BMC Bioinformatics
Research article
1 Identifying hypermethylated CpG islands using a quantile regression model
Sun S, Chen Z, Yan PS, Huang YW, Huang THM, Lin S
BMC Bioinformatics 2011, 12:54 (15 February 2011)
[Abstract] [Provisional PDF]
2.
Research
Genome-wide discovery of missing genes in biological pathways of prokaryotes
Chen Y, Mao F, Li G, Xu Y
BMC Bioinformatics 2011, 12(Suppl 1):S1 (15 February 2011)
[Abstract] [Full text] [PDF]
3.
Research
Gene-gene interaction filtering with ensemble of filters
Yang P, Ho JWK, Yang YH, Zhou BB
BMC Bioinformatics 2011, 12(Suppl 1):S10 (15 February 2011)
[Abstract] [Full text] [PDF]
4.
Research
An efficient algorithmic approach for mass spectrometry-based disulfide
connectivity determination using multi-ion analysis
Murad W, Singh R, Yen TY
BMC Bioinformatics 2011, 12(Suppl 1):S12 (15 February 2011)
[Abstract] [Full text] [PDF]
5.
Research
Integrating multiple protein-protein interaction networks to prioritize disease
genes: a Bayesian regression approach
Zhang W, Sun F, Jiang R
BMC Bioinformatics 2011, 12(Suppl 1):S11 (15 February 2011)
[Abstract] [Full text] [PDF]
6.
Research
An ILP solution for the gene duplication problem
Chang WC, Burleigh GJ, Fernández-Baca DF, Eulenstein O
BMC Bioinformatics 2011, 12(Suppl 1):S14 (15 February 2011)
[Abstract] [Full text] [PDF]
7.
Research
SOMEA: self-organizing map based extraction algorithm for DNA motif
identification with heterogeneous model
Lee NK, Wang D
BMC Bioinformatics 2011, 12(Suppl 1):S16 (15 February 2011)
[Abstract] [Full text] [PDF]
8.
Research
Enhanced stochastic optimization algorithm for finding effective multi-target
therapeutics
Yoon BJ
BMC Bioinformatics 2011, 12(Suppl 1):S18 (15 February 2011)
[Abstract] [Full text] [PDF]
9.
Research
Score regularization for peptide identification
He Z, Zhao H, Yu W
BMC Bioinformatics 2011, 12(Suppl 1):S2 (15 February 2011)
[Abstract] [Full text] [PDF]
10.
Research
Functional analysis of metagenomes and metatranscriptomes using SEED and
KEGG
Mitra S, Rupek P, Richter DC, Urich T, Gilbert JA, Meyer F, Wilke A, Huson DH
BMC Bioinformatics 2011, 12(Suppl 1):S21 (15 February 2011)
[Abstract] [Full text] [PDF]
11.
Research
The G protein-coupled receptors in the pufferfish Takifugu rubripes
Sarkar A, Kumar S, Sundar D
BMC Bioinformatics 2011, 12(Suppl 1):S3 (15 February 2011)
[Abstract] [Full text] [PDF]
12.
Research
Predicting gene expression in T cell differentiation from histone modifications and
transcription factor binding affinities by linear mixture models
Costa IG, Roider HG, do Rego TG, de Carvalho FAT
BMC Bioinformatics 2011, 12(Suppl 1):S29 (15 February 2011)
[Abstract] [Full text] [PDF]
13.
Research
Potent bace-1 inhibitor design using pharmacophore modeling, in silico screening
and molecular docking studies
John S, Thangapandian S, Sakkiah S, Lee KW
BMC Bioinformatics 2011, 12(Suppl 1):S28 (15 February 2011)
[Abstract] [Full text] [PDF]
14.
Research
Reconstructing phylogeny from metabolic substrate-product relationships
Chang CW, Lyu PC, Arita M
BMC Bioinformatics 2011, 12(Suppl 1):S27 (15 February 2011)
[Abstract] [Full text] [PDF]
15.
Research
The choice of null distributions for detecting gene-gene interactions in genome-
wide association studies
Yang C, Wan X, He Z, Yang Q, Xue H, Yu W
BMC Bioinformatics 2011, 12(Suppl 1):S26 (15 February 2011)
[Abstract] [Full text] [PDF]
16.
Research
GARNET – gene set analysis with exploration of annotation relations
Rho K, Kim B, Jang Y, Lee S, Bae T, Seo J, Seo C, Lee J, Kang H, Yu U, Kim S,
Lee S, Kim WK
BMC Bioinformatics 2011, 12(Suppl 1):S25 (15 February 2011)
[Abstract] [Full text] [PDF]
17.
Research
Strobe sequence design for haplotype assembly
Lo C, Bashir A, Bansal V, Bafna V
BMC Bioinformatics 2011, 12(Suppl 1):S24 (15 February 2011)
[Abstract] [Full text] [PDF]
18.
Research
Modeling allosteric signal propagation using protein structure networks
Park K, Kim D
BMC Bioinformatics 2011, 12(Suppl 1):S23 (15 February 2011)
[Abstract] [Full text] [PDF]
19.
Research
Motif-All: discovering all phosphorylation motifs
He Z, Yang C, Guo G, Li N, Yu W
BMC Bioinformatics 2011, 12(Suppl 1):S22 (15 February 2011)
[Abstract] [Full text] [PDF]
20.
Research
PicXAA-R: Efficient structural alignment of multiple RNA sequences using a
greedy approach
Sahraeian SME, Yoon BJ
BMC Bioinformatics 2011, 12(Suppl 1):S38 (15 February 2011)
[Abstract] [Full text] [PDF]
21.
Research
Query-based biclustering of gene expression data using Probabilistic Relational
Models
Zhao H, Cloots L, Van den Bulcke T, Wu Y, De Smet R, Storms V, Meysman P,
Engelen K, Marchal K
BMC Bioinformatics 2011, 12(Suppl 1):S37 (15 February 2011)
[Abstract] [Full text] [PDF]
22.
Research
Integrated metabolome and transcriptome analysis of the NCI60 dataset
Su G, Burant CF, Beecher CW, Athey BD, Meng F
BMC Bioinformatics 2011, 12(Suppl 1):S36 (15 February 2011)
[Abstract] [Full text] [PDF]
23.
Research
Ligand binding site superposition and comparison based on Atomic Property
Fields: identification of distant homologues, convergent evolution and PDB-wide
clustering of binding sites
Totrov M
BMC Bioinformatics 2011, 12(Suppl 1):S35 (15 February 2011)
[Abstract] [Full text] [PDF]
24.
Research
Learning probabilistic models of hydrogen bond stability from molecular
dynamics simulation trajectories
Chikalov I, Yao P, Moshkov M, Latombe JC
BMC Bioinformatics 2011, 12(Suppl 1):S34 (15 February 2011)
[Abstract] [Full text] [PDF]
25.
Research
iGEMDOCK: a graphical environment of enhancing GEMDOCK using
pharmacological interactions and post-screening analysis
Hsu KC, Chen YF, Lin SR, Yang JM
BMC Bioinformatics 2011, 12(Suppl 1):S33 (15 February 2011)
[Abstract] [Full text] [PDF]
26.
Research
A study on the flexibility of enzyme active sites
Weng YZ, Chang DTH, Huang YF, Lin CW
BMC Bioinformatics 2011, 12(Suppl 1):S32 (15 February 2011)
[Abstract] [Full text] [PDF]
27.
Research
Changed epitopes drive the antigenic drift for influenza A (H3N2) viruses
Huang JW, Yang JM
BMC Bioinformatics 2011, 12(Suppl 1):S31 (15 February 2011)
[Abstract] [Full text] [PDF]
28.
Research
Hsp90/Cdc37 Chaperone/co-chaperone complex, a novel junction anticancer target
elucidated by the mode of action of herbal drug Withaferin A
Grover A, Shandilya A, Agrawal V, Pratik P, Bhasme D, Bisaria VS, Sundar D
BMC Bioinformatics 2011, 12(Suppl 1):S30 (15 February 2011)
[Abstract] [Full text] [PDF]
29.
Research
High-throughput peptide quantification using mTRAQ reagent triplex
Yoon JY, Yeom J, Lee H, Kim K, Na S, Park K, Paek E, Lee C
BMC Bioinformatics 2011, 12(Suppl 1):S46 (15 February 2011)
[Abstract] [Full text] [PDF]
30.
Research
Evaluation of methods for detecting conversion events in gene clusters
Song G, Hsu CH, Riemer C, Miller W
BMC Bioinformatics 2011, 12(Suppl 1):S45 (15 February 2011)
[Abstract] [Full text] [PDF]
31.
Research
Resolving the structure of interactomes with hierarchical agglomerative clustering
Park Y, Bader JS
BMC Bioinformatics 2011, 12(Suppl 1):S44 (15 February 2011)
[Abstract] [Full text] [PDF]
32.
Research
HDX-Analyzer: a novel package for statistical analysis of protein structure
dynamics
Liu S, Liu L, Uzuner U, Zhou X, Gu M, Shi W, Zhang Y, Dai SY, Yuan JS
BMC Bioinformatics 2011, 12(Suppl 1):S43 (15 February 2011)
[Abstract] [Full text] [PDF]
33.
Research
A method for supporting retrieval of articles on protein structure analysis
considering users’ intention
Kyogoku R, Fujimoto R, Ozaki T, Ohkawa T
BMC Bioinformatics 2011, 12(Suppl 1):S42 (15 February 2011)
[Abstract] [Full text] [PDF]
34.
Research
Coregulation of transcription factors and microRNAs in human transcriptional
regulatory network
Chen CY, Chen ST, Fuh CS, Juan HF, Huang HC
BMC Bioinformatics 2011, 12(Suppl 1):S41 (15 February 2011)
[Abstract] [Full text] [PDF]
35.
Research
GOChase-II: correcting semantic inconsistencies from Gene Ontology-based
annotations for gene products
Park YR, Kim J, Lee HW, Yoon YJ, Kim JH
BMC Bioinformatics 2011, 12(Suppl 1):S40 (15 February 2011)
[Abstract] [Full text] [PDF]
36.
Research
On the PATHGROUPS approach to rapid small phylogeny
Zheng C, Sankoff D
BMC Bioinformatics 2011, 12(Suppl 1):S4 (15 February 2011)
[Abstract] [Full text] [PDF]
37.
Research
Interaction site prediction by structural similarity to neighboring clusters in
protein-protein interaction networks
Monji H, Koizumi S, Ozaki T, Ohkawa T
BMC Bioinformatics 2011, 12(Suppl 1):S39 (15 February 2011)
[Abstract] [Full text] [PDF]
38.
Research
UMARS: Un-MAppable Reads Solution
Li SC, Chan WC, Lai CH, Tsai KW, Hsu CN, Jou YS, Chen HC, Chen CH, Lin W
BMC Bioinformatics 2011, 12(Suppl 1):S9 (15 February 2011)
[Abstract] [Full text] [PDF]
39.
Research
Ontology-based instance data validation for high-quality curated biological
pathways
Jeong E, Nagasaki M, Ueno K, Miyano S
BMC Bioinformatics 2011, 12(Suppl 1):S8 (15 February 2011)
[Abstract] [Full text] [PDF]
40.
Research
Multi-resolution independent component analysis for high-performance tumor
classification and biomarker discovery
Han H, Li XL
BMC Bioinformatics 2011, 12(Suppl 1):S7 (15 February 2011)
[Abstract] [Full text] [PDF]
41.
Research
A minimal descriptor of an ancestral recombinations graph
Parida L, Palamara PF, Javed A
BMC Bioinformatics 2011, 12(Suppl 1):S6 (15 February 2011)
[Abstract] [Full text] [PDF]
42.
Research
CLOSEST STRING WITH OUTLIERS
Boucher C, Ma B
BMC Bioinformatics 2011, 12(Suppl 1):S55 (15 February 2011)
[Abstract] [Full text] [PDF]
43.
Research
Incorporating Ab Initio energy into threading approaches for protein structure
prediction
Shao M, Wang S, Wang C, Yuan X, Li SC, Zheng W, Bu D
BMC Bioinformatics 2011, 12(Suppl 1):S54 (15 February 2011)
[Abstract] [Full text] [PDF]
44.
Research
Linkage disequilibrium based genotype calling from low-coverage shotgun
sequencing reads
Duitama J, Kennedy J, Dinakar S, Hernández Y, Wu Y, Măndoiu II
BMC Bioinformatics 2011, 12(Suppl 1):S53 (15 February 2011)
[Abstract] [Full text] [PDF]
45.
Research
Repeat-aware modeling and correction of short read errors
Yang X, Aluru S, Dorman KS
BMC Bioinformatics 2011, 12(Suppl 1):S52 (15 February 2011)
[Abstract] [Full text] [PDF]
46.
Research
Semantically enabled and statistically supported biological hypothesis testing with
tissue microarray databases
Song YS, Park CH, Chung HJ, Shin H, Kim J, Kim JH
BMC Bioinformatics 2011, 12(Suppl 1):S51 (15 February 2011)
[Abstract] [Full text] [PDF]
47.
Research
A regression analysis of gene expression in ES cells reveals two gene classes that
are significantly different in epigenetic patterns
Park SJ, Nakai K
BMC Bioinformatics 2011, 12(Suppl 1):S50 (15 February 2011)
[Abstract] [Full text] [PDF]
48.
Research
FPGA accelerator for protein secondary structure prediction based on the GOR
algorithm
Xia F, Dou Y, Lei G, Tan Y
BMC Bioinformatics 2011, 12(Suppl 1):S5 (15 February 2011)
[Abstract] [Full text] [PDF]
49.
Research
Discriminative structural approaches for enzyme active-site prediction
Kato T, Nagano N
BMC Bioinformatics 2011, 12(Suppl 1):S49 (15 February 2011)
[Abstract] [Full text] [PDF]
50.
Research
Fast and accurate clustering of noncoding RNAs using ensembles of sequence
alignments and secondary structures
Saito Y, Sato K, Sakakibara Y
BMC Bioinformatics 2011, 12(Suppl 1):S48 (15 February 2011)
[Abstract] [Full text] [PDF]
51.
Research
Predicting and analyzing DNA-binding domains using a systematic approach to
identifying a set of informative physicochemical and biochemical properties
Huang HL, Lin IC, Liou YF, Tsai CT, Hsu KT, Huang WL, Ho SJ, Ho SY
BMC Bioinformatics 2011, 12(Suppl 1):S47 (15 February 2011)
[Abstract] [Full text] [PDF]
52.
Research
Characterization and sequence prediction of structural variations in α-helix
Tendulkar AV, Wangikar PP
BMC Bioinformatics 2011, 12(Suppl 1):S20 (15 February 2011)
[Abstract] [Full text] [PDF]
53.
Research
Comparative analysis of protein interaction networks reveals that conserved
pathways are susceptible to HIV-1 interception
Qian X, Yoon BJ
BMC Bioinformatics 2011, 12(Suppl 1):S19 (15 February 2011)
[Abstract] [Full text] [PDF]
54.
Research
A genetic algorithm-based boolean delay model of intracellular signal transduction
in inflammation
Kang CC, Chuang YJ, Tung KC, Chao CC, Tang CY, Peng SC, Wong DSH
BMC Bioinformatics 2011, 12(Suppl 1):S17 (15 February 2011)
[Abstract] [Full text] [PDF]
55.
Research
Maximum likelihood models and algorithms for gene tree evolution with
duplications and losses
Górecki P, Burleigh GJ, Eulenstein O
BMC Bioinformatics 2011, 12(Suppl 1):S15 (15 February 2011)
[Abstract] [Full text] [PDF]
56.
Research
A clique-based method for the edit distance between unordered trees and its
application to analysis of glycan structures
Fukagawa D, Tamura T, Takasu A, Tomita E, Akutsu T
BMC Bioinformatics 2011, 12(Suppl 1):S13 (15 February 2011)
[Abstract] [Full text] [PDF]
57.
Methodology article
Estimating developmental states of tumors and normal tissues using a linear timeordered model
Zhang B, Chen B, Wu T, Xuan Z, Zhu X, Chen R
BMC Bioinformatics 2011, 12:53 (11 February 2011)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
58.
Software
RedundancyMiner: De-replication of redundant GO categories in microarray and
proteomics analysis
Zeeberg BR, Liu H, Kahn AB, Ehler M, Rajapakse VN, Bonner RF, Brown JD,
Brooks BP, Larionov VL, Reinhold W, Weinstein JN, Pommier YG
BMC Bioinformatics 2011, 12:52 (10 February 2011)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
59.
Software
Tree Pruner: An efficient tool for selecting data from a biased genetic database
Krishnamoorthy M, Patel P, Dimitrijevic M, Dietrich J, Green M, Macken C
BMC Bioinformatics 2011, 12:51 (9 February 2011)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
60.
Database
Dr. PIAS: an integrative system for assessing the druggability of protein-protein
interactions
Sugaya N, Furuya T
BMC Bioinformatics 2011, 12:50 (9 February 2011)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
61.
Methodology article
A novel approach to the clustering of microarray data via nonparametric density
estimation
De Bin R, Risso D
BMC Bioinformatics 2011, 12:49 (8 February 2011)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
62.
Research article
A quality metric for homology modeling: the H-factor
di Luccio E, Koehl P
BMC Bioinformatics 2011, 12:48 (4 February 2011)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
63.
Research article
Accurate statistics for local sequence alignment with position-dependent scoring by
rare-event sampling
Wolfsheimer S, Herms I, Rahmann S, Hartmann AK
BMC Bioinformatics 2011, 12:47 (3 February 2011)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
64.
Database
GCOD - GeneChip Oncology Database
Liu F, White JA, Antonescu C, Quackenbush J
BMC Bioinformatics 2011, 12:46 (3 February 2011)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
65.
Research article
Hierarchical graphs for rule-based modeling of biochemical systems
Lemons NW, Hu B, Hlavacek WS
BMC Bioinformatics 2011, 12:45 (2 February 2011)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
66.
Methodology article
Gene ontology based transfer learning for protein subcellular localization
Mei S, Fei W, Zhou S
BMC Bioinformatics 2011, 12:44 (2 February 2011)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
67.
Research article
DoBo: Protein domain boundary prediction by integrating evolutionary signals
and machine learning
Eickholt J, Deng X, Cheng J
BMC Bioinformatics 2011, 12:43 (1 February 2011)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
68.
Methodology article
Multivariate analysis of microarray data: differential expression and differential
connection
Kiiveri HT
BMC Bioinformatics 2011, 12:42 (1 February 2011)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
69.
Research article
RAIphy: Phylogenetic classification of metagenomics samples using iterative
refinement of relative abundance index profiles
Nalbantoglu OU, Way SF, Hinrichs SH, Sayood K
BMC Bioinformatics 2011, 12:41 (31 January 2011)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
70.
Research article
nocoRNAc: Characterization of non-coding RNAs in prokaryotes
Herbig A, Nieselt K
BMC Bioinformatics 2011, 12:40 (31 January 2011)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
71.
Research article
ChIPseqR: Analysis of ChIP-seq Experiments
Humburg P, Helliwell CA, Bulger D, Stone G
BMC Bioinformatics 2011, 12:39 (31 January 2011)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
72.
Research article
Removing Noise From Pyrosequenced Amplicons
Quince C, Lanzen A, Davenport RJ, Turnbaugh PJ
BMC Bioinformatics 2011, 12:38 (28 January 2011)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
73.
Research article
Statistical learning techniques applied to epidemiology: a simulated case-control
comparison study with logistic regression
Heine JJ, Land WH, Egan KM
BMC Bioinformatics 2011, 12:37 (27 January 2011)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
74.
Research article
ASPDock: protein-protein docking algorithm using atomic solvation parameters
model
Li L, Guo D, Huang Y, Liu S, Xiao Y
BMC Bioinformatics 2011, 12:36 (27 January 2011)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
75.
Software
VennDiagram: a package for the generation of highly-customizable Venn and
Euler diagrams in R
Chen H, Boutros PC
BMC Bioinformatics 2011, 12:35 (26 January 2011)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
76.
Software
Gepoclu: a software tool for identifying and analyzing gene positional clusters in
large-scale gene expression analysis.
Dottorini T, Senin N, Mazzoleni G, Magnusson K, Crisanti A
BMC Bioinformatics 2011, 12:34 (26 January 2011)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
77.
Methodology article
A genetic algorithm-Bayesian network approach for the analysis of metabolomics
and spectroscopic data: application to the rapid detection of Bacillus spores and
identification of Bacillus species
Correa E, Goodacre R
BMC Bioinformatics 2011, 12:33 (26 January 2011)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
78.
Methodology article
Worm Phenotype Ontology: Integrating phenotype data within and beyond the C.
elegans community
Schindelman G, Fernandes JS, Bastiani CA, Yook K, Sternberg PW
BMC Bioinformatics 2011, 12:32 (24 January 2011)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
79.
Software
PileLine: a toolbox to handle genome position information in next-generation
sequencing studies
Glez-Peña D, Gómez-López G, Reboiro-Jato M, Fdez-Riverola F, Pisano DG
BMC Bioinformatics 2011, 12:31 (24 January 2011)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
80.
Software
iPhy: an integrated phylogenetic workbench for supermatrix analyses
Jones MO, Koutsovoulos GD, Blaxter ML
BMC Bioinformatics 2011, 12:30 (24 January 2011)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
81.
Research article
Investigating the effect of paralogs on microarray gene-set analysis
Faure AJ, Seoighe C, Mulder NJ
BMC Bioinformatics 2011, 12:29 (24 January 2011)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
82.
Software
FASIMU: flexible software for flux-balance computation series in large metabolic
networks
Hoppe A, Hoffmann S, Gerasch A, Gille C, Holzhütter HG
BMC Bioinformatics 2011, 12:28 (22 January 2011)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
83.
Software
CODA (crossover distribution analyzer): quantitative characterization of
crossover position patterns along chromosomes
Gauthier F, Martin OC, Falque M
BMC Bioinformatics 2011, 12:27 (20 January 2011)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
84.
Research article
Predicting functionally important SNP classes based on negative selection
Levenstien MA, Klein RJ
BMC Bioinformatics 2011, 12:26 (19 January 2011)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
85.
Methodology article
Systematic error detection in experimental high-throughput screening
Dragiev P, Nadon R, Makarenkov V
BMC Bioinformatics 2011, 12:25 (19 January 2011)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
86.
Software
GraphCrunch 2: Software tool for network modeling, alignment and clustering
Kuchaiev O, Stevanović A, Hayes W, Pržulj N
BMC Bioinformatics 2011, 12:24 (19 January 2011)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
87.
Software
easyDAS: Automatic creation of DAS servers
Gel Moreno B, Jenkinson AM, Jimenez RC, Messeguer Peypoch X, Hermjakob H
BMC Bioinformatics 2011, 12:23 (18 January 2011)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
88.
Research article
Revision history aware repositories of computational models of biological systems
Miller AK, Yu T, Britten R, Cooling MT, Lawson J, Cowan D, Garny A, Halstead
MDB, Hunter PJ, Nickerson DP, Nunns G, Wimalaratne SM, F Nielsen PM
BMC Bioinformatics 2011, 12:22 (14 January 2011)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
89.
Research article
NClassG+: A classifier for non-classically secreted Gram-positive bacterial
proteins
Restrepo-Montoya D, Pino C, Nino LF, Patarroyo ME, Patarroyo MA
BMC Bioinformatics 2011, 12:21 (14 January 2011)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
90.
Research article
Combining gene prediction methods to improve metagenomic gene annotation
Yok NG, Rosen GL
BMC Bioinformatics 2011, 12:20 (13 January 2011)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
91.
Research article
Context-dependent transcriptional regulations between signal transduction
pathways
Hwang S, Kim S, Shin H, Lee D
BMC Bioinformatics 2011, 12:19 (13 January 2011)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
92.
Research article
Analysis on the reconstruction accuracy of the Fitch method for inferring ancestral
states
Yang J, Li J, Dong L, Grünewald S
BMC Bioinformatics 2011, 12:18 (13 January 2011)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
93.
Research article
Pathway-based analysis using reduced gene subsets in genome-wide association
studies
Zhao J, Gupta S, Seielstad M, Liu J, Thalamuthu A
BMC Bioinformatics 2011, 12:17 (12 January 2011)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
94.
Research article
A hierarchical Bayesian network approach for linkage disequilibrium modeling
and data-dimensionality reduction prior to genome-wide association studies
Mourad R, Sinoquet C, Leray P
BMC Bioinformatics 2011, 12:16 (12 January 2011)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
95.
Methodology article
Shape-based peak identification for ChIP-Seq
Hower V, Evans SN, Pachter L
BMC Bioinformatics 2011, 12:15 (12 January 2011)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
96.
Research article
Predicting disease-associated substitution of a single amino acid by analyzing
residue interactions
Li Y, Wen Z, Xiao J, Yin H, Yu L, Yang L, Li M
BMC Bioinformatics 2011, 12:14 (12 January 2011)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
97.
Software
A Platform for Processing Expression of Short Time Series (PESTS)
Sinha A, Markatou M
BMC Bioinformatics 2011, 12:13 (11 January 2011)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
98.
Research article
N-gram analysis of 970 microbial organisms reveals presence of biological
language models
Osmanbeyoglu HU, Ganapathiraju MK
BMC Bioinformatics 2011, 12:12 (10 January 2011)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
99.
Software
OrthoInspector: comprehensive orthology analysis and visual exploration
Linard B, Thompson JD, Poch O, Lecompte O
BMC Bioinformatics 2011, 12:11 (10 January 2011)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
100.
Methodology article
PICS-Ord: unlimited coding of ambiguous regions by pairwise identity and cost
scores ordination
Lücking R, Hodkinson BP, Stamatakis A, Cartwright RA
BMC Bioinformatics 2011, 12:10 (7 January 2011)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
101.
Methodology article
Robust joint analysis allowing for model uncertainty in two-stage genetic
association studies
Pan D, Li Q, Jiang N, Liu A, Yu K
BMC Bioinformatics 2011, 12:9 (7 January 2011)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
102.
Research article
Flexible taxonomic assignment of ambiguous sequencing reads
Clemente JC, Jansson J, Valiente G
BMC Bioinformatics 2011, 12:8 (7 January 2011)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
103.
Research article
Using Stochastic Causal Trees to Augment Bayesian Networks for Modeling eQTL
Datasets
Chipman KC, Singh AK
BMC Bioinformatics 2011, 12:7 (6 January 2011)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
104.
Methodology article
Logical Development of the Cell Ontology
Meehan TF, Masci AM, Abdulla A, Cowell LG, Blake JA, Mungall CJ, Diehl AD
BMC Bioinformatics 2011, 12:6 (5 January 2011)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
105.
Methodology article
Combinatorial analysis and algorithms for quasispecies reconstruction using nextgeneration sequencing
Prosperi MCF, Prosperi L, Bruselles A, Abbate I, Rozera G, Vincenti D, Solmone
MC, Capobianchi MR, Ulivi G
BMC Bioinformatics 2011, 12:5 (5 January 2011)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
106.
Software
CNV-WebStore: Online CNV Analysis, Storage and Interpretation
Vandeweyer G, Reyniers E, Wuyts W, Rooms L, Kooy RF
BMC Bioinformatics 2011, 12:4 (5 January 2011)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
107.
Software
R2R - software to speed the depiction of aesthetic consensus RNA secondary
structures
Weinberg Z, Breaker RR
BMC Bioinformatics 2011, 12:3 (4 January 2011)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
108.
Methodology article
Clustering gene expression data with a penalized graph-based metric
Bayá AE, Granitto PM
BMC Bioinformatics 2011, 12:2 (4 January 2011)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
109.
Software
MTML-msBayes: Approximate Bayesian comparative phylogeographic inference
from multiple taxa and multiple loci with rate heterogeneity
Huang W, Takebayashi N, Qi Y, Hickerson MJ
BMC Bioinformatics 2011, 12:1 (3 January 2011)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
110.
Research article
A two-step site and mRNA-level model for predicting microRNA targets
Saito T, Sætrom P
BMC Bioinformatics 2010, 11:612 (31 December 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
111.
Software
SIDEKICK: Genomic data driven analysis and decision-making framework
Doderer MS, Yoon K, Robbins KA
BMC Bioinformatics 2010, 11:611 (30 December 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
112.
Software
BiologicalNetworks 2.0 - an integrative view of genome biology data
Kozhenkov S, Dubinina Y, Sedova M, Gupta A, Ponomarenko J, Baitaluk M
BMC Bioinformatics 2010, 11:610 (29 December 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
113.
Research article
RISCI - Repeat Induced Sequence Changes Identifier: a comprehensive,
comparative genomics-based, in silico subtractive hybridization pipeline to identify
repeat induced sequence changes in closely related genomes
Singh V, Mishra RK
BMC Bioinformatics 2010, 11:609 (26 December 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
114.
Software
MBAT: A scalable informatics system for unifying digital atlasing workflows
Lee D, Ruffins S, Ng Q, Sane N, Anderson S, Toga A
BMC Bioinformatics 2010, 11:608 (22 December 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
115.
Research article
The complexity of gene expression dynamics revealed by permutation entropy
Sun X, Zou Y, Nikiforova V, Kurths J, Walther D
BMC Bioinformatics 2010, 11:607 (22 December 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
116.
Methodology article
Kernel based methods for accelerated failure time model with ultra-high
dimensional data
Liu Z, Chen D, Tan M, Jiang F, Gartenhaus RB
BMC Bioinformatics 2010, 11:606 (21 December 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
117.
Research article
New insights into protein-protein interaction data lead to increased estimates of
the S. cerevisiae interactome size
Sambourg L, Thierry-Mieg N
BMC Bioinformatics 2010, 11:605 (21 December 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
118.
Research article
Computing DNA duplex instability profiles efficiently with a two-state model:
trends of promoters and binding sites
Kantorovitz MR, Rapti Z, Gelev V, Usheva A
BMC Bioinformatics 2010, 11:604 (21 December 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
119.
Research article
Content-based microarray search using differential expression profiles
Engreitz JM, Morgan AA, Dudley JT, Chen R, Thathoo R, Altman RB, Butte AJ
BMC Bioinformatics 2010, 11:603 (21 December 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
120.
Proceedings
An overview of the Hadoop/MapReduce/HBase framework and its current
applications in bioinformatics
Taylor RC
BMC Bioinformatics 2010, 11(Suppl 12):S1 (21 December 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
121.
Proceedings
interPopula: a Python API to access the HapMap Project dataset
Antao T
BMC Bioinformatics 2010, 11(Suppl 12):S10 (21 December 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
122.
Proceedings
An intuitive Python interface for Bioconductor libraries demonstrates the utility of
language translators
Gautier L
BMC Bioinformatics 2010, 11(Suppl 12):S11 (21 December 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
123.
Proceedings
The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button
Swertz MA, Dijkstra M, Adamusiak T, van der Velde JK, Kanterakis A, Roos ET,
Lops J, Thorisson GA, Arends D, Byelas G, Muilu J, Brookes AJ, de Brock EO,
Jansen RC, Parkinson H
BMC Bioinformatics 2010, 11(Suppl 12):S12 (21 December 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
124.
Proceedings
IPRStats: visualization of the functional potential of an InterProScan run
Kelly RJ, Vincent DE, Friedberg I
BMC Bioinformatics 2010, 11(Suppl 12):S13 (21 December 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
125.
Proceedings
SeqWare Query Engine: storing and searching sequence data in the cloud
O’Connor BD, Merriman B, Nelson SF
BMC Bioinformatics 2010, 11(Suppl 12):S2 (21 December 2010)
[Abstract] [Full text] [PDF]
126.
Proceedings
Hybrid cloud and cluster computing paradigms for life science applications
Qiu J, Ekanayake J, Gunarathne T, Choi JY, Bae SH, Li H, Zhang B, Wu TL,
Ruan Y, Ekanayake S, Hughes A, Fox G
BMC Bioinformatics 2010, 11(Suppl 12):S3 (21 December 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
127.
Proceedings
Galaxy CloudMan: delivering cloud compute clusters
Afgan E, Baker D, Coraor N, Chapman B, Nekrutenko A, Taylor J
BMC Bioinformatics 2010, 11(Suppl 12):S4 (21 December 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
128.
Proceedings
Community-driven computational biology with Debian Linux
Möller S, Krabbenhöft HN, Tille A, Paleino D, Williams A, Wolstencroft K, Goble
C, Holland R, Belhachemi D, Plessy C
BMC Bioinformatics 2010, 11(Suppl 12):S5 (21 December 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
129.
Proceedings
WordSeeker: concurrent bioinformatics software for discovering genome-wide
patterns and word-based genomic signatures
Lichtenberg J, Kurz K, Liang X, Al-ouran R, Neiman L, Nau LJ, Welch JD, Jacox
E, Bitterman T, Ecker K, Elnitski L, Drews F, Lee SS, Welch LR
BMC Bioinformatics 2010, 11(Suppl 12):S6 (21 December 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
130.
Proceedings
SADI, SHARE, and the in silico scientific method
Wilkinson MD, McCarthy L, Vandervalk B, Withers D, Kawas E, Samadian S
BMC Bioinformatics 2010, 11(Suppl 12):S7 (21 December 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
131.
Proceedings
ONTO-ToolKit: enabling bio-ontology engineering via Galaxy
Antezana E, Venkatesan A, Mungall C, Mironov V, Kuiper M
BMC Bioinformatics 2010, 11(Suppl 12):S8 (21 December 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
132.
Proceedings
The Musite open-source framework for phosphorylation-site prediction
Gao J, Xu D
BMC Bioinformatics 2010, 11(Suppl 12):S9 (21 December 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
133.
Research article
Gene processing control loops suggested by sequencing, splicing, and RNA folding
Jeffries CD, Perkins DO, Guan X
BMC Bioinformatics 2010, 11:602 (20 December 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
134.
Software
SNPexp - A web tool for calculating and visualizing correlation between HapMap
genotypes and gene expression levels
Holm K, Melum E, Franke A, Karlsen TH
BMC Bioinformatics 2010, 11:600 (17 December 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
135.
Methodology article
A genome alignment algorithm based on compression
Cao MD, Dix TI, Allison L
BMC Bioinformatics 2010, 11:599 (16 December 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
136.
Research article
Initial steps towards a production platform for DNA sequence analysis on the grid
Luyf ACM, van Schaik BDC, de Vries M, Baas F, van Kampen AHC, Olabarriaga
SD
BMC Bioinformatics 2010, 11:598 (14 December 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
137.
Research
Detection and reconstruction of tandemly organized de novo copy number
variations
He D, Furlotte N, Eskin E
BMC Bioinformatics 2010, 11(Suppl 11):S12 (14 December 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
138.
Research
Association of tissue lineage and gene expression: conservatively and differentially
expressed genes define common and special functions of tissues
Yu Y, Xu T, Yu Y, Hao P, Li X
BMC Bioinformatics 2010, 11(Suppl 11):S1 (14 December 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
139.
Research
MiRenSVM: towards better prediction of microRNA precursors using an
ensemble SVM classifier with multi-loop features
Ding J, Zhou S, Guan J
BMC Bioinformatics 2010, 11(Suppl 11):S11 (14 December 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
140.
Research
TF-centered downstream gene set enrichment analysis: Inference of causal
regulators by integrating TF-DNA interactions and protein post-translational
modifications information
Liu Q, Tan Y, Huang T, Ding G, Tu Z, Liu L, Li Y, Dai H, Xie L
BMC Bioinformatics 2010, 11(Suppl 11):S5 (14 December 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
141.
Research
Accurate HLA type inference using a weighted similarity graph
Xie M, Li J, Jiang T
BMC Bioinformatics 2010, 11(Suppl 11):S10 (14 December 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
142.
Research
The utility of mass spectrometry-based proteomic data for validation of novel
alternative splice forms reconstructed from RNA-Seq data: a preliminary
assessment
Ning K, Nesvizhskii AI
BMC Bioinformatics 2010, 11(Suppl 11):S14 (14 December 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
143.
Research
Integer programming-based method for grammar-based tree compression and its
application to pattern extraction of glycan tree structures
Zhao Y, Hayashida M, Akutsu T
BMC Bioinformatics 2010, 11(Suppl 11):S4 (14 December 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
144.
Research
Herb network construction and co-module analysis for uncovering the
combination rule of traditional Chinese herbal formulae
Li S, Zhang B, Jiang D, Wei Y, Zhang N
BMC Bioinformatics 2010, 11(Suppl 11):S6 (14 December 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
145.
Research
A novel parametric approach to mine gene regulatory relationship from
microarray datasets
Liu W, Li D, Liu Q, Zhu Y, He F
BMC Bioinformatics 2010, 11(Suppl 11):S15 (14 December 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
146.
Research
Sorting out inherent features of head-to-head gene pairs by evolutionary
conservation
Chen YQ, Yu H, Li YX, Li YY
BMC Bioinformatics 2010, 11(Suppl 11):S16 (14 December 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
147.
Research
Revealing parasite influence in metabolic pathways in Apicomplexa infected
patients
Xu T, Ping J, Yu Y, Yu F, Yu Y, Hao P, Li X
BMC Bioinformatics 2010, 11(Suppl 11):S13 (14 December 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
148.
Research
Large number of phosphotransferase genes in the Clostridium beijerinckii NCIMB
8052 genome and the study on their evolution
Shi Y, Li YX, Li YY
BMC Bioinformatics 2010, 11(Suppl 11):S9 (14 December 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
149.
Research
RecMotif: a novel fast algorithm for weak motif discovery
Sun HQ, Low MYH, Hsu WJ, Rajapakse JC
BMC Bioinformatics 2010, 11(Suppl 11):S8 (14 December 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
150.
Research
Improved protein surface comparison and application to low-resolution protein
structure data
Sael L, Kihara D
BMC Bioinformatics 2010, 11(Suppl 11):S2 (14 December 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
151.
Research
Gene-centric association analysis for the correlation between the guanine-cytosine
content levels and temperature range conditions of prokaryotic species
Zheng H, Wu H
BMC Bioinformatics 2010, 11(Suppl 11):S7 (14 December 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
152.
Research
Prior knowledge based mining functional modules from Yeast PPI networks with
gene ontology
Jing L, Ng MK
BMC Bioinformatics 2010, 11(Suppl 11):S3 (14 December 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
153.
Methodology article
Extending pathways and processes using molecular interaction networks to
analyse cancer genome data
Glaab E, Baudot A, Krasnogor N, Valencia A
BMC Bioinformatics 2010, 11:597 (13 December 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
154.
Research article
PETALS: Proteomic Evaluation and Topological Analysis of a mutated Locus'
Signaling
Bebek G, Patel V, Chance MR
BMC Bioinformatics 2010, 11:596 (13 December 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
155.
Software
BIGSdb: Scalable analysis of bacterial genome variation at the population level
Jolley KA, Maiden MCJ
BMC Bioinformatics 2010, 11:595 (10 December 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
156.
Research article
Addressing the Challenge of Defining Valid Proteomic Biomarkers and Classifiers
Dakna M, Harris K, Kalousis A, Carpentier S, Kolch W, Schanstra JP, Haubitz M,
Vlahou A, Mischak H, Girolami M
BMC Bioinformatics 2010, 11:594 (10 December 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
157.
Research article
Application of Wavelet Packet Transform to detect genetic polymorphisms by the
analysis of inter-Alu PCR patterns
Cardelli M, Nicoli M, Bazzani A, Franceschi C
BMC Bioinformatics 2010, 11:593 (9 December 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
158.
Research article
Haplotype association analyses in resources of mixed structure using Monte Carlo
testing
Abo R, Wong J, Thomas A, Camp NJ
BMC Bioinformatics 2010, 11:592 (9 December 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
159.
Methodology article
An improved machine learning protocol for the identification of correct Sequest
search results
Källberg M, Lu H
BMC Bioinformatics 2010, 11:591 (7 December 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
160.
Poster presentation
Human protein-protein interaction prediction
McDowall MD, Scott MS, Barton GJ
BMC Bioinformatics 2010, 11(Suppl 10):P1 (7 December 2010)
[Abstract] [Full text] [PDF]
161.
Oral presentation
Analysis of the functional properties of the creatine kinase system using a
multiscale ‘sloppy’ modeling approach
Hettling H, Heringa J, van Beek JHGM
BMC Bioinformatics 2010, 11(Suppl 10):O9 (7 December 2010)
[Abstract] [Full text] [PDF]
162.
Oral presentation
A hidden Markov model for detecting multi-gene chromatin domains
Larson J, Yuan G
BMC Bioinformatics 2010, 11(Suppl 10):O5 (7 December 2010)
[Abstract] [Full text] [PDF]
163.
Oral presentation
Bridging the gaps: atomic simulation of macromolecular environment brings
together protein docking, interaction kinetics and the crowding effects
Li XF, Moal IH, Bates PA
BMC Bioinformatics 2010, 11(Suppl 10):O2 (7 December 2010)
[Abstract] [Full text] [PDF]
164.
Oral presentation
Next generation genome annotation with mGene.ngs
Behr J, Bohnert R, Zeller G, Schweikert G, Hartmann L, Rätsch G
BMC Bioinformatics 2010, 11(Suppl 10):O8 (7 December 2010)
[Abstract] [Full text] [PDF]
165.
Oral presentation
A computational pipeline for diagnostic biomarker discovery in the human
pathogen Trypanosoma cruzi
Carmona SJ, Sartor P, Leguizamón MS, Campetella O, Agüero F
BMC Bioinformatics 2010, 11(Suppl 10):O11 (7 December 2010)
[Abstract] [Full text] [PDF]
166.
Oral presentation
Modeling protein-peptide interactions using protein fragments: fitting the pieces?
Vanhee P, Stricher F, Baeten L, Verschueren E, Serrano L, Rousseau F,
Schymkowitz J
BMC Bioinformatics 2010, 11(Suppl 10):O1 (7 December 2010)
[Abstract] [Full text] [PDF]
167.
Oral presentation
A bioengineering approach for rational vaccine design towards the Ebola Virus
Banton S, Roth Z, Pavlovic M
BMC Bioinformatics 2010, 11(Suppl 10):O12 (7 December 2010)
[Abstract] [Full text] [PDF]
168.
Oral presentation
is-rSNP: a novel technique for in silico regulatory SNP detection
Macintyre G, Bailey J, Haviv I, Kowalczyk A
BMC Bioinformatics 2010, 11(Suppl 10):O7 (7 December 2010)
[Abstract] [Full text] [PDF]
169.
Oral presentation
Genome wide association study of nonsynonymous Single Nucleotide
Polymorphisms for seven common diseases
Surendran P, Stanton A, Shields D
BMC Bioinformatics 2010, 11(Suppl 10):O6 (7 December 2010)
[Abstract] [Full text] [PDF]
170.
Oral presentation
Structure-based kernels for the prediction of catalytic residues and their
involvement in human inherited disease
Xin F, Myers S, Li YF, Cooper DN, Mooney SD, Radivojac P
BMC Bioinformatics 2010, 11(Suppl 10):O4 (7 December 2010)
[Abstract] [Full text] [PDF]
171.
Oral presentation
Exploiting physical properties in protein structure alignment
Shah S, Sahinidis N
BMC Bioinformatics 2010, 11(Suppl 10):O3 (7 December 2010)
[Abstract] [Full text] [PDF]
172.
Introduction
Highlights from the 6th International Society for Computational Biology Student
Council Symposium at the 18th Annual International Conference on Intelligent
Systems for Molecular Biology
Klijn C, Michaut M, Abeel T
BMC Bioinformatics 2010, 11(Suppl 10):I1 (7 December 2010)
[Abstract] [Full text] [PDF]
173.
Oral presentation
Designing and implementing chemoinformatic approaches in TDR Targets
Database: linking genes to chemical compounds in tropical disease causing
pathogens
Magariños MP, Overington J, Carmona S, Shanmugam D, Doyle M, Ralph S,
Crowther G, Hertz-Fowler C, Nwaka S, Berriman M, Roos D, Van Voorhis W,
Agüero F
BMC Bioinformatics 2010, 11(Suppl 10):O10 (7 December 2010)
[Abstract] [Full text] [PDF]
174.
Software
Merged consensus clustering to assess and improve class discovery with
microarray data
Simpson TI, Armstrong JD, Jarman AP
BMC Bioinformatics 2010, 11:590 (3 December 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
175.
Methodology article
BrEPS: a flexible and automatic protocol to compute enzyme-specific sequence
profiles for functional annotation
Bannert C, Welfle A, aus dem Spring C, Schomburg D
BMC Bioinformatics 2010, 11:589 (1 December 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
176.
Methodology article
IntelliGO: a new vector-based semantic similarity measure including annotation
origin
Benabderrahmane S, Smail-Tabbone M, Poch O, Napoli A, Devignes MD
BMC Bioinformatics 2010, 11:588 (1 December 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
177.
Research article
Comparison of Beta-value and M-value methods for quantifying methylation levels
by microarray analysis
Du P, Zhang X, Huang CC, Jafari N, Kibbe WA, Hou L, Lin SM
BMC Bioinformatics 2010, 11:587 (30 November 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
178.
Research article
Prediction of RNA secondary structure by maximizing pseudo-expected accuracy
Hamada M, Sato K, Asai K
BMC Bioinformatics 2010, 11:586 (30 November 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
179.
Research article
Knowledge-based matrix factorization temporally resolves the cellular responses
to IL-6 stimulation
Kowarsch A, Blöchl F, Bohl S, Saile M, Gretz N, Klingmüller U, Theis FJ
BMC Bioinformatics 2010, 11:585 (30 November 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
180.
Methodology article
LTC: a novel algorithm to improve the efficiency of contig assembly for physical
mapping in complex genomes
Frenkel Z, Paux E, Mester D, Feuillet C, Korol A
BMC Bioinformatics 2010, 11:584 (30 November 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
181.
Research article
Preprocessing of gene expression data by optimally robust estimators
Kohl M, Deigner HP
BMC Bioinformatics 2010, 11:583 (30 November 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
182.
Methodology article
Systematic integration of experimental data and models in systems biology
Li P, Dada JO, Jameson D, Spasic I, Swainston N, Carroll K, Dunn W, Khan F,
Malys N, Messiha HL, Simeonidis E, Weichart D, Winder C, Wishart J,
Broomhead DS, Goble CA, Gaskell SJ, Kell DB, Westerhoff HV, Mendes P, Paton
NW
BMC Bioinformatics 2010, 11:582 (29 November 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
183.
Software
The INTERPRET Decision-Support System version 3.0 for evaluation of Magnetic
Resonance Spectroscopy data from human brain tumours and other abnormal
brain masses
Pérez-Ruiz A, Julià-Sapé M, Mercadal G, Olier I, Majós C, Arús C
BMC Bioinformatics 2010, 11:581 (29 November 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
184.
Methodology article
A hybrid blob-slice model for accurate and efficient detection of fluorescence
labeled nuclei in 3D
Santella A, Du Z, Nowotschin S, Hadjantonakis AK, Bao Z
BMC Bioinformatics 2010, 11:580 (29 November 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
185.
Software
webPRANK: a phylogeny-aware multiple sequence aligner with interactive
alignment browser
Löytynoja A, Goldman N
BMC Bioinformatics 2010, 11:579 (26 November 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
186.
Research article
Improvements to previous algorithms to predict gene structure and isoform
concentrations using Affymetrix Exon arrays
Anton MA, Aramburu A, Rubio A
BMC Bioinformatics 2010, 11:578 (26 November 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
187.
Research article
Speeding up tandem mass spectrometry-based database searching by longest
common prefix
Zhou C, Chi H, Wang LH, Li Y, Wu YJ, Fu Y, Sun RX, He SM
BMC Bioinformatics 2010, 11:577 (25 November 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
188.
Research article
Validation and characterization of DNA microarray gene expression data
distribution and associated moments
Thomas R, de la Torre L, Chang X, Mehrotra S
BMC Bioinformatics 2010, 11:576 (24 November 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
189.
Research article
Sampling the conformation of protein surface residues for flexible protein docking
Francis-Lyon P, Gu S, Hass J, Amenta N, Koehl P
BMC Bioinformatics 2010, 11:575 (23 November 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
190.
Software
iGTP: A software package for large-scale gene tree parsimony analysis
Chaudhary R, Bansal MS, Wehe A, Fernández-Baca D, Eulenstein O
BMC Bioinformatics 2010, 11:574 (23 November 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
191.
Software
DeltaProt: a software toolbox for comparative genomics
Thorvaldsen S, Flå T, Willassen NP
BMC Bioinformatics 2010, 11:573 (23 November 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
192.
Software
Pash 3.0: A versatile software package for read mapping and integrative analysis
of genomic and epigenomic variation using massively parallel DNA sequencing
Coarfa C, Yu F, Miller CA, Chen Z, Harris RA, Milosavljevic A
BMC Bioinformatics 2010, 11:572 (23 November 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
193.
Methodology article
Probabilistic principal component analysis for metabolomic data
Nyamundanda G, Brennan L, Gormley IC
BMC Bioinformatics 2010, 11:571 (23 November 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
194.
Methodology article
Reticular alignment: A progressive corner-cutting method for multiple sequence
alignment
Szabó A, Novák , Miklós I, Hein J
BMC Bioinformatics 2010, 11:570 (23 November 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
195.
Research article
Knowledge-based biomedical word sense disambiguation: comparison of
approaches
Jimeno-Yepes AJ, Aronson AR
BMC Bioinformatics 2010, 11:569 (22 November 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
196.
Research article
Peptide binding predictions for HLA DR, DP and DQ molecules
Wang P, Sidney J, Kim Y, Sette A, Lund O, Nielsen M, Peters B
BMC Bioinformatics 2010, 11:568 (22 November 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
197.
Research article
Comparative study of unsupervised dimension reduction techniques for the
visualization of microarray gene expression data
Bartenhagen C, Klein HU, Ruckert C, Jiang X, Dugas M
BMC Bioinformatics 2010, 11:567 (18 November 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
198.
Research article
Semi-automatic identification of punching areas for tissue microarray building:
the tubular breast cancer pilot study
Viti F, Merelli I, Timmermans M, den Bakker M, Beltrame F, Riegman P,
Milanesi L
BMC Bioinformatics 2010, 11:566 (18 November 2010)
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199.
Research article
Reanalyze unassigned reads in Sanger based metagenomic data using conserved
gene adjacency
Weng FC, Su CH, Hsu MT, Wang TY, Tsai HK, Wang D
BMC Bioinformatics 2010, 11:565 (18 November 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
200.
Research article
Empirical bayes analysis of sequencing-based transcriptional profiling without
replicates
Wu Z, Jenkins BD, Rynearson TA, Dyhrman ST, Saito MA, Mercier M, Whitney
LAP
BMC Bioinformatics 2010, 11:564 (16 November 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
201.
Methodology article
A factorization method for the classification of infrared spectra
Henneges C, Laskov P, Darmawan E, Backhaus J, Kammerer B, Zell A
BMC Bioinformatics 2010, 11:561 (15 November 2010)
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202.
Research article
Efficient parallel and out of core algorithms for constructing large bi-directed de Bruijn
graphs
Kundeti VK, Rajasekaran S, Dinh H, Vaughn M, Thapar V
BMC Bioinformatics 2010, 11:560 (15 November 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
203.
Methodology article
Quantification and deconvolution of asymmetric LC-MS peaks using the bi-Gaussian mixture
model and statistical model selection
Yu T, Peng H
BMC Bioinformatics 2010, 11:559 (12 November 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
204.
Methodology article
Leukocyte nucleus segmentation and nucleus lobe counting
Chan YK, Tsai MH, Huang DC, Zheng ZH, Hung KD
BMC Bioinformatics 2010, 11:558 (12 November 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
205.
Research article
Epigenetic domains found in mouse embryonic stem cells via a hidden Markov model
Larson JL, Yuan GC
BMC Bioinformatics 2010, 11:557 (12 November 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
206.
Methodology article
Assessment and optimisation of normalisation methods for dual-colour antibody
microarrays
Sill M, Schröder C, Hoheisel JD, Benner A, Zucknick M
BMC Bioinformatics 2010, 11:556 (12 November 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
207.
Methodology article
The LabelHash algorithm for substructure matching
Moll M, Bryant DH, Kavraki LE
BMC Bioinformatics 2010, 11:555 (11 November 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
208.
Software
FITBAR: a web tool for the robust prediction of prokaryotic regulons
Oberto J
BMC Bioinformatics 2010, 11:554 (11 November 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
209.
Research article
Algorithm-driven Artifacts in median polish summarization of Microarray data
Giorgi FM, Bolger AM, Lohse M, Usadel B
BMC Bioinformatics 2010, 11:553 (11 November 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
210.
Research article
Bayesian inference of the number of factors in gene-expression analysis: application to
human virus challenge studies
Chen B, Chen M, Paisley J, Zaas A, Woods C, Ginsburg GS, Hero A, Lucas J, Dunson D, Carin L
BMC Bioinformatics 2010, 11:552 (9 November 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
211.
Research article
An intuitionistic approach to scoring DNA sequences against transcription factor binding site
motifs
Garcia-Alcalde F, Blanco A, Shepherd AJ
BMC Bioinformatics 2010, 11:551 (8 November 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
212.
Research article
Localizing triplet periodicity in DNA and cDNA sequences
Wang L, Stein LD
BMC Bioinformatics 2010, 11:550 (8 November 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
213.
Research article
The Text-mining based PubChem Bioassay neighboring analysis
Han L, Suzek TO, Wang Y, Bryant SH
BMC Bioinformatics 2010, 11:549 (8 November 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
214.
Methodology article
Protein structure analysis of mutations causing inheritable diseases. An e-Science approach
with life scientist friendly interfaces
Venselaar H, te Beek TAH, Kuipers RKP, Hekkelman ML, Vriend G
BMC Bioinformatics 2010, 11:548 (8 November 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
215.
Research article
Thermodynamically consistent Bayesian analysis of closed biochemical reaction systems
Jenkinson G, Zhong X, Goutsias J
BMC Bioinformatics 2010, 11:547 (5 November 2010)
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216.
Methodology article
Optimizing transformations for automated, high throughput analysis of flow cytometry data
Finak G, Perez JM, Weng A, Gottardo R
BMC Bioinformatics 2010, 11:546 (4 November 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
217.
Methodology article
Bioactive conformational generation of small molecules: A comparative analysis between
force-field and multiple empirical criteria based methods
Bai F, Liu X, Li J, Zhang H, Jiang H, Wang X, Li H
BMC Bioinformatics 2010, 11:545 (4 November 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
218.
Methodology article
Clustering metagenomic sequences with interpolated Markov models
Kelley DR, Salzberg SL
BMC Bioinformatics 2010, 11:544 (2 November 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
219.
Methodology article
Predicting success of oligomerized pool engineering (OPEN) for zinc finger target site
sequences
Sander JD, Reyon D, Maeder ML, Foley JE, Thibodeau-Beganny S, Li X, Regan MR, Dahlborg
EJ, Goodwin MJ, Fu F, Voytas DF, Joung JK, Dobbs D
BMC Bioinformatics 2010, 11:543 (2 November 2010)
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220.
Software
CaGrid Workflow Toolkit: A taverna based workflow tool for cancer grid
Tan W, Madduri R, Nenadic A, Soiland-Reyes S, Sulakhe D, Foster I, Goble CA
BMC Bioinformatics 2010, 11:542 (2 November 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
221.
Correction
Correction: PathEx: A novel multi factors based datasets selector web tool
Bareke E, Pierre M, Gaigneaux A, De Meulder B, Depiereux S, Berger F, Habra N, Depiereux E
BMC Bioinformatics 2010, 11:541 (2 November 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
222.
Research article
Circadian signatures in rat liver: from gene expression to pathways
Ovacik MA, Sukumaran S, Almon RR, DuBois DC, Jusko WJ, Androulakis IP
BMC Bioinformatics 2010, 11:540 (1 November 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
223.
Methodology article
Detection of copy number variation from array intensity and sequencing read depth using a
stepwise Bayesian model
Zhang ZD, Gerstein MB
BMC Bioinformatics 2010, 11:539 (31 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
224.
Methodology article
pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences
onto a fixed reference tree
Matsen FA, Kodner RB, Armbrust EV
BMC Bioinformatics 2010, 11:538 (30 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
225.
Research article
Predicting domain-domain interaction based on domain profiles with feature selection and
support vector machines
González AJ, Liao L
BMC Bioinformatics 2010, 11:537 (29 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
226.
Research article
Incorporating significant amino acid pairs to identify O-linked glycosylation sites on
transmembrane proteins and non-transmembrane proteins
Chen SA, Lee TY, Ou YY
BMC Bioinformatics 2010, 11:536 (29 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
227.
Research article
Optimizing structural modeling for a specific protein scaffold: knottins or inhibitor cystine
knots
Gracy J, Chiche L
BMC Bioinformatics 2010, 11:535 (28 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
228.
Proceedings
Feasibility of incorporating genomic knowledge into electronic medical records for
pharmacogenomic clinical decision support
Overby CL, Tarczy-Hornoch P, Hoath JI, Kalet IJ, Veenstra DL
BMC Bioinformatics 2010, 11(Suppl 9):S10 (28 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
229.
Proceedings
Multi-dimensional discovery of biomarker and phenotype complexes
Payne PRO, Huang K, Keen-Circle K, Kundu A, Zhang J, Borlawsky TB
BMC Bioinformatics 2010, 11(Suppl 9):S3 (28 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
230.
Proceedings
Using gene co-expression network analysis to predict biomarkers for chronic lymphocytic
leukemia
Zhang J, Xiang Y, Ding L, Keen-Circle K, Borlawsky TB, Ozer HG, Jin R, Payne P, Huang K
BMC Bioinformatics 2010, 11(Suppl 9):S5 (28 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
231.
Proceedings
Mapping transcription mechanisms from multimodal genomic data
Chang HH, McGeachie M, Alterovitz G, Ramoni MF
BMC Bioinformatics 2010, 11(Suppl 9):S2 (28 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
232.
Proceedings
Stromal microenvironment processes unveiled by biological component analysis of gene
expression in xenograft tumor models
Yang X, Lee Y, Huang Y, Chen JL, Xing RH, Lussier YA
BMC Bioinformatics 2010, 11(Suppl 9):S11 (28 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
233.
Proceedings
Mining multi-item drug adverse effect associations in spontaneous reporting systems
Harpaz R, Chase HS, Friedman C
BMC Bioinformatics 2010, 11(Suppl 9):S7 (28 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
234.
Proceedings
Comparison of multiplex meta analysis techniques for understanding the acute rejection of
solid organ transplants
Morgan AA, Khatri P, Jones RH, Sarwal MM, Butte AJ
BMC Bioinformatics 2010, 11(Suppl 9):S6 (28 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
235.
Introduction
Selected proceedings of the 2010 Summit on Translational Bioinformatics
Mendonça EA, Tarczy-Hornoch P
BMC Bioinformatics 2010, 11(Suppl 9):S1 (28 October 2010)
[Abstract] [Full text] [PDF]
236.
Proceedings
Latent physiological factors of complex human diseases revealed by independent component
analysis of clinarrays
Chen DP, Dudley JT, Butte AJ
BMC Bioinformatics 2010, 11(Suppl 9):S4 (28 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
237.
Proceedings
Assessment of genetic variation for the LINE-1 retrotransposon from next generation
sequence data
Rouchka E, Montoya-Durango DE, Stribinskis V, Ramos K, Kalbfleisch T
BMC Bioinformatics 2010, 11(Suppl 9):S12 (28 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
238.
Proceedings
An integrative method for scoring candidate genes from association studies: application to
warfarin dosing
Tatonetti NP, Dudley JT, Sagreiya H, Butte AJ, Altman RB
BMC Bioinformatics 2010, 11(Suppl 9):S9 (28 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
239.
Proceedings
Assessing the quality of annotations in asthma gene expression experiments
Lacson R, Mbagwu M, Yousif H, Ohno-Machado L
BMC Bioinformatics 2010, 11(Suppl 9):S8 (28 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
240.
Research article
Subdivision of the MDR superfamily of medium-chain dehydrogenases/reductases through
iterative hidden Markov model refinement
Hedlund J, Jörnvall H, Persson B
BMC Bioinformatics 2010, 11:534 (27 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
241.
Research article
Integrated prediction of one-dimensional structural features and their relationships with
conformational flexibility in helical membrane proteins
Ahmad S, Singh YH, Paudel Y, Mori T, Sugita Y, Mizuguchi K
BMC Bioinformatics 2010, 11:533 (27 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
242.
Research
Graphical models for inferring single molecule dynamics
Bronson JE, Hofman JM, Fei J, Gonzalez RL, Wiggins CH
BMC Bioinformatics 2010, 11(Suppl 8):S2 (26 October 2010)
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243.
Research
Efficient motif finding algorithms for large-alphabet inputs
Kuksa PP, Pavlovic V
BMC Bioinformatics 2010, 11(Suppl 8):S1 (26 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
244.
Research
Inferring latent task structure for Multitask Learning by Multiple Kernel Learning
Widmer C, Toussaint NC, Altun Y, Rätsch G
BMC Bioinformatics 2010, 11(Suppl 8):S5 (26 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
245.
Research
A machine learning pipeline for quantitative phenotype prediction from genotype data
Guzzetta G, Jurman G, Furlanello C
BMC Bioinformatics 2010, 11(Suppl 8):S3 (26 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
246.
Research
Infinite mixture-of-experts model for sparse survival regression with application to breast
cancer
Raman S, Fuchs TJ, Wild PJ, Dahl E, Buhmann JM, Roth V
BMC Bioinformatics 2010, 11(Suppl 8):S8 (26 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
247.
Research
Classifying and scoring of molecules with the NGN: new datasets, significance tests, and
generalization
Ma EYT, Cameron CJF, Kremer SC
BMC Bioinformatics 2010, 11(Suppl 8):S4 (26 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
248.
Research
Exploiting physico-chemical properties in string kernels
Toussaint NC, Widmer C, Kohlbacher O, Rätsch G
BMC Bioinformatics 2010, 11(Suppl 8):S7 (26 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
249.
Research
Semi-supervised prediction of protein subcellular localization using abstraction augmented
Markov models
Caragea C, Caragea D, Silvescu A, Honavar V
BMC Bioinformatics 2010, 11(Suppl 8):S6 (26 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
250.
Software
Estimating time since infection in early homogeneous HIV-1 samples using a poisson model
Giorgi EE, Funkhouser B, Athreya G, Perelson AS, Korber BT, Bhattacharya T
BMC Bioinformatics 2010, 11:532 (25 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
251.
Software
BALL - biochemical algorithms library 1.3
Hildebrandt A, Dehof AK, Rurainski A, Bertsch A, Schumann M, Toussaint NC, Moll A, Stöckel
D, Nickels S, Mueller SC, Lenhof HP, Kohlbacher O
BMC Bioinformatics 2010, 11:531 (25 October 2010)
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252.
Methodology article
Formalization of taxon-based constraints to detect inconsistencies in annotation and
ontology development
Deegan (née Clark) JI, Dimmer EC, Mungall CJ
BMC Bioinformatics 2010, 11:530 (25 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
253.
Research article
Genomic selection and complex trait prediction using a fast EM algorithm applied to
genome-wide markers
Shepherd RK, Meuwissen THE, Woolliams JA
BMC Bioinformatics 2010, 11:529 (22 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
254.
Database
PathEx: a novel multi factors based datasets selector web tool
Bareke E, Pierre M, Gaigneaux A, Meulder BD, Depiereux S, Habra N, Depiereux E
BMC Bioinformatics 2010, 11:528 (22 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
255.
Software
CCRaVAT and QuTie - enabling analysis of rare variants in large-scale case control and
quantitative trait association studies
Lawrence R, Day-Williams AG, Elliott KS, Morris AP, Zeggini E
BMC Bioinformatics 2010, 11:527 (21 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
256.
Methodology article
A statistical approach to finding overlooked genetic associations
Rider AK, Siwo G, Chawla NV, Ferdig M, Emrich SJ
BMC Bioinformatics 2010, 11:526 (21 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
257.
Database
solQTL: a tool for QTL analysis, visualization and linking to genomes at SGN database
Tecle IY, Menda N, Buels RM, van der Knaap E, Mueller LA
BMC Bioinformatics 2010, 11:525 (21 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
258.
Methodology article
A genetic ensemble approach for gene-gene interaction identification
Yang P, Ho JWK, Zomaya AY, Zhou BB
BMC Bioinformatics 2010, 11:524 (21 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
259.
Research article
Class prediction for high-dimensional class-imbalanced data
Blagus R, Lusa L
BMC Bioinformatics 2010, 11:523 (20 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
260.
Methodology article
Structuring heterogeneous biological information using fuzzy clustering of k-partite graphs
Hartsperger ML, Blöchl F, Stümpflen V, Theis FJ
BMC Bioinformatics 2010, 11:522 (20 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
261.
Research article
Discover Protein Complexes in Protein-Protein Interaction Networks Using Parametric Local
Modularity
Kim J, Tan K
BMC Bioinformatics 2010, 11:521 (19 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
262.
Research article
Comparative study of discretization methods of microarray data for inferring transcriptional
regulatory networks
Li Y, Liu L, Bai X, Cai H, Ji W, Guo D, Zhu Y
BMC Bioinformatics 2010, 11:520 (19 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
263.
Research article
Statistical analysis and molecular dynamics simulations of ambivalent α -helices
Bhattacharjee N, Biswas P
BMC Bioinformatics 2010, 11:519 (18 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
264.
Methodology article
Accurate peak list extraction from proteomic mass spectra for identification and profiling
studies
Barbarini N, Magni P
BMC Bioinformatics 2010, 11:518 (16 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
265.
Methodology article
Inferring gene regression networks with model trees
Nepomuceno-Chamorro IA, Aguilar-Ruiz JS, Riquelme JC
BMC Bioinformatics 2010, 11:517 (15 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
266.
Software
QTLminer: identifying genes regulating quantitative traits
Alberts R, Schughart K
BMC Bioinformatics 2010, 11:516 (15 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
267.
Proceedings
Integrating diverse biological and computational sources for reliable protein-protein
interactions
Wu M, Li X, Chua HN, Kwoh CK, Ng SK
BMC Bioinformatics 2010, 11(Suppl 7):S8 (15 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
268.
Proceedings
Modeling the competition between lung metastases and the immune system using agents
Pennisi M, Pappalardo F, Palladini A, Nicoletti G, Nanni P, Lollini PL, Motta S
BMC Bioinformatics 2010, 11(Suppl 7):S13 (15 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
269.
Proceedings
Identification of a better Homo sapiens Class II HDAC inhibitor through binding energy
calculations and descriptor analysis
Tambunan USF, Wulandari EK
BMC Bioinformatics 2010, 11(Suppl 7):S16 (15 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
270.
Proceedings
DODO: an efficient orthologous genes assignment tool based on domain architectures.
Domain based ortholog detection
Chen T, Wu TH, Ng WV, Lin W
BMC Bioinformatics 2010, 11(Suppl 7):S6 (15 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
271.
Proceedings
Modularity of Escherichia coli sRNA regulation revealed by sRNA-target and protein network
analysis
Wu TH, Chang IYF, Chu LJ, Huang HC, Ng WV
BMC Bioinformatics 2010, 11(Suppl 7):S11 (15 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
272.
Proceedings
Network analysis of human protein location
Kumar G, Ranganathan S
BMC Bioinformatics 2010, 11(Suppl 7):S9 (15 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
273.
Proceedings
Intrinsically disordered domains deviate significantly from random sequences in mammalian
proteins
Teraguchi S, Patil A, Standley DM
BMC Bioinformatics 2010, 11(Suppl 7):S7 (15 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
274.
Proceedings
A quantitatively-modeled homozygosity mapping algorithm, qHomozygosityMapping,
utilizing whole genome single nucleotide polymorphism genotyping data
Huqun* , Fukuyama S, Morino H, Miyazawa H, Tanaka T, Suzuki T, Kohda M, Kawakami H,
Okazaki Y, Seyama K, Hagiwara K
BMC Bioinformatics 2010, 11(Suppl 7):S5 (15 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
275.
Proceedings
Robust and accurate prediction of noncoding RNAs from aligned sequences
Saito Y, Sato K, Sakakibara Y
BMC Bioinformatics 2010, 11(Suppl 7):S3 (15 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
276.
Proceedings
Gradual transition from mosaic to global DNA methylation patterns during deuterostome
evolution
Okamura K, Matsumoto KA, Nakai K
BMC Bioinformatics 2010, 11(Suppl 7):S2 (15 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
277.
Proceedings
DiScRIBinATE: a rapid method for accurate taxonomic classification of metagenomic
sequences
Ghosh TS, Haque M M, Mande SS
BMC Bioinformatics 2010, 11(Suppl 7):S14 (15 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
278.
Proceedings
Sensitivity analysis of dynamic biological systems with time-delays
Wu WH, Wang FS, Chang MS
BMC Bioinformatics 2010, 11(Suppl 7):S12 (15 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
279.
Proceedings
Analysis and verification of the HMGB1 signaling pathway
Gong H, Zuliani P, Komuravelli A, Faeder JR, Clarke EM
BMC Bioinformatics 2010, 11(Suppl 7):S10 (15 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
280.
Proceedings
T3SEdb: data warehousing of virulence effectors secreted by the bacterial Type III Secretion
System
Tay DMM, Govindarajan KR, Khan AM, Ong TYR, Samad HM, Soh WW, Tong M, Zhang F, Tan
TW
BMC Bioinformatics 2010, 11(Suppl 7):S4 (15 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
281.
Proceedings
IKKβ inhibitor identification: a multi-filter driven novel scaffold
Nagarajan S, Choo H, Cho YS, Shin KJ, Oh KS, Lee BH, Pae AN
BMC Bioinformatics 2010, 11(Suppl 7):S15 (15 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
282.
Introduction
InCoB2010 - 9th International Conference on Bioinformatics at Tokyo, Japan, September 2628, 2010
Schönbach C, Nakai K, Tan TW, Ranganathan S
BMC Bioinformatics 2010, 11(Suppl 7):S1 (15 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
283.
Methodology article
Comparative analysis of acute and chronic corticosteroid pharmacogenomic effects in rat
liver: Transcriptional dynamics and regulatory structures
Nguyen TT, Almon RR, DuBois DC, Jusko WJ, Androulakis IP
BMC Bioinformatics 2010, 11:515 (14 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
284.
Research article
Data structures and compression algorithms for high-throughput sequencing technologies
Daily K, Rigor P, Christley S, Xie X, Baldi P
BMC Bioinformatics 2010, 11:514 (14 October 2010)
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285.
Methodology article
Booly: a new data integration platform
Do LH, Esteves FF, Karten HJ, Bier E
BMC Bioinformatics 2010, 11:513 (13 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
286.
Research article
Quadratic variance models for adaptively preprocessing SELDI-TOF mass spectrometry data
Emanuele VA, Gurbaxani BM
BMC Bioinformatics 2010, 11:512 (13 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
287.
Methodology article
Trimming of mammalian transcriptional networks using network component analysis
Tran LM, Hyduke DR, Liao JC
BMC Bioinformatics 2010, 11:511 (13 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
288.
Research article
Functional Analysis: Evaluation of Response Intensities - Tailoring ANOVA for Lists of
Expression Subsets
Berger F, De Meulder B, Gaigneaux A, Depiereux S, Bareke E, Pierre M, De Hertogh B,
Delorenzi M, Depiereux E
BMC Bioinformatics 2010, 11:510 (13 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
289.
Methodology article
Confronting two-pair primer design for enzyme-free SNP genotyping based on a genetic
algorithm
Yang CH, Cheng YH, Chuang LY, Chang HW
BMC Bioinformatics 2010, 11:509 (13 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
290.
Methodology article
GenHtr: a tool for comparative assessment of genetic heterogeneity in microbial genomes
generated by massive short-read sequencing
Yu GX
BMC Bioinformatics 2010, 11:508 (12 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
291.
Research article
Proteome scanning to predict PDZ domain interactions using support vector machines
Hui S, Bader GD
BMC Bioinformatics 2010, 11:507 (12 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
292.
Software
Geoseq: a tool for dissecting deep-sequencing datasets
Gurtowski J, Cancio A, Shah H, Levovitz C, George A, Homann R, Sachidanandam R
BMC Bioinformatics 2010, 11:506 (12 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
293.
Research article
Examination of the relationship between essential genes in PPI network and hub proteins in
reverse nearest neighbor topology
Ning K, Ng HK, Srihari S, Leong HW, Nesvizhskii AI
BMC Bioinformatics 2010, 11:505 (12 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
294.
Research article
MCL-CAw: a refinement of MCL for detecting yeast complexes from weighted PPI networks
by incorporating core-attachment structure
Srihari S, Ning K, Leong HW
BMC Bioinformatics 2010, 11:504 (12 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
295.
Research article
Challenges in microarray class discovery: a comprehensive examination of normalization,
gene selection and clustering
Freyhult E, Landfors M, Önskog J, Hvidsten TR, Rydén P
BMC Bioinformatics 2010, 11:503 (11 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
296.
Methodology article
Misty Mountain clustering: application to fast unsupervised flow cytometry gating
Sugár IP, Sealfon SC
BMC Bioinformatics 2010, 11:502 (9 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
297.
Research article
Predicting enzyme targets for cancer drugs by profiling human Metabolic reactions in NCI-60
cell lines
Li L, Zhou X, Ching WK, Wang P
BMC Bioinformatics 2010, 11:501 (8 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
298.
Research article
Analysis of X-ray Structures of Matrix Metalloproteinases via Chaotic Map Clustering
Giangreco I, Nicolotti O, Carotti A, De Carlo F, Gargano G, Bellotti R
BMC Bioinformatics 2010, 11:500 (8 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
299.
Research article
Bi-directional gene set enrichment and canonical correlation analysis identify key dietsensitive pathways and biomarkers of metabolic syndrome
Morine MJ, McMonagle J, Toomey S, Reynolds CM, Moloney AP, Gormley IC, Gaora PÓ,
Roche HM
BMC Bioinformatics 2010, 11:499 (7 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
300.
Methodology article
Automatic, context-specific generation of Gene Ontology slims
Davis MJ, Sehgal MSB, Ragan MA
BMC Bioinformatics 2010, 11:498 (7 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [1 comment]
301.
Proceedings
Analysis of density based and fuzzy c-means clustering methods on lesion border extraction
in dermoscopy images
Kockara S, Mete M, Chen B, Aydin K
BMC Bioinformatics 2010, 11(Suppl 6):S26 (7 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
302.
Proceedings
Constructing non-stationary Dynamic Bayesian Networks with a flexible lag choosing
mechanism
Jia Y, Huan J
BMC Bioinformatics 2010, 11(Suppl 6):S27 (7 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
303.
Proceedings
Dynamics of protofibril elongation and association involved in Aβ42 peptide aggregation in
Alzheimer’s disease
Ghosh P, Kumar A, Datta B, Rangachari V
BMC Bioinformatics 2010, 11(Suppl 6):S24 (7 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
304.
Proceedings
Lesion detection in demoscopy images with novel density-based and active contour
approaches
Mete M, Sirakov NM
BMC Bioinformatics 2010, 11(Suppl 6):S23 (7 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
305.
Proceedings
Comparative genome analysis of PHB gene family reveals deep evolutionary origins and
diverse gene function
Di C, Xu W, Su Z, Yuan JS
BMC Bioinformatics 2010, 11(Suppl 6):S22 (7 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
306.
Proceedings
A predictive model for secondary RNA structure using graph theory and a neural network
Koessler DR, Knisley DJ, Knisley J, Haynes T
BMC Bioinformatics 2010, 11(Suppl 6):S21 (7 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
307.
Proceedings
A framework for automated enrichment of functionally significant inverted repeats in whole
genomes
Kandoth C, Ercal F, Frank RL
BMC Bioinformatics 2010, 11(Suppl 6):S20 (7 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
308.
Proceedings
Applying internal coordinate mechanics to model the interactions between 8R-lipoxygenase
and its substrate
Bai S, Du T, Khosravi E
BMC Bioinformatics 2010, 11(Suppl 6):S2 (7 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
309.
Proceedings
Phylometrics: a pipeline for inferring phylogenetic trees from a sequence relationship
network perspective
Smits SA, Ouverney CC
BMC Bioinformatics 2010, 11(Suppl 6):S18 (7 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
310.
Proceedings
Promoter prediction in E. coli based on SIDD profiles and Artificial Neural Networks
Bland C, Newsome AS, Markovets AA
BMC Bioinformatics 2010, 11(Suppl 6):S17 (7 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
311.
Proceedings
HPIDB - a unified resource for host-pathogen interactions
Kumar R, Nanduri B
BMC Bioinformatics 2010, 11(Suppl 6):S16 (7 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
312.
Introduction
Proceedings of the 2010 MidSouth Computational Biology and Bioinformatics Society
(MCBIOS) Conference
Wren JD, Kupfer DM, Perkins EJ, Bridges S, Berleant D
BMC Bioinformatics 2010, 11(Suppl 6):S1 (7 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
313.
Proceedings
Analysis of Bovine Viral Diarrhea Viruses-infected monocytes: identification of cytopathic
and non-cytopathic biotype differences
Ammari M, McCarthy FM, Nanduri B, Pinchuk LM
BMC Bioinformatics 2010, 11(Suppl 6):S9 (7 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
314.
Proceedings
Identification of diagnostic subnetwork markers for cancer in human protein-protein
interaction network
Su J, Yoon BJ, Dougherty ER
BMC Bioinformatics 2010, 11(Suppl 6):S8 (7 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
315.
Proceedings
PEPPI: a peptidomic database of human protein isoforms for proteomics experiments
Zhou A, Zhang F, Chen JY
BMC Bioinformatics 2010, 11(Suppl 6):S7 (7 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
316.
Proceedings
Two new ArrayTrack libraries for personalized biomedical research
Xu J, Wise C, Varma V, Fang H, Ning B, Hong H, Tong W, Kaput J
BMC Bioinformatics 2010, 11(Suppl 6):S6 (7 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
317.
Proceedings
The EDKB: an established knowledge base for endocrine disrupting chemicals
Ding D, Xu L, Fang H, Hong H, Perkins R, Harris S, Bearden ED, Shi L, Tong W
BMC Bioinformatics 2010, 11(Suppl 6):S5 (7 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
318.
Proceedings
Next generation models for storage and representation of microbial biological annotation
Quest DJ, Land ML, Brettin TS, Cottingham RW
BMC Bioinformatics 2010, 11(Suppl 6):S15 (7 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
319.
Proceedings
Discovering gene functional relationships using FAUN (Feature Annotation Using
Nonnegative matrix factorization)
Tjioe E, Berry MW, Homayouni R
BMC Bioinformatics 2010, 11(Suppl 6):S14 (7 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
320.
Proceedings
Quail Genomics: a knowledgebase for Northern bobwhite
Rawat A, Gust KA, Elasri MO, Perkins EJ
BMC Bioinformatics 2010, 11(Suppl 6):S13 (7 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
321.
Proceedings
Enzyme structure dynamics of xylanase I from Trichoderma longibrachiatum
Uzuner U, Shi W, Liu L, Liu S, Dai SY, Yuan JS
BMC Bioinformatics 2010, 11(Suppl 6):S12 (7 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
322.
Proceedings
Evaluation of gene expression data generated from expired Affymetrix GeneChip®
microarrays using MAQC reference RNA samples
Wen Z, Wang C, Shi Q, Huang Y, Su Z, Hong H, Tong W, Shi L
BMC Bioinformatics 2010, 11(Suppl 6):S10 (7 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
323.
Proceedings
An FDA bioinformatics tool for microbial genomics research on molecular characterization of
bacterial foodborne pathogens using microarrays
Fang H, Xu J, Ding D, Jackson SA, Patel IR, Frye JG, Zou W, Nayak R, Foley S, Chen J, Su Z, Ye Y,
Turner S, Harris S, Zhou G, Cerniglia C, Tong W
BMC Bioinformatics 2010, 11(Suppl 6):S4 (7 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
324.
Proceedings
Assessing constancy of substitution rates in viruses over evolutionary time
Melcher U
BMC Bioinformatics 2010, 11(Suppl 6):S3 (7 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
325.
Proceedings
Mixed reality simulation of rasping procedure in artificial cervical disc replacement (ACDR)
surgery
Halic T, Kockara S, Bayrak C, Rowe R
BMC Bioinformatics 2010, 11(Suppl 6):S11 (7 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
326.
Proceedings
GOModeler- A tool for hypothesis-testing of functional genomics datasets
Manda P, Freeman MKG, Bridges SM, Jankun-Kelly TJ, Nanduri B, McCarthy FM, Burgess SC
BMC Bioinformatics 2010, 11(Suppl 6):S29 (7 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
327.
Proceedings
Integrated database for identifying candidate genes for Aspergillus flavus resistance in maize
Kelley RY, Gresham C, Harper J, Bridges SM, Warburton ML, Hawkins LK, Pechanova O,
Peethambaran B, Pechan T, Luthe DS, Mylroie JE, Ankala A, Ozkan S, Henry WB, Williams WP
BMC Bioinformatics 2010, 11(Suppl 6):S25 (7 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
328.
Proceedings
IView: introgression library visualization and query tool
Bottoms CA, Flint-Garcia S, McMullen MD
BMC Bioinformatics 2010, 11(Suppl 6):S28 (7 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
329.
Proceedings
Time lagged information theoretic approaches to the reverse engineering of gene regulatory
networks
Chaitankar V, Ghosh P, Perkins EJ, Gong P, Zhang C
BMC Bioinformatics 2010, 11(Suppl 6):S19 (7 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
330.
Methodology article
DiffCoEx: a simple and sensitive method to find differentially coexpressed gene modules
Tesson BM, Breitling R, Jansen RC
BMC Bioinformatics 2010, 11:497 (6 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
331.
Software
MetAssimulo:Simulation of Realistic NMR Metabolic Profiles
Muncey HJ, Jones R, De Iorio M, Ebbels TMD
BMC Bioinformatics 2010, 11:496 (6 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
332.
Research article
An integrated analysis of molecular aberrations in NCI-60 cell lines
Yeang CH
BMC Bioinformatics 2010, 11:495 (6 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
333.
Introduction
Highlights of the BioTM 2010 workshop on advances in bio text mining
Abeel T, Van Landeghem S, Morante R, Van Asch V, Van de Peer Y, Daelemans W, Saeys Y
BMC Bioinformatics 2010, 11(Suppl 5):I1 (6 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
334.
Oral presentation
The PPI affix dictionary (PPIAD) and BioMethod Lexicon: importance of affixes and tags for
recognition of entity mentions and experimental protein interactions
Krallinger M, Tendulkar AV, Leitner F, Chatr-aryamontri A, Valencia A
BMC Bioinformatics 2010, 11(Suppl 5):O1 (6 October 2010)
[Abstract] [Full text] [PDF]
335.
Oral presentation
Integrating text mining into high-throughput assay analysis
Cohen KB
BMC Bioinformatics 2010, 11(Suppl 5):O3 (6 October 2010)
[Abstract] [Full text] [PDF]
336.
Oral presentation
Event extraction on PubMed scale
Ginter F, Björne J, Pyysalo S
BMC Bioinformatics 2010, 11(Suppl 5):O2 (6 October 2010)
[Abstract] [Full text] [PDF]
337.
Oral presentation
Integrating automated literature searches and text mining in biomarker discovery
Ongenaert M, Dehaspe L
BMC Bioinformatics 2010, 11(Suppl 5):O5 (6 October 2010)
[Abstract] [Full text] [PDF]
338.
Poster presentation
Functional variation of alternative splice forms in their protein interaction networks: a
literature mining approach
Kafkas , Varoğlu E, Rebholz-Schuhmann D, Taneri B
BMC Bioinformatics 2010, 11(Suppl 5):P1 (6 October 2010)
[Abstract] [Full text] [PDF]
339.
Poster presentation
Semantic integration of isolation habitat and location in StrainInfo
Verslyppe B, De Smet W, De Vos P, De Baets B, Dawyndt P
BMC Bioinformatics 2010, 11(Suppl 5):P3 (6 October 2010)
[Abstract] [Full text] [PDF]
340.
Poster presentation
Species identification for gene name normalization
Solt I, Tikk D, Leser U
BMC Bioinformatics 2010, 11(Suppl 5):P5 (6 October 2010)
[Abstract] [Full text] [PDF]
341.
Poster presentation
Medie and Info-pubmed: 2010 update
Ohta T, Matsuzaki T, Okazaki N, Miwa M, Sætre R, Pyysalo S, Tsujii J
BMC Bioinformatics 2010, 11(Suppl 5):P7 (6 October 2010)
[Abstract] [Full text] [PDF]
342.
Poster presentation
Extracting drug-drug interactions from biomedical texts
Segura-Bedmar I, Martínez P, de Pablo-Sánchez C
BMC Bioinformatics 2010, 11(Suppl 5):P9 (6 October 2010)
[Abstract] [Full text] [PDF]
343.
Poster presentation
A fast and effective dependency graph kernel for PPI relation extraction
Tikk D, Palaga P, Leser U
BMC Bioinformatics 2010, 11(Suppl 5):P8 (6 October 2010)
[Abstract] [Full text] [PDF]
344.
Poster presentation
BioLMiner and the BioCreative II.5 challenge
Chen Y, Liu F, Manderick B
BMC Bioinformatics 2010, 11(Suppl 5):P6 (6 October 2010)
[Abstract] [Full text] [PDF]
345.
Poster presentation
Identification of concepts bridging diverse biomedical domains
Juršič M, Mozetič I, Grčar M, Cestnik B, Lavrač N
BMC Bioinformatics 2010, 11(Suppl 5):P4 (6 October 2010)
[Abstract] [Full text] [PDF]
346.
Poster presentation
Supporting the search for cross-context links by outlier detection methods
Sluban B, Lavrač N
BMC Bioinformatics 2010, 11(Suppl 5):P2 (6 October 2010)
[Abstract] [Full text] [PDF]
347.
Oral presentation
Pitfalls in applying text mining to scientific literature
Neefs JM
BMC Bioinformatics 2010, 11(Suppl 5):O4 (6 October 2010)
[Abstract] [Full text] [PDF]
348.
Research article
Accurate and efficient gp120 V3 loop structure based models for the determination of HIV-1
co-receptor usage
Masso M, Vaisman II
BMC Bioinformatics 2010, 11:494 (5 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
349.
Methodology article
A systematic study of genome context methods: calibration, normalization and combination
Ferrer L, Dale JM, Karp PD
BMC Bioinformatics 2010, 11:493 (1 October 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
350.
Research article
The structural and content aspects of abstracts versus bodies of full text journal articles are
different
Cohen KB, Johnson HL, Verspoor K, Roeder C, Hunter LE
BMC Bioinformatics 2010, 11:492 (29 September 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
351.
Methodology article
Non-coding RNA detection methods combined to improve usability, reproducibility and
precision
Raasch P, Schmitz U, Patenge N, Vera J, Kreikemeyer B, Wolkenhauer O
BMC Bioinformatics 2010, 11:491 (29 September 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
352.
Methodology article
BPDA - A Bayesian peptide detection algorithm for mass spectrometry
Sun Y, Zhang J, Braga-Neto U, Dougherty ER
BMC Bioinformatics 2010, 11:490 (29 September 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
353.
Software
Computationally efficient flux variability analysis
Gudmundsson S, Thiele I
BMC Bioinformatics 2010, 11:489 (29 September 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
354.
Methodology article
A global optimization algorithm for protein surface alignment
Bertolazzi P, Guerra C, Liuzzi G
BMC Bioinformatics 2010, 11:488 (29 September 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
355.
Research article
Analysis of lifestyle and metabolic predictors of visceral obesity with Bayesian Networks
Aussem A, Tchernof A, de Morais SR, Rome S
BMC Bioinformatics 2010, 11:487 (28 September 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
356.
Methodology article
A semi-nonparametric mixture model for selecting functionally consistent proteins
Yu L, Doerge RW
BMC Bioinformatics 2010, 11:486 (28 September 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
357.
Software
SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data
Cox MP, Peterson DA, Biggs PJ
BMC Bioinformatics 2010, 11:485 (27 September 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
358.
Research article
Protein network prediction and topological analysis in Leishmania major as a tool for drug
target selection
Flórez AF, Park D, Bhak J, Kim BC, Kuchinsky A, Morris JH, Espinosa J, Muskus C
BMC Bioinformatics 2010, 11:484 (27 September 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
359.
Methodology article
Asymmetric microarray data produces gene lists highly predictive of research literature on
multiple cancer types
Dawany NB, Tozeren A
BMC Bioinformatics 2010, 11:483 (27 September 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
360.
Research article
MultiRTA: A simple yet reliable method for predicting peptide binding affinities for multiple
class II MHC allotypes
Bordner AJ, Mittelmann HD
BMC Bioinformatics 2010, 11:482 (24 September 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
361.
Research article
Predicting phenotypic traits of prokaryotes from protein domain frequencies
Lingner T, Mühlhausen S, Gabaldón T, Notredame C, Meinicke P
BMC Bioinformatics 2010, 11:481 (24 September 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
362.
Research article
Using diffusion distances for flexible molecular shape comparison
Liu YS, Li Q, Zheng GQ, Ramani K, Benjamin W
BMC Bioinformatics 2010, 11:480 (24 September 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
363.
Research article
Computational analysis and modeling of cleavage by the immunoproteasome and the
constitutive proteasome
Diez-Rivero CM, Lafuente EM, Reche PA
BMC Bioinformatics 2010, 11:479 (23 September 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
364.
Research article
Detecting variants with Metabolic Design, a new software tool to design probes for
explorative functional DNA microarray development
Terrat S, Peyretaillade E, Gonçalves O, Dugat-Bony E, Gravelat F, Moné A, Biderre-Petit C,
Boucher D, Troquet J, Peyret P
BMC Bioinformatics 2010, 11:478 (23 September 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
365.
Research article
A bi-ordering approach to linking gene expression with clinical annotations in gastric cancer
Shi F, Leckie C, MacIntyre G, Haviv I, Boussioutas A, Kowalczyk A
BMC Bioinformatics 2010, 11:477 (23 September 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
366.
Research article
Improving performance of mammalian microRNA target prediction
Liu H, Yue D, Chen Y, Gao SJ, Huang Y
BMC Bioinformatics 2010, 11:476 (22 September 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
367.
Research article
FragViz: visualization of fragmented networks
Štajdohar M, Mramor M, Zupan B, Demšar J
BMC Bioinformatics 2010, 11:475 (22 September 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
368.
Research article
ModuleOrganizer: detecting modules in families of transposable elements
Tempel S, Rousseau C, Tahi F, Nicolas J
BMC Bioinformatics 2010, 11:474 (22 September 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
369.
Software
PeptideMine - A webserver for the design of peptides for protein-peptide binding studies
derived from protein-protein interactomes
Shameer K, Madan LL, Veeranna S, Gopal B, Sowdhamini R
BMC Bioinformatics 2010, 11:473 (22 September 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
370.
Software
GPFrontend and GPGraphics: graphical analysis tools for genetic association studies
Uebe S, Pasutto F, Krumbiegel M, Schanze D, Ekici AB, Reis A
BMC Bioinformatics 2010, 11:472 (21 September 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
371.
Software
SeqAnt: A web service to rapidly identify and annotate DNA sequence variations
Shetty AC, Athri P, Mondal K, Horner VL, Steinberg KM, Patel V, Caspary T, Cutler DJ, Zwick
ME
BMC Bioinformatics 2010, 11:471 (20 September 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
372.
Research article
Trees on networks: resolving statistical patterns of phylogenetic similarities among
interacting proteins
Kelly WP, Stumpf MPH
BMC Bioinformatics 2010, 11:470 (20 September 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
373.
Oral presentation
Entities, relations, events: representing biomolecular semantics
Pyysalo S
BMC Bioinformatics 2010, 11(Suppl 5):O6 (20 September 2010)
[Abstract] [Full text] [PDF]
374.
Software
MetNetGE: interactive views of biological networks and ontologies
Jia M, Choi SY, Reiners D, Wurtele ES, Dickerson JA
BMC Bioinformatics 2010, 11:469 (17 September 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
375.
Research article
Multivariate meta-analysis of proteomics data from human prostate and colon tumours
Rosenberg LH, Franzén B, Auer G, Lehtiö J, Forshed J
BMC Bioinformatics 2010, 11:468 (17 September 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
376.
Software
ClustalXeed: a GUI-based grid computation version for high performance and terabyte size
multiple sequence alignment
Kim T, Joo H
BMC Bioinformatics 2010, 11:467 (17 September 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [2 comments]
377.
Research article
Investigating the validity of current network analysis on static conglomerate networks by
protein network stratification
Zhang M, Lu LJ
BMC Bioinformatics 2010, 11:466 (16 September 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
378.
Research article
Parallel multiplicity and error discovery rate (EDR) in microarray experiments
Xu WW, Carter CJ
BMC Bioinformatics 2010, 11:465 (16 September 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
379.
Research article
Sigma-2: Multiple sequence alignment of non-coding DNA via an evolutionary model
Jayaraman G, Siddharthan R
BMC Bioinformatics 2010, 11:464 (16 September 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
380.
Correction
Correction: Comparison of codon usage measures and their applicability in prediction of
microbial gene expressivity
Supek F, Vlahoviček K
BMC Bioinformatics 2010, 11:463 (16 September 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
381.
Research article
Context dependent substitution biases vary within the human genome
Nevarez PA, DeBoever CM, Freeland BJ, Quitt MA, Bush EC
BMC Bioinformatics 2010, 11:462 (15 September 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
382.
Software
Pan-genome sequence analysis using Panseq: an online tool for the rapid analysis of core
and accessory genomic regions
Laing C, Buchanan C, Taboada EN, Zhang Y, Kropinski A, Villegas A, Thomas JE, Gannon VPJ
BMC Bioinformatics 2010, 11:461 (15 September 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
383.
Methodology article
Candidate gene prioritization by network analysis of differential expression using machine
learning approaches
Nitsch D, Gonçalves JP, Ojeda F, de Moor B, Moreau Y
BMC Bioinformatics 2010, 11:460 (14 September 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
384.
Research article
Comparative study of three commonly used continuous deterministic methods for modeling
gene regulation networks
Swain MT, Mandel JJ, Dubitzky W
BMC Bioinformatics 2010, 11:459 (14 September 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
385.
Research article
The Neural/Immune Gene Ontology: clipping the Gene Ontology for neurological and
immunological systems
Geifman N, Monsonego A, Rubin E
BMC Bioinformatics 2010, 11:458 (12 September 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
386.
Research article
An algorithm for automated closure during assembly
Koren S, Miller JR, Walenz BP, Sutton G
BMC Bioinformatics 2010, 11:457 (10 September 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
387.
Methodology article
Multivariate Hawkes process models of the occurrence of regulatory elements
Carstensen L, Sandelin A, Winther O, Hansen NR
BMC Bioinformatics 2010, 11:456 (9 September 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
388.
Software
Next generation tools for genomic data generation, distribution, and visualization
Nix DA, Di Sera TL, Dalley BK, Milash BA, Cundick RM, Quinn KS, Courdy SJ
BMC Bioinformatics 2010, 11:455 (9 September 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
389.
Research article
On the Choice and Number of Microarrays for Transcriptional Regulatory Network Inference
Cosgrove EJ, Gardner TS, Kolaczyk ED
BMC Bioinformatics 2010, 11:454 (9 September 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
390.
Research article
A multifactorial analysis of obesity as CVD risk factor: Use of neural network based methods
in a nutrigenetics context
Valavanis IK, Mougiakakou SG, Grimaldi KA, Nikita KS
BMC Bioinformatics 2010, 11:453 (8 September 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
391.
Methodology article
Simple and flexible classification of gene expression microarrays via Swirls and Ripples
Baker SG
BMC Bioinformatics 2010, 11:452 (8 September 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
392.
Software
VIGOR, an annotation program for small viral genomes
Wang S, Sundaram JP, Spiro D
BMC Bioinformatics 2010, 11:451 (7 September 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
393.
Research article
Filtering, FDR and power
van Iterson M, Boer JM, Menezes RX
BMC Bioinformatics 2010, 11:450 (7 September 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
394.
Database
Consistency, comprehensiveness, and compatibility of pathway databases
Soh D, Dong D, Guo Y, Wong L
BMC Bioinformatics 2010, 11:449 (7 September 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [1 comment]
395.
Software
Harvest: an open-source tool for the validation and improvement of peptide identification
metrics and fragmentation exploration
McHugh LC, Arthur JW
BMC Bioinformatics 2010, 11:448 (6 September 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
396.
Research article
Sample size and statistical power considerations in high-dimensionality data settings: a
comparative study of classification algorithms
Guo Y, Graber A, McBurney RN, Balasubramanian R
BMC Bioinformatics 2010, 11:447 (3 September 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
397.
Methodology article
Fast and accurate protein substructure searching with simulated annealing and GPUs
Stivala AD, Stuckey PJ, Wirth AI
BMC Bioinformatics 2010, 11:446 (3 September 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
398.
Research article
Automatic detection of anchor points for multiple sequence alignment
Pitschi F, Devauchelle C, Corel E
BMC Bioinformatics 2010, 11:445 (2 September 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
399.
Software
Genome3D: A viewer-model framework for integrating and visualizing multi-scale
epigenomic information within a three-dimensional genome
Asbury TM, Mitman M, Tang J, Zheng WJ
BMC Bioinformatics 2010, 11:444 (2 September 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
400.
Methodology article
Efficient Bayesian approach for multilocus association mapping including gene-gene
interactions
Marttinen P, Corander J
BMC Bioinformatics 2010, 11:443 (2 September 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
401.
Methodology article
Forward-time simulation of realistic samples for genome-wide association studies
Peng B, Amos CI
BMC Bioinformatics 2010, 11:442 (1 September 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
402.
Methodology article
Relations as patterns: bridging the gap between OBO and OWL
Hoehndorf R, Oellrich A, Dumontier M, Kelso J, Rebholz-Schuhmann D, Herre H
BMC Bioinformatics 2010, 11:441 (31 August 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
403.
Methodology article
An exploratory data analysis method to reveal modular latent structures in high-throughput
data
Yu T
BMC Bioinformatics 2010, 11:440 (27 August 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
404.
Methodology article
CMASA: an accurate algorithm for detecting local protein structural similarity and its
application to enzyme catalytic site annotation
Li GH, Huang JF
BMC Bioinformatics 2010, 11:439 (27 August 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
405.
Software
*omeSOM: a software for clustering and visualization of transcriptional and metabolite data
mined from interspecific crosses of crop plants
Milone DH, Stegmayer GS, Kamenetzky L, López M, Lee JM, Giovannoni JJ, Carrari F
BMC Bioinformatics 2010, 11:438 (26 August 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
406.
Research article
Coherent pipeline for biomarker discovery using mass spectrometry and bioinformatics
Al-Shahib A, Misra R, Ahmod N, Fang M, Shah H, Gharbia S
BMC Bioinformatics 2010, 11:437 (26 August 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
407.
Software
A Dynamic Noise Level Algorithm for Spectral Screening of Peptide MS/MS Spectra
Xu H, Freitas MA
BMC Bioinformatics 2010, 11:436 (23 August 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
408.
Database
CircuitsDB: a database of mixed microRNA/transcription factor feed-forward regulatory
circuits in human and mouse
Friard O, Re A, Taverna D, De Bortoli M, Corá D
BMC Bioinformatics 2010, 11:435 (23 August 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
409.
Methodology article
A classification approach for genotyping viral sequences based on multidimensional scaling
and linear discriminant analysis
Kim J, Ahn Y, Lee K, Park SH, Kim S
BMC Bioinformatics 2010, 11:434 (21 August 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
410.
Software
Gene Expression Browser: large-scale and cross-experiment microarray data integration,
management, search & visualization
Zhang M, Zhang Y, Liu L, Yu L, Tsang S, Tan J, Yao W, Kang MS, An Y, Fan X
BMC Bioinformatics 2010, 11:433 (20 August 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
411.
Research article
rSW-seq: Algorithm for detection of copy number alterations in deep sequencing data
Kim TM, Luquette LJ, Xi R, Park PJ
BMC Bioinformatics 2010, 11:432 (18 August 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
412.
Research article
Hidden Markov model speed heuristic and iterative HMM search procedure
Johnson LS, Eddy SR, Portugaly E
BMC Bioinformatics 2010, 11:431 (18 August 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
413.
Research article
Coverage statistics for sequence census methods
Evans SN, Hower V, Pachter L
BMC Bioinformatics 2010, 11:430 (18 August 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
414.
Research article
Calculation of accurate small angle X-ray scattering curves from coarse-grained protein
models
Stovgaard K, Andreetta C, Ferkinghoff-Borg J, Hamelryck T
BMC Bioinformatics 2010, 11:429 (18 August 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
415.
Methodology article
Clustering of protein families into functional subtypes using Relative Complexity Measure
with reduced amino acid alphabets
Albayrak A, Otu HH, Sezerman UO
BMC Bioinformatics 2010, 11:428 (18 August 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
416.
Methodology article
An adaptive optimal ensemble classifier via bagging and rank aggregation with applications
to high dimensional data
Datta S, Pihur V, Datta S
BMC Bioinformatics 2010, 11:427 (18 August 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
417.
Methodology article
TOPSAN: a collaborative annotation environment for structural genomics
Weekes D, Krishna SS, Bakolitsa C, Wilson IA, Godzik A, Wooley J
BMC Bioinformatics 2010, 11:426 (17 August 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
418.
Methodology article
TF-finder: A software package for identifying transcription factors involved in biological
processes using microarray data and existing knowledge base
Cui X, Wang T, Chen HS, Busov V, Wei H
BMC Bioinformatics 2010, 11:425 (12 August 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
419.
Methodology article
Computing H/D-Exchange rates of single residues from data of proteolytic fragments
Althaus E, Canzar S, Ehrler C, Emmett MR, Karrenbauer A, Marshall AG, Meyer-Bäse A, Tipton
JD, Zhang HM
BMC Bioinformatics 2010, 11:424 (11 August 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
420.
Methodology article
Ranked retrieval of Computational Biology models
Henkel R, Endler L, Peters A, Le Novère N, Waltemath D
BMC Bioinformatics 2010, 11:423 (11 August 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
421.
Research article
baySeq: Empirical Bayesian methods for identifying differential expression in sequence
count data
Hardcastle TJ, Kelly KA
BMC Bioinformatics 2010, 11:422 (10 August 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
422.
Database
Microarray meta-analysis database (M2DB): a uniformly pre-processed, quality controlled,
and manually curated human clinical microarray database
Cheng WC, Tsai ML, Chang CW, Huang CL, Chen CR, Shu WY, Lee YS, Wang TH, Hong JH, Li CY,
Hsu IC
BMC Bioinformatics 2010, 11:421 (10 August 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
423.
Research article
An improved classification of G-protein-coupled receptors using sequence-derived features
Peng ZL, Yang JY, Chen X
BMC Bioinformatics 2010, 11:420 (9 August 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
424.
Methodology article
TAM: A method for enrichment and depletion analysis of a microRNA category in a list of
microRNAs
Lu M, Shi B, Wang J, Cao Q, Cui Q
BMC Bioinformatics 2010, 11:419 (9 August 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
425.
Software
eGIFT: Mining Gene Information from the Literature
Tudor CO, Schmidt CJ, Vijay-Shanker K
BMC Bioinformatics 2010, 11:418 (9 August 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
426.
Methodology article
FACT: Functional annotation transfer between proteins with similar feature architectures
Koestler T, von Haeseler A, Ebersberger I
BMC Bioinformatics 2010, 11:417 (9 August 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
427.
Research article
Survival dimensionality reduction (SDR): development and clinical application of an
innovative approach to detect epistasis in presence of right-censored data
Beretta L, Santaniello A, van Riel PLCM, Coenen MJH, Scorza R
BMC Bioinformatics 2010, 11:416 (6 August 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
428.
Software
PeakAnalyzer: Genome-wide annotation of chromatin binding and modification loci
Salmon-Divon M, Dvinge H, Tammoja K, Bertone P
BMC Bioinformatics 2010, 11:415 (6 August 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
429.
Methodology article
Global parameter estimation methods for stochastic biochemical systems
Poovathingal SK, Gunawan R
BMC Bioinformatics 2010, 11:414 (6 August 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
430.
Research article
Nonparametric identification of regulatory interactions from spatial and temporal gene
expression data
Aswani A, Keränen SVE, Brown J, Fowlkes CC, Knowles DW, Biggin MD, Bickel P, Tomlin CJ
BMC Bioinformatics 2010, 11:413 (4 August 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
431.
Research article
The effect of prior assumptions over the weights in BayesPI with application to study
protein-DNA interactions from ChIP-based high-throughput data
Wang J
BMC Bioinformatics 2010, 11:412 (4 August 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
432.
Research article
Extracting the abstraction pyramid from complex networks
Cheng CY, Hu YJ
BMC Bioinformatics 2010, 11:411 (3 August 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
433.
Methodology article
A method for automatically extracting infectious disease-related primers and probes from
the literature
García-Remesal M, Cuevas A, López-Alonso V, López-Campos G, de la Calle G, de la Iglesia D,
Pérez-Rey D, Crespo J, Martín-Sánchez F, Maojo V
BMC Bioinformatics 2010, 11:410 (3 August 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
434.
Research article
Estimating the individualized HIV-1 genetic barrier to resistance using a nelfinavir fitness
landscape
Theys K, Deforche K, Beheydt G, Moreau Y, van Laethem K, Lemey P, Camacho RJ, Rhee SY,
Shafer RW, Van Wijngaerden E, Vandamme AM
BMC Bioinformatics 2010, 11:409 (3 August 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
435.
Research article
Comparison study of microarray meta-analysis methods
Campain A, Yang YH
BMC Bioinformatics 2010, 11:408 (3 August 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
436.
Research article
Predicting β-turns and their types using predicted backbone dihedral angles and secondary
structures
Kountouris P, Hirst JD
BMC Bioinformatics 2010, 11:407 (31 July 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
437.
Research article
MS4 - Multi-Scale Selector of Sequence Signatures: An alignment-free method for
classification of biological sequences
Corel E, Pitschi F, Laprevotte I, Grasseau G, Didier G, Devauchelle C
BMC Bioinformatics 2010, 11:406 (30 July 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
438.
Software
OpenChrom: a cross-platform open source software for the mass spectrometric analysis of
chromatographic data
Wenig P, Odermatt J
BMC Bioinformatics 2010, 11:405 (30 July 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
439.
Software
RuleMonkey: software for stochastic simulation of rule-based models
Colvin J, Monine MI, Gutenkunst RN, Hlavacek WS, Von Hoff DD, Posner RG
BMC Bioinformatics 2010, 11:404 (30 July 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
440.
Methodology article
Data reduction for spectral clustering to analyze high throughput flow cytometry data
Zare H, Shooshtari P, Gupta A, Brinkman RR
BMC Bioinformatics 2010, 11:403 (28 July 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [1 comment]
441.
Research article
Sequence-based identification of interface residues by an integrative profile combining
hydrophobic and evolutionary information
Chen P, Li J
BMC Bioinformatics 2010, 11:402 (28 July 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
442.
Research article
Inference on population history and model checking using DNA sequence and microsatellite
data with the software DIYABC (v1.0)
Cornuet JM, Ravigné V, Estoup A
BMC Bioinformatics 2010, 11:401 (28 July 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
443.
Research article
Intensity dependent estimation of noise in microarrays improves detection of differentially
expressed genes
Zeisel A, Amir A, Köstler WJ, Domany E
BMC Bioinformatics 2010, 11:400 (27 July 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
444.
Methodology article
Quantized correlation coefficient for measuring reproducibility of ChIP-chip data
Peng S, Kuroda MI, Park PJ
BMC Bioinformatics 2010, 11:399 (27 July 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
445.
Database
CIG-DB: the database for human or mouse immunoglobulin and T cell receptor genes
available for cancer studies
Nakamura Y, Komiyama T, Furue M, Gojobori T, Akiyama Y
BMC Bioinformatics 2010, 11:398 (27 July 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
446.
Methodology article
Simultaneous prediction of transcription factor binding sites in a group of prokaryotic
genomes
Zhang S, Li S, Pham PT, Su Z
BMC Bioinformatics 2010, 11:397 (23 July 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
447.
Research article
Application of machine learning methods to histone methylation ChIP-Seq data reveals
H4R3me2 globally represses gene expression
Xu X, Hoang S, Mayo MW, Bekiranov S
BMC Bioinformatics 2010, 11:396 (23 July 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
448.
Software
MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometrybased molecular profile data
Pluskal T, Castillo S, Villar-Briones A, Orešič M
BMC Bioinformatics 2010, 11:395 (23 July 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
449.
Oral presentation
Genomic analysis of a rare human tumor
Jones SJM, Laskin J, Li YY, Griffith OL, An J, Bilenky M, Butterfield YS, Cezard T, Chuah E,
Corbett R, Fejes A, Griffith M, Yee J, Martin M, Mayo M, Melnyk N, Morin RD, Pugh TJ,
Severson T, Shah SP, Sutcliffe M, Tam A, Terry J, Thiessen N, Thomson T, Varhol R, Zeng T,
Zhao Y, Moore RA, Huntsman DG, Birol I, Hirst M, Holt RA, Marra MA
BMC Bioinformatics 2010, 11(Suppl 4):O3 (23 July 2010)
[Abstract] [Full text] [PDF]
450.
Poster presentation
Pleiotropy of tumor necrosis factor-α in C2C12 myotubes: in vitro studies on genes, networks
and pathways involved in TNF-α induced skeletal muscle atrophy
Bhatnagar S, Panguluri SK, Lundy RF, Kumar A
BMC Bioinformatics 2010, 11(Suppl 4):P13 (23 July 2010)
[Abstract] [Full text] [PDF]
451.
Poster presentation
The HHMI National Genomics Research Initiative at Western Kentucky University
King RA, Rinehart C, Parthasarathy PT
BMC Bioinformatics 2010, 11(Suppl 4):P20 (23 July 2010)
[Abstract] [Full text] [PDF]
452.
Poster presentation
Identifying potential drugs that induce QT prolongation using electronic medical records
Liu M, Denny JC, Mani S, Chen Y, Hu Y, Xu H
BMC Bioinformatics 2010, 11(Suppl 4):P2 (23 July 2010)
[Abstract] [Full text] [PDF]
453.
Oral presentation
Association of genomewide newborn DNA methylation patterns with maternal and newborn
characteristics
Adkins RM, Krushkal J, Zeisel S, Piyathilake C, Tylavsky F, Somes G
BMC Bioinformatics 2010, 11(Suppl 4):O4 (23 July 2010)
[Abstract] [Full text] [PDF]
454.
Oral presentation
Integrating experimental and computational approaches for the proteogenomic
characterizations of microbial communities
Hettich RL, Russell AL, VerBerkmoes NC, Shah M, Fraser-Liggett C, Jansson JK
BMC Bioinformatics 2010, 11(Suppl 4):O6 (23 July 2010)
[Abstract] [Full text] [PDF]
455.
Oral presentation
Analysis of equine protein-coding gene structure and expression by RNA-sequencing
Coleman SJ, Zeng Z, Liu J, MacLeod JN
BMC Bioinformatics 2010, 11(Suppl 4):O8 (23 July 2010)
[Abstract] [Full text] [PDF]
456.
Poster presentation
WebGestalt2: an updated and expanded version of the Web-based Gene Set Analysis Toolkit
Duncan D, Prodduturi N, Zhang B
BMC Bioinformatics 2010, 11(Suppl 4):P10 (23 July 2010)
[Abstract] [Full text] [PDF]
457.
Poster presentation
Integrating neighbor clustering, coexpression clustering and subsystems analysis to define
dynamic changes in regulatory networks associated with group A streptococcal
sociomicrobiology and niche adaptation
Aziz RK, Aronow BJ, Taylor WL, Rowe SL, Kansal R, Walker MJ, Kotb M
BMC Bioinformatics 2010, 11(Suppl 4):P12 (23 July 2010)
[Abstract] [Full text] [PDF]
458.
Poster presentation
Serendipitous discoveries in microarray analysis
Ellingson SR, Phillips CA, Glenn R, Swanson D, Ha T, Goldowitz D, Langston MA
BMC Bioinformatics 2010, 11(Suppl 4):P24 (23 July 2010)
[Abstract] [Full text] [PDF]
459.
Poster presentation
Application of Pearson correlation coefficient (PCC) and Kolmogorov-Smirnov distance (KSD)
metrics to identify disease-specific biomarker genes
Huang HC, Zheng S, Zhao Z
BMC Bioinformatics 2010, 11(Suppl 4):P23 (23 July 2010)
[Abstract] [Full text] [PDF]
460.
Poster presentation
Graph algorithms for machine learning: a case-control study based on prostate cancer
populations and high throughput transcriptomic data
Rogers GL, Moscato P, Langston MA
BMC Bioinformatics 2010, 11(Suppl 4):P21 (23 July 2010)
[Abstract] [Full text] [PDF]
461.
Poster presentation
Understanding molecular recognition and epitope prediction from Information Theoretic
approach
Mitra I, Cui Y
BMC Bioinformatics 2010, 11(Suppl 4):P22 (23 July 2010)
[Abstract] [Full text] [PDF]
462.
Poster presentation
Linking genotype to phenotype with Bayesian network modeling of Chlamydia infection
Ziebarth JD, Li B, Miyairi I, Cui Y
BMC Bioinformatics 2010, 11(Suppl 4):P19 (23 July 2010)
[Abstract] [Full text] [PDF]
463.
Poster presentation
A two-step approach to qPCR experimental design and software for data analysis
Guo H, Tague L, Ray R, Tigyi G
BMC Bioinformatics 2010, 11(Suppl 4):P18 (23 July 2010)
[Abstract] [Full text] [PDF]
464.
Poster presentation
A Bayesian change-point algorithm for detecting copy number alteration
Thomas F, Pounds S
BMC Bioinformatics 2010, 11(Suppl 4):P17 (23 July 2010)
[Abstract] [Full text] [PDF]
465.
Poster presentation
Sequence and annotation of the Wizard007 mycobacterium phage genome
Anyanwu E, Cole K, Driver K, Falcone A, Farnsworth E, Howard B, Howard B, Howard C, King
R, Olberding J, Perkins M, Rinehart C, Sayre H, Scaff T, Schrader S, Parthasarathy PT, Tope C
BMC Bioinformatics 2010, 11(Suppl 4):P15 (23 July 2010)
[Abstract] [Full text] [PDF]
466.
Poster presentation
Developing measures for microbial genome assembly quality control
Adams RM, Harris JB, Jay JJ, Johnson BG, Land ML, Hauser LJ
BMC Bioinformatics 2010, 11(Suppl 4):P14 (23 July 2010)
[Abstract] [Full text] [PDF]
467.
Introduction
Proceedings of the ninth annual UT-ORNL-KBRIN Bioinformatics Summit 2010
Rouchka EC, Flight RM, Rinehart C
BMC Bioinformatics 2010, 11(Suppl 4):I1 (23 July 2010)
[Abstract] [Full text] [PDF]
468.
Poster presentation
Experimenting with database segmentation size vs time performance for mpiBLAST on an
IBM HS21 blade cluster
Harris D, Jaromczyk JW, Schardl CL
BMC Bioinformatics 2010, 11(Suppl 4):P9 (23 July 2010)
[Abstract] [Full text] [PDF]
469.
Poster presentation
In silico analysis of a family of extracellular polysaccharide deacetylases involved in virulence
of pathogenic gram-positive cocci
Aziz RK
BMC Bioinformatics 2010, 11(Suppl 4):P8 (23 July 2010)
[Abstract] [Full text] [PDF]
470.
Poster presentation
Comparative functional genomic study of substrate specificity evolution of the SABATH
family of methyltransferases in plants
Zhao N, Ferrer JL, Zhuang X, Chen F
BMC Bioinformatics 2010, 11(Suppl 4):P7 (23 July 2010)
[Abstract] [Full text] [PDF]
471.
Poster presentation
Phylotree – a toolkit for computing experiments with distance-based methods for genome
coevolution
Arnaoudova E, Jaromczyk JW, Moore N, Schardl CL, Yoshida R
BMC Bioinformatics 2010, 11(Suppl 4):P6 (23 July 2010)
[Abstract] [Full text] [PDF]
472.
Poster presentation
Slim-Prim: an integrated data system for clinical and translational research
Viangteeravat T, Brooks IM, Vuthipadadon S, Kuscu E, Nagisetty N, Smith E, Homayouni R,
McDonald CS
BMC Bioinformatics 2010, 11(Suppl 4):P5 (23 July 2010)
[Abstract] [Full text] [PDF]
473.
Poster presentation
SNPlotz: a generic genome plot tool to aid the SNP association studies
Hu ZL, Fernando R, Garrick D, Reecy JM
BMC Bioinformatics 2010, 11(Suppl 4):P4 (23 July 2010)
[Abstract] [Full text] [PDF]
474.
Poster presentation
Design of a DNA-based shift register
Gearheart CM, Rouchka EC, Arazi B
BMC Bioinformatics 2010, 11(Suppl 4):P31 (23 July 2010)
[Abstract] [Full text] [PDF]
475.
Poster presentation
Statistical analysis of multiple significance test methods for differential proteomics
Wang B, Mohammad F, Zhang J, Yin X, Rouchka E, Zhang X
BMC Bioinformatics 2010, 11(Suppl 4):P30 (23 July 2010)
[Abstract] [Full text] [PDF]
476.
Poster presentation
Molecular analysis of Trypanosoma cruzi isolates obtained from raccoons in Warren and
Barren counties of Kentucky
Bi LP, Groce C, Davis C
BMC Bioinformatics 2010, 11(Suppl 4):P3 (23 July 2010)
[Abstract] [Full text] [PDF]
477.
Poster presentation
Enabling proteomics-based identification of human cancer variations
Li J, Ma Z, Slebos RJC, Tabb DL, Liebler DC, Zhang B
BMC Bioinformatics 2010, 11(Suppl 4):P29 (23 July 2010)
[Abstract] [Full text] [PDF]
478.
Poster presentation
Do pathogenic bacteria encode more secreted proteins than their non-pathogenic relatives?
Mahmoud AAB, Aziz RK
BMC Bioinformatics 2010, 11(Suppl 4):P28 (23 July 2010)
[Abstract] [Full text] [PDF]
479.
Poster presentation
Development of tools for the automated analysis of spectra generated by tandem mass
spectrometry
Ellingson S, Hughes J, Storey D, Weber R, VerBerkmoes N
BMC Bioinformatics 2010, 11(Suppl 4):P27 (23 July 2010)
[Abstract] [Full text] [PDF]
480.
Poster presentation
Growth hormone induces proliferation in the zebrafish inner ear
Smith ME, Sun H, Schuck JB, Moriyama S
BMC Bioinformatics 2010, 11(Suppl 4):P26 (23 July 2010)
[Abstract] [Full text] [PDF]
481.
Poster presentation
The UofL Microarray Facility: merger and new location
Waigel S, Li X, Chen Y, Arumugam V, Cooper NGF, Zacharias W
BMC Bioinformatics 2010, 11(Suppl 4):P25 (23 July 2010)
[Abstract] [Full text] [PDF]
482.
Poster presentation
Next-gen sequencing of multi-drug resistant Acinetobacter baumannii to determine
antibiotic resistance genotypes
Dent L, Marshall D, Hulette R, Pratap S
BMC Bioinformatics 2010, 11(Suppl 4):P16 (23 July 2010)
[Abstract] [Full text] [PDF]
483.
Poster presentation
Bioinformatic analysis of gene regulation in the metal-reducing bacterial family
Geobacteraceae
Krushkal J, Adkins RM, Qu Y, Peeples J, Sontineni S, Leang C, Brown P, Young ND, Ueki T,
Juarez K, Lovley DR
BMC Bioinformatics 2010, 11(Suppl 4):P11 (23 July 2010)
[Abstract] [Full text] [PDF]
484.
Poster presentation
Epigenetic control of signaling networks involved in interleukin-18-induced cardiac
hypertrophy and its attenuation by pan-histone deacetylase inhibitors
Majumdar G, Raghow R
BMC Bioinformatics 2010, 11(Suppl 4):P1 (23 July 2010)
[Abstract] [Full text] [PDF]
485.
Oral presentation
High-throughput sequencing of the DBA/2J mouse genome
Wang X, Agarwala R, Capra JA, Chen Z, Church DM, Ciobanu DC, Li Z, Lu L, Mozhui K, Mulligan
MK, Nelson SF, Pollard KS, Taylor WL, Thomason DB, Williams RW
BMC Bioinformatics 2010, 11(Suppl 4):O7 (23 July 2010)
[Abstract] [Full text] [PDF]
486.
Oral presentation
Inferring gene coexpression networks for low dose ionizing radiation using graph theoretical
algorithms and systems genetics
Naswa S, Rogers GL, Lynch RM, Kania SA, Das S, Chesler EJ, Saxton AM, Voy BH, Langston MA
BMC Bioinformatics 2010, 11(Suppl 4):O5 (23 July 2010)
[Abstract] [Full text] [PDF]
487.
Oral presentation
Subsystems-based servers for rapid annotation of genomes and metagenomes
Aziz RK
BMC Bioinformatics 2010, 11(Suppl 4):O2 (23 July 2010)
[Abstract] [Full text] [PDF]
488.
Oral presentation
Pathway- and network-based analysis of GWAS data revealed susceptibility gene sets to
schizophrenia
Jia P, Zhao Z
BMC Bioinformatics 2010, 11(Suppl 4):O1 (23 July 2010)
[Abstract] [Full text] [PDF]
489.
Research article
A comparison of internal validation techniques for multifactor dimensionality reduction
Winham SJ, Slater AJ, Motsinger-Reif AA
BMC Bioinformatics 2010, 11:394 (22 July 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
490.
Research article
Compartmentalization of the Edinburgh Human Metabolic Network
Hao T, Ma HW, Zhao XM, Goryanin I
BMC Bioinformatics 2010, 11:393 (22 July 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
491.
Research article
Uncovering packaging features of co-regulated modules based on human protein interaction
and transcriptional regulatory networks
Chen L, Wang H, Zhang L, Li W, Wang Q, Shang Y, He Y, He W, Li X, Tai J, Li X
BMC Bioinformatics 2010, 11:392 (22 July 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
492.
Methodology article
Robust test method for time-course microarray experiments
Sohn I, Owzar K, George SL, Kim S, Jung SH
BMC Bioinformatics 2010, 11:391 (22 July 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
493.
Methodology article
Deriving enzymatic and taxonomic signatures of metagenomes from short read data
Weingart U, Persi E, Gophna U, Horn D
BMC Bioinformatics 2010, 11:390 (22 July 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
494.
Software
GeneBrowser 2: an application to explore and identify common biological traits in a set of
genes
Arrais JP, Fernandes J, Pereira J, Oliveira JL
BMC Bioinformatics 2010, 11:389 (21 July 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
495.
Research article
A comparative study of conservation and variation scores
Johansson F, Toh H
BMC Bioinformatics 2010, 11:388 (21 July 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
496.
Research article
S3DB core: a framework for RDF generation and management in bioinformatics
infrastructures
Almeida JS, Deus HF, Maass W
BMC Bioinformatics 2010, 11:387 (20 July 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
497.
Methodology article
Efficiency clustering for low-density microarrays and its application to QPCR
Lock EF, Ziemiecki R, Marron JS, Dittmer DP
BMC Bioinformatics 2010, 11:386 (20 July 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
498.
Research article
Applications of a formal approach to decipher discrete genetic networks
Corblin F, Fanchon E, Trilling L
BMC Bioinformatics 2010, 11:385 (20 July 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
499.
Research article
VIPR: A probabilistic algorithm for analysis of microbial detection microarrays
Allred AF, Wu G, Wulan T, Fischer KF, Holbrook MR, Tesh RB, Wang D
BMC Bioinformatics 2010, 11:384 (20 July 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
500.
Research article
The oligodeoxynucleotide sequences corresponding to never-expressed peptide motifs are
mainly located in the non-coding strand
Capone G, Novello G, Fasano C, Trost B, Bickis M, Kusalik A, Kanduc D
BMC Bioinformatics 2010, 11:383 (20 July 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
501.
Software
Integration and visualization of systems biology data in context of the genome
Bare JC, Koide T, Reiss DJ, Tenenbaum D, Baliga NS
BMC Bioinformatics 2010, 11:382 (19 July 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
502.
Methodology article
EPSVR and EPMeta: prediction of antigenic epitopes using support vector regression and
multiple server results
Liang S, Zheng D, Standley DM, Yao B, Zacharias M, Zhang C
BMC Bioinformatics 2010, 11:381 (16 July 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
503.
Software
R-Gada: a fast and flexible pipeline for copy number analysis in association studies
Pique-Regi R, Cáceres A, González JR
BMC Bioinformatics 2010, 11:380 (16 July 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
504.
Software
MetaPIGA v2.0: maximum likelihood large phylogeny estimation using the metapopulation
genetic algorithm and other stochastic heuristics
Helaers R, Milinkovitch MC
BMC Bioinformatics 2010, 11:379 (15 July 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
505.
Methodology article
Graph-based clustering and characterization of repetitive sequences in next-generation
sequencing data
Novák P, Neumann P, Macas J
BMC Bioinformatics 2010, 11:378 (15 July 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
506.
Software
SEQADAPT: an adaptable system for the tracking, storage and analysis of high throughput
sequencing experiments
Burdick DB, Cavnor CC, Handcock J, Killcoyne S, Lin J, Marzolf B, Ramsey SA, Rovira H,
Bressler R, Shmulevich I, Boyle J
BMC Bioinformatics 2010, 11:377 (14 July 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
507.
Database
The MetabolomeExpress Project: enabling web-based processing, analysis and transparent
dissemination of GC/MS metabolomics datasets
Carroll AJ, Badger MR, Harvey Millar A
BMC Bioinformatics 2010, 11:376 (14 July 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [2 comments]
508.
Database
KID - an algorithm for fast and efficient text mining used to automatically generate a
database containing kinetic information of enzymes
Heinen S, Thielen B, Schomburg D
BMC Bioinformatics 2010, 11:375 (13 July 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
509.
Methodology article
Protein structure modelling and evaluation based on a 4-distance description of side-chain
interactions
Potapov V, Cohen M, Inbar Y, Schreiber G
BMC Bioinformatics 2010, 11:374 (12 July 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
510.
Methodology article
Extended morphological processing: a practical method for automatic spot detection of
biological markers from microscopic images
Kimori Y, Baba N, Morone N
BMC Bioinformatics 2010, 11:373 (8 July 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
511.
Research article
Beyond co-localization: inferring spatial interactions between sub-cellular structures from
microscopy images
Helmuth JA, Paul G, Sbalzarini IF
BMC Bioinformatics 2010, 11:372 (7 July 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
512.
Software
Visualisation tool for peptide fractionation data in proteomics: application to OFFGEL
isoelectric focussing
Azulay DOD, Neubert H, Ocaña MF
BMC Bioinformatics 2010, 11:371 (5 July 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
513.
Software
Predicting changes in protein thermostability brought about by single- or multi-site
mutations
Tian J, Wu N, Chu X, Fan Y
BMC Bioinformatics 2010, 11:370 (2 July 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
514.
Methodology article
HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-Seq data
Qin ZS, Yu J, Shen J, Maher CA, Hu M, Kalyana-Sundaram S, Yu J, Chinnaiyan AM
BMC Bioinformatics 2010, 11:369 (2 July 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
515.
Methodology article
A factor model to analyze heterogeneity in gene expression
Blum Y, Le Mignon G, Lagarrigue S, Causeur D
BMC Bioinformatics 2010, 11:368 (2 July 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
516.
Software
A flexible R package for nonnegative matrix factorization
Gaujoux R, Seoighe C
BMC Bioinformatics 2010, 11:367 (2 July 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
517.
Research article
Dual-functioning transcription factors in the developmental gene network of Drosophila
melanogaster
Bauer DC, Buske FA, Bailey TL
BMC Bioinformatics 2010, 11:366 (2 July 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
518.
Research article
Knowledge-based annotation of small molecule binding sites in proteins
Thangudu RR, Tyagi M, Shoemaker BA, Bryant SH, Panchenko AR, Madej T
BMC Bioinformatics 2010, 11:365 (1 July 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
519.
Research article
Automatic structure classification of small proteins using random forest
Jain P, Hirst JD
BMC Bioinformatics 2010, 11:364 (1 July 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
520.
Research article
Robust probabilistic superposition and comparison of protein structures
Mechelke M, Habeck M
BMC Bioinformatics 2010, 11:363 (1 July 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
521.
Methodology article
Use of historic metabolic biotransformation data as a means of anticipating metabolic sites
using MetaPrint2D and Bioclipse
Carlsson L, Spjuth O, Adams S, Glen RC, Boyer S
BMC Bioinformatics 2010, 11:362 (1 July 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
522.
Correspondence
Scanner calibration revisited
Pozhitkov AE
BMC Bioinformatics 2010, 11:361 (1 July 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
523.
Software
Flexible network reconstruction from relational databases with Cytoscape and CytoSQL
Laukens K, Hollunder J, Dang TH, De Jaeger G, Kuiper M, Witters E, Verschoren A, Van
Leemput K
BMC Bioinformatics 2010, 11:360 (1 July 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
524.
Methodology article
On the use of resampling tests for evaluating statistical significance of binding-site cooccurrence
Huen DS, Russell S
BMC Bioinformatics 2010, 11:359 (30 June 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
525.
Software
MetaBar - a tool for consistent contextual data acquisition and standards compliant
submission
Hankeln W, Buttigieg PL, Fink D, Kottmann R, Yilmaz P, Glöckner FO
BMC Bioinformatics 2010, 11:358 (30 June 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
526.
Research article
Interaction prediction and classification of PDZ domains
Kalyoncu S, Keskin O, Gursoy A
BMC Bioinformatics 2010, 11:357 (30 June 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
527.
Methodology article
Spatial normalization improves the quality of genotype calling for Affymetrix SNP 6.0 arrays
Chai HS, Therneau TM, Bailey KR, Kocher JPA
BMC Bioinformatics 2010, 11:356 (29 June 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
528.
Methodology article
Inference of sparse combinatorial-control networks from gene-expression data: a message
passing approach
Bailly-Bechet M, Braunstein A, Pagnani A, Weigt M, Zecchina R
BMC Bioinformatics 2010, 11:355 (29 June 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
529.
Methodology article
Nonparametric methods for the analysis of single-color pathogen microarrays
Jabado OJ, Conlan S, Quan PL, Hui J, Palacios G, Hornig M, Briese T, Lipkin WI
BMC Bioinformatics 2010, 11:354 (28 June 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
530.
Software
ScreenMill: A freely available software suite for growth measurement, analysis and
visualization of high-throughput screen data
Dittmar JC, Reid RJD, Rothstein R
BMC Bioinformatics 2010, 11:353 (28 June 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
531.
Research article
Protein docking by Rotation-Based Uniform Sampling (RotBUS) with fast computing of
intermolecular contact distance and residue desolvation
Solernou A, Fernandez-Recio J
BMC Bioinformatics 2010, 11:352 (28 June 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
532.
Methodology article
Identifying differentially regulated subnetworks from phosphoproteomic data
Klammer M, Godl K, Tebbe A, Schaab C
BMC Bioinformatics 2010, 11:351 (28 June 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
533.
Methodology article
Protein complex prediction via verifying and reconstructing the topology of domain-domain
interactions
Ozawa Y, Saito R, Fujimori S, Kashima H, Ishizaka M, Yanagawa H, Miyamoto-Sato E, Tomita
M
BMC Bioinformatics 2010, 11:350 (28 June 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
534.
Research article
Modular composition predicts kinase/substrate interactions
Liu Y, Tozeren A
BMC Bioinformatics 2010, 11:349 (25 June 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
535.
Methodology article
Metamotifs - a generative model for building families of nucleotide position weight matrices
Piipari M, Down TA, Hubbard TJP
BMC Bioinformatics 2010, 11:348 (25 June 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
536.
Research article
Local alignment of generalized k-base encoded DNA sequence
Homer N, Nelson SF, Merriman B
BMC Bioinformatics 2010, 11:347 (24 June 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
537.
Methodology article
Predicting nucleosome positioning using a duration Hidden Markov Model
Xi L, Fondufe-Mittendorf Y, Xia L, Flatow J, Widom J, Wang JP
BMC Bioinformatics 2010, 11:346 (24 June 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
538.
Research article
SOPRA: Scaffolding algorithm for paired reads via statistical optimization
Dayarian A, Michael TP, Sengupta AM
BMC Bioinformatics 2010, 11:345 (24 June 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
539.
Research article
Error, reproducibility and sensitivity: a pipeline for data processing of Agilent oligonucleotide
expression arrays
Chain B, Bowen H, Hammond J, Posch W, Rasaiyaah J, Tsang J, Noursadeghi M
BMC Bioinformatics 2010, 11:344 (24 June 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
540.
Research article
A semi-supervised learning approach to predict synthetic genetic interactions by combining
functional and topological properties of functional gene network
You ZH, Yin Z, Han K, Huang DS, Zhou X
BMC Bioinformatics 2010, 11:343 (24 June 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
541.
Software
TabSQL: a MySQL tool to facilitate mapping user data to public databases
Xia XQ, McClelland M, Wang Y
BMC Bioinformatics 2010, 11:342 (23 June 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
542.
Software
TagCleaner: Identification and removal of tag sequences from genomic and metagenomic
datasets
Schmieder R, Lim YW, Rohwer F, Edwards R
BMC Bioinformatics 2010, 11:341 (23 June 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
543.
Software
A high-throughput pipeline for the design of real-time PCR signatures
Vijaya Satya R, Kumar K, Zavaljevski N, Reifman J
BMC Bioinformatics 2010, 11:340 (23 June 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
544.
Research article
Kinome-wide interaction modelling using alignment-based and alignment-independent
approaches for kinase description and linear and non-linear data analysis techniques
Lapins M, Wikberg JES
BMC Bioinformatics 2010, 11:339 (22 June 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
545.
Methodology article
svdPPCS: an effective singular value decomposition-based method for conserved and
divergent co-expression gene module identification
Zhang W, Edwards A, Fan W, Zhu D, Zhang K
BMC Bioinformatics 2010, 11:338 (22 June 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
546.
Research article
Identifying interactions in the time and frequency domains in local and global networks - A
Granger Causality Approach
Zou C, Ladroue C, Guo S, Feng J
BMC Bioinformatics 2010, 11:337 (21 June 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
547.
Methodology article
PCA2GO: a new multivariate statistics based method to identify highly expressed GO-Terms
Bruckskotten M, Looso M, Cemiĉ F, Konzer A, Hemberger J, Krüger M, Braun T
BMC Bioinformatics 2010, 11:336 (21 June 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
548.
Research article
An efficient biological pathway layout algorithm combining grid-layout and spring embedder
for complicated cellular location information
Kojima K, Nagasaki M, Miyano S
BMC Bioinformatics 2010, 11:335 (18 June 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
549.
Research article
An effective approach for generating a three-Cys2His2 zinc-finger-DNA complex model by
docking
Chou CC, Rajasekaran M, Chen C
BMC Bioinformatics 2010, 11:334 (18 June 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
550.
Research article
MPRAP: An accessibility predictor for a-helical transmem-brane proteins that performs well
inside and outside the membrane
Illergård K, Callegari S, Elofsson A
BMC Bioinformatics 2010, 11:333 (18 June 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
551.
Software
VITCOMIC: visualization tool for taxonomic compositions of microbial communities based on
16S rRNA gene sequences
Mori H, Maruyama F, Kurokawa K
BMC Bioinformatics 2010, 11:332 (18 June 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
552.
Software
CGHpower: exploring sample size calculations for chromosomal copy number experiments
Scheinin I, Ferreira JA, Knuutila S, Meijer GA, van de Wiel MA, Ylstra B
BMC Bioinformatics 2010, 11:331 (17 June 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
553.
Software
Computing and visually analyzing mutual information in molecular co-evolution
Bremm S, Schreck T, Boba P, Held S, Hamacher K
BMC Bioinformatics 2010, 11:330 (17 June 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
554.
Software
permGPU: Using graphics processing units in RNA microarray association studies
Shterev ID, Jung SH, George SL, Owzar K
BMC Bioinformatics 2010, 11:329 (16 June 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
555.
Software
MimoSA: a system for minimotif annotation
Vyas J, Nowling RJ, Meusburger T, Sargeant D, Kadaveru K, Gryk MR, Kundeti V, Rajasekaran
S, Schiller MR
BMC Bioinformatics 2010, 11:328 (16 June 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
556.
Software
FRASS: the web-server for RNA structural comparison
Kirillova S, Tosatto SCE, Carugo O
BMC Bioinformatics 2010, 11:327 (16 June 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
557.
Software
PPLook: an automated data mining tool for protein-protein interaction
Zhang SW, Li YJ, Xia L, Pan Q
BMC Bioinformatics 2010, 11:326 (16 June 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
558.
Research article
Classification of G-protein coupled receptors based on support vector machine with
maximum relevance minimum redundancy and genetic algorithm
Li Z, Zhou X, Dai Z, Zou X
BMC Bioinformatics 2010, 11:325 (16 June 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
559.
Methodology article
Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests
Abby SS, Tannier E, Gouy M, Daubin V
BMC Bioinformatics 2010, 11:324 (15 June 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
560.
Methodology article
A boundary delimitation algorithm to approximate cell soma volumes of bipolar cells from
topographical data obtained by scanning probe microscopy
Happel P, Möller K, Kunz R, Dietzel ID
BMC Bioinformatics 2010, 11:323 (15 June 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
561.
Research article
Quantifying the relationship between sequence and three-dimensional structure
conservation in RNA
Capriotti E, Marti-Renom MA
BMC Bioinformatics 2010, 11:322 (15 June 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
562.
Research article
An integrated Bayesian analysis of LOH and copy number data
Rancoita PMV, Hutter M, Bertoni F, Kwee I
BMC Bioinformatics 2010, 11:321 (15 June 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
563.
Software
Pripper: prediction of caspase cleavage sites from whole proteomes
Piippo M, Lietzén N, Nevalainen OS, Salmi J, Nyman TA
BMC Bioinformatics 2010, 11:320 (15 June 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
564.
Software
Accessing the SEED Genome Databases via Web Services API: Tools for Programmers
Disz T, Akhter S, Cuevas D, Olson R, Overbeek R, Vonstein V, Stevens R, Edwards RA
BMC Bioinformatics 2010, 11:319 (14 June 2010)
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565.
Software
CONAN: copy number variation analysis software for genome-wide association studies
Forer L, Schönherr S, Weissensteiner H, Haider F, Kluckner T, Gieger C, Wichmann HE, Specht
G, Kronenberg F, Kloss-Brandstätter A
BMC Bioinformatics 2010, 11:318 (14 June 2010)
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566.
Software
Introducing W.A.T.E.R.S.: a Workflow for the Alignment, Taxonomy, and Ecology of
Ribosomal Sequences
Hartman AL, Riddle S, McPhillips T, Ludäscher B, Eisen JA
BMC Bioinformatics 2010, 11:317 (12 June 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
567.
Research article
A novel chemogenomics analysis of G protein-coupled receptors (GPCRs) and their ligands: a
potential strategy for receptor de-orphanization
van der Horst E, Peironcely JE, IJzerman AP, Beukers MW, Lane JR, van Vlijmen HWT,
Emmerich MTM, Okuno Y, Bender A
BMC Bioinformatics 2010, 11:316 (10 June 2010)
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568.
Software
μ-CS: An extension of the TM4 platform to manage Affymetrix binary data
Guzzi PH, Cannataro M
BMC Bioinformatics 2010, 11:315 (10 June 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
569.
Methodology article
A boosting method for maximizing the partial area under the ROC curve
Komori O, Eguchi S
BMC Bioinformatics 2010, 11:314 (10 June 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
570.
Research article
Functional classification of proteins based on projection of amino acid sequences:
application for prediction of protein kinase substrates
Sobolev B, Filimonov D, Lagunin A, Zakharov A, Koborova O, Kel A, Poroikov V
BMC Bioinformatics 2010, 11:313 (10 June 2010)
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571.
Methodology article
GIGA: a simple, efficient algorithm for gene tree inference in the genomic age
Thomas PD
BMC Bioinformatics 2010, 11:312 (9 June 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
572.
Database
FunctSNP: an R package to link SNPs to functional knowledge and dbAutoMaker: a suite of
Perl scripts to build SNP databases
Goodswen SJ, Gondro C, Watson-Haigh NS, Kadarmideen HN
BMC Bioinformatics 2010, 11:311 (9 June 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
573.
Software
dConsensus: a tool for displaying domain assignments by multiple structure-based
algorithms and for construction of a consensus assignment
Alden K, Veretnik S, Bourne PE
BMC Bioinformatics 2010, 11:310 (9 June 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
574.
Methodology article
L2-norm multiple kernel learning and its application to biomedical data fusion
Yu S, Falck T, Daemen A, Tranchevent LC, Suykens JAK, De Moor B, Moreau Y
BMC Bioinformatics 2010, 11:309 (8 June 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
575.
Methodology article
Computational modeling with forward and reverse engineering links signaling network and
genomic regulatory responses: NF-κB signaling-induced gene expression responses in
inflammation
Peng SC, Wong DSH, Tung KC, Chen YY, Chao CC, Peng CH, Chuang YJ, Tang CY
BMC Bioinformatics 2010, 11:308 (8 June 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
576.
Research article
Rule-based spatial modeling with diffusing, geometrically constrained molecules
Gruenert G, Ibrahim B, Lenser T, Lohel M, Hinze T, Dittrich P
BMC Bioinformatics 2010, 11:307 (7 June 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
577.
Research article
Beyond rotamers: a generative, probabilistic model of side chains in proteins
Harder T, Boomsma W, Paluszewski M, Frellsen J, Johansson KE, Hamelryck T
BMC Bioinformatics 2010, 11:306 (5 June 2010)
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578.
Methodology article
Prediction of epigenetically regulated genes in breast cancer cell lines
Loss LA, Sadanandam A, Durinck S, Nautiyal S, Flaucher D, Carlton VEH, Moorhead M, Lu Y,
Gray JW, Faham M, Spellman P, Parvin B
BMC Bioinformatics 2010, 11:305 (4 June 2010)
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579.
Research article
Scaffold filling, contig fusion and comparative gene order inference
Muñoz A, Zheng C, Zhu Q, Albert VA, Rounsley S, Sankoff D
BMC Bioinformatics 2010, 11:304 (4 June 2010)
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580.
Research article
Detecting internally symmetric protein structures
Kim C, Basner J, Lee B
BMC Bioinformatics 2010, 11:303 (3 June 2010)
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581.
Research article
Saliva Ontology: An ontology-based framework for a Salivaomics Knowledge Base
Ai J, Smith B, Wong DT
BMC Bioinformatics 2010, 11:302 (3 June 2010)
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582.
Research article
Prediction of GTP interacting residues, dipeptides and tripeptides in a protein from its
evolutionary information
Chauhan JS, Mishra NK, Raghava GPS
BMC Bioinformatics 2010, 11:301 (3 June 2010)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
583.
Research article
UFFizi: a generic platform for ranking informative features
Gottlieb A, Varshavsky R, Linial M, Horn D
BMC Bioinformatics 2010, 11:300 (3 June 2010)
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584.
Research article
poolMC: Smart pooling of mRNA samples in microarray experiments
Kainkaryam RM, Bruex A, Gilbert AC, Schiefelbein J, Woolf PJ
BMC Bioinformatics 2010, 11:299 (2 June 2010)
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585.
Research article
An interaction-motif-based scoring function for protein-ligand docking
Xie ZR, Hwang MJ
BMC Bioinformatics 2010, 11:298 (2 June 2010)
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586.
Research article
A classification model for distinguishing copy number variants from cancer-related
alterations
Ostrovnaya I, Nanjangud G, Olshen AB
BMC Bioinformatics 2010, 11:297 (2 June 2010)
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587.
Research article
Super-sparse principal component analyses for high-throughput genomic data
Lee D, Lee W, Lee Y, Pawitan Y
BMC Bioinformatics 2010, 11:296 (2 June 2010)
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588.
Research article
Bayesian integrated modeling of expression data: a case study on RhoG
Gupta R, Greco D, Auvinen P, Arjas E
BMC Bioinformatics 2010, 11:295 (1 June 2010)
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589.
Methodology article
EnvMine: A text-mining system for the automatic extraction of contextual information
Tamames J, de Lorenzo V
BMC Bioinformatics 2010, 11:294 (1 June 2010)
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590.
Research article
Predicting the network of substrate-enzyme-product triads by combining compound
similarity and functional domain composition
Chen L, Feng KY, Cai YD, Chou KC, Li HP
BMC Bioinformatics 2010, 11:293 (31 May 2010)
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591.
Research article
TargetSpy: a supervised machine learning approach for microRNA target prediction
Sturm M, Hackenberg M, Langenberger D, Frishman D
BMC Bioinformatics 2010, 11:292 (28 May 2010)
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592.
Research article
Washing scaling of GeneChip microarray expression
Binder H, Krohn K, Burden CJ
BMC Bioinformatics 2010, 11:291 (28 May 2010)
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593.
Research article
Revealing and avoiding bias in semantic similarity scores for protein pairs
Wang J, Zhou X, Zhu J, Zhou C, Guo Z
BMC Bioinformatics 2010, 11:290 (28 May 2010)
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594.
Research article
Spatio-structural granularity of biological material entities
Vogt L
BMC Bioinformatics 2010, 11:289 (28 May 2010)
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595.
Software
GWAMA: software for genome-wide association meta-analysis
Mägi R, Morris AP
BMC Bioinformatics 2010, 11:288 (28 May 2010)
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596.
Software
Colonyzer: automated quantification of micro-organism growth characteristics on solid agar
Lawless C, Wilkinson DJ, Young A, Addinall SG, Lydall DA
BMC Bioinformatics 2010, 11:287 (28 May 2010)
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597.
Research article
Conserved residue clusters at protein-protein interfaces and their use in binding site
identification
Guharoy M, Chakrabarti P
BMC Bioinformatics 2010, 11:286 (27 May 2010)
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598.
Methodology article
Preferred analysis methods for Affymetrix GeneChips. II. An expanded, balanced, whollydefined spike-in dataset
Zhu Q, Miecznikowski JC, Halfon MS
BMC Bioinformatics 2010, 11:285 (27 May 2010)
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599.
Software
JCoDA: a tool for detecting evolutionary selection
Steinway SN, Dannenfelser R, Laucius CD, Hayes JE, Nayak S
BMC Bioinformatics 2010, 11:284 (27 May 2010)
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600.
Research article
Optimal contact definition for reconstruction of Contact Maps
Duarte JM, Sathyapriya R, Stehr H, Filippis I, Lappe M
BMC Bioinformatics 2010, 11:283 (27 May 2010)
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