Publications by researcher staff with the Bioinformatics Consulting Center
<http://bcc.cbio.psu.edu/> at Penn State University, for the academic year 2003-2004.
This file is temporarily stored at: <http://www.stat.psu.edu/~jlr/BCC/Pubs/>
Istvan Albert
Reka Albert, Istvan Albert and Gary L. Nakarado. (2004)
Structural Vulnerability of the North American Power Grid
Physical Review E, 69, 025103(R)
Istvan Albert and Reka Albert. (2004) Conserved network motifs allow protein-protein
interaction prediction. Bioinformatics, to appear.
related website: http://www.protsuggest.org
Stephen Racunas , Nigam Shah, Istvan Albert and Nina Fedoroff (2004).
HyBrow - A Prototype System for Computer Aided Hypothesis Evaluation,
International Conference for Intelligent Systems for Molecular Biology, ISMB
related website: http://www.hybrow.org
Naomi Altman
Altman, N.S. (2003) Replication, Variation and Normalization in Microarray
Experiments (submitted to Applied Bioinformatics)
Wang, G., Kong, H., Sun, Y., Zhang, X., Zhang, W., Altman, N.S., Ma, H. (2004)
Phylogeny and Expression of Plant Cyclins
Walters, E., Altman, N.S., Elnitski, L., (2004) Are Gene Locations Clustered on
Chromosomes? (submitted to Journal of Computational Statistics and Data Analysis)
Gary Chase
Blacker D, Bertram L, Saunders AJ, Moscarillo TJ, Albert MS, Wiener H, Perry RT,
Collins JS, Harrell LE, Go RCP, Mahoney A, Beaty T, Fallin MD, Avramopoulos D,
Chase GA , Folstein MF, McInnis MG, Bassett SB, Doheny KJ, Pugh EW and Tanzi
RE (The NIMH Genetics Initiative Alzheimer's Disease Study Group): Results of a highresolution genome screen of 437 Alzheimer's Disease families. Human Molecular
Genetics 12: 23-32, 2003.
Rybicki BA, Maliarik MJ, Poisson LM, Sheffer R, Chen KM, Major M, Chase GA,
Iannuzzi MC. The major histocompatibility complex gene region and sarcoidosis
susceptibility in African Americans. American Journal of Respiratory and Critical Care
Medicine 167: 444-449, 2003.
Poisson LM, Rybicki BA, Coon SW, Barnholtz-Sloan JS, Chase GA: Susceptibility
scoring in family-based association testing. BMC Genetics 4 (S1): S49, 2003.
Barnholtz-Sloan JS, Poisson LM, Coon SW, Chase GA, Rybicki BA: Analysis of gene ×
environment interactions in sibships using mixed models. BMC Genetics 4 (S1): S18,
2003.
Francesca Chiaromonte
Schwartz S., Miller W., Chiaromonte F. (2003) Distinguishing regulatory DNA from
neutral sites. Genome Research 13: 64-72.
M., Kent J.W., Weber R., Elnitski L.,
Li J., O Connor M., Kolbe D., Schwartz S., Furey T.S., Whelan S., Goldman N., Smit A.,
Miller W., Chiaromonte F., Haussler D. (2003) Co-variation in frequencies of
substitution, deletion, transposition and recombination during eutherian evolution.
Genome Research 13: 13-26.
Chiaromonte F., Miller W. and Bouhassira E. (2003) Gene length and proximity to
neighbors affect genome-wide expression levels. Genome Research 13: 2602-2608.
Chiaromonte F., Kolbe D., Wang H., Petrykowska H., Elnitski L.,
Yang S., Giardine B., Zhang Y., Riemer C., Schwartz S., Haussler D., Roskin K., Weber
R., Diekhans M., Kent W.J., Weiss M.J., Welch J. and Miller W. (2004) Global
prediction and tests for erythroid regulatory regions. Cold Spring Harbor Symposia in
Quantitative Biology: The Genome of Homo Sapiens 68: 335-345.
Chiaromonte F., Weber R. J., Roskin K.M., Diekhans M., Kent W.J. and Haussler D.
(2004) The share of human genomic DNA under selection estimated from human-mouse
genomic alignments. Cold Spring Harbor Symposia in Quantitative Biology: The
Genome of Homo Sapien. 68: 245-254.
Genome
sequence of the Brown Norway rat yields insights into mammalian evolution. Nature
428: 493-521.
Chiaromonte F. (2004) Insertions and deletions are
male-biased too: a whole-genome analysis in rodents. Genome Research 14: 567-573.
Chiaromonte F. (2004) Regulatory potential scores from genome-wide 3-way
alignments of human, mouse and rat. Genome Research 14: 700-707.
Chiaromonte F., Roskin K. M., Haussler D., Miller
W. and Hardison R.C. (2004) Patterns of insertions and their covariation with
substitutions in the rat, mouse and human genomes. Genome Research 14: 517-527.
Wenlei Liu
Liu W, Bentley CM, Floros J. Study of human SP-A, SP-B and SP-D loci: allele
frequencies, linkage disequilibrium and heterozygosity in different races and ethnic
groups. BMC Genetics 4:13, 2003.
Liu W, Weir BS. Affected sib pair tests in inbred populations. (submitted to Ann
Hum Genet)
Liu W, Icitovic N, Shaffer ML, Chase GA. The impact of population heterogeneity
on genetic counseling. (Submitted to BMC Medical Genetics)
Liu W, Zhao W, Chase GA. Genome scan meta-analysis of Hypertension. (submitted
to Am J Hypertens)
Izabela Makalowska
Veeramachaneni V, Makalowski W, Galdzicki M, Sood R, Makalowska I., (2004)
Mammalian overlapping genes: the comparative perspective. Genome Res;14(2):280-6.
Cohen-Solal KA, Sood R, Marin Y, Crespo-Carbone SM, Sinsimer D, Martino JJ,
Robbins C, Makalowska I, Trent J, Chen S. (2003) Identification and characterization of
mouse Rab32 by mRNA and protein expression analysis. Biochim Biophys Acta.
23;1651(1-2):68-75.
Sood R, Makalowska I, Galdzicki M, Hu P, Eddings E, Robbins CM, Moses T,
Namkoong J, Chen S, Trent JM. (2003) Cloning and characterization of a novel gene,
SHPRH, encoding a conserved putative protein with SNF2/helicase and PHD-finger
domains from the 6q24 region. Genomics. 2003 Aug;82(2):153-61.
Pollock PM, Cohen-Solal K, Sood R, Namkoong J, Martino JJ, Koganti A, Zhu H,
Robbins C, Makalowska I, Shin SS, Marin Y, Roberts KG, Yudt LM, Chen A, Cheng J,
Incao A, Pinkett HW, Graham CL, Dunn K, Crespo-Carbone SM, Mackason KR, Ryan
KB, Sinsimer D, Goydos J, Reuhl KR, Eckhaus M, Meltzer PS, Pavan WJ, Trent JM,
Chen S. (2003) Melanoma mouse model implicates metabotropic glutamate signaling in
melanocytic neoplasia. Nat Genet ;34(1):108-12.
Imanishi T., Itoh T., Suzuki Y., O'Donovan C., Fukuchi S., Koyanagi K, ... Makalowska
I., ..., Gojobori T., Sugano S. (2004) Integrative Annotation of 21, 037 human genes
validated by full-length cDNA clones. PloS Biology, Apr 20;2(6):E162
Manzoor-Ali P.K. Mohideen, lamason R., Wong A.C., Aros M., Humbert J.E.,
Humphreville V., Moore J.L., Grunvald D.J., Makalowska I., Mangini N., Ning G.,
Canfield V., and Cheng K.C. (2004) The zebrafish golden mutation indicates a role for
potassium-dependent sodium-calcium exchange in vertebrate pigmentation. Submitted to
Current Biology.
Geiser D.V., del mar Jimenez-Gasco M., Kang S., Makalowska I., Veeraraghavan N.,
Ward T.J., Zhang N., Kuldau G.A., and O'Donnell K (2004) FUSARIUM-ID v.1.0: A
DNA sequence database for identifying Fusarium. The European Journal of Plant
Pathology. In press