Publications for Jean Yang
Publications for Jean Yang
2016
Jayawardana, K., Schramm, S., Tembe, V.,
Mueller, S., Thompson, J., Scolyer, R., Mann,
G., Yang, J. (2016). Identification, Review, and
Systematic Cross-Validation of microRNA
Prognostic Signatures in Metastatic Melanoma.
Journal of Investigative Dermatology, 136(1),
245-254. <a
href="http://dx.doi.org/10.1038/JID.2015.355">[
More Information]</a>
Yang, P., Humphrey, S., James, D., Yang, J.,
Jothi, R. (2016). Positive-unlabeled ensemble
learning for kinase substrate prediction from
dynamic phosphoproteomics data.
Bioinformatics, 32(2), 252-259. <a
href="http://dx.doi.org/10.1093/bioinformatics/bt
v550">[More Information]</a>
Markus, M., Yang, J., Morris, B. (2016).
Transcriptome-wide targets of alternative
splicing by RBM4 and possible role in cancer.
Genomics, 107(4), 138-144. <a
href="http://dx.doi.org/10.1016/j.ygeno.2016.02.
003">[More Information]</a>
2015
Rahman, W., Tu, T., Budzinska, M., Huang, P.,
Belov, L., Chrisp, J., Christopherson, R., Warner,
F., Bowden, D., Thomspon, A., Bowen, D.,
Strasser, S., Sharland, A., Yang, J., McCaughan,
G., Shackel, N., et al (2015). Analysis of
Post-Liver Transplant Hepatitis C Virus
Recurrence Using Serial Cluster of
differentiation Antibody Microarrays.
Transplantation, 99(9), e120-e126. <a
href="http://dx.doi.org/10.1097/TP.00000000000
00617">[More Information]</a>
Strbenac, D., Mann, G., Ormerod, J., Yang, J.
(2015). ClassifyR: an R package for performance
assessment of classification with applications to
transcriptomics. Bioinformatics, 31(11),
1851-1853. <a
href="http://dx.doi.org/10.1093/bioinformatics/bt
v066">[More Information]</a>
Heinemann, A., Cullinane, C., De Paoli-Iseppi,
R., Wilmott, J., Gunatilake, D., Madore, J.,
Strbenac, D., Yang, J., Gowrishankar, K., Tiffen,
J., Hersey, P., Gallagher, S., et al (2015).
Combining BET and HDAC inhibitors
synergistically induces apoptosis of melanoma
and suppresses AKT and YAP signaling.
Oncotarget, 6(25), 21507-21521.
Chaudhuri, R., Khoo, P., Tonks, K., Junutula, J.,
Kolumam, G., Modrusan, Z., Samocha-Bonet,
D., Meoli, C., Hocking, S., Fazakerley, D.,
Stockli, J., Yang, J., James, D., et al (2015).
Cross-species gene expression analysis identifies
a novel set of genes implicated in human insulin
sensitivity. Npj Systems Biology And
Applications, 1, 1-10. <a
href="http://dx.doi.org/10.1038/npjsba.2015.10"
>[More Information]</a>
Jayawardana, K., Schramm, S., Haydu, L.,
Thompson, J., Scolyer, R., Mann, G., Muller, S.,
Yang, J. (2015). Determination of prognosis in
metastatic melanoma through integration of
clinico-pathologic, mutation, mRNA,
microRNA, and protein information.
International Journal of Cancer, 136(4),
863-874. <a
href="http://dx.doi.org/10.1002/ijc.29047">[Mor
e Information]</a>
Patrick, E., Buckley, M., Mueller, S., Lin, D.,
Yang, J. (2015). Inferring data-specific
micro-RNA function through the joint ranking of
micro-RNA and pathways from matched
micro-RNA and gene expression data.
Bioinformatics, 31(17), 2822-2828. <a
href="http://dx.doi.org/10.1093/bioinformatics/bt
v220">[More Information]</a>
Yang, P., Zheng, X., Jayaswal, V., Hu, G., Yang,
J., Jothi, R. (2015). Knowledge-Based Analysis
for Detecting Key Signaling Events from
Time-Series Phosphoproteomics Data. PLoS
Computational Biology, 11(8), 1-18. <a
href="http://dx.doi.org/10.1371/journal.pcbi.100
4403">[More Information]</a>
Tembe, V., Schramm, S., Stark, M., Patrick, E.,
Jayaswal, V., Tang, Y., Barbour, A., Hayward,
N., Thompson, J., Scolyer, R., Yang, J., Mann,
G. (2015). microRNA and mRNA expression
profiling in metastatic melanoma reveal
associations with BRAF mutation and patient
prognosis. Pigment Cell & Melanoma Research,
28(3), 254-226. <a
href="http://dx.doi.org/10.1111/pcmr.12343">[
More Information]</a>
Chaudhuri, R., Sadrieh, A., Hoffman, N., Parker,
B., Humphrey, S., Stoeckli, J., Hill, A., James,
D., Yang, J. (2015). PhosphOrtholog: a
web-based tool for cross-species mapping of
orthologous protein post-translational
modification. BMC Genomics, 16(1), 1-14. <a
href="http://dx.doi.org/10.1186/s12864-015-182
0-x">[More Information]</a>
Tiffen, J., Gunatilake, D., Gallagher, S.,
Gowrishankar, K., Heinemann, A., Cullinane, C.,
Dutton-Regester, K., Pupo, G., Strbenac, D.,
Yang, J., Madore, J., Mann, G., Hersey, P., et al
(2015). Targeting activating mutations of EZH2
leads to potent cell growth inhibition in human
melanoma by derepression of tumor suppressor
genes. Oncotarget, 6(29), 27023-27036. <a
href="http://dx.doi.org/10.18632/oncotarget.480
9">[More Information]</a>
Publications for Jean Yang
Byrne, M., Koop, D., Cisternas, P., Strbenac, D.,
Yang, J., Wray, G. (2015). Transcriptomic
analysis of Nodal- and BMP-associated genes
during juvenile development of the sea urchin
Heliocidaris erythrogramma. Marine Genomics,
24(1), 41-45. <a
href="http://dx.doi.org/10.1016/j.margen.2015.0
5.019">[More Information]</a>
2014
Yang, P., Patrick, E., Tan, S., Fazakerley, D.,
Burchfield, J., Gribben, C., Prior, M., James, D.,
Yang, J. (2014). Direction pathway analysis of
large-scale proteomics data reveals novel
features of the insulin action pathway.
Bioinformatics, 30(6), 808-814. <a
href="http://dx.doi.org/10.1093/bioinformatics/bt
t616">[More Information]</a>
Palmer, S., Wong, G., Iff, S., Yang, J., Jayaswal,
V., Craig, J., Rochtchina, E., Mitchell, P., Wang,
J., Strippoli, G. (2014). Fluid intake and all-cause
mortality, cardiovascular mortality, and kidney
function: a population-based longitudinal cohort
study. Nephrology, Dialysis, Transplantation,
29(7), 1377-1384. <a
href="http://dx.doi.org/10.1093/ndt/gft507">[Mo
re Information]</a>
O'Connor, K., Parnell, G., Patrick, E., Ahlenstiel,
G., Suppiah, V., van der Poorten, D., Read, S.,
Leung, R., Douglas, M., Yang, J., Stewart, G.,
Liddle, C., George, J., Booth, D. (2014). Hepatic
metallothionein expression in chronic hepatitis C
virus infection is IFNL3 genotype-dependent.
Genes and Immunity, 15(2), 88-94. <a
href="http://dx.doi.org/10.1038/gene.2013.66">[
More Information]</a>
Ma, X., Yang, P., Kaplan, W., Lee, B., Wu, L.,
Yang, J., Yasunaga, M., Sato, K., Chisholm, D.,
James, D. (2014). ISL1 Regulates Peroxisome
Proliferator-Activated Receptor gamma
Activation and Early Adipogenesis via Bone
Morphogenetic Protein 4-Dependent and
-Independent Mechanisms. Molecular and
Cellular Biology, 34(19), 3607-3617. <a
href="http://dx.doi.org/10.1128/MCB.00583-14"
>[More Information]</a>
Barter, R., Schramm, S., Mann, G., Yang, J.
(2014). Network-based biomarkers enhance
classical approaches to prognostic gene
expression signatures. International Conference
on Bioinformatics 2014 (InCoB2014), Australia:
BMC Public Health. <a
href="http://dx.doi.org/10.1186/1752-0509-8-S4S5">[More Information]</a>
Mactier, S., Kaufman (nee Alexander), K.,
Wang, P., Crossett, B., Pupo, G., Kohnke, P.,
Thompson, J., Scolyer, R., Yang, J., Mann, G.,
Christopherson, R. (2014). Protein signatures
correspond to survival outcomes of AJCC stage
III melanoma patients. Pigment Cell &
Melanoma Research, 27(6), 1106-1116. <a
href="http://dx.doi.org/10.1111/pcmr.12290">[
More Information]</a>
Yang, P., Zhou, B., Yang, J., Zomaya, A. (2014).
Stability of Feature Selection Algorithms and
Ensemble Feature Selection Methods in
Bioinformatics. In Mourad Elloumi, Albert Y.
Zomaya (Eds.), Biological Knowledge Discovery
Handbook: Preprocessing, Mining and
Postprocessing of Biological Data, (pp.
333-352). New Jersey: John Wiley & Sons.
Wygoda, J., Yang, J., Byrne, M., Wray, G.
(2014). Transcriptomic analysis of the highly
derived radial body plan of a sea urchin. Genome
Biology and Evolution, 6(4), 964-973. <a
href="http://dx.doi.org/10.1093/gbe/evu070">[M
ore Information]</a>
2013
Oates, J., Casikar, I., Campain, A., Mueller, S.,
Yang, J., Reid, S., Condous, G. (2013). A
prediction model for viability at the end of the
first trimester after a single early pregnancy
evaluation. Australian and New Zealand Journal
of Obstetrics and Gynaecology, 53(1), 51-57. <a
href="http://dx.doi.org/10.1111/ajo.12046">[Mo
re Information]</a>
Mann, G., Pupo, G., Campain, A., Carter, C.,
Schramm, S., Pianova, S., Gerega, S., Desilva,
C., Lai, K., Wilmott, J., Hersey, P., Kefford, R.,
Thompson, J., Yang, J., Scolyer, R., et al (2013).
BRAF Mutation, NRAS Mutation, and the
Absence of an Immune-Related Expressed Gene
Profile Predict Poor Outcome in Patients with
Stage III Melanoma. Journal of Investigative
Dermatology, 133(2), 509-517. <a
href="http://dx.doi.org/10.1038/jid.2012.283">[
More Information]</a>
Strbenac, D., Armstrong, N., Yang, J. (2013).
Correction: Detection and classification of peaks
in 5' cap RNA sequencing data. BMC Genetics,
14(1), Art. 767-1. <a
href="http://dx.doi.org/10.1186/1471-2164-14-7
67">[More Information]</a>
Strbenac, D., Armstrong, N., Yang, J. (2013).
Detection and classification of peaks in 5’ cap
RNA sequencing data. BMC Genomics, 14(Suppl
5), 1-11. <a
href="http://dx.doi.org/10.1186/1471-2164-14-S
5-S9">[More Information]</a>
Chung, S., Shen, W., Jayawardana, K., Wang, P.,
Yang, J., Shackel, N., Gillies, M. (2013).
Differential gene expression profiling after
conditional müller-cell ablation in a novel
transgenic model. Investigative Ophthalmology
and Visual Science, 54(3), 2142-2152. <a
href="http://dx.doi.org/10.1167/iovs.12-1155">[
Publications for Jean Yang
More Information]</a>
Schramm, S., Li, S., Jayaswal, V., Fung, D.,
Campain, A., Pang, C., Scolyer, R., Yang, J.,
Mann, G., Wilkins, M. (2013). Disturbed
protein-protein interaction networks in metastatic
melanoma are associated with worse prognosis
and increased functional mutation burden.
Pigment Cell & Melanoma Research, 26(5),
708-722. <a
href="http://dx.doi.org/10.1111/pcmr.12126">[
More Information]</a>
Humphrey, S., Yang, G., Yang, P., Fazakerley,
D., Stockli, J., Yang, J., James, D. (2013).
Dynamic adipocyte phosphoproteome reveals
that akt directly regulates mTORC2. Cell
Metabolism, 17(6), 1009-1020. <a
href="http://dx.doi.org/10.1016/j.cmet.2013.04.0
10">[More Information]</a>
Patrick, E., Buckley, M., Yang, J. (2013).
Estimation of data-specific constitutive exons
with RNA-Seq data. BMC Bioinformatics,
14(31), 1-10. <a
href="http://dx.doi.org/10.1186/1471-2105-14-3
1">[More Information]</a>
Patrick, E., Buckley, M., Lin, D., Yang, J.
(2013). Improved moderation for gene-wise
variance estimation in RNA-Seq via the
exploitation of external information. BMC
Genomics, 14(Suppl 1), S1-S9. <a
href="http://dx.doi.org/10.1186/1471-2164-14-S
1-S9">[More Information]</a>
Wang, P., Yang, J., Raftery, M., Zhong, L.,
Wilson, S. (2013). Latin Square Dataset for
Evaluating the Accuracy of Mass
Spectrometry-based Protein Identification and
Quantification. 2013 IEEE International
Conference on Bioinformatics and Biomedicine
(BIBM2013), Piscataway, United States: (IEEE)
Institute of Electrical and Electronics Engineers.
<a
href="http://dx.doi.org/10.1109/BIBM.2013.673
2765">[More Information]</a>
Schramm, S., Jayaswal, V., Goel, A., Li, S.,
Yang, J., Mann, G., Wilkins, M. (2013).
Molecular interaction networks for the analysis
of human disease: utility, limitations, and
considerations. Proteomics, 13(23-24),
3393-3405. <a
href="http://dx.doi.org/10.1002/pmic.201200570
">[More Information]</a>
Neff, C., Yang, J. (2013). Shark bites and public
attitudes: Policy implications from the first
before and after shark bite survey. Marine
Policy, 38, 545-547. <a
href="http://dx.doi.org/10.1016/j.marpol.2012.06
.017">[More Information]</a>
Jayaswal, V., Schramm, S., Mann, G., Wilkins,
M., Yang, J. (2013). VAN: an R package for
identifying biologically perturbed networks via
differential variability analysis. BMC Research
Notes, 6(1), 1-9. <a
href="http://dx.doi.org/10.1186/1756-0500-6-43
0">[More Information]</a>
Yang, J., Markus, A., Mangs, A., Raitskin, O.,
Sperling, R., Morris, B. (2013). ZRANB2
localizes to supraspliceosomes and influences the
alternative splicing of multiple genes in the
transcriptome. Molecular Biology Reports, 40(9),
5381-5395. <a
href="http://dx.doi.org/10.1007/s11033-013-263
7-9">[More Information]</a>
2012
Yang, P., Ma, J., Wang, P., Zhu, Y., Zhou, B.,
Yang, J. (2012). Improving X!Tandem on
peptide identification from mass spectrometry by
self-boosted percolator. IEEE - ACM
Transactions on Computational Biology and
Bioinformatics, 9(5), 1273-1280. <a
href="http://dx.doi.org/10.1109/TCBB.2012.86"
>[More Information]</a>
Jayaswal, V., Lutherborrow, M., Yang, J. (2012).
Measures of Association for Identifying
MicroRNA-mRNA Pairs of Biological Interest.
PloS One, 7(1), e29612-1-e29612-10. <a
href="http://dx.doi.org/10.1371/journal.pone.002
9612">[More Information]</a>
Bryant, A., Palma, C., Jayaswal, V., Yang, J.,
Lutherborrow, M., Ma, D. (2012). miR-10a is
aberrantly overexpressed in Nucleophosmin1
mutated acute myeloid leukaemia and its
suppression induces cell death. Molecular
Cancer, 11(8), 1-9. <a
href="http://dx.doi.org/10.1186/1476-4598-11-8"
>[More Information]</a>
Wang, P., Yang, P., Yang, J. (2012). OCAP: an
open comprehensive analysis pipeline for
iTRAQ. Bioinformatics, 28(10), 1404-1405. <a
href="http://dx.doi.org/10.1093/bioinformatics/bt
s150">[More Information]</a>
Yang, P., Humphrey, S., Fazakerley, D., Prior,
M., Yang, G., James, D., Yang, J. (2012).
Re-Fraction: A machine learning approach for
deterministic identification of protein
homologues and splice variants in large-scale
MS-based proteomics. Journal of Proteome
Research, 11(5), 3035-3045. <a
href="http://dx.doi.org/10.1021/pr300072j">[Mo
re Information]</a>
Schramm, S., Campain, A., Scolyer, R., Yang, J.,
Mann, G. (2012). Review and Cross-Validation
of Gene Expression Signatures and Melanoma
Prognosis. Journal of Investigative Dermatology,
132(2), 274-283. <a
href="http://dx.doi.org/10.1038/jid.2011.305">[
Publications for Jean Yang
More Information]</a>
.00009.2011">[More Information]</a>
2011
Jayaswal, V., Lutherborrow, M., Ma, D., Yang,
J. (2011). Identification of microRNA-mRNA
modules using microarray data. BMC Genomics,
12(138), 1-32. <a
href="http://dx.doi.org/10.1186/1471-2164-12-1
38">[More Information]</a>
Loi, T., Campain, A., Bryant, A., Molloy, T.,
Lutherborrow, M., Turner, J., Yang, J., Ma, D.
(2011). Discriminating lymphomas and reactive
lymphadenopathy in lymph node biopsies by
gene expression profiling. BMC Medical
Genomics, 4(27), 1-10. <a
href="http://dx.doi.org/10.1186/1755-8794-4-27"
>[More Information]</a>
Lutherborrow, M., Bryant, A., Jayaswal, V.,
Agapiou, D., PALMA, C., Yang, J., Ma, D.
(2011). Expression Profiling of Cytogenetically
Normal Acute Myeloid Leukemia Identifies
MicroRNAs that Target Genes Involved in
Monocytic Differentiation. American Journal Of
Hematology, 86(1), 2-11. <a
href="http://dx.doi.org/10.1002/ajh.21864">[Mo
re Information]</a>
Marques, F., Campain, A., Tomaszewski, M.,
Zukowska-Szczechowska, E., Yang, J.,
Charchar, F., Morris, B. (2011). Gene Expression
Profiling Reveals Renin mRNA Overexpression
in Human Hypertensive Kidneys and a Role for
MicroRNAs. Hypertension, 58(6), 1093-1098. <a
href="http://dx.doi.org/10.1161/HYPERTENSIO
NAHA.111.180729">[More Information]</a>
Yang, P., Ho, J., Yang, J., Zhou, B. (2011).
Gene-gene interaction filtering with ensemble
of filters. BMC Bioinformatics, 12(Supp 1: S10),
1-10. <a
href="http://dx.doi.org/10.1186/1471-2105-12-S
1-S10">[More Information]</a>
Marques, F., Campain, A., Davern, P., Yang, J.,
Head, G., Morris, B. (2011). Genes Influencing
Circadian Differences in Blood
Pressure in Hypertensive Mice. PloS One, 6(4),
e19203-1-e19203-9. <a
href="http://dx.doi.org/10.1371/journal.pone.001
9203">[More Information]</a>
Wu, J., Dwyer, D., Dyer, W., Yang, J., Wang, B.,
Saksena, N. (2011). Genome-wide analysis of
primary CD4+ and CD8+
T cell transcriptomes shows evidence for a
network of enriched pathways associated with
HIV disease. Retrovirology, 8(18), 1-21. <a
href="http://dx.doi.org/10.1186/1742-4690-8-18"
>[More Information]</a>
Marques, F., Campain, A., Davern, P., Yang, J.,
Head, G., Morris, B. (2011). Global
identification of the genes and pathways
differentially expressed in hypothalamus in early
and established neurogenic hypertension.
Physiological Genomics, 43(12), 766-771. <a
href="http://dx.doi.org/10.1152/physiolgenomics
Collinson, E., Wimmer-Kleikamp, S., Gerega, S.,
Yang, J., Parish, C., Dawes, I., Stocker, R.
(2011). The Yeast Homolog of Heme
Oxygenase-1 Affords Cellular Antioxidant
Protection via the Transcriptional Regulation of
Known Antioxidant Genes. Journal of Biological
Chemistry, 286(3), 2205-2214. <a
href="http://dx.doi.org/10.1074/jbc.M110.18706
2">[More Information]</a>
Peters, T., Bulger, D., Loi, T., Yang, J., Ma, D.
(2011). Two-Step Cross-Entropy Feature
Selection For Microarrays-Power Through
Complementarity. IEEE - ACM Transactions on
Computational Biology and Bioinformatics, 8(4),
1148-1151. <a
href="http://dx.doi.org/10.1109/TCBB.2011.30"
>[More Information]</a>
2010
Wang, P., Yang, P., Arthur, J., Yang, J. (2010).
A dynamic wavelet-based algorithm for
pre-processing tandem mass spectrometry data.
Bioinformatics, 26(18), 2242-2249. <a
href="http://dx.doi.org/10.1093/bioinformatics/bt
q403">[More Information]</a>
Yang, P., Yang, J., Zhou, B., Zomaya, A. (2010).
A Review of Ensemble Methods in
Bioinformatics. Current Bioinformatics, 5(4),
296-308. <a
href="http://dx.doi.org/10.2174/1574893107940
72508">[More Information]</a>
Jensen, S., Apisiridej, S., Kwong, S., Yang, J.,
Skurray, R., Firth, N. (2010). Analysis of the
prototypical Staphylococcus aureus
multiresistance plasmid pSK1. Plasmid, 64(3),
135-142. <a
href="http://dx.doi.org/10.1016/j.plasmid.2010.0
6.001">[More Information]</a>
Campain, A., Yang, J. (2010). Comparison study
of microarray meta-analysis methods. BMC
Bioinformatics, 11(408), 1-11. <a
href="http://dx.doi.org/10.1186/1471-2105-11-4
08">[More Information]</a>
Marques, F., Campain, A., Yang, J., Morris, B.
(2010). Meta-Analysis of Genome-Wide Gene
Expression Differences in Onset and
Maintenance Phases of Genetic Hypertension.
Hypertension, 56(2), 319-324. <a
href="http://dx.doi.org/10.1161/HYPERTENSIO
NAHA.110.155366">[More Information]</a>
Publications for Jean Yang
Karim, R., Gerega, S., Yang, J., Spillane, A.,
Carmalt, H., Scolyer, R., Lee, C. (2010). p16 and
pRb immunohistochemical expression increases
with increasing tumour grade in mammary
phyllodes tumours. Histopathology, 56(7),
868-875. <a
href="http://dx.doi.org/10.1111/j.1365-2559.201
0.03562.x">[More Information]</a>
2009
Jayaswal, V., Lutherborrow, M., Ma, D., Yang,
J. (2009). Identification of microRNAs with
regulatory potential using a matched microRNA
-mRNA time-course data. Nucleic Acids
Research, 37(8), e60-e60. <a
href="http://dx.doi.org/10.1093/nar/gkp153">[M
ore Information]</a>
Karim, R., Gerega, S., Yang, J., Spillane, A.,
Carmalt, H., Scolyer, R., Lee, C. (2009).
Phyllodes tumours of the breast: a
clinicopathological analysis of 65 cases from a
single institution. The Breast, 18(3), 165-170. <a
href="http://dx.doi.org/10.1016/j.breast.2009.03.
001">[More Information]</a>
Karim, R., Gerega, S., Yang, J., Horvath, L.,
Spillane, A., Carmalt, H., Scolyer, R., Lee, C.
(2009). Proteins from the Wnt pathway are
involved in the pathogenesis and progression of
mammary phyllodes tumours. Journal of Clinical
Pathology, 62(11), 1016-1020. <a
href="http://dx.doi.org/10.1136/jcp.2009.066977
">[More Information]</a>
Karim, R., Li, W., Sanki, A., Colman, M., Yang,
J., Thompson, J., Scolyer, R. (2009). Reduced
p16 and increased cyclin D1 and pRb expression
are correlated with progression in cutaneous
melanocytic tumors. International Journal of
Surgical Pathology, 17(5), 361-367. <a
href="http://dx.doi.org/10.1177/1066896909336
177">[More Information]</a>
2008
Genomics, 9(SUPPL. 2, Article number 551),
1-15. <a
href="http://dx.doi.org/10.1186/1471-2164-9-55
1">[More Information]</a>
Wu, J., Dwyer, D., Dyer, W., Yang, J., Wang, B.,
Saksena, N. (2008). Transcriptional profiles in
CD8+ T cells from HIV+ progressors on
HAART are characterized by coordinated
up-regulation of oxidative phosphorylation
enzymes and interferon responses. Virology,
380(1), 124-135. <a
href="http://dx.doi.org/10.1016/j.virol.2008.06.0
39">[More Information]</a>
2007
Xiao, Y., Segal, M., Yang, J., Yeh, R. (2007). A
multi-array multi-SNP genotyping algorithm for
Affymetrix SNP microarrays. Bioinformatics,
23(12), 1459-1467.
Winn, V., Haimov-Kochman, R., Paquet, A.,
Yang, J., Madhusudhan, M., Gormley, M., Feng,
K., Bernlohr, D., McDonagh, S., Pereira, L., et al
(2007). Gene expression profiling of the human
maternal-fetal interface reveals dramatic changes
between midgestation and term. Endocrinology,
148(3), 1059-1079.
Woodruff, P., Boushey, H., Dolganov, G.,
Barker, C., Yang, J., Donnelly, S., Ellwanger, A.,
Sidhu, S., Dao-Pick, T., Pantoja, C., et al (2007).
Genome-wide profiling identifies elpithelial cell
genes associated with asthma and with treatment
response to corticosteroids. Proceedings of the
National Academy of Sciences of the United
States of America (PNAS), 104(40),
15858-15863.
Williams, E., Xiao, Y., Sickles, H., Shafer, P.,
Yona, G., Yang, J., Lin, D. (2007). Novel
subdomains of the mouse olfactory bulb defined
by molecular heterogeneity in the nascent
external plexiform and glomerular layers. BMC
Developmental Biology, 7(article no. 48), 1-15.
Lewis, C., Yang, J., Huang, X., Banerjee, S.,
Balckburn, M., Baluk, P., McDonald, D.,
Blackwell, T., Nagabhushanam, V., Peters, W.,
et al (2008). Disease specific gene expression
profiling in multiple models of lung disease.
American Journal of Respiratory and Critical
Care Medicine, 177(4), 376-387. <a
href="http://dx.doi.org/10.1164/rccm.200702-33
3OC">[More Information]</a>
2005
Yang, J. (2008). Microarrays - Planning your
experiment. In Ronald J.A. Trent (Eds.),
Clinical Bioinformatics: Methods in Molecular
Medicine, (pp. 71-85). New Jersey: Humana
Press.
Xiao, Y., Yang, J., Burckin, T., Shiue, L.,
Hartzog, G., Segal, M. (2005). Analysis of a
Splice Array Experiment Elucidates Roles of
Chromatin Elongation Factor Spt4-5 in Splicing.
PLoS Computational Biology, 1(4),
e39-0276-e39-0288. <a
href="http://dx.doi.org/10.1371/journal.pcbi.001
0039">[More Information]</a>
Kechris, K., Yang, J., Yeh, R. (2008). Prediction
of alternatively skipped exons and splicing
enhancers from exon junction arrays. BMC
Woodruff, P., Koth, L., Yang, J., Rodriguez, M.,
Favoreto, S., Dolganov, G., Paquet, A., Erle, D.
(2005). A distinctive alveolar macrophage
activation state
induced by cigarette smoking. American Journal
of Respiratory and Critical Care Medicine,
172(11), 1383-1392.
Publications for Jean Yang
Kuperman, D., Lewis, C., Woodruff, P.,
Rodriguez, M., Yang, J., Dolganov, G., Fahy, J.,
Erle, D. (2005). Dissecting asthma using focused
transgenic modeling and functional genomics.
Journal of Allergy and Clinical Immunology,
116(2), 305-311. <a
href="http://dx.doi.org/10.1016/j.jaci.2005.03.02
4">[More Information]</a>
Gonzalez, R., Griffin, C., Yang, J., Allen, L.,
Tigue, Z., Dobbs, L. (2005). Freshly isolated rat
alveolar type I cells, type II cells, and cultured
type II cells have distinct molecular phenotypes.
American Journal of Physiology: Lung Cellular
and Molecular Physiology, 288(1), L179-L189.
Yang, J., Xiao, Y., Segal, M. (2005). Identifying
differentially expressed genes from microarray
experiments via statistic synthesis.
Bioinformatics, 21(7), 1084-1093.
Barker, C., Griffin, C., Dolganov, G., Hanspers,
K., Yang, J., Erle, D. (2005). Increased DNA
microarray hybridization specificity using
sscDNA targets. BMC Genomics, 6(57), 571-57- 8.
Yang, J., Paquet, A. (2005). Preprocessing
Two-Color Spotted Arrays. In R. Gentleman,
V. Carey, S. Dudoit, R. Irizarry, W. Huber
(Eds.), Bioinformatics and Computational
Biology Solutions using R and Bioconductor,
(pp. 49-70). New York: Springer.
Xiao, Y., Segal, M., Yang, J. (2005). Stepwise
Normalization of Two-Channel Spotted
Microarrays. Statistical Applications in Genetics
and Molecular Biology, 4(1), 4-1-4-29.
2004
Gentleman, R., Carey, V., Bates, D., Bolstad, B.,
Dettling, M., Dudoit, S., Ellis, B., Gautier, L.,
Ge, Y., Gentry, J., Yang, J., et al (2004).
Bioconductor: open software development for
computational biology and bioinformatics.
Genome Biology, 5(10), R80.1-R80.16.
Rodriguez, M., Paquet, A., Yang, J., Erle, D.
(2004). Differential gene expression by integrin
ß7+ and ß7-memory T helper cells. BMC
Immunology, 5(13), 1-11.
Lin, D., Yang, J., Scolnick, J., Brunet, L., Marsh,
H., Peng, V., Okazaki, Y., Hayashizaki, Y.,
Speed, T., Ngai, J. (2004). Spatial patterns of
gene expression in the olfactory bulb.
Proceedings of the National Academy of
Sciences of the United States of America (PNAS),
101(34), 12718-12723.
2003
Diaz, E., Yang, J., Ferreira, T., Loh, K., Okazaki,
Y., Hayashizaki, Y., Tessier-Lavigne, M., Speed,
T., Ngai, J. (2003). Analysis of gene expression
in the developing
mouse retina. Proceedings of the National
Academy of Sciences of the United States of
America (PNAS), 100(9), 5491-5496.
Erle, D., Yang, J. (2003). Asthma investigators
begin to reap the fruits of genomics. Genome
Biology, 4(11), 232.1-232.3.
Yang, J., Speed, T. (2003). Bioconductor R
packages for exploratory analysis and
normalization of cDNA microarray data. In G.
Parmigiani, E. S. Garrett, R. A. Irizarry and S. L.
Zeger (Eds.), The Analysis of Gene Expression
Data: Methods and Software, (pp. 73-101). New
York: Springer.
Yang, J., Speed, T. (2003). Design and Analysis
of Comparative Microarray Experiments. In T.
P. Speed (Eds.), Statistical Analysis of Gene
Expression Microarray Data, (pp. 35-92).
Chapman & Hall.
Yang, J., Thorne, N. (2003). Normalization for
Two-color cDNA Microarray Data. In Darlene
R Goldstein (Eds.), Science and Statistics: A
Festschrift for Terry Speed, (pp. 403-418).
Beachwood, Ohio: Institute of Mathematical
Statistics.
Smyth, G., Yang, J., Speed, T. (2003). Statistical
issues in cDNA microarray data analysis. In M.
J. Brownstein and A. B. Khodursky (Eds.),
Functional Genomics: Methods and Protocols,
(pp. 111-136). New Jersey: Humana Press.
2002
Ball, C., Chen, Y., Panavally, S., Sherlock, G.,
Speed, T., Spellman, P., Yang, J. (2002). An
introduction to microarray bioinformatics. In D.
Bowtell and J. Sambrook (Eds.), DNA
Microarrays: A Molecular Cloning Manual, (pp.
509-602). New York: Cold Spring Harbor
Laboratory Press.
Yang, J., Buckley, M., Dudoit, S., Speed, T.
(2002). Comparison of methods for image
analysis on cDNA microarray data. Journal of
Computational and Graphical Statistics, 11(1),
108-136.
Yang, J., Speed, T. (2002). Design issues for
cDNA microarray experiments. Nature Reviews
Genetics, 3(8), 579-588.
Speed, T., Yang, J. (2002). Direct versus indirect
designs for cDNA microarray experiments.
Sankhya: The Indian Journal of Statistics,
64(Series A, Pt. 3), 707-721.
Diaz, E., Ge, Y., Yang, J., Loh, K., Serafini, T.,
Okazaki, Y., Hayashizaki, Y., Speed, T., Ngai,
J., Scheiffele, P. (2002). Molecular Analysis of
Gene Expression in the
Developing Pontocerebellar Projection System.
Neuron, 36(3), 417-434.
Publications for Jean Yang
Yang, J., Dudoit, S., Luu, P., Lin, D., Peng, V.,
Ngai, J., Speed, T. (2002). Normalization for
cDNA microarray data: a robust composite
method addressing single and multiple slide
systematic variation. Nucleic Acids Research,
30(4), e15.
Dudoit, S., Yang, J., Callow, M., Speed, T.
(2002). Statistical methods for identifying
differentially expressed genes in replicated
cDNA microarray experiments. Statistica Sinica,
12, 111-139.
Dudoit, S., Yang, J., Bolstad, B. (2002). Using R
for the Analysis of DNA Microarray Data. R
News.
2001
Yang, J., Buckley, M., Speed, T. (2001).
Analysis of cDNA microarray images. Briefings
in Bioinformatics, 2(4), 341-349.