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** Dataset: manually curated Human Signaling Network dataset (Updated April, 2013, HumanSignalingNetwork_v5.txt, ~6,300 proteins and ~63,000 relations). ** New Book: Wang E (ed), Cancer Systems Biology, CRC Mathematical and Computational Biology Series, 2010 [Link]. ** Internal computational tools and data resources (password is required) |
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Scientific Highlights
- Personalized medicine for cancer patients.
Dimensions Magazine, 2011 [HTML]
- A novel algorithm for finding robust cancer gene markers.
NRC Highlights, 2010 [HTML]; also in Genetic Engineering & Biotech News, 2010 [PDF]
- The bioinformatics components in plant genome research.
NRC Highlights, 2009 [HTML]
Gene expression map of Arabidopsis embryo development [HTML]
- From tumor genome sequencing to human cancer signaling maps.
Highlighted in Genome Technology Magazine [PDF]. Selected by NRC Highlights, 2008 [HTML]
Publications
- Cancer systems biology in the genome sequencing era (Invited Review).
Wang et al.
Seminars in Cancer Biology, 2013 [Paper]
- Understanding genomic alterations in cancer genomes using an integrative network approach (Invited Review).
Wang Edwin
Cancer Letter, in press, 2012 [Paper]
- A Mass spectrometry-based plasma protein panel targeting the tumor microenvironment in patients with breast cancer.
Cohen et al.
,J. Proteomics, in press, 2012
- An upstream interacting context based framework for the computational inference of microRNA functions.
Qiu C, Wang D, Wang E and Cui Q.
Molecular BioSystems, 8:1492-8, 2012
- Target of rapamycin signaling regulates metabolism, growth and lifespan in Arabidopsis.
Ren et al.
Plant Cell, in press, 2012
- The human phosphotyrosine signaling network-evolution and hotspots of hijacking in cancer.
Lei Li, Chabane Tibiche, Cong Fu, Tomonori Kaneko, Michael Moran, Martin Schiller, Shawn Li & Edwin Wang.
Genome Research, 2011 [PDF] Curated and predicted phosphotyrosine signaling circuits [XLS]
Presented in RECOME::DREAM, 2011 [ppt].
- Dynamic modeling and analysis of cancer cellular network motifs.
Cloutier and Wang.
Integrative Biology, 3:724-732, 2011 (Invited Review) [Paper] // [Supplementary Methods]
- A Multiple Survival Screening algorithm (MSS) for identifying high-quality cancer prognostic markers.
Li and Wang.
Protocol Exchange, doi:10.1038/protex.2011.211, 2011 (Protocol) [Link]
- Dynamic rewiring of the Androgen Receptor interaction networks correlates with prosate cancer clinical outcomes.
Paliouuras M et al.
Integrative Biology, 3:1020-1032, 2011 [pdf]
- Identification of vascular breast tumor markers by laser capture microdissection and label-free LC-MS.
Hill JJ et al.
Journal of Proteome Research, 10:2479-2493, 2011
- Functions in auxin pathway to regulate embryonic body plan and meristem organization in Arabidopsis.
Xiang D et al.
Plant Cell, 23:4348-67, 2011
- Genome-wide analysis reveals gene expression and metabolic network dynamics during embryo development in Arabidopsis.
Xiang D et al.
Plant Physiol, 156:346-356, 2011
- Gene expression analysis of flax seed development.
Venglat et al.
BMC Plant Biology, 11:74, 2011
2010
- Identification of high-quality cancer prognostic markers and metastasis network modules.
Li J, Lenferink AE, Deng Y, Cantin C, Cui Q, Purisima EO, O'Connor-McCourt MD, Wang E.
Nature Communications, 1:34, 2010
The paper is freely available in Nature Communications. Highlighted in GenomeWeb-This Week in Nature [HTML]; also in SciBX: Science-Business eXchange, 2010 [HTML]; also in GEN's Tech Tips: Protein Biomarker Discovery, 2010 [PDF] A pratical protocol of the algorithm [Protocol] [Software]
- microRNA evolution in a human transcription factor and microRNA regulatory network.
Qiu C., Wang J., Yao P., Wang E., Cui Q.
BMC Systems Biology, 4:90, 2010
The paper is freely available in BMC Systems Biology.
- Transcriptome profiling of a TGF-beta-induced epithelial-to-mesenchymal transition reveals extracellular clusterin as a target for therapeutic antibodies.
Lenferink AE, Cantin C, Nantel A, Wang E, Durocher Y, Banville M, Paul-Roc B, Marcil A, Wilson MR, O'Connor-McCourt MD.
Oncogene, 29:831–844, 2010
2009
- A roadmap of cancer systems biology.
Edwin Wang
Cancer Systems Biology (Wang, E. ed), Chapman & Hall/CRC Press [PDF]
- From tumor genome sequencing to cancer signaling maps.
Cong Fu and Edwin Wang
Cancer Systems Biology (Wang, E. ed), Chapman & Hall/CRC Press [PDF]
- Signaling network analysis of ubiquitin-mediated proteins suggests correlations between the 26S proteasome and tumor progression.
Cong Fu, Jie Li and Edwin Wang
Molecular BioSystems, 5:1809-1816, 2009 [PDF], [HTML]
- Protein evolution on a human signaling network.
Qinghua Cui, Enrico Purisima and Edwin Wang
BMC Systems Biology, 3:21, 2009
The paper is freely available in BMC Systems Biology.
- Cepred: predicting the co-expression patterns of the human intronic microRNAs with their host genes.
D. Wang, M. Lu, J. Miao, T. Li, E. Wang and Q. Cui
PLoS ONE, 4:e4421, 2009
The paper is freely available in PLoS ONE.
2008
- MicroRNA Regulatory Patterns on the Human Metabolic Network.
Chabane Tibiche and Edwin Wang
The Open Systems Biology Journal, 1:1-8, 2008 [PDF]
- Computational methods in cancer gene networking.
Edwin Wang
Nutrigenomics and Proteomics in Health and Disease, Blackwell, 367-374, 2008 [PDF]
- MicroRNA systems biology.
Edwin Wang
RNA Technologies in Cardiovascular Medicine and Research, Springer, 69-86, 2008 [PDF]
- An overview of microRNA.
Edwin Wang
RNA Technologies in Cardiovascular Medicine and Research, Springer, 1-16, 2008 [PDF]
2007
- A map of human cancer signaling (A network-based signaling mechanism of cancer developement and progression).
Cui, Q., Ma, Y., Jaramillo, M., Bari, H., Awan, A., Yang, S., Zhang, S., Liu, L., Lu, M., O'Connor-McCourt, M., Purisima, E. and Wang, E.
Nature-EMBO Molecular Systems Biology, 3:152, 2007
Abstract , human signaling network dataset , cancer-signaling-map dataset, and access the paper in MSB, a new journal from EMBO and Nature. Highlighted in Genome Technology Magazine [PDF]. Selected by NRC Highlights [webLink]. News in Genomics and Proteomics [PDF]. Selected in Highlight Track, 16th International Conference of ISMB, 2008 [Presentation in Nature Precedings].
- Cancer systems biology: exploring cancer-associated genes on cellular networks.
Wang, E., Lenferink, AE.,and O'Connor-McCourt, MD.
Cellular and Molecular Life Sciences (CMLS), 64:1752-1762, 2007, [invited review] [PDF]
- Regulatory network motifs and hotspots of cancer genes in
a mammalian cellular signaling network.
Awan, A., H. Bari, F. Yan, S. Mokin, S. Yang, S. Chowdhury, Q. Cui, Z. Yu, E. Purisima and E. Wang
IET Systems Biology, 1:292-297, 2007
Click this link to view the supplementary material page.
- MicroRNA systems biology.
Edwin Wang
A book chapter in: "RNA Technologies in Cardiovascular Medicine and Research", Springer, in press [PDF]
- Aberrant allele frequencies of the SNPs located in microRNA target sites are potentially associated with human cancers.
Yu, Z., Zhen, L., Jolicoeur, N., Zhang, L., Fortin, Y., Wang, E., Shen, S.
Nuclei Acids Research, 35:4535-4541, 2007
The paper is freely available in NAR.
- MicroRNA regulation and interspecific variation of gene expression.
Qinghua Cui, Zhenbao Yu, Enrico Purisima and Edwin Wang
Trends Genet., 23:372-375, 2007
Abstract , paper and supplementary materials.
- Global analysis of microRNA target gene expression
reveals that miRNA targets are lower expressed in mature mouse and Drosophila tissues than in the embryos.
Zhenbao Yu, Zhaofeng Jian, Shi-Hsiang Shen, Enrico Purisima and Edwin Wang
Nuclei Acids Research, 35:152-164, 2007
The paper is freely available in NAR. Picked up by Faculty of 1000 Biology.
- MicroRNAs preferentially target the genes with high
transcriptional regulation complexity.
Qinghua Cui, Zhenbao Yu, Youlian Pan, Enrico Purisima and Edwin Wang
Biochem Biophys Res Commun., 352:733-738, 2007
Abstract , paper and supplementary materials.
2006
- Principles of microRNA regulation of a human cellular
signaling network.
Qinghua Cui, Zhenbao Yu, Enrico Purisima and Edwin Wang
Nature-EMBO Molecular Systems Biology, 2:46, 2006
Supplementary materials and access the paper in MSB, a new journal from EMBO and Nature.
2005
- Network motifs are enriched with transcription factors
whose transcripts have short half-lives.
Edwin Wang and Enrico Purisima
Trends Genet., 21:492-495, 2005
Abstract , paper and supplementary materials.
- A Human-Curated Annotation of the Candida albicans
Genome.
Braun BR et al.,
PLoS Genet., 1:36-57, 2005
Supplementary materials and the paper is freely available in PLoS Genetics.
- Tumor geneome sequencing paper track: enter here.