SELECTED PUBLICATIONS

Books 

Edwin Wang (ed), Cancer Systems Biology, CRC Press, 2010(The first book of the cancer systems biology field), In AmazonCRC PressWiki for Cancer Systems Biology 

Selected Research Articles

Milanese JS., ..  Wang E., Germline variants associated with leukocyte-genes predict tumor recurrence in breast cancer patients,  npj (Nature Partner Journal) Precision Oncology, 3:28, 2019; paper online, PMID: 31701019; bioRxiv, News from the GenomeWebBlog at Nature Research Cancer (blog), Selected by NEJM (New England Journal of Medicine) Journal Watch (link

Xu X., ..  Wang E., Association of germline variants in natural killers cells with tumor immune microenvironment subtypes, tumor-infiltrating lymphocytes, immunotherapy response, clinical outcomes, and cancer risk, JAMA Network Open2:e199292, 2019paper onlineSupplemental Materials, PMID: 31483464, Blog at Nature Research Cancer (blog

Gao, Tibiche, Zou, Zaman, Trifiro, O'Connor-McCourt and Wang, Identification and Construction of Combinatory Cancer Hallmark-Based Gene Signature Sets to Predict Recurrence and Chemotherapy Benefit in Stage II Colorectal Cancer, JAMA Oncology2:37-45, 2016,  paper onlineSupplemental Materials  (JAMA, NEJM and Lancet are the 3 top clinical journals)Reuters NewsPMID: 26502222

Zaman N. . Edwin Wang, Signaling network assessment of mutations and copy number variations predict breast cancer subtype-specific drug targets, Cell Reports (a new Cell sister journal), 5:216-223, 2013, Paper in Cell Press, PMID: 24075989 

Li L., Fu C., Tibiche C., Kaneko T., Schiller M., Li S., Wang, EdwinThe human phosphotyrosine signaling network: evolution and hotspots of hijacking in cancer, Genome Research, 22:1222-30, 2012, Paper in Genome ResHighlighted in 7th Annual RECOMB Systems Biology, 2011, PMID: 22194470

 Li. J., Lenferink, AE., Cantin, C., Purisima EO., O'Connor-McCourt, MD., and Edwin Wang, Identification of high quality cancer prognostic markers and metastasis network modules, Nature Communications1:34, 2010, Paper in Nature Communications. GEN's Tech Tips: Protein Biomarker Discovery, 2010. Commentary,NRC HighlightsPMID: 20975711

Cui Q, Ma Y, Jaramillo M, Bari H, Awan A, Yang S, Zhang S, Liu L, Lu M, O'Connor-McCourt M, Purisima EO, Edwin Wang, A map of human cancer signaling, (Nature/EMBO) Molecular Systems Biology3:152, 2007, Paper in Molecular Systems Biology (MSB)Highlighted in Genome Technology Magazine (PDF),  Highlight Track in 16th International Conference of ISMB, 2008, NRC Highlights PMID:16969338

Cui Q, Yu Z, Purisima EO, Wang Edwin, MicroRNA regulation and cross-species variation of gene expression, Trends Genet.23:372-375, 2007, PDFPaper in Cell Press

Cui Q, Yu Z, Purisima EO, Wang Edwin, Principles of microRNA regulation of a human cellular signaling network, (Nature/EMBO) Molecular Systems Biology, 2:46, 2006Paper in Molecular Systems Biology (MSB) PMID:16969338

Edwin Wang*, Purisima E., Network motifs are enriched with transcription factors whose transcripts have short half-lives, Trends Genet. 21:492-495, 2005, PDFPaper in Cell Press 

Selected Visionary Essays

Milanese and Wang, Germline mutations and their applications in cancer (Editorial), Future Medicine, 2019, paper online 

Edwin Wang* et al., Predictive Genomics: A cancer hallmark network framework for predicting tumor clinical phenotypes using genome sequencing data, Seminars in Cancer Biology (Invited review), 2014, PDF, preprint, PMID: 24747696, Blog at Nature Research Cancer (blog

Edwin Wang* et al., Cancer systems biology in the genome sequencing era: Part 1, dissecting and modeling of tumor clones and their networks, Seminars in Cancer Biology (Invited Review), 23:279-285,2013, PDF, PMID: 23791722 

Edwin Wang* et al., Cancer systems biology in the genome sequencing era: Part 2, evolutionary dynamics of tumor clonal networks and drug resistance, Seminars in Cancer Biology (Invited Review), 23:286-292,2013, PDF, PMID: 23792107 

Edwin Wang, A roadmap of cancer systems biology, In Edwin Wang (ed), Cancer Systems Biology, CRC Press, 2010, PDFNature Precedings, 2010 

Edwin Wang et al., Cancer systems biology: exploring cancer-associated genes on cellular networks (invited review), Cellular and Molecular Life Sciences (CMLS), 64:1752-1762, 2007PDF

 More Publications

Research Article Preprints

Feng et al., Germline genomic patterns are associated with cancer risk, oncogenic pathways and clinical outcomes, doi: https://doi.org/10.1101/616268, 2019, paper online

Zou and Wang, eTumorRisk, an algorithm predicts cancer risk based on co-mutated gene networks in an individual's germline genome, doi: https://doi.org/10.1101/393090, 2018, paper online  

Milanese et al., eTumorMetastatsis, a network-based algorithm predicts clinical outcomes using whole-exome sequencing data of cancer patientsdoi: https://doi.org/10.1101/268680, 2018, paper online 

Research Articles and Reviews

Xiang et al., The transcriptional landscape of polyploid wheats and their diploid ancestors during embryogenesis and grain development, Plant Cell, 31:2888-2911, 2019, paper online

Milanese, ..  Wang E., Germline variants associated with leukocyte-genes predict tumor recurrence in breast cancer patients, npj (Nature Partner Journal) Precision Oncology, 3:28, 2019, paper onlinebioRxiv

Xu X., ..  Wang E., Association of germline variants in natural killers cells with tumor immune microenvironment subtypes, tumor-infiltrating lymphocytes, immunotherapy response, clinical outcomes, and cancer risk, JAMA Network Open, 2:e199292, 2019,  on-lineSupplemental Materials

Feng et al., Gene expression-based predictive markers for paclitaxel treatment in ER+ and ER- breast cancer, Frontiers in Genetics, 2019, paper online

Hao et al., The protein-protein interaction network of Litopenaeus vannamei haemocyte, Frontiers in Physiol, 10: 156, 2019 , paper online

Gao et al., Gene expression atlas of embryo development in Arabidopsis, Plant Reprod, 32:93-104, 2019 , paper online

Peter et al., Putting benchmarks in their rightful place: The heart of computational biology, PLoS Computational Biology, e1006494, 2018, paper online

Hao et al., Analyzing of molecular networks for human diseases and drug discovery, Current Topics in Medicinal Chemistry, 18: 8, 2018, paper online

Zou and Wang, Cancer biomarker discovery for precision medicine: new progresses, Current Medicinal Chemistry, 2018

Hao et al., The genome-scale integrated networks in microorganisms, Frontiers in Microbiology, 9: 296, 2018, paper online

Zou et al., A protocol for epigenetic imprinting analysis with RNA-seq data, Methods Molecular Biology, 1751: 199-208, 2018

Zou and Wang, eTumorType, an algorithm of discriminating cancer types for circulating tumor cells or cell-free DNAs in blood,  Genomics, Proteomics Bioinformatics,  15:130-140, 2017, paper online

McGee et al., Network analysis reveals a singling regulatory loop in the PIK3CA-mutated breast cancer predicting survival outcome,  Genomics, Proteomics Bioinformatics,  15:121-129, 2017, paper online

Wang et al., Disease biomarkers for precision medicine: challenges and future opportunities,  Genomics, Proteomics Bioinformatics,  15:57-58, 2017, paper online

Han et al., Gene Regulatory network rewiring in the immune cells associated with cancer, Genes, 8:308, 2017, paper online  

You et al., The multivalent histone binder BRPF1 is essential for development of fetal hematopoietic stem cells, J Clinical Investigations (JCI), 126:3247-62, 2016, paper online

Gao et al., Identification and construction of combinatory cancer-hallmark-based gene signature sets that predict recurrence and chemotherapy benefit in stage II colorectal cancer, JAMA Oncology, 2015, paper onlineSupplemental Material2015

Schweitzer et al., Characterization of the NPC1L1 gene and proteome from an exceptional responder to ezetimibe,  Atherosclerosis,  246:78-86, 2016, paper online

Phuong et al., Molecular Characterization of the Vasculature of Patients with Infiltrating Ductal Carcinoma Generates a Gene Signature Predictive of Breast Cancer Survival, Journal of Cancer Biology and Research, 3:1068, 2015, paper online

You et al., The lysine acetylation activator Brpf1 governs dentate gyrus development through neural progenitors and stem cells, PLoS Genetics, 11: e1005034, 2015, paper online

Hill et al., Glycoproteomic Comparison of Clinical Triple-Negative and Luminal Breast Tumors, J. Proteome Res, 14: 1376-1388, 2015

 You et al., The chromatin regulator Brpf1 regulates embryo development and cell proliferation, J. Biol Chem, 290:11349-64, 2015

 You et al., Deficiency of the multivalent chromatin regulator Brpf1 causes abnormal brain development, J. Biol Chem, 290: 7114-7129, 2015

 Edwin Wang* et al., Predictive Genomics: A cancer hallmark network framework for predicting tumor clinical phenotype using genome sequencing data, Seminars in Cancer Biology (Invited review), 30:4-12, 2015, PDF,

 Masoudi-Nejad and Edwin Wang, Cancer modeling and network biology: Accelerating toward personalized medicine, Seminars in Cancer Biology (Invited review), 30:1-3, 2015

 Masoudi-Nejad, .. and Edwin Wang, Cancer systems biology and modeling: Microscopic scale and multiscale approaches, Seminars in Cancer Biology (Invited review), 30:60-69, 2015

Zaman et al., Proteomic-Coupled-Network Analysis of T877A-Androgen Receptor Interactomes Can Predict Clinical Prostate Cancer Outcomes between White (Non-Hispanic) and African-American Groups, PLoS One, e113190,  2014

Zaman N. …. Edwin Wang*, Signaling network assessment of mutations and copy number variations predict breast cancer subtype-specific drug targets, Cell Reports (a new Cell sister journal), 5:216-223, 2013, Paper in Cell Press,

 Edwin Wang* et al., Cancer systems biology in the genome sequencing era: Part 1, dissecting and modeling of tumor clones and their networks, Seminars in Cancer Biology (Invited Review), 23:279-285, 2013PDF, PMID:23791722

  Edwin Wang* et al., Cancer systems biology in the genome sequencing era: Part 2, evolutionary dynamics of tumor clonal networks and drug resistance, Seminars in Cancer Biology (Invited Review), 23:286-292, 2013PDF, PMID:23792107

  Edwin Wang, Understanding genomic alterations in cancer genomes using an integrative network approach, Cancer Letters (Invited Review), 340: 261-9, 2013,PDFPMID:23266571 

Cohen,.. Edwin Wang, .. et al., A Mass spectrometry-based plasma protein panel targeting the tumor microenvironment in patients with breast cancer, J. Proteomics, 81:135-47, 2013paper link,

Li L., Fu C., Tibiche C., Kaneko T., Schiller M., Li S., Edwin WangThe human phosphotyrosine signaling network: evolution and hotspots of hijacking in cancer, Genome Research, 22:1222-30, 2012Paper in Genome Res

 Qiu C, Wang D, Edwin Wang and Cui Q., An upstream interacting context based framework for the computational inference of microRNA functions, Mol Biosyst, 8:1492-8, 2012

Ren, .. Edwin Wang, .. et al, Target of rapamycin signaling regulates metabolism, growth, and life span in Arabidopsis, Plant Cell, 24:2850-74, 2012 

Paliouuras, .. Edwin Wang.. et al., Dynamic rewiring of the Androgen Receptor interaction networks correlates with prostate cancer clinical outcomes, Integrative Biology, 3:1020-1032, 2011, PMID:21901193

Xiang, .. Edwin Wang, .. et al, POPCORN functions in the auxin pathway to regulate embryonic body plan and meristem organization in arabidopsis, Plant Cell, 23:4348-67, 2011

 Cloutier M and Wang Edwin, Dynamic modeling and analysis of cancer cellular network motifs, Integrative Biology, (Invited review) 3:724-732, 2011, PDF, PMID:21674097

Hill, .. Edwin Wang, .. et al., Identification of vascular breast tumor markers by laser capture microdissection and label-free LC-MS, Journal of Proteome Research, 10:2479-2493, 2011paper link,

 Xiang, .. Edwin Wang, .. et al., Genome-wide analysis reveals gene expression and metabolic network dynamics during embryo development in Arabidopsis, Plant Physiol, 156:346-356, 2011

 Venglat P… Edwin Wang, .. et al., Gene expression analysis of flax seed development, BMC Plant Biology, 11: 74, 2011

Li and Wang, A Multiple Survival Screening algorithm (MSS) for identifying high-quality cancer prognostic markers (Protocol),doi:10.1038/protex.2011.211, 2011

Li. J., Lenferink, AE., Cantin, C., Purisima EO., O’Connor-McCourt, MD., and Edwin Wang, Identification of high quality cancer prognostic markers and metastasis network modules, Nature Communications, 1:34, 2010, Paper in Nature Communications

Qiu C., Wang J., Yao P., Edwin Wang, Cui Q., microRNA evolution in a human transcription factor and microRNA regulatory network, BMC Systems Biology, 4:90, 2010 (Highly Accessed noted by the journal website),

Lenferink, AE., Cantin, C., Nantel, A., Edwin Wang, Durocher, Y., Banville, M., Collins, C., Wilson, MR., O’Connor-McCourt, MD., Transcriptome profiling of a TGF-beta-induced epithelial-to-mesenchymal transition reveals extracellular clusterin as a target for therapeutic antibodies, Oncogene, 29:831–844, 2010

Fu, C., Li, J., Edwin Wang, Signaling network analysis of ubiquitin-mediated proteins suggests correlations between the 26S proteasome and tumor progression, Molecular BioSystems, 5:1809-1816, 2009paper link, PMID:19593471

 Cui, Q., Purisima EO., Wang, Edwin, Protein evolution on a human signaling network, BMC Systems Biology, 3:21, 2009 (Highly Accessed noted by the journal website), paper in BMC Systems Biology

 Wang D, Lu M, Miao J, Li T, Wang Edwin, Cui Q, Cepred: Predicting the co-expression patterns of the human intronic microRNAs with their host genes. PLoS ONE 4: e4421, 2009

 Yang, H., Xiang, D., Venglat, SP., Cao, Y., Wang, Edwin, Selvaraj, G., and Datla, R., PolA2 is required for embryo development in Arabidopsis, Botany, 87:626-634, 2009 

 Tibiche, C. and Edwin Wang, MicroRNA regulatory patterns on the human metabolic network, The Open Systems Biology Journal, 1:1-8, 2008Paper in the Systems Biology Journal

Cui Q, Ma Y, Jaramillo M, Bari H, Awan A, Yang S, Zhang S, Liu L, Lu M, O'Connor-McCourt M, Purisima EO, Edwin Wang, A map of human cancer signaling, (Nature/EMBO) Molecular Systems Biology, 3:152, 2007, Paper in Molecular Systems Biology (MSB) 

 Awan A, Bari H, Yan F, Moksong S, Yang S, Chowdhury S, Cui Q, Yu Z, Purisima EO, Edwin Wang, Regulatory network motifs and hotspots of cancer genes in a mammalian cellular signaling network, IET Systems Biology, 1:292-297, 2007, PDF

Cui Q, Yu Z, Purisima EO, Edwin Wang, MicroRNA regulation and cross-species variation of gene expression, Trends Genet., 23:372-375, 2007PDFPaper in Cell Press

Edwin Wang*, Lenferink A, O'Connor-McCourt M., Cancer systems biology: exploring cancer-associated genes on cellular networks (invited review), Cellular and Molecular Life Sciences (CMLS), 64:1752-1762, 2007PDF

Yu Z, Jian Z, Shen SH, Purisima E, Edwin Wang, Global analysis of microRNA target gene expression reveals that miRNA targets are lower expressed in mature mouse and Drosophila tissues than in the embryos, Nuclei Acids Research, 35:152-164, 2007 (Selected by Faculty of Biology 1000), Paper in the journal 

Yu Z, Li Z, Jolicoeur N, Zhang L, Fortin Y, Edwin Wang, Shen SH., Aberrant allele frequencies of the SNPs located in microRNA target sites are potentially associated with human cancers, Nuclei Acids Research, 35:4535-4541, 2007Paper in the journal

Cui Q, Yu Z, Pan Y, Purisima EO, Edwin Wang, MicroRNAs preferentially target the genes with high transcriptional regulation complexity,Biochem Biophys Res Commun., 352:733-738, 2007PDF

Cui Q, Yu Z, Purisima EO, Edwin Wang, Principles of microRNA regulation of a human cellular signaling network, (Nature/EMBO) Molecular Systems Biology, 2:46, 2006Paper in Molecular Systems Biology (MSB) 

Edwin Wang*, Purisima E., Network motifs are enriched with transcription factors whose transcripts have short half-lives, Trends Genet.21:492-495, 2005PDFPaper in Cell Press 

Braun, B.... Edwin Wang ...et al., 2005, A human-curated annotation of the Candida albicans genome, PLoS Genet. 1: e1, 2005