SELECTED PUBLICATIONS
Books
Edwin Wang (ed), Cancer Systems Biology, CRC Press, 2010, (The first book of the cancer systems biology field), In Amazon, CRC Press, Wiki for Cancer Systems Biology
Selected Research Articles
Xu, .. Wang E, Germline genomic patterns are associated with cancer risk, oncogenic pathways and clinical outcomes, Science Advances, 6:eaba4905, 2020, paper online, PDF, News from Yahoo News and MSN-Microsoft News.
Milanese JS., .. Wang E., Genome-wide 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 GenomeWeb, Blog 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 Open, 2:e199292, 2019, paper online, Supplemental 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 Oncology, 2:37-45, 2016, paper-PDF, Supplemental Materials (JAMA, NEJM and Lancet are the 3 top clinical journals), Reuters News, PMID: 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, Edwin, The human phosphotyrosine signaling network: evolution and hotspots of hijacking in cancer, Genome Research, 22:1222-30, 2012, Paper in Genome Res, Highlighted 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 Communications, 1:34, 2010, Paper in Nature Communications. GEN's Tech Tips: Protein Biomarker Discovery, 2010. Commentary,NRC Highlights, PMID: 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 Biology, 3:152, 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, PDF, Paper 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, 2006, Paper 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, PDF, Paper in Cell Press
Selected Visionary Essays
Jiang et al., Germline genomes have a dominant-heritable contribution to cancer immune evasion and immunotherapy response (Invited Review), Quantitative Biology, 8:216-227, 2020 , PDF , 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, PDF, Nature 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, 2007, PDF
More Publications
Research Article Preprints
Jiang et al., Is a 14-day quarantine period optimal for effectively controlling coronavirus disease 2019 (Covid-19)? doi: https://doi.org/10.1101/2020.03.15.20036533, paper online, News1, News2, The bmj Opinion,
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 patients, doi: https://doi.org/10.1101/268680, 2018, paper online
Research Articles and Reviews
Xian et al., Distinct immune escape and microenvironment between RG-like and pri-OPC-like glioma revealed by single-cell RNA-seq analysis, Frontiers of Medicine, 2023, paper online
Ji et al., Deciphering gene contributions and etiologies of somatic mutational signatures of cancer , Briefings in Bioinformatics, bbad017, 2023
Jiang et al., A Self-attention Graph Convolutional Network for Precision Multi-tumor Early Diagnostics with DNA Methylation Data, Computational Life Sciences, in press, 2023
Koczka et la., Comparing the associations between host and tumour factors with survival outcomes with anti-PD-1 immunotherapy in metastatic melanoma, Cancer Medicine, 12:2427-39, 2023
Li et al., An ensemble prediction model for COVID-19 mortality risk, Biology Methods and Protocols, 7:bpac029, 2022
Xu et al., A single cell potency inference method based on the local cell-specific network entropy, IEEE International Conference on Bioinformatics and Biomedicine (BIBM), doi:10.1109/BIBM55620.2022.9995196, 2022
Wang et al., A comparison on predicting functional impact of genomic variants, NAR Genomics and Bioinformatics, 4: lqab122, 2022
Wei et la., TAIGET: a small-molecule target identification and annotation webserver, Frontiers in Pharmacology, 13: doi.org/10.3389/fphar.2022.898519, 2022
Milanese et al., eTumorMetastatsis, a network-based algorithm predicts clinical outcomes using whole-exome sequencing data of cancer patients, Genomics, Proteomics Bioinformatics, 19:, 2021, paper online, Pre-print, paper online
Xu, .. Wang E, Germline genomic patterns are associated with cancer risk, oncogenic pathways and clinical outcomes, Science Advances, 6:eaba4905, 2020, paper link, PDF, bioRxiv
Koti, Berman, Siemens, Lange, Wang, Toren, Eigl, Hardy, Purves, Fradet, Mansure, Kassouf, Black et al., Building a Canadian translational bladder cancer network, Can Urol Assoc J (CUAJ), 14:E475-81, 2020, PDF_online
Milanese and Wang, Germline genetics in cancer: the new frontier (Book Chapter) in Systems Medicine: Integrative, Qualitative and Computational Approaches (Book), Elsevier Press, 2020, PDF_online
Jiang et al., Germline genomes have a dominant-heritable contribution to cancer immune evasion and immunotherapy response (Invited Review), Quantitative Biology, 8:216-227, 2020 , PDF online
Alabi et al., Methylation-based signatures for gastroesophageal tumor classification, Cancers 12:1208, 2020, paper online
Mealey et al., Mutational landscape differences between young-onset and older-onset breast cancer patients, BMC Cancer 20:212, 2020, paper online
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 online, bioRxiv
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-line, Supplemental 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 online, Supplemental Material, 2015
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, 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, Understanding genomic alterations in cancer genomes using an integrative network approach, Cancer Letters (Invited Review), 340: 261-9, 2013,PDF, PMID: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, 2013, paper link,
Li L., Fu C., Tibiche C., Kaneko T., Schiller M., Li S., Edwin Wang, The human phosphotyrosine signaling network: evolution and hotspots of hijacking in cancer, Genome Research, 22:1222-30, 2012, Paper 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, 2011, paper 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, Dataset
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, 2009, paper 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, 2008, Paper 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, 2007, PDF, Paper 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, 2007, PDF
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, 2007, Paper 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, 2007, PDF
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, 2006, Paper 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, 2005, PDF, Paper in Cell Press
Braun, B.... Edwin Wang ...et al., 2005, A human-curated annotation of the Candida albicans genome, PLoS Genet. 1: e1, 2005