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Yan Zhou, PhD, MSE
About
Education and Training
Educational Background
- MSE, Biotechnology, University of Pennsylvania, Philadelphia, PA, 2002
- PhD, Biochemistry, Institute of Basic Medical Sciences, CAMS&PUMC, Beijing, 1999
- BS, Molecular Biology, Nankai University, Tianjin, China, 1994
Memberships
- International Society of Computational Biology and Bioinformatics
Research Profile
Research Program
Research Interests
- Implement computational and statistical methods to analyze and interpret complex, high-throughput biological and genomic data
- Apply the most advanced pathway and network analysis to elucidate the perturbation of cellular mechanisms through observed genomic changes in different biological and disease conditions
Lab Overview
Work closely with biologists as well as clinical research teams to identify critical questions that can be addressed via computational approaches. Define and implement computational analysis plans to advance our research in cancer biology and also the development of potential novel translational therapeutic agents.
Analysis of various –omic-scale data including RNA-Seq, Exome and Whole Genome Sequencing and high throughput screening in order to nominate novel drug targets, enable patient enrichment strategies, understand mechanisms of resistance to therapies.
Integration and mining of large scale external data sets (TCGA, 1KG, EXAC, Cosmic) to further our understanding of the relationship between tumor genetics, the tumor microenvironment, and response to therapies.
Publications
Selected Publications
Gabbasov R, Xiao F, Howe CG, Bickel LE, O'Brien SW, Benrubi D, Do TV, Zhou Y, Nicolas E, Cai KQ, Litwin S, Seo S, Golemis EA, Connolly DC. NEDD9 promotes oncogenic signaling, a stem/mesenchymal gene signature, and aggressive ovarian cancer growth in mice. Oncogene, 2018. PubMed
Chang W.L., Jackson C., Riel S., Cooper H.S., Devarajan K., Hensley H.H., Zhou Y., Vanderveer L.A., Nguyen M.T. ,Clapper M.L., Differential preventive activity of sulindac and atorvastatin in apc(+/min-fccc)mice with or without colorectal adenomas. Gut. 67(7): 1290-1298, 2018.P MC6031273. 17.943
Hayakawa K., Formica A.M., Zhou Y., Ichikawa D., Asano M., Li Y.S., Shinton S.A., Brill-Dashoff J., Nunez G., Hardy R.R., Nlr nod1 signaling promotes survival of bcr-engaged mature b cells through up-regulated nod1 as a positive outcome. J Exp Med. 214(10): 3067-3083, 2017. PMC5626402. 10.892
Lulla A.R., Slifker M.J., Zhou Y., Lev A., Einarson M.B., Dicker D.T., El-Deiry W.S., Mir-6883 family mirnas target cdk4/6 to induce g1 phase cell cycle arrest in colon cancer cells. Cancer Res. 77(24): 6902-6913, 2017. 8.378
Jiang Z, Slater CM, Zhou Y, Devarajan K, Ruth KJ, Li Y, Cai KQ, Daly M, Chen X. LincIN, a novel NF90-binding long non-coding RNA, is overexpressed in advanced breast tumors and involved in metastasis. Breast Cancer Res. 2017 May 30;19(1):62. doi: 10.1186/s13058-017-0853-2. PubMed PMID: 28558830.
Zook P, Pathak HB, Belinsky MG, Gersz L, Devarajan K, Zhou Y, Godwin AK, von Mehren M, Rink L. Combination of Imatinib Mesylate and AKT Inhibitor Provides Synergistic Effects in Preclinical Study of Gastrointestinal Stromal Tumor. Clin Cancer Res. 2017 Jan 1;23(1):171-180. doi: 10.1158/1078-0432.CCR-16-0529. Epub 2016 Jul 1. PubMed PMID: 27370604; PubMed Central PMCID: PMC5203981
Beglyarova N, Banina E, Zhou Y, Mukhamadeeva R, Andrianov G, Bobrov E, Lysenko E, Skobeleva N, Gabitova L, Restifo D, et al. Screening of Conditionally Reprogrammed Patient-Derived Carcinoma Cells Identifies ERCC3-MYC Interactions as a Target in Pancreatic Cancer. Clin Cancer Res. 2016 Dec 15;22(24):6153-6163. Epub 2016 Jul 6. PubMed PMID: 27384421; PubMed Central PMCID: PMC5161635.
Zhou Y, Li YS, Bandi SR, Tang L, Shinton SA, Hayakawa K, Hardy RR. Lin28b promotes fetal B lymphopoiesis through the transcription factor Arid3a. J Exp Med. 2015 Apr 6;212(4):569-80. PubMed PMID: 25753579; PubMed Central PMCID: PMC4387290.
Zhou Y, Moon BG, Shinton SA, Hayakawa K, Hardy RR. Molecular Biology of B Cells. Second ed. Alt FW, Honjo T, Radbruch A, Reth M, editors. London: Elsevier; 2015. Chapter 4, Relationships among B cell populations revealed by global gene analysis; p.55-63.
Pathak HB, Zhou Y, Sethi G, Hirst J, Schilder RJ, Golemis EA, Godwin AK. A Synthetic Lethality Screen Using a Focused siRNA Library to Identify Sensitizers to Dasatinib Therapy for the Treatment of Epithelial Ovarian Cancer. PLoS One. 2015 Dec 4;10(12):e0144126. PubMed PMID: 26637171; PubMed Central PMCID: PMC4670180.
Li YS, Zhou Y, Tang L, Shinton SA, Hayakawa K, Hardy RR. A developmental switch between fetal and adult B lymphopoiesis. Ann N Y Acad Sci. 2015 Dec;1362:8-15. doi: 10.1111/nyas.12769. Epub 2015 Apr 30. Review. PubMed PMID: 25931205.
Arora S, Yan H, Cho I, Fan HY, Luo B, Gai X, Bodian DL, Vockley JG, Zhou Y, Handorf EA, Egleston BL, Andrake MD, Nicolas E, Serebriiskii IG, Yen TJ, Hall MJ, Golemis EA, Enders GH. Genetic Variants That Predispose to DNA Double-Strand Breaks in Lymphocytes From a Subset of Patients With Familial Colorectal Carcinomas. Gastroenterology. 2015 Dec;149(7):1872-1883.e9. PubMed PMID: 26344056; PubMed Central PMCID: PMC4663158.
Plimack ER, Dunbrack RL, Brennan TA, Andrake MD, Zhou Y, Serebriiskii IG, Slifker M, Alpaugh K, Dulaimi E, Palma N, Hoffman-Censits J, Bilusic M, Wong YN, Kutikov A, Viterbo R, Greenberg RE, Chen DY, Lallas CD, Trabulsi EJ, Yelensky R, McConkey DJ, Miller VA, Golemis EA, Ross EA. Defects in DNA Repair Genes Predict Response to Neoadjuvant Cisplatin-based Chemotherapy in Muscle-invasive Bladder Cancer. Eur Urol. 2015 Dec;68(6):959-67. PubMed PMID: 26238431; PubMed Central PMCID: PMC4764095.
Nicolas E, Arora S, Zhou Y, Serebriiskii IG, Andrake MD, Handorf ED, Bodian DL, Vockley JG, Dunbrack RL, Ross EA, Egleston BL, Hall MJ, Golemis EA, Giri VN, Daly MB. Systematic evaluation of underlying defects in DNA repair as an approach to case-only assessment of familial prostate cancer. Oncotarget. 2015 Nov 24;6(37):39614-33. PubMed PMID: 26485759; PubMed Central PMCID: PMC4741850.
Bhattacharjee V, Zhou Y, Yen TJ. A synthetic lethal screen identifies the Vitamin D receptor as a novel gemcitabine sensitizer in pancreatic cancer cells. Cell Cycle. 2014;13(24):3839-56. PubMed PMID: 25558828; PubMed Central PMCID: PMC4615005.
Gowrishankar B, Ibragimova I, Zhou Y, Slifker MJ, Devarajan K, Al-Saleem T, Uzzo RG, Cairns P. MicroRNA expression signatures of stage, grade, and progression in clear cell RCC. Cancer Biol Ther. 2014 Mar 1;15(3):329-41. PubMed PMID: 24351440; PubMed Central PMCID: PMC3974834.
Rink L, Ochs MF, Zhou Y, von Mehren M, Godwin AK. ZNF-mediated resistance to imatinib mesylate in gastrointestinal stromal tumor. PLoS One. 2013;8(1):e54477. PubMed PMID: 23372733; PubMed Central PMCID: PMC3556080.
Additional Publications
Contact Information
Office Phone: 215-214-3780
Lab Phone: 215-728-2553
Office: R431
Contact Information
Office Phone: 215-214-3780
Lab Phone: 215-728-2553
Office: R431
Assistant Professor
Research Program
Education
Educational Background
- MSE, Biotechnology, University of Pennsylvania, Philadelphia, PA, 2002
- PhD, Biochemistry, Institute of Basic Medical Sciences, CAMS&PUMC, Beijing, 1999
- BS, Molecular Biology, Nankai University, Tianjin, China, 1994
Memberships
- International Society of Computational Biology and Bioinformatics
Research Profile
Research Interests
- Implement computational and statistical methods to analyze and interpret complex, high-throughput biological and genomic data
- Apply the most advanced pathway and network analysis to elucidate the perturbation of cellular mechanisms through observed genomic changes in different biological and disease conditions
Lab Overview
Work closely with biologists as well as clinical research teams to identify critical questions that can be addressed via computational approaches. Define and implement computational analysis plans to advance our research in cancer biology and also the development of potential novel translational therapeutic agents.
Analysis of various –omic-scale data including RNA-Seq, Exome and Whole Genome Sequencing and high throughput screening in order to nominate novel drug targets, enable patient enrichment strategies, understand mechanisms of resistance to therapies.
Integration and mining of large scale external data sets (TCGA, 1KG, EXAC, Cosmic) to further our understanding of the relationship between tumor genetics, the tumor microenvironment, and response to therapies.
Publications
Selected Publications
Gabbasov R, Xiao F, Howe CG, Bickel LE, O'Brien SW, Benrubi D, Do TV, Zhou Y, Nicolas E, Cai KQ, Litwin S, Seo S, Golemis EA, Connolly DC. NEDD9 promotes oncogenic signaling, a stem/mesenchymal gene signature, and aggressive ovarian cancer growth in mice. Oncogene, 2018. PubMed
Chang W.L., Jackson C., Riel S., Cooper H.S., Devarajan K., Hensley H.H., Zhou Y., Vanderveer L.A., Nguyen M.T. ,Clapper M.L., Differential preventive activity of sulindac and atorvastatin in apc(+/min-fccc)mice with or without colorectal adenomas. Gut. 67(7): 1290-1298, 2018.P MC6031273. 17.943
Hayakawa K., Formica A.M., Zhou Y., Ichikawa D., Asano M., Li Y.S., Shinton S.A., Brill-Dashoff J., Nunez G., Hardy R.R., Nlr nod1 signaling promotes survival of bcr-engaged mature b cells through up-regulated nod1 as a positive outcome. J Exp Med. 214(10): 3067-3083, 2017. PMC5626402. 10.892
Lulla A.R., Slifker M.J., Zhou Y., Lev A., Einarson M.B., Dicker D.T., El-Deiry W.S., Mir-6883 family mirnas target cdk4/6 to induce g1 phase cell cycle arrest in colon cancer cells. Cancer Res. 77(24): 6902-6913, 2017. 8.378
Jiang Z, Slater CM, Zhou Y, Devarajan K, Ruth KJ, Li Y, Cai KQ, Daly M, Chen X. LincIN, a novel NF90-binding long non-coding RNA, is overexpressed in advanced breast tumors and involved in metastasis. Breast Cancer Res. 2017 May 30;19(1):62. doi: 10.1186/s13058-017-0853-2. PubMed PMID: 28558830.
Zook P, Pathak HB, Belinsky MG, Gersz L, Devarajan K, Zhou Y, Godwin AK, von Mehren M, Rink L. Combination of Imatinib Mesylate and AKT Inhibitor Provides Synergistic Effects in Preclinical Study of Gastrointestinal Stromal Tumor. Clin Cancer Res. 2017 Jan 1;23(1):171-180. doi: 10.1158/1078-0432.CCR-16-0529. Epub 2016 Jul 1. PubMed PMID: 27370604; PubMed Central PMCID: PMC5203981
Beglyarova N, Banina E, Zhou Y, Mukhamadeeva R, Andrianov G, Bobrov E, Lysenko E, Skobeleva N, Gabitova L, Restifo D, et al. Screening of Conditionally Reprogrammed Patient-Derived Carcinoma Cells Identifies ERCC3-MYC Interactions as a Target in Pancreatic Cancer. Clin Cancer Res. 2016 Dec 15;22(24):6153-6163. Epub 2016 Jul 6. PubMed PMID: 27384421; PubMed Central PMCID: PMC5161635.
Zhou Y, Li YS, Bandi SR, Tang L, Shinton SA, Hayakawa K, Hardy RR. Lin28b promotes fetal B lymphopoiesis through the transcription factor Arid3a. J Exp Med. 2015 Apr 6;212(4):569-80. PubMed PMID: 25753579; PubMed Central PMCID: PMC4387290.
Zhou Y, Moon BG, Shinton SA, Hayakawa K, Hardy RR. Molecular Biology of B Cells. Second ed. Alt FW, Honjo T, Radbruch A, Reth M, editors. London: Elsevier; 2015. Chapter 4, Relationships among B cell populations revealed by global gene analysis; p.55-63.
Pathak HB, Zhou Y, Sethi G, Hirst J, Schilder RJ, Golemis EA, Godwin AK. A Synthetic Lethality Screen Using a Focused siRNA Library to Identify Sensitizers to Dasatinib Therapy for the Treatment of Epithelial Ovarian Cancer. PLoS One. 2015 Dec 4;10(12):e0144126. PubMed PMID: 26637171; PubMed Central PMCID: PMC4670180.
Li YS, Zhou Y, Tang L, Shinton SA, Hayakawa K, Hardy RR. A developmental switch between fetal and adult B lymphopoiesis. Ann N Y Acad Sci. 2015 Dec;1362:8-15. doi: 10.1111/nyas.12769. Epub 2015 Apr 30. Review. PubMed PMID: 25931205.
Arora S, Yan H, Cho I, Fan HY, Luo B, Gai X, Bodian DL, Vockley JG, Zhou Y, Handorf EA, Egleston BL, Andrake MD, Nicolas E, Serebriiskii IG, Yen TJ, Hall MJ, Golemis EA, Enders GH. Genetic Variants That Predispose to DNA Double-Strand Breaks in Lymphocytes From a Subset of Patients With Familial Colorectal Carcinomas. Gastroenterology. 2015 Dec;149(7):1872-1883.e9. PubMed PMID: 26344056; PubMed Central PMCID: PMC4663158.
Plimack ER, Dunbrack RL, Brennan TA, Andrake MD, Zhou Y, Serebriiskii IG, Slifker M, Alpaugh K, Dulaimi E, Palma N, Hoffman-Censits J, Bilusic M, Wong YN, Kutikov A, Viterbo R, Greenberg RE, Chen DY, Lallas CD, Trabulsi EJ, Yelensky R, McConkey DJ, Miller VA, Golemis EA, Ross EA. Defects in DNA Repair Genes Predict Response to Neoadjuvant Cisplatin-based Chemotherapy in Muscle-invasive Bladder Cancer. Eur Urol. 2015 Dec;68(6):959-67. PubMed PMID: 26238431; PubMed Central PMCID: PMC4764095.
Nicolas E, Arora S, Zhou Y, Serebriiskii IG, Andrake MD, Handorf ED, Bodian DL, Vockley JG, Dunbrack RL, Ross EA, Egleston BL, Hall MJ, Golemis EA, Giri VN, Daly MB. Systematic evaluation of underlying defects in DNA repair as an approach to case-only assessment of familial prostate cancer. Oncotarget. 2015 Nov 24;6(37):39614-33. PubMed PMID: 26485759; PubMed Central PMCID: PMC4741850.
Bhattacharjee V, Zhou Y, Yen TJ. A synthetic lethal screen identifies the Vitamin D receptor as a novel gemcitabine sensitizer in pancreatic cancer cells. Cell Cycle. 2014;13(24):3839-56. PubMed PMID: 25558828; PubMed Central PMCID: PMC4615005.
Gowrishankar B, Ibragimova I, Zhou Y, Slifker MJ, Devarajan K, Al-Saleem T, Uzzo RG, Cairns P. MicroRNA expression signatures of stage, grade, and progression in clear cell RCC. Cancer Biol Ther. 2014 Mar 1;15(3):329-41. PubMed PMID: 24351440; PubMed Central PMCID: PMC3974834.
Rink L, Ochs MF, Zhou Y, von Mehren M, Godwin AK. ZNF-mediated resistance to imatinib mesylate in gastrointestinal stromal tumor. PLoS One. 2013;8(1):e54477. PubMed PMID: 23372733; PubMed Central PMCID: PMC3556080.