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CV of Rong Chen
CV of Rong Chen
CV of Rong Chen
CV of Rong Chen
CV of Rong Chen
CV of Rong Chen
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CV of Rong Chen


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  • 1. Rong Chen, Ph.D. 1 CURRICULUM VITAE RONG CHENWork Address:Director of Predictive MedicinePersonalis Inc.530 Lytton AvenuePalo Alto, CA 94301Telephone: (858)837-2265 Email: rongch60@gmail.comHomepage: Profile: @RongChenBioinfoGoogle Citations: (citations 2160; h-index 18)Research Interests:Use systems medicine to transform personalized medicine and accelerate the discovery ofdiagnostic biomarkers and therapeutic targetsHighlights:• Published 50 papers in top tier journals, including Lancet, Cell, Nature Biotechnology, Nature Methods, PLoS Genetics, PLoS Computational Biology, Genome Biology, and PNAS• Invented numerous patents, software, and databases on translational medicine o Varimed is the foundation for a VC-supported startup company, Personalis Inc o ZDOCKpro is the standard method to investigate protein-protein interaction with million-dollar sale o AILUN built tera-bytes of databases on multi-omics disease-specific molecular measurements and enabled numerous translational discoveries in the Butte Lab• Have been regularly invited to lecture on personalized medicine, biomarker discovery, and translational bioinformatics worldwideEducation:1999-2003 Boston University, Boston, MA, USA Ph.D., M.S. in Bioinformatics (Advisor: Zhiping Weng)1994-1997 Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai M.S. in Analytic Chemistry / Protein Crystallography1989-1994 University of Science and Technology of China, Hefei, Anhui, China B.S. in Chemical PhysicsProfessional Appointments:2011-current Director of Predictive Medicine, Personalis Inc., Palo Alto, CA2005-2011 Bioinformatics Scientist, Division of Systems Medicine, Department of Pediatrics, Stanford University, CA (Supervisor: Atul Butte)2006-2007 Principal Software Engineer, Nichols Institute, Quest Diagnostic, San Juan Capistrano, CA2004-2005 Senior Computational Biologist, Abgenix / Amgen Inc., Fremont, CA2003-2004 Scientist, Life Science R & D , Accelrys Inc, San Diego, CAHonors and Professional Services:• ICHG Young Investigator Awards, International Congress of Human Genetics, 2011• Works reported by MIT Technology Review, BBC News, and Business Week, GenomeWeb News, NPR radio, Wall Street Journal, Market Watch
  • 2. Rong Chen, Ph.D. 2• A paper on “Clinical assessment incorporating personal genome sequence” has been identified by Thomson Reuters Essential Science IndicatorsSM as a featured New Hot Paper in the field of Clinical Medicine• Interviewed by Science, Genome Technology, GenomeWeb, ebiotrade• Reviewer for Proteins, BMC Bioinformatics, J. of Structural Biolog, Evolutionary Bioinformatics, Biology Direct, Pacific Symposium on Biocomputing, and RECOMB, J. translational Medicine, J of Biomedical Informatics, PLoS One, Database, ISMB, AMIA TBI, New England Journal of Medicine• Committee for The Life Science Computational Systems Bioinformatics Conference• Committee for Biomedical Computation at Stanford Symposium• ASHG member (American Society of Human Genetics)• AMIA member (American Medical Informatics Association)Peer Reviewed Research Papers:1. Patel C.J., Chen R., Ioannidis J.P.A., Butte A.J. Systematic identification of interaction effects between validated genome- and environment-wide association on Type 2 Diabetes Mellitus (under review)2. Keiichi K., Horikoshi M., Toda K., Yamada S., Irie J., Sirota M., Morgan A.A., Chen R., Ohtsu H., Hara K., Maeda S., Kadowaki T., Butte A.J. (2012) Expression-based genome-wide association study links CD44 in adipose tissue with type 2 diabetes PNAS (in press)3. Chen R., Corona E., Sikora M., Dudley J.T., Morgan A.A., Moreno-Estrada A., Nilsen G.B., Ruau D., Lincoln S.E., Bustamante C.D., Butte A.J. (2012) Type 2 diabetes risk alleles show extreme directional differentiation among human populations, compared to other diseases PLoS Genetics (in press)4. Li L, Wozniak L.J., Rodder S., Heish S., Talisetti A., Wang Q., Esquivel C., Cox K., Chen R., McDiarmid S.V., Sarwal M.M. (2012) A common peripheral blood gene set for diagnosis of operational tolerance in pediatric and adult liver transplantation. Am. J. of Transplant. Doi:10.11115. Dudley J., Chen R., Sanderford M., Butte A.J., Kumar S. (2012) Evolutionary meta-analysis of association studies reveals ancient constraints affecting disease marker discovery Molecular Biology and Evolution6. Chen R., Mias G.I., Li-Pook-Than J., Jiang L., Lam H.Y.K., Chen R., Miriami E., Karczewski K.J., Hariharan M., Dewey F.E., Habegger L., Clark M.J., Balasubramanian S., Cheng Y., O’Huallachain M., Dudley J.T., Hillenmeyer S., Haraksingh R., Sharon D., Euskirchen G., Lacroute P., Bettinger K., Im H., Boyle A.P., Kasowski M., Grubert F., Seki S., Garcia M., Whirl-Carrillo M., Gallardo M., Blasco M.A., Greenberg P.L., Snyder P., Klein T.E., Altman R.B., Butte A.J., Ashley E.A., Nadeau K.C., Gerstein M., Tang H., Snyder M. (2012) Personal omics profiling reveals dynamic molecular and medical phenotypes Cell 148:1293-3077. Rothbard J.B., Kurnellas M.P., Adams C.M., Su L., Chen R., Fathman C.G., Robinson W.H., Steinman L. (2012) Therapeutic effects of systemic administration of the chaperone alpha B crystallin associated with binding proinflammatory plasma proteins The Journal of Biological Chemistry 287:9708-97218. Chen R., Dudley J.T., Ruau D., Butte A.J. (2012) Quantifying multi-ethnic representation in genetic studies of high mortality diseases AMIA Summit on Translational Bioinformatics9. Morgan A.A., Chen R., Butte A.J. (2012) Clinical utility of sequence-based genotype compared with that derivable from genotyping arrays AMIA Summit on Translational Bioinformatics (Marco Ramoni award for the best paper)10. Kang H.P., Morgan A.A., Chen R., Schadt E.E., Butte A.J. (2012) Coanalysis of GWAS with eQTL reveals disease-tissue associations AMIA Summit on Translational Bioinformatics11. Lam H.Y.K., Clark M.J., Chen R., Chen R., Natsoulis G., O’Huallachain M., Dewey F.,
  • 3. Rong Chen, Ph.D. 3 Habegger L., Ashley E., Gerstein M.B., Butte A.J., Ji H., Snyder M. (2011) Comparison of two genome sequencing platforms Nature Biotechnology doi:10.103812. Pan S., Dewey F., Perez M., Knowles J., Chen R., Butte A.J., Ashley E. (2011) Personalized medicine and cardiovascular disease: from genome to bedside Current Cardiovascular Risk Reports doi:10.100713. Engreitz J.M., Chen R., Morgan A.A., Dudley J.T., Mallelwar R., Butte A.J. (2011) ProfileChaser: searching microarray repositories based on genome-wide patterns of differential expression Bioinformatics 27: 331714. Clark M.J., Chen R., Lam H., Karczewski K.J., Chen R., Euskirchen G., Butte A.J., Snyder M. (2011) Performance comparison of Exome DNA sequencing technologies Nature Biotechnology 29:dio:10.103815. Dewey F.E., Chen R., Cordero S.P., Ormond K.E., Caleshu C., Karczewski K.J., Carrillo M.W., Wheeler M.T., Dudley J.T., Bynes J.K., Cornejo O.E., Knowles J.W., Woon M., Sangkuhl K., Gong L., Thorn C.F., Hebert J.M., Capriotti E., David S.P., Pavlovic A., West A.,West J.S., Thakuria J.V., Ball M.P., Zaranek A.W., Rehm H.L., Church G.M., Bustamante C.D., Snyder M.P., Altman R.B., Klein T.E., Butte A.J., Ashley E.A. (2011) Phased whole genome genetic risk in a family quartet using a major allele reference sequence PLoS Genetics 7:e100228016. Naesens M., Khatri P., Li L., Sigdel T., Chen R., Vitalone M., Butte A.J., Salvatierra O., Sarwal M.M. (2011) Progressive histological damage in renal allografts is associated with expression of innate and adaptive immunity genes Kidney International 80:doi:10.1038/ki2011.24517. Chen R., Butte A.J. (2011) The reference human genome demonstrates high risk of type 1 diabetes and other disorders Pac Symp Biocomputp 2011:231-4218. Dudley J.T., Chen R., Butte A.J. (2011) Matching cancer genomes to established cell lines for personalized oncology Pac Symp Biocomputp 2011:243-5219. Engereitz J.M., Morgan A.A., Dudley J.T., Chen R., Thathoo R., Altman R.B., Butte A.J. (2010) Content-based microarray search using differential expression profiles BMC Bioinfo 11:60320. Chen R., Davydov E.V., Sirota M., Butte A.J. (2010) Non-synonymous and synonymous coding SNPs show similar likelihood and effect size of human disease association PLoS One 5:e1357421. Chen R., Sigdel T.K., Li L., Kambham N., Dudley J.T., Heish S.C., Klassen R.B., Chen A., Caohuu T., Morgan A.A., Valantine H.A., Khush K.K., Sarwal M.M., Butte A.J. (2010) Differentially expressed RNA from public microarray data identifies serum biomarkers for cross-organ transplant rejection and other conditions PLoS Computational. Biology 6: e100094022. Morgan A.A., Chen R., Butte A.J., Ashley E.A. (2010) Clinical assessment incorporating a personal genome – Authors’ reply Lancet 376:869-7023. Dudley J.T., Pouliot Y., Chen R., Morgan A.A., Butte A.J. (2010) Translational Bioinformatics in the cloud: an affordable alternative Genome Medicine 2:5124. Shi L., Campbell G., Jones W.D., Campagne F., Wen Z., Walker S.J., Su Z., Chu T.,. . Chen R., ...Puri R.K., Scherf U., Tong W., Wolfinger R.D. (2010) The MAQC-II Project: A comprehensive study of common practices for the development and validation of microarray- based predictive models Nature Biotechnology 28:827-3825. Morgan A.A., Chen R., Butte A. J. (2010) Likelihood Ratios for Genome Medicine Genome Medicine 2:3026. Ashley EA, Butte AJ, Wheeler MT, Chen R., Klein TE, Dewey FE, Dudley JT, Ormond KE, Pavlovic A, Hudgins L, Gong L, Hodges LM, Berlin DS, Thorn CF, Sangkuhl K, Hebert JM, Woon M, Sagreiya H, Whaley R, Morgan AA, Pushkarev D, Neff NF, Knowles JW, Chou M, Thakuria J, Rosenbaum A, Zaranek AW, Church G, Greely HT, Quake SR, Altman RB (2010) Clinical assessment incorporating a personal genome Lancet 375:1525-35
  • 4. Rong Chen, Ph.D. 427. Suthram S., Dudley J.T., Chaing A.P., Chen R., Hastie T.J., Butte A.J. (2010) Network-based elucidation of human disease similarity reveals common functional modules enriched for pluripotent drug targets PLoS Computational Biology. 6:e100066228. Li L., Chen A., Chaudhuri A., Kambham N., Sigdel T., Chen R., Sarwal M. (2010) Compartmental Localization and Clinical Relevance of MICA Antibodies after Renal Transplantation Transplantation 89: 312-929. Cai J.J., Borenstein E., Chen R., Petrov D.A (2009) Similarly strong purifying selection acts on human disease genes of all evolutionary ages Genome Biology & Evolution 2009:131-14430. Becker L., Salameh W., Sferruzza A., Zhang K., Chen R., Malik R., Reitz R., Nasser I. Afdhal N.H. (2009) Validation of Hepascore, compared to simple indices of fibrosis, in US patients with chronic hepatitis C virus infection. Clinical Gastroenterology and Hepatology 7: 696-70131. Li L., Wadia P., Chen R., Kambham N, Naesens M., Sigdel T., Miklos D., Sarwal M., Butte A.J. (2009) Identifying Compartment-specific Alloimmune Targets After Renal Transplantation by Integrating Transcriptome and Antibodyome Measures. PNAS 106:4148-5332. Shah N.H., Jonquet C., Chiang A.P., Butte A.J., Chen R., Musen M.A. (2009) Ontology-driven Indexing of Public Datasets for Translational Bioinformatics BMC Bioinformatics 10 (supple 2): S133. Chen R., Mallelwar R., Thosar A., Venkatasubrahmanyam S., Butte A.J. (2008) GeneChaser: identifying all biological and clinical conditions in which genes of interest are differentially expressed. BMC Bioinformatics 9: 54834. Chen R., Morgan A., Dudley J., Deshpande T., Li L., Kodma K., Chiang A., Butte A.J. (2008) FitSNPs: Highly Differentially Expressed Genes are More Likely to Have Variants Associated With Disease. Genome Biology 9: R17035. Shah N., Chiang A., Butte A.J., Chen R., Musen M., Ontology-driven Indexing of Public Datasets for Translational Bioinformatics (2008) AMIA Symposium on Translational Bioinformatics36. Li L., Ying LH., Naesens M., Xiao W., Hsieh S., Sigdel T., Martin J., Chen R., Liu K., Sarwal M. (2008) Interference of globin genes with biomarker discovery for allograft rejection in peripheral blood samples. Physiological Genomics 32: 190-19737. Chen R., Li L, Butte A.J. (2007), AILUN: Reannotating Gene Expression Data Automatically. Nature Methods 4: 87938. Lin Y., Chiang A., Yao P., Chen R., Butte A., Lin R., Methodology for Exacting Functional Pharmacogenomic Experiments from International Repository (2007) AMIA Annual Symp Proc 2007:463-46739. Mintseris J., Pierce B., Wiehe K., Anderson R., Chen R., Weng Z., (2007) Integrating statistical pair potentials into protein complex prediction. Proteins 69:511-52040. Butte A.J., Chen R., (2006) Finding Disease-Related Genomic Experiments Within an International Repository: First Steps in Translational Bioinformatics, AMIA Annu Symp Proc. 2006:106-11041. Wiehe K., Pierce B., Mintseris J., Tong W., Anderson R., Chen R., Weng Z. (2005) ZDOCK and RDOCK Performance in CAPRI Rounds 3, 4, and 5. Proteins 60: 207-21342. Mintseris J., Wiehe K., Pierce B., Anderson R., Chen R., Janin J., Weng Z. (2005) Protein-Protein Docking Benchmark 2.0: an Update. Proteins 60: 214-21643. Li L., Chen R. (joint first authors), Weng Z. (2003) RDOCK: Refinement of Rigid-body Protein Docking Predictions. Proteins 53: 693-70744. Chen R., Li L., Weng Z. (2003) ZDOCK: An Initial-stage Protein-Docking Algorithm. Proteins, 52:80- 8745. Chen R., Tong W., Mintseris J., Li L., Weng Z. (2003) ZDOCK Predictions for the CAPRI Challenge. Proteins, 52:68-7346. Chen R., Mintseris J., Janin J., Weng Z. (2003) A Protein-Protein Docking Benchmark. Proteins, 52:88- 9147. Chen R., Weng Z. (2003) A Novel Shape Complementarity Scoring Function For Protein-Protein Docking. Proteins, 51:397-40848. Chen R., Weng Z. (2002) Docking Unbound Proteins Using Shape Complementarity, Desolvation, and Electorstatics. Proteins, 47:281-29449. Chen R., Xu YZ, Wu J,Pu Z, Jin SW, Liu WY, Xia ZX (1999) Purification and Characterization of
  • 5. Rong Chen, Ph.D. 5 Trichomaglin-A Novel Ribosomal-inactivating Protein with Abortificient Activity. Biochem. Mol. Biol. Int. 47:185-9350. Wang XQ, Chen R., Wang YL, He TJ, Liu FC (1998) Theoretical Studies on Electrocompression of Electrodeposited Halid Monolayer on Au(111) Surface. J. Phys. Chem. B 102:7568-76Patents and Software • Patent: methods and composition for monitoring an allograft recipient for a rejection response (13/148,458, 61/152199, PCT/US 10/24023) • Patent: self organizing map in clinical diagnostics (11/617303, US 2008/0221395 A1) • Inventor for system and database for personalized medicine (VariMed), licensed to Personalis Inc. • Inventor for method to integrate population and familial haplotype phasing into estimates of genome-wide genetic of gene product risk, licensed to Personalis Inc. • Inventor for software to identify differentially expressed conditions for a gene or set of genes, licensed to Personalis Inc. • Inventor for protein docking software ZDOCK & RDOCK, licensed to Accelrys Inc. with multi- million dollar marketTeaching:1. Spring 2011, BMI 217, Translational Bioinformatics, Stanford University. Lecture Title: “Using Systems Medicine to Transform Biomarker Discovery and Personalized Medicine”2. Jan. 20, 2011, International workshop on Bioinformatics: Advanced course on High Throughput Sequencing Data with R and Bioconductor, The University of the West Indies, Thrinidad and Tobago. Lecture Title: “Disease Risk Assessment of Personal Genome sequence”3. Fall 2010, BMI 205, Biomedical Informatics for Medicine, Stanford University. Lecture Title: “Disease Risk Assessment of Personal Genome Sequences”3. Fall 2009, BMI 205, Biomedical Informatics for Medicine, Stanford University. Lecture Title: “Biomarker Discovery from Public Gene Expression Data”4. Fall 2002, BE703, Dept. of Biomedical Engineering, Boston University. Lecture Title: “Protein-protein Docking”Invited Talks and Oral Presentations:1. Mar. 20, 2012, Talk in 2012 AMIA Summit on Translational Bioinformatics (TBI), San Francisco, CA. Title: “Quantifying multi-ethnic representation in genetic studies of high mortality diseases”2. Feb. 23, 2012, Session chair and invited talk in the 19th International Molecular Medicine Tri- conference, San Francisco, CA. Title: “Type 2 diabetes risk alleles show extreme directional differentiation among human populations, compared to other diseases”.3. Feb. 22, 2012, Invited talk in the 19th International Molecular Medicine Tri-conference, San Francisco, CA. Title: “Use public molecular measurements to drive the discovery of diagnostic protein biomarkers”.4. Feb. 16, 2012, Plenary talk in 13th annual Advances in Genome Biology and Technology (AGBT), Marco Island, FL. Title: “Type 2 diabetes risk alleles show extreme directional differentiation among human populations, compared to other diseases”5. Oct. 13, 2011, Talk in 12th International Congress of Human Genetics / American Society of Human Genetics 61th annual meeting, Montreal, Canada. Title: “Type 2 diabetes risk alleles show extreme directional differentiation among human populations, compared to other diseases”6. Sep. 14, 2011, Invited talk in Clinical Sequencing Standards Symposium in HL7, San Diego, CA. Title: “Standardizing Genetic Reports for Medical Assessment of Personal Genome Sequences”
  • 6. Rong Chen, Ph.D. 67. Sep. 8, 2011, Session chair and Invited talk and session chair in Biomarker Discovery Informatics, Philadelphia, PA. Title: “Using Public Molecular Measurements to Drive Biomarker Discovery”8. Apr. 14, 2011, Session chair and Invited talk and session chair in BioIT World Conference, Boston, MA. Title: “Using Systems Medicine to Transform Biomarker Discovery and Personalized Medicine”9. Apr. 12, 2011, Invited talk in Agios Pharmaceutical, Cambridge, MA. Title: “Using Systems Medicine to Transform Biomarker Discovery and Personalized Medicine”10. Mar. 18, 2011, Invited talk in 3rd NIH / Scripps Genomics for Transplantation Symposium, San Diego, CA. Title: “Using public molecular measurements to drive discover of biomarkers for cross-organ transplant rejection”11. Mar. 14, 2011, Invited talk in 2nd International Conference on Transplantomics and Biomarkers in Organ Transplantation, Barcelona, Spain. Title: “The clinical utility of whole genome sequencing”12. Mar. 15, 2011, Talk in 2nd International Conference on Transplantomics and Biomarkers in Organ Transplantation, Barcelona, Spain. Title: “Differentially Expressed RNA from Public Microarray Data Identifies Serum Protein Biomarkers for Cross-organ Transplant Rejection and Other Conditions”.13. Mar. 8, 2011, 2011 Talk in AMIA Summit on Translational Bioinformatics, San Francisco, CA. Title: “Non-synonymous and Synonymous Coding SNPs Show Similar Likelihood and Effect Size of Human Disease Association”.14. Feb. 27, 2011, Invited talk in Biomarkers for Brain Disorders: Challenges and Opportunities, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK. Title: “Translating Publically- available molecular Data into Diagnostics and Personalized Medicine”15. Feb. 3, 2011, Invited talk by Complete Genomics in 12th annual Advances in Genome Biology and Technology (AGBT), Marco Island, FL. Title: “Genetics explains the ethnic disparity of incidence rate of Melanoma and Pancreatic cancer”.16. Jan. 4, 2011, Talk in Pacific Symposium on Biocomputing (PSB), Big island of Hawaii. Title: “Is the Reference Human Genome a Good Representation of a Healthy Control and Consensus?”17. Jun. 11, 2010, Invited Lecture in 13th Annual International Toronto Heart Summit, 21 Avenue Rd, Toronto, Ontario, Canada. Title: “Bioinformatics Approaches Yielding Biomarkers for Personalized Medicine”18. Aug. 11, 2010, Invited talk in Xiameng University, Xiameng, Fujian, China. Title: “Translating Publically-available molecular Data into Diagnostics and Personalized Medicine”19. Mar. 9, 2009, Invited Talk in FDA / National Center for Toxicological Research, 3900 NCTR Road, Jefferson, AR. Title: “Biomarker Discovery from Public Gene Expression Data”20. May 12 2008, Invited Talk in Indiana University School of Medicine, Indianapolis, IN. Title: “Differentially Expressed Genes are Most Likely to have Variants Associated With Disease”21. Jun. 12, 2004, Invited Talk in Biogeometry workshop, ACM Symposium on Computational Geometry, New York, NY. Title: “An Integrated Approach to Protein-Protein Docking”22. Sep. 19, 2002, Invited Talk in First CAPRI Evaluation Meeting, Agelonde, La Londe-des- Maures, France. Title: "ZDOCK Predictions for the CAPRI Challenge"23. Jul. 25, 2002, Talk in Boston University-Humboldt University Workshop, Boston, MA. Title: "A Novel Shape Complementarity Scoring Function for Protein Docking"24. Dec. 1, 2001, Invited Talk in Computational Genomics Conference, Baltimore, Maryland. Title: "An Integrated Approach to Predictive Protein-protein Docking"