CV of Rong Chen


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Rong Chen, Director of Clinical Genome Informatics at Icahn School of Medicine at Mount Sinai.

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CV of Rong Chen

  1. 1. Rong Chen, Ph.D. 1 CURRICULUM VITAE RONG CHEN Work Address: Assistant Professor, Director of Clinical Genome Informatics Department of genetics and Genomic Sciences Icahn School of Medicine at Mount Sinai 1255 5th Avenue, New York, NY Telephone: (858)837-2265 Email: Homepage: Google Citations: (citations 6136; h-index 36) Summary: A recognized expert with 15 years of experience on translational bioinformatics and genomics, specialized on developing databases, genome repositories, pipeline, clinical application, and commercial products to analyze next generation sequencing data, and interpret personal genomes for clinical diagnosis, protective alleles, precision medicine, and predictive disease risk. Highlights: • Built clinical genome informatics teams from scratch at Mount Sinai and Personalis • Science team to launch a startup company LifeMap Solutions for mobile health • Launched a startup company Personalis and won the VA's contract for the Million Veteran Genome project • Scientific advisor for various next generation sequencing companies, including Bina Technologies and Tute Genomics • Developed NGS products for the precision medicine of cancer, clinical diagnosis of rare diseases, and disease risk assessment of healthy individuals • Supervises genome, exome, RNA-Seq, and Panel sequencing and analysis including clinical, research, and production sequencing at Mount Sinai • Published over 70 papers in top tier journals, including Lancet, Cell, Nature Biotechnology, Nature Methods, Science Translational Research, American J Human Genetics, PLoS Genetics, PLoS Computational Biology, Genomic Research, Genome Biology, PNAS, American J Transplant, J Clinical Investigation • Invented many patents, software, and databases on translational medicine Education: 1999-2003 Boston University, Boston, MA, USA Ph.D., M.S. in Bioinformatics 1994-1997 Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai M.S. in Structural Biology 1989-1994 University of Science and Technology of China, Hefei, Anhui, China B.S. in Chemical Physics Work Experience: Icahn School of Medicine at Mount Sinai, New York, NY 06/13-Present Directors of Clinical Genome Informatics, Assistant Professor, Dept. of Genetics and Genomic Sciences • Build and lead a clinical genome informatics team with over 10 bioinformatics scientists and software engineers • Build databases, genome repositories, and clinical applications to interpret personal genome for precision medicine, clinical diagnosis, protective alleles, and disease mechanism
  2. 2. Rong Chen, Ph.D. 2 • Lead personalized cancer therapy project, build a pipeline to sequence, analyze, and interpret tumor samples and create clinical reports to recommend personalized therapeutics and clinical trials for patients with colon cancer, breast cancer, and other tumor types • Identify protective alleles as therapeutics for Alzheimer’s disease, cardiovascular diseases • Identify driver landscape of parathyroid carcinoma • Lead the resilience project, build Mendelian disease mutation panel, search 600,000 genomes, and identify 13 unexpected heroes who are resilient to childhood diseases • Build a reference variant store with 470 million genetic variants with observed frequencies in a wide variety of disease and healthy states using Hadoop-based infrastructure • Mine 30 million abstracts and 3 million full text and build VarImpact database with comprehensive phenotypic impact of genetic variants at gene, protein, pathway, cellular, and organism levels • Build disease networks through integrating genetic, EMR, and literature • Build NGS panels and evaluate the performance between HiSeq and Proton • Catalog and identify breast cancer risk variants through large scale sequencing • Develop chrGeneticist to enable clinical geneticists to distribute, annotate, review, and assign pathogenicity to genetic variants in clinical sequencing Personalis, Menlo Park, CA 12/11-05/13 Directors of Predictive Medicine • Built a team of Bioinformatics Scientist, Software Engineer, Database Developer, and Statistical Geneticist to interpret human genomes for rare variant discovery, disease risk assessment, and clinical diagnosis on personal genome, family-based studies, and large case/control studies • Designed and developed several NGS products, including genome annotation, rare variant discovery, and personal genome report • Built a comprehensive disease-variant database from 20,000 human genetic papers through manual curation Stanford University, Stanford, CA 11/05-02/06, 03/07-11/11 Bioinformatics Scientist, Butte Lab • Built comprehensive data warehouse on genetics, genomics, epidemiology, evolutionary, and clinics, which enabled many startups, diagnostic biomarkers, novel therapeutics, and patents from Butte Lab • Led a large curation team to build a comprehensive disease-variant database Varimed from literature • Built a pipeline to interpret human genome and predict personal risk on hundreds of diseases • Built AILUN to extract, annotate, and analyze millions of gene expression data across thousands of platforms in GEO, and identified and validated many diagnostic biomarkers • Identified and validated several protein biomarkers for the diagnosis of cross-organ transplant rejection • Developed several tools to integrate various types of molecular measurements to drive the discovery of diagnostic biomarkers and therapeutic targets Quest Diagnostics Nichols Institute, San Juan Capistrano, CA 03/06-02/07 Principal Software Engineer • Supervised two bioinformatics programmers • Developed diagnostic assays on Cancer of Unknown Primary Origin, Thyroid Carcinoma, Prostate Carcinoma, and Liver Fibrosis
  3. 3. Rong Chen, Ph.D. 3 • Developed a web portal to assess the clinical significance of DNA mutations by integrating sequence, structure, alternative splicing, and evolutionary data Abgenix (bought by Amgen), Fremont, CA 07/04-11/05 Senior Computational Biologist • Developed a pipeline to build high-quality atomic structure of antibodies from sequences to support therapeutic antibody discovery on oncology • Classified the CDR regions of thousands of antibodies into novel canonical structures Accelrys (became BIOVIA), San Diego, CA 08/03-06/04 Senior Computational Biologist • Development of a high-throughput genomic structure prediction and functional annotation software GeneAtlas in DS Modeling Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, China 08/97-08/98 Research Associate • Protein chemistry and crystallography analysis on two ribosome-inactivating proteins Honors and Professional Services: • Scientific Advisor and founding member, LifeMap Solutions (http://www.lifemap- ), New York, NY, 2014-Present, • Scientific Advisor, Bina Technologies ( , Redwood City, CA, 2014-Present • Scientific Advisor, Tute Genomics ( , Provo, UT, 2013-Present • 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 • 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 Peer Reviewed Research Papers: 1. Ayers K.A., Reva B., Chen R., Assessment of cancer mutational burden from the 1000 genomes sequencing data (in preparation) 2. Hakenberg J., Cheng W., Thomas P., Chen R., A global repository for genetic variants allows platform-independent integration of annotation (under review) 3. Glicksberg B., Li L., Badgeley M.A., Kosoy R., Hakenberg J., Beckmann N.D., Hoffman G.E., Ruderfer D.M., Ayers K.L., Ma M., Shameer K., Schadt E.E., Loos R.J., Pho N., Patel C.J., Chen R.*, Dudley J.T.*, Integrative analysis of demographic factors underlying disease comorbidity networks (under review) (* co-corresponding authors) 4. Chen R., Shi L., Hakenberg J., Brian N., Sklar P., Zhang J., Zhou H., Tian L., Prakash O., Lemire M., Sleiman P., Cheng W., Chen W., Shah H., Shen Y., Fromer M., Omberg L., Deardorff M.A., Zackai E., Bobe J.R., Levin E., Hudson T., Groop L., Wang J., Hakonarson H.,
  4. 4. Rong Chen, Ph.D. 4 Wojcicki A., Diaz G.A., Edelmann L., Schadt E.E., Friend S., A systematic retrospective search of 589,306 genomes for individuals resilient to severe childhood diseases (under review) 5. Li L., Cheng W., Glicksberg B.S., Gottesman O., Tamler R., Chen R., Bottinger E.P., Dudley J.T., Identification of type 2 diabetes patient subtypes and molecular markers through topological analysis of patient similarity networks (under review) 6. Cheng W., Hakenberg J., Li S., Chen R., DIVAS: a centralized genetic variant repository representing 150,000 individuals from multiple disease cohorts Bioinformatics (in press) 7. Wang J., Liao J., Zhang J., Cheng W., Hakenberg J., Ma M., Webb B.D., Ramasamudram- chakravarthi R., Karger L., Mehta L., Kornreich R., Diaz G.A., Li S., Edelmann L., Chen R., ClinLabGeneticist: A tool for clinical management of genetic variants from whole exome sequencing in clinical genetic laboratories Genome Med 2015 7:7 8. Luo W., Obeidat M., Di Narzo A.F., Chen R., Sin D.D., Pare P.D., Hao K. Airway epithelial expression quantitative trait loci reveal genes underlying asthma and other airway diseases Am J Respir Cell Mol Biol. 2015 Jun 23. 9. Hao K., Di Narzo A.F., Ho L., Luo W., Li S., Chen R., Li T., Dubner L., Pasinetti G.M., Shared genetic etiology underlying Alzheimer’s Disease and type 2 diabetes Mol Aspects Med. 2015 June 23. Pii:S0098-2997(15)00041-2. Doi: 10.1016/j.mam.2015.06.006. 10. Ma M., Ru Y., Chuang L., Hsu N., Shi L., Hakenberg J., Cheng W., Uzilov A., Ding W., Chen R., Disease-associated variants in different categories of disease locating in distinct regulatory elements BMC Genomics 2015;16(Suppl 8):S3 11. Glicksberg B.S., Li L., Cheng W., Shameer K., Hakenberg J., Castellanos R., Meng M., Shi L., Shah H., Dudley J.T., Chen R., an integrated pipeline for multi-modal discovery of disease relationships Pac Symp Biocomputp 2015:407-18 12. Menon M.C., Chuang P.Y., Li Z., Wei C., Zhang W., Luan Y., Yi Z., Xiong H., Woytovich C., Greene I., Overbey J., Rosales I., Bagiella E., Chen R., Ma M., Li L., Ding W., Djamali A., Saminego M., O'Connell P.J., Gallon L., Colvin R., Schroppel B., He J.C., Murphy B. Intronic locus determines SHROOM3 expression and potentiates renal allograft fibrosis. J Clin Invest. 2014 Dec 1. 13. Enns G.M., Shashi V., Bainbridge M., Gambello M.J., Zahir F.R., Bast T., Crimian R., Schoch K., Platt J., Cox R., Bernstein J.A., Scavina M., Walter R.S., Bibb A., Jones M., Hegde M., Graham B.H., Need A.C., Oviedo A., Schaaf C.P., Boyle S., Butte A.J., Chen R., Clark M.J., Haraksingh R., Cowan T.M., He P., Langlois S., Zoghbi H.Y., Snyder M., Gibbs R.A., Freeze H.H., Goldstein D.B. Mutations in NGLY1 cause an inherited disorder of the endoplasmic reticulum-associated degradation pathway. Genet Med. 2014 Mar 20. doi: 10.1038/gim.2014.22. 14. SEQC/MAQC-III Consortium. A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium. Nat Biotechnol. 2014 Sep;32(9):903-14. doi: 10.1038/nbt.2957. 15. Li L., Ruau D.J., Patel C.J., Weber S.C., Chen R., Tatonetti N.P., Dudley J.T., Butte A.J., Disease risk factors identified through shared genetic architecture and electronic medical records. Science translational medicine 2014 Apr 30; 6(234):234ra57-234ra57 16. Patel C.J., Sivadas A., Tabassum R., Preeprem T., Zhao J., Arafat D., Chen R., Morgan A.A., Martin G.S., Brigham K.L., Butte A.J., Gibson G. Whole genome sequencing in support of wellness and health maintenance. Genome Med 2013 Jun27; 5(6):58. 17. Hsu I., Chen R., Ramesh A., Corona E., Kang H.P., Ruau D., Butte A.J. Systematic identification of DNA variants associated with ultraviolet radiation using a novel Geographic- Wide Association Study (GeoWAS). BMC Med Genet. 2013 Jun 20;14(1):62. 18. Corona E., Chen R., Sikora M., Morgan A.A., Patel C.J., Ramesh A., Bustamante C.D., Butte A.J. Analysis of the genetic basis of disease in the context of worldwide human relationships and migration. PLoS Genet. 2013 May;9(5):e1003447 19. Karczewski K.J., Dudley J.T., Kukurba K.R., Chen R., Butte A.J., Montgomery S.B., Snyder
  5. 5. Rong Chen, Ph.D. 5 M. Systematic functional regulatory assessment of disease-associated variants. Proc Natl Acad Sci U S A 2013 May 20 20. Sigdel T.K., Shoemaker L.D., Chen R., Li L., Butte A.J. Immune response profiling identified autoantibodies specific to Moyamoya patients. Orphanet J Rare Dis. 2013 Mar 21;8:45. 21. Patel C.J., Chen R., Kodama K., Ioannidis J.P., Butte A.J. Systematic identification of interaction effects between genome- and environment-wide associations in type 2 diabetes mellitus. Hum Genet. 2013 May;132(5):495-508. 22. Li L., Ruau D., Chen R., Weber S., Butte A.J. Systematic identification of risk factors for Alzheimer’s disease through shared genetic architecture and electronic medical records. Pac Symp Biocomput. 2013:224-35. 23. Li L., Khatri P., Sigdel T.K., Tran T., Ying L., Vitalone M.J., Chen A., Hsieh S., Dai H., Zhang M., Naesens M., Zarkhin V., Sansanwal P., Chen R., Mindrinos M., Xiao W., Benfield M., Ettenger R.B., Dharnidharka V., Mathias R., Portale A., McDonald R., Harmon W., Kershaw D., Vehaskari V.M., Kamil E., Baluarte H.J., Warady B., Davis R., Butte A.J., Salvatierra O., Sarwal M.M. A peripheral blood diagnostic test for acute rejection in renal transplantation. Am J Transplant. 2012 Oct;12(10):2710-8. 24. Kidd J.M., Gravel S., Byrnes J., Moreno-Estrada A., Musharoff S., Bryc K., Degenhardt J.D., Brisbin A., Sheth V., Chen R., McLaughlin S.F., Peckham H.E., Omberg L., Chung C.A.B., Stanley S., Pearlstein K., Levandowsky E., Acevedo-Acevedo S., Auton A., Keinan A., Acuña- Alonzo V., Barquera-Lozano R., Canizales-Quinteros S., Eng C., Burchard E.G., Russell A., Reynolds A., Clark A.G., Reese M.G., Lincoln S.E., Butte A.J., Vega FMDL, Bustamante C.D.. Population genetic inference from personal genome data: impact of ancestry and admixture on human genomic variation. Am J Hum Genet. 2012 Oct 5;91(4):660-71. 25. Gupta R., Ratan A., Rajesh C., Chen R., Kim H.L., Burhans R., Miller W., Santhosh S., Davuluri R.V., Butte A.J., Schuster S.C., Seshagiri S., Thomas G. Sequencing and analysis of a South Asian-Indian personal genome. BMC Genomics. 2012 Aug 31;13:440. 26. Morgan A.A., Chen R., Butte A.J. Clinical utility of sequence-based genotype compared with that derivable from genotyping arrays. J Am Med Inform Assoc. 2012 Jun;19(e1):e21-e27. 27. Patel C.J., Chen R., Butte A.J. Data-driven integration of epidemiological and toxicological data to select candidate interacting genes and environmental factors in association with disease. Bioinformatics. 2012 Jun 15;28(12):i121-6. 28. Ruau D, Dudley, JT, Chen R, Phillips NG, Swan GE, Lazzeroni LC, Clark JD, Butte AJ, Angst MS. Integrative approach to pain genetics identifies pain sensitivity loci across diseases. PLoS Comput Biol. 2012;8(6):e1002538. 29. Dudley JT, Kim Y, Liu L, Markov GJ, Gerold K, Chen R, Butte AJ, Kumar S. Human genomic disease variants: A neutral evolutionary explanation. Genome Res. 2012 Aug;22(8):1383-94. 30. Kang HP, Yang X, Chen R, Zhang B, Corona E, Schadt EE, Butte AJ. Integration of disease- specific single nucleotide polymorphisms, expression quantitative trait loci and coexpression networks reveal novel candidate genes for type 2 diabetes. Diabetologia. 2012 Aug;55(8):2205- 13. 31. Keiichi K, Horikoshi M, Toda K, Yamada S, Irie J, Sirota M, Morgan AA, Chen R, Ohtsu H, Hara K, Maeda S, Kadowaki T, Butte AJ. Expression-based genome-wide association study links CD44 in adipose tissue with type 2 diabetes. Proc Natl Acad Sci U S A. 2012 May 1;109(18):7049-54. 32. Chen R, Corona E, Sikora M, Dudley JT, Morgan AA, Moreno-Estrada A, Nilsen GB, Ruau D, Lincoln SE, Bustamante CD, Butte AJ. Type 2 diabetes risk alleles show extreme directional differentiation among human populations, compared to other diseases. PLoS Genet. 2012;8(4):e1002621. 33. Li L, Wozniak LJ, Rodder S, Heish S, Talisetti A, Wang Q, Esquivel C, Cox K, Chen R, McDiarmid SV, Sarwal MM. A common peripheral blood gene set for diagnosis of operational tolerance in pediatric and adult liver transplantation. Am J Transplant. 2012 May;12(5):1218-
  6. 6. Rong Chen, Ph.D. 6 28. 34. Dudley J, Chen R, Sanderford M, Butte AJ, Kumar S. Evolutionary meta-analysis of association studies reveals ancient constraints affecting disease marker discovery. Mol Biol Evol 2012 Sep;29(9)2087-94. 35. Chen R, Mias GI, Li-Pook-Than J, Jiang L, Lam HYK, Chen R, Miriami E, Karczewski KJ, Hariharan M, Dewey FE, Habegger L, Clark MJ, Balasubramanian S, Cheng Y, O’Huallachain M, Dudley JT, Hillenmeyer S, Haraksingh R, Sharon D, Euskirchen G, Lacroute P, Bettinger K, Im H, Boyle AP, Kasowski M, Grubert F, Seki S, Garcia M, Whirl-Carrillo M, Gallardo M, Blasco MA, Greenberg PL, Snyder P, Klein TE, Altman RB, Butte AJ, Ashley EA, Nadeau KC, Gerstein M, Tang H, Snyder M. Personal omics profiling reveals dynamic molecular and medical phenotypes. Cell. 2012 Mar 16;148(6):1293-307. (Responsible for the methods and analysis on risk prediction on all complex diseases) 36. Rothbard JB, Kurnellas MP, Adams CM, Su L, Chen R, Fathman CG, Robinson WH, Steinman L. Therapeutic effects of systemic administration of the chaperone alpha B crystallin associated with binding proinflammatory plasma proteins. J Biol Chem 2012 Mar 23;287(3):9708-21. 37. Chen R, Dudley JT, Ruau D, Butte AJ. Quantifying multi-ethnic representation in genetic studies of high mortality diseases. AMIA Summits Transl Sci Proc. 2012;2012:11-8. 38. Lam H.Y.K., Clark M.J., Chen R., Chen R., Natsoulis G., O’Huallachain M., Dewey F., Habegger L., Ashley E., Gerstein M.B., Butte A.J., Ji H., Snyder M. (2011) Comparison of two genome sequencing platforms Nature Biotechnology doi:10.1038 39. 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:10.1007 40. 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: doi:10.1093 41. 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:10.1038 42. 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:e1002280 43. 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/ki2011.245 44. Chen R., Butte A.J. (2011) The reference human genome demonstrates high risk of type 1 diabetes and other disorders Pac Symp Biocomputp 2011:231-42 45. Dudley J.T., Chen R., Butte A.J. (2011) Matching cancer genomes to established cell lines for personalized oncology Pac Symp Biocomputp 2011:243-52 46. 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 11:603 47. 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:e13574 48. 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)
  7. 7. Rong Chen, Ph.D. 7 Differentially expressed RNA from public microarray data identifies serum biomarkers for cross-organ transplant rejection and other conditions PLoS Computational. Biology 6: e1000940 49. Morgan A.A., Chen R., Butte A.J., Ashley E.A. (2010) Clinical assessment incorporating a personal genome – Authors’ reply Lancet 376:869-70 50. Dudley J.T., Pouliot Y., Chen R., Morgan A.A., Butte A.J. (2010) Translational Bioinformatics in the cloud: an affordable alternative Genome Medicine 2:51 51. 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 28:827-38 52. Morgan A.A., Chen R., Butte A. J. (2010) Likelihood Ratios for Genome Medicine Genome Medicine 2:30 53. 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 54. 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:e1000662 55. 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: 312-9 56. 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 2009:131-144 57. 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: 696-701 58. 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 106:4148-53 59. 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): S1 60. 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: 548 61. 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: R170 62. 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 Bioinformatics 63. 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: 190-197 64. Chen R., Li L, Butte A.J. (2007), AILUN: Reannotating Gene Expression Data Automatically. Nature Methods 4: 879 65. 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 2007:463-467 66. Mintseris J., Pierce B., Wiehe K., Anderson R., Chen R., Weng Z., (2007) Integrating statistical pair potentials into protein complex prediction. Proteins 69:511-520
  8. 8. Rong Chen, Ph.D. 8 67. Butte A.J., Chen R., (2006) Finding Disease-Related Genomic Experiments Within an International Repository: First Steps in Translational Bioinformatics, AMIA Annu Symp Proc. 2006:106-110 68. 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: 207-213 69. 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: 214-216 70. Li L., Chen R. (joint first authors), Weng Z. (2003) RDOCK: Refinement of Rigid-body Protein Docking Predictions. Proteins 53: 693-707 71. Chen R., Li L., Weng Z. (2003) ZDOCK: An Initial-stage Protein-Docking Algorithm. Proteins, 52:80- 87 72. Chen R., Tong W., Mintseris J., Li L., Weng Z. (2003) ZDOCK Predictions for the CAPRI Challenge. Proteins, 52:68-73 73. Chen R., Mintseris J., Janin J., Weng Z. (2003) A Protein-Protein Docking Benchmark. Proteins, 52:88- 91 74. Chen R., Weng Z. (2003) A Novel Shape Complementarity Scoring Function For Protein-Protein Docking. Proteins, 51:397-408 75. Chen R., Weng Z. (2002) Docking Unbound Proteins Using Shape Complementarity, Desolvation, and Electorstatics. Proteins, 47:281-294 76. Chen R., Xu YZ, Wu J,Pu Z, Jin SW, Liu WY, Xia ZX (1999) Purification and Characterization of Trichomaglin-A Novel Ribosomal-inactivating Protein with Abortificient Activity. Biochem. Mol. Biol. Int. 47:185-93 77. 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 102:7568-76 Patents and Software • Patent: methods and composition for monitoring an allograft recipient for a rejection response (61/152199, PCT/US 10/24023) • Patent: self organizing map in clinical diagnostics (11/617303) • 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 market Invited Talks and Oral Presentations: 1. June 24, 2015, Invited Talk in Five Point Lecture Series in New York Genome Center, New York, NY. Title: “Using Big Data to Interpret Genomes for Diagnosis, Therapeutics, and Precision Medicine”. 2. May 21, 2015, Invited Talk in Functional Genomics & Predictive Medicine, Boston, MA. Title: “Searching for Protective Alleles as Therapeutic Targets in Genomes with Electronic Medical Records”. 3. May 5, 2015. Section Chair and Invited Talk in Biomarkers & Diagnostics World Congress 2015, Philadelphia, PA. Talk Title: “Using Big Data to Interpret Genomes for Disease Variant Discovery, Precision Medicine and Novel Therapeutics”. 4. April 1, 2015, Invited Talk in School of Life Science, Fudan University, Shanghai, China. Talk Title: Using Big Data to Interpret Genomes for Diagnosis, Therapeutics, and Precision Medicine”.
  9. 9. Rong Chen, Ph.D. 9 5. April 1, 2015, Invited Talk in School of Pharmacy, Fudan University, Shanghai, China. Talk Title: “Using Big Data to Interpret Genomes for Diagnosis, Therapeutics, and Precision Medicine”. 6. March 30, 2015, Invited Talk in Second Military Medical University, Shanghai, China. Talk Title: “Genetic Landscape of Prostate Cancer in Chinese Population”. 7. March 3, 2015, Invited Talk in School of Medicine, Columbia University, New York, NY. Talk Title: “Using Big Data to Interpret Genomes for Protective Alleles and Precision Medicine”. 8. December 13, 2014, Invited Talk in Inaugural Personalized Medicine Conference: Implementation of Next Generation Sequencing into Clinical Care, Buffalo, NY. Title “Drug- centric Personalized Cancer Therapy Report”. 9. October 20, 2014, Talk in The American Society of Human Genetics, San Diego, CA. Title “Using Big Data to Interpret Personal Genome for Precision Medicine”. 10. August 20, 2014, Invited Talk in Next Generation Dx Summit Moving Assays to the Clinic, Capital Hilton, Washington, DC. Title “Using Big Data to Interpret Personal Genome for Precision Medicine and Novel Therapeutics”. 11. July 11, 2014, Invited Talk in World Transplant Congress, San Francisco, CA. Title: “Building databases, genome repositories, and tools to interpret personal genomes for clinical diagnosis, precision medicine, and preventative care” 12. Jan 30, 2014, Invited Talk in Clinical Genomics conference, Boston, MA. Title: “Driving Personalized Medicine and Clinical Diagnosis Using Genome Sequencing, Exome Sequencing and Integrative Genomics” 13. Jan 27, 2014, Invited Talk in The Children’s Hospital of Philadelphia, Philadelphia, PA. Title: “A worldwide search for the resilient buffered from childhood genetic diseases as a means to identify novel therapeutic and preventive interventions” 14. Mar. 4, 2013, Invited Talk in Automated Personal Genome Analysis for Clinical Advisors: Challenges and Solutions, Carnegie Mellon University, Pittsburgh, PA 15. Mar. 20, 2012, Oral presentation in 2012 AMIA Summit on Translational Bioinformatics (TBI), San Francisco, CA. Title: “Quantifying multi-ethnic representation in genetic studies of high mortality diseases” 16. Feb. 19, 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” 17. Oct. 13, 2011, Oral presentation 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” 18. 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” 19. 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” 20. 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” 21. Apr. 12, 2011, Invited talk in Agios Pharmaceutical, Cambridge, MA. Title: “Using Systems Medicine to Transform Biomarker Discovery and Personalized Medicine” 22. 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”
  10. 10. Rong Chen, Ph.D. 10 23. 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” 24. Mar. 15, 2011, Oral presentation 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”. 25. Mar. 8, 2011, 2011 Oral presentation 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”. 26. 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” 27. 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”. 28. Jan. 4, 2011, Oral presentation, Pacific Symposium on Biocomputing (PSB), Big island of Hawaii. Title: “Is the Reference Human Genome a Good Representation of a Healthy Control and Consensus?” 29. 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” 30. Aug. 11, 2010, Invited talk in Xiameng University, Xiameng, Fujian, China. Title: “Translating Publically-available molecular Data into Diagnostics and Personalized Medicine” 31. 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” 32. 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” 33. Jun. 12, 2004, Invited Talk in Biogeometry workshop, ACM Symposium on Computational Geometry, New York, NY. Title: “An Integrated Approach to Protein-Protein Docking” 34. Sep. 19, 2002, Invited Talk in First CAPRI Evaluation Meeting, Agelonde, La Londe-des- Maures, France. Title: "ZDOCK Predictions for the CAPRI Challenge" 35. Jul. 25, 2002, Oral presentation in Boston University-Humboldt University Workshop, Boston, MA. Title: "A Novel Shape Complementarity Scoring Function for Protein Docking" 36. Dec. 1, 2001, Invited Talk in Computational Genomics Conference, Baltimore, Maryland. Title: "An Integrated Approach to Predictive Protein-protein Docking"