Publications

2019

Glicksberg BS et al. Integrative analysis of loss-of-function variants in clinical and genomic data reveals novel genes associated with cardiovascular traits. Supplementary Materials and Supplemental Tables revision

2018

Ayers KL, Benjamin S. Glicksberg BS, Garfield AS, Longerich S, White JA, Yang PW, Du L, Chittenden TW, Gulcher JR, Roy S, Fiedorek F, Gottesdiener K, Cohen S, North KE, Schadt EE, Li SD*, Chen R* and Van der Ploeg LHT*. Melanocortin 4 Receptor Pathway Dysfunction in Obesity: Patient Stratification Aimed at MC4R Agonist Treatment. J Clin Endocrinol Metab, 2018,103(7):2601–2612 (* co-corresponding authors).
Smith MR, Glicksberg BS, Li L, Chen R, Morishita H, Dudley JT. Loss-of-function of neuroplasticity-related genes confers risk for human neurodevelopmental disorders. Pac Symp Biocomput. 2018,23:68-79
Glicksberg BS, Miotto R, Johnson KW, Shameer K, Li L, Chen R, Dudley JT. Automated disease cohort selection using word embeddings from Electronic Health Records. Pac Symp Biocomput. 2018,23:145-156.

2017

Scott SA, Owusu Obeng A, Botton MR, Yang Y, Scott ER, Ellis SB, Wallsten R, Kaszemacher T, Zhou X, Chen R, Nicoletti P, Naik H, Kenny EE, Vega A, Waite E, Diaz GA, Dudley J, Halperin JL, Edelmann L, Kasarskis A, Hulot JS, Peter I, Bottinger EP, Hirschhorn K, Sklar P, Cho JH, Desnick RJ, Schadt EE. Institutional profile: translational pharmacogenomics at the Icahn School of Medicine at Mount Sinai. Pharmacogenomics. 2017,18(15):1381-1386. doi: 10.2217/pgs-2017-0137
Li SD, Ma M, Li H, Waluszko A, Sidorenko T, Schadt EE, Zhang DY, Chen R
and Ye F. Cancer gene profiling in non-small cell lung cancers reveals activating mutations in JAK2 and JAK3 with therapeutic implications. Genome Medicine 2017,9:89
Schrock AB, Li SD, Frampton GM, Suh J, Braun E, Mehra R, Buck SC, Bufill JA, Peled N, Karim NA, Hsieh KC, Doria M, Knost J, Chen R, Ou SI, Ross JS, Stephens PJ, Fishkin P, Miller VA, Ali SM, Halmos B, Liu JJ. Pulmonary Sarcomatoid Carcinomas Commonly Harbor Either Potentially Targetable Genomic Alterations or High Tumor Mutational Burden as Observed by Comprehensive Genomic Profiling. J Thorac Oncol. 2017 Jun;12(6):932-942. doi: 10.1016/j.jtho.2017.03.005. Epub 2017 Mar 16.
Wang H., Bender A., Wang P., Karaoke E., Inabnet W. B., Libutti S. K., Amold A., Lambertini L., Stang M., Chen H,. Kasal Y., Mahajan M., Kinoshita Y., Ranvier G F., Becker T. C., Takane K. K., Walker L. A., Saul S., Chen R., Scott D. K., Ferrer J., Antipin Y., Donovan M., Uzilov A. V., Reva B., Schadt E.E., Losic B., Argmann C., Stewart A. F. Insights into beta cell regeneration for diabetes via integration of molecular landscapes in human insulinomas. Nature Communications. 2017(8) 767.
Pandya C., Andrew V. Uzilov A.V., Justin Bellizzi J., Lau C.Y., Moe A.S., Strah M, Hamou W., Newman L. C., Fink M. Y., Antipin Y., Yu W., Stevenson M., Cavaco B.M.,Teh B.T, Thakker R.V., Morreau H, Schadt E.E, Sebra R, Li SD, Arnold A. and Chen R. Genomic profiling reveals mutational landscape in parathyroid carcinomas. JCI Insight. 2017;2(6):e92061.
Uzilov A.V, Cheesman K.C, Fink M.Y, Newman LC, Chetanya Pandya C, Lalazar Y, Hefti M, Fowkes M,Deikus G,Lau C.Y, AMoe A.S, Kinoshita Y, Kasai Y, Zweig M, Gupta A,Starcevic D, Mahajan M,Schadt E.E,Post K, Donovan M, Sebra R.P, Chen R * and Geer E.B *. Identification of a novel RASD1 somatic mutation in a USP8-mutated corticotroph adenoma. Molecular Case Studies. Published in Advance March 3, 2017, doi: 10.1101/mcs.a001602 (*co-corresponding authors)
Shameer K., Glicksberg BS., Hodos R., Johnson KW., Badgeley MA., Readhead B., Tomlinson MS.,O’Connor T., Miotto R., Kidd BA, Chen R, Avi Ma’ayan and Dudley JT. Systematic analyses of drugs and disease indications in RepurposeDB reveal pharmacological, biological and epidemiological factors influencing drug repositioning. Briefings in Bioinformatics, 2016, 1–23
Li L*, Greene I., Readhead B, Menon M.C.,Kidd B.A.,Uzilov A. V., Wei C.G, Philippe N, Schroppe B., He J.C., Chen R, Dudley J.T., Murphy B. Novel Therapeutics Identification for Fibrosis in Renal Allograft Using Integrative Informatics Approach. Scientific Reports ,2017, 7:3948

2016

Chen B, Solis-Villa C, Hakenberg J, Qiao W, Srinivasan R.R, Yasuda M, Balwani M, Doheny D, Peter I, Chen R, Desnick R.J. Acute Intermittent Porphyria: Predicted Pathogenicity of HMBS Variants Indicates Extremely Low Penetrance of the Autosomal Dominant Disease. Hum Mutat. 2016 Nov;37(11):1215-1222.
Chen Y, Camacho S.C.,Silvers T.R., Razak A.RA,Gabrail N.Y., Gerecitano J.F.,Kalir E., Pereira E.,Evans B.R., Ramus S.J., Huang F.,Priedigkeit N., Rodriguez E., Donovan M.,Khan F., Kalir T., Sebra R.,Uzilov A., Chen R.,Sinha R.,Halpert R., Billaud J.N., Shacham S., McCauley D., Landesman Y., Rashal T., Kauffman M., Mirza M.R., Mau-Sørensen M., Dottino P., Martignetti J.A. Inhibition of the nuclear export receptor XPO1 as a therapeutic target for platinum resistant ovarian cancer. Clinical Cancer Research. 2016. Published Online First September 23, 2016 doi: 10.1158/1078-0432.CCR-16-1333
Ayers K. L., Mirshahi U. L., Wardeh A.H., Murray M.F, Hao K., Glicksberg B.S., Li S.Y., Carey D. J. and Chen R. A loss of function variant in CASP7 protects against Alzheimer’s disease in homozygous APOE ε4 allele carriers. BMC Genomics 2016, 17(Suppl 2):445
Glicksberg B S. ,Li L ,Badgeley M A.,Shameer K ,Kosoy R ,Beckmann N D. , Pho N,Hakenberg J, Ma M, Ayers K L., Hoffman G E., Li S D, Schadt E E., Patel C J., Chen R* and Dudley J T*. Comparative analyses of population-scale phenomic data in electronic medical records reveal race-specific disease networks. Bioinformatics. 2016, 32, i101–i110 (*co-corresponding authors)
Uzilov A. V. , Ding W., Fink M. Y., Antipin Y., Brohl A. S., Davis C., Lau C.Y., Pandya C., Shah H., Kasai Y., Powell J., Micchelli M., Castellanos R., Zhang ZY, Linderman M., Kinoshita Y., Zweig M., Raustad K., Cheung K., Castillo D., Wooten M., Bourzgui I., Newman L. C., Deikus G., Mathew B., Zhu J., Glicksberg B. S., Moe A. S., Liao J, Edelmann L., Dudley J. T., Maki R.G., Kasarskis A., Holcombe R. F., Mahajan M., Hao K., Reva B., Longtine J., Starcevic D., Sebra R., Donovan M. J., Li SY., Schadt E. E*. and Chen R*. Development and clinical application of an integrative genomic approach to personalized cancer therapy. Genome Medicine. 2016, 8:62 (*co-corresponding authors)
Liu P, Ping YL, Ma M, Zhang D, Liu C., Zaidid S., Gao S, Ji YY, Lou F, Yu FY, Lu P, Stachnik A, Bai M, Wei CG, Zhang LR, Wang K, Chen R, New M. I., Rowe D. W., Yuen T, Sun L and Zaidi M. Anabolic actions of Notch on mature bone. PNAS. 2016, 1603399113
Chen R*, Shi LS, Hakenberg J., Naughton B., Sklar P., Zhang J.G., Zhou HL, Tian LF, Prakash O., Lemire M., Sleiman P., Cheng WY, Chen W.T., Shah H. Shen YL., Fromer M.,Omberg L., Deardorff M. A, Zackai E., Bobe J. R, Levin E., Hudson T. J., Groop L., Wang J.,Hakonarson H., Wojcicki A., Diaz G. A., Edelmann L., Schadt E. E.* & Friend S. H.* Analysis of 589,306 genomes identifies individuals resilient to severe Mendelian childhood diseases. Nature Biotechnology. 2016,doi:10.1038/nbt.3514 (*co-corresponding authors)
Hakenberg J, Cheng WY, Thomas P, Wang YC, Uzilov A. V. and Chen R. Integrating 400 million variants from 80,000 human samples with extensive annotations: towards a knowledge base to analyze disease cohorts. BMC Bioinformatics. 2016,17:24.
Cheng WY, Hakenberg J, Li SD, Chen R. DIVAS: a centralized genetic variant repository representing 150,000 individuals from multiple disease cohorts. Bioinformatics, 32(1), 2016, 151–153
Qiao W, Wang J, Pullman BS, Chen R, Yang Y and Scott SA. The CYP2D6 VCF Translator. The Pharmacogenomics Journal (2016), 1–3

2015

Pereira E, Vanegas OC, Anand S, Sebra R, Camacho SC, Wortzel LG, Nair N, Moshier E, Wooten M, Uzilov A. V., Chen R, Hayes MP, Zakashansky K, Beddoe AM, Schadt E, Dottino P, Martignett JA. Personalized Circulating Tumor DNA Biomarkers Dynamically Predict Treatment Response and Survival In Gynecologic Cancers. PLOS ONE. 2015, DOI:10.1371/journal.pone.0145754
Shoemaker LD, Clark MJ, Patwardhan A, Chandratillake G, Garcia S,Chen R, Morgan A.A, Leng N, Kirk S, Chen R, Cook D.J, Snyder M and Steinberg GK. Disease Variant Landscape of a Large Multi-ethnic Population of Moyamoya Patients by Exome Sequencing. G3: Genes|Genomes|Genetics. 2015, doi:10.1534/g3.115.020321
Li L, Cheng WY, Glicksberg B.S., Gottesman O, Tamler R, Chen R, Bottinger E. P. and Dudley J.T. Identification of type 2 diabetes subgroups through topological analysis of patient similarity. Science Translational Medicine. 2015:Vol. 7, Issue 311, pp. 311ra174
Wang JL, Liao J, Zhang JL, Cheng WY, Hakenberg J, Ma M, Webb BD, Ramasamudram-chakravarthi R, Karger L, Mehta L, Kornreich R, Diaz GA, Li SY, Edelmann L and Chen R. ClinLabGeneticist: a tool for clinical management of genetic variants from whole exome sequencing in clinical genetic laboratories. Genome Medicine 2015, 7:7.
Luo W, Obeidat M, Di Narzo AF, Chen R, Sin DD, Paré PD, 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.
Hao K, Di Narzo AF, Ho L, Luo W, Li S, Chen R, Li T, Dubner L, Pasinetti GM. Shared genetic etiology underlying alzheimer’s Disease and type 2 Diabetes. Mol Aspects Med. 2015 Jun 23. pii: S0098-2997(15)00041-2. doi: 10.1016/j.mam.2015.06.006.
Ma M, Ru Y, Chuang LS, Hsu NY, Shi LS, Hakenberg J, Cheng WY, Uzilov A.V., Ding W, Glicksberg B.S. and Chen R. Disease-associated variants in different categories of disease located in distinct regulatory elements. BMC Genomics 2015, 16(Suppl 8):S3.
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

2014

Menon MC, Chuang PY, 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 PJ, Gallon L, Colvin R, Schroppel B, He JC, Murphy B. Intronic locus determines SHROOM3 expression and potentiates renal allograft fibrosis. J Clin Invest. 2014 Dec 1.
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. Epub 2014 Aug 24. Chen R is in SEQC consortium.
Enns GM, Shashi V, Bainbridge M, Gambello MJ, Zahir FR, Bast T, Crimian R, Schoch K, Platt J, Cox R, Bernstein JA, Scavina M, Walter RS, Bibb A, Jones M, Hegde M, Graham BH, Need AC, Oviedo A, Schaaf CP, Boyle S, Butte AJ, Chen R, Clark MJ, Haraksingh R; FORGE Canada Consortium, Cowan TM, He P, Langlois S, Zoghbi HY, Snyder M, Gibbs RA, Freeze HH,Goldstein DB. Mutations in NGLY1 cause an inherited disorder of the endoplasmic reticulum-associated degradation pathway. Genet Med. 2014 Oct;16(10):751-8.
Li L, Ruau DJ, Patel CJ, Weber SC, Chen R, Tatonetti NP, Dudley JT, Butte AJ. Disease Risk Factors Identified Through Shared Genetic Architecture and Electronic Medical Records. Science Translational Medicine 30 April 2014 6:234ra57.

2013

Hsu I, Chen R, Ramesh A, Corona E, Kang HP, Ruau D, Butte AJ. 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.
Corona E, Chen R, Sikora M, Morgan AA, Patel CJ, Ramesh A, Bustamante CD, Butte AJ. Analysis of the genetic basis of disease in the context of worldwide human relationships and migration. PLoS Genet. 2013 May;9(5):e1003447.
Karczewski KJ, Dudley JT, Kukurba KR, Chen R, Butte AJ,Montgomery SB,Synder M. Systematic functional regulatory assessment of disease-associated variants. Proc Natl Acad Sci U S A 2013 May 20.
Patel CJ, Chen R, Kodama K, Ioannidis JP, Butte AJ. Systematic identification of interaction effects between genome- and environment-wide associations in type 2 diabetes mellitus. Hum Genet. 2013 May;132(5):495-508.
Sigdel TK, Shoemaker LD, Chen R, Li L, Butte AJ. Immune response profiling identified autoantibodies specific to Moyamoya patients. Orphanet J Rare Dis. 2013 Mar 21;8:45.
Li L, Ruau D, Chen R, Weber S, Butte AJ. Systematic identification of risk factors for Alzheimer’s disease through shared genetic architecture and electronic medical records. Pac Symp Biocomput. 2013:224-35.
Patel CJ, Sivadas A, Tabassum R, Preeprem T, Zhao J, Arafat D, Chen R, Morgan AA, Martin GS, Brigham KL, Butte AJ, Gibson G. Whole genome sequencing in support of wellness and health maintenance. Genome Med. 2013 Jun 27;5(6):58

2012

Li L, Khatri P, Sigdel TK, Tran T, Ying L, Vitalone MJ, Chen A, Hsieh S, Dai H, Zhang M, Naesens M, Zarkhin V, Sansanwal P, Chen R, Mindrinos M, Xiao W, Benfield M, Ettenger RB, Dharnidharka V, Mathias R, Portale A, McDonald R, Harmon W, Kershaw D, Vehaskari VM, Kamil E, Baluarte HJ, Warady B, Davis R, Butte AJ, Salvatierra O, Sarwal MM. A peripheral blood diagnostic test for acute rejection in renal transplantation. Am J Transplant. 2012 Oct;12(10):2710-8.
Kidd JM, Gravel S, Byrnes J, Moreno-Estrada A, Musharoff S, Bryc K, Degenhardt JD, Brisbin A, Sheth V, Chen R, McLaughlin SF, Peckham HE, Omberg L, Chung CAB, 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 EG, Russell A, Reynolds A, Clark AG, Reese MG, Lincoln SE, Butte AJ, Vega FMDL, Bustamante CD. 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.
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.
Gupta R, Ratan A, Rajesh C, Chen R, Kim HL, Burhans R, Miller W, Santhosh S, Davuluri RV, Butte AJ, Schuster SC, Seshagiri S, Thomas G. Sequencing and analysis of a South Asian-Indian personal genome. BMC Genomics. 2012 Aug 31;13:440.
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.
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.
Morgan AA, Chen R, Butte AJ. Clinical utility of sequence-based genotype compared with that derivable from genotyping arrays. J Am Med Inform Assoc. 2012 Jun;19(e1):e21-e27.
Patel CJ, Chen R, Butte AJ. 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.
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.
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):1218-28.
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.
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.
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).
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.
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.
Kang HP, Morgan AA, Chen R, Schadt EE, Butte AJ. Coanalysis of GWAS with eQTL reveals disease-tissue associations. AMIA Summits Transl Sci Proc. 2012;2012:35-41.

2011

Lam HYK, Clark MJ, Chen R, Chen R, Natsoulis G, O’Huallachain M, Dewey F, Habegger L, Ashley EA, Gerstein MB, Butte AJ, Ji H, Snyder M. Performance comparison of whole-genome sequencing platforms. Nat Biotechnol. 2011 Dec 18;30(1):78-82.
Pan S, Dewey F, Perez M, Knowles J, Chen R, Butte AJ, Ashley EA. Personalized medicine and cardiovascular disease: from genome to bedside. Curr Cardiovasc Risk Rep 2011;5:542-551.
Naesens M, Khatri P, Li L, Sigdel T, Chen R, Vitalone M, Butte AJ, Salvatierra O, Sarwal MM. Progressive histological damage in renal allografts is associated with expression of innate and adaptive immunity genes. Kidney Int. 2011 Dec;80(12):1364-76.
Engreitz JM, Chen R, Morgan AA, Dudley JT, Mallelwar R, Butte AJ. ProfileChaser: searching microarray repositories based on genome-wide patterns of differential expression. Bioinformatics. 2011 dec 1;27(23):3317-8.
Clark MJ, Chen R, Lam H, Karczewski KJ, Chen R, Euskirchen G, Butte AJ, Snyder M. Performance comparison of exome DNA sequencing technologies. Nat Biotechnol. 2011 Sep 25;29(10):908-14.
Dewey FE, Chen R, Cordero SP, Ormond KE, Caleshu C, Karczewski KJ, Carrillo MW, Wheeler MT, Dudley JT, Bynes JK, Cornejo OE, Knowles JW, Woon M, Sangkuhl K, Gong L, Thorn CF, Hebert JM, Capriotti E, David SP, Pavlovic A, West A, West JS, Thakuria JV, Ball MP, Zaranek AW, Rehm HL, Church GM, Bustamante CD, Snyder MP, Altman RB, Klein TE, Butte AJ, Ashley EA. Phased whole genome genetic risk in a family quartet using a major allele reference sequence. PLoS Genet. 2011 Sep;7(9):e1002280.
Chen R, Butte AJ. The reference human genome demonstrates high risk of type 1 diabetes and other disorders. Pac Symp Biocomput. 2011:231-42.
Dudley JT, Chen R, Butte AJ. Matching cancer genomes to established cell lines for personalized oncology. Pac Symp Biocomput.2011:243-52.

2010

Engereitz JM, Morgan AA, Dudley JT, Chen R, Thathoo R, Altman RB, Butte AJ. Content-based microarray search using differential expression profiles. BMC Bioinformatics. 2010 Dec 21;11:603.
Chen R, Davydov EV, Sirota M, Butte AJ. Non-synonymous and synonymous coding SNPs show similar likelihood and effect size of human disease association. PLoS One 2010 Oct 22;5(10):e1 574.
Chen R, Sigdel TK, Li L, Kambham N, Dudley JT, Heish SC, Klassen RB, Chen A, Caohuu T, Morgan AA, Valantine HA, Khush KK, Sarwal MM, Butte AJ. Differentially expressed RNA from public microarray data identifies serum biomarkers for cross-organ transplant rejection and other conditions. PLoS Computat Biol. 2010 Sep 23;6(9):e1000940.
Dudley JT, Pouliot Y, Chen R, Morgan AA, Butte AJ. Translational Bioinformatics in the cloud: an affordable alternative. Genome Med.2010 Aug 6;2(8):51.
Shi L, Campbell G, Jones WD, Campagne F, Wen Z, Walker SJ, Su Z, Chu TM, Goodsaid FM, Pusztai L, Shaughbessy JD Jr, Oberthuer A,Chen R, Puri RK, Scherf U, Tong W, Wolfinger RD, MAQC Consortium. The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray- based predictive models. Nat Biotechnol 2010 Aug;28(8):827-38.
Morgan AA, Chen R, Butte AJ. Likelihood Ratios for Genome Medicine. Genome Med. 2010 May 17;2(5):30.
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. Clinical assessment incorporating a personal genome. Lancet. 2010 May 1;375(9725):1525-35. (Responsible for the methods and analysis on risk prediction on all complex diseases)
Li L, Chen A, Chaudhuri A, Kambham N, Sigdel T, Chen R, Sarwal MM. Compartmental Localization and Clinical Relevance of MICA Antibodies after Renal Transplantation. Transplantation. 2010 Feb 15;89(3):312-9.
Suthram S, Dudley JT, Chaing AP, Chen R, Hastie TJ, Butte AJ. Network-based elucidation of human disease similarity reveals common functional modules enriched for pluripotent drug targets. PLoS Comput Biol. 2010 Feb 5;6(2):e1000662.

2009

Becker L, Salameh W, Sferruzza A, Zhang K, Chen R, Malik R, Reitz R, Nasser I, Afdhal NH. Validation of Hepascore, compared to simple indices of fibrosis, in US patients with chronic hepatitis C virus infection. Clin Gastroenterol Hepatol. 2009 Jun;7(6):696-701.
Cai JJ, Borenstein E, Chen R, Petrov DA. Similarly strong purifying selection acts on human disease genes of all evolutionary ages. Genome Biol Evol. 2009 May 27;1:131-144.
Li L, Wadia P, Chen R, Kambham N, Naesens M, Sigdel T, Miklos D, Sarwal MM, Butte AJ. Identifying compartment-specific alloimmune targets after renal transplantation by integrating transcriptome and antibodyome measures. Proc Natl Acad Sc U S A. 2009 Mar 17;106(11):4148-53.
Shah NH, Jonquet C, Chiang AP, Butte AJ, Chen R, Musen MA. Ontology-driven indexing of public datasets for translational bioinformatics. BMC Bioinformatics. 2009 Feb 5;10 supple 2:S1.

2008

Chen R, Mallelwar R, Thosar A, Venkatasubrahmanyam S, Butte AJ. GeneChaser: identifying all biological and clinical conditions in which genes of interest are differentially expressed. BMC Bioinformatics 2008 Dec 18;9:548.
Chen R, Morgan AA, Dudley J, Deshpande T, Li L, Kodma K, Chiang A, Butte AJ.FitSNPs: highly differentially expressed genes are more likely to have variants associated with disease. Genome Biol. 2008;9(12):R170.
Li L, Ying LH, Naesens M, Xiao W, Hsieh S, Sigdel T, Martin J, Chen R, Liu K, Sarwal MM. Interference of globin genes with biomarker discovery for allograft rejection in peripheral blood samples. Physiol Genomics 2008 Jan 17;32(2):190-197.

2007

Mintseris J, Pierce B, Wiehe K, Anderson R, Chen R, Weng Z. Integrating statistical pair potentials into protein complex prediction. Proteins. 2007 Nov 15;69(3):511-20.
Chen R, Li L, Butte AJ. AILUN: reannotating gene expression data automatically. Nat Methods. 2007 Nov;4(11):879.
Lin Y, Chiang A, Yao P, Chen R, Butte AJ, Lin R. Methodology for exacting functional pharmacogenomic experiments from international repository. AMIA Annu Symp Proc. 2007 Oct 11:463-7.

2006

Butte AJ, Chen R. Finding disease-related genomic experiments within an international repository: first steps in translational bioinformatics. AMIA Annu Symp Proc. 2006:106-110.

2005

Wiehe K, Pierce B, Mintseris J, Tong W, Anderson R, Chen R, Weng Z. ZDOCK and RDOCK performance in CAPRI rounds 3, 4, and 5. Proteins. 2005 Aug 1;60(2):207-13.
Mintseris J, Wiehe K, Pierce B, Anderson R, Chen R, Janin J, Weng Z. Protein-protein docking benchmark 2.0: an update. Proteins. 2005 Aug 1;60(2):214-6.

2003

Li L, Chen R (joint first authors), Weng Z. RDOCK: refinement of rigid-body protein docking predictions. Proteins. 2003 Nov 15;53(3):693-707.
Chen R, Li L, Weng Z. ZDOCK: an initial-stage protein-docking algorithm. Proteins. 2003 Jul 1; 52(1):80-7.
Chen R, Tong W, Mintseris J, Li L, Weng Z. ZDOCK predictions for the CAPRI challenge. Proteins. 2003 Jul 1;52(1):68-73.
Chen R, Mintseris J, Janin J, Weng Z. A protein-protein docking benchmark. Proteins. 2003 Jul 1;52(1):88-91.
Chen R, Weng Z. A novel shape complementarity scoring function for protein-protein docking. Proteins. 2003 May 15;51(3):397-408.

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