Atul J. Butte, MD, PhD - Publications

Affiliations: 
Stanford Center for Biomedical Informatics, Department of Medicine and Department of Pediatrics Stanford University School of Medicine, Palo Alto, CA, United States 
 Bakar Computational Health Sciences Institute University of California, San Francisco, San Francisco, CA 

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Year Citation  Score
2019 Norgeot B, Glicksberg BS, Trupin L, Lituiev D, Gianfrancesco M, Oskotsky B, Schmajuk G, Yazdany J, Butte AJ. Assessment of a Deep Learning Model Based on Electronic Health Record Data to Forecast Clinical Outcomes in Patients With Rheumatoid Arthritis. Jama Network Open. 2: e190606. PMID 30874779 DOI: 10.1001/jamanetworkopen.2019.0606  0.88
2019 Lussier YA, Butte AJ, Li H, Chen R, Moore JH. Translational informatics of population health: How large biomolecular and clinical datasets unite. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 24: 455-459. PMID 30864347  0.48
2019 Norgeot B, Glicksberg BS, Butte AJ. A call for deep-learning healthcare. Nature Medicine. 25: 14-15. PMID 30617337 DOI: 10.1038/s41591-018-0320-3  0.88
2018 Zalocusky KA, Kan MJ, Hu Z, Dunn P, Thomson E, Wiser J, Bhattacharya S, Butte AJ. The 10,000 Immunomes Project: Building a Resource for Human Immunology. Cell Reports. 25: 1995. PMID 30428364 DOI: 10.1016/j.celrep.2018.11.013  0.56
2018 Zalocusky KA, Kan MJ, Hu Z, Dunn P, Thomson E, Wiser J, Bhattacharya S, Butte AJ. The 10,000 Immunomes Project: Building a Resource for Human Immunology. Cell Reports. 25: 513-522.e3. PMID 30304689 DOI: 10.1016/j.celrep.2018.09.021  0.56
2018 Hu Z, Glicksberg BS, Butte AJ. Robust prediction of clinical outcomes using cytometry data. Bioinformatics (Oxford, England). PMID 30169745 DOI: 10.1093/bioinformatics/bty768  0.88
2018 Hu Z, Jujjavarapu C, Hughey JJ, Andorf S, Lee HC, Gherardini PF, Spitzer MH, Thomas CG, Campbell J, Dunn P, Wiser J, Kidd BA, Dudley JT, Nolan GP, Bhattacharya S, ... Butte AJ, et al. MetaCyto: A Tool for Automated Meta-analysis of Mass and Flow Cytometry Data. Cell Reports. 24: 1377-1388. PMID 30067990 DOI: 10.1016/j.celrep.2018.07.003  0.72
2018 Bhattacharya S, Dunn P, Thomas CG, Smith B, Schaefer H, Chen J, Hu Z, Zalocusky KA, Shankar RD, Shen-Orr SS, Thomson E, Wiser J, Butte AJ. ImmPort, toward repurposing of open access immunological assay data for translational and clinical research. Scientific Data. 5: 180015. PMID 29485622 DOI: 10.1038/sdata.2018.15  0.56
2018 Kido T, Sikora-Wohlfeld W, Kawashima M, Kikuchi S, Kamatani N, Patwardhan A, Chen R, Sirota M, Kodama K, Hadley D, Butte AJ. Are minor alleles more likely to be risk alleles? Bmc Medical Genomics. 11: 3. PMID 29351777 DOI: 10.1186/s12920-018-0322-5  0.48
2017 Aran D, Hu Z, Butte AJ. xCell: digitally portraying the tissue cellular heterogeneity landscape. Genome Biology. 18: 220. PMID 29141660 DOI: 10.1186/s13059-017-1349-1  0.56
2016 Rennert RC, Januszyk M, Sorkin M, Rodrigues M, Maan ZN, Duscher D, Whittam AJ, Kosaraju R, Chung MT, Paik K, Li AY, Findlay M, Glotzbach JP, Butte AJ, Gurtner GC. Microfluidic single-cell transcriptional analysis rationally identifies novel surface marker profiles to enhance cell-based therapies. Nature Communications. 7: 11945. PMID 27324848 DOI: 10.1038/ncomms11945  0.48
2016 Kosti I, Jain N, Aran D, Butte AJ, Sirota M. Cross-tissue Analysis of Gene and Protein Expression in Normal and Cancer Tissues. Scientific Reports. 6: 24799. PMID 27142790 DOI: 10.1038/srep24799  0.48
2016 Bagley SC, Sirota M, Chen R, Butte AJ, Altman RB. Constraints on Biological Mechanism from Disease Comorbidity Using Electronic Medical Records and Database of Genetic Variants. Plos Computational Biology. 12: e1004885. PMID 27115429 DOI: 10.1371/journal.pcbi.1004885  0.48
2016 Kodama K, Zhao Z, Toda K, Yip L, Fuhlbrigge R, Miao D, Fathman CG, Yamada S, Butte AJ, Yu L. Expression-based Genome-Wide Association Study Links Vitamin D Binding Protein with Autoantigenicity in Type 1 Diabetes. Diabetes. PMID 26983959 DOI: 10.2337/db15-1308  0.48
2016 Hughey JJ, Hastie T, Butte AJ. ZeitZeiger: supervised learning for high-dimensional data from an oscillatory system. Nucleic Acids Research. PMID 26819407 DOI: 10.1093/nar/gkw030  0.48
2015 Li X, Kang J, Pan Q, Sikora-Wohlfeld W, Zhao D, Meng C, Bai C, Patwardhan A, Chen R, Ren H, Butte AJ, Ding K. Genetic analysis in a patient with nine primary malignant neoplasms: a rare case of Li-Fraumeni syndrome. Oncology Reports. PMID 26707089 DOI: 10.3892/or.2015.4501  0.48
2015 Geifman N, Bollyky J, Bhattacharya S, Butte AJ. Opening clinical trial data: are the voluntary data-sharing portals enough? Bmc Medicine. 13: 280. PMID 26560699 DOI: 10.1186/s12916-015-0525-y  0.48
2015 Tan Z, Hu Z, Cai EY, Alev C, Yang T, Li Z, Sung J, El-Sayed YY, Shaw GM, Stevenson DK, Butte AJ, Sheng G, Sylvester KG, Cohen HJ, Ling XB. Serological Targeted Analysis of an ITIH4 Peptide Isoform: A Preterm Birth Biomarker and Its Associated SNP Implications. Journal of Genetics and Genomics = Yi Chuan Xue Bao. 42: 507-10. PMID 26408095 DOI: 10.1016/j.jgg.2015.06.001  0.48
2015 Nasrallah M, Pouliot Y, Hartmann B, Dunn P, Thomson E, Wiser J, Butte AJ. Reanalysis of the Rituximab in ANCA-Associated Vasculitis trial identifies granulocyte subsets as a novel early marker of successful treatment. Arthritis Research & Therapy. 17: 262. PMID 26387933 DOI: 10.1186/s13075-015-0778-z  0.48
2015 Patwardhan A, Harris J, Leng N, Bartha G, Church DM, Luo S, Haudenschild C, Pratt M, Zook J, Salit M, Tirch J, Morra M, Chervitz S, Li M, Clark M, ... ... Butte AJ, et al. Achieving high-sensitivity for clinical applications using augmented exome sequencing. Genome Medicine. 7: 71. PMID 26269718 DOI: 10.1186/s13073-015-0197-4  0.48
2015 Chen B, Sirota M, Fan-Minogue H, Hadley D, Butte AJ. Relating hepatocellular carcinoma tumor samples and cell lines using gene expression data in translational research. Bmc Medical Genomics. 8: S5. PMID 26043652 DOI: 10.1186/1755-8794-8-S2-S5  0.48
2015 Liu LF, Kodama K, Wei K, Tolentino LL, Choi O, Engleman EG, Butte AJ, McLaughlin T. The receptor CD44 is associated with systemic insulin resistance and proinflammatory macrophages in human adipose tissue. Diabetologia. 58: 1579-86. PMID 25952479 DOI: 10.1007/s00125-015-3603-y  0.48
2015 Li J, Zheng S, Chen B, Butte AJ, Swamidass SJ, Lu Z. A survey of current trends in computational drug repositioning. Briefings in Bioinformatics. PMID 25832646 DOI: 10.1093/bib/bbv020  0.48
2015 Hughey JJ, Butte AJ. Robust meta-analysis of gene expression using the elastic net. Nucleic Acids Research. PMID 25829177 DOI: 10.1093/nar/gkv229  0.48
2015 Paik H, Chung AY, Park HC, Park RW, Suk K, Kim J, Kim H, Lee K, Butte AJ. Repurpose terbutaline sulfate for amyotrophic lateral sclerosis using electronic medical records. Scientific Reports. 5: 8580. PMID 25739475 DOI: 10.1038/srep08580  0.48
2015 Bollyky JB, Xu P, Butte AJ, Wilson DM, Beam CA, Greenbaum CJ. Heterogeneity in recent-onset type 1 diabetes - a clinical trial perspective. Diabetes/Metabolism Research and Reviews. PMID 25689602 DOI: 10.1002/dmrr.2643  0.48
2015 Brodin P, Jojic V, Gao T, Bhattacharya S, Angel CJ, Furman D, Shen-Orr S, Dekker CL, Swan GE, Butte AJ, Maecker HT, Davis MM. Variation in the human immune system is largely driven by non-heritable influences. Cell. 160: 37-47. PMID 25594173 DOI: 10.1016/j.cell.2014.12.020  0.48
2015 Fan-Minogue H, Chen B, Sikora-Wohlfeld W, Sirota M, Butte AJ. A systematic assessment of linking gene expression with genetic variants for prioritizing candidate targets. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 383-94. PMID 25592598  0.48
2014 Ehmer U, Zmoos AF, Auerbach RK, Vaka D, Butte AJ, Kay MA, Sage J. Organ size control is dominant over Rb family inactivation to restrict proliferation in vivo. Cell Reports. 8: 371-81. PMID 25017070 DOI: 10.1016/j.celrep.2014.06.025  0.48
2014 Mazur PK, Reynoird N, Khatri P, Jansen PW, Wilkinson AW, Liu S, Barbash O, Van Aller GS, Huddleston M, Dhanak D, Tummino PJ, Kruger RG, Garcia BA, Butte AJ, Vermeulen M, et al. SMYD3 links lysine methylation of MAP3K2 to Ras-driven cancer. Nature. 510: 283-7. PMID 24847881 DOI: 10.1038/nature13320  0.48
2014 Bhattacharya S, Andorf S, Gomes L, Dunn P, Schaefer H, Pontius J, Berger P, Desborough V, Smith T, Campbell J, Thomson E, Monteiro R, Guimaraes P, Walters B, Wiser J, ... Butte AJ, et al. ImmPort: disseminating data to the public for the future of immunology. Immunologic Research. 58: 234-9. PMID 24791905 DOI: 10.1007/s12026-014-8516-1  0.48
2014 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. 6: 234ra57. PMID 24786325 DOI: 10.1126/scitranslmed.3007191  0.72
2014 Shaikh AR, Butte AJ, Schully SD, Dalton WS, Khoury MJ, Hesse BW. Collaborative biomedicine in the age of big data: the case of cancer. Journal of Medical Internet Research. 16: e101. PMID 24711045 DOI: 10.2196/jmir.2496  0.48
2014 de Jesus Perez VA, Yuan K, Lyuksyutova MA, Dewey F, Orcholski ME, Shuffle EM, Mathur M, Yancy L, Rojas V, Li CG, Cao A, Alastalo TP, Khazeni N, Cimprich KA, Butte AJ, et al. Whole-exome sequencing reveals TopBP1 as a novel gene in idiopathic pulmonary arterial hypertension. American Journal of Respiratory and Critical Care Medicine. 189: 1260-72. PMID 24702692 DOI: 10.1164/rccm.201310-1749OC  0.48
2014 Chen R, Khatri P, Mazur PK, Polin M, Zheng Y, Vaka D, Hoang CD, Shrager J, Xu Y, Vicent S, Butte AJ, Sweet-Cordero EA. A meta-analysis of lung cancer gene expression identifies PTK7 as a survival gene in lung adenocarcinoma. Cancer Research. 74: 2892-902. PMID 24654231 DOI: 10.1158/0008-5472.CAN-13-2775  0.48
2014 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, ... ... Butte AJ, et al. Mutations in NGLY1 cause an inherited disorder of the endoplasmic reticulum-associated degradation pathway. Genetics in Medicine : Official Journal of the American College of Medical Genetics. 16: 751-8. PMID 24651605 DOI: 10.1038/gim.2014.22  0.48
2014 Dewey FE, Grove ME, Pan C, Goldstein BA, Bernstein JA, Chaib H, Merker JD, Goldfeder RL, Enns GM, David SP, Pakdaman N, Ormond KE, Caleshu C, Kingham K, Klein TE, ... ... Butte AJ, et al. Clinical interpretation and implications of whole-genome sequencing. Jama. 311: 1035-45. PMID 24618965 DOI: 10.1001/jama.2014.1717  0.48
2014 Patel CJ, Yang T, Hu Z, Wen Q, Sung J, El-Sayed YY, Cohen H, Gould J, Stevenson DK, Shaw GM, Ling XB, Butte AJ. Investigation of maternal environmental exposures in association with self-reported preterm birth. Reproductive Toxicology (Elmsford, N.Y.). 45: 1-7. PMID 24373932 DOI: 10.1016/j.reprotox.2013.12.005  0.48
2013 Patel CJ, Chen R, Kodama K, Ioannidis JP, Butte AJ. Systematic identification of interaction effects between validated genome- and environment-wide associations on Type 2 Diabetes Mellitus. Amia Joint Summits On Translational Science Proceedings Amia Summit On Translational Science. 2013: 135. PMID 24303322  0.48
2013 Liu LY, Yang T, Ji J, Wen Q, Morgan AA, Jin B, Chen G, Lyell DJ, Stevenson DK, Ling XB, Butte AJ. Integrating multiple 'omics' analyses identifies serological protein biomarkers for preeclampsia. Bmc Medicine. 11: 236. PMID 24195779 DOI: 10.1186/1741-7015-11-236  0.48
2013 Khatri P, Roedder S, Kimura N, De Vusser K, Morgan AA, Gong Y, Fischbein MP, Robbins RC, Naesens M, Butte AJ, Sarwal MM. A common rejection module (CRM) for acute rejection across multiple organs identifies novel therapeutics for organ transplantation. The Journal of Experimental Medicine. 210: 2205-21. PMID 24127489 DOI: 10.1084/jem.20122709  0.48
2013 Jahchan NS, Dudley JT, Mazur PK, Flores N, Yang D, Palmerton A, Zmoos AF, Vaka D, Tran KQ, Zhou M, Krasinska K, Riess JW, Neal JW, Khatri P, Park KS, ... Butte AJ, et al. A drug repositioning approach identifies tricyclic antidepressants as inhibitors of small cell lung cancer and other neuroendocrine tumors. Cancer Discovery. 3: 1364-77. PMID 24078773 DOI: 10.1158/2159-8290.CD-13-0183  0.48
2013 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 Medicine. 5: 58. PMID 23806097 DOI: 10.1186/gm462  0.48
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 Medical Genetics. 14: 62. PMID 23786662 DOI: 10.1186/1471-2350-14-62  0.48
2013 Butte AJ, Ohno-Machado L. Making it personal: translational bioinformatics. Journal of the American Medical Informatics Association : Jamia. 20: 595-6. PMID 23757438 DOI: 10.1136/amiajnl-2013-002028  0.32
2013 Auerbach RK, Chen B, Butte AJ. Relating genes to function: identifying enriched transcription factors using the ENCODE ChIP-Seq significance tool. Bioinformatics (Oxford, England). 29: 1922-4. PMID 23732275 DOI: 10.1093/bioinformatics/btt316  0.48
2013 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 Genetics. 9: e1003447. PMID 23717210 DOI: 10.1371/journal.pgen.1003447  0.48
2013 Karczewski KJ, Dudley JT, Kukurba KR, Chen R, Butte AJ, Montgomery SB, Snyder M. Systematic functional regulatory assessment of disease-associated variants. Proceedings of the National Academy of Sciences of the United States of America. 110: 9607-12. PMID 23690573 DOI: 10.1073/pnas.1219099110  0.72
2013 Sigdel TK, Shoemaker LD, Chen R, Li L, Butte AJ, Sarwal MM, Steinberg GK. Immune response profiling identifies autoantibodies specific to Moyamoya patients. Orphanet Journal of Rare Diseases. 8: 45. PMID 23518061 DOI: 10.1186/1750-1172-8-45  0.48
2013 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. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 224-35. PMID 23424127  0.48
2013 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. Human Genetics. 132: 495-508. PMID 23334806 DOI: 10.1007/s00439-012-1258-z  0.48
2012 Salih DA, Rashid AJ, Colas D, de la Torre-Ubieta L, Zhu RP, Morgan AA, Santo EE, Ucar D, Devarajan K, Cole CJ, Madison DV, Shamloo M, Butte AJ, Bonni A, Josselyn SA, et al. FoxO6 regulates memory consolidation and synaptic function. Genes & Development. 26: 2780-801. PMID 23222102 DOI: 10.1101/gad.208926.112  0.48
2012 Tzoulaki I, Patel CJ, Okamura T, Chan Q, Brown IJ, Miura K, Ueshima H, Zhao L, Van Horn L, Daviglus ML, Stamler J, Butte AJ, Ioannidis JP, Elliott P. A nutrient-wide association study on blood pressure. Circulation. 126: 2456-64. PMID 23093587 DOI: 10.1161/CIRCULATIONAHA.112.114058  0.48
2012 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, Bormann Chung CA, Stanley S, ... ... Butte AJ, et al. Population genetic inference from personal genome data: impact of ancestry and admixture on human genomic variation. American Journal of Human Genetics. 91: 660-71. PMID 23040495 DOI: 10.1016/j.ajhg.2012.08.025  0.48
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, ... ... Butte AJ, et al. A peripheral blood diagnostic test for acute rejection in renal transplantation. American Journal of Transplantation : Official Journal of the American Society of Transplantation and the American Society of Transplant Surgeons. 12: 2710-8. PMID 23009139 DOI: 10.1111/j.1600-6143.2012.04253.x  0.48
2012 Vicent S, Sayles LC, Vaka D, Khatri P, Gevaert O, Chen R, Zheng Y, Gillespie AK, Clarke N, Xu Y, Shrager J, Hoang CD, Plevritis S, Butte AJ, Sweet-Cordero EA. Cross-species functional analysis of cancer-associated fibroblasts identifies a critical role for CLCF1 and IL-6 in non-small cell lung cancer in vivo. Cancer Research. 72: 5744-56. PMID 22962265 DOI: 10.1158/0008-5472.CAN-12-1097  0.48
2012 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. 13: 440. PMID 22938532 DOI: 10.1186/1471-2164-13-440  0.48
2012 Haeberle H, Dudley JT, Liu JT, Butte AJ, Contag CH. Identification of cell surface targets through meta-analysis of microarray data. Neoplasia (New York, N.Y.). 14: 666-9. PMID 22904683 DOI: 10.1593/neo.12634  0.48
2012 Califano A, Butte AJ, Friend S, Ideker T, Schadt E. Leveraging models of cell regulation and GWAS data in integrative network-based association studies. Nature Genetics. 44: 841-7. PMID 22836096 DOI: 10.1038/ng.2355  0.48
2012 Kang HP, Morgan AA, Chen R, Schadt EE, Butte AJ. Coanalysis of GWAS with eQTLs reveals disease-tissue associations. Amia Joint Summits On Translational Science Proceedings Amia Summit On Translational Science. 2012: 35-41. PMID 22779046  0.48
2012 Chen R, Dudley JT, Ruau D, Butte AJ. Quantifying multi-ethnic representation in genetic studies of high mortality diseases. Amia Joint Summits On Translational Science Proceedings Amia Summit On Translational Science. 2012: 11-8. PMID 22779041  0.72
2012 Morgan AA, Chen R, Butte AJ. Clinical utility of sequence-based genotype compared with that derivable from genotyping arrays. Journal of the American Medical Informatics Association : Jamia. 19: e21-7. PMID 22718036 DOI: 10.1136/amiajnl-2011-000737  0.48
2012 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 (Oxford, England). 28: i121-6. PMID 22689751 DOI: 10.1093/bioinformatics/bts229  0.48
2012 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 Computational Biology. 8: e1002538. PMID 22685391 DOI: 10.1371/journal.pcbi.1002538  0.48
2012 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 Research. 22: 1383-94. PMID 22665443 DOI: 10.1101/gr.133702.111  0.48
2012 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. 55: 2205-13. PMID 22584726 DOI: 10.1007/s00125-012-2568-3  0.48
2012 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 demonstrate extreme directional differentiation among human populations, compared to other diseases. Plos Genetics. 8: e1002621. PMID 22511877 DOI: 10.1371/journal.pgen.1002621  0.72
2012 Kodama K, Horikoshi M, Toda K, Yamada S, Hara K, Irie J, Sirota M, Morgan AA, Chen R, Ohtsu H, Maeda S, Kadowaki T, Butte AJ. Expression-based genome-wide association study links the receptor CD44 in adipose tissue with type 2 diabetes. Proceedings of the National Academy of Sciences of the United States of America. 109: 7049-54. PMID 22499789 DOI: 10.1073/pnas.1114513109  0.48
2012 Chen R, Mias GI, Li-Pook-Than J, Jiang L, Lam HY, Chen R, Miriami E, Karczewski KJ, Hariharan M, Dewey FE, Cheng Y, Clark MJ, Im H, Habegger L, Balasubramanian S, ... ... Butte AJ, et al. Personal omics profiling reveals dynamic molecular and medical phenotypes. Cell. 148: 1293-307. PMID 22424236 DOI: 10.1016/j.cell.2012.02.009  0.48
2012 Dudley JT, Chen R, Sanderford M, Butte AJ, Kumar S. Evolutionary meta-analysis of association studies reveals ancient constraints affecting disease marker discovery. Molecular Biology and Evolution. 29: 2087-94. PMID 22389448 DOI: 10.1093/molbev/mss079  0.48
2012 Khatri P, Sirota M, Butte AJ. Ten years of pathway analysis: current approaches and outstanding challenges. Plos Computational Biology. 8: e1002375. PMID 22383865 DOI: 10.1371/journal.pcbi.1002375  0.48
2012 Morgan AA, Pyrgos VJ, Nadeau KC, Williamson PR, Butte AJ. Multiplex meta-analysis of RNA expression to identify genes with variants associated with immune dysfunction. Journal of the American Medical Informatics Association : Jamia. 19: 284-8. PMID 22319178 DOI: 10.1136/amiajnl-2011-000657  0.48
2012 Lam HY, Clark MJ, Chen R, Chen R, Natsoulis G, O'Huallachain M, Dewey FE, Habegger L, Ashley EA, Gerstein MB, Butte AJ, Ji HP, Snyder M. Performance comparison of whole-genome sequencing platforms. Nature Biotechnology. 30: 78-82. PMID 22178993 DOI: 10.1038/nbt.2065  0.48
2012 Liu LY, Schaub MA, Sirota M, Butte AJ. Sex differences in disease risk from reported genome-wide association study findings. Human Genetics. 131: 353-64. PMID 21858542 DOI: 10.1007/s00439-011-1081-y  0.48
2012 Liu LY, Schaub MA, Sirota M, Butte AJ. Transmission distortion in Crohn's disease risk gene ATG16L1 leads to sex difference in disease association. Inflammatory Bowel Diseases. 18: 312-22. PMID 21618365 DOI: 10.1002/ibd.21781  0.48
2011 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 (Oxford, England). 27: 3317-8. PMID 21967760 DOI: 10.1093/bioinformatics/btr548  0.48
2011 Clark MJ, Chen R, Lam HY, Karczewski KJ, Chen R, Euskirchen G, Butte AJ, Snyder M. Performance comparison of exome DNA sequencing technologies. Nature Biotechnology. 29: 908-14. PMID 21947028 DOI: 10.1038/nbt.1975  0.48
2011 Dewey FE, Chen R, Cordero SP, Ormond KE, Caleshu C, Karczewski KJ, Whirl-Carrillo M, Wheeler MT, Dudley JT, Byrnes JK, Cornejo OE, Knowles JW, Woon M, Sangkuhl K, Gong L, ... ... Butte AJ, et al. Phased whole-genome genetic risk in a family quartet using a major allele reference sequence. Plos Genetics. 7: e1002280. PMID 21935354 DOI: 10.1371/journal.pgen.1002280  0.72
2011 Naesens M, Khatri P, Li L, Sigdel TK, Vitalone MJ, Chen R, Butte AJ, Salvatierra O, Sarwal MM. Progressive histological damage in renal allografts is associated with expression of innate and adaptive immunity genes. Kidney International. 80: 1364-76. PMID 21881554 DOI: 10.1038/ki.2011.245  0.48
2011 Sirota M, Dudley JT, Kim J, Chiang AP, Morgan AA, Sweet-Cordero A, Sage J, Butte AJ. Discovery and preclinical validation of drug indications using compendia of public gene expression data. Science Translational Medicine. 3: 96ra77. PMID 21849665 DOI: 10.1126/scitranslmed.3001318  0.48
2011 Dudley JT, Sirota M, Shenoy M, Pai RK, Roedder S, Chiang AP, Morgan AA, Sarwal MM, Pasricha PJ, Butte AJ. Computational repositioning of the anticonvulsant topiramate for inflammatory bowel disease. Science Translational Medicine. 3: 96ra76. PMID 21849664 DOI: 10.1126/scitranslmed.3002648  0.48
2011 Yu M, Eckart MR, Morgan AA, Mukai K, Butte AJ, Tsai M, Galli SJ. Identification of an IFN-γ/mast cell axis in a mouse model of chronic asthma. The Journal of Clinical Investigation. 121: 3133-43. PMID 21737883 DOI: 10.1172/JCI43598  0.48
2011 Khatri P, Sarwal MM, Butte AJ. Applications of translational bioinformatics in transplantation. Clinical Pharmacology and Therapeutics. 90: 323-7. PMID 21716268 DOI: 10.1038/clpt.2011.120  0.48
2011 Dudley JT, Deshpande T, Butte AJ. Exploiting drug-disease relationships for computational drug repositioning. Briefings in Bioinformatics. 12: 303-11. PMID 21690101 DOI: 10.1093/bib/bbr013  0.48
2011 Butte AJ, Shah NH. Computationally translating molecular discoveries into tools for medicine: translational bioinformatics articles now featured in JAMIA. Journal of the American Medical Informatics Association : Jamia. 18: 352-3. PMID 21672904 DOI: 10.1136/amiajnl-2011-000343  0.48
2011 Sarkar IN, Butte AJ, Lussier YA, Tarczy-Hornoch P, Ohno-Machado L. Translational bioinformatics: linking knowledge across biological and clinical realms. Journal of the American Medical Informatics Association : Jamia. 18: 354-7. PMID 21561873 DOI: 10.1136/amiajnl-2011-000245  0.48
2011 Ruau D, Mbagwu M, Dudley JT, Krishnan V, Butte AJ. Comparison of automated and human assignment of MeSH terms on publicly-available molecular datasets. Journal of Biomedical Informatics. 44: S39-43. PMID 21420508 DOI: 10.1016/j.jbi.2011.03.007  0.72
2011 Sarwal MM, Benjamin J, Butte AJ, Davis MM, Wood K, Chapman J. Transplantomics and biomarkers in organ transplantation: a report from the first international conference. Transplantation. 91: 379-82. PMID 21278631 DOI: 10.1097/TP.0b013e3182105fb8  0.48
2011 Sharaf RN, Butte AJ, Montgomery KD, Pai R, Dudley JT, Pasricha PJ. Computational prediction and experimental validation associating FABP-1 and pancreatic adenocarcinoma with diabetes. Bmc Gastroenterology. 11: 5. PMID 21251264 DOI: 10.1186/1471-230X-11-5  0.48
2011 Dudley JT, Chen R, Butte AJ. Matching cancer genomes to established cell lines for personalized oncology. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 243-52. PMID 21121052  0.72
2011 Chen R, Butte AJ. The reference human genome demonstrates high risk of type 1 diabetes and other disorders. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 231-42. PMID 21121051  0.48
2010 Engreitz JM, Morgan AA, Dudley JT, Chen R, Thathoo R, Altman RB, Butte AJ. Content-based microarray search using differential expression profiles. Bmc Bioinformatics. 11: 603. PMID 21172034 DOI: 10.1186/1471-2105-11-603  0.48
2010 Dudley JT, Butte AJ. In silico research in the era of cloud computing. Nature Biotechnology. 28: 1181-5. PMID 21057489 DOI: 10.1038/nbt1110-1181  0.72
2010 Tatonetti NP, Dudley JT, Sagreiya H, Butte AJ, Altman RB. An integrative method for scoring candidate genes from association studies: application to warfarin dosing. Bmc Bioinformatics. 11: S9. PMID 21044367 DOI: 10.1186/1471-2105-11-S9-S9  0.72
2010 Morgan AA, Khatri P, Jones RH, Sarwal MM, Butte AJ. Comparison of multiplex meta analysis techniques for understanding the acute rejection of solid organ transplants. Bmc Bioinformatics. 11: S6. PMID 21044364 DOI: 10.1186/1471-2105-11-S9-S6  0.48
2010 Chen DP, Dudley JT, Butte AJ. Latent physiological factors of complex human diseases revealed by independent component analysis of clinarrays. Bmc Bioinformatics. 11: S4. PMID 21044362 DOI: 10.1186/1471-2105-11-S9-S4  0.48
2010 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. 5: e13574. PMID 21042586 DOI: 10.1371/journal.pone.0013574  0.48
2010 Chen R, Sigdel TK, Li L, Kambham N, Dudley JT, Hsieh 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 protein biomarkers for cross-organ transplant rejection and other conditions. Plos Computational Biology. 6. PMID 20885780 DOI: 10.1371/journal.pcbi.1000940  0.48
2010 Zheng M, Ravindran P, Wang J, Epstein RH, Chen DP, Butte AJ, Peltz G. Special article: an optimistic prognosis for the clinical utility of laboratory test data. Anesthesia and Analgesia. 111: 1026-35. PMID 20810674 DOI: 10.1213/ANE.0b013e3181efff0c  0.48
2010 Corona E, Dudley JT, Butte AJ. Extreme evolutionary disparities seen in positive selection across seven complex diseases. Plos One. 5: e12236. PMID 20808933 DOI: 10.1371/journal.pone.0012236  0.48
2010 Wilson KD, Hu S, Venkatasubrahmanyam S, Fu JD, Sun N, Abilez OJ, Baugh JJ, Jia F, Ghosh Z, Li RA, Butte AJ, Wu JC. Dynamic microRNA expression programs during cardiac differentiation of human embryonic stem cells: role for miR-499. Circulation. Cardiovascular Genetics. 3: 426-35. PMID 20733065 DOI: 10.1161/CIRCGENETICS.109.934281  0.48
2010 Dudley JT, Pouliot Y, Chen R, Morgan AA, Butte AJ. Translational bioinformatics in the cloud: an affordable alternative. Genome Medicine. 2: 51. PMID 20691073 DOI: 10.1186/gm172  0.48
2010 Dudley JT, Schadt E, Sirota M, Butte AJ, Ashley E. Drug discovery in a multidimensional world: systems, patterns, and networks. Journal of Cardiovascular Translational Research. 3: 438-47. PMID 20677029 DOI: 10.1007/s12265-010-9214-6  0.72
2010 Dudley JT, Butte AJ. Biomarker and drug discovery for gastroenterology through translational bioinformatics. Gastroenterology. 139: 735-41, 741.e1. PMID 20650279 DOI: 10.1053/j.gastro.2010.07.024  0.72
2010 Ober C, Butte AJ, Elias JA, Lusis AJ, Gan W, Banks-Schlegel S, Schwartz D. Getting from genes to function in lung disease: a National Heart, Lung, and Blood Institute workshop report. American Journal of Respiratory and Critical Care Medicine. 182: 732-7. PMID 20558629 DOI: 10.1164/rccm.201002-0180PP  0.48
2010 Morgan AA, Chen R, Butte AJ. Likelihood ratios for genome medicine. Genome Medicine. 2: 30. PMID 20497613 DOI: 10.1186/gm151  0.48
2010 Ashley EA, Butte AJ, Wheeler MT, Chen R, Klein TE, Dewey FE, Dudley JT, Ormond KE, Pavlovic A, Morgan AA, Pushkarev D, Neff NF, Hudgins L, Gong L, Hodges LM, et al. Clinical assessment incorporating a personal genome. Lancet (London, England). 375: 1525-35. PMID 20435227 DOI: 10.1016/S0140-6736(10)60452-7  0.72
2010 Shen-Orr SS, Tibshirani R, Khatri P, Bodian DL, Staedtler F, Perry NM, Hastie T, Sarwal MM, Davis MM, Butte AJ. Cell type-specific gene expression differences in complex tissues. Nature Methods. 7: 287-9. PMID 20208531 DOI: 10.1038/nmeth.1439  0.48
2010 Suthram S, Dudley JT, Chiang AP, Chen R, Hastie TJ, Butte AJ. Network-based elucidation of human disease similarities reveals common functional modules enriched for pluripotent drug targets. Plos Computational Biology. 6: e1000662. PMID 20140234 DOI: 10.1371/journal.pcbi.1000662  0.48
2009 Dudley JT, Butte AJ. A quick guide for developing effective bioinformatics programming skills. Plos Computational Biology. 5: e1000589. PMID 20041221 DOI: 10.1371/journal.pcbi.1000589  0.72
2006 Butte AJ, Kohane IS. Creation and implications of a phenome-genome network. Nature Biotechnology. 24: 55-62. PMID 16404398 DOI: 10.1038/nbt1150  0.76
2005 Wolfe CJ, Kohane IS, Butte AJ. Systematic survey reveals general applicability of "guilt-by-association" within gene coexpression networks. Bmc Bioinformatics. 6: 227. PMID 16162296 DOI: 10.1186/1471-2105-6-227  0.76
2004 Kho AT, Zhao Q, Cai Z, Butte AJ, Kim JY, Pomeroy SL, Rowitch DH, Kohane IS. Conserved mechanisms across development and tumorigenesis revealed by a mouse development perspective of human cancers. Genes & Development. 18: 629-40. PMID 15075291 DOI: 10.1101/gad.1182504  0.48
2004 Allocco DJ, Kohane IS, Butte AJ. Quantifying the relationship between co-expression, co-regulation and gene function. Bmc Bioinformatics. 5: 18. PMID 15053845 DOI: 10.1186/1471-2105-5-18  0.76
2003 Patti ME, Butte AJ, Crunkhorn S, Cusi K, Berria R, Kashyap S, Miyazaki Y, Kohane I, Costello M, Saccone R, Landaker EJ, Goldfine AB, Mun E, DeFronzo R, Finlayson J, et al. Coordinated reduction of genes of oxidative metabolism in humans with insulin resistance and diabetes: Potential role of PGC1 and NRF1. Proceedings of the National Academy of Sciences of the United States of America. 100: 8466-71. PMID 12832613 DOI: 10.1073/pnas.1032913100  0.48
2003 Nimgaonkar A, Sanoudou D, Butte AJ, Haslett JN, Kunkel LM, Beggs AH, Kohane IS. Reproducibility of gene expression across generations of Affymetrix microarrays. Bmc Bioinformatics. 4: 27. PMID 12823866 DOI: 10.1186/1471-2105-4-27  0.76
2003 Lee K, Kohane IS, Butte AJ. PGAGENE: integrating quantitative gene-specific results from the NHLBI programs for genomic applications. Bioinformatics (Oxford, England). 19: 778-9. PMID 12691993  0.76
2002 Park PJ, Butte AJ, Kohane IS. Comparing expression profiles of genes with similar promoter regions. Bioinformatics (Oxford, England). 18: 1576-84. PMID 12490441  0.76
2002 Kuo WP, Jenssen TK, Butte AJ, Ohno-Machado L, Kohane IS. Analysis of matched mRNA measurements from two different microarray technologies. Bioinformatics (Oxford, England). 18: 405-12. PMID 11934739  0.76
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