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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
2023 Zack T, Lehman E, Suzgun M, Rodriguez JA, Celi LA, Gichoya J, Jurafsky D, Szolovits P, Bates DW, Abdulnour RE, Butte AJ, Alsentzer E. Assessing the potential of GPT-4 to perpetuate racial and gender biases in health care: a model evaluation study. The Lancet. Digital Health. 6: e12-e22. PMID 38123252 DOI: 10.1016/S2589-7500(23)00225-X  0.509
2023 Yeung AWK, Torkamani A, Butte AJ, Glicksberg BS, Schuller B, Rodriguez B, Ting DSW, Bates D, Schaden E, Peng H, Willschke H, van der Laak J, Car J, Rahimi K, Celi LA, et al. The promise of digital healthcare technologies. Frontiers in Public Health. 11: 1196596. PMID 37822534 DOI: 10.3389/fpubh.2023.1196596  0.631
2021 Rudrapatna VA, Glicksberg BS, Butte AJ. Utility of routinely collected electronic health records data to support effectiveness evaluations in inflammatory bowel disease: a pilot study of tofacitinib. Bmj Health & Care Informatics. 28. PMID 34011632 DOI: 10.1136/bmjhci-2021-100337  0.658
2020 Madhavan S, Bastarache L, Brown JS, Butte AJ, Dorr DA, Embi PJ, Friedman CP, Johnson KB, Moore JH, Kohane IS, Payne PRO, Tenenbaum JD, Weiner MG, Wilcox AB, Ohno-Machado L. Use of electronic health records to support a public health response to the COVID-19 pandemic in the United States: a perspective from 15 academic medical centers. Journal of the American Medical Informatics Association : Jamia. PMID 33260207 DOI: 10.1093/jamia/ocaa287  0.425
2020 Norgeot B, Quer G, Beaulieu-Jones BK, Torkamani A, Dias R, Gianfrancesco M, Arnaout R, Kohane IS, Saria S, Topol E, Obermeyer Z, Yu B, Butte AJ. Minimum information about clinical artificial intelligence modeling: the MI-CLAIM checklist. Nature Medicine. 26: 1320-1324. PMID 32908275 DOI: 10.1038/S41591-020-1041-Y  0.449
2020 Hu Z, Tang A, Singh J, Bhattacharya S, Butte AJ. A robust and interpretable end-to-end deep learning model for cytometry data. Proceedings of the National Academy of Sciences of the United States of America. PMID 32801215 DOI: 10.1073/Pnas.2003026117  0.31
2020 Norgeot B, Muenzen K, Peterson TA, Fan X, Glicksberg BS, Schenk G, Rutenberg E, Oskotsky B, Sirota M, Yazdany J, Schmajuk G, Ludwig D, Goldstein T, Butte AJ. Protected Health Information filter (Philter): accurately and securely de-identifying free-text clinical notes. Npj Digital Medicine. 3: 57. PMID 32337372 DOI: 10.1038/s41746-020-0258-y  0.676
2020 Rudrapatna VA, Glicksberg BS, Avila P, Harding-Theobald E, Wang C, Butte AJ. Accuracy of medical billing data against the electronic health record in the measurement of colorectal cancer screening rates. Bmj Open Quality. 9. PMID 32209595 DOI: 10.1136/bmjoq-2019-000856  0.645
2020 Rudrapatna VA, Butte AJ. Opportunities and challenges in using real-world data for health care. The Journal of Clinical Investigation. 130: 565-574. PMID 32011317 DOI: 10.1172/Jci129197  0.313
2019 Glicksberg BS, Oskotsky B, Giangreco N, Thangaraj PM, Rudrapatna V, Datta D, Frazier R, Lee N, Larsen R, Tatonetti NP, Butte AJ. ROMOP: a light-weight R package for interfacing with OMOP-formatted electronic health record data. Jamia Open. 2: 10-14. PMID 31633087 DOI: 10.1093/jamiaopen/ooy059  0.65
2019 Paik H, Kan MJ, Rappoport N, Hadley D, Sirota M, Chen B, Manber U, Cho SB, Butte AJ. Tracing diagnosis trajectories over millions of patients reveal an unexpected risk in schizophrenia. Scientific Data. 6: 201. PMID 31615985 DOI: 10.1038/S41597-019-0220-5  0.317
2019 Glicksberg BS, Oskotsky B, Thangaraj PM, Giangreco N, Badgeley MA, Johnson KW, Datta D, Rudrapatna V, Rappoport N, Shervey MM, Miotto R, Goldstein TC, Rutenberg E, Frazier R, Lee N, ... ... Butte AJ, et al. PatientExploreR: an extensible application for dynamic visualization of patient clinical history from Electronic Health Records in the OMOP Common Data Model Title. Bioinformatics (Oxford, England). PMID 31214700 DOI: 10.1093/Bioinformatics/Btz409  0.766
2019 Schüssler-Fiorenza Rose SM, Contrepois K, Moneghetti KJ, Zhou W, Mishra T, Mataraso S, Dagan-Rosenfeld O, Ganz AB, Dunn J, Hornburg D, Rego S, Perelman D, Ahadi S, Sailani MR, Zhou Y, ... ... Butte AJ, et al. A longitudinal big data approach for precision health. Nature Medicine. 25: 792-804. PMID 31068711 DOI: 10.1038/S41591-019-0414-6  0.337
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  0.642
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  0.352
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  0.642
2019 Cheng F, Liang H, Butte AJ, Eng C, Nussinov R. Personal Mutanomes Meet Modern Oncology Drug Discovery and Precision Health. Pharmacological Reviews. 71: 1-19. PMID 30545954 DOI: 10.1124/Pr.118.016253  0.34
2019 Datta D, Goldstein T, Butte A. Assessing real-world outcomes in precision oncology by linking clinical genomic testing to electronic medical records. Journal of Clinical Oncology. 37. DOI: 10.1200/Jco.2019.37.15_Suppl.E18091  0.313
2019 Rudrapatna V, Glicksberg B, Avila P, Harding-Theobald E, Wang C, Butte A. Tu1650 – Accuracy of Electronic Health Record Billing Data in the Measurement of Colorectal Cancer Screening Rates Gastroenterology. 156: S-1075-S-1076. DOI: 10.1016/S0016-5085(19)39654-4  0.659
2018 Rajkomar A, Oren E, Chen K, Dai AM, Hajaj N, Hardt M, Liu PJ, Liu X, Marcus J, Sun M, Sundberg P, Yee H, Zhang K, Zhang Y, Flores G, ... ... Butte AJ, et al. Scalable and accurate deep learning with electronic health records. Npj Digital Medicine. 1: 18. PMID 31304302 DOI: 10.1038/S41746-018-0029-1  0.301
2018 Sirota M, Thomas CG, Liu R, Zuhl M, Banerjee P, Wong RJ, Quaintance CC, Leite R, Chubiz J, Anderson R, Chappell J, Kim M, Grobman W, Zhang G, Rokas A, ... ... Butte AJ, et al. Enabling precision medicine in neonatology, an integrated repository for preterm birth research. Scientific Data. 5: 180219. PMID 30398470 DOI: 10.1038/Sdata.2018.219  0.309
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  0.679
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  0.651
2018 Rudrapatna VA, Butte AJ. Open data informatics and data repurposing for IBD. Nature Reviews. Gastroenterology & Hepatology. PMID 30061595 DOI: 10.1038/S41575-018-0050-5  0.326
2018 Bhattacharya S, Li J, Sockell A, Kan MJ, Bava FA, Chen SC, Ávila-Arcos MC, Ji X, Smith E, Asadi NB, Lachman RS, Lam HYK, Bustamante CD, Butte AJ, Nolan GP. Whole-genome sequencing of Atacama skeleton shows novel mutations linked with dysplasia. Genome Research. PMID 29567674 DOI: 10.1101/Gr.223693.117  0.311
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  0.32
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  0.309
2018 Rappoport N, Toung J, Hadley D, Wong RJ, Fujioka K, Reuter J, Abbott CW, Oh S, Hu D, Eng C, Huntsman S, Bodian DL, Niederhuber JE, Hong X, Zhang G, ... ... Butte AJ, et al. A genome-wide association study identifies only two ancestry specific variants associated with spontaneous preterm birth. Scientific Reports. 8: 226. PMID 29317701 DOI: 10.1038/S41598-017-18246-5  0.306
2017 Hadley D, Pan J, El-Sayed O, Aljabban J, Aljabban I, Azad TD, Hadied MO, Raza S, Rayikanti BA, Chen B, Paik H, Aran D, Spatz J, Himmelstein D, Panahiazar M, ... ... Butte AJ, et al. Precision annotation of digital samples in NCBI's gene expression omnibus. Scientific Data. 4: 170125. PMID 28925997 DOI: 10.1038/Sdata.2017.125  0.356
2017 Butte AJ. Big data opens a window onto wellness. Nature Biotechnology. 35: 720-721. PMID 28787419 DOI: 10.1038/Nbt.3934  0.323
2017 Chen B, Ma L, Paik H, Sirota M, Wei W, Chua MS, So S, Butte AJ. Reversal of cancer gene expression correlates with drug efficacy and reveals therapeutic targets. Nature Communications. 8: 16022. PMID 28699633 DOI: 10.1038/Ncomms16022  0.359
2017 Lasry A, Aran D, Butte AJ, Ben-Neriah Y. Cancer Cell-Autonomous Parainflammation Mimics Immune Cell Infiltration. Cancer Research. PMID 28667073 DOI: 10.1158/0008-5472.Can-16-3383  0.3
2017 Datta D, Goldstein T, Gu Z, Butte A. Abstract LB-006: Oncology model fidelity scores Cancer Research. 77. DOI: 10.1158/1538-7445.Am2017-Lb-006  0.323
2016 Pessetto ZY, Chen B, Alturkmani H, Hyter S, Flynn CA, Baltezor M, Ma Y, Rosenthal HG, Neville KA, Weir SJ, Butte AJ, Godwin AK. In silico and in vitro drug screening identifies new therapeutic approaches for Ewing sarcoma. Oncotarget. PMID 27863422 DOI: 10.18632/Oncotarget.13385  0.301
2016 Butte AJ. It takes a genome to understand a village: Population scale precision medicine. Proceedings of the National Academy of Sciences of the United States of America. 113: 12344-12346. PMID 27791179 DOI: 10.1073/Pnas.1615329113  0.311
2016 Amor M, Moreno-Viedma V, Sarabi A, Grün NG, Itariu B, Leitner L, Steiner I, Bilban M, Kodama K, Butte AJ, Staffler G, Zeyda M, Stulnig TM. Identification of matrix metalloproteinase-12 as a candidate molecule for prevention and treatment of cardiometabolic disease. Molecular Medicine (Cambridge, Mass.). 22. PMID 27385318 DOI: 10.2119/Molmed.2016.00068  0.307
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  0.317
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  0.342
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  0.308
2016 Godec J, Tan Y, Liberzon A, Tamayo P, Bhattacharya S, Butte AJ, Mesirov JP, Haining WN. Compendium of Immune Signatures Identifies Conserved and Species-Specific Biology in Response to Inflammation. Immunity. PMID 26795250 DOI: 10.1016/J.Immuni.2015.12.006  0.332
2016 Ma Y, Chen B, Weir SJ, Butte A, Godwin AK. Abstract B20: In silico and in vitro drug screening identifies new therapeutic approaches targeting DNA double-strand breaks repair in Ewing sarcoma Cancer Research. 76. DOI: 10.1158/1538-7445.Pedca15-B20  0.329
2015 Geifman N, Bhattacharya S, Butte AJ. Immune modulators in disease: integrating knowledge from the biomedical literature and gene expression. Journal of the American Medical Informatics Association : Jamia. PMID 26661719 DOI: 10.1093/Jamia/Ocv166  0.378
2015 Chen B, Butte AJ. Leveraging Big Data to Transform Target Selection and Drug Discovery. Clinical Pharmacology and Therapeutics. PMID 26659699 DOI: 10.1002/Cpt.318  0.342
2015 Aran D, Sirota M, Butte AJ. Systematic pan-cancer analysis of tumour purity. Nature Communications. 6: 8971. PMID 26634437 DOI: 10.1038/Ncomms9971  0.308
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  0.358
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  0.319
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  0.352
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  0.337
2015 Mazur PK, Reynoird N, Khatri P, Butte AJ, Wilkinson A, Garcia B, Liu S, Vermeulen M, Jansen PWTC, Tummino PJ, Kruger RG, Aller GSV, Barbash O, Huddleston M, Gozani O, et al. Abstract A23: SMYD3 links methylation of MAP3K2 to Ras-driven tumors Cancer Research. 75. DOI: 10.1158/1538-7445.Panca2014-A23  0.501
2015 Januszyk M, Jahchan N, Khatri P, Rennert RC, Sorkin M, Sage J, Longaker MT, Butte AJ, Gurtner GC. Abstract 172 Plastic and Reconstructive Surgery. 135: 120-121. DOI: 10.1097/01.Prs.0000465620.23775.46  0.444
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  0.489
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  0.335
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  0.709
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  0.539
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  0.357
2014 Jahchan NS, Dudley JT, Mazur PK, Flores N, Yang D, Palmerton A, Zmoos A, Vaka D, Tran KQt, Zhou M, Krasinska K, Riess JW, Neal JW, Khatri P, Park KS, ... Butte AJ, et al. Abstract 4610: A drug repositioning approach identifies tricyclic antidepressants as inhibitors of small cell lung cancer and other neuroendocrine tumors Cancer Research. 74: 4610-4610. DOI: 10.1158/1538-7445.Am2014-4610  0.542
2014 Jahchan N, Joel D, Mazur P, Neal J, Khatri P, Butte A, Sage J. Abstract IA02: A drug repositioning approach identifies tricyclic antidepressants as inhibitors of small cell lung cancer. Clinical Cancer Research. 20: IA02-IA02. DOI: 10.1158/1078-0432.14AACRIASLC-IA02  0.452
2014 Januszyk M, Rennert R, Sorkin M, Khatri P, Butte A, Gurtner G. Integration of Public Microarray Data with Single Cell Gene Expression Profiling Facilitates Identification of Transcriptionally-Defined Subpopulations in Small Cell Lung Cancer Journal of Surgical Research. 186: 558-559. DOI: 10.1016/J.Jss.2013.11.471  0.546
2014 Butte AJ. Translating a Trillion Points of Data into Therapies, Diagnostics, and New Insights into Disease Biophysical Journal. 106. DOI: 10.1016/J.Bpj.2013.11.1353  0.372
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  0.515
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  0.713
2013 Kido T, Kawashima M, Nishino S, Swan M, Kamatani N, Butte AJ. Systematic evaluation of personal genome services for Japanese individuals. Journal of Human Genetics. 58: 734-41. PMID 24067293 DOI: 10.1038/Jhg.2013.96  0.324
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  0.457
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  0.412
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  0.348
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  0.317
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  0.418
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  0.71
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  0.446
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  0.433
2013 Szabo LA, Khatri P, Liu X, Hu Z, Ling B, Butte AJ. Abstract B20: Identification of novel biomarkers for early detection of ovarian cancer Clinical Cancer Research. 19. DOI: 10.1158/1078-0432.Ovca13-B20  0.548
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  0.42
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  0.581
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  0.465
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  0.443
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  0.661
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  0.355
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  0.67
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  0.4
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  0.441
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  0.688
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  0.705
2012 Butte AJ, Ito S. Translational bioinformatics: data-driven drug discovery and development. Clinical Pharmacology and Therapeutics. 91: 949-52. PMID 22609903 DOI: 10.1038/Clpt.2012.55  0.359
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  0.339
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  0.67
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  0.417
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  0.7
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  0.703
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  0.545
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  0.353
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  0.42
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  0.346
2012 Vicent S, Gillespie AK, Vakaa D, Khatri P, Chen R, Gevaert O, Clarke N, Plevritis S, Butte A, Sweet-Cordero A. Abstract A41: SOX11 transcriptionally regulates a cytokine-based gene signature in lung cancer-associated fibroblasts (LCAF) to promote tumor growth Clinical Cancer Research. 18: A41-A41. DOI: 10.1158/1078-0432.12Aacriaslc-A41  0.539
2012 Vitalone M, Khatri P, Hsieh S, Naesens M, Butte A, Sarwal M. Specific miRNAʼs and their Downstream Targets Are Associated with Acute Rejection in Pediatric Renal Allografts Transplantation Journal. 94: 116. DOI: 10.1097/00007890-201211271-00214  0.476
2012 Lam HYK, 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. Erratum: Corrigendum: Performance comparison of whole-genome sequencing platforms Nature Biotechnology. 30: 562-562. DOI: 10.1038/Nbt0612-562E  0.366
2011 Kim Y, Khatri P, Park K, Dudley J, Sage J, Butte A. Identification of serum protein biomarkers for small cell lung cancer. Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology. 29: e21005. PMID 28022393 DOI: 10.1200/Jco.2011.29.15_Suppl.E21005  0.715
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  0.701
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  0.397
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  0.685
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  0.568
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  0.665
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  0.662
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  0.514
2011 Sirota M, Butte AJ. The role of bioinformatics in studying rheumatic and autoimmune disorders. Nature Reviews. Rheumatology. 7: 489-94. PMID 21691330 DOI: 10.1038/Nrrheum.2011.87  0.377
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  0.654
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  0.355
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  0.359
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  0.667
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  0.636
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  0.668
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  0.356
2011 Califano A, Butte A, Friend S, Ideker T, Schadt EE. Integrative Network-based Association Studies: Leveraging cell regulatory models in the post-GWAS era Nature Precedings. DOI: 10.1038/Npre.2011.5732.1  0.379
2011 Pan S, Dewey FE, Perez MV, Knowles JW, Chen R, Butte AJ, Ashley EA. Personalized Medicine and Cardiovascular Disease: From Genome to Bedside Current Cardiovascular Risk Reports. 5: 542-551. DOI: 10.1007/S12170-011-0202-4  0.326
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  0.701
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  0.606
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  0.66
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  0.516
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  0.662
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  0.423
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  0.689
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  0.658
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  0.682
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  0.657
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  0.633
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  0.361
2010 Patel CJ, Bhattacharya J, Butte AJ. An Environment-Wide Association Study (EWAS) on type 2 diabetes mellitus. Plos One. 5: e10746. PMID 20505766 DOI: 10.1371/Journal.Pone.0010746  0.315
2010 Morgan AA, Chen R, Butte AJ. Likelihood ratios for genome medicine. Genome Medicine. 2: 30. PMID 20497613 DOI: 10.1186/Gm151  0.448
2010 Lussier YA, Butte AJ, Hunter L. Current methodologies for translational bioinformatics. Journal of Biomedical Informatics. 43: 355-7. PMID 20470899 DOI: 10.1016/J.Jbi.2010.05.002  0.354
2010 Patel CJ, Butte AJ. Predicting environmental chemical factors associated with disease-related gene expression data. Bmc Medical Genomics. 3: 17. PMID 20459635 DOI: 10.1186/1755-8794-3-17  0.351
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  0.682
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  0.53
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  0.706
2010 Morgan AA, Dudley JT, Deshpande T, Butte AJ. Dynamism in gene expression across multiple studies. Physiological Genomics. 40: 128-40. PMID 19920211 DOI: 10.1152/Physiolgenomics.90403.2008  0.656
2010 Morgan AA, Chen R, Butte AJ, Ashley EA. Clinical assessment incorporating a personal genome – Authors' reply The Lancet. 376: 869-870. DOI: 10.1016/S0140-6736(10)61405-5  0.393
2010 Sharaf R, Butte AJ, Montgomery KD, Pai RK, Dudley JT, Pasricha PJ. 103 Computational Prediction and Experimental Validation of FABP-1 as a Putative Biomarker for Pancreatic Adenocarcinoma: A Novel Approach to Biomarker Discovery for Gastrointestinal Disorders Gastroenterology. 138: S-19. DOI: 10.1016/S0016-5085(10)60086-8  0.627
2010 Shen-Orr S, Gaidarski A, Tibshirani R, Khatri P, Davis M, Butte A. Extracting Cell-type-specific Gene Expression Differences from Complex Tissues Clinical Immunology. 135: S10. DOI: 10.1016/J.Clim.2010.03.037  0.504
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  0.624
2009 Sirota M, Schaub MA, Batzoglou S, Robinson WH, Butte AJ. Autoimmune disease classification by inverse association with SNP alleles. Plos Genetics. 5: e1000792. PMID 20041220 DOI: 10.1371/Journal.Pgen.1000792  0.344
2009 Sridhar K, Ross DT, Tibshirani R, Butte AJ, Greenberg PL. Relationship of differential gene expression profiles in CD34+ myelodysplastic syndrome marrow cells to disease subtype and progression. Blood. 114: 4847-58. PMID 19801443 DOI: 10.1182/Blood-2009-08-236422  0.329
2009 Dudley JT, Tibshirani R, Deshpande T, Butte AJ. Disease signatures are robust across tissues and experiments. Molecular Systems Biology. 5: 307. PMID 19756046 DOI: 10.1038/Msb.2009.66  0.668
2009 Butte AJ. Translational bioinformatics applications in genome medicine. Genome Medicine. 1: 64. PMID 19566916 DOI: 10.1186/Gm64  0.355
2009 Schaub MA, Kaplow IM, Sirota M, Do CB, Butte AJ, Batzoglou S. A Classifier-based approach to identify genetic similarities between diseases. Bioinformatics (Oxford, England). 25: i21-9. PMID 19477990 DOI: 10.1093/Bioinformatics/Btp226  0.343
2009 Aebersold R, Auffray C, Baney E, Barillot E, Brazma A, Brett C, Brunak S, Butte A, Califano A, Celis J, Cufer T, Ferrell J, Galas D, Gallahan D, Gatenby R, et al. Report on EU-USA workshop: how systems biology can advance cancer research (27 October 2008). Molecular Oncology. 3: 9-17. PMID 19383362 DOI: 10.1016/J.Molonc.2008.11.003  0.343
2009 Li L, Wadia P, Chen R, Kambham N, Naesens M, Sigdel TK, Miklos DB, Sarwal MM, Butte AJ. Identifying compartment-specific non-HLA targets after renal transplantation by integrating transcriptome and "antibodyome" measures. Proceedings of the National Academy of Sciences of the United States of America. 106: 4148-53. PMID 19251643 DOI: 10.1073/Pnas.0900563106  0.382
2009 Dudley JT, Butte AJ. Identification of discriminating biomarkers for human disease using integrative network biology. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 27-38. PMID 19209693  0.648
2009 Shah NH, Jonquet C, Chiang AP, Butte AJ, Chen R, Musen MA. Ontology-driven indexing of public datasets for translational bioinformatics. Bmc Bioinformatics. 10: S1. PMID 19208184 DOI: 10.1186/1471-2105-10-S2-S1  0.472
2009 Chiang AP, Butte AJ. Data-driven methods to discover molecular determinants of serious adverse drug events. Clinical Pharmacology and Therapeutics. 85: 259-68. PMID 19177064 DOI: 10.1038/Clpt.2008.274  0.353
2009 English SB, Shih SC, Ramoni MF, Smith LE, Butte AJ. Use of Bayesian networks to probabilistically model and improve the likelihood of validation of microarray findings by RT-PCR. Journal of Biomedical Informatics. 42: 287-95. PMID 18790084 DOI: 10.1016/J.Jbi.2008.08.009  0.304
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. 9: 548. PMID 19094235 DOI: 10.1186/1471-2105-9-548  0.469
2008 Chen R, Morgan AA, Dudley J, Deshpande T, Li L, Kodama K, Chiang AP, Butte AJ. FitSNPs: highly differentially expressed genes are more likely to have variants associated with disease. Genome Biology. 9: R170. PMID 19061490 DOI: 10.1186/Gb-2008-9-12-R170  0.697
2008 Tenenbaum JD, Walker MG, Utz PJ, Butte AJ. Expression-based Pathway Signature Analysis (EPSA): mining publicly available microarray data for insight into human disease. Bmc Medical Genomics. 1: 51. PMID 18937865 DOI: 10.1186/1755-8794-1-51  0.364
2008 Kodama K, Butte AJ, Creusot RJ, Su L, Sheng D, Hartnett M, Iwai H, Soares LR, Fathman CG. Tissue- and age-specific changes in gene expression during disease induction and progression in NOD mice. Clinical Immunology (Orlando, Fla.). 129: 195-201. PMID 18801706 DOI: 10.1016/J.Clim.2008.07.028  0.315
2008 Butte AJ. Translational bioinformatics: coming of age. Journal of the American Medical Informatics Association. 15: 709-714. PMID 18755990 DOI: 10.1197/Jamia.M2824  0.314
2008 Butte AJ. Medicine. The ultimate model organism. Science (New York, N.Y.). 320: 325-7. PMID 18420921 DOI: 10.1126/Science.1158343  0.318
2008 Dudley J, Butte AJ. Enabling integrative genomic analysis of high-impact human diseases through text mining Pacific Symposium On Biocomputing 2008, Psb 2008. 580-591. PMID 18229717  0.666
2008 Chen R, Li L, Butte AJ. AILUN: reannotating gene expression data automatically. Nature Methods. 4: 879. PMID 17971777 DOI: 10.1038/Nmeth1107-879  0.425
2008 Sarwal M, Li L, Wadia P, Chen R, Naesens M, Miklos D, Butte A. INTEGRATIVE GENOMICS TO IDENTIFY NON-HLA ALLOGENIC KIDNEY-SPECIFIC TARGETS AFTER KIDNEY TRANSPLANTATION Transplantation. 86: 13. DOI: 10.1097/01.Tp.0000332715.73087.A0  0.386
2007 Lin YA, Chiang A, Lin R, Yao P, Chen R, Butte AJ. Methodologies for extracting functional pharmacogenomic experiments from international repository. Amia ... Annual Symposium Proceedings / Amia Symposium. Amia Symposium. 463-7. PMID 18693879  0.364
2007 English SB, Butte AJ. Evaluation and integration of 49 genome-wide experiments and the prediction of previously unknown obesity-related genes Bioinformatics. 23: 2910-2917. PMID 17921495 DOI: 10.1093/Bioinformatics/Btm483  0.304
2007 Butte AJ, Chen R. Finding disease-related genomic experiments within an international repository: first steps in translational bioinformatics. Amia ... Annual Symposium Proceedings. Amia Symposium. 106-10. PMID 17238312  0.385
2007 Kodama K, Dang D, Holness C, Iwai H, Hartnett M, Butte A, Fathman CG. Identification of Candidate IDDM Disease Susceptibility Genes in the Idd Regions of NOD Mice by Temporal Microarray Gene Expression Data Analysis Clinical Immunology. 123: S19. DOI: 10.1016/J.Clim.2007.03.222  0.333
2006 Balboni I, Chan SM, Kattah M, Tenenbaum JD, Butte AJ, Utz PJ. Multiplexed protein array platforms for analysis of autoimmune diseases. Annual Review of Immunology. 24: 391-418. PMID 16551254 DOI: 10.1146/Annurev.Immunol.24.021605.090709  0.341
2006 Butte AJ, Kohane IS. Creation and implications of a phenome-genome network. Nature Biotechnology. 24: 55-62. PMID 16404398 DOI: 10.1038/Nbt1150  0.532
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  0.504
2004 Csoka AB, English SB, Simkevich CP, Ginzinger DG, Butte AJ, Schatten GP, Rothman FG, Sedivy JM. Genome-scale expression profiling of Hutchinson-Gilford progeria syndrome reveals widespread transcriptional misregulation leading to mesodermal/mesenchymal defects and accelerated atherosclerosis. Aging Cell. 3: 235-43. PMID 15268757 DOI: 10.1111/J.1474-9728.2004.00105.X  0.339
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  0.486
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  0.507
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  0.454
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  0.506
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 DOI: 10.1093/Bioinformatics/Btg066  0.529
2002 Park PJ, Butte AJ, Kohane IS. Comparing expression profiles of genes with similar promoter regions. Bioinformatics (Oxford, England). 18: 1576-84. PMID 12490441 DOI: 10.1093/Bioinformatics/18.12.1576  0.483
2002 Butte A. The use and analysis of microarray data. Nature Reviews. Drug Discovery. 1: 951-60. PMID 12461517 DOI: 10.1038/Nrd961  0.4
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 DOI: 10.1093/Bioinformatics/18.3.405  0.464
2001 Butte AJ, Bao L, Reis BY, Watkins TW, Kohane IS. Comparing the similarity of time-series gene expression using signal processing metrics Journal of Biomedical Informatics. 34: 396-405. PMID 12198759 DOI: 10.1006/Jbin.2002.1037  0.472
2001 Butte AJ, Dzau VJ, Glueck SB. Further defining housekeeping, or "maintenance," genes Focus on "A compendium of gene expression in normal human tissues" Physiological Genomics. 7: 95-96. PMID 11773595 DOI: 10.1152/Physiolgenomics.2001.7.2.95  0.31
2001 Riva A, Mandl KD, Oh DH, Nigrin DJ, Butte AJ, Szolovits P, Kohane IS. The personal internetworked notary and guardian. International Journal of Medical Informatics. 62: 27-40. PMID 11340004 DOI: 10.1016/S1386-5056(00)00136-2  0.652
2001 Butte AJ, Reis B, Kho A, Sun Y, Kohane IS. Analyzing functional genomic differences yields oncogenes and chromosomal breakpoints in ALL and AML Nature Genetics. 27: 45-45. DOI: 10.1038/87022  0.45
2000 Butte AJ, Tamayo P, Slonim D, Golub TR, Kohane IS. Discovering functional relationships between RNA expression and chemotherapeutic susceptibility using relevance networks. Proceedings of the National Academy of Sciences of the United States of America. 97: 12182-6. PMID 11027309 DOI: 10.1073/Pnas.220392197  0.498
2000 Butte AJ, Kohane IS. Mutual information relevance networks: functional genomic clustering using pairwise entropy measurements. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 418-29. PMID 10902190 DOI: 10.1142/9789814447331_0040  0.432
1999 Butte AJ, Kohane IS. Using Cross-Validation to Find the Optimal Polynomial Model for Pediatric Anthropometric Time-Series Data Pediatric Research. 45: 86-86. DOI: 10.1203/00006450-199904020-00513  0.438
1999 Butte AJ, Kohane IS. Increasing Frequency of Diabetes Clinic Visits Is Associated with Improving Hemoglobin A1c Pediatric Research. 45: 86A-86A. DOI: 10.1203/00006450-199904020-00512  0.434
1999 Butte AJ, Kohane IS. The Relationship of Arm Span Vs. Height in Boys with Constitutional Delay and Boys and Girls with Short Stature Pediatric Research. 45: 86A-86A. DOI: 10.1203/00006450-199904020-00511  0.396
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