Atul Butte, MD, PhD

Professor

Atul Butte, MD, PhD
Priscilla Chan and Mark Zuckerberg Distinguished Professor of Pediatrics, Bioengineering and Therapeutic Sciences, and Epidemiology and Biostatistics at UCSF
Director, Bakar Computational Health Sciences Institute, UCSF
Chief Data Scientist, University of California Health System (UC Health)

Atul Butte, MD, PhD is the Priscilla Chan and Mark Zuckerberg Distinguished Professor and inaugural Director of the Bakar Computational Health Sciences Institute (bchsi.ucsf.edu) at the University of California, San Francisco (UCSF). Dr. Butte is also the Chief Data Scientist for the entire University of California Health System, the tenth largest by revenue in the United States, with 20 health professional schools, 6 medical schools, 6 academic health centers, 10 hospitals, and over 1000 care delivery sites. Dr. Butte has been continually funded by NIH for 20 years, is an inventor on 24 patents, and has authored nearly 300 publications, with research repeatedly featured in the New York Times, Wall Street Journal, and Wired Magazine. Dr. Butte was elected into the National Academy of Medicine in 2015, and in 2013, he was recognized by the Obama Administration as a White House Champion of Change in Open Science for promoting science through publicly available data. Dr. Butte is also a co-founder of three investor-backed data-driven companies: Personalis (IPO, 2019), providing medical genome sequencing services, Carmenta (acquired by Progenity, 2015), discovering diagnostics for pregnancy complications, and NuMedii, finding new uses for drugs through open molecular data. Dr. Butte trained in Computer Science at Brown University, worked as a software engineer at Apple and Microsoft, received his MD at Brown University, trained in Pediatrics and Pediatric Endocrinology at Children's Hospital Boston, then received his PhD from Harvard Medical School and MIT.
Education
Ph.D., 2004 - Health Sciences and Technology (HST), Harvard Medical School
M.D., 05/1995 - Medicine, Brown University School of Medicine
A.B. (Honors), 05/1991 - Computer Science, Brown University
Honors and Awards
  • Elected as Fellow, American Association for the Advancement of Science (AAAS), American Association for the Advancement of Science, 2023
  • Elected as Fellow, International Society for Computational Biology (ISCB), International Society for Computational Biology, 2021
  • Elected into the American Institute for Medical and Biological Engineering (AIMBE), American Institute for Medical and Biological Engineering, 2019
  • Elected into the American Institute for Medical and Biological Engineering (AIMBE), American Institute for Medical and Biological Engineering, 2019
  • Ruth B. Sauber Distinguished Medical Alumni Lecture and Award, Brown University School of Medicine, 2015
  • Elected into the National Academy of Medicine, National Academy of Medicine, 2015
  • WorldView Top 100 Most Influential People in Biotech, Scientific American, 2015
  • E. Mead Johnson Award, Society for Pediatric Research, 2014
  • Elected into the American Society of Clinical Investigation (ASCI), American Society of Clinical Investigation, 2013
  • Champion of Change in Open Science, Obama Administration White House, 2013
  • Eagle Scout, Boy Scouts of America, 1984
Websites
Publications

  1. Mehandru N, Miao BY, Almaraz ER, Sushil M, Butte AJ, Alaa A. Evaluating large language models as agents in the clinic. 2024. PMID: 38570554


  2. Silverman AL, Bhasuran B, Mosenia A, Yasini F, Ramasamy G, Banerjee I, Gupta S, Mardirossian T, Narain R, Sewell J, Butte AJ, Rudrapatna VA. Accurate, Robust, and Scalable Machine Abstraction of Mayo Endoscopic Subscores From Colonoscopy Reports. 2024. PMID: 38533919


  3. Patel PV, Zhang A, Bhasuran B, Ravindranath VG, Heyman MB, Verstraete SG, Butte AJ, Rosen MJ, Rudrapatna VA, ImproveCareNow Pediatric IBD Learning Health System. Real-world effectiveness of ustekinumab and vedolizumab in TNF-exposed pediatric patients with ulcerative colitis. 2024. PMID: 38482890


  4. Silverman AL, Sushil M, Bhasuran B, Ludwig D, Buchanan J, Racz R, Parakala M, El-Kamary S, Ahima O, Belov A, Choi L, Billings M, Li Y, Habal N, Liu Q, Tiwari J, Butte AJ, Rudrapatna VA. Algorithmic Identification of Treatment-Emergent Adverse Events From Clinical Notes Using Large Language Models: A Pilot Study in Inflammatory Bowel Disease. 2024. PMID: 38459719


  5. Miao BY, Sushil M, Xu A, Wang M, Arneson D, Berkley E, Subash M, Vashisht R, Rudrapatna V, Butte AJ. Characterisation of digital therapeutic clinical trials: a systematic review with natural language processing. 2024. PMID: 38395542


  6. Goldberg CB, Adams L, Blumenthal D, Brennan PF, Brown N, Butte AJ, Cheatham M, deBronkart D, Dixon J, Drazen J, Evans BJ, Hoffman SM, Holmes C, Lee P, Manrai AK, Omenn GS, Perlin JB, Ramoni R, Sapiro G, Sarkar R, Sood H, Vayena E, Kohane IS, RAISE Consortium. To do no harm - and the most good - with AI in health care. 2024. PMID: 38388841


  8. Sushil M, Zack T, Mandair D, Zheng Z, Wali A, Yu YN, Quan Y, Butte AJ. A comparative study of zero-shot inference with large language models and supervised modeling in breast cancer pathology classification. 2024. PMID: 38405831


  9. Zrubka Z, Kertész G, Gulácsi L, Czere J, Hölgyesi Á, Nezhad HM, Mosavi A, Kovács L, Butte AJ, Péntek M. The Reporting Quality of Machine Learning Studies on Pediatric Diabetes Mellitus: Systematic Review. 2024. PMID: 38241075


  10. Sushil M, Butte AJ, Schuit E, van Smeden M, Leeuwenberg AM. Cross-institution natural language processing for reliable clinical association studies: a methodological exploration. 2024. PMID: 38219811


  11. Sun S, Zack T, Williams CYK, Sushil M, Butte AJ. Topic modeling on clinical social work notes for exploring social determinants of health factors. 2024. PMID: 38223407


  12. 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. 2024. PMID: 38123252


  13. Wang Q, Tang T, Youlton N, Weldy C, Kenney A, Ronen O, Hughes J, Chin E, Sutton S, Agarwal A, Li X, Behr M, Kumbier K, Moravec C, Tang WHW, Margulies K, Cappola T, Butte A, Arnaout R, Brown J, Priest J, Parikh V, Yu B, Ashley E. Epistasis regulates genetic control of cardiac hypertrophy. 2023. PMID: 38045390


  14. Rudrapatna VA, Ravindranath VG, Arneson DV, Mosenia A, Butte AJ, Wang S. Personalizing treatment selection in Crohn's disease: a meta-analysis of individual participant data from fifteen randomized controlled trials. 2023. PMID: 37986977


  15. Wang Q, Tang TM, Youlton N, Weldy CS, Kenney AM, Ronen O, Hughes JW, Chin ET, Sutton SC, Agarwal A, Li X, Behr M, Kumbier K, Moravec CS, Tang WHW, Margulies KB, Cappola TP, Butte AJ, Arnaout R, Brown JB, Priest JR, Parikh VN, Yu B, Ashley EA. Epistasis regulates genetic control of cardiac hypertrophy. 2023. PMID: 37987017


  16. Rudrapatna VA, Ravindranath VG, Arneson DV, Mosenia A, Butte AJ, Wang S. Sequential regression and simulation: a method for estimating causal effects from heterogeneous clinical trials without a common control group. 2023. PMID: 37789257


  17. Vashisht R, Patel A, Dahm L, Han C, Medders KE, Mowers R, Byington CL, Koliwad SK, Butte AJ. Second-Line Pharmaceutical Treatments for Patients with Type 2 Diabetes. 2023. PMID: 37782497


  19. 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, Banach M, Kletecka-Pulker M, Kimberger O, Eils R, Islam SMS, Wong ST, Wong TY, Gao W, Brunak S, Atanasov AG. The promise of digital healthcare technologies. 2023. PMID: 37822534


  20. Silverman AL, Sushil M, Bhasuran B, Ludwig D, Buchanan J, Racz R, Parakala M, El-Kamary S, Ahima O, Belov A, Choi L, Billings M, Li Y, Habal N, Liu Q, Tiwari J, Butte AJ, Rudrapatna VA. Algorithmic identification of treatment-emergent adverse events from clinical notes using large language models: a pilot study in inflammatory bowel disease. 2023. PMID: 37732220


  21. Khera R, Butte AJ, Berkwits M, Hswen Y, Flanagin A, Park H, Curfman G, Bibbins-Domingo K. AI in Medicine-JAMA's Focus on Clinical Outcomes, Patient-Centered Care, Quality, and Equity. 2023. PMID: 37566406


  23. Patel S, Sparman NZR, Arneson D, Alvarsson A, Santos LC, Duesman SJ, Centonze A, Hathaway E, Ahn IS, Diamante G, Cely I, Cho CH, Talari NK, Rajbhandari AK, Goedeke L, Wang P, Butte AJ, Blanpain C, Chella Krishnan K, Lusis AJ, Stanley SA, Yang X, Rajbhandari P. Mammary duct luminal epithelium controls adipocyte thermogenic programme. 2023. PMID: 37495690


  24. Radhakrishnan L, Schenk G, Muenzen K, Oskotsky B, Ashouri Choshali H, Plunkett T, Israni S, Butte AJ. A certified de-identification system for all clinical text documents for information extraction at scale. 2023. PMID: 37416449


  25. Wang M, Slatter S, Sussell J, Lin CW, Ogale S, Datta D, Butte AJ, Bazhenova L, Rudrapatna VA. ALK Inhibitor Treatment Patterns and Outcomes in Real-World Patients with ALK-Positive Non-Small-Cell Lung Cancer: A Retrospective Cohort Study. 2023. PMID: 37341856


  27. Wang M, Goldgof GM, Patel A, Whitaker B, Belov A, Chan B, Phelps E, Rubin B, Anderson S, Butte AJ. Novel computational methods on electronic health record yields new estimates of transfusion-associated circulatory overload in populations enriched with high-risk patients. 2023. PMID: 37248741


  28. Farrand E, Gologorskaya O, Mills H, Radhakrishnan L, Collard HR, Butte AJ. Machine Learning Algorithm to Improve Cohort Identification in Interstitial Lung Disease. 2023. PMID: 36943196


  29. Kany S, Rämö JT, Hou C, Jurgens SJ, Nauffal V, Cunningham J, Lau ES, Butte AJ, Ho JE, Olgin JE, Elmariah S, Lindsay ME, Ellinor PT, Pirruccello JP. Assessment of valvular function in over 47,000 people using deep learning-based flow measurements. 2023. PMID: 37205587


  30. Binvignat M, Emond P, Mifsud F, Miao B, Courties A, Lef?vre A, Maheu E, Crema MD, Klatzmann D, Kloppenburg M, Richette P, Butte AJ, Mariotti-Ferrandiz E, Berenbaum F, Sokol H, Sellam J. Serum Tryptophan Metabolites are Associated with Erosive Hand Osteoarthritis and Pain: Results from the DIGICOD Cohort. 2023. PMID: 37105396


  31. Loy CJ, Sotomayor-Gonzalez A, Servellita V, Nguyen J, Lenz J, Bhattacharya S, Williams ME, Cheng AP, Bliss A, Saldhi P, Brazer N, Streithorst J, Suslovic W, Hsieh CJ, Bahar B, Wood N, Foresythe A, Gliwa A, Bhakta K, Perez MA, Hussaini L, Anderson EJ, Chahroudi A, Delaney M, Butte AJ, DeBiasi RL, Rostad CA, De Vlaminck I, Chiu CY. Nucleic acid biomarkers of immune response and cell and tissue damage in children with COVID-19 and MIS-C. 2023. PMID: 37279751


  32. Voss EA, Shoaibi A, Yin Hui Lai L, Blacketer C, Alshammari T, Makadia R, Haynes K, Sena AG, Rao G, van Sandijk S, Fraboulet C, Boyer L, Le Carrour T, Horban S, Morales DR, Martínez Roldán J, Ramírez-Anguita JM, Mayer MA, de Wilde M, John LH, Duarte-Salles T, Roel E, Pistillo A, Kolde R, Maljkovic F, Denaxas S, Papez V, Kahn MG, Natarajan K, Reich C, Secora A, Minty EP, Shah NH, Posada JD, Garcia Morales MT, Bosca D, Cadenas Juanino H, Diaz Holgado A, Pedrera Jiménez M, Serrano Balazote P, García Barrio N, Sen S, Üresin AY, Erdogan B, Belmans L, Byttebier G, Malbrain MLNG, Dedman DJ, Cuccu Z, Vashisht R, Butte AJ, Patel A, Dahm L, Han C, Bu F, Arshad F, Ostropolets A, Nyberg F, Hripcsak G, Suchard MA, Prieto-Alhambra D, Rijnbeek PR, Schuemie MJ, Ryan PB. Contextualising adverse events of special interest to characterise the baseline incidence rates in 24 million patients with COVID-19 across 26 databases: a multinational retrospective cohort study. 2023. PMID: 37034358


  33. Zack T, Losert KP, Maisel SM, Wild J, Yaqubie A, Herman M, Knox JJ, Mayer RJ, Venook AP, Butte A, O'Neill AF, Abou-Alfa GK, Gordan JD. Defining incidence and complications of fibrolamellar liver cancer through tiered computational analysis of clinical data. 2023. PMID: 36959495


  34. Rudrapatna VA, Cheng YW, Feuille C, Mosenia A, Shih J, Shi Y, Roberson O, Rubin B, Butte AJ, Mahadevan U, Skomrock N, Erondu N, Chehoud C, Rahim S, Apfel D, Curran M, Khan NS, O'Brien C, Terry N, Martini BD. Creation of an ustekinumab external control arm for Crohn's disease using electronic health records data: A pilot study. 2023. PMID: 36862717


  35. Bauchner H, McDermott MM, Butte AJ. Data Sharing Enters a New Era. 2023. PMID: 36848652


  36. Goldgof GM, Sun S, Van Cleave J, Wang L, Lucas F, Brown L, Spector JD, Boiocchi L, Baik J, Zhu M, Ardon O, Lu CM, Dogan A, Goldgof DB, Carmichael I, Prakash S, Butte AJ. DeepHeme: A generalizable, bone marrow classifier with hematopathologist-level performance. 2023. PMID: 36865216


  37. Rodriguez-Watson CV, Sheils NE, Louder AM, Eldridge EH, Lin ND, Pollock BD, Gatz JL, Grannis SJ, Vashisht R, Ghauri K, Valo G, Chakravarty AG, Lasky T, Jung M, Lovell SL, Major JM, Kabelac C, Knepper C, Leonard S, Embi PJ, Jenkinson WG, Klesh R, Garner OB, Patel A, Dahm L, Barin A, Cooper DM, Andriola T, Byington CL, Crews BO, Butte AJ, Allen J. Real-world utilization of SARS-CoV-2 serological testing in RNA positive patients across the United States. 2023. PMID: 36763574


  38. Rodriguez-Watson CV, Louder AM, Kabelac C, Frederick CM, Sheils NE, Eldridge EH, Lin ND, Pollock BD, Gatz JL, Grannis SJ, Vashisht R, Ghauri K, Knepper C, Leonard S, Embi PJ, Jenkinson G, Klesh R, Garner OB, Patel A, Dahm L, Barin A, Cooper DM, Andriola T, Byington CL, Crews BO, Butte AJ, Allen J. Real-world performance of SARS-Cov-2 serology tests in the United States, 2020. 2023. PMID: 36735683


  39. Binvignat M, Pires G, Tchitchek N, Costantino F, Courties A, Klatzmann D, Butte AJ, Combe B, Dougados M, Richette P, Mariotti-Ferrandiz E, Berenbaum F, Sellam J. Identification of Symptom Phenotypes of Hand Osteoarthritis Using Hierarchical Clustering: Results From the DIGICOD Cohort. 2022. PMID: 36263851


  40. Aras MA, Abreau S, Mills H, Radhakrishnan L, Klein L, Mantri N, Rubin B, Barrios J, Chehoud C, Kogan E, Gitton X, Nnewihe A, Quinn D, Bridges C, Butte AJ, Olgin JE, Tison GH. Electrocardiogram Detection of Pulmonary Hypertension Using Deep Learning. 2023. PMID: 36706977


  42. Huie JR, Vashisht R, Galivanche A, Hadjadj C, Morshed S, Butte AJ, Ferguson AR, O'Neill C. Toward a causal model of chronic back pain: Challenges and opportunities. 2023. PMID: 36714527


  43. Arvisais-Anhalt S, Ravi A, Weia B, Aarts J, Ahmad HB, Araj E, Bauml JA, Benham-Hutchins M, Boyd AD, Brecht-Doscher A, Butler-Henderson K, Butte A, Cardillo AB, Chilukuri N, Cho MK, Cohen JK, Craven CK, Crusco SJ, Dadabhoy F, Dash D, DeBolt C, Elkin PL, Fayanju OA, Fochtmann L, Graham JV, Hanna J, Hersh W, Hoffard MR, Hron J, Huang SS, Jackson BR, Kaplan B, Kelly W, Ko K, Koppel R, Kurapati N, Labbad G, Lee J, Lehmann CU, Leitner S, Liao ZC, Medford RJ, Melnick ER, Muniyappa AN, Murray S, Neinstein A, Nichols-Johnson V, Novak L, Ogan WS, Ozeran L, Pageler N, Pandita D, Perumbeti A, Petersen C, Pierce L, Puttagunta R, Ramaswamy P, Rogers KM, Rosenbloom T, Ryan A, Saleh S, Sarabu C, Schreiber R, Shaw KA, Sim I, Sirintrapun SJ, Solomonides A, Spector JD, Starren JB, Stoffel M, Subbian V, Swanson K, Tomes A, Trang K, Unertl KM, Weon JL, Whooley M, Wiley K, Williamson DF, Winkelstein P, Wong J, Xie J, Yarahuan JKW, Yung N, Zera C, Ratanawongsa N, Sadasivaiah S. Paging the Clinical Informatics Community: Respond STAT to Dobbs v Jackson's Women's Health Organization. 2022. PMID: 36535703


  45. Hu Z, van der Ploeg K, Chakraborty S, Arunachalam PS, Mori DAM, Jacobson KB, Bonilla H, Parsonnet J, Andrews JR, Holubar M, Subramanian A, Khosla C, Maldonado Y, Hedlin H, de la Parte L, Press K, Ty M, Tan GS, Blish C, Takahashi S, Rodriguez-Barraquer I, Greenhouse B, Butte AJ, Singh U, Pulendran B, Wang TT, Jagannathan P. Early immune markers of clinical, virological, and immunological outcomes in patients with COVID-19: a multi-omics study. 2022. PMID: 36239699


  47. Kornblith AE, Singh C, Devlin G, Addo N, Streck CJ, Holmes JF, Kuppermann N, Grupp-Phelan J, Fineman J, Butte AJ, Yu B. Predictability and stability testing to assess clinical decision instrument performance for children after blunt torso trauma. 2022. PMID: 36812570


  48. Padula WV, Kreif N, Vanness DJ, Adamson B, Rueda JD, Felizzi F, Jonsson P, IJzerman MJ, Butte A, Crown W. Machine Learning Methods in Health Economics and Outcomes Research-The PALISADE Checklist: A Good Practices Report of an ISPOR Task Force. 2022. PMID: 35779937


  49. Abernethy A, Adams L, Barrett M, Bechtel C, Brennan P, Butte A, Faulkner J, Fontaine E, Friedhoff S, Halamka J, Howell M, Johnson K, Long P, McGraw D, Miller R, Lee P, Perlin J, Rucker D, Sandy L, Savage L, Stump L, Tang P, Topol E, Tuckson R, Valdes K. The Promise of Digital Health: Then, Now, and the Future. 2022. PMID: 36177208


  50. Wong DR, Conrad J, Johnson N, Ayers J, Laeremans A, Lee JC, Lee J, Prusiner SB, Bandyopadhyay S, Butte AJ, Paras NA, Keiser MJ. Trans-channel fluorescence learning improves high-content screening for Alzheimer's disease therapeutics. 2022. PMID: 36276634


  51. Wong DR, Tang Z, Mew NC, Das S, Athey J, McAleese KE, Kofler JK, Flanagan ME, Borys E, White CL, Butte AJ, Dugger BN, Keiser MJ. Deep learning from multiple experts improves identification of amyloid neuropathologies. 2022. PMID: 35484610


  52. Binvignat M, Pedoia V, Butte AJ, Louati K, Klatzmann D, Berenbaum F, Mariotti-Ferrandiz E, Sellam J. Use of machine learning in osteoarthritis research: a systematic literature review. 2022. PMID: 35296530


  53. Maruthamuthu S, Rajalingam K, Kaur N, Morvan MG, Soto J, Lee N, Kong D, Hu Z, Reyes K, Ng D, Butte AJ, Chiu C, Rajalingam R. Individualized Constellation of Killer Cell Immunoglobulin-Like Receptors and Cognate HLA Class I Ligands that Controls Natural Killer Cell Antiviral Immunity Predisposes COVID-19. 2022. PMID: 35273641


  54. Hu Z, van der Ploeg K, Chakraborty S, Arunachalam P, Mori D, Jacobson K, Bonilla H, Parsonnet J, Andrews J, Hedlin H, de la Parte L, Dantzler K, Ty M, Tan G, Blish C, Takahashi S, Rodriguez-Barraquer I, Greenhouse B, Butte A, Singh U, Pulendran B, Wang T, Jagannathan P. Early immune responses have long-term associations with clinical, virologic, and immunologic outcomes in patients with COVID-19. 2022. PMID: 35132407


  56. Miao BY, Arneson D, Wang M, Butte AJ. Open challenges in developing digital therapeutics in the United States. 2022. PMID: 36812515


  58. Hu Z, Bhattacharya S, Butte AJ. Application of Machine Learning for Cytometry Data. 2022. PMID: 35046945


  59. Bishara A, Chiu C, Whitlock EL, Douglas VC, Lee S, Butte AJ, Leung JM, Donovan AL. Postoperative delirium prediction using machine learning models and preoperative electronic health record data. 2022. PMID: 34979919


  60. Cefalu WT, Andersen DK, Arreaza-Rubín G, Pin CL, Sato S, Verchere CB, Woo M, Rosenblum ND, Symposium planning committee, moderators, and speakers:, Rosenblum N, Cefalu W, Andersen DK, Arreaza-Rubín G, Dhara C, James SP, Makarchuk MJ, Pin CL, Sato S, Verchere B, Woo M, Powers A, Estall J, Hoesli C, Millman J, Linnemann A, Johnson J, Pin CL, Hawkins M, Woo M, Gloyn A, Cefalu W, Rosenblum N, Huising MO, Benninger RKP, Almaça J, Hull-Meichle RL, MacDonald P, Lynn F, Melero-Martin J, Yoshihara E, Stabler C, Sander M, Evans-Molina C, Engin F, Thompson P, Shalev A, Redondo MJ, Nadeau K, Bellin M, Udler MS, Dennis J, Dash S, Zhou W, Snyder M, Booth G, Butte A, Florez J. Heterogeneity of Diabetes: β-Cells, Phenotypes, and Precision Medicine: Proceedings of an International Symposium of the Canadian Institutes of Health Research's Institute of Nutrition, Metabolism and Diabetes and the U.S. National Institutes of Health's 2022. PMID: 34782355


  61. Bishara A, Wong A, Wang L, Chopra M, Fan W, Lin A, Fong N, Palacharla A, Spinner J, Armstrong R, Pletcher MJ, Lituiev D, Hadley D, Butte A. Opal: an implementation science tool for machine learning clinical decision support in anesthesia. 2021. PMID: 34837585


  62. Cefalu WT, Andersen DK, Arreaza-Rubín G, Pin CL, Sato S, Verchere CB, Woo M, Rosenblum ND, Symposium planning committee, moderators, and speakers:, Rosenblum N, Cefalu W, Andersen DK, Arreaza-Rubín G, Dhara C, James SP, Makarchuk MJ, Pin CL, Sato S, Verchere B, Woo M, Powers A, Estall J, Hoesli C, Millman J, Linnemann A, Johnson J, Pin CL, Hawkins M, Woo M, Gloyn A, Cefalu W, Rosenblum N, Huising MO, Benninger RKP, Almaça J, Hull-Meichle RL, MacDonald P, Lynn F, Melero-Martin J, Yoshihara E, Stabler C, Sander M, Evans-Molina C, Engin F, Thompson P, Shalev A, Redondo MJ, Nadeau K, Bellin M, Udler MS, Dennis J, Dash S, Zhou W, Snyder M, Booth G, Butte A, Florez J. Heterogeneity of Diabetes: β-Cells, Phenotypes, and Precision Medicine: Proceedings of an International Symposium of the Canadian Institutes of Health Research's Institute of Nutrition, Metabolism and Diabetes and the U.S. National Institutes of Health's 2021. PMID: 34957490


  63. Kornblith AE, Addo N, Dong R, Rogers R, Grupp-Phelan J, Butte A, Gupta P, Callcut RA, Arnaout R. Development and Validation of a Deep Learning Strategy for Automated View Classification of Pediatric Focused Assessment With Sonography for Trauma. 2021. PMID: 34741469


  64. Zhang B, Silverman AL, Bangaru S, Arneson D, Dasharathy S, Nguyen N, Rodden D, Shih J, Butte AJ, El-Nachef WN, Boland BS, Rudrapatna VA. Case-control study of the association of chronic acid suppression and social determinants of health with COVID-19 infection. 2021. PMID: 34697319


  65. Butte KD, Bahmani A, Butte AJ, Li X, Snyder MP. Five-year pediatric use of a digital wearable fitness device: lessons from a pilot case study. 2021. PMID: 34350390


  67. Kaur N, Bhattacharya S, Butte AJ. Big Data in Nephrology. 2021. PMID: 34194006


  69. Liu X, Anstey J, Li R, Sarabu C, Sono R, Butte AJ. Rethinking PICO in the Machine Learning Era: ML-PICO. 2021. PMID: 34010977


  71. Bhattacharya S, Hu Z, Butte AJ. Opportunities and Challenges in Democratizing Immunology Datasets. 2021. PMID: 33936065


  72. 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. 2020. PMID: 33260207


  74. Kwon DH, Vashisht R, Borno HT, Aggarwal RR, Small EJ, Butte AJ, Huang FW. Androgen deprivation therapy and SARS-CoV-2 in men with prostate cancer: findings from the University of California Health System registry. 2021. PMID: 33571636


  76. Vashisht R, Patel A, Crews BO, Garner OB, Dahm L, Wilson C, Butte AJ. Age- and Sex-Associated Variations in the Sensitivity of Serological Tests Among Individuals Infected With SARS-CoV-2. 2021. PMID: 33576815


  77. Nelson CA, Acuna AU, Paul AM, Scott RT, Butte AJ, Cekanaviciute E, Baranzini SE, Costes SV. Knowledge Network Embedding of Transcriptomic Data from Spaceflown Mice Uncovers Signs and Symptoms Associated with Terrestrial Diseases. 2021. PMID: 33445483


  80. Reznikov LR, Norris MH, Vashisht R, Bluhm AP, Li D, Liao YJ, Brown A, Butte AJ, Ostrov DA. Identification of antiviral antihistamines for COVID-19 repurposing. 2020. PMID: 33309272


  81. Moron-Lopez S, Telwatte S, Sarabia I, Battivelli E, Montano M, Macedo AB, Aran D, Butte AJ, Jones RB, Bosque A, Verdin E, Greene WC, Wong JK, Yukl SA. Human splice factors contribute to latent HIV infection in primary cell models and blood CD4+ T cells from ART-treated individuals. 2020. PMID: 33253324


  82. Arneson D, Elliott M, Mosenia A, Oskotsky B, Solodar S, Vashisht R, Zack T, Bleicher P, Butte AJ, Rudrapatna VA. CovidCounties is an interactive real time tracker of the COVID19 pandemic at the level of US counties. 2020. PMID: 33199721


  84. 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. 2020. PMID: 32908275


  85. Hu Z, Tang A, Singh J, Bhattacharya S, Butte AJ. A robust and interpretable end-to-end deep learning model for cytometry data. 2020. PMID: 32801215


  86. Arneson D, Elliott M, Mosenia A, Oskotsky B, Vashisht R, Zack T, Bleicher P, Butte AJ, Rudrapatna VA. CovidCounties - an interactive, real-time tracker of the COVID-19 pandemic at the level of US counties. 2020. PMID: 32511606


  87. 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. Volume 3. 2020. PMID: 32337372


  88. Rough K, Dai AM, Zhang K, Xue Y, Vardoulakis LM, Cui C, Butte AJ, Howell MD, Rajkomar A. Predicting inpatient medication orders from electronic health record data. Volume 108 of Issue 1. 2020. PMID: 32141068


  89. Kosti I, Lyalina S, Pollard KS, Butte AJ, Sirota M. Meta-Analysis of Vaginal Microbiome Data Provides New Insights Into Preterm Birth. Volume 11. 2020. PMID: 32322240


  90. Sim I, Stebbins M, Bierer BE, Butte AJ, Drazen J, Dzau V, Hernandez AF, Krumholz HM, Lo B, Munos B, Perakslis E, Rockhold F, Ross JS, Terry SF, Yamamoto KR, Zarin DA, Li R. Time for NIH to lead on data sharing. Volume 367 of Issue 6484. 2020. PMID: 32193313


  91. 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. Volume 9 of Issue 1. 2020. PMID: 32209595


  92. Kurnat-Thoma E, Baranova A, Baird P, Brodsky E, Butte AJ, Cheema AK, Cheng F, Dutta S, Grant C, Giordano J, Maitland-van der Zee AH, Fridsma DB, Jarrin R, Kann MG, Keeney J, Loscalzo J, Madhavan G, Maron BA, McBride DK, McKean M, Mun SK, Palmer JC, Patel B, Parakh K, Pariser AR, Pristipino C, Radstake TRDJ, Rajasimha HK, Rouse WB, Rozman D, Saleh A, Schmidt HHHW, Schultz N, Sethi T, Silverman EK, Skopac J, Svab I, Trujillo S, Valentine JE, Verma D, West BJ, Vasudevan S. Recent Advances in Systems and Network Medicine: Meeting Report from the First International Conference in Systems and Network Medicine. Volume 3 of Issue 1. 2020. PMID: 32226924


  94. Rudrapatna VA, Butte AJ. Opportunities and challenges in using real-world data for health care. Volume 130 of Issue 2. 2020. PMID: 32011317


  95. Farrand E, Vittinghoff E, Ley B, Butte AJ, Collard HR. Corticosteroid use is not associated with improved outcomes in acute exacerbation of IPF. Volume 25 of Issue 6. 2019. PMID: 31846126


  96. Telwatte S, Morón-López S, Aran D, Kim P, Hsieh C, Joshi S, Montano M, Greene WC, Butte AJ, Wong JK, Yukl SA. Heterogeneity in HIV and cellular transcription profiles in cell line models of latent and productive infection: implications for HIV latency. Volume 16 of Issue 1. 2019. PMID: 31711503


  97. Glicksberg BS, Oskotsky B, Thangaraj PM, Giangreco N, Badgeley MA, Johnson KW, Datta D, Rudrapatna VA, Rappoport N, Shervey MM, Miotto R, Goldstein TC, Rutenberg E, Frazier R, Lee N, Israni S, Larsen R, Percha B, Li L, Dudley JT, Tatonetti NP, Butte AJ. PatientExploreR: an extensible application for dynamic visualization of patient clinical history from electronic health records in the OMOP common data model. Volume 35 of Issue 21. 2019. PMID: 31214700


  98. 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. Volume 6 of Issue 1. 2019. PMID: 31615985


  99. Yu K, Chen B, Aran D, Charalel J, Yau C, Wolf DM, van 't Veer LJ, Butte AJ, Goldstein T, Sirota M. Comprehensive transcriptomic analysis of cell lines as models of primary tumors across 22 tumor types. Volume 10 of Issue 1. 2019. PMID: 31395879


  101. 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, Leopold SR, Chen J, Ashland M, Christle JW, Avina M, Limcaoco P, Ruiz C, Tan M, Butte AJ, Weinstock GM, Slavich GM, Sodergren E, McLaughlin TL, Haddad F, Snyder MP. A longitudinal big data approach for precision health. Volume 25 of Issue 5. 2019. PMID: 31068711


  102. Farrand E, Anstrom KJ, Bernard G, Butte AJ, Iribarren C, Ley B, Martinez FJ, Collard HR. Closing the Evidence Gap in Interstitial Lung Disease. The Promise of Real-World Data. Volume 199 of Issue 9. 2019. PMID: 30452876


  103. Chen J, Bhattacharya S, Sirota M, Laiudompitak S, Schaefer H, Thomson E, Wiser J, Sarwal MM, Butte AJ. Assessment of Postdonation Outcomes in US Living Kidney Donors Using Publicly Available Data Sets. Volume 2 of Issue 4. 2019. PMID: 30977847


  104. Hu Z, Glicksberg BS, Butte AJ. Robust prediction of clinical outcomes using cytometry data. Volume 35 of Issue 7. 2019. PMID: 30169745


  105. 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. Volume 2 of Issue 3. 2019. PMID: 30874779


  106. Andorf S, Bhattacharya S, Gaudilliere B, Shaw GM, Stevenson DK, Butte AJ, Sirota M. A pilot study showing a stronger H1N1 influenza vaccination response during pregnancy in women who subsequently deliver preterm. Volume 132. 2019. PMID: 30852461


  107. Wong DR, Bhattacharya S, Butte AJ. Prototype of running clinical trials in an untrustworthy environment using blockchain. Volume 10 of Issue 1. 2019. PMID: 30796226


  108. Aran D, Looney AP, Liu L, Wu E, Fong V, Hsu A, Chak S, Naikawadi RP, Wolters PJ, Abate AR, Butte AJ, Bhattacharya M. Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage. Volume 20 of Issue 2. 2019. PMID: 30643263


  109. 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. Volume 2 of Issue 1. 2019. PMID: 31633087


  110. Norgeot B, Glicksberg BS, Butte AJ. A call for deep-learning healthcare. Volume 25 of Issue 1. 2019. PMID: 30617337


  111. Saria S, Butte A, Sheikh A. Better medicine through machine learning: What's real, and what's artificial? Volume 15 of Issue 12. 2018. PMID: 30596635


  112. 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, Muglia LJ, Ober C, England SK, Macones G, Driscoll D, Parry S, Shaw GM, Stevenson DK, Simpson JL, Thomson E, Butte AJ. Author Correction: Enabling precision medicine in neonatology, an integrated repository for preterm birth research. Volume 5 of Issue 1. 2018. PMID: 30563979


  113. Cheng F, Liang H, Butte AJ, Eng C, Nussinov R. Personal Mutanomes Meet Modern Oncology Drug Discovery and Precision Health. Volume 71 of Issue 1. 2018. PMID: 30545954


  114. Rudrapatna VA, Butte AJ. Open data informatics and data repurposing for IBD. Volume 15 of Issue 12. 2018. PMID: 30061595


  115. 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. Volume 25 of Issue 7. 2018. PMID: 30428364


  116. 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, England SK, Parry S, Shaw GM, Simpson JL, Thomson E, Butte AJ. Enabling precision medicine in neonatology, an integrated repository for preterm birth research. Volume 5. 2018. PMID: 30398470


  117. Rappoport N, Paik H, Oskotsky B, Tor R, Ziv E, Zaitlen N, Butte AJ. Comparing Ethnicity-Specific Reference Intervals for Clinical Laboratory Tests from EHR Data. 2018. PMID: 33636914


  118. 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. Volume 25 of Issue 2. 2018. PMID: 30304689


  119. 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. MetaCyto: A Tool for Automated Meta-analysis of Mass and Flow Cytometry Data. Volume 24 of Issue 5. 2018. PMID: 30067990


  120. 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, Duggan GE, Irvine J, Le Q, Litsch K, Mossin A, Tansuwan J, Wexler J, Wilson J, Ludwig D, Volchenboum SL, Chou K, Pearson M, Madabushi S, Shah NH, Butte AJ, Howell MD, Cui C, Corrado GS, Dean J. Scalable and accurate deep learning with electronic health records. Volume 1. 2018. PMID: 31304302


  121. Nolan G, Butte A. The Atacama skeleton. Volume 28 of Issue 5. 2018. PMID: 29602903


  122. 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. Volume 28 of Issue 4. 2018. PMID: 29567674


  123. 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. Volume 5. 2018. PMID: 29485622


  124. 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? Volume 11 of Issue 1. 2018. PMID: 29351777


  125. 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, Sikora-Wohfeld W, Gignoux CR, Wang H, Oehlert J, Jelliffe-Pawlowski LL, Gould JB, Darmstadt GL, Wang X, Bustamante CD, Snyder MP, Ziv E, Patsopoulos NA, Muglia LJ, Burchard E, Shaw GM, O'Brodovich HM, Stevenson DK, Butte AJ, Sirota M. A genome-wide association study identifies only two ancestry specific variants associated with spontaneous preterm birth. Volume 8 of Issue 1. 2018. PMID: 29317701


  126. Wise PH, Shaw GM, Druzin ML, Darmstadt GL, Quaintance C, Mäkinen E, Relman DA, Quake SR, Butte AJ, Angst MS, Muglia LJ, Macones G, Driscoll D, Ober C, Simpson JL, Katz M, Howse J, Stevenson DK. Risky Business: Meeting the Structural Needs of Transdisciplinary Science. Volume 191. 2017. PMID: 29173314


  127. Aran D, Hu Z, Butte AJ. xCell: digitally portraying the tissue cellular heterogeneity landscape. Volume 18 of Issue 1. 2017. PMID: 29141660


  128. Mirza AN, Fry MA, Urman NM, Atwood SX, Roffey J, Ott GR, Chen B, Lee A, Brown AS, Aasi SZ, Hollmig T, Ator MA, Dorsey BD, Ruggeri BR, Zificsak CA, Sirota M, Tang JY, Butte A, Epstein E, Sarin KY, Oro AE. Combined inhibition of atypical PKC and histone deacetylase 1 is cooperative in basal cell carcinoma treatment. Volume 2 of Issue 21. 2017. PMID: 29093271


  129. Meehan TF, Conte N, Goldstein T, Inghirami G, Murakami MA, Brabetz S, Gu Z, Wiser JA, Dunn P, Begley DA, Krupke DM, Bertotti A, Bruna A, Brush MH, Byrne AT, Caldas C, Christie AL, Clark DA, Dowst H, Dry JR, Doroshow JH, Duchamp O, Evrard YA, Ferretti S, Frese KK, Goodwin NC, Greenawalt D, Haendel MA, Hermans E, Houghton PJ, Jonkers J, Kemper K, Khor TO, Lewis MT, Lloyd KCK, Mason J, Medico E, Neuhauser SB, Olson JM, Peeper DS, Rueda OM, Seong JK, Trusolino L, Vinolo E, Wechsler-Reya RJ, Weinstock DM, Welm A, Weroha SJ, Amant F, Pfister SM, Kool M, Parkinson H, Butte AJ, Bult CJ. PDX-MI: Minimal Information for Patient-Derived Tumor Xenograft Models. Volume 77 of Issue 21. 2017. PMID: 29092942


  130. Jaffee EM, Dang CV, Agus DB, Alexander BM, Anderson KC, Ashworth A, Barker AD, Bastani R, Bhatia S, Bluestone JA, Brawley O, Butte AJ, Coit DG, Davidson NE, Davis M, DePinho RA, Diasio RB, Draetta G, Frazier AL, Futreal A, Gambhir SS, Ganz PA, Garraway L, Gerson S, Gupta S, Heath J, Hoffman RI, Hudis C, Hughes-Halbert C, Ibrahim R, Jadvar H, Kavanagh B, Kittles R, Le QT, Lippman SM, Mankoff D, Mardis ER, Mayer DK, McMasters K, Meropol NJ, Mitchell B, Naredi P, Ornish D, Pawlik TM, Peppercorn J, Pomper MG, Raghavan D, Ritchie C, Schwarz SW, Sullivan R, Wahl R, Wolchok JD, Wong SL, Yung A. Future cancer research priorities in the USA: a Lancet Oncology Commission. Volume 18 of Issue 11. 2017. PMID: 29208398


  131. Aran D, Camarda R, Odegaard J, Paik H, Oskotsky B, Krings G, Goga A, Sirota M, Butte AJ. Comprehensive analysis of normal adjacent to tumor transcriptomes. Volume 8 of Issue 1. 2017. PMID: 29057876


  132. 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, Bhattacharya S, Sirota M, Musen MA, Butte AJ. Precision annotation of digital samples in NCBI's gene expression omnibus. Volume 4. 2017. PMID: 28925997


  133. Butte AJ. Big data opens a window onto wellness. Volume 35 of Issue 8. 2017. PMID: 28787419


  134. 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. Volume 8. 2017. PMID: 28699633


  135. Lasry A, Aran D, Butte AJ, Ben-Neriah Y. Cancer Cell-Autonomous Parainflammation Mimics Immune Cell Infiltration. Volume 77 of Issue 14. 2017. PMID: 28667073


  136. Shankar RD, Bhattacharya S, Jujjavarapu C, Andorf S, Wiser JA, Butte AJ. RImmPort: an R/Bioconductor package that enables ready-for-analysis immunology research data. Volume 33 of Issue 7. 2017. PMID: 28057685


  138. Geifman N, Brinton RD, Kennedy RE, Schneider LS, Butte AJ. Evidence for benefit of statins to modify cognitive decline and risk in Alzheimer's disease. Volume 9 of Issue 1. 2017. PMID: 28212683


  139. 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. Volume 8 of Issue 3. 2017. PMID: 27863422


  140. Vodovotz Y, Xia A, Read EL, Bassaganya-Riera J, Hafler DA, Sontag E, Wang J, Tsang JS, Day JD, Kleinstein SH, Butte AJ, Altman MC, Hammond R, Sealfon SC. Solving Immunology? Volume 38 of Issue 2. 2016. PMID: 27986392


  141. Paik H, Chen B, Sirota M, Hadley D, Butte AJ. Integrating Clinical Phenotype and Gene Expression Data to Prioritize Novel Drug Uses. Volume 5 of Issue 11. 2016. PMID: 27860440


  142. Butte AJ. It takes a genome to understand a village: Population scale precision medicine. Volume 113 of Issue 44. 2016. PMID: 27791179


  143. Shen-Orr SS, Furman D, Kidd BA, Hadad F, Lovelace P, Huang YW, Rosenberg-Hasson Y, Mackey S, Grisar FA, Pickman Y, Maecker HT, Chien YH, Dekker CL, Wu JC, Butte AJ, Davis MM. Defective Signaling in the JAK-STAT Pathway Tracks with Chronic Inflammation and Cardiovascular Risk in Aging Humans. Volume 3 of Issue 4. 2016. PMID: 27746093


  144. Hughey JJ, Butte AJ. Differential Phasing between Circadian Clocks in the Brain and Peripheral Organs in Humans. Volume 31 of Issue 6. 2016. PMID: 27702781


  145. Aran D, Butte AJ. Digitally deconvolving the tumor microenvironment. Volume 17 of Issue 1. 2016. PMID: 27549319


  146. Aran D, Lasry A, Zinger A, Biton M, Pikarsky E, Hellman A, Butte AJ, Ben-Neriah Y. Widespread parainflammation in human cancer. Volume 17 of Issue 1. 2016. PMID: 27386949


  147. 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. Volume 22. 2016. PMID: 27385318


  148. 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. Volume 7. 2016. PMID: 27324848


  150. Kosti I, Jain N, Aran D, Butte AJ, Sirota M. Cross-tissue Analysis of Gene and Protein Expression in Normal and Cancer Tissues. Volume 6. 2016. PMID: 27142790


  151. 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. Volume 12 of Issue 4. 2016. PMID: 27115429


  152. 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. Volume 65 of Issue 5. 2016. PMID: 26983959


  153. Chen B, Butte AJ. Leveraging big data to transform target selection and drug discovery. Volume 99 of Issue 3. 2016. PMID: 26659699


  154. Aran D, Sirota M, Butte AJ. Corrigendum: Systematic pan-cancer analysis of tumour purity. Volume 7. 2016. PMID: 26848121


  155. Hughey JJ, Hastie T, Butte AJ. ZeitZeiger: supervised learning for high-dimensional data from an oscillatory system. Volume 44 of Issue 8. 2016. PMID: 26819407


  156. 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. Volume 44 of Issue 1. 2016. PMID: 26795250


  158. 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. Volume 35 of Issue 3. 2015. PMID: 26707089


  159. Geifman N, Bhattacharya S, Butte AJ. Immune modulators in disease: integrating knowledge from the biomedical literature and gene expression. Volume 23 of Issue 3. 2015. PMID: 26661719


  160. Aran D, Sirota M, Butte AJ. Systematic pan-cancer analysis of tumour purity. Volume 6. 2015. PMID: 26634437


  161. Geifman N, Bollyky J, Bhattacharya S, Butte AJ. Opening clinical trial data: are the voluntary data-sharing portals enough? Volume 13. 2015. PMID: 26560699


  162. Chen B, Greenside P, Paik H, Sirota M, Hadley D, Butte AJ. Relating Chemical Structure to Cellular Response: An Integrative Analysis of Gene Expression, Bioactivity, and Structural Data Across 11,000 Compounds. Volume 4 of Issue 10. 2015. PMID: 26535158


  163. 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. Volume 17. 2015. PMID: 26387933


  164. 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, Garcia S, Chandratillake G, Kirk S, Ashley E, Snyder M, Altman R, Bustamante C, Butte AJ, West J, Chen R. Achieving high-sensitivity for clinical applications using augmented exome sequencing. Volume 7. 2015. PMID: 26269718


  165. 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. Volume 42 of Issue 9. 2015. PMID: 26408095


  166. 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. Volume 8 Suppl 2. 2015. PMID: 26043652


  167. Rehm HL, Berg JS, Brooks LD, Bustamante CD, Evans JP, Landrum MJ, Ledbetter DH, Maglott DR, Martin CL, Nussbaum RL, Plon SE, Ramos EM, Sherry ST, Watson MS. ClinGen--the Clinical Genome Resource. Volume 372 of Issue 23. 2015. PMID: 26014595


  168. 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. Volume 58 of Issue 7. 2015. PMID: 25952479


  169. Bollyky JB, Xu P, Butte AJ, Wilson DM, Beam CA, Greenbaum CJ. Heterogeneity in recent-onset type 1 diabetes - a clinical trial perspective. Volume 31 of Issue 6. 2015. PMID: 25689602


  170. Li J, Zheng S, Chen B, Butte AJ, Swamidass SJ, Lu Z. A survey of current trends in computational drug repositioning. Volume 17 of Issue 1. 2015. PMID: 25832646


  171. Hughey JJ, Butte AJ. Robust meta-analysis of gene expression using the elastic net. Volume 43 of Issue 12. 2015. PMID: 25829177


  172. 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. Volume 5. 2015. PMID: 25739475


  173. 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. Volume 160 of Issue 1-2. 2015. PMID: 25594173


  174. 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. 2015. PMID: 25592598


  176. Duscher D, Rennert RC, Januszyk M, Anghel E, Maan ZN, Whittam AJ, Perez MG, Kosaraju R, Hu MS, Walmsley GG, Atashroo D, Khong S, Butte AJ, Gurtner GC. Aging disrupts cell subpopulation dynamics and diminishes the function of mesenchymal stem cells. Volume 4. 2014. PMID: 25413454


  179. 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. Volume 8 of Issue 2. 2014. PMID: 25017070


  180. 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, Sage J, Gozani O. SMYD3 links lysine methylation of MAP3K2 to Ras-driven cancer. Volume 510 of Issue 7504. 2014. PMID: 24847881


  181. 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, Ashley E, Zamanian RT. Whole-exome sequencing reveals TopBP1 as a novel gene in idiopathic pulmonary arterial hypertension. Volume 189 of Issue 10. 2014. PMID: 24702692


  182. 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. ImmPort: disseminating data to the public for the future of immunology. Volume 58 of Issue 2-3. 2014. PMID: 24791905


  183. 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. Volume 6 of Issue 234. 2014. PMID: 24786325


  184. Januszyk M, Sorkin M, Glotzbach JP, Vial IN, Maan ZN, Rennert RC, Duscher D, Thangarajah H, Longaker MT, Butte AJ, Gurtner GC. Diabetes irreversibly depletes bone marrow-derived mesenchymal progenitor cell subpopulations. Volume 63 of Issue 9. 2014. PMID: 24740572


  185. Shaikh AR, Butte AJ, Schully SD, Dalton WS, Khoury MJ, Hesse BW. Collaborative biomedicine in the age of big data: the case of cancer. Volume 16 of Issue 4. 2014. PMID: 24711045


  186. 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. Volume 74 of Issue 10. 2014. PMID: 24654231


  187. 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, Chen R, Clark MJ, Haraksingh R, 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. Volume 16 of Issue 10. 2014. PMID: 24651605


  188. 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, Whirl-Carrillo M, Sakamoto K, Wheeler MT, Butte AJ, Ford JM, Boxer L, Ioannidis JP, Yeung AC, Altman RB, Assimes TL, Snyder M, Ashley EA, Quertermous T. Clinical interpretation and implications of whole-genome sequencing. Volume 311 of Issue 10. 2014. PMID: 24618965


  189. 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. Volume 45. 2013. PMID: 24373932


  190. Chen B, Butte AJ. Network medicine in disease analysis and therapeutics. Volume 94 of Issue 6. 2013. PMID: 24241637


  191. 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. Volume 11. 2013. PMID: 24195779


  192. 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. Volume 210 of Issue 11. 2013. PMID: 24127489


  193. 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, Sage J. A drug repositioning approach identifies tricyclic antidepressants as inhibitors of small cell lung cancer and other neuroendocrine tumors. Volume 3 of Issue 12. 2013. PMID: 24078773


  194. Kido T, Kawashima M, Nishino S, Swan M, Kamatani N, Butte AJ. Systematic evaluation of personal genome services for Japanese individuals. Volume 58 of Issue 11. 2013. PMID: 24067293


  195. Butte AJ, Ohno-Machado L. Making it personal: translational bioinformatics. Volume 20 of Issue 4. 2013. PMID: 23757438


  196. 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. Volume 5 of Issue 6. 2013. PMID: 23806097


  197. 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). Volume 14. 2013. PMID: 23786662


  198. Wen Q, Liu LY, Yang T, Alev C, Wu S, Stevenson DK, Sheng G, Butte AJ, Ling XB. Peptidomic Identification of Serum Peptides Diagnosing Preeclampsia. Volume 8 of Issue 6. 2013. PMID: 23840341


  199. Auerbach RK, Chen B, Butte AJ. Relating genes to function: identifying enriched transcription factors using the ENCODE ChIP-Seq significance tool. Volume 29 of Issue 15. 2013. PMID: 23732275


  200. Kodama K, Tojjar D, Yamada S, Toda K, Patel CJ, Butte AJ. Ethnic differences in the relationship between insulin sensitivity and insulin response: a systematic review and meta-analysis. Volume 36 of Issue 6. 2013. PMID: 23704681


  201. 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. Volume 9 of Issue 5. 2013. PMID: 23717210


  202. Karczewski KJ, Dudley JT, Kukurba KR, Chen R, Butte AJ, Montgomery SB, Snyder M. Systematic functional regulatory assessment of disease-associated variants. Volume 110 of Issue 23. 2013. PMID: 23690573


  203. Grossman AD, Cohen MJ, Manley GT, Butte AJ. Altering physiological networks using drugs: steps towards personalized physiology. Volume 6 Suppl 2. 2013. PMID: 23819503


  204. Sigdel TK, Shoemaker LD, Chen R, Li L, Butte AJ, Sarwal MM, Steinberg GK. Immune response profiling identifies autoantibodies specific to Moyamoya patients. Volume 8. 2013. PMID: 23518061


  207. 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. Volume 132 of Issue 5. 2013. PMID: 23334806


  209. 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, Brunet A. FoxO6 regulates memory consolidation and synaptic function. Volume 26 of Issue 24. 2012. PMID: 23222102


  210. 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. Volume 126 of Issue 21. 2012. PMID: 23093587


  211. Stevenson DK, Shaw GM, Wise PH, Norton ME, Druzin ML, Valantine HA, McFarland DA. Transdisciplinary translational science and the case of preterm birth. Volume 33 of Issue 4. 2012. PMID: 23079774


  212. 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, 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, De La Vega FM, Bustamante CD. Population genetic inference from personal genome data: impact of ancestry and admixture on human genomic variation. Volume 91 of Issue 4. 2012. PMID: 23040495


  213. 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. Volume 12 of Issue 10. 2012. PMID: 23009139


  214. 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. Volume 72 of Issue 22. 2012. PMID: 22962265


  215. 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. Volume 13. 2012. PMID: 22938532


  216. Califano A, Butte AJ, Friend S, Ideker T, Schadt E. Leveraging models of cell regulation and GWAS data in integrative network-based association studies. Volume 44 of Issue 8. 2012. PMID: 22836096


  217. Haeberle H, Dudley JT, Liu JT, Butte AJ, Contag CH. Identification of cell surface targets through meta-analysis of microarray data. Volume 14 of Issue 7. 2012. PMID: 22904683


  219. 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. Volume 8 of Issue 6. 2012. PMID: 22685391


  220. Dudley JT, Kim Y, Liu L, Markov GJ, Gerold K, Chen R, Butte AJ, Kumar S. Human genomic disease variants: a neutral evolutionary explanation. Volume 22 of Issue 8. 2012. PMID: 22665443


  221. Morgan AA, Chen R, Butte AJ. Clinical utility of sequence-based genotype compared with that derivable from genotyping arrays. Volume 19 of Issue e1. 2012. PMID: 22718036


  222. Butte AJ, Ito S. Translational bioinformatics: data-driven drug discovery and development. Volume 91 of Issue 6. 2012. PMID: 22609903


  224. Palma JP, Benitz WE, Tarczy-Hornoch P, Butte AJ, Longhurst CA. Neonatal Informatics: Transforming Neonatal Care Through Translational Bioinformatics. Volume 13 of Issue 5. 2012. PMID: 22924023


  225. 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. Volume 109 of Issue 18. 2012. PMID: 22499789


  226. 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. Volume 8 of Issue 4. 2012. PMID: 22511877


  227. Kang HP, Morgan AA, Chen R, Schadt EE, Butte AJ. Coanalysis of GWAS with eQTLs reveals disease-tissue associations. Volume 2012. 2012. PMID: 22779046


  228. Chen R, Dudley JT, Ruau D, Butte AJ. Quantifying multi-ethnic representation in genetic studies of high mortality diseases. Volume 2012. 2012. PMID: 22779041


  229. 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, O'Huallachain M, Dudley JT, Hillenmeyer S, Haraksingh R, Sharon D, Euskirchen G, Lacroute P, Bettinger K, 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, Gerstein M, Nadeau KC, Tang H, Snyder M. Personal omics profiling reveals dynamic molecular and medical phenotypes. Volume 148 of Issue 6. 2012. PMID: 22424236


  230. Patel CJ, Cullen MR, Ioannidis JP, Butte AJ. Systematic evaluation of environmental factors: persistent pollutants and nutrients correlated with serum lipid levels. Volume 41 of Issue 3. 2012. PMID: 22421054


  231. Dudley JT, Chen R, Sanderford M, Butte AJ, Kumar S. Evolutionary meta-analysis of association studies reveals ancient constraints affecting disease marker discovery. Volume 29 of Issue 9. 2012. PMID: 22389448


  232. 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. Volume 19 of Issue 2. 2012. PMID: 22319178


  233. Khatri P, Sirota M, Butte AJ. Ten years of pathway analysis: current approaches and outstanding challenges. Volume 8 of Issue 2. 2012. PMID: 22383865


  234. Ruau D, Liu LY, Clark JD, Angst MS, Butte AJ. Sex differences in reported pain across 11,000 patients captured in electronic medical records. Volume 13 of Issue 3. 2012. PMID: 22245360


  235. 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. Volume 30 of Issue 1. 2011. PMID: 22178993


  236. Engreitz JM, Chen R, Morgan AA, Dudley JT, Mallelwar R, Butte AJ. ProfileChaser: searching microarray repositories based on genome-wide patterns of differential expression. Volume 27 of Issue 23. 2011. PMID: 21967760


  237. Clark MJ, Chen R, Lam HY, Karczewski KJ, Chen R, Euskirchen G, Butte AJ, Snyder M. Performance comparison of exome DNA sequencing technologies. Volume 29 of Issue 10. 2011. PMID: 21947028


  238. 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, Thorn CF, Hebert JM, Capriotti E, David SP, Pavlovic A, West A, Thakuria JV, Ball MP, Zaranek AW, Rehm HL, Church GM, West JS, Bustamante CD, Snyder M, Altman RB, Klein TE, Butte AJ, Ashley EA. Phased whole-genome genetic risk in a family quartet using a major allele reference sequence. Volume 7 of Issue 9. 2011. PMID: 21935354


  239. 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. Volume 80 of Issue 12. 2011. PMID: 21881554


  240. Liu LY, Schaub MA, Sirota M, Butte AJ. Sex differences in disease risk from reported genome-wide association study findings. Volume 131 of Issue 3. 2011. PMID: 21858542


  241. 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. Volume 3 of Issue 96. 2011. PMID: 21849664


  242. 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. Volume 3 of Issue 96. 2011. PMID: 21849665


  243. Yu M, Eckart MR, Morgan AA, Mukai K, Butte AJ, Tsai M, Galli SJ. Identification of an IFN-?/mast cell axis in a mouse model of chronic asthma. Volume 121 of Issue 8. 2011. PMID: 21737883


  245. Khatri P, Sarwal MM, Butte AJ. Applications of translational bioinformatics in transplantation. Volume 90 of Issue 2. 2011. PMID: 21716268


  246. Sirota M, Butte AJ. The role of bioinformatics in studying rheumatic and autoimmune disorders. Volume 7 of Issue 8. 2011. PMID: 21691330


  247. Dudley JT, Deshpande T, Butte AJ. Exploiting drug-disease relationships for computational drug repositioning. Volume 12 of Issue 4. 2011. PMID: 21690101


  248. Pouliot Y, Chiang AP, Butte AJ. Predicting adverse drug reactions using publicly available PubChem BioAssay data. Volume 90 of Issue 1. 2011. PMID: 21613989


  249. Liu LY, Schaub MA, Sirota M, Butte AJ. Transmission distortion in Crohn's disease risk gene ATG16L1 leads to sex difference in disease association. Volume 18 of Issue 2. 2011. PMID: 21618365


  250. Sarkar IN, Butte AJ, Lussier YA, Tarczy-Hornoch P, Ohno-Machado L. Translational bioinformatics: linking knowledge across biological and clinical realms. Volume 18 of Issue 4. 2011. PMID: 21561873


  251. Ruau D, Mbagwu M, Dudley JT, Krishnan V, Butte AJ. Comparison of automated and human assignment of MeSH terms on publicly-available molecular datasets. Volume 44 Suppl 1. 2011. PMID: 21420508


  252. 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. Volume 91 of Issue 4. 2011. PMID: 21278631


  253. 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. Volume 11. 2011. PMID: 21251264


  254. Dudley JT, Chen R, Butte AJ. Matching cancer genomes to established cell lines for personalized oncology. 2011. PMID: 21121052


  256. Butte AJ, Sigdel TK, Wadia PP, Miklos DB, Sarwal MM. Protein microarrays discover angiotensinogen and PRKRIP1 as novel targets for autoantibodies in chronic renal disease. Volume 10 of Issue 3. 2010. PMID: 21183621


  257. Engreitz JM, Morgan AA, Dudley JT, Chen R, Thathoo R, Altman RB, Butte AJ. Content-based microarray search using differential expression profiles. Volume 11. 2010. PMID: 21172034


  258. Dudley JT, Butte AJ. In silico research in the era of cloud computing. Volume 28 of Issue 11. 2010. PMID: 21057489


  259. Tatonetti NP, Dudley JT, Sagreiya H, Butte AJ, Altman RB. An integrative method for scoring candidate genes from association studies: application to warfarin dosing. Volume 11 Suppl 9. 2010. PMID: 21044367


  260. 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. Volume 11 Suppl 9. 2010. PMID: 21044364


  262. Chen R, Davydov EV, Sirota M, Butte AJ. Non-synonymous and synonymous coding SNPs show similar likelihood and effect size of human disease association. Volume 5 of Issue 10. 2010. PMID: 21042586


  263. 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. Volume 6 of Issue 9. 2010. PMID: 20885780


  264. 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. Volume 111 of Issue 4. 2010. PMID: 20810674


  265. 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. Volume 3 of Issue 5. 2010. PMID: 20733065


  266. Corona E, Dudley JT, Butte AJ. Extreme evolutionary disparities seen in positive selection across seven complex diseases. Volume 5 of Issue 8. 2010. PMID: 20808933


  267. Dudley JT, Pouliot Y, Chen R, Morgan AA, Butte AJ. Translational bioinformatics in the cloud: an affordable alternative. Volume 2 of Issue 8. 2010. PMID: 20691073


  268. Dudley JT, Schadt E, Sirota M, Butte AJ, Ashley E. Drug discovery in a multidimensional world: systems, patterns, and networks. Volume 3 of Issue 5. 2010. PMID: 20677029


  269. Dudley JT, Butte AJ. Biomarker and drug discovery for gastroenterology through translational bioinformatics. Volume 139 of Issue 3. 2010. PMID: 20650279


  270. 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. Volume 182 of Issue 6. 2010. PMID: 20558629


  271. Patel CJ, Bhattacharya J, Butte AJ. An Environment-Wide Association Study (EWAS) on type 2 diabetes mellitus. Volume 5 of Issue 5. 2010. PMID: 20505766


  272. Morgan AA, Chen R, Butte AJ. Likelihood ratios for genome medicine. Volume 2 of Issue 5. 2010. PMID: 20497613


  273. Lussier YA, Butte AJ, Hunter L. Current methodologies for translational bioinformatics. Volume 43 of Issue 3. 2010. PMID: 20470899


  275. 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, Berlin DS, Thorn CF, Sangkuhl K, Hebert JM, Woon M, Sagreiya H, Whaley R, Knowles JW, Chou MF, Thakuria JV, Rosenbaum AM, Zaranek AW, Church GM, Greely HT, Quake SR, Altman RB. Clinical assessment incorporating a personal genome. Volume 375 of Issue 9725. 2010. PMID: 20435227


  276. Ormond KE, Wheeler MT, Hudgins L, Klein TE, Butte AJ, Altman RB, Ashley EA, Greely HT. Challenges in the clinical application of whole-genome sequencing. Volume 375 of Issue 9727. 2010. PMID: 20434765


  277. 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. Volume 7 of Issue 4. 2010. PMID: 20208531


  278. 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. Volume 6 of Issue 2. 2010. PMID: 20140234


  279. Cohen MJ, Grossman AD, Morabito D, Knudson MM, Butte AJ, Manley GT. Identification of complex metabolic states in critically injured patients using bioinformatic cluster analysis. Volume 14 of Issue 1. 2010. PMID: 20122274


  280. Wadia PP, Coram M, Armstrong RJ, Mindrinos M, Butte AJ, Miklos DB. Antibodies specifically target AML antigen NuSAP1 after allogeneic bone marrow transplantation. Volume 115 of Issue 10. 2010. PMID: 20053754


  281. Dudley JT, Butte AJ. A quick guide for developing effective bioinformatics programming skills. Volume 5 of Issue 12. 2009. PMID: 20041221


  282. Sirota M, Schaub MA, Batzoglou S, Robinson WH, Butte AJ. Autoimmune disease classification by inverse association with SNP alleles. Volume 5 of Issue 12. 2009. PMID: 20041220


  283. Chen DP, Morgan AA, Butte AJ. Validating pathophysiological models of aging using clinical electronic medical records. Volume 43 of Issue 3. 2009. PMID: 19958842


  284. Morgan AA, Dudley JT, Deshpande T, Butte AJ. Dynamism in gene expression across multiple studies. Volume 40 of Issue 3. 2009. PMID: 19920211


  285. Renault VM, Rafalski VA, Morgan AA, Salih DA, Brett JO, Webb AE, Villeda SA, Thekkat PU, Guillerey C, Denko NC, Palmer TD, Butte AJ, Brunet A. FoxO3 regulates neural stem cell homeostasis. Volume 5 of Issue 5. 2009. PMID: 19896443


  286. Sutherland SM, Li L, Sigdel TK, Wadia PP, Miklos DB, Butte AJ, Sarwal MM. Protein microarrays identify antibodies to protein kinase Czeta that are associated with a greater risk of allograft loss in pediatric renal transplant recipients. Volume 76 of Issue 12. 2009. PMID: 19812540


  287. 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. Volume 114 of Issue 23. 2009. PMID: 19801443


  288. Grossman AD, Cohen MJ, Manley GT, Butte AJ. Infection in the intensive care unit alters physiological networks. Volume 10 Suppl 9. 2009. PMID: 19761574


  289. Dudley JT, Tibshirani R, Deshpande T, Butte AJ. Disease signatures are robust across tissues and experiments. Volume 5. 2009. PMID: 19756046


  290. Mani M, Venkatasubrahmanyam S, Sanyal M, Levy S, Butte A, Weinberg K, Jahn T. Wiskott-Aldrich syndrome protein is an effector of Kit signaling. Volume 114 of Issue 14. 2009. PMID: 19643989


  291. Chiang AP, Butte AJ. Systematic evaluation of drug-disease relationships to identify leads for novel drug uses. Volume 86 of Issue 5. 2009. PMID: 19571805


  292. Butte AJ. Translational bioinformatics applications in genome medicine. Volume 1 of Issue 6. 2009. PMID: 19566916


  293. Schaub MA, Kaplow IM, Sirota M, Do CB, Butte AJ, Batzoglou S. A Classifier-based approach to identify genetic similarities between diseases. Volume 25 of Issue 12. 2009. PMID: 19477990


  294. Naesens M, Butte AJ, Sarwal MM. C3 polymorphisms and outcomes of renal allografts. Volume 360 of Issue 23. 2009. PMID: 19504761


  295. Wilson KD, Venkatasubrahmanyam S, Jia F, Sun N, Butte AJ, Wu JC. MicroRNA profiling of human-induced pluripotent stem cells. Volume 18 of Issue 5. 2009. PMID: 19284351


  296. Naesens M, Li L, Ying L, Sansanwal P, Sigdel TK, Hsieh SC, Kambham N, Lerut E, Salvatierra O, Butte AJ, Sarwal MM. Expression of complement components differs between kidney allografts from living and deceased donors. Volume 20 of Issue 8. 2009. PMID: 19443638


  297. 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. Volume 106 of Issue 11. 2009. PMID: 19251643


  298. Shah NH, Jonquet C, Chiang AP, Butte AJ, Chen R, Musen MA. Ontology-driven indexing of public datasets for translational bioinformatics. Volume 10 Suppl 2. 2009. PMID: 19208184


  299. Butte AJ, Sarkar IN, Ramoni M, Lussier Y, Troyanskaya O. Selected proceedings of the First Summit on Translational Bioinformatics 2008. Volume 10 Suppl 2. 2009. PMID: 19208183


  300. Liu YI, Wise PH, Butte AJ. The "etiome": identification and clustering of human disease etiological factors. Volume 10 Suppl 2. 2009. PMID: 19208189


  301. Chiang AP, Butte AJ. Data-driven methods to discover molecular determinants of serious adverse drug events. Volume 85 of Issue 3. 2009. PMID: 19177064


  303. Shen-Orr SS, Goldberger O, Garten Y, Rosenberg-Hasson Y, Lovelace PA, Hirschberg DL, Altman RB, Davis MM, Butte AJ. Towards a cytokine-cell interaction knowledgebase of the adaptive immune system. 2009. PMID: 19209721


  304. 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. Volume 9. 2008. PMID: 19094235


  305. 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, Goldbeter A, Hace N, Henney A, Hood L, Iyengar R, Jackson V, Kallioniemi O, Klingmüller U, Kolar P, Kolch W, Kyriakopoulou C, Laplace F, Lehrach H, Marcus F, Matrisian L, Nolan G, Pelkmans L, Potti A, Sander C, Seljak M, Singer D, Sorger P, Stunnenberg H, Superti-Furga G, Uhlen M, Vidal M, Weinstein J, Wigle D, Williams M, Wolkenhauer O, Zhivotovsky B, Zinovyev A, Zupan B. Report on EU-USA workshop: how systems biology can advance cancer research (27 October 2008). Volume 3 of Issue 1. 2008. PMID: 19383362


  306. 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. Volume 9 of Issue 12. 2008. PMID: 19061490


  308. Viatour P, Somervaille TC, Venkatasubrahmanyam S, Kogan S, McLaughlin ME, Weissman IL, Butte AJ, Passegué E, Sage J. Hematopoietic stem cell quiescence is maintained by compound contributions of the retinoblastoma gene family. Volume 3 of Issue 4. 2008. PMID: 18940733


  309. 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. Volume 129 of Issue 2. 2008. PMID: 18801706


  310. Butte AJ. Translational bioinformatics: coming of age. Volume 15 of Issue 6. 2008. PMID: 18755990


  311. 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. Volume 42 of Issue 2. 2008. PMID: 18790084


  312. Butte AJ. Medicine. The ultimate model organism. Volume 320 of Issue 5874. 2008. PMID: 18420921


  314. Chen DP, Weber SC, Constantinou PS, Ferris TA, Lowe HJ, Butte AJ. Novel integration of hospital electronic medical records and gene expression measurements to identify genetic markers of maturation. 2008. PMID: 18229690


  315. Chen R, Li L, Butte AJ. AILUN: reannotating gene expression data automatically. Volume 4 of Issue 11. 2007. PMID: 17971777


  316. Chen DP, Weber SC, Constantinou PS, Ferris TA, Lowe HJ, Butte AJ. Clinical arrays of laboratory measures, or "clinarrays", built from an electronic health record enable disease subtyping by severity. 2007. PMID: 18693809


  317. Lin YA, Chiang A, Lin R, Yao P, Chen R, Butte AJ. Methodologies for extracting functional pharmacogenomic experiments from international repository. 2007. PMID: 18693879


  319. Butte AJ, Kohane IS. Creation and implications of a phenome-genome network. Volume 24 of Issue 1. 2006. PMID: 16404398


  321. Balboni I, Chan SM, Kattah M, Tenenbaum JD, Butte AJ, Utz PJ. Multiplexed protein array platforms for analysis of autoimmune diseases. Volume 24. 2006. PMID: 16551254


  322. Ichikawa JK, English SB, Wolfgang MC, Jackson R, Butte AJ, Lory S. Genome-wide analysis of host responses to the Pseudomonas aeruginosa type III secretion system yields synergistic effects. Volume 7 of Issue 11. 2005. PMID: 16207250


  324. Tseng YH, Butte AJ, Kokkotou E, Yechoor VK, Taniguchi CM, Kriauciunas KM, Cypess AM, Niinobe M, Yoshikawa K, Patti ME, Kahn CR. Prediction of preadipocyte differentiation by gene expression reveals role of insulin receptor substrates and necdin. Volume 7 of Issue 6. 2005. PMID: 15895078


  325. Pollard J, Butte AJ, Hoberman S, Joshi M, Levy J, Pappo J. A computational model to define the molecular causes of type 2 diabetes mellitus. Volume 7 of Issue 2. 2005. PMID: 15857235


  326. 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. Volume 3 of Issue 4. 2004. PMID: 15268757


  327. 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. Volume 18 of Issue 6. 2004. PMID: 15075291


  328. Allocco DJ, Kohane IS, Butte AJ. Quantifying the relationship between co-expression, co-regulation and gene function. Volume 5. 2004. PMID: 15053845


  329. 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, Kahn CR, Mandarino LJ. Coordinated reduction of genes of oxidative metabolism in humans with insulin resistance and diabetes: Potential role of PGC1 and NRF1. Volume 100 of Issue 14. 2003. PMID: 12832613


  330. Nimgaonkar A, Sanoudou D, Butte AJ, Haslett JN, Kunkel LM, Beggs AH, Kohane IS. Reproducibility of gene expression across generations of Affymetrix microarrays. Volume 4. 2003. PMID: 12823866


  331. Lee K, Kohane IS, Butte AJ. PGAGENE: integrating quantitative gene-specific results from the NHLBI programs for genomic applications. Volume 19 of Issue 6. 2003. PMID: 12691993


  332. Weiner DL, Butte AJ, Hibberd PL, Fleisher GR. Computerized recruiting for clinical trials in real time. Volume 41 of Issue 2. 2003. PMID: 12548275


  333. Park PJ, Butte AJ, Kohane IS. Comparing expression profiles of genes with similar promoter regions. Volume 18 of Issue 12. 2002. PMID: 12490441


  334. Kuo WP, Jenssen TK, Butte AJ, Ohno-Machado L, Kohane IS. Analysis of matched mRNA measurements from two different microarray technologies. Volume 18 of Issue 3. 2002. PMID: 11934739


  337. Riva A, Mandl KD, Oh DH, Nigrin DJ, Butte A, Szolovits P, Kohane IS. The personal internetworked notary and guardian. Volume 62 of Issue 1. 2001. PMID: 11340004


  338. Butte AJ. Challenges in bioinformatics: infrastructure, models and analytics. Volume 19 of Issue 5. 2001. PMID: 11403022


  339. Butte AJ, Ye J, Häring HU, Stumvoll M, White MF, Kohane IS. Determining significant fold differences in gene expression analysis. 2001. PMID: 11262977


  340. Butte AJ, Tamayo P, Slonim D, Golub TR, Kohane IS. Discovering functional relationships between RNA expression and chemotherapeutic susceptibility using relevance networks. Volume 97 of Issue 22. 2000. PMID: 11027309


  341. Huang SA, Tu HM, Harney JW, Venihaki M, Butte AJ, Kozakewich HP, Fishman SJ, Larsen PR. Severe hypothyroidism caused by type 3 iodothyronine deiodinase in infantile hemangiomas. Volume 343 of Issue 3. 2000. PMID: 10900278


  342. Butte AJ, Weinstein DA, Kohane IS. Enrolling patients into clinical trials faster using RealTime Recuiting. 2000. PMID: 11079855


  345. Quon MJ, Butte AJ, Zarnowski MJ, Sesti G, Cushman SW, Taylor SI. Insulin receptor substrate 1 mediates the stimulatory effect of insulin on GLUT4 translocation in transfected rat adipose cells. Volume 269 of Issue 45. 1994. PMID: 7525563


  346. Quon MJ, Butte AJ, Taylor SI. Insulin signal transduction pathways. Volume 5 of Issue 9. 1994. PMID: 18407232


  347. Quon MJ, Guerre-Millo M, Zarnowski MJ, Butte AJ, Em M, Cushman SW, Taylor SI. Tyrosine kinase-deficient mutant human insulin receptors (Met1153-->Ile) overexpressed in transfected rat adipose cells fail to mediate translocation of epitope-tagged GLUT4. Volume 91 of Issue 12. 1994. PMID: 8202531


  348. DePetrillo PB, Butte AJ. Derivation of a scale-independent parameter which characterizes genetic sequence comparisons. Volume 26 of Issue 6. 1993. PMID: 8112054