Atul Butte, MD, PhD
Professor
Pediatrics
School of Medicine

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.

• To do no harm - and the most good - with AI in health care.
  Nature medicine 2024 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 …
• Predictive Modeling of Drug-Related Adverse Events with Real-World Data: A Case Study of Linezolid Hematologic Outcomes.
  Clinical pharmacology and therapeutics 2024 Patel A, Doernberg SB, Zack T, Butte AJ, Radtke KK
• A comparative study of zero-shot inference with large language models and supervised modeling in breast cancer pathology classification.
  Research square 2024 Sushil M, Zack T, Mandair D, Zheng Z, Wali A, Yu YN, Quan Y, Butte AJ
• The Reporting Quality of Machine Learning Studies on Pediatric Diabetes Mellitus: Systematic Review.
  Journal of medical Internet research 2024 Zrubka Z, Kertész G, Gulácsi L, Czere J, Hölgyesi Á, Nezhad HM, Mosavi A, Kovács L, Butte AJ, Péntek M
• Cross-institution natural language processing for reliable clinical association studies: a methodological exploration.
  Journal of clinical epidemiology 2024 Sushil M, Butte AJ, Schuit E, van Smeden M, Leeuwenberg AM
• Topic modeling on clinical social work notes for exploring social determinants of health factors.
  JAMIA open 2024 Sun S, Zack T, Williams CYK, Sushil M, Butte AJ
• Assessing the potential of GPT-4 to perpetuate racial and gender biases in health care: a model evaluation study.
  The Lancet. Digital health 2024 Zack T, Lehman E, Suzgun M, Rodriguez JA, Celi LA, Gichoya J, Jurafsky D, Szolovits P, Bates DW, Abdulnour RE, Butte AJ, Alsentzer E
• Epistasis regulates genetic control of cardiac hypertrophy.
  Research square 2023 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 …
• Personalizing treatment selection in Crohn's disease: a meta-analysis of individual participant data from fifteen randomized controlled trials.
  medRxiv : the preprint server for health sciences 2023 Rudrapatna VA, Ravindranath VG, Arneson DV, Mosenia A, Butte AJ, Wang S
• Epistasis regulates genetic control of cardiac hypertrophy.
  medRxiv : the preprint server for health sciences 2023 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 …
• Sequential regression and simulation: a method for estimating causal effects from heterogeneous clinical trials without a common control group.
  BMC medical research methodology 2023 Rudrapatna VA, Ravindranath VG, Arneson DV, Mosenia A, Butte AJ, Wang S
• Second-Line Pharmaceutical Treatments for Patients with Type 2 Diabetes.
  JAMA network open 2023 Vashisht R, Patel A, Dahm L, Han C, Medders KE, Mowers R, Byington CL, Koliwad SK, Butte AJ
• Artificial Intelligence-From Starting Pilots to Scalable Privilege.
  JAMA oncology 2023 Butte AJ
• The promise of digital healthcare technologies.
  Frontiers in public health 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, Banach M, Kletecka-Pulker M, …
• Algorithmic identification of treatment-emergent adverse events from clinical notes using large language models: a pilot study in inflammatory bowel disease.
  medRxiv : the preprint server for health sciences 2023 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
• AI in Medicine-JAMA's Focus on Clinical Outcomes, Patient-Centered Care, Quality, and Equity.
  JAMA 2023 Khera R, Butte AJ, Berkwits M, Hswen Y, Flanagin A, Park H, Curfman G, Bibbins-Domingo K
• Development of a Machine Learning Model of Postoperative Acute Kidney Injury Using Non-Invasive Time-Sensitive Intraoperative Predictors.
  Bioengineering (Basel, Switzerland) 2023 Zamirpour S, Hubbard AE, Feng J, Butte AJ, Pirracchio R, Bishara A
• Mammary duct luminal epithelium controls adipocyte thermogenic programme.
  Nature 2023 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, …
• A certified de-identification system for all clinical text documents for information extraction at scale.
  JAMIA open 2023 Radhakrishnan L, Schenk G, Muenzen K, Oskotsky B, Ashouri Choshali H, Plunkett T, Israni S, Butte AJ
• ALK Inhibitor Treatment Patterns and Outcomes in Real-World Patients with ALK-Positive Non-Small-Cell Lung Cancer: A Retrospective Cohort Study.
  Targeted oncology 2023 Wang M, Slatter S, Sussell J, Lin CW, Ogale S, Datta D, Butte AJ, Bazhenova L, Rudrapatna VA
• Bottom-up and top-down paradigms of artificial intelligence research approaches to healthcare data science using growing real-world big data.
  Journal of the American Medical Informatics Association : JAMIA 2023 Wang M, Sushil M, Miao BY, Butte AJ
• Novel computational methods on electronic health record yields new estimates of transfusion-associated circulatory overload in populations enriched with high-risk patients.
  Transfusion 2023 Wang M, Goldgof GM, Patel A, Whitaker B, Belov A, Chan B, Phelps E, Rubin B, Anderson S, Butte AJ
• Machine-Learning Algorithm to Improve Cohort Identification in Interstitial Lung Disease.
  American journal of respiratory and critical care medicine 2023 Farrand E, Gologorskaya O, Mills H, Radhakrishnan L, Collard HR, Butte AJ
• Assessment of valvular function in over 47,000 people using deep learning-based flow measurements.
  medRxiv : the preprint server for health sciences 2023 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
• Serum tryptophan metabolites are associated with erosive hand osteoarthritis and pain: results from the DIGICOD cohort.
  Osteoarthritis and cartilage 2023 Binvignat M, Emond P, Mifsud F, Miao B, Courties A, Lefèvre A, Maheu E, Crema MD, Klatzmann D, Kloppenburg M, Richette P, Butte AJ, Mariotti-Ferrandiz E, Berenbaum F, Sokol H, Sellam J
• Nucleic acid biomarkers of immune response and cell and tissue damage in children with COVID-19 and MIS-C.
  Cell reports. Medicine 2023 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, …
• 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.
  EClinicalMedicine 2023 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-…
• Defining incidence and complications of fibrolamellar liver cancer through tiered computational analysis of clinical data.
  NPJ precision oncology 2023 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
• Creation of an ustekinumab external control arm for Crohn's disease using electronic health records data: A pilot study.
  PloS one 2023 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, …
• Data Sharing Enters a New Era.
  Annals of internal medicine 2023 Bauchner H, McDermott MM, Butte AJ
• DeepHeme: A generalizable, bone marrow classifier with hematopathologist-level performance.
  bioRxiv : the preprint server for biology 2023 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
• Real-world utilization of SARS-CoV-2 serological testing in RNA positive patients across the United States.
  PloS one 2023 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 …
• Real-world performance of SARS-Cov-2 serology tests in the United States, 2020.
  PloS one 2023 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, …
• Identification of Symptom Phenotypes of Hand Osteoarthritis Using Hierarchical Clustering: Results From the DIGICOD Cohort.
  Arthritis care & research 2023 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
• Electrocardiogram Detection of Pulmonary Hypertension Using Deep Learning.
  Journal of cardiac failure 2023 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
• Advancing evidence-based treatment of infectious diseases in children with real-world data: Opportunities and challenges.
  Frontiers in pharmacology 2023 Radtke KK, Butte AJ
• Toward a causal model of chronic back pain: Challenges and opportunities.
  Frontiers in computational neuroscience 2023 Huie JR, Vashisht R, Galivanche A, Hadjadj C, Morshed S, Butte AJ, Ferguson AR, O'Neill C
• Paging the Clinical Informatics Community: Respond STAT to Dobbs v. Jackson's Women's Health Organization.
  Applied clinical informatics 2022 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 AJ, Cardilo AB, Chilukuri N, Cho MK, Cohen JK, Craven CK…
• Predictive Models for Length of Stay and Discharge Disposition in Elective Spine Surgery: Development, Validation, and Comparison to the ACS NSQIP Risk Calculator.
  Spine 2022 Arora A, Lituiev D, Jain D, Hadley D, Butte AJ, Berven S, Peterson TA
• Early immune markers of clinical, virological, and immunological outcomes in patients with COVID-19: a multi-omics study.
  eLife 2022 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…
• From Genes to Geography, from Cells to Community, from Biomolecules to Behaviors: The Importance of Social Determinants of Health.
  Biomolecules 2022 Davidson J, Vashisht R, Butte AJ
• Predictability and stability testing to assess clinical decision instrument performance for children after blunt torso trauma.
  PLOS digital health 2022 Kornblith AE, Singh C, Devlin G, Addo N, Streck CJ, Holmes JF, Kuppermann N, Grupp-Phelan J, Fineman J, Butte AJ, Yu B
• Machine Learning Methods in Health Economics and Outcomes Research-The PALISADE Checklist: A Good Practices Report of an ISPOR Task Force.
  Value in health : the journal of the International Society for Pharmacoeconomics and Outcomes Research 2022 Padula WV, Kreif N, Vanness DJ, Adamson B, Rueda JD, Felizzi F, Jonsson P, IJzerman MJ, Butte A, Crown W
• The Promise of Digital Health: Then, Now, and the Future.
  NAM perspectives 2022 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, …
• Trans-channel fluorescence learning improves high-content screening for Alzheimer's disease therapeutics.
  Nature machine intelligence 2022 Wong DR, Conrad J, Johnson N, Ayers J, Laeremans A, Lee JC, Lee J, Prusiner SB, Bandyopadhyay S, Butte AJ, Paras NA, Keiser MJ
• Deep learning from multiple experts improves identification of amyloid neuropathologies.
  Acta neuropathologica communications 2022 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
• Use of machine learning in osteoarthritis research: a systematic literature review.
  RMD open 2022 Binvignat M, Pedoia V, Butte AJ, Louati K, Klatzmann D, Berenbaum F, Mariotti-Ferrandiz E, Sellam J
• Individualized Constellation of Killer Cell Immunoglobulin-Like Receptors and Cognate HLA Class I Ligands that Controls Natural Killer Cell Antiviral Immunity Predisposes COVID-19.
  Frontiers in genetics 2022 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
• Early immune responses have long-term associations with clinical, virologic, and immunologic outcomes in patients with COVID-19.
  Research square 2022 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 …
• Embedding electronic health records onto a knowledge network recognizes prodromal features of multiple sclerosis and predicts diagnosis.
  Journal of the American Medical Informatics Association : JAMIA 2022 Nelson CA, Bove R, Butte AJ, Baranzini SE
• Open challenges in developing digital therapeutics in the United States.
  PLOS digital health 2022 Miao BY, Arneson D, Wang M, Butte AJ
• Systematic identification of ACE2 expression modulators reveals cardiomyopathy as a risk factor for mortality in COVID-19 patients.
  Genome biology 2022 Kaur N, Oskotsky B, Butte AJ, Hu Z
• Application of Machine Learning for Cytometry Data.
  Frontiers in immunology 2022 Hu Z, Bhattacharya S, Butte AJ
• Postoperative delirium prediction using machine learning models and preoperative electronic health record data.
  BMC anesthesiology 2022 Bishara A, Chiu C, Whitlock EL, Douglas VC, Lee S, Butte AJ, Leung JM, Donovan AL
• 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 National Institute of Diabetes and Digestive and Kidney Diseases.
  Diabetes care 2022 Cefalu WT, Andersen DK, Arreaza-Rubín G, Pin CL, Sato S, Verchere CB, Woo M, Rosenblum ND, Symposium planning committee, moderators, and speakers
• Opal: an implementation science tool for machine learning clinical decision support in anesthesia.
  Journal of clinical monitoring and computing 2021 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
• 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 National Institute of Diabetes and Digestive and Kidney Diseases.
  Diabetes 2021 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,…
• Development and Validation of a Deep Learning Strategy for Automated View Classification of Pediatric Focused Assessment With Sonography for Trauma.
  Journal of ultrasound in medicine : official journal of the American Institute of Ultrasound in Medicine 2021 Kornblith AE, Addo N, Dong R, Rogers R, Grupp-Phelan J, Butte A, Gupta P, Callcut RA, Arnaout R
• Case-control study of the association of chronic acid suppression and social determinants of health with COVID-19 infection.
  Scientific reports 2021 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
• Five-year pediatric use of a digital wearable fitness device: lessons from a pilot case study.
  JAMIA open 2021 Butte KD, Bahmani A, Butte AJ, Li X, Snyder MP
• Assessing Clinical Outcomes in a Data-Rich World-A Reality Check on Real-World Data.
  JAMA network open 2021 Hong JC, Butte AJ
• Big Data in Nephrology.
  Nature reviews. Nephrology 2021 Kaur N, Bhattacharya S, Butte AJ
• Impact of Different Approaches to Preparing Notes for Analysis With Natural Language Processing on the Performance of Prediction Models in Intensive Care.
  Critical care explorations 2021 Mahendra M, Luo Y, Mills H, Schenk G, Butte AJ, Dudley RA
• Rethinking PICO in the Machine Learning Era: ML-PICO.
  Applied clinical informatics 2021 Liu X, Anstey J, Li R, Sarabu C, Sono R, 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 2021 Rudrapatna VA, Glicksberg BS, Butte AJ
• Opportunities and Challenges in Democratizing Immunology Datasets.
  Frontiers in immunology 2021 Bhattacharya S, Hu Z, Butte AJ
• 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 2021 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
• Algorithmic Stewardship in Health Care-Reply.
  JAMA 2021 Eaneff S, Obermeyer Z, Butte AJ
• Androgen-deprivation therapy and SARS-CoV-2 in men with prostate cancer: findings from the University of California Health System registry.
  Annals of oncology : official journal of the European Society for Medical Oncology 2021 Kwon DH, Vashisht R, Borno HT, Aggarwal RR, Small EJ, Butte AJ, Huang FW
• Quantifying Variation in Treatment Utilization for Type 2 Diabetes Across Five Major University of California Health Systems.
  Diabetes care 2021 Peterson TA, Fontil V, Koliwad SK, Patel A, Butte AJ
• Age- and Sex-Associated Variations in the Sensitivity of Serological Tests Among Individuals Infected With SARS-CoV-2.
  JAMA network open 2021 Vashisht R, Patel A, Crews BO, Garner OB, Dahm L, Wilson C, Butte AJ
• Knowledge Network Embedding of Transcriptomic Data from Spaceflown Mice Uncovers Signs and Symptoms Associated with Terrestrial Diseases.
  Life (Basel, Switzerland) 2021 Nelson CA, Acuna AU, Paul AM, Scott RT, Butte AJ, Cekanaviciute E, Baranzini SE, Costes SV
• Trials and Tribulations-11 Reasons Why We Need to Promote Clinical Trials Data Sharing.
  JAMA network open 2021 Butte AJ
• Characteristics and challenges of the clinical pipeline of digital therapeutics.
  NPJ digital medicine 2020 Patel NA, Butte AJ
• Identification of antiviral antihistamines for COVID-19 repurposing.
  Biochemical and biophysical research communications 2020 Reznikov LR, Norris MH, Vashisht R, Bluhm AP, Li D, Liao YJ, Brown A, Butte AJ, Ostrov DA
• Human splice factors contribute to latent HIV infection in primary cell models and blood CD4+ T cells from ART-treated individuals.
  PLoS pathogens 2020 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
• CovidCounties is an interactive real time tracker of the COVID19 pandemic at the level of US counties.
  Scientific data 2020 Arneson D, Elliott M, Mosenia A, Oskotsky B, Solodar S, Vashisht R, Zack T, Bleicher P, Butte AJ, Rudrapatna VA
• The Case for Algorithmic Stewardship for Artificial Intelligence and Machine Learning Technologies.
  JAMA 2020 Eaneff S, Obermeyer Z, Butte AJ
• Minimum information about clinical artificial intelligence modeling: the MI-CLAIM checklist.
  Nature medicine 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
• 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 2020 Hu Z, Tang A, Singh J, Bhattacharya S, Butte AJ
• CovidCounties - an interactive, real-time tracker of the COVID-19 pandemic at the level of US counties.
  medRxiv : the preprint server for health sciences 2020 Arneson D, Elliott M, Mosenia A, Oskotsky B, Vashisht R, Zack T, Bleicher P, Butte AJ, Rudrapatna VA
• Protected Health Information filter (Philter): accurately and securely de-identifying free-text clinical notes.
  NPJ digital medicine 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
• Predicting Inpatient Medication Orders From Electronic Health Record Data.
  Clinical pharmacology and therapeutics 2020 Rough K, Dai AM, Zhang K, Xue Y, Vardoulakis LM, Cui C, Butte AJ, Howell MD, Rajkomar A
• Meta-Analysis of Vaginal Microbiome Data Provides New Insights Into Preterm Birth.
  Frontiers in microbiology 2020 Kosti I, Lyalina S, Pollard KS, Butte AJ, Sirota M
• Time for NIH to lead on data sharing.
  Science (New York, N.Y.) 2020 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
• Accuracy of medical billing data against the electronic health record in the measurement of colorectal cancer screening rates.
  BMJ open quality 2020 Rudrapatna VA, Glicksberg BS, Avila P, Harding-Theobald E, Wang C, Butte AJ
• Recent Advances in Systems and Network Medicine: Meeting Report from the First International Conference in Systems and Network Medicine.
  Systems medicine (New Rochelle, N.Y.) 2020 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, …
• Explanatory Model of Dry Eye Disease Using Health and Nutrition Examinations: Machine Learning and Network-Based Factor Analysis From a National Survey.
  JMIR medical informatics 2020 Nam SM, Peterson TA, Butte AJ, Seo KY, Han HW
• Opportunities and challenges in using real-world data for health care.
  The Journal of clinical investigation 2020 Rudrapatna VA, Butte AJ
• Corticosteroid use is not associated with improved outcomes in acute exacerbation of IPF.
  Respirology (Carlton, Vic.) 2019 Farrand E, Vittinghoff E, Ley B, Butte AJ, Collard HR
• Heterogeneity in HIV and cellular transcription profiles in cell line models of latent and productive infection: implications for HIV latency.
  Retrovirology 2019 Telwatte S, Morón-López S, Aran D, Kim P, Hsieh C, Joshi S, Montano M, Greene WC, Butte AJ, Wong JK, Yukl SA
• PatientExploreR: an extensible application for dynamic visualization of patient clinical history from electronic health records in the OMOP common data model.
  Bioinformatics (Oxford, England) 2019 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 …
• Tracing diagnosis trajectories over millions of patients reveal an unexpected risk in schizophrenia.
  Scientific data 2019 Paik H, Kan MJ, Rappoport N, Hadley D, Sirota M, Chen B, Manber U, Cho SB, Butte AJ
• Comprehensive transcriptomic analysis of cell lines as models of primary tumors across 22 tumor types.
  Nature communications 2019 Yu K, Chen B, Aran D, Charalel J, Yau C, Wolf DM, van 't Veer LJ, Butte AJ, Goldstein T, Sirota M
• Integrating biomedical research and electronic health records to create knowledge-based biologically meaningful machine-readable embeddings.
  Nature communications 2019 Nelson CA, Butte AJ, Baranzini SE
• A longitudinal big data approach for precision health.
  Nature medicine 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, Leopold SR, Chen…
• Closing the Evidence Gap in Interstitial Lung Disease. The Promise of Real-World Data.
  American journal of respiratory and critical care medicine 2019 Farrand E, Anstrom KJ, Bernard G, Butte AJ, Iribarren C, Ley B, Martinez FJ, Collard HR
• Assessment of Postdonation Outcomes in US Living Kidney Donors Using Publicly Available Data Sets.
  JAMA network open 2019 Chen J, Bhattacharya S, Sirota M, Laiudompitak S, Schaefer H, Thomson E, Wiser J, Sarwal MM, Butte AJ
• Robust prediction of clinical outcomes using cytometry data.
  Bioinformatics (Oxford, England) 2019 Hu Z, Glicksberg BS, 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 2019 Norgeot B, Glicksberg BS, Trupin L, Lituiev D, Gianfrancesco M, Oskotsky B, Schmajuk G, Yazdany J, Butte AJ
• A pilot study showing a stronger H1N1 influenza vaccination response during pregnancy in women who subsequently deliver preterm.
  Journal of reproductive immunology 2019 Andorf S, Bhattacharya S, Gaudilliere B, Shaw GM, Stevenson DK, Butte AJ, Sirota M
• Prototype of running clinical trials in an untrustworthy environment using blockchain.
  Nature communications 2019 Wong DR, Bhattacharya S, Butte AJ
• Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage.
  Nature immunology 2019 Aran D, Looney AP, Liu L, Wu E, Fong V, Hsu A, Chak S, Naikawadi RP, Wolters PJ, Abate AR, Butte AJ, Bhattacharya M
• ROMOP: a light-weight R package for interfacing with OMOP-formatted electronic health record data.
  JAMIA open 2019 Glicksberg BS, Oskotsky B, Giangreco N, Thangaraj PM, Rudrapatna V, Datta D, Frazier R, Lee N, Larsen R, Tatonetti NP, Butte AJ
• A call for deep-learning healthcare.
  Nature medicine 2019 Norgeot B, Glicksberg BS, Butte AJ
• Better medicine through machine learning: What's real, and what's artificial?
  PLoS medicine 2018 Saria S, Butte A, Sheikh A
• Author Correction: Enabling precision medicine in neonatology, an integrated repository for preterm birth research.
  Scientific data 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, Muglia LJ, Ober C, England SK, Macones G, …
• Personal Mutanomes Meet Modern Oncology Drug Discovery and Precision Health.
  Pharmacological reviews 2018 Cheng F, Liang H, Butte AJ, Eng C, Nussinov R
• Open data informatics and data repurposing for IBD.
  Nature reviews. Gastroenterology & hepatology 2018 Rudrapatna VA, Butte AJ
• The 10,000 Immunomes Project: Building a Resource for Human Immunology.
  Cell reports 2018 Zalocusky KA, Kan MJ, Hu Z, Dunn P, Thomson E, Wiser J, Bhattacharya S, Butte AJ
• Enabling precision medicine in neonatology, an integrated repository for preterm birth research.
  Scientific data 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, England SK, Parry S, Shaw GM, Simpson JL, Thomson…
• Comparing Ethnicity-Specific Reference Intervals for Clinical Laboratory Tests from EHR Data.
  The journal of applied laboratory medicine 2018 Rappoport N, Paik H, Oskotsky B, Tor R, Ziv E, Zaitlen N, Butte AJ
• The 10,000 Immunomes Project: Building a Resource for Human Immunology.
  Cell reports 2018 Zalocusky KA, Kan MJ, Hu Z, Dunn P, Thomson E, Wiser J, Bhattacharya S, Butte AJ
• MetaCyto: A Tool for Automated Meta-analysis of Mass and Flow Cytometry Data.
  Cell reports 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
• Scalable and accurate deep learning with electronic health records.
  NPJ digital medicine 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, Duggan GE, Irvine J, Le Q, Litsch K, Mossin A, Tansuwan J, Wexler J…
• The Atacama skeleton.
  Genome research 2018 Nolan G, Butte A
• Whole-genome sequencing of Atacama skeleton shows novel mutations linked with dysplasia.
  Genome research 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
• ImmPort, toward repurposing of open access immunological assay data for translational and clinical research.
  Scientific data 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
• Are minor alleles more likely to be risk alleles?
  BMC medical genomics 2018 Kido T, Sikora-Wohlfeld W, Kawashima M, Kikuchi S, Kamatani N, Patwardhan A, Chen R, Sirota M, Kodama K, Hadley D, Butte AJ
• A genome-wide association study identifies only two ancestry specific variants associated with spontaneous preterm birth.
  Scientific reports 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, Sikora-Wohfeld W, Gignoux CR, Wang H, Oehlert J, …
• Risky Business: Meeting the Structural Needs of Transdisciplinary Science.
  The Journal of pediatrics 2017 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
• xCell: digitally portraying the tissue cellular heterogeneity landscape.
  Genome biology 2017 Aran D, Hu Z, Butte AJ
• Combined inhibition of atypical PKC and histone deacetylase 1 is cooperative in basal cell carcinoma treatment.
  JCI insight 2017 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 …
• PDX-MI: Minimal Information for Patient-Derived Tumor Xenograft Models.
  Cancer research 2017 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, …
• Future cancer research priorities in the USA: a Lancet Oncology Commission.
  The Lancet. Oncology 2017 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, …
• Comprehensive analysis of normal adjacent to tumor transcriptomes.
  Nature communications 2017 Aran D, Camarda R, Odegaard J, Paik H, Oskotsky B, Krings G, Goga A, Sirota M, Butte AJ
• Precision annotation of digital samples in NCBI's gene expression omnibus.
  Scientific data 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, Bhattacharya S, Sirota M, Musen MA, Butte …
• Big data opens a window onto wellness.
  Nature biotechnology 2017 Butte AJ
• Reversal of cancer gene expression correlates with drug efficacy and reveals therapeutic targets.
  Nature communications 2017 Chen B, Ma L, Paik H, Sirota M, Wei W, Chua MS, So S, Butte AJ
• Cancer Cell-Autonomous Parainflammation Mimics Immune Cell Infiltration.
  Cancer research 2017 Lasry A, Aran D, Butte AJ, Ben-Neriah Y
• RImmPort: an R/Bioconductor package that enables ready-for-analysis immunology research data.
  Bioinformatics (Oxford, England) 2017 Shankar RD, Bhattacharya S, Jujjavarapu C, Andorf S, Wiser JA, Butte AJ
• Computational Discovery of Niclosamide Ethanolamine, a Repurposed Drug Candidate That Reduces Growth of Hepatocellular Carcinoma Cells In Vitro and in Mice by Inhibiting Cell Division Cycle 37 Signaling.
  Gastroenterology 2017 Chen B, Wei W, Ma L, Yang B, Gill RM, Chua MS, Butte AJ, So S
• Evidence for benefit of statins to modify cognitive decline and risk in Alzheimer's disease.
  Alzheimer's research & therapy 2017 Geifman N, Brinton RD, Kennedy RE, Schneider LS, Butte AJ
• In silico and in vitro drug screening identifies new therapeutic approaches for Ewing sarcoma.
  Oncotarget 2017 Pessetto ZY, Chen B, Alturkmani H, Hyter S, Flynn CA, Baltezor M, Ma Y, Rosenthal HG, Neville KA, Weir SJ, Butte AJ, Godwin AK
• Solving Immunology?
  Trends in immunology 2016 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
• Integrating Clinical Phenotype and Gene Expression Data to Prioritize Novel Drug Uses.
  CPT: pharmacometrics & systems pharmacology 2016 Paik H, Chen B, Sirota M, Hadley D, 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 2016 Butte AJ
• Defective Signaling in the JAK-STAT Pathway Tracks with Chronic Inflammation and Cardiovascular Risk in Aging Humans.
  Cell systems 2016 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
• Differential Phasing between Circadian Clocks in the Brain and Peripheral Organs in Humans.
  Journal of biological rhythms 2016 Hughey JJ, Butte AJ
• Digitally deconvolving the tumor microenvironment.
  Genome biology 2016 Aran D, Butte AJ
• Widespread parainflammation in human cancer.
  Genome biology 2016 Aran D, Lasry A, Zinger A, Biton M, Pikarsky E, Hellman A, Butte AJ, Ben-Neriah Y
• Identification of matrix metalloproteinase-12 as a candidate molecule for prevention and treatment of cardiometabolic disease.
  Molecular medicine (Cambridge, Mass.) 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
• Microfluidic single-cell transcriptional analysis rationally identifies novel surface marker profiles to enhance cell-based therapies.
  Nature communications 2016 Rennert RC, Januszyk M, Sorkin M, Rodrigues M, Maan ZN, Duscher D, Whittam AJ, Kosaraju R, Chung MT, Paik K, Li AY, Findlay M, Glotzbach JP, Butte AJ, Gurtner GC
• A patient-level data meta-analysis of standard-of-care treatments from eight prostate cancer clinical trials.
  Scientific data 2016 Geifman N, Butte AJ
• Cross-tissue Analysis of Gene and Protein Expression in Normal and Cancer Tissues.
  Scientific reports 2016 Kosti I, Jain N, Aran D, Butte AJ, Sirota M
• Constraints on Biological Mechanism from Disease Comorbidity Using Electronic Medical Records and Database of Genetic Variants.
  PLoS computational biology 2016 Bagley SC, Sirota M, Chen R, Butte AJ, Altman RB
• Expression-Based Genome-Wide Association Study Links Vitamin D-Binding Protein With Autoantigenicity in Type 1 Diabetes.
  Diabetes 2016 Kodama K, Zhao Z, Toda K, Yip L, Fuhlbrigge R, Miao D, Fathman CG, Yamada S, Butte AJ, Yu L
• Leveraging big data to transform target selection and drug discovery.
  Clinical pharmacology and therapeutics 2016 Chen B, Butte AJ
• Corrigendum: Systematic pan-cancer analysis of tumour purity.
  Nature communications 2016 Aran D, Sirota M, Butte AJ
• ZeitZeiger: supervised learning for high-dimensional data from an oscillatory system.
  Nucleic acids research 2016 Hughey JJ, Hastie T, Butte AJ
• Compendium of Immune Signatures Identifies Conserved and Species-Specific Biology in Response to Inflammation.
  Immunity 2016 Godec J, Tan Y, Liberzon A, Tamayo P, Bhattacharya S, Butte AJ, Mesirov JP, Haining WN
• DO CANCER CLINICAL TRIAL POPULATIONS TRULY REPRESENT CANCER PATIENTS? A COMPARISON OF OPEN CLINICAL TRIALS TO THE CANCER GENOME ATLAS.
  Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2016 Geifman N, Butte AJ
• Genetic analysis in a patient with nine primary malignant neoplasms: a rare case of Li-Fraumeni syndrome.
  Oncology reports 2015 Li X, Kang J, Pan Q, Sikora-Wohlfeld W, Zhao D, Meng C, Bai C, Patwardhan A, Chen R, Ren H, Butte AJ, Ding K
• Immune modulators in disease: integrating knowledge from the biomedical literature and gene expression.
  Journal of the American Medical Informatics Association : JAMIA 2015 Geifman N, Bhattacharya S, Butte AJ
• Systematic pan-cancer analysis of tumour purity.
  Nature communications 2015 Aran D, Sirota M, Butte AJ
• Opening clinical trial data: are the voluntary data-sharing portals enough?
  BMC medicine 2015 Geifman N, Bollyky J, Bhattacharya S, Butte AJ
• Relating Chemical Structure to Cellular Response: An Integrative Analysis of Gene Expression, Bioactivity, and Structural Data Across 11,000 Compounds.
  CPT: pharmacometrics & systems pharmacology 2015 Chen B, Greenside P, Paik H, Sirota M, Hadley D, Butte AJ
• Reanalysis of the Rituximab in ANCA-Associated Vasculitis trial identifies granulocyte subsets as a novel early marker of successful treatment.
  Arthritis research & therapy 2015 Nasrallah M, Pouliot Y, Hartmann B, Dunn P, Thomson E, Wiser J, Butte AJ
• Achieving high-sensitivity for clinical applications using augmented exome sequencing.
  Genome medicine 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, Garcia S, Chandratillake G, Kirk S, Ashley E, Snyder …
• Serological targeted analysis of an ITIH4 peptide isoform: a preterm birth biomarker and its associated SNP implications.
  Journal of genetics and genomics = Yi chuan xue bao 2015 Tan Z, Hu Z, Cai EY, Alev C, Yang T, Li Z, Sung J, El-Sayed YY, Shaw GM, Stevenson DK, Butte AJ, Sheng G, Sylvester KG, Cohen HJ, Ling XB
• Relating hepatocellular carcinoma tumor samples and cell lines using gene expression data in translational research.
  BMC medical genomics 2015 Chen B, Sirota M, Fan-Minogue H, Hadley D, Butte AJ
• ClinGen--the Clinical Genome Resource.
  The New England journal of medicine 2015 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 receptor CD44 is associated with systemic insulin resistance and proinflammatory macrophages in human adipose tissue.
  Diabetologia 2015 Liu LF, Kodama K, Wei K, Tolentino LL, Choi O, Engleman EG, Butte AJ, McLaughlin T
• Heterogeneity in recent-onset type 1 diabetes - a clinical trial perspective.
  Diabetes/metabolism research and reviews 2015 Bollyky JB, Xu P, Butte AJ, Wilson DM, Beam CA, Greenbaum CJ, Type 1 Diabetes TrialNet Study Group
• A survey of current trends in computational drug repositioning.
  Briefings in bioinformatics 2015 Li J, Zheng S, Chen B, Butte AJ, Swamidass SJ, Lu Z
• Robust meta-analysis of gene expression using the elastic net.
  Nucleic acids research 2015 Hughey JJ, Butte AJ
• Repurpose terbutaline sulfate for amyotrophic lateral sclerosis using electronic medical records.
  Scientific reports 2015 Paik H, Chung AY, Park HC, Park RW, Suk K, Kim J, Kim H, Lee K, Butte AJ
• Variation in the human immune system is largely driven by non-heritable influences.
  Cell 2015 Brodin P, Jojic V, Gao T, Bhattacharya S, Angel CJ, Furman D, Shen-Orr S, Dekker CL, Swan GE, Butte AJ, Maecker HT, Davis MM
• A systematic assessment of linking gene expression with genetic variants for prioritizing candidate targets.
  Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2015 Fan-Minogue H, Chen B, Sikora-Wohlfeld W, Sirota M, Butte AJ
• Characteristics of drug combination therapy in oncology by analyzing clinical trial data on ClinicalTrials.gov.
  Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2015 Wu M, Sirota M, Butte AJ, Chen B
• Aging disrupts cell subpopulation dynamics and diminishes the function of mesenchymal stem cells.
  Scientific reports 2014 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
• Anti-CD44 antibody treatment lowers hyperglycemia and improves insulin resistance, adipose inflammation, and hepatic steatosis in diet-induced obese mice.
  Diabetes 2014 Kodama K, Toda K, Morinaga S, Yamada S, Butte AJ
• The Integrative Human Microbiome Project: dynamic analysis of microbiome-host omics profiles during periods of human health and disease.
  Cell host & microbe 2014 Integrative HMP (iHMP) Research Network Consortium
• Organ size control is dominant over Rb family inactivation to restrict proliferation in vivo.
  Cell reports 2014 Ehmer U, Zmoos AF, Auerbach RK, Vaka D, Butte AJ, Kay MA, Sage J
• SMYD3 links lysine methylation of MAP3K2 to Ras-driven cancer.
  Nature 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, Sage J, Gozani O
• Whole-exome sequencing reveals TopBP1 as a novel gene in idiopathic pulmonary arterial hypertension.
  American journal of respiratory and critical care medicine 2014 de Jesus Perez VA, Yuan K, Lyuksyutova MA, Dewey F, Orcholski ME, Shuffle EM, Mathur M, Yancy L, Rojas V, Li CG, Cao A, Alastalo TP, Khazeni N, Cimprich KA, Butte AJ, Ashley E, Zamanian RT
• ImmPort: disseminating data to the public for the future of immunology.
  Immunologic research 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
• Disease risk factors identified through shared genetic architecture and electronic medical records.
  Science translational medicine 2014 Li L, Ruau DJ, Patel CJ, Weber SC, Chen R, Tatonetti NP, Dudley JT, Butte AJ
• Diabetes irreversibly depletes bone marrow-derived mesenchymal progenitor cell subpopulations.
  Diabetes 2014 Januszyk M, Sorkin M, Glotzbach JP, Vial IN, Maan ZN, Rennert RC, Duscher D, Thangarajah H, Longaker MT, Butte AJ, Gurtner GC
• Collaborative biomedicine in the age of big data: the case of cancer.
  Journal of medical Internet research 2014 Shaikh AR, Butte AJ, Schully SD, Dalton WS, Khoury MJ, Hesse BW
• A meta-analysis of lung cancer gene expression identifies PTK7 as a survival gene in lung adenocarcinoma.
  Cancer research 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
• 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 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, Hegde M, Graham BH, Need AC, Oviedo A, Schaaf …
• Clinical interpretation and implications of whole-genome sequencing.
  JAMA 2014 Dewey FE, Grove ME, Pan C, Goldstein BA, Bernstein JA, Chaib H, Merker JD, Goldfeder RL, Enns GM, David SP, Pakdaman N, Ormond KE, Caleshu C, Kingham K, Klein TE, Whirl-Carrillo M, Sakamoto K, Wheeler…
• Investigation of maternal environmental exposures in association with self-reported preterm birth.
  Reproductive toxicology (Elmsford, N.Y.) 2013 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, March of Dimes Prematurity Research Center at Stanford University School of Medicine
• Network medicine in disease analysis and therapeutics.
  Clinical pharmacology and therapeutics 2013 Chen B, Butte AJ
• Integrating multiple 'omics' analyses identifies serological protein biomarkers for preeclampsia.
  BMC medicine 2013 Liu LY, Yang T, Ji J, Wen Q, Morgan AA, Jin B, Chen G, Lyell DJ, Stevenson DK, Ling XB, Butte AJ
• A common rejection module (CRM) for acute rejection across multiple organs identifies novel therapeutics for organ transplantation.
  The Journal of experimental medicine 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 drug repositioning approach identifies tricyclic antidepressants as inhibitors of small cell lung cancer and other neuroendocrine tumors.
  Cancer discovery 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, Sage J
• Systematic evaluation of personal genome services for Japanese individuals.
  Journal of human genetics 2013 Kido T, Kawashima M, Nishino S, Swan M, Kamatani N, Butte AJ
• Making it personal: translational bioinformatics.
  Journal of the American Medical Informatics Association : JAMIA 2013 Butte AJ, Ohno-Machado L
• Whole genome sequencing in support of wellness and health maintenance.
  Genome medicine 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
• Systematic identification of DNA variants associated with ultraviolet radiation using a novel Geographic-Wide Association Study (GeoWAS).
  BMC medical genetics 2013 Hsu I, Chen R, Ramesh A, Corona E, Kang HP, Ruau D, Butte AJ
• Peptidomic Identification of Serum Peptides Diagnosing Preeclampsia.
  PloS one 2013 Wen Q, Liu LY, Yang T, Alev C, Wu S, Stevenson DK, Sheng G, Butte AJ, Ling XB
• Relating genes to function: identifying enriched transcription factors using the ENCODE ChIP-Seq significance tool.
  Bioinformatics (Oxford, England) 2013 Auerbach RK, Chen B, Butte AJ
• Ethnic differences in the relationship between insulin sensitivity and insulin response: a systematic review and meta-analysis.
  Diabetes care 2013 Kodama K, Tojjar D, Yamada S, Toda K, Patel CJ, Butte AJ
• Analysis of the genetic basis of disease in the context of worldwide human relationships and migration.
  PLoS genetics 2013 Corona E, Chen R, Sikora M, Morgan AA, Patel CJ, Ramesh A, Bustamante CD, Butte AJ
• Systematic functional regulatory assessment of disease-associated variants.
  Proceedings of the National Academy of Sciences of the United States of America 2013 Karczewski KJ, Dudley JT, Kukurba KR, Chen R, Butte AJ, Montgomery SB, Snyder M
• Altering physiological networks using drugs: steps towards personalized physiology.
  BMC medical genomics 2013 Grossman AD, Cohen MJ, Manley GT, Butte AJ
• Immune response profiling identifies autoantibodies specific to Moyamoya patients.
  Orphanet journal of rare diseases 2013 Sigdel TK, Shoemaker LD, Chen R, Li L, Butte AJ, Sarwal MM, Steinberg GK
• Database integration of 4923 publicly-available samples of breast cancer molecular and clinical data.
  AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science 2013 Planey CR, Butte AJ
• Systematic identification of interaction effects between validated genome- and environment-wide associations on Type 2 Diabetes Mellitus.
  AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science 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 2013 Patel CJ, Chen R, Kodama K, Ioannidis JP, Butte AJ
• Systematic identification of risk factors for Alzheimer's disease through shared genetic architecture and electronic medical records.
  Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2013 Li L, Ruau D, Chen R, Weber S, Butte AJ
• FoxO6 regulates memory consolidation and synaptic function.
  Genes & development 2012 Salih DA, Rashid AJ, Colas D, de la Torre-Ubieta L, Zhu RP, Morgan AA, Santo EE, Ucar D, Devarajan K, Cole CJ, Madison DV, Shamloo M, Butte AJ, Bonni A, Josselyn SA, Brunet A
• A nutrient-wide association study on blood pressure.
  Circulation 2012 Tzoulaki I, Patel CJ, Okamura T, Chan Q, Brown IJ, Miura K, Ueshima H, Zhao L, Van Horn L, Daviglus ML, Stamler J, Butte AJ, Ioannidis JP, Elliott P
• Transdisciplinary translational science and the case of preterm birth.
  Journal of perinatology : official journal of the California Perinatal Association 2012 Stevenson DK, Shaw GM, Wise PH, Norton ME, Druzin ML, Valantine HA, McFarland DA, March of Dimes Prematurity Research Center at Stanford University School of Medicine
• Population genetic inference from personal genome data: impact of ancestry and admixture on human genomic variation.
  American journal of human genetics 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, Pearlstein K, …
• 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 2012 Li L, Khatri P, Sigdel TK, Tran T, Ying L, Vitalone MJ, Chen A, Hsieh S, Dai H, Zhang M, Naesens M, Zarkhin V, Sansanwal P, Chen R, Mindrinos M, Xiao W, Benfield M, Ettenger RB, Dharnidharka V, …
• 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 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
• Sequencing and analysis of a South Asian-Indian personal genome.
  BMC genomics 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
• Leveraging models of cell regulation and GWAS data in integrative network-based association studies.
  Nature genetics 2012 Califano A, Butte AJ, Friend S, Ideker T, Schadt E
• Identification of cell surface targets through meta-analysis of microarray data.
  Neoplasia (New York, N.Y.) 2012 Haeberle H, Dudley JT, Liu JT, Butte AJ, Contag CH
• Data-driven integration of epidemiological and toxicological data to select candidate interacting genes and environmental factors in association with disease.
  Bioinformatics (Oxford, England) 2012 Patel CJ, Chen R, Butte AJ
• Integrative approach to pain genetics identifies pain sensitivity loci across diseases.
  PLoS computational biology 2012 Ruau D, Dudley JT, Chen R, Phillips NG, Swan GE, Lazzeroni LC, Clark JD, Butte AJ, Angst MS
• Human genomic disease variants: a neutral evolutionary explanation.
  Genome research 2012 Dudley JT, Kim Y, Liu L, Markov GJ, Gerold K, Chen R, Butte AJ, Kumar S
• Clinical utility of sequence-based genotype compared with that derivable from genotyping arrays.
  Journal of the American Medical Informatics Association : JAMIA 2012 Morgan AA, Chen R, Butte AJ
• Translational bioinformatics: data-driven drug discovery and development.
  Clinical pharmacology and therapeutics 2012 Butte AJ, Ito S
• Integration of disease-specific single nucleotide polymorphisms, expression quantitative trait loci and coexpression networks reveal novel candidate genes for type 2 diabetes.
  Diabetologia 2012 Kang HP, Yang X, Chen R, Zhang B, Corona E, Schadt EE, Butte AJ
• Neonatal Informatics: Transforming Neonatal Care Through Translational Bioinformatics.
  NeoReviews 2012 Palma JP, Benitz WE, Tarczy-Hornoch P, Butte AJ, Longhurst CA
• 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 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
• Type 2 diabetes risk alleles demonstrate extreme directional differentiation among human populations, compared to other diseases.
  PLoS genetics 2012 Chen R, Corona E, Sikora M, Dudley JT, Morgan AA, Moreno-Estrada A, Nilsen GB, Ruau D, Lincoln SE, Bustamante CD, Butte AJ
• Coanalysis of GWAS with eQTLs reveals disease-tissue associations.
  AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science 2012 Kang HP, Morgan AA, Chen R, Schadt EE, Butte AJ
• Quantifying multi-ethnic representation in genetic studies of high mortality diseases.
  AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science 2012 Chen R, Dudley JT, Ruau D, Butte AJ
• Personal omics profiling reveals dynamic molecular and medical phenotypes.
  Cell 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, O'Huallachain M, Dudley JT, …
• Systematic evaluation of environmental factors: persistent pollutants and nutrients correlated with serum lipid levels.
  International journal of epidemiology 2012 Patel CJ, Cullen MR, Ioannidis JP, Butte AJ
• Evolutionary meta-analysis of association studies reveals ancient constraints affecting disease marker discovery.
  Molecular biology and evolution 2012 Dudley JT, Chen R, Sanderford M, Butte AJ, Kumar S
• Multiplex meta-analysis of RNA expression to identify genes with variants associated with immune dysfunction.
  Journal of the American Medical Informatics Association : JAMIA 2012 Morgan AA, Pyrgos VJ, Nadeau KC, Williamson PR, Butte AJ
• Ten years of pathway analysis: current approaches and outstanding challenges.
  PLoS computational biology 2012 Khatri P, Sirota M, Butte AJ
• Sex differences in reported pain across 11,000 patients captured in electronic medical records.
  The journal of pain 2012 Ruau D, Liu LY, Clark JD, Angst MS, Butte AJ
• Performance comparison of whole-genome sequencing platforms.
  Nature biotechnology 2011 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
• ProfileChaser: searching microarray repositories based on genome-wide patterns of differential expression.
  Bioinformatics (Oxford, England) 2011 Engreitz JM, Chen R, Morgan AA, Dudley JT, Mallelwar R, Butte AJ
• Performance comparison of exome DNA sequencing technologies.
  Nature biotechnology 2011 Clark MJ, Chen R, Lam HY, Karczewski KJ, Chen R, Euskirchen G, Butte AJ, Snyder M
• Phased whole-genome genetic risk in a family quartet using a major allele reference sequence.
  PLoS genetics 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, Thorn CF, Hebert JM, …
• Progressive histological damage in renal allografts is associated with expression of innate and adaptive immunity genes.
  Kidney international 2011 Naesens M, Khatri P, Li L, Sigdel TK, Vitalone MJ, Chen R, Butte AJ, Salvatierra O, Sarwal MM
• Sex differences in disease risk from reported genome-wide association study findings.
  Human genetics 2011 Liu LY, Schaub MA, Sirota M, Butte AJ
• Computational repositioning of the anticonvulsant topiramate for inflammatory bowel disease.
  Science translational medicine 2011 Dudley JT, Sirota M, Shenoy M, Pai RK, Roedder S, Chiang AP, Morgan AA, Sarwal MM, Pasricha PJ, Butte AJ
• Discovery and preclinical validation of drug indications using compendia of public gene expression data.
  Science translational medicine 2011 Sirota M, Dudley JT, Kim J, Chiang AP, Morgan AA, Sweet-Cordero A, Sage J, Butte AJ
• Identification of an IFN-γ/mast cell axis in a mouse model of chronic asthma.
  The Journal of clinical investigation 2011 Yu M, Eckart MR, Morgan AA, Mukai K, Butte AJ, Tsai M, Galli SJ
• Computationally translating molecular discoveries into tools for medicine: translational bioinformatics articles now featured in JAMIA.
  Journal of the American Medical Informatics Association : JAMIA 2011 Butte AJ, Shah NH
• Applications of translational bioinformatics in transplantation.
  Clinical pharmacology and therapeutics 2011 Khatri P, Sarwal MM, Butte AJ
• The role of bioinformatics in studying rheumatic and autoimmune disorders.
  Nature reviews. Rheumatology 2011 Sirota M, Butte AJ
• Exploiting drug-disease relationships for computational drug repositioning.
  Briefings in bioinformatics 2011 Dudley JT, Deshpande T, Butte AJ
• Predicting adverse drug reactions using publicly available PubChem BioAssay data.
  Clinical pharmacology and therapeutics 2011 Pouliot Y, Chiang AP, Butte AJ
• Transmission distortion in Crohn's disease risk gene ATG16L1 leads to sex difference in disease association.
  Inflammatory bowel diseases 2011 Liu LY, Schaub MA, Sirota M, Butte AJ
• Translational bioinformatics: linking knowledge across biological and clinical realms.
  Journal of the American Medical Informatics Association : JAMIA 2011 Sarkar IN, Butte AJ, Lussier YA, Tarczy-Hornoch P, Ohno-Machado L
• Comparison of automated and human assignment of MeSH terms on publicly-available molecular datasets.
  Journal of biomedical informatics 2011 Ruau D, Mbagwu M, Dudley JT, Krishnan V, Butte AJ
• Transplantomics and biomarkers in organ transplantation: a report from the first international conference.
  Transplantation 2011 Sarwal MM, Benjamin J, Butte AJ, Davis MM, Wood K, Chapman J
• Computational prediction and experimental validation associating FABP-1 and pancreatic adenocarcinoma with diabetes.
  BMC gastroenterology 2011 Sharaf RN, Butte AJ, Montgomery KD, Pai R, Dudley JT, Pasricha PJ
• Matching cancer genomes to established cell lines for personalized oncology.
  Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2011 Dudley JT, 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 2011 Chen R, Butte AJ
• Protein microarrays discover angiotensinogen and PRKRIP1 as novel targets for autoantibodies in chronic renal disease.
  Molecular & cellular proteomics : MCP 2010 Butte AJ, Sigdel TK, Wadia PP, Miklos DB, Sarwal MM
• Content-based microarray search using differential expression profiles.
  BMC bioinformatics 2010 Engreitz JM, Morgan AA, Dudley JT, Chen R, Thathoo R, Altman RB, Butte AJ
• In silico research in the era of cloud computing.
  Nature biotechnology 2010 Dudley JT, Butte AJ
• An integrative method for scoring candidate genes from association studies: application to warfarin dosing.
  BMC bioinformatics 2010 Tatonetti NP, Dudley JT, Sagreiya H, Butte AJ, Altman RB
• Comparison of multiplex meta analysis techniques for understanding the acute rejection of solid organ transplants.
  BMC bioinformatics 2010 Morgan AA, Khatri P, Jones RH, Sarwal MM, Butte AJ
• Latent physiological factors of complex human diseases revealed by independent component analysis of clinarrays.
  BMC bioinformatics 2010 Chen DP, Dudley JT, Butte AJ
• Non-synonymous and synonymous coding SNPs show similar likelihood and effect size of human disease association.
  PloS one 2010 Chen R, Davydov EV, Sirota M, Butte AJ
• Differentially expressed RNA from public microarray data identifies serum protein biomarkers for cross-organ transplant rejection and other conditions.
  PLoS computational biology 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
• Special article: an optimistic prognosis for the clinical utility of laboratory test data.
  Anesthesia and analgesia 2010 Zheng M, Ravindran P, Wang J, Epstein RH, Chen DP, Butte AJ, Peltz G
• Dynamic microRNA expression programs during cardiac differentiation of human embryonic stem cells: role for miR-499.
  Circulation. Cardiovascular genetics 2010 Wilson KD, Hu S, Venkatasubrahmanyam S, Fu JD, Sun N, Abilez OJ, Baugh JJ, Jia F, Ghosh Z, Li RA, Butte AJ, Wu JC
• Extreme evolutionary disparities seen in positive selection across seven complex diseases.
  PloS one 2010 Corona E, Dudley JT, Butte AJ
• Translational bioinformatics in the cloud: an affordable alternative.
  Genome medicine 2010 Dudley JT, Pouliot Y, Chen R, Morgan AA, Butte AJ
• Drug discovery in a multidimensional world: systems, patterns, and networks.
  Journal of cardiovascular translational research 2010 Dudley JT, Schadt E, Sirota M, Butte AJ, Ashley E
• Biomarker and drug discovery for gastroenterology through translational bioinformatics.
  Gastroenterology 2010 Dudley JT, Butte AJ
• 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 2010 Ober C, Butte AJ, Elias JA, Lusis AJ, Gan W, Banks-Schlegel S, Schwartz D
• An Environment-Wide Association Study (EWAS) on type 2 diabetes mellitus.
  PloS one 2010 Patel CJ, Bhattacharya J, Butte AJ
• Likelihood ratios for genome medicine.
  Genome medicine 2010 Morgan AA, Chen R, Butte AJ
• Current methodologies for translational bioinformatics.
  Journal of biomedical informatics 2010 Lussier YA, Butte AJ, Hunter L
• Predicting environmental chemical factors associated with disease-related gene expression data.
  BMC medical genomics 2010 Patel CJ, Butte AJ
• Clinical assessment incorporating a personal genome.
  Lancet (London, England) 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, Berlin DS, Thorn CF, Sangkuhl K, Hebert JM…
• Challenges in the clinical application of whole-genome sequencing.
  Lancet (London, England) 2010 Ormond KE, Wheeler MT, Hudgins L, Klein TE, Butte AJ, Altman RB, Ashley EA, Greely HT
• Cell type-specific gene expression differences in complex tissues.
  Nature methods 2010 Shen-Orr SS, Tibshirani R, Khatri P, Bodian DL, Staedtler F, Perry NM, Hastie T, Sarwal MM, Davis MM, Butte AJ
• Network-based elucidation of human disease similarities reveals common functional modules enriched for pluripotent drug targets.
  PLoS computational biology 2010 Suthram S, Dudley JT, Chiang AP, Chen R, Hastie TJ, Butte AJ
• Identification of complex metabolic states in critically injured patients using bioinformatic cluster analysis.
  Critical care (London, England) 2010 Cohen MJ, Grossman AD, Morabito D, Knudson MM, Butte AJ, Manley GT
• Antibodies specifically target AML antigen NuSAP1 after allogeneic bone marrow transplantation.
  Blood 2010 Wadia PP, Coram M, Armstrong RJ, Mindrinos M, Butte AJ, Miklos DB
• A quick guide for developing effective bioinformatics programming skills.
  PLoS computational biology 2009 Dudley JT, Butte AJ
• Autoimmune disease classification by inverse association with SNP alleles.
  PLoS genetics 2009 Sirota M, Schaub MA, Batzoglou S, Robinson WH, Butte AJ
• Validating pathophysiological models of aging using clinical electronic medical records.
  Journal of biomedical informatics 2009 Chen DP, Morgan AA, Butte AJ
• Dynamism in gene expression across multiple studies.
  Physiological genomics 2009 Morgan AA, Dudley JT, Deshpande T, Butte AJ
• FoxO3 regulates neural stem cell homeostasis.
  Cell stem cell 2009 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
• Protein microarrays identify antibodies to protein kinase Czeta that are associated with a greater risk of allograft loss in pediatric renal transplant recipients.
  Kidney international 2009 Sutherland SM, Li L, Sigdel TK, Wadia PP, Miklos DB, Butte AJ, Sarwal MM
• Relationship of differential gene expression profiles in CD34+ myelodysplastic syndrome marrow cells to disease subtype and progression.
  Blood 2009 Sridhar K, Ross DT, Tibshirani R, Butte AJ, Greenberg PL
• Infection in the intensive care unit alters physiological networks.
  BMC bioinformatics 2009 Grossman AD, Cohen MJ, Manley GT, Butte AJ
• Disease signatures are robust across tissues and experiments.
  Molecular systems biology 2009 Dudley JT, Tibshirani R, Deshpande T, Butte AJ
• Wiskott-Aldrich syndrome protein is an effector of Kit signaling.
  Blood 2009 Mani M, Venkatasubrahmanyam S, Sanyal M, Levy S, Butte A, Weinberg K, Jahn T
• Systematic evaluation of drug-disease relationships to identify leads for novel drug uses.
  Clinical pharmacology and therapeutics 2009 Chiang AP, Butte AJ
• Translational bioinformatics applications in genome medicine.
  Genome medicine 2009 Butte AJ
• A Classifier-based approach to identify genetic similarities between diseases.
  Bioinformatics (Oxford, England) 2009 Schaub MA, Kaplow IM, Sirota M, Do CB, Butte AJ, Batzoglou S
• C3 polymorphisms and outcomes of renal allografts.
  The New England journal of medicine 2009 Naesens M, Butte AJ, Sarwal MM
• MicroRNA profiling of human-induced pluripotent stem cells.
  Stem cells and development 2009 Wilson KD, Venkatasubrahmanyam S, Jia F, Sun N, Butte AJ, Wu JC
• Expression of complement components differs between kidney allografts from living and deceased donors.
  Journal of the American Society of Nephrology : JASN 2009 Naesens M, Li L, Ying L, Sansanwal P, Sigdel TK, Hsieh SC, Kambham N, Lerut E, Salvatierra O, Butte AJ, Sarwal MM
• 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 2009 Li L, Wadia P, Chen R, Kambham N, Naesens M, Sigdel TK, Miklos DB, Sarwal MM, Butte AJ
• Ontology-driven indexing of public datasets for translational bioinformatics.
  BMC bioinformatics 2009 Shah NH, Jonquet C, Chiang AP, Butte AJ, Chen R, Musen MA
• Selected proceedings of the First Summit on Translational Bioinformatics 2008.
  BMC bioinformatics 2009 Butte AJ, Sarkar IN, Ramoni M, Lussier Y, Troyanskaya O
• The "etiome": identification and clustering of human disease etiological factors.
  BMC bioinformatics 2009 Liu YI, Wise PH, Butte AJ
• Data-driven methods to discover molecular determinants of serious adverse drug events.
  Clinical pharmacology and therapeutics 2009 Chiang AP, Butte AJ
• Identification of discriminating biomarkers for human disease using integrative network biology.
  Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2009 Dudley JT, Butte AJ
• Towards a cytokine-cell interaction knowledgebase of the adaptive immune system.
  Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2009 Shen-Orr SS, Goldberger O, Garten Y, Rosenberg-Hasson Y, Lovelace PA, Hirschberg DL, Altman RB, Davis MM, Butte AJ
• GeneChaser: identifying all biological and clinical conditions in which genes of interest are differentially expressed.
  BMC bioinformatics 2008 Chen R, Mallelwar R, Thosar A, Venkatasubrahmanyam S, Butte AJ
• Report on EU-USA workshop: how systems biology can advance cancer research (27 October 2008).
  Molecular oncology 2008 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, …
• FitSNPs: highly differentially expressed genes are more likely to have variants associated with disease.
  Genome biology 2008 Chen R, Morgan AA, Dudley J, Deshpande T, Li L, Kodama K, Chiang AP, Butte AJ
• Expression-based Pathway Signature Analysis (EPSA): mining publicly available microarray data for insight into human disease.
  BMC medical genomics 2008 Tenenbaum JD, Walker MG, Utz PJ, Butte AJ
• Hematopoietic stem cell quiescence is maintained by compound contributions of the retinoblastoma gene family.
  Cell stem cell 2008 Viatour P, Somervaille TC, Venkatasubrahmanyam S, Kogan S, McLaughlin ME, Weissman IL, Butte AJ, Passegué E, Sage J
• Tissue- and age-specific changes in gene expression during disease induction and progression in NOD mice.
  Clinical immunology (Orlando, Fla.) 2008 Kodama K, Butte AJ, Creusot RJ, Su L, Sheng D, Hartnett M, Iwai H, Soares LR, Fathman CG
• Translational bioinformatics: coming of age.
  Journal of the American Medical Informatics Association : JAMIA 2008 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 2008 English SB, Shih SC, Ramoni MF, Smith LE, Butte AJ
• Medicine. The ultimate model organism.
  Science (New York, N.Y.) 2008 Butte AJ
• Enabling integrative genomic analysis of high-impact human diseases through text mining.
  Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2008 Dudley J, Butte AJ
• Novel integration of hospital electronic medical records and gene expression measurements to identify genetic markers of maturation.
  Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2008 Chen DP, Weber SC, Constantinou PS, Ferris TA, Lowe HJ, Butte AJ
• AILUN: reannotating gene expression data automatically.
  Nature methods 2007 Chen R, Li L, Butte AJ
• Clinical arrays of laboratory measures, or "clinarrays", built from an electronic health record enable disease subtyping by severity.
  AMIA ... Annual Symposium proceedings. AMIA Symposium 2007 Chen DP, Weber SC, Constantinou PS, Ferris TA, Lowe HJ, Butte AJ
• Methodologies for extracting functional pharmacogenomic experiments from international repository.
  AMIA ... Annual Symposium proceedings. AMIA Symposium 2007 Lin YA, Chiang A, Lin R, Yao P, Chen R, Butte AJ
• Evaluation and integration of 49 genome-wide experiments and the prediction of previously unknown obesity-related genes.
  Bioinformatics (Oxford, England) 2007 English SB, Butte AJ
• Creation and implications of a phenome-genome network.
  Nature biotechnology 2006 Butte AJ, Kohane IS
• Finding disease-related genomic experiments within an international repository: first steps in translational bioinformatics.
  AMIA ... Annual Symposium proceedings. AMIA Symposium 2006 Butte AJ, Chen R
• Multiplexed protein array platforms for analysis of autoimmune diseases.
  Annual review of immunology 2006 Balboni I, Chan SM, Kattah M, Tenenbaum JD, Butte AJ, Utz PJ
• Genome-wide analysis of host responses to the Pseudomonas aeruginosa type III secretion system yields synergistic effects.
  Cellular microbiology 2005 Ichikawa JK, English SB, Wolfgang MC, Jackson R, Butte AJ, Lory S
• Systematic survey reveals general applicability of "guilt-by-association" within gene coexpression networks.
  BMC bioinformatics 2005 Wolfe CJ, Kohane IS, Butte AJ
• Prediction of preadipocyte differentiation by gene expression reveals role of insulin receptor substrates and necdin.
  Nature cell biology 2005 Tseng YH, Butte AJ, Kokkotou E, Yechoor VK, Taniguchi CM, Kriauciunas KM, Cypess AM, Niinobe M, Yoshikawa K, Patti ME, Kahn CR
• A computational model to define the molecular causes of type 2 diabetes mellitus.
  Diabetes technology & therapeutics 2005 Pollard J, Butte AJ, Hoberman S, Joshi M, Levy J, Pappo J
• Genome-scale expression profiling of Hutchinson-Gilford progeria syndrome reveals widespread transcriptional misregulation leading to mesodermal/mesenchymal defects and accelerated atherosclerosis.
  Aging cell 2004 Csoka AB, English SB, Simkevich CP, Ginzinger DG, Butte AJ, Schatten GP, Rothman FG, Sedivy JM
• Conserved mechanisms across development and tumorigenesis revealed by a mouse development perspective of human cancers.
  Genes & development 2004 Kho AT, Zhao Q, Cai Z, Butte AJ, Kim JY, Pomeroy SL, Rowitch DH, Kohane IS
• Quantifying the relationship between co-expression, co-regulation and gene function.
  BMC bioinformatics 2004 Allocco DJ, Kohane IS, Butte AJ
• 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 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, Kahn CR, Mandarino LJ
• Reproducibility of gene expression across generations of Affymetrix microarrays.
  BMC bioinformatics 2003 Nimgaonkar A, Sanoudou D, Butte AJ, Haslett JN, Kunkel LM, Beggs AH, Kohane IS
• PGAGENE: integrating quantitative gene-specific results from the NHLBI programs for genomic applications.
  Bioinformatics (Oxford, England) 2003 Lee K, Kohane IS, Butte AJ
• Computerized recruiting for clinical trials in real time.
  Annals of emergency medicine 2003 Weiner DL, Butte AJ, Hibberd PL, Fleisher GR
• Comparing expression profiles of genes with similar promoter regions.
  Bioinformatics (Oxford, England) 2002 Park PJ, Butte AJ, Kohane IS
• Analysis of matched mRNA measurements from two different microarray technologies.
  Bioinformatics (Oxford, England) 2002 Kuo WP, Jenssen TK, Butte AJ, Ohno-Machado L, Kohane IS
• Further defining housekeeping, or "maintenance," genes Focus on "A compendium of gene expression in normal human tissues".
  Physiological genomics 2001 Butte AJ, Dzau VJ, Glueck SB
• Strict interpretation of vaccination guidelines with computerized algorithms and improper timing of administered doses.
  The Pediatric infectious disease journal 2001 Butte AJ, Shaw JS, Bernstein H
• The personal internetworked notary and guardian.
  International journal of medical informatics 2001 Riva A, Mandl KD, Oh DH, Nigrin DJ, Butte A, Szolovits P, Kohane IS
• Challenges in bioinformatics: infrastructure, models and analytics.
  Trends in biotechnology 2001 Butte AJ
• Determining significant fold differences in gene expression analysis.
  Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2001 Butte AJ, Ye J, Häring HU, Stumvoll M, White MF, 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 2000 Butte AJ, Tamayo P, Slonim D, Golub TR, Kohane IS
• Severe hypothyroidism caused by type 3 iodothyronine deiodinase in infantile hemangiomas.
  The New England journal of medicine 2000 Huang SA, Tu HM, Harney JW, Venihaki M, Butte AJ, Kozakewich HP, Fishman SJ, Larsen PR
• Enrolling patients into clinical trials faster using RealTime Recuiting.
  Proceedings. AMIA Symposium 2000 Butte AJ, Weinstein DA, Kohane IS
• Mutual information relevance networks: functional genomic clustering using pairwise entropy measurements.
  Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2000 Butte AJ, Kohane IS
• Unsupervised knowledge discovery in medical databases using relevance networks.
  Proceedings. AMIA Symposium 1999 Butte AJ, Kohane IS
• Insulin receptor substrate 1 mediates the stimulatory effect of insulin on GLUT4 translocation in transfected rat adipose cells.
  The Journal of biological chemistry 1994 Quon MJ, Butte AJ, Zarnowski MJ, Sesti G, Cushman SW, Taylor SI
• Insulin signal transduction pathways.
  Trends in endocrinology and metabolism: TEM 1994 Quon MJ, Butte AJ, 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.
  Proceedings of the National Academy of Sciences of the United States of America 1994 Quon MJ, Guerre-Millo M, Zarnowski MJ, Butte AJ, Em M, Cushman SW, Taylor SI
• Derivation of a scale-independent parameter which characterizes genetic sequence comparisons.
  Computers and biomedical research, an international journal 1993 DePetrillo PB, Butte AJ