Atul Butte, MD, PhD

Director of the Bakar Computational Health Sciences Institute
Professor of Pediatrics
Element Lead:Computational Health Sciences
Committee Members

Atul Butte, MD, PhD is the Priscilla Chan and Mark Zuckerberg Distinguished Professor and inaugural Director of the Bakar Computational Health Sciences Institute ( at the University of California, San Francisco (UCSF). Dr. Butte is also the Chief Data Scientist for the entire University of California Health System, with 20 health professional schools, 6 medical centers, and 10 hospitals. Dr. Butte has been continually funded by NIH for 20 years, and has authored over 200 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 founder of three investor-backed data-driven companies: Personalis, providing medical genome sequencing services, Carmenta (acquired by Progenity), discovering diagnostics for pregnancy complications, and NuMedii, finding new uses for drugs through open molecular data. Dr. Butte is a principal investigator of two major programs: (1) the California Initiative to Advance Precision Medicine, implementing Governor Brown’s vision to promote precision medicine in California; and (2) ImmPort, the clinical and molecular data repository for the National Institute of Allergy and Infectious Diseases. 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.


Evaluating large language models as agents in the clinic.

NPJ digital medicine

Mehandru N, Miao BY, Almaraz ER, Sushil M, Butte AJ, Alaa A

Accurate, Robust, and Scalable Machine Abstraction of Mayo Endoscopic Subscores From Colonoscopy Reports.

Inflammatory bowel diseases

Silverman AL, Bhasuran B, Mosenia A, Yasini F, Ramasamy G, Banerjee I, Gupta S, Mardirossian T, Narain R, Sewell J, Butte AJ, Rudrapatna VA

Real-world effectiveness of ustekinumab and vedolizumab in TNF-exposed pediatric patients with ulcerative colitis.

Journal of pediatric gastroenterology and nutrition

Patel PV, Zhang A, Bhasuran B, Ravindranath VG, Heyman MB, Verstraete SG, Butte AJ, Rosen MJ, Rudrapatna VA, ImproveCareNow Pediatric IBD Learning Health System

Algorithmic Identification of Treatment-Emergent Adverse Events From Clinical Notes Using Large Language Models: A Pilot Study in Inflammatory Bowel Disease.

Clinical pharmacology and therapeutics

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

Characterisation of digital therapeutic clinical trials: a systematic review with natural language processing.

The Lancet. Digital health

Miao BY, Sushil M, Xu A, Wang M, Arneson D, Berkley E, Subash M, Vashisht R, Rudrapatna V, Butte AJ

To do no harm - and the most good - with AI in health care.

Nature medicine

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

Predictive Modeling of Drug-Related Adverse Events with Real-World Data: A Case Study of Linezolid Hematologic Outcomes.

Clinical pharmacology and therapeutics

Patel A, Doernberg SB, Zack T, Butte AJ, Radtke KK

The Reporting Quality of Machine Learning Studies on Pediatric Diabetes Mellitus: Systematic Review.

Journal of medical Internet research

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

Sushil M, Butte AJ, Schuit E, van Smeden M, Leeuwenberg AM

Assessing the potential of GPT-4 to perpetuate racial and gender biases in health care: a model evaluation study.

The Lancet. Digital health

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

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

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

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

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

Sequential regression and simulation: a method for estimating causal effects from heterogeneous clinical trials without a common control group.

BMC medical research methodology

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

Vashisht R, Patel A, Dahm L, Han C, Medders KE, Mowers R, Byington CL, Koliwad SK, Butte AJ

The promise of digital healthcare technologies.

Frontiers in public health

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

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

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.


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)

Zamirpour S, Hubbard AE, Feng J, Butte AJ, Pirracchio R, Bishara A

Mammary duct luminal epithelium controls adipocyte thermogenic programme.


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

A certified de-identification system for all clinical text documents for information extraction at scale.

JAMIA open

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

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

Wang M, Sushil M, Miao BY, Butte AJ

Machine Learning Algorithm to Improve Cohort Identification in Interstitial Lung Disease.

American journal of respiratory and critical care medicine

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

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

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

Nucleic acid biomarkers of immune response and cell and tissue damage in children with COVID-19 and MIS-C.

Cell reports. Medicine

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

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.


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

Defining incidence and complications of fibrolamellar liver cancer through tiered computational analysis of clinical data.

NPJ precision oncology

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

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

Data Sharing Enters a New Era.

Annals of internal medicine

Bauchner H, McDermott MM, Butte AJ

DeepHeme: A generalizable, bone marrow classifier with hematopathologist-level performance.

bioRxiv : the preprint server for biology

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

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 performance of SARS-Cov-2 serology tests in the United States, 2020.

PloS one

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

Identification of Symptom Phenotypes of Hand Osteoarthritis Using Hierarchical Clustering: Results From the DIGICOD Cohort.

Arthritis care & research

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

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

Toward a causal model of chronic back pain: Challenges and opportunities.

Frontiers in computational neuroscience

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

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

Early immune markers of clinical, virological, and immunological outcomes in patients with COVID-19: a multi-omics study.


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

Predictability and stability testing to assess clinical decision instrument performance for children after blunt torso trauma.

PLOS digital health

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

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

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

Trans-channel fluorescence learning improves high-content screening for Alzheimer's disease therapeutics.

Nature machine intelligence

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

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

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

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

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

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

Nelson CA, Bove R, Butte AJ, Baranzini SE

Open challenges in developing digital therapeutics in the United States.

PLOS digital health

Miao BY, Arneson D, Wang M, Butte AJ

Application of Machine Learning for Cytometry Data.

Frontiers in immunology

Hu Z, Bhattacharya S, Butte AJ

Postoperative delirium prediction using machine learning models and preoperative electronic health record data.

BMC anesthesiology

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

Diabetes care

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

Opal: an implementation science tool for machine learning clinical decision support in anesthesia.

Journal of clinical monitoring and computing

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


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

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

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

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

Big Data in Nephrology.

Nature reviews. Nephrology

Kaur N, Bhattacharya S, Butte AJ

Rethinking PICO in the Machine Learning Era: ML-PICO.

Applied clinical informatics

Liu X, Anstey J, Li R, Sarabu C, Sono R, Butte AJ

Opportunities and Challenges in Democratizing Immunology Datasets.

Frontiers in immunology

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

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

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

Kwon DH, Vashisht R, Borno HT, Aggarwal RR, Small EJ, Butte AJ, Huang FW

Age- and Sex-Associated Variations in the Sensitivity of Serological Tests Among Individuals Infected With SARS-CoV-2.

JAMA network open

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)

Nelson CA, Acuna AU, Paul AM, Scott RT, Butte AJ, Cekanaviciute E, Baranzini SE, Costes SV

Identification of antiviral antihistamines for COVID-19 repurposing.

Biochemical and biophysical research communications

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

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

Arneson D, Elliott M, Mosenia A, Oskotsky B, Solodar S, Vashisht R, Zack T, Bleicher P, Butte AJ, Rudrapatna VA

Minimum information about clinical artificial intelligence modeling: the MI-CLAIM checklist.

Nature medicine

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

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

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

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

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

Kosti I, Lyalina S, Pollard KS, Butte AJ, Sirota M

Time for NIH to lead on data sharing.

Science (New York, N.Y.)

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

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.)

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

Opportunities and challenges in using real-world data for health care.

The Journal of clinical investigation

Rudrapatna VA, Butte AJ

Corticosteroid use is not associated with improved outcomes in acute exacerbation of IPF.

Respirology (Carlton, Vic.)

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.


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)

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

Tracing diagnosis trajectories over millions of patients reveal an unexpected risk in schizophrenia.

Scientific data

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

Yu K, Chen B, Aran D, Charalel J, Yau C, Wolf DM, van 't Veer LJ, Butte AJ, Goldstein T, Sirota M

A longitudinal big data approach for precision health.

Nature medicine

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

Closing the Evidence Gap in Interstitial Lung Disease. The Promise of Real-World Data.

American journal of respiratory and critical care medicine

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

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)

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

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

Andorf S, Bhattacharya S, Gaudilliere B, Shaw GM, Stevenson DK, Butte AJ, Sirota M

Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage.

Nature immunology

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

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

Norgeot B, Glicksberg BS, Butte AJ

Author Correction: Enabling precision medicine in neonatology, an integrated repository for preterm birth research.

Scientific data

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

Personal Mutanomes Meet Modern Oncology Drug Discovery and Precision Health.

Pharmacological reviews

Cheng F, Liang H, Butte AJ, Eng C, Nussinov R

Open data informatics and data repurposing for IBD.

Nature reviews. Gastroenterology & hepatology

Rudrapatna VA, Butte AJ

The 10,000 Immunomes Project: Building a Resource for Human Immunology.

Cell reports

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

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

Comparing Ethnicity-Specific Reference Intervals for Clinical Laboratory Tests from EHR Data.

The journal of applied laboratory medicine

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

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

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

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

The Atacama skeleton.

Genome research

Nolan G, Butte A

Whole-genome sequencing of Atacama skeleton shows novel mutations linked with dysplasia.

Genome research

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

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

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

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

Risky Business: Meeting the Structural Needs of Transdisciplinary Science.

The Journal of pediatrics

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

Combined inhibition of atypical PKC and histone deacetylase 1 is cooperative in basal cell carcinoma treatment.

JCI insight

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

PDX-MI: Minimal Information for Patient-Derived Tumor Xenograft Models.

Cancer research

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

Future cancer research priorities in the USA: a Lancet Oncology Commission.

The Lancet. Oncology

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

Comprehensive analysis of normal adjacent to tumor transcriptomes.

Nature communications

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

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

Big data opens a window onto wellness.

Nature biotechnology

Butte AJ

Reversal of cancer gene expression correlates with drug efficacy and reveals therapeutic targets.

Nature communications

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

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)

Shankar RD, Bhattacharya S, Jujjavarapu C, Andorf S, Wiser JA, Butte AJ

Evidence for benefit of statins to modify cognitive decline and risk in Alzheimer's disease.

Alzheimer's research & therapy

Geifman N, Brinton RD, Kennedy RE, Schneider LS, Butte AJ

In silico and in vitro drug screening identifies new therapeutic approaches for Ewing sarcoma.


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

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

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

Butte AJ

Defective Signaling in the JAK-STAT Pathway Tracks with Chronic Inflammation and Cardiovascular Risk in Aging Humans.

Cell systems

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

Widespread parainflammation in human cancer.

Genome biology

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.)

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

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

Cross-tissue Analysis of Gene and Protein Expression in Normal and Cancer Tissues.

Scientific reports

Kosti I, Jain N, Aran D, Butte AJ, Sirota M

Expression-Based Genome-Wide Association Study Links Vitamin D-Binding Protein With Autoantigenicity in Type 1 Diabetes.


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

Chen B, Butte AJ

Corrigendum: Systematic pan-cancer analysis of tumour purity.

Nature communications

Aran D, Sirota M, Butte AJ

Compendium of Immune Signatures Identifies Conserved and Species-Specific Biology in Response to Inflammation.


Godec J, Tan Y, Liberzon A, Tamayo P, Bhattacharya S, Butte AJ, Mesirov JP, Haining WN


Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing

Geifman N, Butte AJ

Genetic analysis in a patient with nine primary malignant neoplasms: a rare case of Li-Fraumeni syndrome.

Oncology reports

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

Geifman N, Bhattacharya S, Butte AJ

Systematic pan-cancer analysis of tumour purity.

Nature communications

Aran D, Sirota M, Butte AJ

Opening clinical trial data: are the voluntary data-sharing portals enough?

BMC medicine

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

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

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

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

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

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

ClinGen--the Clinical Genome Resource.

The New England journal of medicine

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

The receptor CD44 is associated with systemic insulin resistance and proinflammatory macrophages in human adipose tissue.


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

Bollyky JB, Xu P, Butte AJ, Wilson DM, Beam CA, Greenbaum CJ

A survey of current trends in computational drug repositioning.

Briefings in bioinformatics

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

Hughey JJ, Butte AJ

Repurpose terbutaline sulfate for amyotrophic lateral sclerosis using electronic medical records.

Scientific reports

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.


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

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

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing

Wu M, Sirota M, Butte AJ, Chen B

Aging disrupts cell subpopulation dynamics and diminishes the function of mesenchymal stem cells.

Scientific reports

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

Organ size control is dominant over Rb family inactivation to restrict proliferation in vivo.

Cell reports

Ehmer U, Zmoos AF, Auerbach RK, Vaka D, Butte AJ, Kay MA, Sage J

SMYD3 links lysine methylation of MAP3K2 to Ras-driven cancer.


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

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

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

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.


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

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

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

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

Clinical interpretation and implications of whole-genome sequencing.


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

Investigation of maternal environmental exposures in association with self-reported preterm birth.

Reproductive toxicology (Elmsford, N.Y.)

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

Network medicine in disease analysis and therapeutics.

Clinical pharmacology and therapeutics

Chen B, Butte AJ

Integrating multiple 'omics' analyses identifies serological protein biomarkers for preeclampsia.

BMC medicine

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

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

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

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

Butte AJ, Ohno-Machado L

Whole genome sequencing in support of wellness and health maintenance.

Genome medicine

Patel CJ, Sivadas A, Tabassum R, Preeprem T, Zhao J, Arafat D, Chen R, Morgan AA, Martin GS, Brigham KL, Butte AJ, Gibson G

Peptidomic Identification of Serum Peptides Diagnosing Preeclampsia.

PloS one

Wen Q, Liu LY, Yang T, Alev C, Wu S, Stevenson DK, Sheng G, Butte AJ, Ling XB

Analysis of the genetic basis of disease in the context of worldwide human relationships and migration.

PLoS genetics

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

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

Grossman AD, Cohen MJ, Manley GT, Butte AJ

Immune response profiling identifies autoantibodies specific to Moyamoya patients.

Orphanet journal of rare diseases

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

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

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

Li L, Ruau D, Chen R, Weber S, Butte AJ

FoxO6 regulates memory consolidation and synaptic function.

Genes & development

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.


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

Stevenson DK, Shaw GM, Wise PH, Norton ME, Druzin ML, Valantine HA, McFarland DA

Population genetic inference from personal genome data: impact of ancestry and admixture on human genomic variation.

American journal of human genetics

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

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

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

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

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

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

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.)

Haeberle H, Dudley JT, Liu JT, Butte AJ, Contag CH

Integrative approach to pain genetics identifies pain sensitivity loci across diseases.

PLoS computational biology

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

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

Morgan AA, Chen R, Butte AJ

Translational bioinformatics: data-driven drug discovery and development.

Clinical pharmacology and therapeutics

Butte AJ, Ito S

Neonatal Informatics: Transforming Neonatal Care Through Translational Bioinformatics.


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

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

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

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

Chen R, Dudley JT, Ruau D, Butte AJ

Personal omics profiling reveals dynamic molecular and medical phenotypes.


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

Systematic evaluation of environmental factors: persistent pollutants and nutrients correlated with serum lipid levels.

International journal of epidemiology

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

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

Morgan AA, Pyrgos VJ, Nadeau KC, Williamson PR, Butte AJ

Ten years of pathway analysis: current approaches and outstanding challenges.

PLoS computational biology

Khatri P, Sirota M, Butte AJ

Sex differences in reported pain across 11,000 patients captured in electronic medical records.

The journal of pain : official journal of the American Pain Society

Ruau D, Liu LY, Clark JD, Angst MS, Butte AJ

Performance comparison of whole-genome sequencing platforms.

Nature biotechnology

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)

Engreitz JM, Chen R, Morgan AA, Dudley JT, Mallelwar R, Butte AJ

Performance comparison of exome DNA sequencing technologies.

Nature biotechnology

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

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

Progressive histological damage in renal allografts is associated with expression of innate and adaptive immunity genes.

Kidney international

Naesens M, Khatri P, Li L, Sigdel TK, Vitalone MJ, Chen R, Butte AJ, Salvatierra O, Sarwal MM

Computational repositioning of the anticonvulsant topiramate for inflammatory bowel disease.

Science translational medicine

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

Sirota M, Dudley JT, Kim J, Chiang AP, Morgan AA, Sweet-Cordero A, Sage J, Butte AJ

Identification of an IFN-?/mast cell axis in a mouse model of chronic asthma.

The Journal of clinical investigation

Yu M, Eckart MR, Morgan AA, Mukai K, Butte AJ, Tsai M, Galli SJ

Applications of translational bioinformatics in transplantation.

Clinical pharmacology and therapeutics

Khatri P, Sarwal MM, Butte AJ

Exploiting drug-disease relationships for computational drug repositioning.

Briefings in bioinformatics

Dudley JT, Deshpande T, Butte AJ

Predicting adverse drug reactions using publicly available PubChem BioAssay data.

Clinical pharmacology and therapeutics

Pouliot Y, Chiang AP, Butte AJ

Translational bioinformatics: linking knowledge across biological and clinical realms.

Journal of the American Medical Informatics Association : JAMIA

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

Ruau D, Mbagwu M, Dudley JT, Krishnan V, Butte AJ

Transplantomics and biomarkers in organ transplantation: a report from the first international conference.


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

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

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

Chen R, Butte AJ

Protein microarrays discover angiotensinogen and PRKRIP1 as novel targets for autoantibodies in chronic renal disease.

Molecular & cellular proteomics : MCP

Butte AJ, Sigdel TK, Wadia PP, Miklos DB, Sarwal MM

Content-based microarray search using differential expression profiles.

BMC bioinformatics

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

Dudley JT, Butte AJ

An integrative method for scoring candidate genes from association studies: application to warfarin dosing.

BMC bioinformatics

Tatonetti NP, Dudley JT, Sagreiya H, Butte AJ, Altman RB

Differentially expressed RNA from public microarray data identifies serum protein biomarkers for cross-organ transplant rejection and other conditions.

PLoS computational biology

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

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

Wilson KD, Hu S, Venkatasubrahmanyam S, Fu JD, Sun N, Abilez OJ, Baugh JJ, Jia F, Ghosh Z, Li RA, Butte AJ, Wu JC

Translational bioinformatics in the cloud: an affordable alternative.

Genome medicine

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

Dudley JT, Schadt E, Sirota M, Butte AJ, Ashley E

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

Ober C, Butte AJ, Elias JA, Lusis AJ, Gan W, Banks-Schlegel S, Schwartz D

Likelihood ratios for genome medicine.

Genome medicine

Morgan AA, Chen R, Butte AJ

Current methodologies for translational bioinformatics.

Journal of biomedical informatics

Lussier YA, Butte AJ, Hunter L

Clinical assessment incorporating a personal genome.

Lancet (London, England)

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

Challenges in the clinical application of whole-genome sequencing.

Lancet (London, England)

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

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

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)

Cohen MJ, Grossman AD, Morabito D, Knudson MM, Butte AJ, Manley GT

Antibodies specifically target AML antigen NuSAP1 after allogeneic bone marrow transplantation.


Wadia PP, Coram M, Armstrong RJ, Mindrinos M, Butte AJ, Miklos DB

Autoimmune disease classification by inverse association with SNP alleles.

PLoS genetics

Sirota M, Schaub MA, Batzoglou S, Robinson WH, Butte AJ

Validating pathophysiological models of aging using clinical electronic medical records.

Journal of biomedical informatics

Chen DP, Morgan AA, Butte AJ

Dynamism in gene expression across multiple studies.

Physiological genomics

Morgan AA, Dudley JT, Deshpande T, Butte AJ

FoxO3 regulates neural stem cell homeostasis.

Cell stem cell

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

Infection in the intensive care unit alters physiological networks.

BMC bioinformatics

Grossman AD, Cohen MJ, Manley GT, Butte AJ

Disease signatures are robust across tissues and experiments.

Molecular systems biology

Dudley JT, Tibshirani R, Deshpande T, Butte AJ

Wiskott-Aldrich syndrome protein is an effector of Kit signaling.


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

Chiang AP, Butte AJ

A Classifier-based approach to identify genetic similarities between diseases.

Bioinformatics (Oxford, England)

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

Naesens M, Butte AJ, Sarwal MM

MicroRNA profiling of human-induced pluripotent stem cells.

Stem cells and development

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

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

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

Shah NH, Jonquet C, Chiang AP, Butte AJ, Chen R, Musen MA

Selected proceedings of the First Summit on Translational Bioinformatics 2008.

BMC bioinformatics

Butte AJ, Sarkar IN, Ramoni M, Lussier Y, Troyanskaya O

Data-driven methods to discover molecular determinants of serious adverse drug events.

Clinical pharmacology and therapeutics

Chiang AP, Butte AJ

Identification of discriminating biomarkers for human disease using integrative network biology.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing

Dudley JT, Butte AJ

Towards a cytokine-cell interaction knowledgebase of the adaptive immune system.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing

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

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

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

FitSNPs: highly differentially expressed genes are more likely to have variants associated with disease.

Genome biology

Chen R, Morgan AA, Dudley J, Deshpande T, Li L, Kodama K, Chiang AP, Butte AJ

Hematopoietic stem cell quiescence is maintained by compound contributions of the retinoblastoma gene family.

Cell stem cell

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.)

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

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

English SB, Shih SC, Ramoni MF, Smith LE, Butte AJ

Medicine. The ultimate model organism.

Science (New York, N.Y.)

Butte AJ

Enabling integrative genomic analysis of high-impact human diseases through text mining.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing

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

Chen DP, Weber SC, Constantinou PS, Ferris TA, Lowe HJ, Butte AJ

AILUN: reannotating gene expression data automatically.

Nature methods

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

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

Lin YA, Chiang A, Lin R, Yao P, Chen R, Butte AJ

Creation and implications of a phenome-genome network.

Nature biotechnology

Butte AJ, Kohane IS

Multiplexed protein array platforms for analysis of autoimmune diseases.

Annual review of immunology

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

Ichikawa JK, English SB, Wolfgang MC, Jackson R, Butte AJ, Lory S

Prediction of preadipocyte differentiation by gene expression reveals role of insulin receptor substrates and necdin.

Nature cell biology

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

Pollard J, Butte AJ, Hoberman S, Joshi M, Levy J, Pappo J

Conserved mechanisms across development and tumorigenesis revealed by a mouse development perspective of human cancers.

Genes & development

Kho AT, Zhao Q, Cai Z, Butte AJ, Kim JY, Pomeroy SL, Rowitch DH, Kohane IS

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

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

Nimgaonkar A, Sanoudou D, Butte AJ, Haslett JN, Kunkel LM, Beggs AH, Kohane IS

Computerized recruiting for clinical trials in real time.

Annals of emergency medicine

Weiner DL, Butte AJ, Hibberd PL, Fleisher GR

Comparing expression profiles of genes with similar promoter regions.

Bioinformatics (Oxford, England)

Park PJ, Butte AJ, Kohane IS

Analysis of matched mRNA measurements from two different microarray technologies.

Bioinformatics (Oxford, England)

Kuo WP, Jenssen TK, Butte AJ, Ohno-Machado L, Kohane IS

The personal internetworked notary and guardian.

International journal of medical informatics

Riva A, Mandl KD, Oh DH, Nigrin DJ, Butte A, Szolovits P, Kohane IS

Determining significant fold differences in gene expression analysis.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing

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

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

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

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

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

Quon MJ, Butte AJ, Zarnowski MJ, Sesti G, Cushman SW, Taylor SI

Insulin signal transduction pathways.

Trends in endocrinology and metabolism: TEM

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

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

DePetrillo PB, Butte AJ