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Atul Butte, MD, PhD

TitleProfessor
SchoolUCSF School of Medicine
DepartmentPediatrics
Address550 16th Street
San Francisco CA 94158
Phone415-514-0528
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    Collapse Biography 
    Collapse Education and Training
    Brown University, Providence, RIA.B. (Honors)05/1991Computer Science
    Brown University School of Medicine, Providence, RIM.D.05/1995Medicine
    Harvard Medical School, Boston, MAPh.D.2004Health Sciences and Technology (HST)

    Collapse Overview 
    Collapse Overview
    Atul Butte, MD, PhD is the Priscilla Chan and Mark Zuckerberg Distinguished Professor and inaugural Director of the Institute for Computational Health Sciences (ichs.ucsf.edu) at the University of California, San Francisco (UCSF). Dr. Butte is also the Executive Director for Clinical Informatics across the six University of California Medical Schools and Medical Centers. Dr. Butte 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 an Open Science Champion of Change 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 three major programs: the California Initiative to Advance Precision Medicine; ImmPort, the clinical and molecular data repository for the National Institute of Allergy and Infectious Diseases; and the California Precision Medicine Consortium, helping recruit tens of thousands of participants into President Obama's Precision Medicine Initiative. 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.


    Collapse Research 
    Collapse Research Activities and Funding
    California Precision Medicine Consortium
    NIH OT2OD024611Sep 27, 2016 - Aug 31, 2017
    Role: Co-Principal Investigator
    Integrative Analysis of Genomic, Epigenomic and Phenotypic Data for Disease Stratification of Endometriosis
    NIH/NICHD R01HD089511Sep 26, 2016 - Apr 30, 2021
    Role: Principal Investigator
    Stanford and Northrop Grumman proposal for the Oncology Models Forum
    NIH/NCI U24CA195858Sep 1, 2015 - Aug 31, 2020
    Role: Principal Investigator
    Biorepository of Human iPSCs for Studying Dilated and Hypertrophic Cardiomyopathy
    NIH/NHLBI R24HL117756Apr 15, 2014 - Mar 31, 2019
    Role: Co-Principal Investigator
    Vaccination and infection: indicators of immunological health and responsiveness
    NIH U19AI090019Jul 12, 2010 - Jun 30, 2016
    Role: Co-Investigator
    Integrating Microarray and Proteomic Data by Ontology-based Annotation
    NIH/NLM R01LM009719Sep 30, 2008 - Sep 29, 2013
    Role: Principal Investigator
    Comparative functional genomics for lung cancer gene discovery
    NIH/NCI R01CA138256Sep 23, 2008 - Jul 31, 2014
    Role: Co-Principal Investigator
    Enabling new translational discoveries using a genomic data-driven nosology
    NIH/NIGMS R01GM079719Sep 30, 2006 - Mar 31, 2016
    Role: Principal Investigator
    CREATION AND APPLICATION OF A DIABETES KNOWLEDGE BASE
    NIH/NLM K22LM008261Jan 15, 2005 - May 31, 2008
    Role: Principal Investigator
    Adaptive and Innate Immunity, Memory and Repertoire in Vaccination and Infection
    NIH U19AI057229Sep 1, 2003 - Mar 31, 2019
    Role: Co-Investigator

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    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
    List All   |   Timeline
    1. Chen B, Wei W, Ma L, Yang B, Gill RM, Chua MS, Butte A, So S. Computational Discovery of Niclosamide Ethanolamine, A Repurposed Drug Candidate That Reduces Growth of Hepatocellular Carcinoma Cells in Vitro and in Mice by Inhibiting CDC37 Signaling. Gastroenterology. 2017 Mar 08. PMID: 28284560.
      View in: PubMed
    2. Shankar RD, Bhattacharya S, Jujjavarapu C, Andorf S, Wiser JA, Butte A. RImmPort: an R/Bioconductor package that enables ready-for-analysis immunology research data. Bioinformatics. 2017 Jan 05. PMID: 28057685.
      View in: PubMed
    3. Vodovotz Y, Xia A, Read EL, Bassaganya-Riera J, Hafler DA, Sontag E, Wang J, Tsang JS, Day JD, Kleinstein SH, Butte A, Altman MC, Hammond R, Sealfon SC. Solving Immunology? Trends Immunol. 2016 Dec 13. PMID: 27986392.
      View in: PubMed
    4. Pessetto ZY, Chen B, Alturkmani H, Hyter S, Flynn CA, Baltezor M, Ma Y, Rosenthal HG, Neville KA, Weir SJ, Butte A, Godwin AK. In silico and in vitro drug screening identifies new therapeutic approaches for Ewing sarcoma. Oncotarget. 2016 Nov 16. PMID: 27863422.
      View in: PubMed
    5. Paik H, Chen B, Sirota M, Hadley D, Butte A. Integrating Clinical Phenotype and Gene Expression Data to Prioritize Novel Drug Uses. CPT Pharmacometrics Syst Pharmacol. 2016 Nov 14. PMID: 27860440.
      View in: PubMed
    6. Butte A. It takes a genome to understand a village: Population scale precision medicine. Proc Natl Acad Sci U S A. 2016 Nov 1; 113(44):12344-12346. PMID: 27791179.
      View in: PubMed
    7. 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 A, Davis MM. Defective Signaling in the JAK-STAT Pathway Tracks with Chronic Inflammation and Cardiovascular Risk in Aging Humans. Cell Syst. 2016 Oct 26; 3(4):374-384.e4. PMID: 27746093.
      View in: PubMed
    8. Hughey JJ, Butte A. Differential Phasing between Circadian Clocks in the Brain and Peripheral Organs in Humans. J Biol Rhythms. 2016 Oct 4. PMID: 27702781.
      View in: PubMed
    9. Aran D, Butte A. Digitally deconvolving the tumor microenvironment. Genome Biol. 2016; 17(1):175. PMID: 27549319.
      View in: PubMed
    10. Aran D, Lasry A, Zinger A, Biton M, Pikarsky E, Hellman A, Butte A, Ben-Neriah Y, et al. Widespread parainflammation in human cancer. Genome Biol. 2016; 17(1):145. PMID: 27386949.
      View in: PubMed
    11. Amor M, Moreno-Viedma V, Sarabi A, Grün NG, Itariu B, Leitner L, Steiner I, Bilban M, Kodama K, Butte A, Staffler G, Zeyda M, Stulnig TM, et al. Identification of matrix metalloproteinase-12 as a candidate molecule for prevention and treatment of cardiometabolic disease. Mol Med. 2016 Jun 30; 22. PMID: 27385318.
      View in: PubMed
    12. Geifman N, Butte A. A patient-level data meta-analysis of standard-of-care treatments from eight prostate cancer clinical trials. Sci Data. 2016; 3:160027. PMID: 27163794.
      View in: PubMed
    13. Kosti I, Jain N, Aran D, Butte A, Sirota M. Cross-tissue Analysis of Gene and Protein Expression in Normal and Cancer Tissues. Sci Rep. 2016; 6:24799. PMID: 27142790.
      View in: PubMed
    14. Bagley SC, Sirota M, Chen R, Butte A, Altman RB. Constraints on Biological Mechanism from Disease Comorbidity Using Electronic Medical Records and Database of Genetic Variants. PLoS Comput Biol. 2016 Apr; 12(4):e1004885. PMID: 27115429.
      View in: PubMed
    15. Kodama K, Zhao Z, Toda K, Yip L, Fuhlbrigge R, Miao D, Fathman CG, Yamada S, Butte A, Yu L. Expression-Based Genome-Wide Association Study Links Vitamin D-Binding Protein With Autoantigenicity in Type 1 Diabetes. Diabetes. 2016 May; 65(5):1341-9. PMID: 26983959.
      View in: PubMed
    16. Chen B, Butte A. Leveraging big data to transform target selection and drug discovery. Clin Pharmacol Ther. 2016 Mar; 99(3):285-97. PMID: 26659699.
      View in: PubMed
    17. Aran D, Sirota M, Butte A. Corrigendum: Systematic pan-cancer analysis of tumour purity. Nat Commun. 2016; 7:10707. PMID: 26848121.
      View in: PubMed
    18. Hughey JJ, Hastie T, Butte A. ZeitZeiger: supervised learning for high-dimensional data from an oscillatory system. Nucleic Acids Res. 2016 May 5; 44(8):e80. PMID: 26819407.
      View in: PubMed
    19. Godec J, Tan Y, Liberzon A, Tamayo P, Bhattacharya S, Butte A, Mesirov JP, Haining WN. Compendium of Immune Signatures Identifies Conserved and Species-Specific Biology in Response to Inflammation. Immunity. 2016 Jan 19; 44(1):194-206. PMID: 26795250.
      View in: PubMed
    20. Geifman N, Butte A. DO CANCER CLINICAL TRIAL POPULATIONS TRULY REPRESENT CANCER PATIENTS? A COMPARISON OF OPEN CLINICAL TRIALS TO THE CANCER GENOME ATLAS. Pac Symp Biocomput. 2016; 21:309-20. PMID: 26776196.
      View in: PubMed
    21. Li X, Kang J, Pan Q, Sikora-Wohlfeld W, Zhao D, Meng C, Bai C, Patwardhan A, Chen R, Ren H, Butte A, Ding K. Genetic analysis in a patient with nine primary malignant neoplasms: a rare case of Li-Fraumeni syndrome. Oncol Rep. 2016 Mar; 35(3):1519-28. PMID: 26707089.
      View in: PubMed
    22. Geifman N, Bhattacharya S, Butte A. Immune modulators in disease: integrating knowledge from the biomedical literature and gene expression. J Am Med Inform Assoc. 2016 May; 23(3):617-26. PMID: 26661719.
      View in: PubMed
    23. Aran D, Sirota M, Butte A. Systematic pan-cancer analysis of tumour purity. Nat Commun. 2015; 6:8971. PMID: 26634437; PMCID: PMC4671203 [Available on 06/04/16].
    24. Geifman N, Bollyky J, Bhattacharya S, Butte A. Opening clinical trial data: are the voluntary data-sharing portals enough? BMC Med. 2015; 13:280. PMID: 26560699; PMCID: PMC4642633.
    25. Chen B, Greenside P, Paik H, Sirota M, Hadley D, Butte A. Relating Chemical Structure to Cellular Response: An Integrative Analysis of Gene Expression, Bioactivity, and Structural Data Across 11,000 Compounds. CPT Pharmacometrics Syst Pharmacol. 2015 Oct; 4(10):576-84. PMID: 26535158; PMCID: PMC4625862.
    26. Nasrallah M, Pouliot Y, Hartmann B, Dunn P, Thomson E, Wiser J, Butte A. Reanalysis of the Rituximab in ANCA-Associated Vasculitis trial identifies granulocyte subsets as a novel early marker of successful treatment. Arthritis Res Ther. 2015; 17:262. PMID: 26387933; PMCID: PMC4576403.
    27. 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 A, West J, Chen R. Achieving high-sensitivity for clinical applications using augmented exome sequencing. Genome Med. 2015; 7(1):71. PMID: 26269718; PMCID: PMC4534066.
    28. Tan Z, Hu Z, Cai EY, Alev C, Yang T, Li Z, Sung J, El-Sayed YY, Shaw GM, Stevenson DK, Butte A, Sheng G, Sylvester KG, Cohen HJ, Ling XB. Serological Targeted Analysis of an ITIH4 Peptide Isoform: A Preterm Birth Biomarker and Its Associated SNP Implications. J Genet Genomics. 2015 Sep 20; 42(9):507-10. PMID: 26408095.
      View in: PubMed
    29. Chen B, Sirota M, Fan-Minogue H, Hadley D, Butte A. Relating hepatocellular carcinoma tumor samples and cell lines using gene expression data in translational research. BMC Med Genomics. 2015; 8 Suppl 2:S5. PMID: 26043652; PMCID: PMC4460709.
    30. Rehm HL, Berg JS, Brooks LD, Bustamante CD, Evans JP, Landrum MJ, Ledbetter DH, Maglott DR, Martin CL, Nussbaum RL, Plon SE, Ramos EM, Sherry ST, Watson MS. ClinGen--the Clinical Genome Resource. N Engl J Med. 2015 Jun 4; 372(23):2235-42. PMID: 26014595; PMCID: PMC4474187 [Available on 12/04/15].
    31. Liu LF, Kodama K, Wei K, Tolentino LL, Choi O, Engleman EG, Butte A, McLaughlin T. The receptor CD44 is associated with systemic insulin resistance and proinflammatory macrophages in human adipose tissue. Diabetologia. 2015 Jul; 58(7):1579-86. PMID: 25952479.
      View in: PubMed
    32. Bollyky JB, Xu P, Butte A, Wilson DM, Beam CA, Greenbaum CJ. Heterogeneity in recent-onset type 1 diabetes - a clinical trial perspective. Diabetes Metab Res Rev. 2015 Sep; 31(6):588-94. PMID: 25689602.
      View in: PubMed
    33. Li J, Zheng S, Chen B, Butte A, Swamidass SJ, Lu Z. A survey of current trends in computational drug repositioning. Brief Bioinform. 2016 Jan; 17(1):2-12. PMID: 25832646.
      View in: PubMed
    34. Hughey JJ, Butte A. Robust meta-analysis of gene expression using the elastic net. Nucleic Acids Res. 2015 Jul 13; 43(12):e79. PMID: 25829177; PMCID: PMC4499117.
    35. Paik H, Chung AY, Park HC, Park RW, Suk K, Kim J, Kim H, Lee K, Butte A. Repurpose terbutaline sulfate for amyotrophic lateral sclerosis using electronic medical records. Sci Rep. 2015; 5:8580. PMID: 25739475.
      View in: PubMed
    36. Brodin P, Jojic V, Gao T, Bhattacharya S, Angel CJ, Furman D, Shen-Orr S, Dekker CL, Swan GE, Butte A, Maecker HT, Davis MM. Variation in the human immune system is largely driven by non-heritable influences. Cell. 2015 Jan 15; 160(1-2):37-47. PMID: 25594173; PMCID: PMC4302727 [Available on 01/15/16].
    37. Fan-Minogue H, Chen B, Sikora-Wohlfeld W, Sirota M, Butte A. A systematic assessment of linking gene expression with genetic variants for prioritizing candidate targets. Pac Symp Biocomput. 2015; 383-94. PMID: 25592598; PMCID: PMC4299914 [Available on 01/01/16].
    38. Wu M, Sirota M, Butte A, Chen B. Characteristics of drug combination therapy in oncology by analyzing clinical trial data on ClinicalTrials.gov. Pac Symp Biocomput. 2015; 68-79. PMID: 25592569; PMCID: PMC4361221.
    39. 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 A, Gurtner GC. Aging disrupts cell subpopulation dynamics and diminishes the function of mesenchymal stem cells. Sci Rep. 2014; 4:7144. PMID: 25413454; PMCID: PMC4239576.
    40. Kodama K, Toda K, Morinaga S, Yamada S, Butte A. Anti-CD44 antibody treatment lowers hyperglycemia and improves insulin resistance, adipose inflammation, and hepatic steatosis in diet-induced obese mice. Diabetes. 2015 Mar; 64(3):867-75. PMID: 25294945; PMCID: PMC4392898 [Available on 03/01/16].
    41. The Integrative Human Microbiome Project: dynamic analysis of microbiome-host omics profiles during periods of human health and disease. Cell Host Microbe. 2014 Sep 10; 16(3):276-89. PMID: 25211071.
      View in: PubMed
    42. Ehmer U, Zmoos AF, Auerbach RK, Vaka D, Butte A, Kay MA, Sage J. Organ size control is dominant over Rb family inactivation to restrict proliferation in vivo. Cell Rep. 2014 Jul 24; 8(2):371-81. PMID: 25017070; PMCID: PMC4128252.
    43. 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 A, Vermeulen M, Sage J, Gozani O. SMYD3 links lysine methylation of MAP3K2 to Ras-driven cancer. Nature. 2014 Jun 12; 510(7504):283-7. PMID: 24847881; PMCID: PMC4122675.
    44. 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 A, Ashley E, Zamanian RT. Whole-exome sequencing reveals TopBP1 as a novel gene in idiopathic pulmonary arterial hypertension. Am J Respir Crit Care Med. 2014 May 15; 189(10):1260-72. PMID: 24702692; PMCID: PMC4225850.
    45. 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 A. ImmPort: disseminating data to the public for the future of immunology. Immunol Res. 2014 May; 58(2-3):234-9. PMID: 24791905.
      View in: PubMed
    46. Li L, Ruau DJ, Patel CJ, Weber SC, Chen R, Tatonetti NP, Dudley JT, Butte A. Disease risk factors identified through shared genetic architecture and electronic medical records. Sci Transl Med. 2014 Apr 30; 6(234):234ra57. PMID: 24786325; PMCID: PMC4323098.
    47. Januszyk M, Sorkin M, Glotzbach JP, Vial IN, Maan ZN, Rennert RC, Duscher D, Thangarajah H, Longaker MT, Butte A, Gurtner GC. Diabetes irreversibly depletes bone marrow-derived mesenchymal progenitor cell subpopulations. Diabetes. 2014 Sep; 63(9):3047-56. PMID: 24740572; PMCID: PMC4429348.
    48. Shaikh AR, Butte A, Schully SD, Dalton WS, Khoury MJ, Hesse BW. Collaborative biomedicine in the age of big data: the case of cancer. J Med Internet Res. 2014; 16(4):e101. PMID: 24711045; PMCID: PMC4004150.
    49. Chen R, Khatri P, Mazur PK, Polin M, Zheng Y, Vaka D, Hoang CD, Shrager J, Xu Y, Vicent S, Butte A, Sweet-Cordero EA. A meta-analysis of lung cancer gene expression identifies PTK7 as a survival gene in lung adenocarcinoma. Cancer Res. 2014 May 15; 74(10):2892-902. PMID: 24654231; PMCID: PMC4084668.
    50. 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 A, Chen R, Clark MJ, Haraksingh R, Cowan TM, He P, Langlois S, Zoghbi HY, Snyder M, Gibbs RA, Freeze HH, Goldstein DB. Mutations in NGLY1 cause an inherited disorder of the endoplasmic reticulum-associated degradation pathway. Genet Med. 2014 Oct; 16(10):751-8. PMID: 24651605; PMCID: PMC4243708.
    51. 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 A, Ford JM, Boxer L, Ioannidis JP, Yeung AC, Altman RB, Assimes TL, Snyder M, Ashley EA, Quertermous T. Clinical interpretation and implications of whole-genome sequencing. JAMA. 2014 Mar 12; 311(10):1035-45. PMID: 24618965; PMCID: PMC4119063.
    52. Patel CJ, Yang T, Hu Z, Wen Q, Sung J, El-Sayed YY, Cohen H, Gould J, Stevenson DK, Shaw GM, Ling XB, Butte A. Investigation of maternal environmental exposures in association with self-reported preterm birth. Reprod Toxicol. 2014 Jun; 45:1-7. PMID: 24373932; PMCID: PMC4316205.
    53. Chen B, Butte A. Network medicine in disease analysis and therapeutics. Clin Pharmacol Ther. 2013 Dec; 94(6):627-9. PMID: 24241637.
      View in: PubMed
    54. Liu LY, Yang T, Ji J, Wen Q, Morgan AA, Jin B, Chen G, Lyell DJ, Stevenson DK, Ling XB, Butte A. Integrating multiple 'omics' analyses identifies serological protein biomarkers for preeclampsia. BMC Med. 2013; 11:236. PMID: 24195779; PMCID: PMC4226208.
    55. Khatri P, Roedder S, Kimura N, De Vusser K, Morgan AA, Gong Y, Fischbein MP, Robbins RC, Naesens M, Butte A, Sarwal MM. A common rejection module (CRM) for acute rejection across multiple organs identifies novel therapeutics for organ transplantation. J Exp Med. 2013 Oct 21; 210(11):2205-21. PMID: 24127489; PMCID: PMC3804941.
    56. Kido T, Kawashima M, Nishino S, Swan M, Kamatani N, Butte A. Systematic evaluation of personal genome services for Japanese individuals. J Hum Genet. 2013 Nov; 58(11):734-41. PMID: 24067293.
      View in: PubMed
    57. 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 A, Sage J. A drug repositioning approach identifies tricyclic antidepressants as inhibitors of small cell lung cancer and other neuroendocrine tumors. Cancer Discov. 2013 Dec; 3(12):1364-77. PMID: 24078773; PMCID: PMC3864571.
    58. Butte A, Ohno-Machado L. Making it personal: translational bioinformatics. J Am Med Inform Assoc. 2013 Jul-Aug; 20(4):595-6. PMID: 23757438; PMCID: PMC3721179.
    59. Patel CJ, Sivadas A, Tabassum R, Preeprem T, Zhao J, Arafat D, Chen R, Morgan AA, Martin GS, Brigham KL, Butte A, Gibson G. Whole genome sequencing in support of wellness and health maintenance. Genome Med. 2013; 5(6):58. PMID: 23806097; PMCID: PMC3967117.
    60. Hsu I, Chen R, Ramesh A, Corona E, Kang HP, Ruau D, Butte A. Systematic identification of DNA variants associated with ultraviolet radiation using a novel Geographic-Wide Association Study (GeoWAS). BMC Med Genet. 2013; 14:62. PMID: 23786662; PMCID: PMC3699381.
    61. Wen Q, Liu LY, Yang T, Alev C, Wu S, Stevenson DK, Sheng G, Butte A, Ling XB. Peptidomic Identification of Serum Peptides Diagnosing Preeclampsia. PLoS One. 2013; 8(6):e65571. PMID: 23840341.
      View in: PubMed
    62. Auerbach RK, Chen B, Butte A. Relating genes to function: identifying enriched transcription factors using the ENCODE ChIP-Seq significance tool. Bioinformatics. 2013 Aug 1; 29(15):1922-4. PMID: 23732275; PMCID: PMC3712221.
    63. Kodama K, Tojjar D, Yamada S, Toda K, Patel CJ, Butte A. Ethnic differences in the relationship between insulin sensitivity and insulin response: a systematic review and meta-analysis. Diabetes Care. 2013 Jun; 36(6):1789-96. PMID: 23704681; PMCID: PMC3661854.
    64. Corona E, Chen R, Sikora M, Morgan AA, Patel CJ, Ramesh A, Bustamante CD, Butte A. Analysis of the genetic basis of disease in the context of worldwide human relationships and migration. PLoS Genet. 2013 May; 9(5):e1003447. PMID: 23717210; PMCID: PMC3662561.
    65. Karczewski KJ, Dudley JT, Kukurba KR, Chen R, Butte A, Montgomery SB, Snyder M. Systematic functional regulatory assessment of disease-associated variants. Proc Natl Acad Sci U S A. 2013 Jun 4; 110(23):9607-12. PMID: 23690573; PMCID: PMC3677437.
    66. Grossman AD, Cohen MJ, Manley GT, Butte A. Altering physiological networks using drugs: steps towards personalized physiology. BMC Med Genomics. 2013; 6 Suppl 2:S7. PMID: 23819503; PMCID: PMC3654899.
    67. Sigdel TK, Shoemaker LD, Chen R, Li L, Butte A, Sarwal MM, Steinberg GK. Immune response profiling identifies autoantibodies specific to Moyamoya patients. Orphanet J Rare Dis. 2013; 8:45. PMID: 23518061; PMCID: PMC3648437.
    68. Patel CJ, Chen R, Kodama K, Ioannidis JP, Butte A. Systematic identification of interaction effects between validated genome- and environment-wide associations on Type 2 Diabetes Mellitus. AMIA Jt Summits Transl Sci Proc. 2013; 2013:135. PMID: 24303322.
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    69. Planey CR, Butte A. Database integration of 4923 publicly-available samples of breast cancer molecular and clinical data. AMIA Jt Summits Transl Sci Proc. 2013; 2013:138-42. PMID: 24303324; PMCID: PMC3814460.
    70. Patel CJ, Chen R, Kodama K, Ioannidis JP, Butte A. Systematic identification of interaction effects between genome- and environment-wide associations in type 2 diabetes mellitus. Hum Genet. 2013 May; 132(5):495-508. PMID: 23334806; PMCID: PMC3625410.
    71. Li L, Ruau D, Chen R, Weber S, Butte A. Systematic identification of risk factors for Alzheimer's disease through shared genetic architecture and electronic medical records. Pac Symp Biocomput. 2013; 224-35. PMID: 23424127.
      View in: PubMed
    72. 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 A, Bonni A, Josselyn SA, Brunet A. FoxO6 regulates memory consolidation and synaptic function. Genes Dev. 2012 Dec 15; 26(24):2780-801. PMID: 23222102; PMCID: PMC3533081.
    73. Tzoulaki I, Patel CJ, Okamura T, Chan Q, Brown IJ, Miura K, Ueshima H, Zhao L, Van Horn L, Daviglus ML, Stamler J, Butte A, Ioannidis JP, Elliott P. A nutrient-wide association study on blood pressure. Circulation. 2012 Nov 20; 126(21):2456-64. PMID: 23093587; PMCID: PMC4105584.
    74. Stevenson DK, Shaw GM, Wise PH, Norton ME, Druzin ML, Valantine HA, McFarland DA. Transdisciplinary translational science and the case of preterm birth. J Perinatol. 2013 Apr; 33(4):251-8. PMID: 23079774; PMCID: PMC3613736.
    75. 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 A, De La Vega FM, Bustamante CD. Population genetic inference from personal genome data: impact of ancestry and admixture on human genomic variation. Am J Hum Genet. 2012 Oct 5; 91(4):660-71. PMID: 23040495; PMCID: PMC3484644.
    76. 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 A, Salvatierra O, Sarwal MM. A peripheral blood diagnostic test for acute rejection in renal transplantation. Am J Transplant. 2012 Oct; 12(10):2710-8. PMID: 23009139; PMCID: PMC4148014.
    77. 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 A, Sweet-Cordero EA. Cross-species functional analysis of cancer-associated fibroblasts identifies a critical role for CLCF1 and IL-6 in non-small cell lung cancer in vivo. Cancer Res. 2012 Nov 15; 72(22):5744-56. PMID: 22962265; PMCID: PMC3856949.
    78. Gupta R, Ratan A, Rajesh C, Chen R, Kim HL, Burhans R, Miller W, Santhosh S, Davuluri RV, Butte A, Schuster SC, Seshagiri S, Thomas G. Sequencing and analysis of a South Asian-Indian personal genome. BMC Genomics. 2012; 13:440. PMID: 22938532; PMCID: PMC3534380.
    79. Califano A, Butte A, Friend S, Ideker T, Schadt E. Leveraging models of cell regulation and GWAS data in integrative network-based association studies. Nat Genet. 2012 Aug; 44(8):841-7. PMID: 22836096; PMCID: PMC3593099.
    80. Haeberle H, Dudley JT, Liu JT, Butte A, Contag CH. Identification of cell surface targets through meta-analysis of microarray data. Neoplasia. 2012 Jul; 14(7):666-9. PMID: 22904683; PMCID: PMC3421962.
    81. Patel CJ, Chen R, Butte A. Data-driven integration of epidemiological and toxicological data to select candidate interacting genes and environmental factors in association with disease. Bioinformatics. 2012 Jun 15; 28(12):i121-6. PMID: 22689751; PMCID: PMC3371861.
    82. Ruau D, Dudley JT, Chen R, Phillips NG, Swan GE, Lazzeroni LC, Clark JD, Butte A, Angst MS. Integrative approach to pain genetics identifies pain sensitivity loci across diseases. PLoS Comput Biol. 2012; 8(6):e1002538. PMID: 22685391; PMCID: PMC3369906.
    83. Dudley JT, Kim Y, Liu L, Markov GJ, Gerold K, Chen R, Butte A, Kumar S. Human genomic disease variants: a neutral evolutionary explanation. Genome Res. 2012 Aug; 22(8):1383-94. PMID: 22665443; PMCID: PMC3409252.
    84. Butte A, Ito S. Translational bioinformatics: data-driven drug discovery and development. Clin Pharmacol Ther. 2012 Jun; 91(6):949-52. PMID: 22609903.
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    85. Morgan AA, Chen R, Butte A. Clinical utility of sequence-based genotype compared with that derivable from genotyping arrays. J Am Med Inform Assoc. 2012 Jun; 19(e1):e21-7. PMID: 22718036; PMCID: PMC3392859.
    86. Kang HP, Yang X, Chen R, Zhang B, Corona E, Schadt EE, Butte A. Integration of disease-specific single nucleotide polymorphisms, expression quantitative trait loci and coexpression networks reveal novel candidate genes for type 2 diabetes. Diabetologia. 2012 Aug; 55(8):2205-13. PMID: 22584726; PMCID: PMC3390705.
    87. Palma JP, Benitz WE, Tarczy-Hornoch P, Butte A, Longhurst CA. Neonatal Informatics: Transforming Neonatal Care Through Translational Bioinformatics. Neoreviews. 2012 May 1; 13(5):e281-e284. PMID: 22924023.
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    88. 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 A. Expression-based genome-wide association study links the receptor CD44 in adipose tissue with type 2 diabetes. Proc Natl Acad Sci U S A. 2012 May 1; 109(18):7049-54. PMID: 22499789; PMCID: PMC3344989.
    89. Chen R, Corona E, Sikora M, Dudley JT, Morgan AA, Moreno-Estrada A, Nilsen GB, Ruau D, Lincoln SE, Bustamante CD, Butte A. Type 2 diabetes risk alleles demonstrate extreme directional differentiation among human populations, compared to other diseases. PLoS Genet. 2012; 8(4):e1002621. PMID: 22511877; PMCID: PMC3325177.
    90. Chen R, Dudley JT, Ruau D, Butte A. Quantifying multi-ethnic representation in genetic studies of high mortality diseases. AMIA Jt Summits Transl Sci Proc. 2012; 2012:11-8. PMID: 22779041; PMCID: PMC3392055.
    91. Kang HP, Morgan AA, Chen R, Schadt EE, Butte A. Coanalysis of GWAS with eQTLs reveals disease-tissue associations. AMIA Jt Summits Transl Sci Proc. 2012; 2012:35-41. PMID: 22779046; PMCID: PMC3392070.
    92. 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 A, Ashley EA, Gerstein M, Nadeau KC, Tang H, Snyder M. Personal omics profiling reveals dynamic molecular and medical phenotypes. Cell. 2012 Mar 16; 148(6):1293-307. PMID: 22424236; PMCID: PMC3341616.
    93. Patel CJ, Cullen MR, Ioannidis JP, Butte A. Systematic evaluation of environmental factors: persistent pollutants and nutrients correlated with serum lipid levels. Int J Epidemiol. 2012 Jun; 41(3):828-43. PMID: 22421054; PMCID: PMC3396318.
    94. Morgan AA, Pyrgos VJ, Nadeau KC, Williamson PR, Butte A. Multiplex meta-analysis of RNA expression to identify genes with variants associated with immune dysfunction. J Am Med Inform Assoc. 2012 Mar-Apr; 19(2):284-8. PMID: 22319178; PMCID: PMC3277634.
    95. Dudley JT, Chen R, Sanderford M, Butte A, Kumar S. Evolutionary meta-analysis of association studies reveals ancient constraints affecting disease marker discovery. Mol Biol Evol. 2012 Sep; 29(9):2087-94. PMID: 22389448; PMCID: PMC3424407.
    96. Khatri P, Sirota M, Butte A. Ten years of pathway analysis: current approaches and outstanding challenges. PLoS Comput Biol. 2012; 8(2):e1002375. PMID: 22383865; PMCID: PMC3285573.
    97. Ruau D, Liu LY, Clark JD, Angst MS, Butte A. Sex differences in reported pain across 11,000 patients captured in electronic medical records. J Pain. 2012 Mar; 13(3):228-34. PMID: 22245360; PMCID: PMC3293998.
    98. Lam HY, Clark MJ, Chen R, Chen R, Natsoulis G, O'Huallachain M, Dewey FE, Habegger L, Ashley EA, Gerstein MB, Butte A, Ji HP, Snyder M. Performance comparison of whole-genome sequencing platforms. Nat Biotechnol. 2012 Jan; 30(1):78-82. PMID: 22178993; PMCID: PMC4076012.
    99. Engreitz JM, Chen R, Morgan AA, Dudley JT, Mallelwar R, Butte A. ProfileChaser: searching microarray repositories based on genome-wide patterns of differential expression. Bioinformatics. 2011 Dec 1; 27(23):3317-8. PMID: 21967760; PMCID: PMC3223361.
    100. Clark MJ, Chen R, Lam HY, Karczewski KJ, Chen R, Euskirchen G, Butte A, Snyder M. Performance comparison of exome DNA sequencing technologies. Nat Biotechnol. 2011 Oct; 29(10):908-14. PMID: 21947028; PMCID: PMC4127531.
    101. 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 A, Ashley EA. Phased whole-genome genetic risk in a family quartet using a major allele reference sequence. PLoS Genet. 2011 Sep; 7(9):e1002280. PMID: 21935354; PMCID: PMC3174201.
    102. Naesens M, Khatri P, Li L, Sigdel TK, Vitalone MJ, Chen R, Butte A, Salvatierra O, Sarwal MM. Progressive histological damage in renal allografts is associated with expression of innate and adaptive immunity genes. Kidney Int. 2011 Dec; 80(12):1364-76. PMID: 21881554; PMCID: PMC4492284.
    103. Liu LY, Schaub MA, Sirota M, Butte A. Sex differences in disease risk from reported genome-wide association study findings. Hum Genet. 2012 Mar; 131(3):353-64. PMID: 21858542; PMCID: PMC3260375.
    104. Sirota M, Dudley JT, Kim J, Chiang AP, Morgan AA, Sweet-Cordero A, Sage J, Butte A. Discovery and preclinical validation of drug indications using compendia of public gene expression data. Sci Transl Med. 2011 Aug 17; 3(96):96ra77. PMID: 21849665; PMCID: PMC3502016.
    105. Dudley JT, Sirota M, Shenoy M, Pai RK, Roedder S, Chiang AP, Morgan AA, Sarwal MM, Pasricha PJ, Butte A. Computational repositioning of the anticonvulsant topiramate for inflammatory bowel disease. Sci Transl Med. 2011 Aug 17; 3(96):96ra76. PMID: 21849664; PMCID: PMC3479650.
    106. Yu M, Eckart MR, Morgan AA, Mukai K, Butte A, Tsai M, Galli SJ. Identification of an IFN-?/mast cell axis in a mouse model of chronic asthma. J Clin Invest. 2011 Aug; 121(8):3133-43. PMID: 21737883; PMCID: PMC3148724.
    107. Butte A, Shah NH. Computationally translating molecular discoveries into tools for medicine: translational bioinformatics articles now featured in JAMIA. J Am Med Inform Assoc. 2011 Jul-Aug; 18(4):352-3. PMID: 21672904; PMCID: PMC3128419.
    108. Khatri P, Sarwal MM, Butte A. Applications of translational bioinformatics in transplantation. Clin Pharmacol Ther. 2011 Aug; 90(2):323-7. PMID: 21716268; PMCID: PMC3476839.
    109. Sirota M, Butte A. The role of bioinformatics in studying rheumatic and autoimmune disorders. Nat Rev Rheumatol. 2011 Aug; 7(8):489-94. PMID: 21691330.
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    110. Dudley JT, Deshpande T, Butte A. Exploiting drug-disease relationships for computational drug repositioning. Brief Bioinform. 2011 Jul; 12(4):303-11. PMID: 21690101; PMCID: PMC3137933.
    111. Liu LY, Schaub MA, Sirota M, Butte A. Transmission distortion in Crohn's disease risk gene ATG16L1 leads to sex difference in disease association. Inflamm Bowel Dis. 2012 Feb; 18(2):312-22. PMID: 21618365; PMCID: PMC3165065.
    112. Pouliot Y, Chiang AP, Butte A. Predicting adverse drug reactions using publicly available PubChem BioAssay data. Clin Pharmacol Ther. 2011 Jul; 90(1):90-9. PMID: 21613989; PMCID: PMC3464971.
    113. Sarkar IN, Butte A, Lussier YA, Tarczy-Hornoch P, Ohno-Machado L. Translational bioinformatics: linking knowledge across biological and clinical realms. J Am Med Inform Assoc. 2011 Jul-Aug; 18(4):354-7. PMID: 21561873; PMCID: PMC3128415.
    114. Ruau D, Mbagwu M, Dudley JT, Krishnan V, Butte A. Comparison of automated and human assignment of MeSH terms on publicly-available molecular datasets. J Biomed Inform. 2011 Dec; 44 Suppl 1:S39-43. PMID: 21420508; PMCID: PMC3155012.
    115. Sarwal MM, Benjamin J, Butte A, Davis MM, Wood K, Chapman J. Transplantomics and biomarkers in organ transplantation: a report from the first international conference. Transplantation. 2011 Feb 27; 91(4):379-82. PMID: 21278631; PMCID: PMC3762499.
    116. Sharaf RN, Butte A, Montgomery KD, Pai R, Dudley JT, Pasricha PJ. Computational prediction and experimental validation associating FABP-1 and pancreatic adenocarcinoma with diabetes. BMC Gastroenterol. 2011; 11:5. PMID: 21251264; PMCID: PMC3037918.
    117. Chen R, Butte A. The reference human genome demonstrates high risk of type 1 diabetes and other disorders. Pac Symp Biocomput. 2011; 231-42. PMID: 21121051; PMCID: PMC3732491.
    118. Dudley JT, Chen R, Butte A. Matching cancer genomes to established cell lines for personalized oncology. Pac Symp Biocomput. 2011; 243-52. PMID: 21121052; PMCID: PMC3477496.
    119. Butte A, Sigdel TK, Wadia PP, Miklos DB, Sarwal MM. Protein microarrays discover angiotensinogen and PRKRIP1 as novel targets for autoantibodies in chronic renal disease. Mol Cell Proteomics. 2011 Mar; 10(3):M110.000497. PMID: 21183621; PMCID: PMC3047141.
    120. Engreitz JM, Morgan AA, Dudley JT, Chen R, Thathoo R, Altman RB, Butte A. Content-based microarray search using differential expression profiles. BMC Bioinformatics. 2010; 11:603. PMID: 21172034; PMCID: PMC3022631.
    121. Dudley JT, Butte A. In silico research in the era of cloud computing. Nat Biotechnol. 2010 Nov; 28(11):1181-5. PMID: 21057489; PMCID: PMC3755123.
    122. Morgan AA, Khatri P, Jones RH, Sarwal MM, Butte A. Comparison of multiplex meta analysis techniques for understanding the acute rejection of solid organ transplants. BMC Bioinformatics. 2010; 11 Suppl 9:S6. PMID: 21044364; PMCID: PMC2967747.
    123. Chen DP, Dudley JT, Butte A. Latent physiological factors of complex human diseases revealed by independent component analysis of clinarrays. BMC Bioinformatics. 2010; 11 Suppl 9:S4. PMID: 21044362; PMCID: PMC2967745.
    124. Tatonetti NP, Dudley JT, Sagreiya H, Butte A, Altman RB. An integrative method for scoring candidate genes from association studies: application to warfarin dosing. BMC Bioinformatics. 2010; 11 Suppl 9:S9. PMID: 21044367; PMCID: PMC2967750.
    125. Chen R, Davydov EV, Sirota M, Butte A. Non-synonymous and synonymous coding SNPs show similar likelihood and effect size of human disease association. PLoS One. 2010; 5(10):e13574. PMID: 21042586; PMCID: PMC2962641.
    126. 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 A. Differentially expressed RNA from public microarray data identifies serum protein biomarkers for cross-organ transplant rejection and other conditions. PLoS Comput Biol. 2010; 6(9). PMID: 20885780; PMCID: PMC2944782.
    127. Zheng M, Ravindran P, Wang J, Epstein RH, Chen DP, Butte A, Peltz G. Special article: an optimistic prognosis for the clinical utility of laboratory test data. Anesth Analg. 2010 Oct; 111(4):1026-35. PMID: 20810674.
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    128. Wilson KD, Hu S, Venkatasubrahmanyam S, Fu JD, Sun N, Abilez OJ, Baugh JJ, Jia F, Ghosh Z, Li RA, Butte A, Wu JC. Dynamic microRNA expression programs during cardiac differentiation of human embryonic stem cells: role for miR-499. Circ Cardiovasc Genet. 2010 Oct; 3(5):426-35. PMID: 20733065; PMCID: PMC3057038.
    129. Corona E, Dudley JT, Butte A. Extreme evolutionary disparities seen in positive selection across seven complex diseases. PLoS One. 2010; 5(8):e12236. PMID: 20808933; PMCID: PMC2923198.
    130. Dudley JT, Pouliot Y, Chen R, Morgan AA, Butte A. Translational bioinformatics in the cloud: an affordable alternative. Genome Med. 2010; 2(8):51. PMID: 20691073; PMCID: PMC2945008.
    131. Dudley JT, Schadt E, Sirota M, Butte A, Ashley E. Drug discovery in a multidimensional world: systems, patterns, and networks. J Cardiovasc Transl Res. 2010 Oct; 3(5):438-47. PMID: 20677029.
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    132. Dudley JT, Butte A. Biomarker and drug discovery for gastroenterology through translational bioinformatics. Gastroenterology. 2010 Sep; 139(3):735-41, 741.e1. PMID: 20650279.
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    133. Ober C, Butte A, Elias JA, Lusis AJ, Gan W, Banks-Schlegel S, Schwartz D. Getting from genes to function in lung disease: a National Heart, Lung, and Blood Institute workshop report. Am J Respir Crit Care Med. 2010 Sep 15; 182(6):732-7. PMID: 20558629; PMCID: PMC2949401.
    134. Patel CJ, Bhattacharya J, Butte A. An Environment-Wide Association Study (EWAS) on type 2 diabetes mellitus. PLoS One. 2010; 5(5):e10746. PMID: 20505766; PMCID: PMC2873978.
    135. Morgan AA, Chen R, Butte A. Likelihood ratios for genome medicine. Genome Med. 2010; 2(5):30. PMID: 20497613; PMCID: PMC2887074.
    136. Lussier YA, Butte A, Hunter L. Current methodologies for translational bioinformatics. J Biomed Inform. 2010 Jun; 43(3):355-7. PMID: 20470899; PMCID: PMC2894568.
    137. Patel CJ, Butte A. Predicting environmental chemical factors associated with disease-related gene expression data. BMC Med Genomics. 2010; 3:17. PMID: 20459635; PMCID: PMC2880288.
    138. Ashley EA, Butte A, Wheeler MT, Chen R, Klein TE, Dewey FE, Dudley JT, Ormond KE, Pavlovic A, Morgan AA, Pushkarev D, Neff NF, Hudgins L, Gong L, Hodges LM, Berlin DS, Thorn CF, Sangkuhl K, Hebert JM, Woon M, Sagreiya H, Whaley R, Knowles JW, Chou MF, Thakuria JV, Rosenbaum AM, Zaranek AW, Church GM, Greely HT, Quake SR, Altman RB. Clinical assessment incorporating a personal genome. Lancet. 2010 May 1; 375(9725):1525-35. PMID: 20435227; PMCID: PMC2937184.
    139. Ormond KE, Wheeler MT, Hudgins L, Klein TE, Butte A, Altman RB, Ashley EA, Greely HT. Challenges in the clinical application of whole-genome sequencing. Lancet. 2010 May 15; 375(9727):1749-51. PMID: 20434765.
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    140. Shen-Orr SS, Tibshirani R, Khatri P, Bodian DL, Staedtler F, Perry NM, Hastie T, Sarwal MM, Davis MM, Butte A. Cell type-specific gene expression differences in complex tissues. Nat Methods. 2010 Apr; 7(4):287-9. PMID: 20208531; PMCID: PMC3699332.
    141. Suthram S, Dudley JT, Chiang AP, Chen R, Hastie TJ, Butte A. Network-based elucidation of human disease similarities reveals common functional modules enriched for pluripotent drug targets. PLoS Comput Biol. 2010 Feb; 6(2):e1000662. PMID: 20140234; PMCID: PMC2816673.
    142. Cohen MJ, Grossman AD, Morabito D, Knudson MM, Butte A, Manley GT. Identification of complex metabolic states in critically injured patients using bioinformatic cluster analysis. Crit Care. 2010; 14(1):R10. PMID: 20122274; PMCID: PMC2875524.
    143. Wadia PP, Coram M, Armstrong RJ, Mindrinos M, Butte A, Miklos DB. Antibodies specifically target AML antigen NuSAP1 after allogeneic bone marrow transplantation. Blood. 2010 Mar 11; 115(10):2077-87. PMID: 20053754; PMCID: PMC2837325.
    144. Dudley JT, Butte A. A quick guide for developing effective bioinformatics programming skills. PLoS Comput Biol. 2009 Dec; 5(12):e1000589. PMID: 20041221; PMCID: PMC2791169.
    145. Sirota M, Schaub MA, Batzoglou S, Robinson WH, Butte A. Autoimmune disease classification by inverse association with SNP alleles. PLoS Genet. 2009 Dec; 5(12):e1000792. PMID: 20041220; PMCID: PMC2791168.
    146. Chen DP, Morgan AA, Butte A. Validating pathophysiological models of aging using clinical electronic medical records. J Biomed Inform. 2010 Jun; 43(3):358-64. PMID: 19958842; PMCID: PMC2878870.
    147. Morgan AA, Dudley JT, Deshpande T, Butte A. Dynamism in gene expression across multiple studies. Physiol Genomics. 2010 Feb 4; 40(3):128-40. PMID: 19920211; PMCID: PMC2825768.
    148. Renault VM, Rafalski VA, Morgan AA, Salih DA, Brett JO, Webb AE, Villeda SA, Thekkat PU, Guillerey C, Denko NC, Palmer TD, Butte A, Brunet A. FoxO3 regulates neural stem cell homeostasis. Cell Stem Cell. 2009 Nov 6; 5(5):527-39. PMID: 19896443; PMCID: PMC2775802.
    149. Sutherland SM, Li L, Sigdel TK, Wadia PP, Miklos DB, Butte A, Sarwal MM. Protein microarrays identify antibodies to protein kinase Czeta that are associated with a greater risk of allograft loss in pediatric renal transplant recipients. Kidney Int. 2009 Dec; 76(12):1277-83. PMID: 19812540; PMCID: PMC4464694.
    150. Sridhar K, Ross DT, Tibshirani R, Butte A, Greenberg PL. Relationship of differential gene expression profiles in CD34+ myelodysplastic syndrome marrow cells to disease subtype and progression. Blood. 2009 Nov 26; 114(23):4847-58. PMID: 19801443; PMCID: PMC2786292.
    151. Grossman AD, Cohen MJ, Manley GT, Butte A. Infection in the intensive care unit alters physiological networks. BMC Bioinformatics. 2009; 10 Suppl 9:S4. PMID: 19761574; PMCID: PMC2745691.
    152. Dudley JT, Tibshirani R, Deshpande T, Butte A. Disease signatures are robust across tissues and experiments. Mol Syst Biol. 2009; 5:307. PMID: 19756046; PMCID: PMC2758720.
    153. Mani M, Venkatasubrahmanyam S, Sanyal M, Levy S, Butte A, Weinberg K, Jahn T. Wiskott-Aldrich syndrome protein is an effector of Kit signaling. Blood. 2009 Oct 1; 114(14):2900-8. PMID: 19643989; PMCID: PMC2756200.
    154. Chiang AP, Butte A. Systematic evaluation of drug-disease relationships to identify leads for novel drug uses. Clin Pharmacol Ther. 2009 Nov; 86(5):507-10. PMID: 19571805; PMCID: PMC2836384.
    155. Butte A. Translational bioinformatics applications in genome medicine. Genome Med. 2009; 1(6):64. PMID: 19566916; PMCID: PMC2703873.
    156. Schaub MA, Kaplow IM, Sirota M, Do CB, Butte A, Batzoglou S. A Classifier-based approach to identify genetic similarities between diseases. Bioinformatics. 2009 Jun 15; 25(12):i21-9. PMID: 19477990; PMCID: PMC2687980.
    157. Naesens M, Butte A, Sarwal MM. C3 polymorphisms and outcomes of renal allografts. N Engl J Med. 2009 Jun 4; 360(23):2478; author reply 2478-9. PMID: 19504761.
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    158. Wilson KD, Venkatasubrahmanyam S, Jia F, Sun N, Butte A, Wu JC. MicroRNA profiling of human-induced pluripotent stem cells. Stem Cells Dev. 2009 Jun; 18(5):749-58. PMID: 19284351; PMCID: PMC3135181.
    159. Naesens M, Li L, Ying L, Sansanwal P, Sigdel TK, Hsieh SC, Kambham N, Lerut E, Salvatierra O, Butte A, Sarwal MM. Expression of complement components differs between kidney allografts from living and deceased donors. J Am Soc Nephrol. 2009 Aug; 20(8):1839-51. PMID: 19443638; PMCID: PMC2723986.
    160. Li L, Wadia P, Chen R, Kambham N, Naesens M, Sigdel TK, Miklos DB, Sarwal MM, Butte A. Identifying compartment-specific non-HLA targets after renal transplantation by integrating transcriptome and "antibodyome" measures. Proc Natl Acad Sci U S A. 2009 Mar 17; 106(11):4148-53. PMID: 19251643; PMCID: PMC2657434.
    161. Butte A, Sarkar IN, Ramoni M, Lussier Y, Troyanskaya O. Selected proceedings of the First Summit on Translational Bioinformatics 2008. BMC Bioinformatics. 2009; 10 Suppl 2:I1. PMID: 19208183; PMCID: PMC2646246.
    162. Liu YI, Wise PH, Butte A. The "etiome": identification and clustering of human disease etiological factors. BMC Bioinformatics. 2009; 10 Suppl 2:S14. PMID: 19208189; PMCID: PMC2646245.
    163. Shah NH, Jonquet C, Chiang AP, Butte A, Chen R, Musen MA. Ontology-driven indexing of public datasets for translational bioinformatics. BMC Bioinformatics. 2009; 10 Suppl 2:S1. PMID: 19208184; PMCID: PMC2646250.
    164. Chiang AP, Butte A. Data-driven methods to discover molecular determinants of serious adverse drug events. Clin Pharmacol Ther. 2009 Mar; 85(3):259-68. PMID: 19177064; PMCID: PMC2726746.
    165. Dudley JT, Butte A. Identification of discriminating biomarkers for human disease using integrative network biology. Pac Symp Biocomput. 2009; 27-38. PMID: 19209693; PMCID: PMC2749008.
    166. Shen-Orr SS, Goldberger O, Garten Y, Rosenberg-Hasson Y, Lovelace PA, Hirschberg DL, Altman RB, Davis MM, Butte A. Towards a cytokine-cell interaction knowledgebase of the adaptive immune system. Pac Symp Biocomput. 2009; 439-50. PMID: 19209721; PMCID: PMC2709757.
    167. Chen R, Mallelwar R, Thosar A, Venkatasubrahmanyam S, Butte A. GeneChaser: identifying all biological and clinical conditions in which genes of interest are differentially expressed. BMC Bioinformatics. 2008; 9:548. PMID: 19094235; PMCID: PMC2629779.
    168. Aebersold R, Auffray C, Baney E, Barillot E, Brazma A, Brett C, Brunak S, Butte A, Califano A, Celis J, Cufer T, Ferrell J, Galas D, Gallahan D, Gatenby R, Goldbeter A, Hace N, Henney A, Hood L, Iyengar R, Jackson V, Kallioniemi O, Klingmüller U, Kolar P, Kolch W, Kyriakopoulou C, Laplace F, Lehrach H, Marcus F, Matrisian L, Nolan G, Pelkmans L, Potti A, Sander C, Seljak M, Singer D, Sorger P, Stunnenberg H, Superti-Furga G, Uhlen M, Vidal M, Weinstein J, Wigle D, Williams M, Wolkenhauer O, Zhivotovsky B, Zinovyev A, Zupan B. Report on EU-USA workshop: how systems biology can advance cancer research (27 October 2008). Mol Oncol. 2009 Feb; 3(1):9-17. PMID: 19383362; PMCID: PMC2930781.
    169. Chen R, Morgan AA, Dudley J, Deshpande T, Li L, Kodama K, Chiang AP, Butte A. FitSNPs: highly differentially expressed genes are more likely to have variants associated with disease. Genome Biol. 2008; 9(12):R170. PMID: 19061490; PMCID: PMC2646274.
    170. Tenenbaum JD, Walker MG, Utz PJ, Butte A. Expression-based Pathway Signature Analysis (EPSA): mining publicly available microarray data for insight into human disease. BMC Med Genomics. 2008; 1:51. PMID: 18937865; PMCID: PMC2588448.
    171. Viatour P, Somervaille TC, Venkatasubrahmanyam S, Kogan S, McLaughlin ME, Weissman IL, Butte A, Passegué E, Sage J. Hematopoietic stem cell quiescence is maintained by compound contributions of the retinoblastoma gene family. Cell Stem Cell. 2008 Oct 9; 3(4):416-28. PMID: 18940733; PMCID: PMC2646421.
    172. Kodama K, Butte A, Creusot RJ, Su L, Sheng D, Hartnett M, Iwai H, Soares LR, Fathman CG. Tissue- and age-specific changes in gene expression during disease induction and progression in NOD mice. Clin Immunol. 2008 Nov; 129(2):195-201. PMID: 18801706; PMCID: PMC2592195.
    173. Butte A. Translational bioinformatics: coming of age. J Am Med Inform Assoc. 2008 Nov-Dec; 15(6):709-14. PMID: 18755990; PMCID: PMC2585538.
    174. English SB, Shih SC, Ramoni MF, Smith LE, Butte A. Use of Bayesian networks to probabilistically model and improve the likelihood of validation of microarray findings by RT-PCR. J Biomed Inform. 2009 Apr; 42(2):287-95. PMID: 18790084; PMCID: PMC3962641.
    175. Butte A. Medicine. The ultimate model organism. Science. 2008 Apr 18; 320(5874):325-7. PMID: 18420921; PMCID: PMC2749009.
    176. Chen DP, Weber SC, Constantinou PS, Ferris TA, Lowe HJ, Butte A. Novel integration of hospital electronic medical records and gene expression measurements to identify genetic markers of maturation. Pac Symp Biocomput. 2008; 243-54. PMID: 18229690; PMCID: PMC2716394.
    177. Dudley J, Butte A. Enabling integrative genomic analysis of high-impact human diseases through text mining. Pac Symp Biocomput. 2008; 580-91. PMID: 18229717; PMCID: PMC2735266.
    178. Chen R, Li L, Butte A. AILUN: reannotating gene expression data automatically. Nat Methods. 2007 Nov; 4(11):879. PMID: 17971777; PMCID: PMC2716375.
    179. Chen DP, Weber SC, Constantinou PS, Ferris TA, Lowe HJ, Butte A. Clinical arrays of laboratory measures, or "clinarrays", built from an electronic health record enable disease subtyping by severity. AMIA Annu Symp Proc. 2007; 115-9. PMID: 18693809; PMCID: PMC2655832.
    180. Lin YA, Chiang A, Lin R, Yao P, Chen R, Butte A. Methodologies for extracting functional pharmacogenomic experiments from international repository. AMIA Annu Symp Proc. 2007; 463-7. PMID: 18693879; PMCID: PMC2655846.
    181. English SB, Butte A. Evaluation and integration of 49 genome-wide experiments and the prediction of previously unknown obesity-related genes. Bioinformatics. 2007 Nov 1; 23(21):2910-7. PMID: 17921495; PMCID: PMC2839901.
    182. Balboni I, Chan SM, Kattah M, Tenenbaum JD, Butte A, Utz PJ. Multiplexed protein array platforms for analysis of autoimmune diseases. Annu Rev Immunol. 2006; 24:391-418. PMID: 16551254.
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    183. Butte A, Kohane IS. Creation and implications of a phenome-genome network. Nat Biotechnol. 2006 Jan; 24(1):55-62. PMID: 16404398; PMCID: PMC2716377.
    184. Butte A, Chen R. Finding disease-related genomic experiments within an international repository: first steps in translational bioinformatics. AMIA Annu Symp Proc. 2006; 106-10. PMID: 17238312; PMCID: PMC1839582.
    185. Ichikawa JK, English SB, Wolfgang MC, Jackson R, Butte A, Lory S. Genome-wide analysis of host responses to the Pseudomonas aeruginosa type III secretion system yields synergistic effects. Cell Microbiol. 2005 Nov; 7(11):1635-46. PMID: 16207250.
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    186. Wolfe CJ, Kohane IS, Butte A. Systematic survey reveals general applicability of "guilt-by-association" within gene coexpression networks. BMC Bioinformatics. 2005; 6:227. PMID: 16162296; PMCID: PMC1239911.
    187. Tseng YH, Butte A, Kokkotou E, Yechoor VK, Taniguchi CM, Kriauciunas KM, Cypess AM, Niinobe M, Yoshikawa K, Patti ME, Kahn CR. Prediction of preadipocyte differentiation by gene expression reveals role of insulin receptor substrates and necdin. Nat Cell Biol. 2005 Jun; 7(6):601-11. PMID: 15895078.
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    188. Pollard J, Butte A, Hoberman S, Joshi M, Levy J, Pappo J. A computational model to define the molecular causes of type 2 diabetes mellitus. Diabetes Technol Ther. 2005 Apr; 7(2):323-36. PMID: 15857235.
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    189. Csoka AB, English SB, Simkevich CP, Ginzinger DG, Butte A, Schatten GP, Rothman FG, Sedivy JM. Genome-scale expression profiling of Hutchinson-Gilford progeria syndrome reveals widespread transcriptional misregulation leading to mesodermal/mesenchymal defects and accelerated atherosclerosis. Aging Cell. 2004 Aug; 3(4):235-43. PMID: 15268757.
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    190. Kho AT, Zhao Q, Cai Z, Butte A, Kim JY, Pomeroy SL, Rowitch DH, Kohane IS. Conserved mechanisms across development and tumorigenesis revealed by a mouse development perspective of human cancers. Genes Dev. 2004 Mar 15; 18(6):629-40. PMID: 15075291; PMCID: PMC387239.
    191. Allocco DJ, Kohane IS, Butte A. Quantifying the relationship between co-expression, co-regulation and gene function. BMC Bioinformatics. 2004 Feb 25; 5:18. PMID: 15053845; PMCID: PMC375525.
    192. Patti ME, Butte A, Crunkhorn S, Cusi K, Berria R, Kashyap S, Miyazaki Y, Kohane I, Costello M, Saccone R, Landaker EJ, Goldfine AB, Mun E, DeFronzo R, Finlayson J, Kahn CR, Mandarino LJ. Coordinated reduction of genes of oxidative metabolism in humans with insulin resistance and diabetes: Potential role of PGC1 and NRF1. Proc Natl Acad Sci U S A. 2003 Jul 8; 100(14):8466-71. PMID: 12832613; PMCID: PMC166252.
    193. Nimgaonkar A, Sanoudou D, Butte A, Haslett JN, Kunkel LM, Beggs AH, Kohane IS. Reproducibility of gene expression across generations of Affymetrix microarrays. BMC Bioinformatics. 2003 Jun 25; 4:27. PMID: 12823866; PMCID: PMC165600.
    194. Lee K, Kohane IS, Butte A. PGAGENE: integrating quantitative gene-specific results from the NHLBI programs for genomic applications. Bioinformatics. 2003 Apr 12; 19(6):778-9. PMID: 12691993.
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    195. Weiner DL, Butte A, Hibberd PL, Fleisher GR. Computerized recruiting for clinical trials in real time. Ann Emerg Med. 2003 Feb; 41(2):242-6. PMID: 12548275.
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    196. Butte A. The use and analysis of microarray data. Nat Rev Drug Discov. 2002 Dec; 1(12):951-60. PMID: 12461517.
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    197. Park PJ, Butte A, Kohane IS. Comparing expression profiles of genes with similar promoter regions. Bioinformatics. 2002 Dec; 18(12):1576-84. PMID: 12490441.
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    198. Kuo WP, Jenssen TK, Butte A, Ohno-Machado L, Kohane IS. Analysis of matched mRNA measurements from two different microarray technologies. Bioinformatics. 2002 Mar; 18(3):405-12. PMID: 11934739.
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    199. Butte A, Dzau VJ, Glueck SB. Further defining housekeeping, or "maintenance," genes Focus on "A compendium of gene expression in normal human tissues". Physiol Genomics. 2001 Dec 21; 7(2):95-6. PMID: 11773595.
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    200. Butte A, Bao L, Reis BY, Watkins TW, Kohane IS. Comparing the similarity of time-series gene expression using signal processing metrics. J Biomed Inform. 2001 Dec; 34(6):396-405. PMID: 12198759.
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    201. Riva A, Mandl KD, Oh DH, Nigrin DJ, Butte A, Szolovits P, Kohane IS. The personal internetworked notary and guardian. Int J Med Inform. 2001 Jun; 62(1):27-40. PMID: 11340004.
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    202. Butte A, Shaw JS, Bernstein H. Strict interpretation of vaccination guidelines with computerized algorithms and improper timing of administered doses. Pediatr Infect Dis J. 2001 Jun; 20(6):561-5. PMID: 11419495.
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    203. Butte A. Challenges in bioinformatics: infrastructure, models and analytics. Trends Biotechnol. 2001 May; 19(5):159-60. PMID: 11403022.
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    204. Butte A, Ye J, Häring HU, Stumvoll M, White MF, Kohane IS. Determining significant fold differences in gene expression analysis. Pac Symp Biocomput. 2001; 6-17. PMID: 11262977.
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    205. Butte A, Tamayo P, Slonim D, Golub TR, Kohane IS. Discovering functional relationships between RNA expression and chemotherapeutic susceptibility using relevance networks. Proc Natl Acad Sci U S A. 2000 Oct 24; 97(22):12182-6. PMID: 11027309; PMCID: PMC17315.
    206. Huang SA, Tu HM, Harney JW, Venihaki M, Butte A, Kozakewich HP, Fishman SJ, Larsen PR. Severe hypothyroidism caused by type 3 iodothyronine deiodinase in infantile hemangiomas. N Engl J Med. 2000 Jul 20; 343(3):185-9. PMID: 10900278.
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    207. Butte A, Kohane IS. Mutual information relevance networks: functional genomic clustering using pairwise entropy measurements. Pac Symp Biocomput. 2000; 418-29. PMID: 10902190.
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    208. Butte A, Weinstein DA, Kohane IS. Enrolling patients into clinical trials faster using RealTime Recuiting. Proc AMIA Symp. 2000; 111-5. PMID: 11079855; PMCID: PMC2244056.
    209. Butte A, Kohane IS. Unsupervised knowledge discovery in medical databases using relevance networks. Proc AMIA Symp. 1999; 711-5. PMID: 10566452; PMCID: PMC2232846.
    210. Mahdi NA, Pathan AZ, Harrell L, Leon MN, Lopez J, Butte A, Ferrell M, Gold HK, Palacios IF. Directional coronary atherectomy for the treatment of Palmaz-Schatz in-stent restenosis. Am J Cardiol. 1998 Dec 1; 82(11):1345-51. PMID: 9856917.
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    211. Goldberg N, Schifter D, Butte A, Stein R. Comparison of ST-segment/heart rate slope analysis with standard ST-segment measurement criteria to outcome of exercise thallium-201 imaging. Am J Cardiol. 1995 Nov 15; 76(14):1097-8. PMID: 7484875.
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    212. Quon MJ, Butte A, Zarnowski MJ, Sesti G, Cushman SW, Taylor SI. Insulin receptor substrate 1 mediates the stimulatory effect of insulin on GLUT4 translocation in transfected rat adipose cells. J Biol Chem. 1994 Nov 11; 269(45):27920-4. PMID: 7525563.
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    213. Quon MJ, Butte A, Taylor SI. Insulin signal transduction pathways. Trends Endocrinol Metab. 1994 Nov; 5(9):369-76. PMID: 18407232.
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    214. Quon MJ, Guerre-Millo M, Zarnowski MJ, Butte A, Em M, Cushman SW, Taylor SI. Tyrosine kinase-deficient mutant human insulin receptors (Met1153-->Ile) overexpressed in transfected rat adipose cells fail to mediate translocation of epitope-tagged GLUT4. Proc Natl Acad Sci U S A. 1994 Jun 7; 91(12):5587-91. PMID: 8202531; PMCID: PMC44041.
    215. DePetrillo PB, Butte A. Derivation of a scale-independent parameter which characterizes genetic sequence comparisons. Comput Biomed Res. 1993 Dec; 26(6):517-40. PMID: 8112054.
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