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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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      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.
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      1. Aran D, Butte AJ. Digitally deconvolving the tumor microenvironment. Genome Biol. 2016; 17(1):175. PMID: 27549319.
        View in: PubMed
      2. Aran D, Lasry A, Zinger A, Biton M, Pikarsky E, Hellman A, Butte AJ, Ben-Neriah Y, et al. Widespread parainflammation in human cancer. Genome Biol. 2016; 17(1):145. PMID: 27386949.
        View in: PubMed
      3. 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, 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.
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      4. Rennert RC, Januszyk M, Sorkin M, Rodrigues M, Maan ZN, Duscher D, Whittam AJ, Kosaraju R, Chung MT, Paik K, Li AY, Findlay M, Glotzbach JP, Butte AJ, Gurtner GC. Microfluidic single-cell transcriptional analysis rationally identifies novel surface marker profiles to enhance cell-based therapies. Nat Commun. 2016; 7:11945. PMID: 27324848.
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      5. Geifman N, Butte AJ. A patient-level data meta-analysis of standard-of-care treatments from eight prostate cancer clinical trials. Sci Data. 2016; 3:160027. PMID: 27163794.
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      6. Kosti I, Jain N, Aran D, Butte AJ, Sirota M. Cross-tissue Analysis of Gene and Protein Expression in Normal and Cancer Tissues. Sci Rep. 2016; 6:24799. PMID: 27142790.
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      7. Bagley SC, Sirota M, Chen R, Butte AJ, Altman RB. Constraints on Biological Mechanism from Disease Comorbidity Using Electronic Medical Records and Database of Genetic Variants. PLoS Comput Biol. 2016 Apr; 12(4):e1004885. PMID: 27115429.
        View in: PubMed
      8. Kodama K, Zhao Z, Toda K, Yip L, Fuhlbrigge R, Miao D, Fathman CG, Yamada S, Butte AJ, Yu L. Expression-Based Genome-Wide Association Study Links Vitamin D-Binding Protein With Autoantigenicity in Type 1 Diabetes. Diabetes. 2016 May; 65(5):1341-9. PMID: 26983959.
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      9. Chen B, Butte AJ. Leveraging big data to transform target selection and drug discovery. Clin Pharmacol Ther. 2016 Mar; 99(3):285-97. PMID: 26659699.
        View in: PubMed
      10. Aran D, Sirota M, Butte AJ. Corrigendum: Systematic pan-cancer analysis of tumour purity. Nat Commun. 2016; 7:10707. PMID: 26848121.
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      11. Hughey JJ, Hastie T, Butte AJ. ZeitZeiger: supervised learning for high-dimensional data from an oscillatory system. Nucleic Acids Res. 2016 May 5; 44(8):e80. PMID: 26819407.
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      12. Godec J, Tan Y, Liberzon A, Tamayo P, Bhattacharya S, Butte AJ, Mesirov JP, Haining WN. Compendium of Immune Signatures Identifies Conserved and Species-Specific Biology in Response to Inflammation. Immunity. 2016 Jan 19; 44(1):194-206. PMID: 26795250.
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      13. Geifman N, Butte AJ. 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.
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      14. Li X, Kang J, Pan Q, Sikora-Wohlfeld W, Zhao D, Meng C, Bai C, Patwardhan A, Chen R, Ren H, Butte AJ, Ding K. Genetic analysis in a patient with nine primary malignant neoplasms: a rare case of Li-Fraumeni syndrome. Oncol Rep. 2016 Mar; 35(3):1519-28. PMID: 26707089.
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      15. Geifman N, Bhattacharya S, Butte AJ. 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
      16. Aran D, Sirota M, Butte AJ. Systematic pan-cancer analysis of tumour purity. Nat Commun. 2015; 6:8971. PMID: 26634437; PMCID: PMC4671203 [Available on 06/04/16].
      17. Geifman N, Bollyky J, Bhattacharya S, Butte AJ. Opening clinical trial data: are the voluntary data-sharing portals enough? BMC Med. 2015; 13:280. PMID: 26560699; PMCID: PMC4642633.
      18. Chen B, Greenside P, Paik H, Sirota M, Hadley D, Butte AJ. Relating Chemical Structure to Cellular Response: An Integrative Analysis of Gene Expression, Bioactivity, and Structural Data Across 11,000 Compounds. CPT Pharmacometrics Syst Pharmacol. 2015 Oct; 4(10):576-84. PMID: 26535158; PMCID: PMC4625862.
      19. Nasrallah M, Pouliot Y, Hartmann B, Dunn P, Thomson E, Wiser J, Butte AJ. Reanalysis of the Rituximab in ANCA-Associated Vasculitis trial identifies granulocyte subsets as a novel early marker of successful treatment. Arthritis Res Ther. 2015; 17:262. PMID: 26387933; PMCID: PMC4576403.
      20. Patwardhan A, Harris J, Leng N, Bartha G, Church DM, Luo S, Haudenschild C, Pratt M, Zook J, Salit M, Tirch J, Morra M, Chervitz S, Li M, Clark M, Garcia S, Chandratillake G, Kirk S, Ashley E, Snyder M, Altman R, Bustamante C, Butte AJ, West J, Chen R. Achieving high-sensitivity for clinical applications using augmented exome sequencing. Genome Med. 2015; 7(1):71. PMID: 26269718; PMCID: PMC4534066.
      21. Tan Z, Hu Z, Cai EY, Alev C, Yang T, Li Z, Sung J, El-Sayed YY, Shaw GM, Stevenson DK, Butte AJ, Sheng G, Sylvester KG, Cohen HJ, Ling XB. Serological Targeted Analysis of an ITIH4 Peptide Isoform: A Preterm Birth Biomarker and Its Associated SNP Implications. J Genet Genomics. 2015 Sep 20; 42(9):507-10. PMID: 26408095.
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      22. Chen B, Sirota M, Fan-Minogue H, Hadley D, Butte AJ. Relating hepatocellular carcinoma tumor samples and cell lines using gene expression data in translational research. BMC Med Genomics. 2015; 8 Suppl 2:S5. PMID: 26043652; PMCID: PMC4460709.
      23. 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].
      24. Liu LF, Kodama K, Wei K, Tolentino LL, Choi O, Engleman EG, Butte AJ, McLaughlin T. The receptor CD44 is associated with systemic insulin resistance and proinflammatory macrophages in human adipose tissue. Diabetologia. 2015 Jul; 58(7):1579-86. PMID: 25952479.
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      25. Bollyky JB, Xu P, Butte AJ, 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.
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      26. Li J, Zheng S, Chen B, Butte AJ, Swamidass SJ, Lu Z. A survey of current trends in computational drug repositioning. Brief Bioinform. 2016 Jan; 17(1):2-12. PMID: 25832646.
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      27. Hughey JJ, Butte AJ. Robust meta-analysis of gene expression using the elastic net. Nucleic Acids Res. 2015 Jul 13; 43(12):e79. PMID: 25829177; PMCID: PMC4499117.
      28. Paik H, Chung AY, Park HC, Park RW, Suk K, Kim J, Kim H, Lee K, Butte AJ. Repurpose terbutaline sulfate for amyotrophic lateral sclerosis using electronic medical records. Sci Rep. 2015; 5:8580. PMID: 25739475.
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      29. Brodin P, Jojic V, Gao T, Bhattacharya S, Angel CJ, Furman D, Shen-Orr S, Dekker CL, Swan GE, Butte AJ, Maecker HT, Davis MM. Variation in the human immune system is largely driven by non-heritable influences. Cell. 2015 Jan 15; 160(1-2):37-47. PMID: 25594173; PMCID: PMC4302727 [Available on 01/15/16].
      30. Fan-Minogue H, Chen B, Sikora-Wohlfeld W, Sirota M, Butte AJ. A systematic assessment of linking gene expression with genetic variants for prioritizing candidate targets. Pac Symp Biocomput. 2015; 383-94. PMID: 25592598; PMCID: PMC4299914 [Available on 01/01/16].
      31. Wu M, Sirota M, Butte AJ, 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.
      32. Duscher D, Rennert RC, Januszyk M, Anghel E, Maan ZN, Whittam AJ, Perez MG, Kosaraju R, Hu MS, Walmsley GG, Atashroo D, Khong S, Butte AJ, Gurtner GC. Aging disrupts cell subpopulation dynamics and diminishes the function of mesenchymal stem cells. Sci Rep. 2014; 4:7144. PMID: 25413454; PMCID: PMC4239576.
      33. Kodama K, Toda K, Morinaga S, Yamada S, Butte AJ. 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].
      34. 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.
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      35. Ehmer U, Zmoos AF, Auerbach RK, Vaka D, Butte AJ, Kay MA, Sage J. Organ size control is dominant over Rb family inactivation to restrict proliferation in vivo. Cell Rep. 2014 Jul 24; 8(2):371-81. PMID: 25017070; PMCID: PMC4128252.
      36. Mazur PK, Reynoird N, Khatri P, Jansen PW, Wilkinson AW, Liu S, Barbash O, Van Aller GS, Huddleston M, Dhanak D, Tummino PJ, Kruger RG, Garcia BA, Butte AJ, Vermeulen M, Sage J, Gozani O. SMYD3 links lysine methylation of MAP3K2 to Ras-driven cancer. Nature. 2014 Jun 12; 510(7504):283-7. PMID: 24847881; PMCID: PMC4122675.
      37. de Jesus Perez VA, Yuan K, Lyuksyutova MA, Dewey F, Orcholski ME, Shuffle EM, Mathur M, Yancy L, Rojas V, Li CG, Cao A, Alastalo TP, Khazeni N, Cimprich KA, Butte AJ, Ashley E, Zamanian RT. Whole-exome sequencing reveals TopBP1 as a novel gene in idiopathic pulmonary arterial hypertension. Am J Respir Crit Care Med. 2014 May 15; 189(10):1260-72. PMID: 24702692; PMCID: PMC4225850.
      38. Bhattacharya S, Andorf S, Gomes L, Dunn P, Schaefer H, Pontius J, Berger P, Desborough V, Smith T, Campbell J, Thomson E, Monteiro R, Guimaraes P, Walters B, Wiser J, Butte AJ. ImmPort: disseminating data to the public for the future of immunology. Immunol Res. 2014 May; 58(2-3):234-9. PMID: 24791905.
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      39. Li L, Ruau DJ, Patel CJ, Weber SC, Chen R, Tatonetti NP, Dudley JT, Butte AJ. Disease risk factors identified through shared genetic architecture and electronic medical records. Sci Transl Med. 2014 Apr 30; 6(234):234ra57. PMID: 24786325; PMCID: PMC4323098.
      40. Januszyk M, Sorkin M, Glotzbach JP, Vial IN, Maan ZN, Rennert RC, Duscher D, Thangarajah H, Longaker MT, Butte AJ, Gurtner GC. Diabetes irreversibly depletes bone marrow-derived mesenchymal progenitor cell subpopulations. Diabetes. 2014 Sep; 63(9):3047-56. PMID: 24740572; PMCID: PMC4429348.
      41. Shaikh AR, Butte AJ, 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.
      42. Chen R, Khatri P, Mazur PK, Polin M, Zheng Y, Vaka D, Hoang CD, Shrager J, Xu Y, Vicent S, Butte AJ, Sweet-Cordero EA. A meta-analysis of lung cancer gene expression identifies PTK7 as a survival gene in lung adenocarcinoma. Cancer Res. 2014 May 15; 74(10):2892-902. PMID: 24654231; PMCID: PMC4084668.
      43. 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, 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.
      44. Dewey FE, Grove ME, Pan C, Goldstein BA, Bernstein JA, Chaib H, Merker JD, Goldfeder RL, Enns GM, David SP, Pakdaman N, Ormond KE, Caleshu C, Kingham K, Klein TE, Whirl-Carrillo M, Sakamoto K, Wheeler MT, Butte AJ, Ford JM, Boxer L, Ioannidis JP, Yeung AC, Altman RB, Assimes TL, Snyder M, Ashley EA, Quertermous T. Clinical interpretation and implications of whole-genome sequencing. JAMA. 2014 Mar 12; 311(10):1035-45. PMID: 24618965; PMCID: PMC4119063.
      45. Patel CJ, Yang T, Hu Z, Wen Q, Sung J, El-Sayed YY, Cohen H, Gould J, Stevenson DK, Shaw GM, Ling XB, Butte AJ. Investigation of maternal environmental exposures in association with self-reported preterm birth. Reprod Toxicol. 2014 Jun; 45:1-7. PMID: 24373932; PMCID: PMC4316205.
      46. Chen B, Butte AJ. Network medicine in disease analysis and therapeutics. Clin Pharmacol Ther. 2013 Dec; 94(6):627-9. PMID: 24241637.
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      47. Liu LY, Yang T, Ji J, Wen Q, Morgan AA, Jin B, Chen G, Lyell DJ, Stevenson DK, Ling XB, Butte AJ. Integrating multiple 'omics' analyses identifies serological protein biomarkers for preeclampsia. BMC Med. 2013; 11:236. PMID: 24195779; PMCID: PMC4226208.
      48. Khatri P, Roedder S, Kimura N, De Vusser K, Morgan AA, Gong Y, Fischbein MP, Robbins RC, Naesens M, Butte AJ, Sarwal MM. A common rejection module (CRM) for acute rejection across multiple organs identifies novel therapeutics for organ transplantation. J Exp Med. 2013 Oct 21; 210(11):2205-21. PMID: 24127489; PMCID: PMC3804941.
      49. Kido T, Kawashima M, Nishino S, Swan M, Kamatani N, Butte AJ. Systematic evaluation of personal genome services for Japanese individuals. J Hum Genet. 2013 Nov; 58(11):734-41. PMID: 24067293.
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      50. Jahchan NS, Dudley JT, Mazur PK, Flores N, Yang D, Palmerton A, Zmoos AF, Vaka D, Tran KQ, Zhou M, Krasinska K, Riess JW, Neal JW, Khatri P, Park KS, Butte AJ, Sage J. A drug repositioning approach identifies tricyclic antidepressants as inhibitors of small cell lung cancer and other neuroendocrine tumors. Cancer Discov. 2013 Dec; 3(12):1364-77. PMID: 24078773; PMCID: PMC3864571.
      51. Butte AJ, Ohno-Machado L. Making it personal: translational bioinformatics. J Am Med Inform Assoc. 2013 Jul-Aug; 20(4):595-6. PMID: 23757438; PMCID: PMC3721179.
      52. Patel CJ, Sivadas A, Tabassum R, Preeprem T, Zhao J, Arafat D, Chen R, Morgan AA, Martin GS, Brigham KL, Butte AJ, Gibson G. Whole genome sequencing in support of wellness and health maintenance. Genome Med. 2013; 5(6):58. PMID: 23806097; PMCID: PMC3967117.
      53. Hsu I, Chen R, Ramesh A, Corona E, Kang HP, Ruau D, Butte AJ. Systematic identification of DNA variants associated with ultraviolet radiation using a novel Geographic-Wide Association Study (GeoWAS). BMC Med Genet. 2013; 14:62. PMID: 23786662; PMCID: PMC3699381.
      54. Wen Q, Liu LY, Yang T, Alev C, Wu S, Stevenson DK, Sheng G, Butte AJ, Ling XB. Peptidomic Identification of Serum Peptides Diagnosing Preeclampsia. PLoS One. 2013; 8(6):e65571. PMID: 23840341.
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      55. Auerbach RK, Chen B, Butte AJ. 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.
      56. Kodama K, Tojjar D, Yamada S, Toda K, Patel CJ, Butte AJ. Ethnic differences in the relationship between insulin sensitivity and insulin response: a systematic review and meta-analysis. Diabetes Care. 2013 Jun; 36(6):1789-96. PMID: 23704681; PMCID: PMC3661854.
      57. Corona E, Chen R, Sikora M, Morgan AA, Patel CJ, Ramesh A, Bustamante CD, Butte AJ. Analysis of the genetic basis of disease in the context of worldwide human relationships and migration. PLoS Genet. 2013 May; 9(5):e1003447. PMID: 23717210; PMCID: PMC3662561.
      58. Karczewski KJ, Dudley JT, Kukurba KR, Chen R, Butte AJ, 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.
      59. Grossman AD, Cohen MJ, Manley GT, Butte AJ. Altering physiological networks using drugs: steps towards personalized physiology. BMC Med Genomics. 2013; 6 Suppl 2:S7. PMID: 23819503; PMCID: PMC3654899.
      60. Sigdel TK, Shoemaker LD, Chen R, Li L, Butte AJ, Sarwal MM, Steinberg GK. Immune response profiling identifies autoantibodies specific to Moyamoya patients. Orphanet J Rare Dis. 2013; 8:45. PMID: 23518061; PMCID: PMC3648437.
      61. Patel CJ, Chen R, Kodama K, Ioannidis JP, Butte AJ. 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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      62. Planey CR, Butte AJ. 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.
      63. Patel CJ, Chen R, Kodama K, Ioannidis JP, Butte AJ. Systematic identification of interaction effects between genome- and environment-wide associations in type 2 diabetes mellitus. Hum Genet. 2013 May; 132(5):495-508. PMID: 23334806; PMCID: PMC3625410.
      64. Li L, Ruau D, Chen R, Weber S, Butte AJ. 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.
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      65. Salih DA, Rashid AJ, Colas D, de la Torre-Ubieta L, Zhu RP, Morgan AA, Santo EE, Ucar D, Devarajan K, Cole CJ, Madison DV, Shamloo M, Butte AJ, Bonni A, Josselyn SA, Brunet A. FoxO6 regulates memory consolidation and synaptic function. Genes Dev. 2012 Dec 15; 26(24):2780-801. PMID: 23222102; PMCID: PMC3533081.
      66. Tzoulaki I, Patel CJ, Okamura T, Chan Q, Brown IJ, Miura K, Ueshima H, Zhao L, Van Horn L, Daviglus ML, Stamler J, Butte AJ, Ioannidis JP, Elliott P. A nutrient-wide association study on blood pressure. Circulation. 2012 Nov 20; 126(21):2456-64. PMID: 23093587; PMCID: PMC4105584.
      67. 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.
      68. Kidd JM, Gravel S, Byrnes J, Moreno-Estrada A, Musharoff S, Bryc K, Degenhardt JD, Brisbin A, Sheth V, Chen R, McLaughlin SF, Peckham HE, Omberg L, Bormann Chung CA, Stanley S, Pearlstein K, Levandowsky E, Acevedo-Acevedo S, Auton A, Keinan A, Acuña-Alonzo V, Barquera-Lozano R, Canizales-Quinteros S, Eng C, Burchard EG, Russell A, Reynolds A, Clark AG, Reese MG, Lincoln SE, Butte AJ, De La Vega FM, Bustamante CD. Population genetic inference from personal genome data: impact of ancestry and admixture on human genomic variation. Am J Hum Genet. 2012 Oct 5; 91(4):660-71. PMID: 23040495; PMCID: PMC3484644.
      69. Li L, Khatri P, Sigdel TK, Tran T, Ying L, Vitalone MJ, Chen A, Hsieh S, Dai H, Zhang M, Naesens M, Zarkhin V, Sansanwal P, Chen R, Mindrinos M, Xiao W, Benfield M, Ettenger RB, Dharnidharka V, Mathias R, Portale A, McDonald R, Harmon W, Kershaw D, Vehaskari VM, Kamil E, Baluarte HJ, Warady B, Davis R, Butte AJ, Salvatierra O, Sarwal MM. A peripheral blood diagnostic test for acute rejection in renal transplantation. Am J Transplant. 2012 Oct; 12(10):2710-8. PMID: 23009139; PMCID: PMC4148014.
      70. Vicent S, Sayles LC, Vaka D, Khatri P, Gevaert O, Chen R, Zheng Y, Gillespie AK, Clarke N, Xu Y, Shrager J, Hoang CD, Plevritis S, Butte AJ, Sweet-Cordero EA. Cross-species functional analysis of cancer-associated fibroblasts identifies a critical role for CLCF1 and IL-6 in non-small cell lung cancer in vivo. Cancer Res. 2012 Nov 15; 72(22):5744-56. PMID: 22962265; PMCID: PMC3856949.
      71. Gupta R, Ratan A, Rajesh C, Chen R, Kim HL, Burhans R, Miller W, Santhosh S, Davuluri RV, Butte AJ, Schuster SC, Seshagiri S, Thomas G. Sequencing and analysis of a South Asian-Indian personal genome. BMC Genomics. 2012; 13:440. PMID: 22938532; PMCID: PMC3534380.
      72. Califano A, Butte AJ, 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.
      73. Haeberle H, Dudley JT, Liu JT, Butte AJ, Contag CH. Identification of cell surface targets through meta-analysis of microarray data. Neoplasia. 2012 Jul; 14(7):666-9. PMID: 22904683; PMCID: PMC3421962.
      74. Patel CJ, Chen R, Butte AJ. Data-driven integration of epidemiological and toxicological data to select candidate interacting genes and environmental factors in association with disease. Bioinformatics. 2012 Jun 15; 28(12):i121-6. PMID: 22689751; PMCID: PMC3371861.
      75. Ruau D, Dudley JT, Chen R, Phillips NG, Swan GE, Lazzeroni LC, Clark JD, Butte AJ, Angst MS. Integrative approach to pain genetics identifies pain sensitivity loci across diseases. PLoS Comput Biol. 2012; 8(6):e1002538. PMID: 22685391; PMCID: PMC3369906.
      76. Dudley JT, Kim Y, Liu L, Markov GJ, Gerold K, Chen R, Butte AJ, Kumar S. Human genomic disease variants: a neutral evolutionary explanation. Genome Res. 2012 Aug; 22(8):1383-94. PMID: 22665443; PMCID: PMC3409252.
      77. Butte AJ, 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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      78. Morgan AA, Chen R, Butte AJ. 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.
      79. Kang HP, Yang X, Chen R, Zhang B, Corona E, Schadt EE, Butte AJ. Integration of disease-specific single nucleotide polymorphisms, expression quantitative trait loci and coexpression networks reveal novel candidate genes for type 2 diabetes. Diabetologia. 2012 Aug; 55(8):2205-13. PMID: 22584726; PMCID: PMC3390705.
      80. Palma JP, Benitz WE, Tarczy-Hornoch P, Butte AJ, Longhurst CA. Neonatal Informatics: Transforming Neonatal Care Through Translational Bioinformatics. Neoreviews. 2012 May 1; 13(5):e281-e284. PMID: 22924023.
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      81. Kodama K, Horikoshi M, Toda K, Yamada S, Hara K, Irie J, Sirota M, Morgan AA, Chen R, Ohtsu H, Maeda S, Kadowaki T, Butte AJ. Expression-based genome-wide association study links the receptor CD44 in adipose tissue with type 2 diabetes. Proc Natl Acad Sci U S A. 2012 May 1; 109(18):7049-54. PMID: 22499789; PMCID: PMC3344989.
      82. Chen R, Corona E, Sikora M, Dudley JT, Morgan AA, Moreno-Estrada A, Nilsen GB, Ruau D, Lincoln SE, Bustamante CD, Butte AJ. Type 2 diabetes risk alleles demonstrate extreme directional differentiation among human populations, compared to other diseases. PLoS Genet. 2012; 8(4):e1002621. PMID: 22511877; PMCID: PMC3325177.
      83. Chen R, Dudley JT, Ruau D, Butte AJ. 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.
      84. Kang HP, Morgan AA, Chen R, Schadt EE, Butte AJ. Coanalysis of GWAS with eQTLs reveals disease-tissue associations. AMIA Jt Summits Transl Sci Proc. 2012; 2012:35-41. PMID: 22779046; PMCID: PMC3392070.
      85. Chen R, Mias GI, Li-Pook-Than J, Jiang L, Lam HY, Chen R, Miriami E, Karczewski KJ, Hariharan M, Dewey FE, Cheng Y, Clark MJ, Im H, Habegger L, Balasubramanian S, O'Huallachain M, Dudley JT, Hillenmeyer S, Haraksingh R, Sharon D, Euskirchen G, Lacroute P, Bettinger K, Boyle AP, Kasowski M, Grubert F, Seki S, Garcia M, Whirl-Carrillo M, Gallardo M, Blasco MA, Greenberg PL, Snyder P, Klein TE, Altman RB, Butte AJ, Ashley EA, Gerstein M, Nadeau KC, Tang H, Snyder M. Personal omics profiling reveals dynamic molecular and medical phenotypes. Cell. 2012 Mar 16; 148(6):1293-307. PMID: 22424236; PMCID: PMC3341616.
      86. Patel CJ, Cullen MR, Ioannidis JP, Butte AJ. 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.
      87. Morgan AA, Pyrgos VJ, Nadeau KC, Williamson PR, Butte AJ. Multiplex meta-analysis of RNA expression to identify genes with variants associated with immune dysfunction. J Am Med Inform Assoc. 2012 Mar-Apr; 19(2):284-8. PMID: 22319178; PMCID: PMC3277634.
      88. Dudley JT, Chen R, Sanderford M, Butte AJ, 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.
      89. Khatri P, Sirota M, Butte AJ. Ten years of pathway analysis: current approaches and outstanding challenges. PLoS Comput Biol. 2012; 8(2):e1002375. PMID: 22383865; PMCID: PMC3285573.
      90. Ruau D, Liu LY, Clark JD, Angst MS, Butte AJ. 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.
      91. Lam HY, Clark MJ, Chen R, Chen R, Natsoulis G, O'Huallachain M, Dewey FE, Habegger L, Ashley EA, Gerstein MB, Butte AJ, Ji HP, Snyder M. Performance comparison of whole-genome sequencing platforms. Nat Biotechnol. 2012 Jan; 30(1):78-82. PMID: 22178993; PMCID: PMC4076012.
      92. Engreitz JM, Chen R, Morgan AA, Dudley JT, Mallelwar R, Butte AJ. ProfileChaser: searching microarray repositories based on genome-wide patterns of differential expression. Bioinformatics. 2011 Dec 1; 27(23):3317-8. PMID: 21967760; PMCID: PMC3223361.
      93. Clark MJ, Chen R, Lam HY, Karczewski KJ, Chen R, Euskirchen G, Butte AJ, Snyder M. Performance comparison of exome DNA sequencing technologies. Nat Biotechnol. 2011 Oct; 29(10):908-14. PMID: 21947028; PMCID: PMC4127531.
      94. Dewey FE, Chen R, Cordero SP, Ormond KE, Caleshu C, Karczewski KJ, Whirl-Carrillo M, Wheeler MT, Dudley JT, Byrnes JK, Cornejo OE, Knowles JW, Woon M, Sangkuhl K, Gong L, Thorn CF, Hebert JM, Capriotti E, David SP, Pavlovic A, West A, Thakuria JV, Ball MP, Zaranek AW, Rehm HL, Church GM, West JS, Bustamante CD, Snyder M, Altman RB, Klein TE, Butte AJ, Ashley EA. Phased whole-genome genetic risk in a family quartet using a major allele reference sequence. PLoS Genet. 2011 Sep; 7(9):e1002280. PMID: 21935354; PMCID: PMC3174201.
      95. Naesens M, Khatri P, Li L, Sigdel TK, Vitalone MJ, Chen R, Butte AJ, Salvatierra O, Sarwal MM. Progressive histological damage in renal allografts is associated with expression of innate and adaptive immunity genes. Kidney Int. 2011 Dec; 80(12):1364-76. PMID: 21881554; PMCID: PMC4492284.
      96. Liu LY, Schaub MA, Sirota M, Butte AJ. Sex differences in disease risk from reported genome-wide association study findings. Hum Genet. 2012 Mar; 131(3):353-64. PMID: 21858542; PMCID: PMC3260375.
      97. Sirota M, Dudley JT, Kim J, Chiang AP, Morgan AA, Sweet-Cordero A, Sage J, Butte AJ. Discovery and preclinical validation of drug indications using compendia of public gene expression data. Sci Transl Med. 2011 Aug 17; 3(96):96ra77. PMID: 21849665; PMCID: PMC3502016.
      98. Dudley JT, Sirota M, Shenoy M, Pai RK, Roedder S, Chiang AP, Morgan AA, Sarwal MM, Pasricha PJ, Butte AJ. Computational repositioning of the anticonvulsant topiramate for inflammatory bowel disease. Sci Transl Med. 2011 Aug 17; 3(96):96ra76. PMID: 21849664; PMCID: PMC3479650.
      99. Yu M, Eckart MR, Morgan AA, Mukai K, Butte AJ, Tsai M, Galli SJ. Identification of an IFN-?/mast cell axis in a mouse model of chronic asthma. J Clin Invest. 2011 Aug; 121(8):3133-43. PMID: 21737883; PMCID: PMC3148724.
      100. Butte AJ, 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.
      101. Khatri P, Sarwal MM, Butte AJ. Applications of translational bioinformatics in transplantation. Clin Pharmacol Ther. 2011 Aug; 90(2):323-7. PMID: 21716268; PMCID: PMC3476839.
      102. Sirota M, Butte AJ. 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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      103. Dudley JT, Deshpande T, Butte AJ. Exploiting drug-disease relationships for computational drug repositioning. Brief Bioinform. 2011 Jul; 12(4):303-11. PMID: 21690101; PMCID: PMC3137933.
      104. Liu LY, Schaub MA, Sirota M, Butte AJ. 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.
      105. Pouliot Y, Chiang AP, Butte AJ. Predicting adverse drug reactions using publicly available PubChem BioAssay data. Clin Pharmacol Ther. 2011 Jul; 90(1):90-9. PMID: 21613989; PMCID: PMC3464971.
      106. Sarkar IN, Butte AJ, 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.
      107. Ruau D, Mbagwu M, Dudley JT, Krishnan V, Butte AJ. 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.
      108. Sarwal MM, Benjamin J, Butte AJ, Davis MM, Wood K, Chapman J. Transplantomics and biomarkers in organ transplantation: a report from the first international conference. Transplantation. 2011 Feb 27; 91(4):379-82. PMID: 21278631; PMCID: PMC3762499.
      109. Sharaf RN, Butte AJ, Montgomery KD, Pai R, Dudley JT, Pasricha PJ. Computational prediction and experimental validation associating FABP-1 and pancreatic adenocarcinoma with diabetes. BMC Gastroenterol. 2011; 11:5. PMID: 21251264; PMCID: PMC3037918.
      110. Chen R, Butte AJ. The reference human genome demonstrates high risk of type 1 diabetes and other disorders. Pac Symp Biocomput. 2011; 231-42. PMID: 21121051; PMCID: PMC3732491.
      111. Dudley JT, Chen R, Butte AJ. Matching cancer genomes to established cell lines for personalized oncology. Pac Symp Biocomput. 2011; 243-52. PMID: 21121052; PMCID: PMC3477496.
      112. Butte AJ, Sigdel TK, Wadia PP, Miklos DB, Sarwal MM. Protein microarrays discover angiotensinogen and PRKRIP1 as novel targets for autoantibodies in chronic renal disease. Mol Cell Proteomics. 2011 Mar; 10(3):M110.000497. PMID: 21183621; PMCID: PMC3047141.
      113. Engreitz JM, Morgan AA, Dudley JT, Chen R, Thathoo R, Altman RB, Butte AJ. Content-based microarray search using differential expression profiles. BMC Bioinformatics. 2010; 11:603. PMID: 21172034; PMCID: PMC3022631.
      114. Dudley JT, Butte AJ. In silico research in the era of cloud computing. Nat Biotechnol. 2010 Nov; 28(11):1181-5. PMID: 21057489; PMCID: PMC3755123.
      115. Morgan AA, Khatri P, Jones RH, Sarwal MM, Butte AJ. Comparison of multiplex meta analysis techniques for understanding the acute rejection of solid organ transplants. BMC Bioinformatics. 2010; 11 Suppl 9:S6. PMID: 21044364; PMCID: PMC2967747.
      116. Chen DP, Dudley JT, Butte AJ. 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.
      117. Tatonetti NP, Dudley JT, Sagreiya H, Butte AJ, Altman RB. An integrative method for scoring candidate genes from association studies: application to warfarin dosing. BMC Bioinformatics. 2010; 11 Suppl 9:S9. PMID: 21044367; PMCID: PMC2967750.
      118. Chen R, Davydov EV, Sirota M, Butte AJ. Non-synonymous and synonymous coding SNPs show similar likelihood and effect size of human disease association. PLoS One. 2010; 5(10):e13574. PMID: 21042586; PMCID: PMC2962641.
      119. Chen R, Sigdel TK, Li L, Kambham N, Dudley JT, Hsieh SC, Klassen RB, Chen A, Caohuu T, Morgan AA, Valantine HA, Khush KK, Sarwal MM, Butte AJ. Differentially expressed RNA from public microarray data identifies serum protein biomarkers for cross-organ transplant rejection and other conditions. PLoS Comput Biol. 2010; 6(9). PMID: 20885780; PMCID: PMC2944782.
      120. Zheng M, Ravindran P, Wang J, Epstein RH, Chen DP, Butte AJ, Peltz G. Special article: an optimistic prognosis for the clinical utility of laboratory test data. Anesth Analg. 2010 Oct; 111(4):1026-35. PMID: 20810674.
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      121. Wilson KD, Hu S, Venkatasubrahmanyam S, Fu JD, Sun N, Abilez OJ, Baugh JJ, Jia F, Ghosh Z, Li RA, Butte AJ, Wu JC. Dynamic microRNA expression programs during cardiac differentiation of human embryonic stem cells: role for miR-499. Circ Cardiovasc Genet. 2010 Oct; 3(5):426-35. PMID: 20733065; PMCID: PMC3057038.
      122. Corona E, Dudley JT, Butte AJ. Extreme evolutionary disparities seen in positive selection across seven complex diseases. PLoS One. 2010; 5(8):e12236. PMID: 20808933; PMCID: PMC2923198.
      123. Dudley JT, Pouliot Y, Chen R, Morgan AA, Butte AJ. Translational bioinformatics in the cloud: an affordable alternative. Genome Med. 2010; 2(8):51. PMID: 20691073; PMCID: PMC2945008.
      124. Dudley JT, Schadt E, Sirota M, Butte AJ, 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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      125. Dudley JT, Butte AJ. Biomarker and drug discovery for gastroenterology through translational bioinformatics. Gastroenterology. 2010 Sep; 139(3):735-41, 741.e1. PMID: 20650279.
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      126. Ober C, Butte AJ, Elias JA, Lusis AJ, Gan W, Banks-Schlegel S, Schwartz D. Getting from genes to function in lung disease: a National Heart, Lung, and Blood Institute workshop report. Am J Respir Crit Care Med. 2010 Sep 15; 182(6):732-7. PMID: 20558629; PMCID: PMC2949401.
      127. Patel CJ, Bhattacharya J, Butte AJ. An Environment-Wide Association Study (EWAS) on type 2 diabetes mellitus. PLoS One. 2010; 5(5):e10746. PMID: 20505766; PMCID: PMC2873978.
      128. Morgan AA, Chen R, Butte AJ. Likelihood ratios for genome medicine. Genome Med. 2010; 2(5):30. PMID: 20497613; PMCID: PMC2887074.
      129. Lussier YA, Butte AJ, Hunter L. Current methodologies for translational bioinformatics. J Biomed Inform. 2010 Jun; 43(3):355-7. PMID: 20470899; PMCID: PMC2894568.
      130. Patel CJ, Butte AJ. Predicting environmental chemical factors associated with disease-related gene expression data. BMC Med Genomics. 2010; 3:17. PMID: 20459635; PMCID: PMC2880288.
      131. Ashley EA, Butte AJ, Wheeler MT, Chen R, Klein TE, Dewey FE, Dudley JT, Ormond KE, Pavlovic A, Morgan AA, Pushkarev D, Neff NF, Hudgins L, Gong L, Hodges LM, Berlin DS, Thorn CF, Sangkuhl K, Hebert JM, Woon M, Sagreiya H, Whaley R, Knowles JW, Chou MF, Thakuria JV, Rosenbaum AM, Zaranek AW, Church GM, Greely HT, Quake SR, Altman RB. Clinical assessment incorporating a personal genome. Lancet. 2010 May 1; 375(9725):1525-35. PMID: 20435227; PMCID: PMC2937184.
      132. Ormond KE, Wheeler MT, Hudgins L, Klein TE, Butte AJ, Altman RB, Ashley EA, Greely HT. Challenges in the clinical application of whole-genome sequencing. Lancet. 2010 May 15; 375(9727):1749-51. PMID: 20434765.
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      133. Shen-Orr SS, Tibshirani R, Khatri P, Bodian DL, Staedtler F, Perry NM, Hastie T, Sarwal MM, Davis MM, Butte AJ. Cell type-specific gene expression differences in complex tissues. Nat Methods. 2010 Apr; 7(4):287-9. PMID: 20208531; PMCID: PMC3699332.
      134. Suthram S, Dudley JT, Chiang AP, Chen R, Hastie TJ, Butte AJ. Network-based elucidation of human disease similarities reveals common functional modules enriched for pluripotent drug targets. PLoS Comput Biol. 2010 Feb; 6(2):e1000662. PMID: 20140234; PMCID: PMC2816673.
      135. Cohen MJ, Grossman AD, Morabito D, Knudson MM, Butte AJ, Manley GT. Identification of complex metabolic states in critically injured patients using bioinformatic cluster analysis. Crit Care. 2010; 14(1):R10. PMID: 20122274; PMCID: PMC2875524.
      136. Wadia PP, Coram M, Armstrong RJ, Mindrinos M, Butte AJ, 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.
      137. Dudley JT, Butte AJ. A quick guide for developing effective bioinformatics programming skills. PLoS Comput Biol. 2009 Dec; 5(12):e1000589. PMID: 20041221; PMCID: PMC2791169.
      138. Sirota M, Schaub MA, Batzoglou S, Robinson WH, Butte AJ. Autoimmune disease classification by inverse association with SNP alleles. PLoS Genet. 2009 Dec; 5(12):e1000792. PMID: 20041220; PMCID: PMC2791168.
      139. Chen DP, Morgan AA, Butte AJ. Validating pathophysiological models of aging using clinical electronic medical records. J Biomed Inform. 2010 Jun; 43(3):358-64. PMID: 19958842; PMCID: PMC2878870.
      140. Morgan AA, Dudley JT, Deshpande T, Butte AJ. Dynamism in gene expression across multiple studies. Physiol Genomics. 2010 Feb 4; 40(3):128-40. PMID: 19920211; PMCID: PMC2825768.
      141. Renault VM, Rafalski VA, Morgan AA, Salih DA, Brett JO, Webb AE, Villeda SA, Thekkat PU, Guillerey C, Denko NC, Palmer TD, Butte AJ, Brunet A. FoxO3 regulates neural stem cell homeostasis. Cell Stem Cell. 2009 Nov 6; 5(5):527-39. PMID: 19896443; PMCID: PMC2775802.
      142. Sutherland SM, Li L, Sigdel TK, Wadia PP, Miklos DB, Butte AJ, Sarwal MM. Protein microarrays identify antibodies to protein kinase Czeta that are associated with a greater risk of allograft loss in pediatric renal transplant recipients. Kidney Int. 2009 Dec; 76(12):1277-83. PMID: 19812540; PMCID: PMC4464694.
      143. Sridhar K, Ross DT, Tibshirani R, Butte AJ, Greenberg PL. Relationship of differential gene expression profiles in CD34+ myelodysplastic syndrome marrow cells to disease subtype and progression. Blood. 2009 Nov 26; 114(23):4847-58. PMID: 19801443; PMCID: PMC2786292.
      144. Grossman AD, Cohen MJ, Manley GT, Butte AJ. Infection in the intensive care unit alters physiological networks. BMC Bioinformatics. 2009; 10 Suppl 9:S4. PMID: 19761574; PMCID: PMC2745691.
      145. Dudley JT, Tibshirani R, Deshpande T, Butte AJ. Disease signatures are robust across tissues and experiments. Mol Syst Biol. 2009; 5:307. PMID: 19756046; PMCID: PMC2758720.
      146. 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.
      147. Chiang AP, Butte AJ. 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.
      148. Butte AJ. Translational bioinformatics applications in genome medicine. Genome Med. 2009; 1(6):64. PMID: 19566916; PMCID: PMC2703873.
      149. Schaub MA, Kaplow IM, Sirota M, Do CB, Butte AJ, Batzoglou S. A Classifier-based approach to identify genetic similarities between diseases. Bioinformatics. 2009 Jun 15; 25(12):i21-9. PMID: 19477990; PMCID: PMC2687980.
      150. Naesens M, Butte AJ, 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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      151. Wilson KD, Venkatasubrahmanyam S, Jia F, Sun N, Butte AJ, Wu JC. MicroRNA profiling of human-induced pluripotent stem cells. Stem Cells Dev. 2009 Jun; 18(5):749-58. PMID: 19284351; PMCID: PMC3135181.
      152. Naesens M, Li L, Ying L, Sansanwal P, Sigdel TK, Hsieh SC, Kambham N, Lerut E, Salvatierra O, Butte AJ, Sarwal MM. Expression of complement components differs between kidney allografts from living and deceased donors. J Am Soc Nephrol. 2009 Aug; 20(8):1839-51. PMID: 19443638; PMCID: PMC2723986.
      153. Li L, Wadia P, Chen R, Kambham N, Naesens M, Sigdel TK, Miklos DB, Sarwal MM, Butte AJ. Identifying compartment-specific non-HLA targets after renal transplantation by integrating transcriptome and "antibodyome" measures. Proc Natl Acad Sci U S A. 2009 Mar 17; 106(11):4148-53. PMID: 19251643; PMCID: PMC2657434.
      154. Butte AJ, 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.
      155. Liu YI, Wise PH, Butte AJ. The "etiome": identification and clustering of human disease etiological factors. BMC Bioinformatics. 2009; 10 Suppl 2:S14. PMID: 19208189; PMCID: PMC2646245.
      156. Shah NH, Jonquet C, Chiang AP, Butte AJ, Chen R, Musen MA. Ontology-driven indexing of public datasets for translational bioinformatics. BMC Bioinformatics. 2009; 10 Suppl 2:S1. PMID: 19208184; PMCID: PMC2646250.
      157. Chiang AP, Butte AJ. 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.
      158. Dudley JT, Butte AJ. Identification of discriminating biomarkers for human disease using integrative network biology. Pac Symp Biocomput. 2009; 27-38. PMID: 19209693; PMCID: PMC2749008.
      159. Shen-Orr SS, Goldberger O, Garten Y, Rosenberg-Hasson Y, Lovelace PA, Hirschberg DL, Altman RB, Davis MM, Butte AJ. Towards a cytokine-cell interaction knowledgebase of the adaptive immune system. Pac Symp Biocomput. 2009; 439-50. PMID: 19209721; PMCID: PMC2709757.
      160. Chen R, Mallelwar R, Thosar A, Venkatasubrahmanyam S, Butte AJ. GeneChaser: identifying all biological and clinical conditions in which genes of interest are differentially expressed. BMC Bioinformatics. 2008; 9:548. PMID: 19094235; PMCID: PMC2629779.
      161. 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.
      162. Chen R, Morgan AA, Dudley J, Deshpande T, Li L, Kodama K, Chiang AP, Butte AJ. FitSNPs: highly differentially expressed genes are more likely to have variants associated with disease. Genome Biol. 2008; 9(12):R170. PMID: 19061490; PMCID: PMC2646274.
      163. Tenenbaum JD, Walker MG, Utz PJ, Butte AJ. Expression-based Pathway Signature Analysis (EPSA): mining publicly available microarray data for insight into human disease. BMC Med Genomics. 2008; 1:51. PMID: 18937865; PMCID: PMC2588448.
      164. Viatour P, Somervaille TC, Venkatasubrahmanyam S, Kogan S, McLaughlin ME, Weissman IL, Butte AJ, Passegué E, Sage J. Hematopoietic stem cell quiescence is maintained by compound contributions of the retinoblastoma gene family. Cell Stem Cell. 2008 Oct 9; 3(4):416-28. PMID: 18940733; PMCID: PMC2646421.
      165. Kodama K, Butte AJ, Creusot RJ, Su L, Sheng D, Hartnett M, Iwai H, Soares LR, Fathman CG. Tissue- and age-specific changes in gene expression during disease induction and progression in NOD mice. Clin Immunol. 2008 Nov; 129(2):195-201. PMID: 18801706; PMCID: PMC2592195.
      166. Butte AJ. Translational bioinformatics: coming of age. J Am Med Inform Assoc. 2008 Nov-Dec; 15(6):709-14. PMID: 18755990; PMCID: PMC2585538.
      167. English SB, Shih SC, Ramoni MF, Smith LE, Butte AJ. Use of Bayesian networks to probabilistically model and improve the likelihood of validation of microarray findings by RT-PCR. J Biomed Inform. 2009 Apr; 42(2):287-95. PMID: 18790084; PMCID: PMC3962641.
      168. Butte AJ. Medicine. The ultimate model organism. Science. 2008 Apr 18; 320(5874):325-7. PMID: 18420921; PMCID: PMC2749009.
      169. Chen DP, Weber SC, Constantinou PS, Ferris TA, Lowe HJ, Butte AJ. Novel integration of hospital electronic medical records and gene expression measurements to identify genetic markers of maturation. Pac Symp Biocomput. 2008; 243-54. PMID: 18229690; PMCID: PMC2716394.
      170. Dudley J, Butte AJ. Enabling integrative genomic analysis of high-impact human diseases through text mining. Pac Symp Biocomput. 2008; 580-91. PMID: 18229717; PMCID: PMC2735266.
      171. Chen R, Li L, Butte AJ. AILUN: reannotating gene expression data automatically. Nat Methods. 2007 Nov; 4(11):879. PMID: 17971777; PMCID: PMC2716375.
      172. Chen DP, Weber SC, Constantinou PS, Ferris TA, Lowe HJ, Butte AJ. Clinical arrays of laboratory measures, or "clinarrays", built from an electronic health record enable disease subtyping by severity. AMIA Annu Symp Proc. 2007; 115-9. PMID: 18693809; PMCID: PMC2655832.
      173. Lin YA, Chiang A, Lin R, Yao P, Chen R, Butte AJ. Methodologies for extracting functional pharmacogenomic experiments from international repository. AMIA Annu Symp Proc. 2007; 463-7. PMID: 18693879; PMCID: PMC2655846.
      174. English SB, Butte AJ. 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.
      175. Balboni I, Chan SM, Kattah M, Tenenbaum JD, Butte AJ, Utz PJ. Multiplexed protein array platforms for analysis of autoimmune diseases. Annu Rev Immunol. 2006; 24:391-418. PMID: 16551254.
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      176. Butte AJ, Kohane IS. Creation and implications of a phenome-genome network. Nat Biotechnol. 2006 Jan; 24(1):55-62. PMID: 16404398; PMCID: PMC2716377.
      177. Butte AJ, 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.
      178. Ichikawa JK, English SB, Wolfgang MC, Jackson R, Butte AJ, Lory S. Genome-wide analysis of host responses to the Pseudomonas aeruginosa type III secretion system yields synergistic effects. Cell Microbiol. 2005 Nov; 7(11):1635-46. PMID: 16207250.
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      179. Wolfe CJ, Kohane IS, Butte AJ. Systematic survey reveals general applicability of "guilt-by-association" within gene coexpression networks. BMC Bioinformatics. 2005; 6:227. PMID: 16162296; PMCID: PMC1239911.
      180. Tseng YH, Butte AJ, Kokkotou E, Yechoor VK, Taniguchi CM, Kriauciunas KM, Cypess AM, Niinobe M, Yoshikawa K, Patti ME, Kahn CR. Prediction of preadipocyte differentiation by gene expression reveals role of insulin receptor substrates and necdin. Nat Cell Biol. 2005 Jun; 7(6):601-11. PMID: 15895078.
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      181. Pollard J, Butte AJ, Hoberman S, Joshi M, Levy J, Pappo J. A computational model to define the molecular causes of type 2 diabetes mellitus. Diabetes Technol Ther. 2005 Apr; 7(2):323-36. PMID: 15857235.
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      182. Csoka AB, English SB, Simkevich CP, Ginzinger DG, Butte AJ, Schatten GP, Rothman FG, Sedivy JM. Genome-scale expression profiling of Hutchinson-Gilford progeria syndrome reveals widespread transcriptional misregulation leading to mesodermal/mesenchymal defects and accelerated atherosclerosis. Aging Cell. 2004 Aug; 3(4):235-43. PMID: 15268757.
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      183. Kho AT, Zhao Q, Cai Z, Butte AJ, Kim JY, Pomeroy SL, Rowitch DH, Kohane IS. Conserved mechanisms across development and tumorigenesis revealed by a mouse development perspective of human cancers. Genes Dev. 2004 Mar 15; 18(6):629-40. PMID: 15075291; PMCID: PMC387239.
      184. Allocco DJ, Kohane IS, Butte AJ. Quantifying the relationship between co-expression, co-regulation and gene function. BMC Bioinformatics. 2004 Feb 25; 5:18. PMID: 15053845; PMCID: PMC375525.
      185. Patti ME, Butte AJ, Crunkhorn S, Cusi K, Berria R, Kashyap S, Miyazaki Y, Kohane I, Costello M, Saccone R, Landaker EJ, Goldfine AB, Mun E, DeFronzo R, Finlayson J, Kahn CR, Mandarino LJ. Coordinated reduction of genes of oxidative metabolism in humans with insulin resistance and diabetes: Potential role of PGC1 and NRF1. Proc Natl Acad Sci U S A. 2003 Jul 8; 100(14):8466-71. PMID: 12832613; PMCID: PMC166252.
      186. Nimgaonkar A, Sanoudou D, Butte AJ, Haslett JN, Kunkel LM, Beggs AH, Kohane IS. Reproducibility of gene expression across generations of Affymetrix microarrays. BMC Bioinformatics. 2003 Jun 25; 4:27. PMID: 12823866; PMCID: PMC165600.
      187. Lee K, Kohane IS, Butte AJ. 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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      188. Weiner DL, Butte AJ, 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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      189. 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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      190. Park PJ, Butte AJ, Kohane IS. Comparing expression profiles of genes with similar promoter regions. Bioinformatics. 2002 Dec; 18(12):1576-84. PMID: 12490441.
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      191. Kuo WP, Jenssen TK, Butte AJ, 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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      192. Butte AJ, 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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      193. Butte AJ, 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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      194. 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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      195. Butte AJ, 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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      196. Butte AJ. Challenges in bioinformatics: infrastructure, models and analytics. Trends Biotechnol. 2001 May; 19(5):159-60. PMID: 11403022.
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      197. Butte AJ, 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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      198. Butte AJ, 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.
      199. Huang SA, Tu HM, Harney JW, Venihaki M, Butte AJ, Kozakewich HP, Fishman SJ, Larsen PR. Severe hypothyroidism caused by type 3 iodothyronine deiodinase in infantile hemangiomas. N Engl J Med. 2000 Jul 20; 343(3):185-9. PMID: 10900278.
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      200. Butte AJ, Kohane IS. Mutual information relevance networks: functional genomic clustering using pairwise entropy measurements. Pac Symp Biocomput. 2000; 418-29. PMID: 10902190.
        View in: PubMed
      201. Butte AJ, Weinstein DA, Kohane IS. Enrolling patients into clinical trials faster using RealTime Recuiting. Proc AMIA Symp. 2000; 111-5. PMID: 11079855; PMCID: PMC2244056.
      202. Butte AJ, Kohane IS. Unsupervised knowledge discovery in medical databases using relevance networks. Proc AMIA Symp. 1999; 711-5. PMID: 10566452; PMCID: PMC2232846.
      203. 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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      204. 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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      205. Quon MJ, Butte AJ, Zarnowski MJ, Sesti G, Cushman SW, Taylor SI. Insulin receptor substrate 1 mediates the stimulatory effect of insulin on GLUT4 translocation in transfected rat adipose cells. J Biol Chem. 1994 Nov 11; 269(45):27920-4. PMID: 7525563.
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      206. Quon MJ, Butte AJ, Taylor SI. Insulin signal transduction pathways. Trends Endocrinol Metab. 1994 Nov; 5(9):369-76. PMID: 18407232.
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      207. Quon MJ, Guerre-Millo M, Zarnowski MJ, Butte AJ, Em M, Cushman SW, Taylor SI. Tyrosine kinase-deficient mutant human insulin receptors (Met1153-->Ile) overexpressed in transfected rat adipose cells fail to mediate translocation of epitope-tagged GLUT4. Proc Natl Acad Sci U S A. 1994 Jun 7; 91(12):5587-91. PMID: 8202531; PMCID: PMC44041.
      208. DePetrillo PB, Butte AJ. 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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