Atul Butte

Publications

• Disease signatures are robust across tissues and experiments. Dudley JT, Tibshirani R, Deshpande T, Butte AJ. Mol Syst Biol. 2009: 5 307
• Data-driven methods to discover molecular determinants of serious adverse drug events. Chiang AP, Butte AJ. Clin Pharmacol Ther. 2009; 85 (3): 259-68
• Translational bioinformatics: coming of age. Butte AJ, J Am Med Inform Assoc. 2008 Nov-Dec; 15 (6): 709-14
• Medicine. The ultimate model organism. Butte AJ, Science. 2008; 320 (5874): 325-7
• Evaluation and integration of 49 genome-wide experiments and the prediction of previously unknown obesity-related genes. English SB, Butte AJ. Bioinformatics. 2007; 23 (21): 2910-7
• AILUN: reannotating gene expression data automatically. Chen R, Li L, Butte AJ. Nat Methods. 2007; 4 (11): 879
• Creation and implications of a phenome-genome network. Butte AJ, Kohane IS. Nat Biotechnol. 2006; 24 (1): 55-62
• Prediction of preadipocyte differentiation by gene expression reveals role of insulin receptor substrates and necdin. Tseng YH, Butte AJ, Kokkotou E, Yechoor VK, Taniguchi CM, Kriauciunas KM, Cypess AM, Niinobe M, Yoshikawa K, Patti ME, Kahn CR. Nat Cell Biol. 2005; 7 (6): 601-11
• Coordinated reduction of genes of oxidative metabolism in humans with insulin resistance and diabetes: Potential role of PGC1 and NRF1. 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. Proc Natl Acad Sci U S A. 2003; 100 (14): 8466-71
• The use and analysis of microarray data. Butte A, Nat Rev Drug Discov. 2002; 1 (12): 951-60
• Discovering functional relationships between RNA expression and chemotherapeutic susceptibility using relevance networks. Butte AJ, Tamayo P, Slonim D, Golub TR, Kohane IS. Proc Natl Acad Sci U S A. 2000; 97 (22): 12182-6
• Selected proceedings of the First Summit on Translational Bioinformatics 2008. Butte AJ, Sarkar IN, Ramoni M, Lussier Y, Troyanskaya O. BMC Bioinformatics. 2009: 10 Suppl 2 I1
• Ontology-driven indexing of public datasets for translational bioinformatics. Shah NH, Jonquet C, Chiang AP, Butte AJ, Chen R, Musen MA. BMC Bioinformatics. 2009: 10 Suppl 2 S1
• The "etiome": identification and clustering of human disease etiological factors. Liu YI, Wise PH, Butte AJ. BMC Bioinformatics. 2009: 10 Suppl 2 S14
• Identification of discriminating biomarkers for human disease using integrative network biology. Dudley JT, Butte AJ. Pac Symp Biocomput. 2009: 27-38
• Towards a cytokine-cell interaction knowledgebase of the adaptive immune system. Shen-Orr SS, Goldberger O, Garten Y, Rosenberg-Hasson Y, Lovelace PA, Hirschberg DL, Altman RB, Davis MM, Butte AJ. Pac Symp Biocomput. 2009: 439-50
• Use of Bayesian networks to probabilistically model and improve the likelihood of validation of microarray findings by RT-PCR. English SB, Shih SC, Ramoni MF, Smith LE, Butte AJ. J Biomed Inform. 2009; 42 (2): 287-95
• MicroRNA profiling of human-induced pluripotent stem cells. Wilson KD, Venkatasubrahmanyam S, Jia F, Sun N, Butte AJ, Wu JC. Stem Cells Dev. 2009; 18 (5): 749-58
• Expression of complement components differs between kidney allografts from living and deceased donors. Naesens M, Li L, Ying L, Sansanwal P, Sigdel TK, Hsieh SC, Kambham N, Lerut E, Salvatierra O, Butte AJ, Sarwal MM. J Am Soc Nephrol. 2009; 20 (8): 1839-51
• A Classifier-based approach to identify genetic similarities between diseases. Schaub MA, Kaplow IM, Sirota M, Do CB, Butte AJ, Batzoglou S. Bioinformatics. 2009; 25 (12): i21-9
• Translational bioinformatics applications in genome medicine. Butte AJ, Genome Med. 2009; 1 (6): 64
• Systematic evaluation of drug-disease relationships to identify leads for novel drug uses. Chiang AP, Butte AJ. Clin Pharmacol Ther. 2009; 86 (5): 507-10
• Infection in the intensive care unit alters physiological networks. Grossman AD, Cohen MJ, Manley GT, Butte AJ. BMC Bioinformatics. 2009: 10 Suppl 9 S4
• Wiskott-Aldrich syndrome protein is an effector of Kit signaling. Mani M, Venkatasubrahmanyam S, Sanyal M, Levy S, Butte A, Weinberg K, Jahn T. Blood. 2009; 114 (14): 2900-8
• C3 polymorphisms and outcomes of renal allografts. Naesens M, Butte AJ, Sarwal MM. N Engl J Med. 2009; 360 (23): 2478; author reply 2478-9
• Report on EU-USA workshop: how systems biology can advance cancer research (27 October 2008). Aebersold R, Auffray C, Baney E, Barillot E, Brazma A, Brett C, Brunak S, Butte A, Califano A, Celis J, Cufer T, Ferrell J, Galas D, Gallahan D, Gatenby R, Goldbeter A, Hace N, Henney A, Hood L, 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. Mol Oncol. 2009; 3 (1): 9-17
• Relationship of differential gene expression profiles in CD34+ myelodysplastic syndrome marrow cells to disease subtype and progression. Sridhar K, Ross DT, Tibshirani R, Butte AJ, Greenberg PL. Blood. 2009
• Protein microarrays identify antibodies to protein kinase Czeta that are associated with a greater risk of allograft loss in pediatric renal transplant recipients. Sutherland SM, Li L, Sigdel TK, Wadia PP, Miklos DB, Butte AJ, Sarwal MM. Kidney Int. 2009
• FoxO3 regulates neural stem cell homeostasis. 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. Cell Stem Cell. 2009; 5 (5): 527-39
• Dynamism in Gene Expression Across Multiple Studies. Morgan AA, Dudley JT, Deshpande T, Butte AJ. Physiol Genomics. 2009
• Tissue- and age-specific changes in gene expression during disease induction and progression in NOD mice. Kodama K, Butte AJ, Creusot RJ, Su L, Sheng D, Hartnett M, Iwai H, Soares LR, Fathman CG. Clin Immunol. 2008; 129 (2): 195-201
• Enabling integrative genomic analysis of high-impact human diseases through text mining. Dudley J, Butte AJ. Pac Symp Biocomput. 2008: 580-91
• Hematopoietic stem cell quiescence is maintained by compound contributions of the retinoblastoma gene family. Viatour P, Somervaille TC, Venkatasubrahmanyam S, Kogan S, McLaughlin ME, Weissman IL, Butte AJ, Passegué E, Sage J. Cell Stem Cell. 2008; 3 (4): 416-28
• Novel integration of hospital electronic medical records and gene expression measurements to identify genetic markers of maturation. Chen DP, Weber SC, Constantinou PS, Ferris TA, Lowe HJ, Butte AJ. Pac Symp Biocomput. 2008: 243-54
• Clinical arrays of laboratory measures, or "clinarrays", built from an electronic health record enable disease subtyping by severity. Chen DP, Weber SC, Constantinou PS, Ferris TA, Lowe HJ, Butte AJ. AMIA Annu Symp Proc. 2007: 115-9
• Methodologies for extracting functional pharmacogenomic experiments from international repository. Lin YA, Chiang A, Lin R, Yao P, Chen R, Butte AJ. AMIA Annu Symp Proc. 2007: 463-7
• Multiplexed protein array platforms for analysis of autoimmune diseases. Balboni I, Chan SM, Kattah M, Tenenbaum JD, Butte AJ, Utz PJ. Annu Rev Immunol. 2006: 24 391-418
• Finding disease-related genomic experiments within an international repository: first steps in translational bioinformatics. Butte AJ, Chen R. AMIA Annu Symp Proc. 2006: 106-10
• Systematic survey reveals general applicability of "guilt-by-association" within gene coexpression networks. Wolfe CJ, Kohane IS, Butte AJ. BMC Bioinformatics. 2005: 6 227
• Genome-wide analysis of host responses to the Pseudomonas aeruginosa type III secretion system yields synergistic effects. Ichikawa JK, English SB, Wolfgang MC, Jackson R, Butte AJ, Lory S. Cell Microbiol. 2005; 7 (11): 1635-46
• A computational model to define the molecular causes of type 2 diabetes mellitus. Pollard J, Butte AJ, Hoberman S, Joshi M, Levy J, Pappo J. Diabetes Technol Ther. 2005; 7 (2): 323-36
• Genome-scale expression profiling of Hutchinson-Gilford progeria syndrome reveals widespread transcriptional misregulation leading to mesodermal/mesenchymal defects and accelerated atherosclerosis. Csoka AB, English SB, Simkevich CP, Ginzinger DG, Butte AJ, Schatten GP, Rothman FG, Sedivy JM. Aging Cell. 2004; 3 (4): 235-43
• Quantifying the relationship between co-expression, co-regulation and gene function. Allocco DJ, Kohane IS, Butte AJ. BMC Bioinformatics. 2004: 5 18
• Conserved mechanisms across development and tumorigenesis revealed by a mouse development perspective of human cancers. Kho AT, Zhao Q, Cai Z, Butte AJ, Kim JY, Pomeroy SL, Rowitch DH, Kohane IS. Genes Dev. 2004; 18 (6): 629-40
• PGAGENE: integrating quantitative gene-specific results from the NHLBI programs for genomic applications. Lee K, Kohane IS, Butte AJ. Bioinformatics. 2003; 19 (6): 778-9
• Computerized recruiting for clinical trials in real time. Weiner DL, Butte AJ, Hibberd PL, Fleisher GR. Ann Emerg Med. 2003; 41 (2): 242-6
• Reproducibility of gene expression across generations of Affymetrix microarrays. Nimgaonkar A, Sanoudou D, Butte AJ, Haslett JN, Kunkel LM, Beggs AH, Kohane IS. BMC Bioinformatics. 2003: 4 27
• Analysis of matched mRNA measurements from two different microarray technologies. Kuo WP, Jenssen TK, Butte AJ, Ohno-Machado L, Kohane IS. Bioinformatics. 2002; 18 (3): 405-12
• Comparing expression profiles of genes with similar promoter regions. Park PJ, Butte AJ, Kohane IS. Bioinformatics. 2002; 18 (12): 1576-84
• Comparing the similarity of time-series gene expression using signal processing metrics. Butte AJ, Bao L, Reis BY, Watkins TW, Kohane IS. J Biomed Inform. 2001; 34 (6): 396-405
• Further defining housekeeping, or "maintenance," genes Focus on "A compendium of gene expression in normal human tissues". Butte AJ, Dzau VJ, Glueck SB. Physiol Genomics. 2001; 7 (2): 95-6
• Strict interpretation of vaccination guidelines with computerized algorithms and improper timing of administered doses. Butte AJ, Shaw JS, Bernstein H. Pediatr Infect Dis J. 2001; 20 (6): 561-5
• Challenges in bioinformatics: infrastructure, models and analytics. Butte AJ, Trends Biotechnol. 2001; 19 (5): 159-60
• Determining significant fold differences in gene expression analysis. Butte AJ, Ye J, Häring HU, Stumvoll M, White MF, Kohane IS. Pac Symp Biocomput. 2001: 6-17
• The personal internetworked notary and guardian. Riva A, Mandl KD, Oh DH, Nigrin DJ, Butte A, Szolovits P, Kohane IS. Int J Med Inform. 2001; 62 (1): 27-40
• Extracting knowledge from dynamics in gene expression. Reis BY, Butte AS, Kohane IS. J Biomed Inform. 2001; 34 (1): 15-27
• Mutual information relevance networks: functional genomic clustering using pairwise entropy measurements. Butte AJ, Kohane IS. Pac Symp Biocomput. 2000: 418-29
• Severe hypothyroidism caused by type 3 iodothyronine deiodinase in infantile hemangiomas. Huang SA, Tu HM, Harney JW, Venihaki M, Butte AJ, Kozakewich HP, Fishman SJ, Larsen PR. N Engl J Med. 2000; 343 (3): 185-9
• Enrolling patients into clinical trials faster using RealTime Recuiting. Butte AJ, Weinstein DA, Kohane IS. Proc AMIA Symp. 2000: 111-5
• Unsupervised knowledge discovery in medical databases using relevance networks. Butte AJ, Kohane IS. Proc AMIA Symp. 1999: 711-5
• Insulin receptor substrate 1 mediates the stimulatory effect of insulin on GLUT4 translocation in transfected rat adipose cells. Quon MJ, Butte AJ, Zarnowski MJ, Sesti G, Cushman SW, Taylor SI. J Biol Chem. 1994; 269 (45): 27920-4
• Tyrosine kinase-deficient mutant human insulin receptors (Met1153-->Ile) overexpressed in transfected rat adipose cells fail to mediate translocation of epitope-tagged GLUT4. Quon MJ, Guerre-Millo M, Zarnowski MJ, Butte AJ, Em M, Cushman SW, Taylor SI. Proc Natl Acad Sci U S A. 1994; 91 (12): 5587-91
• Derivation of a scale-independent parameter which characterizes genetic sequence comparisons. DePetrillo PB, Butte AJ. Comput Biomed Res. 1993; 26 (6): 517-40