Atul Butte

Publications

• Expression-based genome-wide association study links the receptor CD44 in adipose tissue with type 2 diabetes. 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. Proc Natl Acad Sci U S A. 2012; 109 (18): 7049-54
• Personal omics profiling reveals dynamic molecular and medical phenotypes. Chen R, Mias GI, Li-Pook-Than J, Jiang L, Lam HY, Chen R, Miriami E, Karczewski KJ, Hariharan M, Dewey FE, Cheng Y, Clark MJ, Im H, Habegger L, Balasubramanian S, O'Huallachain M, Dudley JT, Hillenmeyer S, Haraksingh R, Sharon D, Euskirchen G, Lacroute P, Bettinger K, Boyle AP, Kasowski M, Grubert F, Seki S, Garcia M, Whirl-Carrillo M, Gallardo M, Blasco MA, Greenberg PL, Snyder P, Klein TE, Altman RB, Butte AJ, Ashley EA, Gerstein M, Nadeau KC, Tang H, Snyder M. Cell. 2012; 148 (6): 1293-307
• Computational repositioning of the anticonvulsant topiramate for inflammatory bowel disease. Dudley JT, Sirota M, Shenoy M, Pai RK, Roedder S, Chiang AP, Morgan AA, Sarwal MM, Pasricha PJ, Butte AJ. Sci Transl Med. 2011; 3 (96): 96ra76
• Discovery and preclinical validation of drug indications using compendia of public gene expression data. Sirota M, Dudley JT, Kim J, Chiang AP, Morgan AA, Sweet-Cordero A, Sage J, Butte AJ. Sci Transl Med. 2011; 3 (96): 96ra77
• Performance comparison of exome DNA sequencing technologies. Clark MJ, Chen R, Lam HY, Karczewski KJ, Chen R, Euskirchen G, Butte AJ, Snyder M. Nat Biotechnol. 2011; 29 (10): 908-14
• An Environment-Wide Association Study (EWAS) on type 2 diabetes mellitus. Patel CJ, Bhattacharya J, Butte AJ. PLoS One. 2010; 5 (5): e10746
• Cell type-specific gene expression differences in complex tissues. Shen-Orr SS, Tibshirani R, Khatri P, Bodian DL, Staedtler F, Perry NM, Hastie T, Sarwal MM, Davis MM, Butte AJ. Nat Methods. 2010; 7 (4): 287-9
• Clinical assessment incorporating a personal genome. 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. Lancet. 2010; 375 (9725): 1525-35
• Differentially expressed RNA from public microarray data identifies serum protein biomarkers for cross-organ transplant rejection and other conditions. 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. PLoS Comput Biol. 2010; 6 (9)
• Extreme evolutionary disparities seen in positive selection across seven complex diseases. Corona E, Dudley JT, Butte AJ. PLoS One. 2010; 5 (8): e12236
• 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
• The use and analysis of microarray data. Butte A, Nat Rev Drug Discov. 2002; 1 (12): 951-60
• Systematic identification of interaction effects between genome- and environment-wide associations in type 2 diabetes mellitus. Patel CJ, Chen R, Kodama K, Ioannidis JP, Butte AJ. Hum Genet. 2013; 132 (5): 495-508
• Systematic identification of risk factors for Alzheimer's disease through shared genetic architecture and electronic medical records. Li L, Ruau D, Chen R, Weber S, Butte AJ. Pac Symp Biocomput. 2013: 224-35
• Multiplex meta-analysis of RNA expression to identify genes with variants associated with immune dysfunction. Morgan AA, Pyrgos VJ, Nadeau KC, Williamson PR, Butte AJ. J Am Med Inform Assoc. 2012 Mar-Apr; 19 (2): 284-8
• A peripheral blood diagnostic test for acute rejection in renal transplantation. 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. Am J Transplant. 2012; 12 (10): 2710-8
• Clinical utility of sequence-based genotype compared with that derivable from genotyping arrays. Morgan AA, Chen R, Butte AJ. J Am Med Inform Assoc. 2012; 19 (e1): e21-7
• Coanalysis of GWAS with eQTLs reveals disease-tissue associations. Kang HP, Morgan AA, Chen R, Schadt EE, Butte AJ. AMIA Summits Transl Sci Proc. 2012: 2012 35-41
• 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. 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. Cancer Res. 2012; 72 (22): 5744-56
• Data-driven integration of epidemiological and toxicological data to select candidate interacting genes and environmental factors in association with disease. Patel CJ, Chen R, Butte AJ. Bioinformatics. 2012; 28 (12): i121-6
• Evolutionary meta-analysis of association studies reveals ancient constraints affecting disease marker discovery. Dudley JT, Chen R, Sanderford M, Butte AJ, Kumar S. Mol Biol Evol. 2012; 29 (9): 2087-94
• Human genomic disease variants: a neutral evolutionary explanation. Dudley JT, Kim Y, Liu L, Markov GJ, Gerold K, Chen R, Butte AJ, Kumar S. Genome Res. 2012; 22 (8): 1383-94
• Identification of cell surface targets through meta-analysis of microarray data. Haeberle H, Dudley JT, Liu JT, Butte AJ, Contag CH. Neoplasia. 2012; 14 (7): 666-9
• Integration of disease-specific single nucleotide polymorphisms, expression quantitative trait loci and coexpression networks reveal novel candidate genes for type 2 diabetes. Kang HP, Yang X, Chen R, Zhang B, Corona E, Schadt EE, Butte AJ. Diabetologia. 2012; 55 (8): 2205-13
• Integrative approach to pain genetics identifies pain sensitivity loci across diseases. Ruau D, Dudley JT, Chen R, Phillips NG, Swan GE, Lazzeroni LC, Clark JD, Butte AJ, Angst MS. PLoS Comput Biol. 2012; 8 (6): e1002538
• Leveraging models of cell regulation and GWAS data in integrative network-based association studies. Califano A, Butte AJ, Friend S, Ideker T, Schadt E. Nat Genet. 2012; 44 (8): 841-7
• Neonatal Informatics: Transforming Neonatal Care Through Translational Bioinformatics. Palma JP, Benitz WE, Tarczy-Hornoch P, Butte AJ, Longhurst CA. Neoreviews. 2012; 13 (5): e281-e284
• Population genetic inference from personal genome data: impact of ancestry and admixture on human genomic variation. 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. Am J Hum Genet. 2012; 91 (4): 660-71
• Quantifying multi-ethnic representation in genetic studies of high mortality diseases. Chen R, Dudley JT, Ruau D, Butte AJ. AMIA Summits Transl Sci Proc. 2012: 2012 11-8
• Sequencing and analysis of a South Asian-Indian personal genome. 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. BMC Genomics. 2012: 13 440
• Sex differences in disease risk from reported genome-wide association study findings. Liu LY, Schaub MA, Sirota M, Butte AJ. Hum Genet. 2012; 131 (3): 353-64
• Sex differences in reported pain across 11,000 patients captured in electronic medical records. Ruau D, Liu LY, Clark JD, Angst MS, Butte AJ. J Pain. 2012; 13 (3): 228-34
• Systematic evaluation of environmental factors: persistent pollutants and nutrients correlated with serum lipid levels. Patel CJ, Cullen MR, Ioannidis JP, Butte AJ. Int J Epidemiol. 2012; 41 (3): 828-43
• Ten years of pathway analysis: current approaches and outstanding challenges. Khatri P, Sirota M, Butte AJ. PLoS Comput Biol. 2012; 8 (2): e1002375
• Translational bioinformatics: data-driven drug discovery and development. Butte AJ, Ito S. Clin Pharmacol Ther. 2012; 91 (6): 949-52
• Transmission distortion in Crohn's disease risk gene ATG16L1 leads to sex difference in disease association. Liu LY, Schaub MA, Sirota M, Butte AJ. Inflamm Bowel Dis. 2012; 18 (2): 312-22
• Type 2 diabetes risk alleles demonstrate extreme directional differentiation among human populations, compared to other diseases. Chen R, Corona E, Sikora M, Dudley JT, Morgan AA, Moreno-Estrada A, Nilsen GB, Ruau D, Lincoln SE, Bustamante CD, Butte AJ. PLoS Genet. 2012; 8 (4): e1002621
• Computationally translating molecular discoveries into tools for medicine: translational bioinformatics articles now featured in JAMIA. Butte AJ, Shah NH. J Am Med Inform Assoc. 2011 Jul-Aug; 18 (4): 352-3
• Translational bioinformatics: linking knowledge across biological and clinical realms. Sarkar IN, Butte AJ, Lussier YA, Tarczy-Hornoch P, Ohno-Machado L. J Am Med Inform Assoc. 2011 Jul-Aug; 18 (4): 354-7
• Applications of translational bioinformatics in transplantation. Khatri P, Sarwal MM, Butte AJ. Clin Pharmacol Ther. 2011; 90 (2): 323-7
• Comparison of automated and human assignment of MeSH terms on publicly-available molecular datasets. Ruau D, Mbagwu M, Dudley JT, Krishnan V, Butte AJ. J Biomed Inform. 2011: 44 Suppl 1 S39-43
• Computational prediction and experimental validation associating FABP-1 and pancreatic adenocarcinoma with diabetes. Sharaf RN, Butte AJ, Montgomery KD, Pai R, Dudley JT, Pasricha PJ. BMC Gastroenterol. 2011: 11 5
• Exploiting drug-disease relationships for computational drug repositioning. Dudley JT, Deshpande T, Butte AJ. Brief Bioinform. 2011; 12 (4): 303-11
• Identification of an IFN-γ/mast cell axis in a mouse model of chronic asthma. Yu M, Eckart MR, Morgan AA, Mukai K, Butte AJ, Tsai M, Galli SJ. J Clin Invest. 2011; 121 (8): 3133-43
• Matching cancer genomes to established cell lines for personalized oncology. Dudley JT, Chen R, Butte AJ. Pac Symp Biocomput. 2011: 243-52
• Phased whole-genome genetic risk in a family quartet using a major allele reference sequence. 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. PLoS Genet. 2011; 7 (9): e1002280
• Predicting adverse drug reactions using publicly available PubChem BioAssay data. Pouliot Y, Chiang AP, Butte AJ. Clin Pharmacol Ther. 2011; 90 (1): 90-9
• ProfileChaser: searching microarray repositories based on genome-wide patterns of differential expression. Engreitz JM, Chen R, Morgan AA, Dudley JT, Mallelwar R, Butte AJ. Bioinformatics. 2011; 27 (23): 3317-8
• Progressive histological damage in renal allografts is associated with expression of innate and adaptive immunity genes. Naesens M, Khatri P, Li L, Sigdel TK, Vitalone MJ, Chen R, Butte AJ, Salvatierra O, Sarwal MM. Kidney Int. 2011; 80 (12): 1364-76
• Protein microarrays discover angiotensinogen and PRKRIP1 as novel targets for autoantibodies in chronic renal disease. Butte AJ, Sigdel TK, Wadia PP, Miklos DB, Sarwal MM. Mol Cell Proteomics. 2011; 10 (3): M110.000497
• The reference human genome demonstrates high risk of type 1 diabetes and other disorders. Chen R, Butte AJ. Pac Symp Biocomput. 2011: 231-42
• The role of bioinformatics in studying rheumatic and autoimmune disorders. Sirota M, Butte AJ. Nat Rev Rheumatol. 2011; 7 (8): 489-94
• Transplantomics and biomarkers in organ transplantation: a report from the first international conference. Sarwal MM, Benjamin J, Butte AJ, Davis MM, Wood K, Chapman J. Transplantation. 2011; 91 (4): 379-82
• An integrative method for scoring candidate genes from association studies: application to warfarin dosing. Tatonetti NP, Dudley JT, Sagreiya H, Butte AJ, Altman RB. BMC Bioinformatics. 2010: 11 Suppl 9 S9
• Antibodies specifically target AML antigen NuSAP1 after allogeneic bone marrow transplantation. Wadia PP, Coram M, Armstrong RJ, Mindrinos M, Butte AJ, Miklos DB. Blood. 2010; 115 (10): 2077-87
• Biomarker and drug discovery for gastroenterology through translational bioinformatics. Dudley JT, Butte AJ. Gastroenterology. 2010; 139 (3): 735-41, 741.e1
• Challenges in the clinical application of whole-genome sequencing. Ormond KE, Wheeler MT, Hudgins L, Klein TE, Butte AJ, Altman RB, Ashley EA, Greely HT. Lancet. 2010; 375 (9727): 1749-51
• Comparison of multiplex meta analysis techniques for understanding the acute rejection of solid organ transplants. Morgan AA, Khatri P, Jones RH, Sarwal MM, Butte AJ. BMC Bioinformatics. 2010: 11 Suppl 9 S6
• Content-based microarray search using differential expression profiles. Engreitz JM, Morgan AA, Dudley JT, Chen R, Thathoo R, Altman RB, Butte AJ. BMC Bioinformatics. 2010: 11 603
• Current methodologies for translational bioinformatics. Lussier YA, Butte AJ, Hunter L. J Biomed Inform. 2010; 43 (3): 355-7
• Drug discovery in a multidimensional world: systems, patterns, and networks. Dudley JT, Schadt E, Sirota M, Butte AJ, Ashley E. J Cardiovasc Transl Res. 2010; 3 (5): 438-47
• Dynamic microRNA expression programs during cardiac differentiation of human embryonic stem cells: role for miR-499. Wilson KD, Hu S, Venkatasubrahmanyam S, Fu JD, Sun N, Abilez OJ, Baugh JJ, Jia F, Ghosh Z, Li RA, Butte AJ, Wu JC. Circ Cardiovasc Genet. 2010; 3 (5): 426-35
• Dynamism in gene expression across multiple studies. Morgan AA, Dudley JT, Deshpande T, Butte AJ. Physiol Genomics. 2010; 40 (3): 128-40
• Getting from genes to function in lung disease: a National Heart, Lung, and Blood Institute workshop report. Ober C, Butte AJ, Elias JA, Lusis AJ, Gan W, Banks-Schlegel S, Schwartz D. Am J Respir Crit Care Med. 2010; 182 (6): 732-7
• Identification of complex metabolic states in critically injured patients using bioinformatic cluster analysis. Cohen MJ, Grossman AD, Morabito D, Knudson MM, Butte AJ, Manley GT. Crit Care. 2010; 14 (1): R10
• In silico research in the era of cloud computing. Dudley JT, Butte AJ. Nat Biotechnol. 2010; 28 (11): 1181-5
• Latent physiological factors of complex human diseases revealed by independent component analysis of clinarrays. Chen DP, Dudley JT, Butte AJ. BMC Bioinformatics. 2010: 11 Suppl 9 S4
• Likelihood ratios for genome medicine. Morgan AA, Chen R, Butte AJ. Genome Med. 2010; 2 (5): 30
• Network-based elucidation of human disease similarities reveals common functional modules enriched for pluripotent drug targets. Suthram S, Dudley JT, Chiang AP, Chen R, Hastie TJ, Butte AJ. PLoS Comput Biol. 2010; 6 (2): e1000662
• Non-synonymous and synonymous coding SNPs show similar likelihood and effect size of human disease association. Chen R, Davydov EV, Sirota M, Butte AJ. PLoS One. 2010; 5 (10): e13574
• Predicting environmental chemical factors associated with disease-related gene expression data. Patel CJ, Butte AJ. BMC Med Genomics. 2010: 3 17
• Special article: an optimistic prognosis for the clinical utility of laboratory test data. Zheng M, Ravindran P, Wang J, Epstein RH, Chen DP, Butte AJ, Peltz G. Anesth Analg. 2010; 111 (4): 1026-35
• Translational bioinformatics in the cloud: an affordable alternative. Dudley JT, Pouliot Y, Chen R, Morgan AA, Butte AJ. Genome Med. 2010; 2 (8): 51
• Validating pathophysiological models of aging using clinical electronic medical records. Chen DP, Morgan AA, Butte AJ. J Biomed Inform. 2010; 43 (3): 358-64
• 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
• A quick guide for developing effective bioinformatics programming skills. Dudley JT, Butte AJ. PLoS Comput Biol. 2009; 5 (12): e1000589
• Autoimmune disease classification by inverse association with SNP alleles. Sirota M, Schaub MA, Batzoglou S, Robinson WH, Butte AJ. PLoS Genet. 2009; 5 (12): e1000792
• 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
• Data-driven methods to discover molecular determinants of serious adverse drug events. Chiang AP, Butte AJ. Clin Pharmacol Ther. 2009; 85 (3): 259-68
• Disease signatures are robust across tissues and experiments. Dudley JT, Tibshirani R, Deshpande T, Butte AJ. Mol Syst Biol. 2009: 5 307
• 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
• 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
• Identification of discriminating biomarkers for human disease using integrative network biology. Dudley JT, Butte AJ. Pac Symp Biocomput. 2009: 27-38
• Identifying compartment-specific non-HLA targets after renal transplantation by integrating transcriptome and "antibodyome" measures. Li L, Wadia P, Chen R, Kambham N, Naesens M, Sigdel TK, Miklos DB, Sarwal MM, Butte AJ. Proc Natl Acad Sci U S A. 2009; 106 (11): 4148-53
• Infection in the intensive care unit alters physiological networks. Grossman AD, Cohen MJ, Manley GT, Butte AJ. BMC Bioinformatics. 2009: 10 Suppl 9 S4
• 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
• 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
• 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; 76 (12): 1277-83
• 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; 114 (23): 4847-58
• 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
• 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
• 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
• The "etiome": identification and clustering of human disease etiological factors. Liu YI, Wise PH, Butte AJ. BMC Bioinformatics. 2009: 10 Suppl 2 S14
• 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
• Translational bioinformatics applications in genome medicine. Butte AJ, Genome Med. 2009; 1 (6): 64
• 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
• 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
• Enabling integrative genomic analysis of high-impact human diseases through text mining. Dudley J, Butte AJ. Pac Symp Biocomput. 2008: 580-91
• Expression-based Pathway Signature Analysis (EPSA): mining publicly available microarray data for insight into human disease. Tenenbaum JD, Walker MG, Utz PJ, Butte AJ. BMC Med Genomics. 2008: 1 51
• FitSNPs: highly differentially expressed genes are more likely to have variants associated with disease. Chen R, Morgan AA, Dudley J, Deshpande T, Li L, Kodama K, Chiang AP, Butte AJ. Genome Biol. 2008; 9 (12): R170
• GeneChaser: identifying all biological and clinical conditions in which genes of interest are differentially expressed. Chen R, Mallelwar R, Thosar A, Venkatasubrahmanyam S, Butte AJ. BMC Bioinformatics. 2008: 9 548
• 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
• 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
• AILUN: reannotating gene expression data automatically. Chen R, Li L, Butte AJ. Nat Methods. 2007; 4 (11): 879
• 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
• 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
• 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
• Creation and implications of a phenome-genome network. Butte AJ, Kohane IS. Nat Biotechnol. 2006; 24 (1): 55-62
• 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
• 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
• 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
• 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-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
• 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
• Systematic survey reveals general applicability of "guilt-by-association" within gene coexpression networks. Wolfe CJ, Kohane IS, Butte AJ. BMC Bioinformatics. 2005: 6 227
• 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
• 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
• Computerized recruiting for clinical trials in real time. Weiner DL, Butte AJ, Hibberd PL, Fleisher GR. Ann Emerg Med. 2003; 41 (2): 242-6
• 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
• 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
• 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
• Challenges in bioinformatics: infrastructure, models and analytics. Butte AJ, Trends Biotechnol. 2001; 19 (5): 159-60
• 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
• 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
• Extracting knowledge from dynamics in gene expression. Reis BY, Butte AS, Kohane IS. J Biomed Inform. 2001; 34 (1): 15-27
• 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
• 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
• 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
• Enrolling patients into clinical trials faster using RealTime Recuiting. Butte AJ, Weinstein DA, Kohane IS. Proc AMIA Symp. 2000: 111-5
• 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
• 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
• Insulin signal transduction pathways. Quon MJ, Butte AJ, Taylor SI. Trends Endocrinol Metab. 1994; 5 (9): 369-76
• 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
• Translation of poliovirus RNA in vitro: studies on n-formylmethionine-labeled polypeptides initiated in cell-free extracts prepared from poliovirus infected HeLa cells. Knauert F, Ehrenfeld E. Virology. 1979; 93 (2): 537-46