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Papers authored by Butte AJ

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FoxO3 regulates neural stem cell homeostasis.

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Renault VM, Rafalski VA, Morgan AA, Salih DA, Brett JO, Webb AE, Villeda SA, Thekkat PU, Guillerey C, Denko NC, Palmer TD, Butte AJ, and Brunet A

Cell stem cell 5(5):527-39, 2009 Nov 6 - Who cited this? | PubMed ID: 19896443 | Fulltext

Systematic evaluation of drug-disease relationships to identify leads for novel drug uses.

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Chiang AP and Butte AJ

Clinical pharmacology and therapeutics 86(5):507-10, 2009 Nov - Who cited this? | PubMed ID: 19571805 | Fulltext

Expression of complement components differs between kidney allografts from living and deceased donors.

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Naesens M, Li L, Ying L, Sansanwal P, Sigdel TK, Hsieh SC, Kambham N, Lerut E, Salvatierra O, Butte AJ, and Sarwal MM

Journal of the American Society of Nephrology : JASN 20(8):1839-51, 2009 Aug - Who cited this? | PubMed ID: 19443638 | Fulltext

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

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Schaub MA, Kaplow IM, Sirota M, Do CB, Butte AJ, and Batzoglou S

Bioinformatics (Oxford, England) 25(12):i21-9, 2009 Jun 15 - Who cited this? | PubMed ID: 19477990 | Fulltext

C3 polymorphisms and outcomes of renal allografts.

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Naesens M, Butte AJ, and Sarwal MM

The New England journal of medicine 360(23):2478; author reply 2478-9, 2009 Jun 4 - Who cited this? | PubMed ID: 19504761 | Fulltext

MicroRNA profiling of human-induced pluripotent stem cells.

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Wilson KD, Venkatasubrahmanyam S, Jia F, Sun N, Butte AJ, and Wu JC

Stem cells and development 18(5):749-58, 2009 Jun - Who cited this? | PubMed ID: 19284351 | Fulltext

Identifying compartment-specific non-HLA targets after renal transplantation by integrating transcriptome and "antibodyome" measures.

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Li L, Wadia P, Chen R, Kambham N, Naesens M, Sigdel TK, Miklos DB, Sarwal MM, and Butte AJ

Proceedings of the National Academy of Sciences of the United States of America 106(11):4148-53, 2009 Mar 17 - Who cited this? | PubMed ID: 19251643 | Fulltext

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

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Chiang AP and Butte AJ

Clinical pharmacology and therapeutics 85(3):259-68, 2009 Mar - Who cited this? | PubMed ID: 19177064 | Fulltext

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

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Dudley JT and Butte AJ

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing:27-38, 2009 - Who cited this? | PubMed ID: 19209693 | Fulltext

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

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Shen-Orr SS, Goldberger O, Garten Y, Rosenberg-Hasson Y, Lovelace PA, Hirschberg DL, Altman RB, Davis MM, and Butte AJ

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing:439-50, 2009 - Who cited this? | PubMed ID: 19209721 | Fulltext

Selected proceedings of the First Summit on Translational Bioinformatics 2008.

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

BMC bioinformatics 10 Suppl 2:I1, 2009 - Who cited this? | PubMed ID: 19208183 | Fulltext

Ontology-driven indexing of public datasets for translational bioinformatics.

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

BMC bioinformatics 10 Suppl 2:S1, 2009 - Who cited this? | PubMed ID: 19208184 | Fulltext

The "etiome": identification and clustering of human disease etiological factors.

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Liu YI, Wise PH, and Butte AJ

BMC bioinformatics 10 Suppl 2:S14, 2009 - Who cited this? | PubMed ID: 19208189 | Fulltext

Translational bioinformatics applications in genome medicine.

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Butte AJ

Genome medicine 1(6):64, 2009 - Who cited this? | PubMed ID: 19566916 | Fulltext

Disease signatures are robust across tissues and experiments.

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Dudley JT, Tibshirani R, Deshpande T, and Butte AJ

Molecular systems biology 5:307, 2009 - Who cited this? | PubMed ID: 19756046 | Fulltext

Infection in the intensive care unit alters physiological networks.

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Grossman AD, Cohen MJ, Manley GT, and Butte AJ

BMC bioinformatics 10 Suppl 9:S4, 2009 - Who cited this? | PubMed ID: 19761574 | Fulltext

Expression-based Pathway Signature Analysis (EPSA): Mining publicly available microarray data for insight into human disease.

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Tenenbaum JD, Walker MG, Utz PJ, and Butte AJ

BMC medical genomics 1(1):51, 2008 Oct 20 - Who cited this? | PubMed ID: 18937865 | Fulltext

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

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Viatour P, Somervaille TC, Venkatasubrahmanyam S, Kogan S, McLaughlin ME, Weissman IL, Butte AJ, Passegué E, and Sage J

Cell stem cell 3(4):416-28, 2008 Oct 9 - Who cited this? | PubMed ID: 18940733 | Fulltext

Use of Bayesian networks to probabilistically model and improve the likelihood of validation of microarray findings by RT-PCR.

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

Journal of biomedical informatics, 2008 Aug 26 - Who cited this? | PubMed ID: 18790084 | Fulltext

Medicine. The ultimate model organism.

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Butte AJ

Science (New York, N.Y.) 320(5874):325-7, 2008 Apr 18 - Who cited this? | PubMed ID: 18420921 | Fulltext

Novel integration of hospital electronic medical records and gene expression measurements to identify genetic markers of maturation.

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

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing:243-54, 2008 - Who cited this? | PubMed ID: 18229690 | Fulltext

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

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Dudley J and Butte AJ

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing:580-91, 2008 - Who cited this? | PubMed ID: 18229717 | Fulltext

Translational bioinformatics: coming of age.

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Butte AJ

Journal of the American Medical Informatics Association : JAMIA 15(6):709-14, 2008 - Who cited this? | PubMed ID: 18755990 | Fulltext

GeneChaser: Identifying all biological and clinical conditions in which genes of interest are differentially expressed.

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Chen R, Mallelwar R, Thosar A, Venkatasubrahmanyam S, and Butte AJ

BMC bioinformatics 9:548, 2008 - Who cited this? | PubMed ID: 19094235 | Fulltext

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

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

Genome biology 9(12):R170, 2008 - Who cited this? | PubMed ID: 19061490 | Fulltext

Evaluation and integration of 49 genome-wide experiments and the prediction of previously unknown obesity-related genes.

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English SB and Butte AJ

Bioinformatics (Oxford, England) 23(21):2910, 2007 Nov 1 - Who cited this? | PubMed ID: 17921495 | Fulltext

AILUN: reannotating gene expression data automatically.

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Chen R, Li L, and Butte AJ

Nature methods 4(11):879, 2007 Nov - Who cited this? | PubMed ID: 17971777 | Fulltext

Clinical arrays of laboratory measures, or "clinarrays", built from an electronic health record enable disease subtyping by severity.

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

AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium:115-9, 2007 - Who cited this? | PubMed ID: 18693809 | Fulltext

Methodologies for extracting functional pharmacogenomic experiments from international repository.

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

AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium:463-7, 2007 - Who cited this? | PubMed ID: 18693879 | Fulltext

Finding disease-related genomic experiments within an international repository: first steps in translational bioinformatics.

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Butte AJ and Chen R

AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium:106, 2006 - Who cited this? | PubMed ID: 17238312 | Fulltext

Multiplexed protein array platforms for analysis of autoimmune diseases.

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Balboni I, Chan SM, Kattah M, Tenenbaum JD, Butte AJ, and Utz PJ

Annual review of immunology 24:391, 2006 - Who cited this? | PubMed ID: 16551254 | Fulltext

Creation and implications of a phenome-genome network.

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Butte AJ and Kohane IS

Nature biotechnology 24(1):55, 2006 Jan - Who cited this? | PubMed ID: 16404398 | Fulltext

Genome-wide analysis of host responses to the Pseudomonas aeruginosa type III secretion system yields synergistic effects.

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

Cellular microbiology 7(11):1635, 2005 Nov - Who cited this? | PubMed ID: 16207250 | Fulltext

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

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Tseng YH, Butte AJ, Kokkotou E, Yechoor VK, Taniguchi CM, Kriauciunas KM, Cypess AM, Niinobe M, Yoshikawa K, Patti ME, and Kahn CR

Nature cell biology 7(6):601-11, 2005 Jun - Who cited this? | PubMed ID: 15895078 | Fulltext

A computational model to define the molecular causes of type 2 diabetes mellitus.

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

Diabetes technology & therapeutics 7(2):323-36, 2005 Apr - Who cited this? | PubMed ID: 15857235 | Fulltext

Systematic survey reveals general applicability of "guilt-by-association" within gene coexpression networks.

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Wolfe CJ, Kohane IS, and Butte AJ

BMC bioinformatics 6:227, 2005 - Who cited this? | PubMed ID: 16162296 | Fulltext

Genome-scale expression profiling of Hutchinson-Gilford progeria syndrome reveals widespread transcriptional misregulation leading to mesodermal/mesenchymal defects and accelerated atherosclerosis.

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Csoka AB, English SB, Simkevich CP, Ginzinger DG, Butte AJ, Schatten GP, Rothman FG, and Sedivy JM

Aging cell 3(4):235-43, 2004 Aug - Who cited this? | PubMed ID: 15268757 | Fulltext

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

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

Genes & development 18(6):629-40, 2004 Mar 15 - Who cited this? | PubMed ID: 15075291 | Fulltext

Quantifying the relationship between co-expression, co-regulation and gene function.

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Allocco DJ, Kohane IS, and Butte AJ

BMC bioinformatics 5:18, 2004 Feb 25 - Who cited this? | PubMed ID: 15053845 | Fulltext

Coordinated reduction of genes of oxidative metabolism in humans with insulin resistance and diabetes: Potential role of PGC1 and NRF1.

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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,

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Proceedings of the National Academy of Sciences of the United States of America 100(14):8466, 2003 Jul 8 - Who cited this? | PubMed ID: 12832613 | Fulltext

Reproducibility of gene expression across generations of Affymetrix microarrays.

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

BMC bioinformatics 4:27, 2003 Jun 25 - Who cited this? | PubMed ID: 12823866 | Fulltext

PGAGENE: integrating quantitative gene-specific results from the NHLBI programs for genomic applications.

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Lee K, Kohane IS, and Butte AJ

Bioinformatics (Oxford, England) 19(6):778, 2003 Apr 12 - Who cited this? | PubMed ID: 12691993 | Fulltext

Computerized recruiting for clinical trials in real time.

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Weiner DL, Butte AJ, Hibberd PL, and Fleisher GR

Annals of emergency medicine 41(2):242-6, 2003 Feb - Who cited this? | PubMed ID: 12548275 | Fulltext

Comparing expression profiles of genes with similar promoter regions.

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Park PJ, Butte AJ, and Kohane IS

Bioinformatics (Oxford, England) 18(12):1576, 2002 Dec - Who cited this? | PubMed ID: 12490441 | Fulltext

Analysis of matched mRNA measurements from two different microarray technologies.

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

Bioinformatics (Oxford, England) 18(3):405-12, 2002 Mar - Who cited this? | PubMed ID: 11934739 | Fulltext

Further defining housekeeping, or "maintenance," genes Focus on "A compendium of gene expression in normal human tissues".

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Butte AJ, Dzau VJ, and Glueck SB

Physiological genomics 7(2):95-6, 2001 Dec 21 - Who cited this? | PubMed ID: 11773595 | Fulltext

Comparing the similarity of time-series gene expression using signal processing metrics.

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Butte AJ, Bao L, Reis BY, Watkins TW, and Kohane IS

Journal of biomedical informatics 34(6):396-405, 2001 Dec - Who cited this? | PubMed ID: 12198759 | Fulltext

Strict interpretation of vaccination guidelines with computerized algorithms and improper timing of administered doses.

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Butte AJ, Shaw JS, and Bernstein H

The Pediatric infectious disease journal 20(6):561-5, 2001 Jun - Who cited this? | PubMed ID: 11419495 | Fulltext

Challenges in bioinformatics: infrastructure, models and analytics.

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Butte AJ

Trends in biotechnology 19(5):159-60, 2001 May - Who cited this? | PubMed ID: 11403022 | Fulltext

Determining significant fold differences in gene expression analysis.

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Butte AJ, Ye J, Häring HU, Stumvoll M, White MF, and Kohane IS

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing:6-17, 2001 - Who cited this? | PubMed ID: 11262977 | Fulltext

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