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Publications
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Publications by Atul J. Butte, M.D., Ph.D.
There are 59 publications that list Atul J. Butte as an author.
 - BMIR-2009-1376
- Translational bioinformatics applications in genome medicine
- A. J. Butte
- Genome Medicine, 1, 6, 64. Published in 2009
- BMIR-2009-1372
- Systematic Evaluation of Drug-Disease Relationships to Identify Leads for Novel Drug Uses
- A. P. Chiang, A. J. Butte
- Clinical Pharmacology and Therapeutics. In Press in 2009
 - BMIR-2009-1365
- MicroRNA Profiling of Human-Induced Pluripotent Stem Cells
- K. D. Wilson, S. Venkatasubrahmanyam, F. Jia, N. Sun, A. J. Butte, J. C. Wu
- Stem Cells Dev, 2009 Jan 12. Epub ahead of print., PMID: 19284351. Published in 2009
 - BMIR-2009-1362
- Identifying compartment-specific non-HLA targets after renal transplantation by integrating transcriptome and ‘‘antibodyome’’ measures
- L. Li, P. Wadia, M. Sarwal, N. Kambham, T. Sigdel, D. B. Miklos, R. Chen, M. Naesens, A. J. Butte
- PNAS, 106, 11, 4148-4153. Published in 2009
- BMIR-2009-1359
- The "etiome": identification and clustering of human disease etiological factors
- Y. I. Liu, P. H. Wise, A. J. Butte
- BMC Bioinformatics, 10(suppl 2), S14, (5 February 2009). In Press in 2009
- BMIR-2009-1356
- Ontology-driven Indexing of Public Datasets for Translational Bioinformatics
- N. H. Shah, C. Jonquet, A. P. Chiang, A. J. Butte, R. Chen, M. A. Musen
- BMC Bioinformatics, Volume 10. Published in 2009
- BMIR-2009-1355
- Data-Driven Methods to Discover Molecular Determinants of Serious Adverse Drug Events
- A. P. Chiang, A. J. Butte
- Clinical Pharmacology and Therapeutics, 28 January 2009, Advance online publication, doi:10.1038/clpt.2008.274. Published in 2009
- BMIR-2009-1352
- A Multi-Scale Cell Specific Knowledgebase of the Adaptive Immune System.
- S. Shen-Orr, O. Goldberger, Y. Garten, Y. Rosenberg-Hasson, P. A. Lovelace, D. L. Hirschberg, R. B. Altman, M. M. Davis, A. J. Butte
- Pacific Symposium on Biocomputing, Kohala Coast, HI, World Scientific, 439-450. Published in 2009
- BMIR-2009-1351
- Identification of Discriminating Biomarkers for Human Disease Using Integrative Network Biology.
- J. Dudley, A. J. Butte
- Pacific Symposium on Biocomputing, Kohala Coast, HI, World Scientific, 27-38. Published in 2009
 - BMIR-2009-1342
- Use of Bayesian Networks to Probabilistically Model and Improve the Likelihood of Validation of Microarray Findings by RT-PCR
- , S. Shih, M. F. Ramoni, L. E. Smith, A. J. Butte
- Journal of Biomedical Informatics, JBI, 42, 2, 287-95. Published in 2009
- BMIR-2008-1353
- GeneChaser: Identifying all biological and clinical conditions in which genes of interest are differentially expressed
- R. Chen, R. Mallelwar, A. Thosar, S. Venkatasubrahmanyam, A. J. Butte
- BMC Bioinformatics, 9, 1, 548. (doi:10.1186/1471-2105-9-548). Published in 2008
- BMIR-2008-1347
- Mining publicly available microarray data for insight into human disease.
- J. Tenenbaum, M. G. Walker, P. J. Utz, A. J. Butte
- BMC Medical Genomics, 1, 51, doi:10.1186/1755-8794-1-51. Published in 2008
 - BMIR-2008-1346
- FitSNPs: highly differentially expressed genes are more likely to have variants associated with disease
- R. Chen, A. A. Morgan, J. Dudley, A. M. Deshpande, L. Li, K. Kodama, A. P. Chiang, A. J. Butte
- Genome Biology, 9, 12, R170 (doi:10.1186/gb-2008-9-12-r170). Published in 2008
 - BMIR-2008-1341
- Translational Bioinformatics: Coming of Age
- A. J. Butte
- Journal of the American Medical Informatics Association, JAMIA, 15, 6, 709-14. Published in 2008
 - BMIR-2008-1340
- Tissue- and age-specific changes in gene expression during disease induction and progression in NOD mice
- K. Kodama, A. J. Butte, R. J. Creusot, L. Su, D. Sheng, M. Hartnett, H. Iwai, L. R. Soares, C. G. Fathman
- Clinical Immunology, 129, 2, 195-201. Published in 2008
 - BMIR-2008-1339
- Hematopoietic Stem Cell Quiescence Is Maintained by Compound Contributions of the Retinoblastoma Gene Family
- P. Viatour, T. C. Somervaille, S. Venkatasubrahmanyam, M. E. McLaughlin, A. J. Butte, I. L. Weissman, S. Kogan, E. Passegue, J. Sage
- Cell Stem Cell, Oct 9, 3, 4, 416-28. Published in 2008
- BMIR-2008-1338
- Using SNOMED-CT For Translational Genomics Data Integration
- J. Dudley, D. P. Chen, A. J. Butte
- Ronald Cornet, Kent Spackman (eds.): Representing and sharing knowledge using SNOMED. Proceedings of the 3rd International Conference on Knowledge Rep, Pheonix (AZ), USA, CEUR Workshop Proceedings, ISSN 1613-0073, online CEUR-WS.org/Vol-410/, 91-96. Published in 2008
- BMIR-2008-1306
- Ontology-driven Indexing of Public Datasets for Translational Bioinformatics
- N. H. Shah, A. P. Chiang, A. J. Butte, R. Chen, M. A. Musen
- American Medical Informatics Association Symposium on Translational Bioinformatics, San Francisco, CA, March 10-12, 2008. Published in 2008
 - BMIR-2008-1303
- The Ultimate Model Organism
- A. J. Butte
- Science, 320, 5874, 325-327. Published in 2008
- BMIR-2008-1293
- Novel Integration of Hopsital Electronic Medical Records and Gene Expression Measurements to Identify Genetic Markers of Maturation
- D. P. Chen, S. C. Weber, P. S. Constantinou, T. A. Ferris, H. J. Lowe, A. J. Butte
- Pacific Symposium on Biocomputing, Big Island, Hawaii, 13, 243-254. Published in 2008
- BMIR-2008-1292
- Enabling Integrative Genomic Analysis of High-Impact Human Diseases through Text Mining
- J. Dudley, A. J. Butte
- Pacific Symposium on Biocomputing, Big Island, Hawaii, 13, 580-591. Published in 2008
- BMIR-2007-1297
- Methodologies for Extracting Functional Pharmacogenomic Experiments from International Repository
- Y. Lin, A. P. Chiang, P. Yao, R. Chen, A. J. Butte, R. S. Lin
- AMIA Annual Symposium, Chicago, IL, 463-467. Published in 2007
- BMIR-2007-1296
- Clinical Arrays of Laboratory Measures, or “Clinarrays”, Built from an Electronic Health Record Enable Disease Subtyping by Severity
- D. P. Chen, S. C. Weber, P. S. Constantinou, T. A. Ferris, H. J. Lowe, A. J. Butte
- AMIA Annual Symposium, Chicago, IL, 115-119. Published in 2007
 - BMIR-2007-1295
- AILUN: reannotating gene expression data automatically
- R. Chen, L. Li, A. J. Butte
- Nature Methods, 4, 11, 879. Published in 2007
 - BMIR-2007-1281
- Evaluation and Integration of 49 Genome-wide Experiments and the Prediction of Previously Unknown Obesity-related Genes
- , A. J. Butte
- Bioinformatics, Epub. Published in 2007
 - BMIR-2006-1232
- Finding Disease-Related Genomic Experiments Within an International Repository: First Steps in Translational Bioinformatics
- A. J. Butte, R. Chen
- Annual Symposium of the American Medical Informatics Association, Washington, D.C., 106-10. Published in 2006
- BMIR-2006-1093
- Multiplexed Protein Array Platforms for Analysis of Autoimmune Diseases
- I. Balboni, S. M. Chan, M. Kattah, J. Tenenbaum, A. J. Butte, P. J. Utz
- Annual Review of Immunology, 24, 391-418. Published in 2006
 - BMIR-2006-1090
- Creation and implications of a phenome-genome network
- A. J. Butte, I. S. Kohane
- Nature Biotechnology, 24, 1, 55 - 62. Published in 2006
 - BMIR-2005-1087
- Systematic survey reveals general applicability of "guilt-by-association" within gene coexpression networks.
- C. J. Wolfe, I. S. Kohane, A. J. Butte
- BMC Bioinformatics, 6, 227. Published in 2005
 - BMIR-2005-1083
- Genome-wide analysis of host responses to the Pseudomonas aeruginosa yields synergistic effects
- J. K. Ichikawa, A. J. Butte, R. Jackson, M. C. Wolfgang, S. Lory
- Cellular Microbiology, 7, 11, 1635-1646. Published in 2005
 - BMIR-2005-1057
- A Computational Model to Define the Molecular Causes of Type 2 Diabetes Mellitus
- J. Pollard, A. J. Butte, S. Hoberman, M. Joshi, J. Levy, J. Pappo
- Diabetes Technology & Therapeutics, 7, 2, 323-336. Published in 2005
 - BMIR-2005-1029
- Prediction of preadipocyte differentiation by gene expression reveals role of insulin receptor substrates and necdin
- Y. Tseng, A. J. Butte, E. Kokkotou, V. K. Yechoor, C. M. Taniguchi, K. M. Kriauciunas, A. M. Cypess, M. Niinobe, K. Yoshikawa, M. E. Patti, C. Kahn
- Nature Cell Biology, 7, 6, 601-614. Published in 2005
 - BMIR-2004-1045
- Conserved mechanisms across development and tumorigenesis revealed by a mouse development perspective of human cancers
- A. T. Kho, Q. Zhao, Z. Cai, A. J. Butte, J. Y. Kim, S. L. Pomeroy, D. H. Rowitch, I. S. Kohane
- Genes & Development, 18, 6, 629-640. Published in 2004
 - BMIR-2004-1043
- Genome-scale expression profiling of Hutchinson-Gilford progeria syndrome reveals widespread transcriptional misregulation leading to mesodermal/mesenchymal defects and accelerated atherosclerosis
- A. B. Csoka, C. P. Simkevich, D. G. Ginzinger, A. J. Butte, G. P. Schatten, F. G. Rothman, J. M. Sedivy
- Aging Cell, 3, 4, 235-43. Published in 2004
- BMIR-2004-1030
- Quantifying the relationship between co-expression, co-regulation and gene function
- D. J. Allocco, I. S. Kohane, A. J. Butte
- BMC Bioinformatics, 5, 18. Published in 2004
- BMIR-2003-1054
- Computerized Recruiting for Clinical Trials in Real Time
- D. L. Weiner, A. J. Butte, P. L. Hibberd, G. R. Fleisher
- Annals of Emergency Medicine, 41, 2, 242-246. Published in 2003
 - BMIR-2003-1050
- Coordinated reduction of genes of oxidative metabolism in humans with insulin resistance and diabetes: Potential role of PGC1 and NRF1
- M. E. Patti, A. J. Butte, S. Crunkhorn, K. Cusi, R. Berria, S. Kashyap, Y. Miyazaki, I. S. Kohane, M. Costello, R. Saccone, E. J. Landaker, A. B. Goldfine, E. Mun, R. DeFronzo, J. Finlayson, C. Kahn, L. J. Mandarino
- Proceedings of the National Academy of Sciences, PNAS, 100, 14, 8466-8471. Published in 2003
- BMIR-2003-1048
- Reproducibility of gene expression across generations of Affymetrix microarrays
- A. Nimgaonkar, D. Sanoudou, A. J. Butte, J. N. Haslett, H. M. Kunkel, A. H. Beggs, I. S. Kohane
- BMC Bioinformatics, 4, 1-12. Published in 2003
 - BMIR-2003-1047
- PGAGENE: integrating quantitative gene-specific results from the NHLBI Programs for Genomic Applications
- K. Y. Lee, I. S. Kohane, A. J. Butte
- Bioinformatics, 19, 6, 778-779. Published in 2003
- BMIR-2002-1077
- Automated Assessments in Health Care Quality
- A. J. Butte
- Improving the Quality of Primary Care, 32, 50-62. Published in 2002
 - BMIR-2002-1049
- Comparing expression profiles of genes with similar promoter regions
- P. J. Park, A. J. Butte, I. S. Kohane
- Bioinformatics, 18, 12, 1576-1584. Published in 2002
 - BMIR-2002-1046
- Analysis of matched mRNA measurements from two different microarray technologies
- W. P. Kuo, T. Jenssen, A. J. Butte, L. Ohno-Machado, I. S. Kohane
- Bioinformatics, 18, 3, 405-12. Published in 2002
- BMIR-2002-1036
- Comparing the Similarity of Time-Series Gene Expression Using Signal Processing Metrics
- A. J. Butte, L. Bao, B. Y. Reis, T. W. Watkins, I. S. Kohane
- Journal of Biomedical Informatics, 34, 396-405. Published in 2002
 - BMIR-2002-1034
- The Use and Analysis of Microarray Data
- A. J. Butte
- Nature Reviews: Drug Discovery, 1, 12, 951-960. Published in 2002
- BMIR-2001-1053
- The Personal Internetworked Notary and Guardian
- A. Riva, K. D. Mandl, D. Oh, D. J. Nigrin, A. J. Butte, P. Szolovits, I. S. Kohane
- International Journal of Medical Informatics, 60, 27-40. Published in 2001
- BMIR-2001-1052
- Extracting Knowledge from Dynamics in Gene Expression
- B. Y. Reis, A. J. Butte, I. S. Kohane
- Journal of Biomedical Informatics, 34, 15-27. Published in 2001
- BMIR-2001-1042
- Challenges in bioinformatics: infrastructure, models and analytics
- A. J. Butte
- Trends in Biotechnology, 19, 5, 159-160. Published in 2001
 - BMIR-2001-1041
- Determining Significant Fold Differences in Gene Expression Analysis
- A. J. Butte, J. Ye, G. Niederfellner, K. Rett, H. U. Häring, M. F. White, I. S. Kohane
- Pacific Symposium on Biocomputing, 6-17. Published in 2001
- BMIR-2001-1038
- Strict interpretation of vaccination guidelines with computerized algorithms and improper timing of administered doses
- A. J. Butte, J. S. Shaw, H. Bernstein
- The Pediatric Infectious Disease Journal, 20, 6, 561-565. Published in 2001
- BMIR-2001-1037
- Further defining housekeeping, or "maintenance," genes Focus on "A compendium of gene expression in normal human tissues"
- A. J. Butte, V. J. Dzau, S. B. Glueck
- Physiol Genomics, 7, 95-96. Published in 2001
 - BMIR-2000-1044
- Severe Hypothyroidism Caused by Type 3 Iodothyronine Deiodinase in Infantile Hemangiomas
- S. A. Huang, H. M. Tu, J. W. Harney, M. Venihaki, A. J. Butte, H. P. Kozakewich, S. J. Fishman, P. R. Larson
- The New England Journal of Medicine, 343, 3, 185-189. Published in 2000
 - BMIR-2000-1040
- Mutual Information Relevance Networks: Functional Genomic Clustering Using Pairwise Entropy Measurements
- A. J. Butte, I. S. Kohane
- Pacific Symposium on Biocomputing, 418-29. Published in 2000
 - BMIR-2000-1039
- Discovering functional relationships between RNA expression and chemotherapeutic susceptibility using relevance networks
- A. J. Butte, P. Tamayo, D. Slonim, T. R. Golub, I. S. Kohane
- Proceedings of the National Academy of Sciences, PNAS, 97, 22, 12182-6. Published in 2000
 - BMIR-2000-1032
- Enrolling Patients Into Clinical Trials Faster Using RealTime Recuiting
- A. J. Butte, D. A. Weinstein, I. S. Kohane
- Proceedings of the American Medical Informatics Association Symposium, 111-5. Published in 2000
 - BMIR-1999-1035
- Unsupervised Knowledge Discovery in Medical Databases Using Relevance Networks
- A. J. Butte, I. S. Kohane
- Proceedings of the American Medical Informatics Association Symposium, 111-5. Published in 1999
- BMIR-1994-1055
- Tyrosine kinase-deficient mutant human insulin receptors (Met1153-->Ile) overexpressed in transfected rat adipose cells fail to mediate translocation
- M. J. Quon, M. Guerre-Millo, M. Zarnowski, A. J. Butte, M. Em, S. W. Cushman, S. I. Taylor
- Proceedings of the National Academy of Sciences, 91, 12, 5587-5591. Published in 1994
- BMIR-1994-1051
- Insulin Receptor Substrate 1 Mediates the Stimulatory Effect of Insulin on GLUT4 Translocation in Transfected Rat Adipose Cells
- M. J. Quon, A. J. Butte, M. Zarnowski, G. Sesti, S. W. Cushman, S. I. Taylor
- The Journal of Biological Chemistry, 269, 45, 27920-27924. Published in 1994
- BMIR-1993-1075
- Derivation of Scale-Independent Parameter Which Characterizes Genetic Sequence Comparisons
- P. B. DePetrillo, A. J. Butte
- Computers and Biomedical Research: An International Journal, 26, 6, 517-540. Published in 1993
- BMIR-1992-1076
- A Computer-Simulated "Wet" Laboratory
- B. Rotman, A. J. Butte
- Biochemical Education, 20, 3, 139-141. Published in 1992
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