Russ B. Altman

Publications

• Data-driven prediction of drug effects and interactions. Tatonetti NP, Ye PP, Daneshjou R, Altman RB. Sci Transl Med. 2012; 4 (125): 125ra31
• Discovery and explanation of drug-drug interactions via text mining. Percha B, Garten Y, Altman RB. Pac Symp Biocomput. 2012: 410-21
• Translational bioinformatics: linking the molecular world to the clinical world. Altman RB, Clin Pharmacol Ther. 2012; 91 (6): 994-1000
• 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
• Estimation of the warfarin dose with clinical and pharmacogenetic data. Klein TE, Altman RB, Eriksson N, Gage BF, Kimmel SE, Lee MT, Limdi NA, Page D, Roden DM, Wagner MJ, Caldwell MD, Johnson JA. N Engl J Med. 2009; 360 (8): 753-64
• Informatics confronts drug-drug interactions. Percha B, Altman RB. Trends Pharmacol Sci. 2013; 34 (3): 178-84
• Personal genomic measurements: the opportunity for information integration. Altman RB, Clin Pharmacol Ther. 2013; 93 (1): 21-3
• Valproic acid pathway: pharmacokinetics and pharmacodynamics. Ghodke-Puranik Y, Thorn CF, Lamba JK, Leeder JS, Song W, Birnbaum AK, Altman RB, Klein TE. Pharmacogenet Genomics. 2013; 23 (4): 236-41
• Simbios: an NIH national center for physics-based simulation of biological structures. Delp SL, Ku JP, Pande VS, Sherman MA, Altman RB. J Am Med Inform Assoc. 2012 Mar-Apr; 19 (2): 186-9
• A novel signal detection algorithm for identifying hidden drug-drug interactions in adverse event reports. Tatonetti NP, Fernald GH, Altman RB. J Am Med Inform Assoc. 2012 Jan-Feb; 19 (1): 79-85
• Bioinformatics and variability in drug response: a protein structural perspective. Lahti JL, Tang GW, Capriotti E, Liu T, Altman RB. J R Soc Interface. 2012; 9 (72): 1409-37
• Celecoxib pathways: pharmacokinetics and pharmacodynamics. Gong L, Thorn CF, Bertagnolli MM, Grosser T, Altman RB, Klein TE. Pharmacogenet Genomics. 2012; 22 (4): 310-8
• Chapter 7: Pharmacogenomics. Karczewski KJ, Daneshjou R, Altman RB. PLoS Comput Biol. 2012; 8 (12): e1002817
• Interpretome: a freely available, modular, and secure personal genome interpretation engine. Karczewski KJ, Tirrell RP, Cordero P, Tatonetti NP, Dudley JT, Salari K, Snyder M, Altman RB, Kim SK. Pac Symp Biocomput. 2012: 339-50
• Introduction to translational bioinformatics collection. Altman RB, PLoS Comput Biol. 2012; 8 (12): e1002796
• Metformin pathways: pharmacokinetics and pharmacodynamics. Gong L, Goswami S, Giacomini KM, Altman RB, Klein TE. Pharmacogenet Genomics. 2012; 22 (11): 820-7
• 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
• PharmGKB summary: caffeine pathway. Thorn CF, Aklillu E, McDonagh EM, Klein TE, Altman RB. Pharmacogenet Genomics. 2012; 22 (5): 389-95
• PharmGKB summary: phenytoin pathway. Thorn CF, Whirl-Carrillo M, Leeder JS, Klein TE, Altman RB. Pharmacogenet Genomics. 2012; 22 (6): 466-70
• PharmGKB summary: very important pharmacogene information for CYP1A2. Thorn CF, Aklillu E, Klein TE, Altman RB. Pharmacogenet Genomics. 2012; 22 (1): 73-7
• PharmGKB summary: very important pharmacogene information for CYP3A5. Lamba J, Hebert JM, Schuetz EG, Klein TE, Altman RB. Pharmacogenet Genomics. 2012; 22 (7): 555-8
• PharmGKB summary: very important pharmacogene information for GSTT1. Thorn CF, Ji Y, Weinshilboum RM, Altman RB, Klein TE. Pharmacogenet Genomics. 2012; 22 (8): 646-51
• PharmGKB summary: very important pharmacogene information for cytochrome P-450, family 2, subfamily A, polypeptide 6. McDonagh EM, Wassenaar C, David SP, Tyndale RF, Altman RB, Whirl-Carrillo M, Klein TE. Pharmacogenet Genomics. 2012; 22 (9): 695-708
• PharmGKB summary: very important pharmacogene information for cytochrome P450, family 2, subfamily C, polypeptide 19. Scott SA, Sangkuhl K, Shuldiner AR, Hulot JS, Thorn CF, Altman RB, Klein TE. Pharmacogenet Genomics. 2012; 22 (2): 159-65
• PharmGKB summary: zidovudine pathway. Ghodke Y, Anderson PL, Sangkuhl K, Lamba J, Altman RB, Klein TE. Pharmacogenet Genomics. 2012; 22 (12): 891-4
• Pharmacogenomics knowledge for personalized medicine. Whirl-Carrillo M, McDonagh EM, Hebert JM, Gong L, Sangkuhl K, Thorn CF, Altman RB, Klein TE. Clin Pharmacol Ther. 2012; 92 (4): 414-7
• Very important pharmacogene summary for VDR. Poon AH, Gong L, Brasch-Andersen C, Litonjua AA, Raby BA, Hamid Q, Laprise C, Weiss ST, Altman RB, Klein TE. Pharmacogenet Genomics. 2012; 22 (10): 758-63
• Fast flexible modeling of RNA structure using internal coordinates. Flores SC, Sherman MA, Bruns CM, Eastman P, Altman RB. IEEE/ACM Trans Comput Biol Bioinform. 2011 Sep-Oct; 8 (5): 1247-57
• 2010 translational bioinformatics year in review. Altman RB, Miller KS. J Am Med Inform Assoc. 2011 Jul-Aug; 18 (4): 358-66
• A new disease-specific machine learning approach for the prediction of cancer-causing missense variants. Capriotti E, Altman RB. Genomics. 2011; 98 (4): 310-7
• Bioinformatics challenges for personalized medicine. Fernald GH, Capriotti E, Daneshjou R, Karczewski KJ, Altman RB. Bioinformatics. 2011; 27 (13): 1741-8
• Bisphosphonates pathway. Gong L, Altman RB, Klein TE. Pharmacogenet Genomics. 2011; 21 (1): 50-3
• CAMPAIGN: an open-source library of GPU-accelerated data clustering algorithms. Kohlhoff KJ, Sosnick MH, Hsu WT, Pande VS, Altman RB. Bioinformatics. 2011; 27 (16): 2322-3
• Cooperative transcription factor associations discovered using regulatory variation. Karczewski KJ, Tatonetti NP, Landt SG, Yang X, Slifer T, Altman RB, Snyder M. Proc Natl Acad Sci U S A. 2011; 108 (32): 13353-8
• Detecting drug interactions from adverse-event reports: interaction between paroxetine and pravastatin increases blood glucose levels. Tatonetti NP, Denny JC, Murphy SN, Fernald GH, Krishnan G, Castro V, Yue P, Tsao PS, Tsau PS, Kohane I, Roden DM, Altman RB. Clin Pharmacol Ther. 2011; 90 (1): 133-42
• Doxorubicin pathways: pharmacodynamics and adverse effects. Thorn CF, Oshiro C, Marsh S, Hernandez-Boussard T, McLeod H, Klein TE, Altman RB. Pharmacogenet Genomics. 2011; 21 (7): 440-6
• From pharmacogenomic knowledge acquisition to clinical applications: the PharmGKB as a clinical pharmacogenomic biomarker resource. McDonagh EM, Whirl-Carrillo M, Garten Y, Altman RB, Klein TE. Biomark Med. 2011; 5 (6): 795-806
• Improving the prediction of disease-related variants using protein three-dimensional structure. Capriotti E, Altman RB. BMC Bioinformatics. 2011: 12 Suppl 4 S3
• PharmGKB summary: carbamazepine pathway. Thorn CF, Leckband SG, Kelsoe J, Leeder JS, Müller DJ, Klein TE, Altman RB. Pharmacogenet Genomics. 2011; 21 (12): 906-10
• PharmGKB summary: citalopram pharmacokinetics pathway. Sangkuhl K, Klein TE, Altman RB. Pharmacogenet Genomics. 2011; 21 (11): 769-72
• PharmGKB summary: cytochrome P450, family 2, subfamily J, polypeptide 2: CYP2J2. Berlin DS, Sangkuhl K, Klein TE, Altman RB. Pharmacogenet Genomics. 2011; 21 (5): 308-11
• PharmGKB summary: dopamine receptor D2. Mi H, Thomas PD, Ring HZ, Jiang R, Sangkuhl K, Klein TE, Altman RB. Pharmacogenet Genomics. 2011; 21 (6): 350-6
• PharmGKB summary: fluoropyrimidine pathways. Thorn CF, Marsh S, Carrillo MW, McLeod HL, Klein TE, Altman RB. Pharmacogenet Genomics. 2011; 21 (4): 237-42
• PharmGKB summary: methotrexate pathway. Mikkelsen TS, Thorn CF, Yang JJ, Ulrich CM, French D, Zaza G, Dunnenberger HM, Marsh S, McLeod HL, Giacomini K, Becker ML, Gaedigk R, Leeder JS, Kager L, Relling MV, Evans W, Klein TE, Altman RB. Pharmacogenet Genomics. 2011; 21 (10): 679-86
• PharmGKB summary: very important pharmacogene information for PTGS2. Thorn CF, Grosser T, Klein TE, Altman RB. Pharmacogenet Genomics. 2011; 21 (9): 607-13
• PharmGKB: very important pharmacogene--HMGCR. Medina MW, Sangkuhl K, Klein TE, Altman RB. Pharmacogenet Genomics. 2011; 21 (2): 98-101
• Pharmacogenomics: "noninferiority" is sufficient for initial implementation. Altman RB, Clin Pharmacol Ther. 2011; 89 (3): 348-50
• Pharmacogenomics: will the promise be fulfilled? Altman RB, Kroemer HK, McCarty CA, Ratain MJ, Roden D. Nat Rev Genet. 2011; 12 (1): 69-73
• 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
• Platelet aggregation pathway. Sangkuhl K, Shuldiner AR, Klein TE, Altman RB. Pharmacogenet Genomics. 2011; 21 (8): 516-21
• Remote thioredoxin recognition using evolutionary conservation and structural dynamics. Tang GW, Altman RB. Structure. 2011; 19 (4): 461-70
• Using multiple microenvironments to find similar ligand-binding sites: application to kinase inhibitor binding. Liu T, Altman RB. PLoS Comput Biol. 2011; 7 (12): e1002326
• Very important pharmacogene summary: ABCB1 (MDR1, P-glycoprotein). Hodges LM, Markova SM, Chinn LW, Gow JM, Kroetz DL, Klein TE, Altman RB. Pharmacogenet Genomics. 2011; 21 (3): 152-61
• 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
• 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
• Clopidogrel pathway. Sangkuhl K, Klein TE, Altman RB. Pharmacogenet Genomics. 2010; 20 (7): 463-5
• 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
• Cytochrome P450 2C9-CYP2C9. Van Booven D, Marsh S, McLeod H, Carrillo MW, Sangkuhl K, Klein TE, Altman RB. Pharmacogenet Genomics. 2010; 20 (4): 277-81
• DNATwist: a Web-based tool for teaching middle and high school students about pharmacogenomics. Berlin DS, Person MG, Mittal A, Oppezzo MA, Chin DB, Starr B, Klein TE, Schwartz DL, Altman RB. Clin Pharmacol Ther. 2010; 87 (4): 393-5
• Extending and evaluating a warfarin dosing algorithm that includes CYP4F2 and pooled rare variants of CYP2C9. Sagreiya H, Sagrieya H, Berube C, Wen A, Ramakrishnan R, Mir A, Hamilton A, Altman RB. Pharmacogenet Genomics. 2010; 20 (7): 407-13
• Extraction of genotype-phenotype-drug relationships from text: from entity recognition to bioinformatics application. Coulet A, Shah N, Hunter L, Barral C, Altman RB. Pac Symp Biocomput. 2010: 485-7
• Improving the prediction of pharmacogenes using text-derived drug-gene relationships. Garten Y, Tatonetti NP, Altman RB. Pac Symp Biocomput. 2010: 305-14
• Independent component analysis: mining microarray data for fundamental human gene expression modules. Engreitz JM, Daigle BJ, Marshall JJ, Altman RB. J Biomed Inform. 2010; 43 (6): 932-44
• KCNH2 pharmacogenomics summary. Oshiro C, Thorn CF, Roden DM, Klein TE, Altman RB. Pharmacogenet Genomics. 2010; 20 (12): 775-7
• Maternal-fetal and neonatal pharmacogenomics: a review of current literature. Blumenfeld YJ, Reynolds-May MF, Altman RB, El-Sayed YY. J Perinatol. 2010; 30 (9): 571-9
• PharmGKB summary: very important pharmacogene information for CYP2B6. Thorn CF, Lamba JK, Lamba V, Klein TE, Altman RB. Pharmacogenet Genomics. 2010; 20 (8): 520-3
• PharmGKB summary: very important pharmacogene information for angiotensin-converting enzyme. Thorn CF, Klein TE, Altman RB. Pharmacogenet Genomics. 2010; 20 (2): 143-6
• Pharmacogenomics and bioinformatics: PharmGKB. Thorn CF, Klein TE, Altman RB. Pharmacogenomics. 2010; 11 (4): 501-5
• Predicting RNA structure by multiple template homology modeling. Flores SC, Wan Y, Russell R, Altman RB. Pac Symp Biocomput. 2010: 216-27
• Recent progress in automatically extracting information from the pharmacogenomic literature. Garten Y, Coulet A, Altman RB. Pharmacogenomics. 2010; 11 (10): 1467-89
• SLC19A1 pharmacogenomics summary. Yee SW, Gong L, Badagnani I, Giacomini KM, Klein TE, Altman RB. Pharmacogenet Genomics. 2010; 20 (11): 708-15
• Teaching computers to read the pharmacogenomics literature ... so you don't have to. Garten Y, Altman RB. Pharmacogenomics. 2010; 11 (4): 515-8
• The utility of general purpose versus specialty clinical databases for research: warfarin dose estimation from extracted clinical variables. Sagreiya H, Altman RB. J Biomed Inform. 2010; 43 (5): 747-51
• Thiopurine pathway. Zaza G, Cheok M, Krynetskaia N, Thorn C, Stocco G, Hebert JM, McLeod H, Weinshilboum RM, Relling MV, Evans WE, Klein TE, Altman RB. Pharmacogenet Genomics. 2010; 20 (9): 573-4
• Turning limited experimental information into 3D models of RNA. Flores SC, Altman RB. RNA. 2010; 16 (9): 1769-78
• Using pre-existing microarray datasets to increase experimental power: application to insulin resistance. Daigle BJ, Deng A, McLaughlin T, Cushman SW, Cam MC, Reaven G, Tsao PS, Altman RB. PLoS Comput Biol. 2010; 6 (3): e1000718
• Using text to build semantic networks for pharmacogenomics. Coulet A, Shah NH, Garten Y, Musen M, Altman RB. J Biomed Inform. 2010; 43 (6): 1009-19
• VKORC1 pharmacogenomics summary. Owen RP, Gong L, Sagreiya H, Klein TE, Altman RB. Pharmacogenet Genomics. 2010; 20 (10): 642-4
• Vascular endothelial growth factor pathway. Maitland ML, Lou XJ, Ramirez J, Desai AA, Berlin DS, McLeod HL, Weichselbaum RR, Ratain MJ, Altman RB, Klein TE. Pharmacogenet Genomics. 2010; 20 (5): 346-9
• Very important pharmacogene summary ADRB2. Litonjua AA, Gong L, Duan QL, Shin J, Moore MJ, Weiss ST, Johnson JA, Klein TE, Altman RB. Pharmacogenet Genomics. 2010; 20 (1): 64-9
• Very important pharmacogene summary: thiopurine S-methyltransferase. Wang L, Pelleymounter L, Weinshilboum R, Johnson JA, Hebert JM, Altman RB, Klein TE. Pharmacogenet Genomics. 2010; 20 (6): 401-5
• A general framework for dose optimization. Turcott RG, Sagreiya H, Ashley EA, Altman RB, Das AK. AMIA Annu Symp Proc. 2009: 2009 656-60
• Antiestrogen pathway (aromatase inhibitor). Desta Z, Nguyen A, Flockhart D, Skaar T, Fletcher R, Weinshilboum R, Berlin DS, Klein TE, Altman RB. Pharmacogenet Genomics. 2009; 19 (7): 554-5
• Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters. Jonikas MA, Radmer RJ, Laederach A, Das R, Pearlman S, Herschlag D, Altman RB. RNA. 2009; 15 (2): 189-99
• Codeine and morphine pathway. Thorn CF, Klein TE, Altman RB. Pharmacogenet Genomics. 2009; 19 (7): 556-8
• Cytochrome P450 2D6. Owen RP, Sangkuhl K, Klein TE, Altman RB. Pharmacogenet Genomics. 2009; 19 (7): 559-62
• Direct-to-consumer genetic testing: failure is not an option. Altman RB, Clin Pharmacol Ther. 2009; 86 (1): 15-7
• Etoposide pathway. Yang J, Bogni A, Schuetz EG, Ratain M, Dolan ME, McLeod H, Gong L, Thorn C, Relling MV, Klein TE, Altman RB. Pharmacogenet Genomics. 2009; 19 (7): 552-3
• Generating genome-scale candidate gene lists for pharmacogenomics. Hansen NT, Brunak S, Altman RB. Clin Pharmacol Ther. 2009; 86 (2): 183-9
• Improving structure-based function prediction using molecular dynamics. Glazer DS, Radmer RJ, Altman RB. Structure. 2009; 17 (7): 919-29
• Knowledge-based instantiation of full atomic detail into coarse-grain RNA 3D structural models. Jonikas MA, Radmer RJ, Altman RB. Bioinformatics. 2009; 25 (24): 3259-66
• New feature: pathways and important genes from PharmGKB. Eichelbaum M, Altman RB, Ratain M, Klein TE. Pharmacogenet Genomics. 2009; 19 (6): 403
• Pharmspresso: a text mining tool for extraction of pharmacogenomic concepts and relationships from full text. Garten Y, Altman RB. BMC Bioinformatics. 2009: 10 Suppl 2 S6
• Platinum pathway. Marsh S, McLeod H, Dolan E, Shukla SJ, Rabik CA, Gong L, Hernandez-Boussard T, Lou XJ, Klein TE, Altman RB. Pharmacogenet Genomics. 2009; 19 (7): 563-4
• Predicting drug side-effects by chemical systems biology. Tatonetti NP, Liu T, Altman RB. Genome Biol. 2009; 10 (9): 238
• Prediction of calcium-binding sites by combining loop-modeling with machine learning. Liu T, Altman RB. BMC Struct Biol. 2009: 9 72
• Selective serotonin reuptake inhibitors pathway. Sangkuhl K, Klein TE, Altman RB. Pharmacogenet Genomics. 2009; 19 (11): 907-9
• 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
• Very important pharmacogene summary: sulfotransferase 1A1. Hildebrandt M, Adjei A, Weinshilboum R, Johnson JA, Berlin DS, Klein TE, Altman RB. Pharmacogenet Genomics. 2009; 19 (6): 404-6
• Efficient algorithms to explore conformation spaces of flexible protein loops. Yao P, Dhanik A, Marz N, Propper R, Kou C, Liu G, van den Bedem H, Latombe JC, Halperin-Landsberg I, Altman RB. IEEE/ACM Trans Comput Biol Bioinform. 2008 Oct-Dec; 5 (4): 534-45
• An XML-based interchange format for genotype-phenotype data. Whirl-Carrillo M, Woon M, Thorn CF, Klein TE, Altman RB. Hum Mutat. 2008; 29 (2): 212-9
• Combining molecular dynamics and machine learning to improve protein function recognition. Glazer DS, Radmer RJ, Altman RB. Pac Symp Biocomput. 2008: 332-43
• Commentaries on "Informatics and medicine: from molecules to populations". Altman RB, Balling R, Brinkley JF, Coiera E, Consorti F, Dhansay MA, Geissbuhler A, Hersh W, Kwankam SY, Lorenzi NM, Martin-Sanchez F, Mihalas GI, Shahar Y, Takabayashi K, Wiederhold G. Methods Inf Med. 2008; 47 (4): 296-317
• High-throughput single-nucleotide structural mapping by capillary automated footprinting analysis. Mitra S, Shcherbakova IV, Altman RB, Brenowitz M, Laederach A. Nucleic Acids Res. 2008; 36 (11): e63
• Interview: Russ Altman speaks to Shreeya Nanda, Commissioning Editor. Altman RB, Pharmacogenomics. 2008; 9 (6): 663-5
• M-BISON: microarray-based integration of data sources using networks. Daigle BJ, Altman RB. BMC Bioinformatics. 2008: 9 214
• PharmGKB and the International Warfarin Pharmacogenetics Consortium: the changing role for pharmacogenomic databases and single-drug pharmacogenetics. Owen RP, Altman RB, Klein TE. Hum Mutat. 2008; 29 (4): 456-60
• PharmGKB: an integrated resource of pharmacogenomic data and knowledge. Gong L, Owen RP, Gor W, Altman RB, Klein TE. Curr Protoc Bioinformatics. 2008: Chapter 14 Unit14.7
• PharmGKB: understanding the effects of individual genetic variants. Sangkuhl K, Berlin DS, Altman RB, Klein TE. Drug Metab Rev. 2008; 40 (4): 539-51
• Robust recognition of zinc binding sites in proteins. Ebert JC, Altman RB. Protein Sci. 2008; 17 (1): 54-65
• Semiautomated and rapid quantification of nucleic acid footprinting and structure mapping experiments. Laederach A, Das R, Vicens Q, Pearlman SM, Brenowitz M, Herschlag D, Altman RB. Nat Protoc. 2008; 3 (9): 1395-401
• Structural inference of native and partially folded RNA by high-throughput contact mapping. Das R, Kudaravalli M, Jonikas M, Laederach A, Fong R, Schwans JP, Baker D, Piccirilli JA, Altman RB, Herschlag D. Proc Natl Acad Sci U S A. 2008; 105 (11): 4144-9
• Text mining for biology--the way forward: opinions from leading scientists. Altman RB, Bergman CM, Blake J, Blaschke C, Cohen A, Gannon F, Grivell L, Hahn U, Hersh W, Hirschman L, Jensen LJ, Krallinger M, Mons B, O'Donoghue SI, Peitsch MC, Rebholz-Schuhmann D, Shatkay H, Valencia A. Genome Biol. 2008: 9 Suppl 2 S7
• The FEATURE framework for protein function annotation: modeling new functions, improving performance, and extending to novel applications. Halperin I, Glazer DS, Wu S, Altman RB. BMC Genomics. 2008: 9 Suppl 2 S2
• The SeqFEATURE library of 3D functional site models: comparison to existing methods and applications to protein function annotation. Wu S, Liang MP, Altman RB. Genome Biol. 2008; 9 (1): R8
• The Simbios National Center: Systems Biology in Motion. Schmidt JP, Delp SL, Sherman MA, Taylor CA, Pande VS, Altman RB. Proc IEEE Inst Electr Electron Eng. 2008; 96 (8): 1266
• The chemical genomic portrait of yeast: uncovering a phenotype for all genes. Hillenmeyer ME, Fung E, Wildenhain J, Pierce SE, Hoon S, Lee W, Proctor M, St Onge RP, Tyers M, Koller D, Altman RB, Davis RW, Nislow C, Giaever G. Science. 2008; 320 (5874): 362-5
• The pharmacogenetics and pharmacogenomics knowledge base: accentuating the knowledge. Hernandez-Boussard T, Whirl-Carrillo M, Hebert JM, Gong L, Owen R, Gong M, Gor W, Liu F, Truong C, Whaley R, Woon M, Zhou T, Altman RB, Klein TE. Nucleic Acids Res. 2008; 36 (Database issue): D913-8
• Biomedical informatics training at Stanford in the 21st century. Altman RB, Klein TE. J Biomed Inform. 2007; 40 (1): 55-8
• Clustering protein environments for function prediction: finding PROSITE motifs in 3D. Yoon S, Ebert JC, Chung EY, De Micheli G, Altman RB. BMC Bioinformatics. 2007: 8 Suppl 4 S10
• Coplanar and coaxial orientations of RNA bases and helices. Laederach A, Chan JM, Schwartzman A, Willgohs E, Altman RB. RNA. 2007; 13 (5): 643-50
• Current progress in bioinformatics 2007. Altman RB, Brief Bioinform. 2007; 8 (5): 277-8
• Distinct contribution of electrostatics, initial conformational ensemble, and macromolecular stability in RNA folding. Laederach A, Shcherbakova I, Jonikas MA, Altman RB, Brenowitz M. Proc Natl Acad Sci U S A. 2007; 104 (17): 7045-50
• Extracting subject demographic information from abstracts of randomized clinical trial reports. Xu R, Garten Y, Supekar KS, Das AK, Altman RB, Garber AM. Stud Health Technol Inform. 2007; 129 (Pt 1): 550-4
• Genetic nondiscrimination legislation: a critical prerequisite for pharmacogenomics data sharing. Altman RB, Benowitz N, Gurwitz D, Lunshof J, Relling M, Lamba J, Wieben E, Mooney S, Giacomini K, Weiss S, Johnson JA, McLeod H, Flockhart D, Weinshilboum R, Shuldiner AR, Roden D, Krauss RM, Ratain M. Pharmacogenomics. 2007; 8 (5): 519
• PharmGKB: a logical home for knowledge relating genotype to drug response phenotype. Altman RB, Nat Genet. 2007; 39 (4): 426
• Predicting allosteric communication in myosin via a pathway of conserved residues. Tang S, Liao JC, Dunn AR, Altman RB, Spudich JA, Schmidt JP. J Mol Biol. 2007; 373 (5): 1361-73
• The PharmGKB: integration, aggregation, and annotation of pharmacogenomic data and knowledge. Hodge AE, Altman RB, Klein TE. Clin Pharmacol Ther. 2007; 81 (1): 21-4
• The education potential of the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB). Owen RP, Klein TE, Altman RB. Clin Pharmacol Ther. 2007; 82 (4): 472-5
• Using surface envelopes to constrain molecular modeling. Dugan JM, Altman RB. Protein Sci. 2007; 16 (7): 1266-73
• Drug Targets for Plasmodium falciparum: a post-genomic review/survey. Yeh I, Altman RB. Mini Rev Med Chem. 2006; 6 (2): 177-202
• Integrating large-scale genotype and phenotype data. Hernandez-Boussard T, Woon M, Klein TE, Altman RB. OMICS. 2006; 10 (4): 545-54
• Local kinetic measures of macromolecular structure reveal partitioning among multiple parallel pathways from the earliest steps in the folding of a large RNA molecule. Laederach A, Shcherbakova I, Liang MP, Brenowitz M, Altman RB. J Mol Biol. 2006; 358 (4): 1179-90
• Pharmacogenomics: The relevance of emerging genotyping technologies. Hernandez-Boussard T, Klein TE, Altman RB. MLO Med Lab Obs. 2006; 38 (3): 24, 26-30
• The incidentalome: a threat to genomic medicine. Kohane IS, Masys DR, Altman RB. JAMA. 2006; 296 (2): 212-5
• A statistical approach to scanning the biomedical literature for pharmacogenetics knowledge. Rubin DL, Thorn CF, Klein TE, Altman RB. J Am Med Inform Assoc. 2005 Mar-Apr; 12 (2): 121-9
• Choosing SNPs using feature selection. Phuong TM, Lin Z, Altman RB. Proc IEEE Comput Syst Bioinform Conf. 2005: 301-9
• Health-information altruists--a potentially critical resource. Kohane IS, Altman RB. N Engl J Med. 2005; 353 (19): 2074-7
• PharmGKB: the pharmacogenetics and pharmacogenomics knowledge base. Thorn CF, Klein TE, Altman RB. Methods Mol Biol. 2005: 311 179-91
• SAFA: semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments. Das R, Laederach A, Pearlman SM, Herschlag D, Altman RB. RNA. 2005; 11 (3): 344-54
• Structural characterization of proteins using residue environments. Mooney SD, Liang MH, DeConde R, Altman RB. Proteins. 2005; 61 (4): 741-7
• A resource to acquire and summarize pharmacogenetics knowledge in the literature. Rubin DL, Carrillo M, Woon M, Conroy J, Klein TE, Altman RB. Stud Health Technol Inform. 2004; 107 (Pt 2): 793-7
• Computational analysis of Plasmodium falciparum metabolism: organizing genomic information to facilitate drug discovery. Yeh I, Hanekamp T, Tsoka S, Karp PD, Altman RB. Genome Res. 2004; 14 (5): 917-24
• Eukaryotic regulatory element conservation analysis and identification using comparative genomics. Liu Y, Liu XS, Wei L, Altman RB, Batzoglou S. Genome Res. 2004; 14 (3): 451-8
• Extracting and characterizing gene-drug relationships from the literature. Chang JT, Altman RB. Pharmacogenetics. 2004; 14 (9): 577-86
• Finding haplotype tagging SNPs by use of principal components analysis. Lin Z, Altman RB. Am J Hum Genet. 2004; 75 (5): 850-61
• GAPSCORE: finding gene and protein names one word at a time. Chang JT, Schütze H, Altman RB. Bioinformatics. 2004; 20 (2): 216-25
• Genetics. Genomic research and human subject privacy. Lin Z, Owen AB, Altman RB. Science. 2004; 305 (5681): 183
• Tools for loading MEDLINE into a local relational database. Oliver DE, Bhalotia G, Schwartz AS, Altman RB, Hearst MA. BMC Bioinformatics. 2004: 5 146
• Using surface envelopes for discrimination of molecular models. Dugan JM, Altman RB. Protein Sci. 2004; 13 (1): 15-24
• A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae). Troyanskaya OG, Dolinski K, Owen AB, Altman RB, Botstein D. Proc Natl Acad Sci U S A. 2003; 100 (14): 8348-53
• A functional analysis of disease-associated mutations in the androgen receptor gene. Mooney SD, Klein TE, Altman RB, Trifiro MA, Gottlieb B. Nucleic Acids Res. 2003; 31 (8): e42
• A literature-based method for assessing the functional coherence of a gene group. Raychaudhuri S, Altman RB. Bioinformatics. 2003; 19 (3): 396-401
• A personalized and automated dbSNP surveillance system. Liu S, Lin S, Woon M, Klein TE, Altman RB. Proc IEEE Comput Soc Bioinform Conf. 2003: 2 132-6
• Automated construction of structural motifs for predicting functional sites on protein structures. Liang MP, Brutlag DL, Altman RB. Pac Symp Biocomput. 2003: 204-15
• Complexities of managing biomedical information. Altman RB, OMICS. 2003; 7 (1): 127-9
• Defining bioinformatics and structural bioinformatics. Altman RB, Dugan JM. Methods Biochem Anal. 2003: 44 3-14
• Genetic sequence data for pharmacogenomics. Altman RB, Curr Opin Drug Discov Devel. 2003; 6 (3): 297-303
• Identification of promoter regions in the human genome by using a retroviral plasmid library-based functional reporter gene assay. Khambata-Ford S, Liu Y, Gleason C, Dickson M, Altman RB, Batzoglou S, Myers RM. Genome Res. 2003; 13 (7): 1765-74
• Indexing pharmacogenetic knowledge on the World Wide Web. Altman RB, Flockhart DA, Sherry ST, Oliver DE, Rubin DL, Klein TE. Pharmacogenetics. 2003; 13 (1): 3-5
• Investigating hypoxic tumor physiology through gene expression patterns. Denko NC, Fontana LA, Hudson KM, Sutphin PD, Raychaudhuri S, Altman R, Giaccia AJ. Oncogene. 2003; 22 (37): 5907-14
• Knowledge acquisition, consistency checking and concurrency control for Gene Ontology (GO). Yeh I, Karp PD, Noy NF, Altman RB. Bioinformatics. 2003; 19 (2): 241-8
• Large scale study of protein domain distribution in the context of alternative splicing. Liu S, Altman RB. Nucleic Acids Res. 2003; 31 (16): 4828-35
• Microenvironment analysis and identification of magnesium binding sites in RNA. Banatao DR, Altman RB, Klein TE. Nucleic Acids Res. 2003; 31 (15): 4450-60
• MutDB: annotating human variation with functionally relevant data. Mooney SD, Altman RB. Bioinformatics. 2003; 19 (14): 1858-60
• Ribosomal dynamics inferred from variations in experimental measurements. Gabashvili IS, Whirl-Carrillo M, Bada M, Banatao DR, Altman RB. RNA. 2003; 9 (11): 1301-7
• The computational analysis of scientific literature to define and recognize gene expression clusters. Raychaudhuri S, Chang JT, Imam F, Altman RB. Nucleic Acids Res. 2003; 31 (15): 4553-60
• WebFEATURE: An interactive web tool for identifying and visualizing functional sites on macromolecular structures. Liang MP, Banatao DR, Klein TE, Brutlag DL, Altman RB. Nucleic Acids Res. 2003; 31 (13): 3324-7
• Creating an online dictionary of abbreviations from MEDLINE. Chang JT, Schütze H, Altman RB. J Am Med Inform Assoc. 2002 Nov-Dec; 9 (6): 612-20
• Associating genes with gene ontology codes using a maximum entropy analysis of biomedical literature. Raychaudhuri S, Chang JT, Sutphin PD, Altman RB. Genome Res. 2002; 12 (1): 203-14
• Automating data acquisition into ontologies from pharmacogenetics relational data sources using declarative object definitions and XML. Rubin DL, Hewett M, Oliver DE, Klein TE, Altman RB. Pac Symp Biocomput. 2002: 88-99
• Challenges for biomedical informatics and pharmacogenomics. Altman RB, Klein TE. Annu Rev Pharmacol Toxicol. 2002: 42 113-33
• Determining the genomic locations of repetitive DNA sequences with a whole-genome microarray: IS6110 in Mycobacterium tuberculosis. Kivi M, Liu X, Raychaudhuri S, Altman RB, Small PM. J Clin Microbiol. 2002; 40 (6): 2192-8
• Mining biochemical information: lessons taught by the ribosome. Whirl-Carrillo M, Gabashvili IS, Bada M, Banatao DR, Altman RB. RNA. 2002; 8 (3): 279-89
• Modelling biological processes using workflow and Petri Net models. Peleg M, Yeh I, Altman RB. Bioinformatics. 2002; 18 (6): 825-37
• Nonparametric methods for identifying differentially expressed genes in microarray data. Troyanskaya OG, Garber ME, Brown PO, Botstein D, Altman RB. Bioinformatics. 2002; 18 (11): 1454-61
• Ontology development for a pharmacogenetics knowledge base. Oliver DE, Rubin DL, Stuart JM, Hewett M, Klein TE, Altman RB. Pac Symp Biocomput. 2002: 65-76
• PharmGKB: the Pharmacogenetics Knowledge Base. Hewett M, Oliver DE, Rubin DL, Easton KL, Stuart JM, Altman RB, Klein TE. Nucleic Acids Res. 2002; 30 (1): 163-5
• Promises of text processing: natural language processing meets AI. Chang JT, Altman RB. Drug Discov Today. 2002; 7 (19): 992-3
• RNAML: a standard syntax for exchanging RNA information. Waugh A, Gendron P, Altman R, Brown JW, Case D, Gautheret D, Harvey SC, Leontis N, Westbrook J, Westhof E, Zuker M, Major F. RNA. 2002; 8 (6): 707-17
• Representing genetic sequence data for pharmacogenomics: an evolutionary approach using ontological and relational models. Rubin DL, Shafa F, Oliver DE, Hewett M, Altman RB. Bioinformatics. 2002: 18 Suppl 1 S207-15
• Using binning to maintain confidentiality of medical data. Lin Z, Hewett M, Altman RB. Proc AMIA Symp. 2002: 454-8
• Using text analysis to identify functionally coherent gene groups. Raychaudhuri S, Schütze H, Altman RB. Genome Res. 2002; 12 (10): 1582-90
• Basic microarray analysis: grouping and feature reduction. Raychaudhuri S, Sutphin PD, Chang JT, Altman RB. Trends Biotechnol. 2001; 19 (5): 189-93
• Constrained global optimization for estimating molecular structure from atomic distances. Williams GA, Dugan JM, Altman RB. J Comput Biol. 2001; 8 (5): 523-47
• Diversity of gene expression in adenocarcinoma of the lung. Garber ME, Troyanskaya OG, Schluens K, Petersen S, Thaesler Z, Pacyna-Gengelbach M, van de Rijn M, Rosen GD, Perou CM, Whyte RI, Altman RB, Brown PO, Botstein D, Petersen I. Proc Natl Acad Sci U S A. 2001; 98 (24): 13784-9
• Including biological literature improves homology search. Chang JT, Raychaudhuri S, Altman RB. Pac Symp Biocomput. 2001: 374-83
• Integrating genotype and phenotype information: an overview of the PharmGKB project. Pharmacogenetics Research Network and Knowledge Base. Klein TE, Chang JT, Cho MK, Easton KL, Fergerson R, Hewett M, Lin Z, Liu Y, Liu S, Oliver DE, Rubin DL, Shafa F, Stuart JM, Altman RB. Pharmacogenomics J. 2001; 1 (3): 167-70
• Missing value estimation methods for DNA microarrays. Troyanskaya O, Cantor M, Sherlock G, Brown P, Hastie T, Tibshirani R, Botstein D, Altman RB. Bioinformatics. 2001; 17 (6): 520-5
• Using meta computing tools to facilitate large-scale analyses of biological databases. Waugh A, Williams GA, Wei L, Altman RB. Pac Symp Biocomput. 2001: 360-71
• Whole-genome expression analysis: challenges beyond clustering. Altman RB, Raychaudhuri S. Curr Opin Struct Biol. 2001; 11 (3): 340-7
• The interactions between clinical informatics and bioinformatics: a case study. Altman RB, J Am Med Inform Assoc. 2000 Sep-Oct; 7 (5): 439-43
• Biomedical computation at Stanford University: a larger umbrella for the future. Altman RB, MD Comput. 2000 Nov-Dec; 17 (6): 35-7
• Computational modeling of structural experimental data. Bada MA, Altman RB. Methods Enzymol. 2000: 317 470-91
• Generating interactive molecular documentaries using a library of graphical actions. Pulavarthi P, Chiang R, Altman RB. Pac Symp Biocomput. 2000: 266-77
• Pattern recognition of genomic features with microarrays: site typing of Mycobacterium tuberculosis strains. Raychaudhuri S, Stuart JM, Liu X, Small PM, Altman RB. Proc Int Conf Intell Syst Mol Biol. 2000: 8 286-95
• Principal components analysis to summarize microarray experiments: application to sporulation time series. Raychaudhuri S, Stuart JM, Altman RB. Pac Symp Biocomput. 2000: 455-66
• Automated diagnosis of data-model conflicts using metadata. Chen RO, Altman RB. J Am Med Inform Assoc. 1999 Sep-Oct; 6 (5): 374-92
• Are predicted structures good enough to preserve functional sites? Wei L, Huang ES, Altman RB. Structure. 1999; 7 (6): 643-50
• Using imperfect secondary structure predictions to improve molecular structure computations. Chen CC, Singh JP, Altman RB. Bioinformatics. 1999; 15 (1): 53-65
• A surface measure for probabilistic structural computations. Schmidt JP, Chen CC, Cooper JL, Altman RB. Proc Int Conf Intell Syst Mol Biol. 1998: 6 148-56
• Bioinformatics in support of molecular medicine. Altman RB, Proc AMIA Symp. 1998: 53-61
• Hierarchical organization of molecular structure computations. Chen CC, Singh JP, Altman RB. J Comput Biol. 1998; 5 (3): 409-22
• MHCWeb: converting a WWW database into a knowledge-based collaborative environment. Hon L, Abernethy NF, Brusic V, Chai J, Altman RB. Proc AMIA Symp. 1998: 947-51
• Recognizing protein binding sites using statistical descriptions of their 3D environments. Wei L, Altman RB. Pac Symp Biocomput. 1998: 497-508
• Updating a bibliography using the related articles function within PubMed. Liu X, Altman RB. Proc AMIA Symp. 1998: 750-4
• Informatics in the care of patients: ten notable challenges. Altman RB, West J Med. 1997; 166 (2): 118-22
• LPFC: an Internet library of protein family core structures. Schmidt R, Gerstein M, Altman RB. Protein Sci. 1997; 6 (1): 246-8
• RIBOWEB: linking structural computations to a knowledge base of published experimental data. Chen RO, Felciano R, Altman RB. Proc Int Conf Intell Syst Mol Biol. 1997: 5 84-7
• RNA secondary structure as a reusable interface to biological information resources. Felciano RM, Chen RO, Altman RB. Gene. 1997; 190 (2): GC59-70
• Standardized representations of the literature: combining diverse sources of ribosomal data. Altman RB, Abernethy NF, Chen RO. Proc Int Conf Intell Syst Mol Biol. 1997: 5 15-24
• Using the radial distributions of physical features to compare amino acid environments and align amino acid sequences. Wei L, Altman RB, Chang JT. Pac Symp Biocomput. 1997: 465-76
• A programming course in bioinformatics for computer and information science students. Altman RB, Koza J. Pac Symp Biocomput. 1996: 73-84
• An evaluation of the TransFER model for sharing clinical decision-support applications. Sujansky W, Altman R. Proc AMIA Annu Fall Symp. 1996: 468-72
• Computational methods for defining the allowed conformational space of 16S rRNA based on chemical footprinting data. Fink DL, Chen RO, Noller HF, Altman RB. RNA. 1996; 2 (9): 851-66
• Conserved features in the active site of nonhomologous serine proteases. Bagley SC, Altman RB. Fold Des. 1996; 1 (5): 371-9
• Constraining volume by matching the moments of a distance distribution. Chen CC, Chen RO, Altman RB. Comput Appl Biosci. 1996; 12 (4): 319-26
• Images in clinical medicine. Knotted umbilical cord. Altman RB, Merino JE. N Engl J Med. 1996; 334 (9): 573
• Lamprey: tracking users on the World Wide Web. Felciano RM, Altman RB. Proc AMIA Annu Fall Symp. 1996: 757-61
• Average core structures and variability measures for protein families: application to the immunoglobulins. Gerstein M, Altman RB. J Mol Biol. 1995; 251 (1): 161-75
• Characterizing oriented protein structural sites using biochemical properties. Bagley SC, Wei L, Cheng C, Altman RB. Proc Int Conf Intell Syst Mol Biol. 1995: 3 12-20
• Characterizing the microenvironment surrounding protein sites. Bagley SC, Altman RB. Protein Sci. 1995; 4 (4): 622-35
• Methods for displaying macromolecular structural uncertainty: application to the globins. Altman RB, Hughes C, Gerstein MB. J Mol Graph. 1995; 13 (3): 142-52, 109-2
• Using a measure of structural variation to define a core for the globins. Gerstein M, Altman RB. Comput Appl Biosci. 1995; 11 (6): 633-44
• A survey of patient access to electronic mail: attitudes, barriers, and opportunities. Fridsma DB, Ford P, Altman R. Proc Annu Symp Comput Appl Med Care. 1994: 15-9
• Constraint satisfaction techniques for modeling large complexes: application to the central domain of 16S ribosomal RNA. Altman RB, Weiser B, Noller HF. Proc Int Conf Intell Syst Mol Biol. 1994: 2 10-8
• Extraction of SNOMED concepts from medical record texts. Oliver DE, Altman RB. Proc Annu Symp Comput Appl Med Care. 1994: 179-83
• Finding an average core structure: application to the globins. Altman RB, Gerstein M. Proc Int Conf Intell Syst Mol Biol. 1994: 2 19-27
• Probabilistic constraint satisfaction: application to radiosurgery. Altman RB, Tombropoulos R. Proc Annu Symp Comput Appl Med Care. 1994: 780-4
• Towards a standard query model for sharing decision-support applications. Sujansky W, Altman R. Proc Annu Symp Comput Appl Med Care. 1994: 325-31
• Probabilistic constraint satisfaction with structural models: application to organ modeling by radial contours. Altman RB, Brinkley JF. Proc Annu Symp Comput Appl Med Care. 1993: 492-6
• Probabilistic structure calculations: a three-dimensional tRNA structure from sequence correlation data. Altman RB, Proc Int Conf Intell Syst Mol Biol. 1993: 1 12-20
• A systematic comparison of three structure determination methods from NMR data: dependence upon quality and quantity of data. Liu Y, Zhao D, Altman R, Jardetzky O. J Biomol NMR. 1992; 2 (4): 373-88
• The solution structures of Escherichia coli trp repressor and trp aporepressor at an intermediate resolution. Arrowsmith C, Pachter R, Altman R, Jardetzky O. Eur J Biochem. 1991; 202 (1): 53-66
• Sequence-specific 1H NMR assignments and secondary structure in solution of Escherichia coli trp repressor. Arrowsmith CH, Pachter R, Altman RB, Iyer SB, Jardetzky O. Biochemistry. 1990; 29 (27): 6332-41
• Heuristic refinement method for the derivation of protein solution structures: validation on cytochrome b562. Brinkley JF, Altman RB, Duncan BS, Buchanan BG, Jardetzky O. J Chem Inf Comput Sci. 1988; 28 (4): 194-210
• New strategies for the determination of macromolecular structure in solution. Altman RB, Jardetzky O. J Biochem. 1986; 100 (6): 1403-23
• Quaternary structural changes in aspartate carbamoyltransferase of Escherichia coli at pH 8.3 and pH 5.8. Altman RB, Ladner JE, Lipscomb WN. Biochem Biophys Res Commun. 1982; 108 (2): 592-5