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Papers authored by Altman RB

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Extraction of genotype-phenotype-drug relationships from text: from entity recognition to bioinformatics application.

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Coulet A, Shah N, Hunter L, Barral C, and Altman RB

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing:485-7, 2010 - Who cited this? | PubMed ID: 19904832 | Fulltext

Predicting RNA structure by multiple template homology modeling.

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Flores SC, Wan Y, Russell R, and Altman RB

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing:216-27, 2010 - Who cited this? | PubMed ID: 19908374 | Fulltext

Improving the prediction of pharmacogenes using text-derived drug-gene relationships.

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Garten Y, Tatonetti NP, and Altman RB

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing:305-14, 2010 - Who cited this? | PubMed ID: 19908383 | Fulltext

Generating genome-scale candidate gene lists for pharmacogenomics.

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Hansen NT, Brunak S, and Altman RB

Clinical pharmacology and therapeutics 86(2):183-9, 2009 Aug - Who cited this? | PubMed ID: 19369935 | Fulltext

Improving structure-based function prediction using molecular dynamics.

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Glazer DS, Radmer RJ, and Altman RB

Structure (London, England : 1993) 17(7):919-29, 2009 Jul 15 - Who cited this? | PubMed ID: 19604472 | Fulltext

Direct-to-consumer genetic testing: failure is not an option.

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Altman RB

Clinical pharmacology and therapeutics 86(1):15-7, 2009 Jul - Who cited this? | PubMed ID: 19536117 | Fulltext

Codeine and morphine pathway.

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Thorn CF, Klein TE, and Altman RB

Pharmacogenetics and genomics 19(7):556-8, 2009 Jul - Who cited this? | PubMed ID: 19512957 | Fulltext

Cytochrome P450 2D6.

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Owen RP, Sangkuhl K, Klein TE, and Altman RB

Pharmacogenetics and genomics 19(7):559-62, 2009 Jul - Who cited this? | PubMed ID: 19512959 | Fulltext

Antiestrogen pathway (aromatase inhibitor).

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Desta Z, Nguyen A, Flockhart D, Skaar T, Fletcher R, Weinshilboum R, Berlin DS, Klein TE, and Altman RB

Pharmacogenetics and genomics 19(7):554-5, 2009 Jul - Who cited this? | PubMed ID: 19512956 | Fulltext

Etoposide pathway.

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Yang J, Bogni A, Schuetz EG, Ratain M, Dolan ME, McLeod H, Gong L, Thorn C, Relling MV, Klein TE, and Altman RB

Pharmacogenetics and genomics 19(7):552-3, 2009 Jul - Who cited this? | PubMed ID: 19512958 | Fulltext

Platinum pathway.

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Marsh S, McLeod H, Dolan E, Shukla SJ, Rabik CA, Gong L, Hernandez-Boussard T, Lou XJ, Klein TE, and Altman RB

Pharmacogenetics and genomics 19(7):563-4, 2009 Jul - Who cited this? | PubMed ID: 19525887 | Fulltext

New feature: pathways and important genes from PharmGKB.

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Eichelbaum M, Altman RB, Ratain M, and Klein TE

Pharmacogenetics and genomics 19(6):403, 2009 Jun - Who cited this? | PubMed ID: 19369911 | Fulltext

Very important pharmacogene summary: sulfotransferase 1A1.

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Hildebrandt M, Adjei A, Weinshilboum R, Johnson JA, Berlin DS, Klein TE, and Altman RB

Pharmacogenetics and genomics 19(6):404-6, 2009 Jun - Who cited this? | PubMed ID: 19451861 | Fulltext

Estimation of the warfarin dose with clinical and pharmacogenetic data.

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International Warfarin Pharmacogenetics Consortium, Klein TE, Altman RB, Eriksson N, Gage BF, Kimmel SE, Lee MT, Limdi NA, Page D, Roden DM, Wagner MJ, Caldwell MD, and Johnson JA

The New England journal of medicine 360(8):753-64, 2009 Feb 19 - Who cited this? | PubMed ID: 19228618 | Fulltext

Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters.

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Jonikas MA, Radmer RJ, Laederach A, Das R, Pearlman S, Herschlag D, and Altman RB

RNA (New York, N.Y.) 15(2):189-99, 2009 Feb - Who cited this? | PubMed ID: 19144906 | 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

Pharmspresso: a text mining tool for extraction of pharmacogenomic concepts and relationships from full text.

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Garten Y and Altman RB

BMC bioinformatics 10 Suppl 2:S6, 2009 - Who cited this? | PubMed ID: 19208194 | Fulltext

Predicting drug side-effects by chemical systems biology.

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Tatonetti NP, Liu T, and Altman RB

Genome biology 10(9):238, 2009 - Who cited this? | PubMed ID: 19723347 | Fulltext

PharmGKB: an integrated resource of pharmacogenomic data and knowledge.

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Gong L, Owen RP, Gor W, Altman RB, and Klein TE

Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] Chapter 14:Unit14.7, 2008 Sep - Who cited this? | PubMed ID: 18819074 | Fulltext

Semiautomated and rapid quantification of nucleic acid footprinting and structure mapping experiments.

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Laederach A, Das R, Vicens Q, Pearlman SM, Brenowitz M, Herschlag D, and Altman RB

Nature protocols 3(9):1395, 2008 Aug - Who cited this? | PubMed ID: 18772866 | Fulltext

High-throughput single-nucleotide structural mapping by capillary automated footprinting analysis.

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Mitra S, Shcherbakova IV, Altman RB, Brenowitz M, and Laederach A

Nucleic acids research 36(11), 2008 Jun - Who cited this? | PubMed ID: 18477638 | Fulltext

Interview: Russ Altman speaks to Shreeya Nanda, Commissioning Editor.

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Altman RB

Pharmacogenomics 9(6):663, 2008 Jun - Who cited this? | PubMed ID: 18518843 | Fulltext

The chemical genomic portrait of yeast: uncovering a phenotype for all genes.

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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, and Giaever G

Science (New York, N.Y.) 320(5874):362, 2008 Apr 18 - Who cited this? | PubMed ID: 18420932 | Fulltext

PharmGKB and the International Warfarin Pharmacogenetics Consortium: the changing role for pharmacogenomic databases and single-drug pharmacogenetics.

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Owen RP, Altman RB, and Klein TE

Human mutation 29(4):456, 2008 Apr - Who cited this? | PubMed ID: 18330919 | Fulltext

Structural inference of native and partially folded RNA by high-throughput contact mapping.

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Das R, Kudaravalli M, Jonikas M, Laederach A, Fong R, Schwans JP, Baker D, Piccirilli JA, Altman RB, and Herschlag D

Proceedings of the National Academy of Sciences of the United States of America 105(11):4144, 2008 Mar 18 - Who cited this? | PubMed ID: 18322008 | Fulltext

An XML-based interchange format for genotype-phenotype data.

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Whirl-Carrillo M, Woon M, Thorn CF, Klein TE, and Altman RB

Human mutation 29(2):212, 2008 Feb - Who cited this? | PubMed ID: 17994540 | Fulltext

The SeqFEATURE library of 3D functional site models: comparison to existing methods and applications to protein function annotation.

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Wu S, Liang MP, and Altman RB

Genome biology 9(1), 2008 Jan 16 - Who cited this? | PubMed ID: 18197987 | Fulltext

MScanner: a classifier for retrieving Medline citations.

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Poulter GL, Rubin DL, Altman RB, and Seoighe C

BMC bioinformatics 9:108, 2008 - Who cited this? | PubMed ID: 18284683 | Fulltext

Robust recognition of zinc binding sites in proteins.

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Ebert JC and Altman RB

Protein science : a publication of the Protein Society 17(1):54, 2008 Jan - Who cited this? | PubMed ID: 18042678 | Fulltext

M-BISON: microarray-based integration of data sources using networks.

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Daigle BJ and Altman RB

BMC bioinformatics 9:214, 2008 - Who cited this? | PubMed ID: 18439292 | Fulltext

The pharmacogenetics and pharmacogenomics knowledge base: accentuating the knowledge.

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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, and Klein TE

Nucleic acids research 36(Database issue), 2008 Jan - Who cited this? | PubMed ID: 18032438 | Fulltext

Combining molecular dynamics and machine learning to improve protein function recognition.

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Glazer DS, Radmer RJ, and Altman RB

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing:332, 2008 - Who cited this? | PubMed ID: 18229697 | Fulltext

Commentaries on "Informatics and medicine: from molecules to populations".

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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, and Wiederhold G

Methods of information in medicine 47(4):296-317, 2008 - Who cited this? | PubMed ID: 18690363 | Fulltext

The FEATURE framework for protein function annotation: modeling new functions, improving performance, and extending to novel applications.

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Halperin I, Glazer DS, Wu S, and Altman RB

BMC genomics 9 Suppl 2:S2, 2008 - Who cited this? | PubMed ID: 18831785 | Fulltext

Text mining for biology--the way forward: opinions from leading scientists.

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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,

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Genome biology 9 Suppl 2:S7, 2008 - Who cited this? | PubMed ID: 18834498 | Fulltext

PharmGKB: Understanding the Effects of Individual Genetic Variants.

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Sangkuhl K, Berlin DS, Altman RB, and Klein TE

Drug metabolism reviews 40(4):539-51, 2008 - Who cited this? | PubMed ID: 18949600 | Fulltext

Efficient algorithms to explore conformation spaces of flexible protein loops.

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Yao P, Dhanik A, Marz N, Propper R, Kou C, Liu G, van den Bedem H, Latombe JC, Halperin-Landsberg I, and Altman RB

IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM 5(4):534-45, 2008 - Who cited this? | PubMed ID: 18989041 | Fulltext

Predicting allosteric communication in myosin via a pathway of conserved residues.

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Tang S, Liao JC, Dunn AR, Altman RB, Spudich JA, and Schmidt JP

Journal of molecular biology 373(5):1361, 2007 Nov 9 - Who cited this? | PubMed ID: 17900617 | Fulltext

The education potential of the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB).

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Owen RP, Klein TE, and Altman RB

Clinical pharmacology and therapeutics 82(4):472, 2007 Oct - Who cited this? | PubMed ID: 17713470 | Fulltext

Current progress in bioinformatics 2007.

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Altman RB

Briefings in bioinformatics 8(5):277, 2007 Sep - Who cited this? | PubMed ID: 17724063 | Fulltext

Using surface envelopes to constrain molecular modeling.

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Dugan JM and Altman RB

Protein science : a publication of the Protein Society 16(7):1266, 2007 Jul - Who cited this? | PubMed ID: 17586766 | Fulltext

Genetic nondiscrimination legislation: a critical prerequisite for pharmacogenomics data sharing.

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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,

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Pharmacogenomics 8(5):519, 2007 May - Who cited this? | PubMed ID: 17465717 | Fulltext

Coplanar and coaxial orientations of RNA bases and helices.

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Laederach A, Chan JM, Schwartzman A, Willgohs E, and Altman RB

RNA (New York, N.Y.) 13(5):643, 2007 May - Who cited this? | PubMed ID: 17339576 | Fulltext

Distinct contribution of electrostatics, initial conformational ensemble, and macromolecular stability in RNA folding.

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Laederach A, Shcherbakova I, Jonikas MA, Altman RB, and Brenowitz M

Proceedings of the National Academy of Sciences of the United States of America 104(17):7045, 2007 Apr 24 - Who cited this? | PubMed ID: 17438287 | Fulltext

PharmGKB: a logical home for knowledge relating genotype to drug response phenotype.

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Altman RB

Nature genetics 39(4):426, 2007 Apr - Who cited this? | PubMed ID: 17392795 | Fulltext

The pharmacogenetics research network: from SNP discovery to clinical drug response.

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Giacomini KM, Brett CM, Altman RB, Benowitz NL, Dolan ME, Flockhart DA, Johnson JA, Hayes DF, Klein T, Krauss RM, Kroetz DL, McLeod HL, Nguyen AT, Ratain MJ, Relling MV, Reus V,

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Clinical pharmacology and therapeutics 81(3):328, 2007 Mar - Who cited this? | PubMed ID: 17339863 | Fulltext

Identification of two distinct hybrid state intermediates on the ribosome.

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Munro JB, Altman RB, O'Connor N, and Blanchard SC

Molecular cell 25(4):505, 2007 Feb 23 - Who cited this? | PubMed ID: 17317624 | Fulltext

Biomedical informatics training at Stanford in the 21st century.

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Altman RB and Klein TE

Journal of biomedical informatics 40(1):55, 2007 Feb - Who cited this? | PubMed ID: 16564233 | Fulltext

Extracting subject demographic information from abstracts of randomized clinical trial reports.

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Xu R, Garten Y, Supekar KS, Das AK, Altman RB, and Garber AM

Studies in health technology and informatics 129(Pt 1):550, 2007 - Who cited this? | PubMed ID: 17911777 | Fulltext

The PharmGKB: integration, aggregation, and annotation of pharmacogenomic data and knowledge.

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Hodge AE, Altman RB, and Klein TE

Clinical pharmacology and therapeutics 81(1):21, 2007 Jan - Who cited this? | PubMed ID: 17185992 | Fulltext

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