For a more complete and up-to-date publication list, please visit this page.

2017

  • Working toward precision medicine: Predicting phenotypes from exomes in the Critical Assessment of Genome Interpretation (CAGI) challenges. HUMAN MUTATION. Daneshjou R., Wang Y., Bromberg Y., Bovo S., Martelli P.L., Babbi G., Lena P.Di., Casadio R., Edwards M., Gifford D., Jones D.T., Sundaram L., Bhat R.Rana., Li X., Pal L.R., Kundu K., Yin Y., Moult J., Jiang Y., Pejaver V., Pagel K.A., Li B., Mooney S.D., Radivojac P., Shah S., Carraro M., Gasparini A., Leonardi E., Giollo M., Ferrari C., Bachar E., Azaria J.R., Ofran Y., Unger R., Niroula A., Vihinen M., Chang B., Wang M.H., Franke A., Petersen B., Pirooznia M., Zandi P., McCombie R., Potash J.B., Altman R.B., Klein T.E., Hoskins R.A., Repo S., Brenner S.E. and Morgan A.A. 2017; 38: 1182--1192
  • Artificial intelligence (AI) systems for interpreting complex medical datasets. CLINICAL PHARMACOLOGY AND THERAPEUTICS. Altman R.B. 2017; 101: 585--586
  • Opportunities for developing therapies for rare genetic diseases: focus on gain-of-function and allostery. ORPHANET JOURNAL OF RARE DISEASES. Chen B. and Altman R.B. 2017; 12: 61
  • The Pharmacogenomics Research Network Translational Pharmacogenetics Program: Outcomes and Metrics of Pharmacogenetic Implementations Across Diverse Healthcare Systems. CLINICAL PHARMACOLOGY AND THERAPEUTICS. Luzum J.A., Pakyz R.E., Elsey A.R., Haidar C.E., Peterson J.F., Whirl-Carrillo M., Handelman S.K., Palmer K., Pulley J.M., Beller M., Schildcrout J.S., Field J.R., Weitzel K.W., Cooper-DeHoff R.M., Cavallari L.H., O'Donnell P.H., Altman R.B., Pereira N., Ratain M.J., Roden D.M., Embi P.J., Sadee W., Klein T.E., Johnson J.A., Relling M.V., Wang L., Weinshilboum R.M., Shuldiner A.R. and Freimuth R.R. 2017; 102: 502--510
  • PharmGKB summary: voriconazole pathway, pharmacokinetics. PHARMACOGENETICS AND GENOMICS. Barbarino J.M., Owusu Obeng A., Klein T.E. and Altman R.B. 2017; 27: 201--209
  • Pharmacogenomics-Based Point-of-Care Clinical Decision Support Significantly Alters Drug Prescribing. CLINICAL PHARMACOLOGY AND THERAPEUTICS. O'Donnell P.H., Wadhwa N., Danahey K., Borden B.A., Lee S.M., Hall J.P., Klammer C., Hussain S., Siegler M., Sorrentino M.J., Davis A.M., Sacro Y.A., Nanda R., Polonsky T.S., Koyner J.L., Burnet D.L., Lipstreuer K., Rubin D.T., Mulcahy C., Strek M.E., Harper W., Cifu A.S., Polite B., Patrick-Miller L., Yeo K., Leung E., Volchenboum S.L., Altman R.B., Olopade O.I., Stadler W.M., Meltzer D.O. and Ratain M.J. 2017
  • PharmGKB summary: sorafenib pathways. PHARMACOGENETICS AND GENOMICS. Gong L., Giacomini M.M., Giacomini C., Maitland M.L., Altman R.B. and Klein T.E. 2017; 27: 240--246
  • Imputing gene expression to maximize platform compatibility. BIOINFORMATICS (OXFORD, ENGLAND). Zhou W., Han L. and Altman R.B. 2017; 33: 522--528
  • PharmGKB summary: pazopanib pathway, pharmacokinetics. PHARMACOGENETICS AND GENOMICS. Thorn C.F., Sharma M.R., Altman R.B. and Klein T.E. 2017; 27: 307--312
  • PharmGKB summary: Macrolide antibiotic pathway, pharmacokinetics/pharmacodynamics. PHARMACOGENETICS AND GENOMICS. Fohner A.E., Sparreboom A., Altman R.B. and Klein T.E. 2017; 27: 164--167
  • 3D deep convolutional neural networks for amino acid environment similarity analysis. BMC BIOINFORMATICS. Torng W. and Altman R.B. 2017; 18: 302
  • PharmGKB summary: very important pharmacogene information for ABCG2. PHARMACOGENETICS AND GENOMICS. Fohner A.E., Brackman D.J., Giacomini K.M., Altman R.B. and Klein T.E. 2017
  • Shallow Representation Learning via Kernel PCA Improves QSAR Modelability. JOURNAL OF CHEMICAL INFORMATION AND MODELING. Rensi S.E. and Altman R.B. 2017; 57: 1859--1867
  • Development of an automated assessment tool for MedWatch reports in the FDA adverse event reporting system. JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION : JAMIA. Han L., Ball R., Pamer C.A., Altman R.B. and Proestel S. 2017; 24: 913--920
  • Decaying relevance of clinical data towards future decisions in data-driven inpatient clinical order sets. INTERNATIONAL JOURNAL OF MEDICAL INFORMATICS. Chen J.H., Alagappan M., Goldstein M.K., Asch S.M. and Altman R.B. 2017; 102: 71--79
  • Flexible Analog Search with Kernel PCA Embedded Molecule Vectors. COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL. Rensi S. and Altman R.B. 2017; 15: 320--327

2016

  • Human induced pluripotent stem cell-derived cardiomyocytes recapitulate the predilection of breast cancer patients to doxorubicin-induced cardiotoxicity. NATURE MEDICINE. Burridge P.W., Li Y.Fuga., Matsa E., Wu H., Ong S., Sharma A., Holmstrom A., Chang A.C., Coronado M.J., Ebert A.D., Knowles J.W., Telli M.L., Witteles R.M., Blau H.M., Bernstein D., Altman R.B. and Wu J.C. 2016; 22: 547--556
  • DYNAMICALLY EVOLVING CLINICAL PRACTICES AND IMPLICATIONS FOR PREDICTING MEDICAL DECISIONS. PACIFIC SYMPOSIUM ON BIOCOMPUTING. PACIFIC SYMPOSIUM ON BIOCOMPUTING. Chen J.H., Goldstein M.K., Asch S.M. and Altman R.B. 2016; 21: 195--206
  • PharmGKB summary: very important pharmacogene information for MT-RNR1. PHARMACOGENETICS AND GENOMICS. Barbarino J.M., McGregor T.L., Altman R.B. and Klein T.E. 2016; 26: 558--567
  • Constraints on Biological Mechanism from Disease Comorbidity Using Electronic Medical Records and Database of Genetic Variants. PLOS COMPUTATIONAL BIOLOGY. Bagley S.C., Sirota M., Chen R., Butte A.J. and Altman R.B. 2016; 12: e1004885
  • Response to Open Peer Commentaries on "Human Germline CRISPR-Cas Modification: Toward a Regulatory Framework". THE AMERICAN JOURNAL OF BIOETHICS : AJOB. Evitt N.H., Mascharak S. and Altman R.B. 2016; 16: W1--2
  • Population-specific single-nucleotide polymorphism confers increased risk of venous thromboembolism in African Americans. MOLECULAR GENETICS \& GENOMIC MEDICINE. Daneshjou R., Cavallari L.H., Weeke P.E., Karczewski K.J., Drozda K., Perera M.A., Johnson J.A., Klein T.E., Bustamante C.D., Roden D.M., Shaffer C., Denny J.C., Zehnder J.L. and Altman R.B. 2016; 4: 513--520
  • Predicting non-small cell lung cancer prognosis by fully automated microscopic pathology image features. NATURE COMMUNICATIONS. Yu K., Zhang C., Berry G.J., Altman R.B., Re C., Rubin D.L. and Snyder M. 2016; 7: 12474
  • STAMS: STRING-assisted module search for genome wide association studies and application to autism. BIOINFORMATICS (OXFORD, ENGLAND). Hillenmeyer S., Davis L.K., Gamazon E.R., Cook E.H., Cox N.J. and Altman R.B. 2016; 32: 3815--3822
  • Computing disease incidence, prevalence and comorbidity from electronic medical records. JOURNAL OF BIOMEDICAL INFORMATICS. Bagley S.C. and Altman R.B. 2016; 63: 108--111
  • Predicting inpatient clinical order patterns with probabilistic topic models vs conventional order sets. JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION : JAMIA. Chen J.H., Goldstein M.K., Asch S.M., Mackey L. and Altman R.B. 2017; 24: 472--480
  • PharmGKB summary: ivacaftor pathway, pharmacokinetics/pharmacodynamics. PHARMACOGENETICS AND GENOMICS. Fohner A.E., McDonagh E.M., Clancy J.P., Whirl Carrillo M., Altman R.B. and Klein T.E. 2017; 27: 39--42
  • Towards Clinical Bioinformatics: Redux 2015. YEARBOOK OF MEDICAL INFORMATICS. Altman R.B. 2016; Suppl 1: S6--7
  • Estimation of Maximum Recommended Therapeutic Dose Using Predicted Promiscuity and Potency. CLINICAL AND TRANSLATIONAL SCIENCE. Liu T., Oprea T., Ursu O., Hasselgren C. and Altman R.B. 2016; 9: 311--320
  • A research roadmap for next-generation sequencing informatics. SCIENCE TRANSLATIONAL MEDICINE. Altman R.B., Prabhu S., Sidow A., Zook J.M., Goldfeder R., Litwack D., Ashley E., Asimenos G., Bustamante C.D., Donigan K., Giacomini K.M., Johansen E., Khuri N., Lee E., Liang X.Sharon., Salit M., Serang O., Tezak Z., Wall D.P., Mansfield E. and Kass-Hout T. 2016; 8: 335ps10
  • PharmGKB summary: very important pharmacogene information for RYR1. PHARMACOGENETICS AND GENOMICS. Alvarellos M.L., Krauss R.M., Wilke R.A., Altman R.B. and Klein T.E. 2016; 26: 138--144
  • SEPARATING THE CAUSES AND CONSEQUENCES IN DISEASE TRANSCRIPTOME. PACIFIC SYMPOSIUM ON BIOCOMPUTING. PACIFIC SYMPOSIUM ON BIOCOMPUTING. Li Y.Fuga., Xin F. and Altman R.B. 2016; 21: 381--392
  • PharmGKB summary: isoniazid pathway, pharmacokinetics. PHARMACOGENETICS AND GENOMICS. Klein D.J., Boukouvala S., McDonagh E.M., Shuldiner S.R., Laurieri N., Thorn C.F., Altman R.B. and Klein T.E. 2016; 26: 436--444

2015

  • Human Germline CRISPR-Cas Modification: Toward a Regulatory Framework. AMERICAN JOURNAL OF BIOETHICS. Evitt, N. H., Mascharak, S., Altman, R. B. 2015; 15 (12): 25-29
  • Unmet needs: Research helps regulators do their jobs. SCIENCE TRANSLATIONAL MEDICINE. Altman, R. B., Khuri, N., Salit, M., Giacomini, K. M.
  • Sequence to Medical Phenotypes: A Framework for Interpretation of Human Whole Genome DNA Sequence Data. PLoS genetics. Dewey, F. E., Grove, M. E., Priest, J. R., Waggott, D., Batra, P., Miller, C. L., Wheeler, M., Zia, A., Pan, C., Karzcewski, K. J., Miyake, C., Whirl-Carrillo, M., Klein, T. E., Datta, S., Altman, R. B., Snyder, M., Quertermous, T., Ashley, E. A. 2015; 11 (10)
  • Sequence to Medical Phenotypes: A Framework for Interpretation of Human Whole Genome DNA Sequence Data. PLOS GENETICS Dewey, F. E., Grove, M. E., Priest, J. R., Waggott, D., Batra, P., Miller, C. L., Wheeler, M., Zia, A., Pan, C., Karzcewski, K. J., Miyake, C., Whirl-Carrillo, M., Klein, T. E., Datta, S., Altman, R. B., Snyder, M., Quertermous, T., Ashley, E. A. 2015; 11 (10)
  • PharmGKB summary: peginterferon-alpha pathway. PHARMACOGENETICS AND GENOMICS. Shuldiner, S. R., Gong, L., Muir, A. J., Altman, R. B., Klein, T. E. 2015; 25 (9): 465-474
  • High Resolution Prediction of Calcium-Binding Sites in 3D Protein Structures Using FEATURE. Journal of chemical information and modeling. Zhou, W., Tang, G. W., Altman, R. B. 2015; 55 (8): 1663-1672
  • Learning the Structure of Biomedical Relationships from Unstructured Text. PLoS computational biology. Percha, B., Altman, R. B. 2015; 11 (7)
  • Relating Essential Proteins to Drug Side-Effects Using Canonical Component Analysis: A Structure-Based Approach. JOURNAL OF CHEMICAL INFORMATION AND MODELING. Liu, T., Altman, R. B. 2015; 55 (7): 1483-1494

Before 2015

  • PharmGKB summary: gemcitabine pathway. PHARMACOGENETICS AND GENOMICS. Alvarellos, M. L., Lamba, J., Sangkuhl, K., Thorn, C. F., Wang, L., Klein, D. J., Altman, R. B., Klein, T. E. 2014; 24 (11): 564-574
  • Genetic variant in folate homeostasis is associated with lower warfarin dose in African Americans. BLOOD. Daneshjou, R., Gamazon, E. R., Burkley, B., Cavallari, L. H., Johnson, J. A., Klein, T. E., Limdi, N., Hillenmeyer, S., Percha, B., Karczewski, K. J., Langaee, T., Patel, S. R., Bustamante, C. D., Altman, R. B., Perera, M. A. 2014; 124 (14): 2298-2305
  • PharmGKB summary: uric acid-lowering drugs pathway, pharmacodynamics. PHARMACOGENETICS AND GENOMICS. McDonagh, E. M., Thorn, C. F., Callaghan, J. T., Altman, R. B., Klein, T. E. 2014; 24 (9): 464-476
  • PharmGKB summary: very important pharmacogene information for N-acetyltransferase 2. PHARMACOGENETICS AND GENOMICS. McDonagh, E. M., Boukouvala, S., Aklillu, E., Hein, D. W., Altman, R. B., Klein, T. E. 2014; 24 (8): 409-425
  • Interpreting the CYP2D6 results from the International Tamoxifen Pharmacogenetics Consortium. Clinical pharmacology & therapeutics. Province, M. A., Altman, R. B., Klein, T. E. 2014; 96 (2): 144-146
  • Integrating Systems Biology Sources Illuminates Drug Action. CLINICAL PHARMACOLOGY & THERAPEUTICS. Gottlieb, A., Altman, R. B. 2014; 95 (6): 663-669
  • Reconstruction of the Mouse Otocyst and Early Neuroblast Lineage at Single-Cell Resolution. CELL. Durruthy-Durruthy, R., Gottlieb, A., Hartman, B. H., Waldhaus, J., Laske, R. D., Altman, R., Heller, S. 2014; 157 (4): 964-978
  • Translational Bioinformatics: Linking the Molecular World to the Clinical World. CLINICAL PHARMACOLOGY & THERAPEUTICS. Altman, R. B. 2012; 91 (6): 994-1000
  • Data-Driven Prediction of Drug Effects and Interactions. SCIENCE TRANSLATIONAL MEDICINE. Tatonetti, N. P., Ye, P. P., Daneshjou, R., Altman, R. B. 2012; 4 (125)
  • Clinical assessment incorporating a personal genome. LANCET. Ashley, E. A., Butte, A. J., Wheeler, M. T., Chen, R., Klein, T. E., Dewey, F. E., Dudley, J. T., Ormond, K. E., Pavlovic, A., Morgan, A. A., Pushkarev, D., Neff, N. F., Hudgins, L., Gong, L., Hodges, L. M., Berlin, D. S., Thorn, C. F., Sangkuhl, K., Hebert, J. M., Woon, M., Sagreiya, H., Whaley, R., Knowles, J. W., Chou, M. F., Thakuria, J. V., Rosenbaum, A. M., Zaranek, A. W., Church, G. M., Greely, H. T., Quake, S. R., Altman, R. B. 2010; 375 (9725): 1525-1535

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