Russ B Altman

Russ B Altman

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Russ B Altman

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Essential Characteristics of Pharmacogenomics Study Publications.

Clin Pharmacol Ther 2019 Jan;105(1):86-91

Department of Biomedical Data Sciences, Stanford University, Stanford, California, USA.

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http://doi.wiley.com/10.1002/cpt.1279
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http://dx.doi.org/10.1002/cpt.1279DOI Listing
January 2019

Standardized biogeographic grouping system for annotating populations in pharmacogenetic research.

Clin Pharmacol Ther 2018 Dec 1. Epub 2018 Dec 1.

Department of Biomedical Data Science, Stanford University, Stanford, CA, 94305, USA.

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http://doi.wiley.com/10.1002/cpt.1322
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http://dx.doi.org/10.1002/cpt.1322DOI Listing
December 2018

PharmGKB summary: oxycodone pathway, pharmacokinetics.

Pharmacogenet Genomics 2018 Oct;28(10):230-237

Departments of Biomedical Data Sciences.

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http://dx.doi.org/10.1097/FPC.0000000000000351DOI Listing
October 2018

PharmGKB summary: clozapine pathway, pharmacokinetics.

Pharmacogenet Genomics 2018 Sep;28(9):214-222

Departments of Biomedical Data Sciences.

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http://dx.doi.org/10.1097/FPC.0000000000000347DOI Listing
September 2018

Data-driven human transcriptomic modules determined by independent component analysis.

BMC Bioinformatics 2018 Sep 17;19(1):327. Epub 2018 Sep 17.

Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA.

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http://dx.doi.org/10.1186/s12859-018-2338-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6142401PMC
September 2018

Chemical reaction vector embeddings: towards predicting drug metabolism in the human gut microbiome.

Pac Symp Biocomput 2018 ;23:56-67

Biomedical Informatics Training Program, Stanford University, Stanford, CA 94305, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5771676PMC
August 2018

GeneDive: A gene interaction search and visualization tool to facilitate precision medicine.

Pac Symp Biocomput 2018 ;23:590-601

Department of Computer Science, San Francisco State University, San Francisco, California 94132, U.S.A.,

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5807065PMC
August 2018

A global network of biomedical relationships derived from text.

Bioinformatics 2018 Aug;34(15):2614-2624

Department of Bioengineering, Stanford University, Stanford, CA, USA.

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http://dx.doi.org/10.1093/bioinformatics/bty114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6061699PMC
August 2018

Machine learning in chemoinformatics and drug discovery.

Drug Discov Today 2018 08 8;23(8):1538-1546. Epub 2018 May 8.

Department of Bioengineering, Stanford University, Stanford, CA, USA. Electronic address:

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http://dx.doi.org/10.1016/j.drudis.2018.05.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6078794PMC
August 2018

PharmGKB: A worldwide resource for pharmacogenomic information.

Wiley Interdiscip Rev Syst Biol Med 2018 07 23;10(4):e1417. Epub 2018 Feb 23.

Department of Biomedical Data Sciences, Stanford University, Stanford, California.

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http://dx.doi.org/10.1002/wsbm.1417DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6002921PMC
July 2018

Expanding a radiology lexicon using contextual patterns in radiology reports.

J Am Med Inform Assoc 2018 Jun;25(6):679-685

Department of Radiology, Stanford University, Stanford, CA, USA.

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http://dx.doi.org/10.1093/jamia/ocx152DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5978019PMC
June 2018

Pharmacogenomics and big genomic data: from lab to clinic and back again.

Hum Mol Genet 2018 May;27(R1):R72-R78

Department of Genetics, Stanford University, Stanford, CA 94305, USA.

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http://dx.doi.org/10.1093/hmg/ddy116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5946941PMC
May 2018

PharmGKB summary: clobazam pathway, pharmacokinetics.

Pharmacogenet Genomics 2018 04;28(4):110-115

Departments of Biomedical Data Sciences.

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http://dx.doi.org/10.1097/FPC.0000000000000327DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5914180PMC
April 2018

Application of a Dynamic Map for Learning, Communicating, Navigating, and Improving Therapeutic Development.

Clin Transl Sci 2018 03 22;11(2):166-174. Epub 2017 Dec 22.

National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland, USA.

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http://dx.doi.org/10.1111/cts.12531DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5866991PMC
March 2018

Reversals and limitations on high-intensity, life-sustaining treatments.

PLoS One 2018 28;13(2):e0190569. Epub 2018 Feb 28.

Center for Biomedical Informatics Research and Division of Hospital Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0190569PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5830043PMC
March 2018

Challenges for Training Translational Researchers in the Era of Ubiquitous Data.

Authors:
Russ B Altman

Clin Pharmacol Ther 2018 Feb 14;103(2):171-173. Epub 2017 Nov 14.

Departments of Bioengineering, Genetics, Medicine & Biomedical Data Science, Stanford University, Stanford, California, USA.

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http://dx.doi.org/10.1002/cpt.918DOI Listing
February 2018

Biomarkers: Delivering on the expectation of molecularly driven, quantitative health.

Exp Biol Med (Maywood) 2018 02 3;243(3):313-322. Epub 2017 Dec 3.

1 171702 Bioengineering Department, Stanford University , Stanford, CA 94305, USA.

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http://dx.doi.org/10.1177/1535370217744775DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5813871PMC
February 2018

A dynamic map for learning, communicating, navigating and improving therapeutic development.

Nat Rev Drug Discov 2018 Feb 22;17(2):150. Epub 2017 Dec 22.

National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland 20817, USA.

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http://dx.doi.org/10.1038/nrd.2017.217DOI Listing
February 2018

Mendelian Disease Associations Reveal Novel Insights into Inflammatory Bowel Disease.

Inflamm Bowel Dis 2018 02;24(3):471-481

Biomedical Informatics Training Program, Stanford University, Stanford, CA.

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http://dx.doi.org/10.1093/ibd/izx087DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6037048PMC
February 2018

Systematic target function annotation of human transcription factors.

BMC Biol 2018 01 10;16(1). Epub 2018 Jan 10.

Department of Bioengineering, Stanford University, Stanford, CA, USA.

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http://dx.doi.org/10.1186/s12915-017-0469-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5795274PMC
January 2018

Association of Omics Features with Histopathology Patterns in Lung Adenocarcinoma.

Cell Syst 2017 Dec 15;5(6):620-627.e3. Epub 2017 Nov 15.

Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2017.10.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5746468PMC
December 2017

PharmGKB summary: very important pharmacogene information for ABCG2.

Pharmacogenet Genomics 2017 11;27(11):420-427

Departments of aGenetics bBioengineering, School of Medicine, Stanford University, Stanford cDepartment of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, USA.

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http://dx.doi.org/10.1097/FPC.0000000000000305DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5788016PMC
November 2017

Development of an automated assessment tool for MedWatch reports in the FDA adverse event reporting system.

J Am Med Inform Assoc 2017 Sep;24(5):913-920

Office of Surveillance and Epidemiology, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA.

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http://dx.doi.org/10.1093/jamia/ocx022DOI Listing
September 2017

PharmGKB summary: pazopanib pathway, pharmacokinetics.

Pharmacogenet Genomics 2017 08;27(8):307-312

Departments of aBiomedical Data Sciences bBiomedical Engineering cGenetics, Stanford University, Stanford, California dDepartment of Medicine, University of Chicago, Chicago, Illinois, USA.

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http://dx.doi.org/10.1097/FPC.0000000000000292DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5862561PMC
August 2017

Shallow Representation Learning via Kernel PCA Improves QSAR Modelability.

J Chem Inf Model 2017 08 7;57(8):1859-1867. Epub 2017 Aug 7.

Department of Bioengineering, Stanford University , Shriram Center, Room 213, 443 Via Ortega MC 4245, Stanford, California 94305, United States.

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http://dx.doi.org/10.1021/acs.jcim.6b00694DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5942586PMC
August 2017

PharmGKB summary: sorafenib pathways.

Pharmacogenet Genomics 2017 06;27(6):240-246

Departments of aBiomedical Data Science bBiomedical Engineering cGenetics Stanford University, Stanford dGilead Sciences, Foster City eEvviva Sciences, San Francisco, California fInova Schar Cancer Institute and Therapeutics, Center for Personalized Health, Falls Church, Virginia, USA.

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http://dx.doi.org/10.1097/FPC.0000000000000279DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5418090PMC
June 2017

Decaying relevance of clinical data towards future decisions in data-driven inpatient clinical order sets.

Int J Med Inform 2017 06 18;102:71-79. Epub 2017 Mar 18.

Department of Medicine, Stanford University, Stanford, CA, USA; Departments of Bioengineering and Genetics, Stanford University, Stanford, CA, USA.

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http://dx.doi.org/10.1016/j.ijmedinf.2017.03.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5459355PMC
June 2017

3D deep convolutional neural networks for amino acid environment similarity analysis.

BMC Bioinformatics 2017 Jun 14;18(1):302. Epub 2017 Jun 14.

Deparment of Bioengineering, Stanford University, Stanford, CA, 94305, USA.

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http://dx.doi.org/10.1186/s12859-017-1702-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5472009PMC
June 2017

PharmGKB summary: voriconazole pathway, pharmacokinetics.

Pharmacogenet Genomics 2017 05;27(5):201-209

Departments of aBiomedical Data Science bBioengineering, Stanford University, Stanford, California cIcahn School of Medicine at Mount Sinai, The Charles Bronfman Institute for Personalized Medicine dDepartment of Medicine, Division of General Internal Medicine, Icahn School of Medicine at Mount Sinai eDepartment of Pharmacy, The Mount Sinai Hospital, New York, New York, USA.

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http://dx.doi.org/10.1097/FPC.0000000000000276DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5405706PMC
May 2017

PharmGKB summary: Macrolide antibiotic pathway, pharmacokinetics/pharmacodynamics.

Pharmacogenet Genomics 2017 04;27(4):164-167

Departments of aGenetics bBioengineering, School of Medicine, Stanford University, Stanford, California cDivision of Pharmaceutics, College of Pharmacy and Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, USA.

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http://dx.doi.org/10.1097/FPC.0000000000000270DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5346035PMC
April 2017

Opportunities for developing therapies for rare genetic diseases: focus on gain-of-function and allostery.

Orphanet J Rare Dis 2017 04 17;12(1):61. Epub 2017 Apr 17.

Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.

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http://dx.doi.org/10.1186/s13023-017-0614-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5392956PMC
April 2017

Flexible Analog Search with Kernel PCA Embedded Molecule Vectors.

Comput Struct Biotechnol J 2017 24;15:320-327. Epub 2017 Mar 24.

Department of Bioengineering, Stanford University, Shriram Center Room 213, 443 Via Ortega MC 4245, Stanford, CA 94305, United States.

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http://dx.doi.org/10.1016/j.csbj.2017.03.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5396859PMC
March 2017

Imputing gene expression to maximize platform compatibility.

Bioinformatics 2017 02;33(4):522-528

Department of Bioengineering.

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http://dx.doi.org/10.1093/bioinformatics/btw664DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5408923PMC
February 2017

PharmGKB summary: ivacaftor pathway, pharmacokinetics/pharmacodynamics.

Pharmacogenet Genomics 2017 01;27(1):39-42

Departments of aGenetics bBioengineering, Stanford University, Stanford, California cDepartment of Pediatrics, Cincinnati Children's Hospital Medical Center and University of Cincinnati, Cincinnati, Ohio, USA dGenomics England, Queen Mary University of London, London, UK.

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http://dx.doi.org/10.1097/FPC.0000000000000246DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5140711PMC
January 2017

STAMS: STRING-assisted module search for genome wide association studies and application to autism.

Bioinformatics 2016 12 19;32(24):3815-3822. Epub 2016 Aug 19.

Departments of Bioengineering and Genetics, Stanford University, Stanford, CA, USA.

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http://dx.doi.org/10.1093/bioinformatics/btw530DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5167061PMC
December 2016

PharmGKB summary: very important pharmacogene information for MT-RNR1.

Pharmacogenet Genomics 2016 12;26(12):558-567

Departments of aGenetics bBioengineering, Stanford University, Stanford, California cDepartment of Pediatrics, Division of Medical Genetics and Genomic Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5083147PMC
http://dx.doi.org/10.1097/FPC.0000000000000247DOI Listing
December 2016

DYNAMICALLY EVOLVING CLINICAL PRACTICES AND IMPLICATIONS FOR PREDICTING MEDICAL DECISIONS.

Pac Symp Biocomput 2016 ;21:195-206

Center for Innovation to Implementation (Ci2i), Veteran Affairs Palo Alto Health Care System, Palo Alto, CA 94304, USA2Center for Primary Care and Outcomes Research (PCOR), Stanford University, Stanford, CA 94305, USA,

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http://psb.stanford.edu/psb-online/proceedings/psb16/chen.pd
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4719775PMC
October 2016

SEPARATING THE CAUSES AND CONSEQUENCES IN DISEASE TRANSCRIPTOME.

Pac Symp Biocomput 2016 ;21:381-92

Department of Bioengineering, Stanford University, USA2Stanford Genome Technology Center, Stanford University, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4722949PMC
October 2016

Computing disease incidence, prevalence and comorbidity from electronic medical records.

J Biomed Inform 2016 10 4;63:108-111. Epub 2016 Aug 4.

Departments of Bioengineering and Genetics, Stanford University, Shriram Room 209, MC 4245, 443 Via Ortega Drive, Stanford, CA 94305-4145, USA. Electronic address:

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http://dx.doi.org/10.1016/j.jbi.2016.08.005DOI Listing
October 2016

PharmGKB summary: isoniazid pathway, pharmacokinetics.

Pharmacogenet Genomics 2016 09;26(9):436-44

Departments of aGenetics bBioengineering, Stanford University, Stanford cKeck School of Medicine of University of Southern California, Los Angeles, California, USA dDepartment of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece eDepartment of Pharmacology, University of Oxford, Oxford, UK.

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http://dx.doi.org/10.1097/FPC.0000000000000232DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4970941PMC
September 2016

Population-specific single-nucleotide polymorphism confers increased risk of venous thromboembolism in African Americans.

Mol Genet Genomic Med 2016 Sep 21;4(5):513-20. Epub 2016 Jun 21.

Department of GeneticsStanford University School of MedicineStanfordCalifornia94305; Department of BioengineeringStanford University School of MedicineStanfordCalifornia94305.

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http://dx.doi.org/10.1002/mgg3.226DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5023936PMC
September 2016

Predicting non-small cell lung cancer prognosis by fully automated microscopic pathology image features.

Nat Commun 2016 08 16;7:12474. Epub 2016 Aug 16.

Department of Genetics, Stanford University, 300 Pasteur Dr, M-344, Stanford 94305-5120, California, USA.

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http://dx.doi.org/10.1038/ncomms12474DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4990706PMC
August 2016

A twentieth anniversary tribute to PSB.

Pac Symp Biocomput 2015 :1-7

Stanford University, Shriram Center for Bioengineering and Chemical Engineering, 443 Via Ortega, Stanford, CA 94305, USA.

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April 2016

Training the next generation of quantitative biologists in the era of big data.

Pac Symp Biocomput 2015 :488-92

Institute for Quantitative Biomedical Sciences, Dartmouth College, Hanover, NH 03755, USA.

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April 2016

Constraints on Biological Mechanism from Disease Comorbidity Using Electronic Medical Records and Database of Genetic Variants.

PLoS Comput Biol 2016 Apr 26;12(4):e1004885. Epub 2016 Apr 26.

Department of Genetics, Stanford University, Stanford, California, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1004885DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4846031PMC
April 2016

OrderRex: clinical order decision support and outcome predictions by data-mining electronic medical records.

J Am Med Inform Assoc 2016 Mar 21;23(2):339-48. Epub 2015 Jul 21.

Departments of Bioengineering, Genetics, and Medicine, Stanford University, Stanford, CA, USA

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https://academic.oup.com/jamia/article-lookup/doi/10.1093/ja
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http://dx.doi.org/10.1093/jamia/ocv091DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5009921PMC
March 2016

PharmGKB summary: very important pharmacogene information for RYR1.

Pharmacogenet Genomics 2016 Mar;26(3):138-44

Departments of aGenetics bBioengineering, Stanford University, Stanford cChildren's Hospital Oakland Research Institute and UCSF, Oakland, California dDepartment of Medicine, University of North Dakota, Fargo, North Dakota eIMAGENETICS, Sanford Healthcare, Sioux Falls, South Dakota, USA.

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http://dx.doi.org/10.1097/FPC.0000000000000198DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4738161PMC
March 2016

Large-scale extraction of gene interactions from full-text literature using DeepDive.

Bioinformatics 2016 Jan 3;32(1):106-13. Epub 2015 Sep 3.

Department of Bioengineering, Department of Genetics and Department of Medicine, Stanford University, Stanford, CA 94305, USA.

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http://dx.doi.org/10.1093/bioinformatics/btv476DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4681986PMC
January 2016

PharmGKB summary: succinylcholine pathway, pharmacokinetics/pharmacodynamics.

Pharmacogenet Genomics 2015 Dec;25(12):622-30

Departments of aGenetics bBioengineering, Stanford University, Stanford, California cDepartment of Anesthesiology dMoffitt Cancer Center, DeBartolo Family Personalized Medicine Institute, Tampa, Florida, USA eGenomics England, Queen Mary University of London, London, UK.

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http://dx.doi.org/10.1097/FPC.0000000000000170DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4631707PMC
December 2015

Unmet needs: Research helps regulators do their jobs.

Sci Transl Med 2015 Nov;7(315):315ps22

Department of Bioengineering and Therapeutic Sciences, Schools of Pharmacy and Medicine, University of California San Francisco, San Francisco, CA 94143-2911, USA. Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94143, USA.

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http://dx.doi.org/10.1126/scitranslmed.aac4369DOI Listing
November 2015

Sequence to Medical Phenotypes: A Framework for Interpretation of Human Whole Genome DNA Sequence Data.

PLoS Genet 2015 Oct 8;11(10):e1005496. Epub 2015 Oct 8.

Stanford Center for Inherited Cardiovascular Disease, Stanford University, Stanford, California, United States of America; Stanford Cardiovascular Institute, Stanford University, Stanford, California, United States of America; Division of Cardiovascular Medicine, Stanford University, Stanford, California, United States of America; Department of Genetics, Stanford University, Stanford, California, United States of America.

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http://dx.plos.org/10.1371/journal.pgen.1005496
Publisher Site
http://dx.doi.org/10.1371/journal.pgen.1005496DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4598191PMC
October 2015

MEDICINE. Personalization in practice.

Science 2015 Oct;350(6258):282-3

Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.

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http://dx.doi.org/10.1126/science.aad5204DOI Listing
October 2015

PharmGKB summary: peginterferon-α pathway.

Pharmacogenet Genomics 2015 Sep;25(9):465-74

Departments of aGenetics bBioengineering, Stanford University, Stanford, California cDuke Clinical Research Institute, Duke University, Durham, North Carolina, USA.

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http://pdfs.journals.lww.com/jpharmacogenetics/2015/09000/Ph
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http://content.wkhealth.com/linkback/openurl?sid=WKPTLP:land
Publisher Site
http://dx.doi.org/10.1097/FPC.0000000000000158DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4757589PMC
September 2015

PharmGKB summary: pathways of acetaminophen metabolism at the therapeutic versus toxic doses.

Pharmacogenet Genomics 2015 Aug;25(8):416-26

aDepartment of Systems Pharmacology and Translational Therapeutics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania Departments of bGenetics cBioengineering, Stanford University Medical Center, Stanford University, Stanford, California, USA.

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http://dx.doi.org/10.1097/FPC.0000000000000150DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4498995PMC
August 2015

An ontology for Autism Spectrum Disorder (ASD) to infer ASD phenotypes from Autism Diagnostic Interview-Revised data.

J Biomed Inform 2015 Aug 4;56:333-47. Epub 2015 Jul 4.

Department of Genetics, Stanford University, Stanford, CA 94305, United States.

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http://dx.doi.org/10.1016/j.jbi.2015.06.026DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4532604PMC
August 2015

Assessment of the Radiation Effects of Cardiac CT Angiography Using Protein and Genetic Biomarkers.

JACC Cardiovasc Imaging 2015 Aug 22;8(8):873-84. Epub 2015 Jul 22.

Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, California; Department of Medicine, Division of Cardiology, Stanford University School of Medicine, Stanford, California; Department of Radiology, Stanford University School of Medicine, Stanford, California. Electronic address:

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http://dx.doi.org/10.1016/j.jcmg.2015.04.016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5019957PMC
August 2015

High Resolution Prediction of Calcium-Binding Sites in 3D Protein Structures Using FEATURE.

J Chem Inf Model 2015 Aug 10;55(8):1663-72. Epub 2015 Aug 10.

Department of Bioengineering, Stanford University , 443 Via Ortega, Stanford, California 94305-4145, United States.

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http://dx.doi.org/10.1021/acs.jcim.5b00367DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4731830PMC
August 2015

Data-Mining Electronic Medical Records for Clinical Order Recommendations: Wisdom of the Crowd or Tyranny of the Mob?

AMIA Jt Summits Transl Sci Proc 2015 25;2015:435-9. Epub 2015 Mar 25.

Department of Medicine, Stanford University, Stanford, CA ; Departments of Bioengineering and Genetics, Stanford University, Stanford, CA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4525236PMC
August 2015

PharmGKB summary: Efavirenz pathway, pharmacokinetics.

Pharmacogenet Genomics 2015 Jul;25(7):363-76

Departments of aGenetics bBioengineering, School of Medicine, Stanford University, Stanford, California, USA cDepartment of Immunology, University of Toronto, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1097/FPC.0000000000000145DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4461466PMC
July 2015

Relating Essential Proteins to Drug Side-Effects Using Canonical Component Analysis: A Structure-Based Approach.

J Chem Inf Model 2015 Jul 16;55(7):1483-94. Epub 2015 Jul 16.

‡Department of Genetics and Department of Bioengineering, Stanford University, Stanford, California 94305, United States.

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http://dx.doi.org/10.1021/acs.jcim.5b00030DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4875781PMC
July 2015

Potential Adverse Effects of Anesthesia in Children--Reply.

JAMA 2015 Jul;314(4):409

Stanford University, Stanford, California.

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http://dx.doi.org/10.1001/jama.2015.7387DOI Listing
July 2015

Learning the Structure of Biomedical Relationships from Unstructured Text.

PLoS Comput Biol 2015 Jul 28;11(7):e1004216. Epub 2015 Jul 28.

Departments of Medicine, Genetics and Bioengineering, Stanford University, Stanford, California, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1004216DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4517797PMC
July 2015

Evidence for Clinical Implementation of Pharmacogenomics in Cardiac Drugs.

Mayo Clin Proc 2015 Jun;90(6):716-29

Center for Personalized Therapeutics, The University of Chicago, Chicago, IL; Department of Medicine, The University of Chicago, Chicago, IL; Committee on Clinical Pharmacology and Pharmacogenomics, The University of Chicago, Chicago, IL. Electronic address:

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http://dx.doi.org/10.1016/j.mayocp.2015.03.016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4475352PMC
June 2015

PharmGKB summary: very important pharmacogene information for human leukocyte antigen B.

Pharmacogenet Genomics 2015 Apr;25(4):205-21

Departments of aGenetics bBioengineering, Stanford University, Stanford cDepartment of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, USA.

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http://dx.doi.org/10.1097/FPC.0000000000000118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4356642PMC
April 2015

Neurotoxicity of generic anesthesia agents in infants and children: an orphan research question in search of a sponsor.

JAMA 2015 Apr;313(15):1515-6

Department of Bioengineering, Stanford University, Stanford, California6Department of Genetics and Medicine, Stanford University, Stanford, California.

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http://dx.doi.org/10.1001/jama.2015.1149DOI Listing
April 2015

PharmGKB summary: very important pharmacogene information for CFTR.

Pharmacogenet Genomics 2015 Mar;25(3):149-56

Departments of aGenetics, Stanford School of Medicine bBioengineering, Stanford University, Stanford, California cDivision of Pulmonary Medicine, Cincinnati Children's Hospital Medical Center dDepartment of Pediatrics, University of Cincinnati, Cincinnati, Ohio, USA.

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http://dx.doi.org/10.1097/FPC.0000000000000112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4336773PMC
March 2015

Predicting cancer drug response: advancing the DREAM.

Authors:
Russ B Altman

Cancer Discov 2015 Mar 26;5(3):237-8. Epub 2015 Jan 26.

Departments of Bioengineering and Genetics, Stanford University, Stanford, California

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http://dx.doi.org/10.1158/2159-8290.CD-15-0093DOI Listing
March 2015

Ranking adverse drug reactions with crowdsourcing.

J Med Internet Res 2015 Mar 23;17(3):e80. Epub 2015 Mar 23.

Department of Genetics, Stanford University, Stanford, CA, United States.

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http://dx.doi.org/10.2196/jmir.3962DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4387295PMC
March 2015

Variations in the binding pocket of an inhibitor of the bacterial division protein FtsZ across genotypes and species.

PLoS Comput Biol 2015 Mar 26;11(3):e1004117. Epub 2015 Mar 26.

Department of Bioengineering, Stanford University, Stanford, California, United States of America; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1004117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4374959PMC
March 2015

PharmGKB summary: ibuprofen pathways.

Pharmacogenet Genomics 2015 Feb;25(2):96-106

aDepartment of Systems Pharmacology and Translational Therapeutics bInstitute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania Departments of cGenetics dBioengineering, Stanford University, Stanford, California, USA.

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http://dx.doi.org/10.1097/FPC.0000000000000113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4355401PMC
February 2015

Automated physician order recommendations and outcome predictions by data-mining electronic medical records.

AMIA Jt Summits Transl Sci Proc 2014 7;2014:206-10. Epub 2014 Apr 7.

Department of Medicine, Stanford University, Stanford, CA 94305, USA. ; Departments of Bioengineering and Genetics, Stanford University, Stanford, CA 94305, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4333710PMC
February 2015

PharmGKB summary: very important pharmacogene information for CYP4F2.

Pharmacogenet Genomics 2015 Jan;25(1):41-7

Departments of aGenetics bBioengineering, Stanford University, Stanford, California, USA.

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http://dx.doi.org/10.1097/FPC.0000000000000100DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4261059PMC
January 2015

Using "big data" to dissect clinical heterogeneity.

Circulation 2015 Jan;131(3):232-3

From the Departments of Bioengineering, Genetics, and Medicine (R.B.A.) and Departments of Medicine, Genetics, and Pathology (E.A.A.), Stanford University, Stanford, CA.

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http://dx.doi.org/10.1161/CIRCULATIONAHA.114.014106DOI Listing
January 2015

High precision prediction of functional sites in protein structures.

PLoS One 2014 14;9(3):e91240. Epub 2014 Mar 14.

Department of Computer Science, San Francisco State University, San Francisco, California, United States of America; Center for Computing for Life Sciences, San Francisco State University, San Francisco, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0091240PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3954699PMC
December 2014

PharmGKB summary: gemcitabine pathway.

Pharmacogenet Genomics 2014 Nov;24(11):564-74

Departments of aGenetics bBioengineering, Stanford University, Stanford, California, USA cDepartment of Pharmacotherapy and Translational Research dCenter for Pharmacogenomics, College of Pharmacy, University of Florida, Gainesville, Florida eDepartment of Molecular Pharmacology & Experimental Therapeutics, Division of Clinical Pharmacology, Mayo Clinic, Rochester, Minnesota, USA.

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http://dx.doi.org/10.1097/FPC.0000000000000086DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4189987PMC
November 2014

PharmGKB summary: uric acid-lowering drugs pathway, pharmacodynamics.

Pharmacogenet Genomics 2014 Sep;24(9):464-76

Departments of aGenetics bBioengineering, Stanford University, Stanford, California cACOS for Research, Department of Veterans Affairs Medical Center Departments of dMedicine ePharmacology/Toxicology, Indiana University School of Medicine, Indianapolis, Indiana, USA.

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http://dx.doi.org/10.1097/FPC.0000000000000058DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4122637PMC
September 2014

PharmGKB summary: very important pharmacogene information for N-acetyltransferase 2.

Pharmacogenet Genomics 2014 Aug;24(8):409-25

Departments of aGenetics bBioengineering, Stanford University, Palo Alto, California cDepartment of Pharmacology and Toxicology and James Graham Brown Cancer Center, University of Louisville, Kentucky, USA dDepartment of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece eDepartment of Laboratory Medicine, Division of Clinical Pharmacology, Karolinska Institutet, Stockholm, Sweden.

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http://dx.doi.org/10.1097/FPC.0000000000000062DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4109976PMC
August 2014

PharmGKB summary: tramadol pathway.

Pharmacogenet Genomics 2014 Jul;24(7):374-80

Departments of aGenetics bBioengineering, Stanford University, Stanford, California, USA cDepartment of Anaesthesiology and Pain Medicine, Inselspital dDepartment of Clinical Research, University of Bern, Bern, Switzerland eInstitute of Clinical Pharmacology, University Medical Center, Göttingen, Germany.

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http://dx.doi.org/10.1097/FPC.0000000000000057DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4100774PMC
July 2014

PharmGKB summary: very important pharmacogene information for SLC22A1.

Pharmacogenet Genomics 2014 Jun;24(6):324-8

aDepartment of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco Departments of bGenetics cBioengineering, Stanford University, Palo Alto, California, USA.

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http://dx.doi.org/10.1097/FPC.0000000000000048DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4035531PMC
June 2014

Knowledge-based fragment binding prediction.

PLoS Comput Biol 2014 Apr 24;10(4):e1003589. Epub 2014 Apr 24.

Department of Bioengineering, Stanford University, Stanford, California, United States of America; Department of Genetics, Stanford University, Stanford, California, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1003589DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3998881PMC
April 2014

Environmental and state-level regulatory factors affect the incidence of autism and intellectual disability.

PLoS Comput Biol 2014 Mar 13;10(3):e1003518. Epub 2014 Mar 13.

Departments of Medicine and Health Studies, the University of Chicago, Center for Health Statistics, Chicago, Illinois, United States of America.

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http://dx.plos.org/10.1371/journal.pcbi.1003518
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http://dx.doi.org/10.1371/journal.pcbi.1003518DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3952819PMC
March 2014