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Items: 1 to 50 of 465

1.

Pharmacogenomics Clinical Annotation Tool (PharmCAT).

Sangkuhl K, Whirl-Carrillo M, Whaley RM, Woon M, Lavertu A, Altman RB, Carter L, Verma A, Ritchie MD, Klein TE.

Clin Pharmacol Ther. 2019 Jul 15. doi: 10.1002/cpt.1568. [Epub ahead of print]

PMID:
31306493
2.

PathFXweb: a web application for identifying drug safety and efficacy phenotypes.

Wilson JL, Wong M, Chalke A, Stepanov N, Petkovic D, Altman RB.

Bioinformatics. 2019 May 22. pii: btz419. doi: 10.1093/bioinformatics/btz419. [Epub ahead of print]

PMID:
31114840
3.

High precision protein functional site detection using 3D convolutional neural networks.

Torng W, Altman RB.

Bioinformatics. 2019 May 1;35(9):1503-1512. doi: 10.1093/bioinformatics/bty813.

4.

Pharmacogenomics in dermatology: tools for understanding gene-drug associations.

Daneshjou R, Huddart R, Klein TE, Altman RB.

Semin Cutan Med Surg. 2019 Mar 1;38(1):E19-E24. doi: 10.12788/j.sder.2019.009.

5.

PharmGKB summary: methylphenidate pathway, pharmacokinetics/pharmacodynamics.

Stevens T, Sangkuhl K, Brown JT, Altman RB, Klein TE.

Pharmacogenet Genomics. 2019 Aug;29(6):136-154. doi: 10.1097/FPC.0000000000000376. No abstract available.

PMID:
30950912
6.

Pocket similarity identifies selective estrogen receptor modulators as microtubule modulators at the taxane site.

Lo YC, Cormier O, Liu T, Nettles KW, Katzenellenbogen JA, Stearns T, Altman RB.

Nat Commun. 2019 Mar 4;10(1):1033. doi: 10.1038/s41467-019-08965-w.

7.

Research Projects Supported by the University of California, San Francisco-Stanford Center of Excellence in Regulatory Science and Innovation.

Giacomini KM, Lin L, Altman RB.

Clin Pharmacol Ther. 2019 Apr;105(4):815-818. doi: 10.1002/cpt.1308. Epub 2019 Feb 17. No abstract available.

PMID:
30773618
8.

PharmGKB summary: Ondansetron and tropisetron pathways, pharmacokinetics and pharmacodynamics.

Huddart R, Altman RB, Klein TE.

Pharmacogenet Genomics. 2019 Jun;29(4):91-97. doi: 10.1097/FPC.0000000000000369. No abstract available.

PMID:
30672837
9.

The association of obesity and coronary artery disease genes with response to SSRIs treatment in major depression.

Amare AT, Schubert KO, Tekola-Ayele F, Hsu YH, Sangkuhl K, Jenkins G, Whaley RM, Barman P, Batzler A, Altman RB, Arolt V, Brockmöller J, Chen CH, Domschke K, Hall-Flavin DK, Hong CJ, Illi A, Ji Y, Kampman O, Kinoshita T, Leinonen E, Liou YJ, Mushiroda T, Nonen S, Skime MK, Wang L, Kato M, Liu YL, Praphanphoj V, Stingl JC, Bobo WV, Tsai SJ, Kubo M, Klein TE, Weinshilboum RM, Biernacka JM, Baune BT.

J Neural Transm (Vienna). 2019 Jan;126(1):35-45. doi: 10.1007/s00702-018-01966-x. Epub 2019 Jan 4.

PMID:
30610379
10.

Standardized Biogeographic Grouping System for Annotating Populations in Pharmacogenetic Research.

Huddart R, Fohner AE, Whirl-Carrillo M, Wojcik GL, Gignoux CR, Popejoy AB, Bustamante CD, Altman RB, Klein TE.

Clin Pharmacol Ther. 2019 May;105(5):1256-1262. doi: 10.1002/cpt.1322. Epub 2019 Jan 21.

PMID:
30506572
11.

ERASE: a novel surface reconditioning strategy for single-molecule experiments.

Broadwater DWB, Altman RB, Blanchard SC, Kim HD.

Nucleic Acids Res. 2019 Feb 20;47(3):e14. doi: 10.1093/nar/gky1168.

12.

Essential Characteristics of Pharmacogenomics Study Publications.

Thorn CF, Whirl-Carrillo M, Hachad H, Johnson JA, McDonagh EM, Ratain MJ, Relling MV, Scott SA, Altman RB, Klein TE.

Clin Pharmacol Ther. 2019 Jan;105(1):86-91. doi: 10.1002/cpt.1279. Review.

PMID:
30406943
13.

The Pioglitazone Trek via Human PPAR Gamma: From Discovery to a Medicine at the FDA and Beyond.

Devchand PR, Liu T, Altman RB, FitzGerald GA, Schadt EE.

Front Pharmacol. 2018 Oct 4;9:1093. doi: 10.3389/fphar.2018.01093. eCollection 2018. Review.

14.

Endogenous rRNA Sequence Variation Can Regulate Stress Response Gene Expression and Phenotype.

Kurylo CM, Parks MM, Juette MF, Zinshteyn B, Altman RB, Thibado JK, Vincent CT, Blanchard SC.

Cell Rep. 2018 Oct 2;25(1):236-248.e6. doi: 10.1016/j.celrep.2018.08.093.

15.

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

Zhou W, Altman RB.

BMC Bioinformatics. 2018 Sep 17;19(1):327. doi: 10.1186/s12859-018-2338-4.

16.

PharmGKB summary: oxycodone pathway, pharmacokinetics.

Huddart R, Clarke M, Altman RB, Klein TE.

Pharmacogenet Genomics. 2018 Oct;28(10):230-237. doi: 10.1097/FPC.0000000000000351. No abstract available.

PMID:
30222708
17.

PharmGKB summary: clozapine pathway, pharmacokinetics.

Thorn CF, Müller DJ, Altman RB, Klein TE.

Pharmacogenet Genomics. 2018 Sep;28(9):214-222. doi: 10.1097/FPC.0000000000000347. No abstract available.

PMID:
30134346
18.

Computational analysis of kinase inhibitor selectivity using structural knowledge.

Lo YC, Liu T, Morrissey KM, Kakiuchi-Kiyota S, Johnson AR, Broccatelli F, Zhong Y, Joshi A, Altman RB.

Bioinformatics. 2019 Jan 15;35(2):235-242. doi: 10.1093/bioinformatics/bty582.

PMID:
29985971
19.

Machine learning in chemoinformatics and drug discovery.

Lo YC, Rensi SE, Torng W, Altman RB.

Drug Discov Today. 2018 Aug;23(8):1538-1546. doi: 10.1016/j.drudis.2018.05.010. Epub 2018 May 8. Review.

20.

Genome-wide and candidate gene approaches of clopidogrel efficacy using pharmacodynamic and clinical end points-Rationale and design of the International Clopidogrel Pharmacogenomics Consortium (ICPC).

Bergmeijer TO, Reny JL, Pakyz RE, Gong L, Lewis JP, Kim EY, Aradi D, Fernandez-Cadenas I, Horenstein RB, Lee MTM, Whaley RM, Montaner J, Gensini GF, Cleator JH, Chang K, Holmvang L, Hochholzer W, Roden DM, Winter S, Altman RB, Alexopoulos D, Kim HS, Déry JP, Gawaz M, Bliden K, Valgimigli M, Marcucci R, Campo G, Schaeffeler E, Dridi NP, Wen MS, Shin JG, Simon T, Fontana P, Giusti B, Geisler T, Kubo M, Trenk D, Siller-Matula JM, Ten Berg JM, Gurbel PA, Hulot JS, Mitchell BD, Schwab M, Ritchie MD, Klein TE, Shuldiner AR; ICPC Investigators.

Am Heart J. 2018 Apr;198:152-159. doi: 10.1016/j.ahj.2017.12.010. Epub 2017 Dec 17. Review.

21.

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

Lavertu A, McInnes G, Daneshjou R, Whirl-Carrillo M, Klein TE, Altman RB.

Hum Mol Genet. 2018 May 1;27(R1):R72-R78. doi: 10.1093/hmg/ddy116. Review.

22.

HIV-1 Env trimer opens through an asymmetric intermediate in which individual protomers adopt distinct conformations.

Ma X, Lu M, Gorman J, Terry DS, Hong X, Zhou Z, Zhao H, Altman RB, Arthos J, Blanchard SC, Kwong PD, Munro JB, Mothes W.

Elife. 2018 Mar 21;7. pii: e34271. doi: 10.7554/eLife.34271.

23.

Association of the Polygenic Scores for Personality Traits and Response to Selective Serotonin Reuptake Inhibitors in Patients with Major Depressive Disorder.

Amare AT, Schubert KO, Tekola-Ayele F, Hsu YH, Sangkuhl K, Jenkins G, Whaley RM, Barman P, Batzler A, Altman RB, Arolt V, Brockmöller J, Chen CH, Domschke K, Hall-Flavin DK, Hong CJ, Illi A, Ji Y, Kampman O, Kinoshita T, Leinonen E, Liou YJ, Mushiroda T, Nonen S, Skime MK, Wang L, Kato M, Liu YL, Praphanphoj V, Stingl JC, Bobo WV, Tsai SJ, Kubo M, Klein TE, Weinshilboum RM, Biernacka JM, Baune BT.

Front Psychiatry. 2018 Mar 6;9:65. doi: 10.3389/fpsyt.2018.00065. eCollection 2018.

24.

PharmGKB summary: clobazam pathway, pharmacokinetics.

Huddart R, Leeder JS, Altman RB, Klein TE.

Pharmacogenet Genomics. 2018 Apr;28(4):110-115. doi: 10.1097/FPC.0000000000000327. No abstract available.

25.

PharmGKB summary: atazanavir pathway, pharmacokinetics/pharmacodynamics.

Alvarellos M, Guillemette C, Altman RB, Klein TE.

Pharmacogenet Genomics. 2018 May;28(5):127-137. doi: 10.1097/FPC.0000000000000331. No abstract available.

26.

A global network of biomedical relationships derived from text.

Percha B, Altman RB.

Bioinformatics. 2018 Aug 1;34(15):2614-2624. doi: 10.1093/bioinformatics/bty114.

27.

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

Chavez G, Richman IB, Kaimal R, Bentley J, Yasukawa LA, Altman RB, Periyakoil VS, Chen JH.

PLoS One. 2018 Feb 28;13(2):e0190569. doi: 10.1371/journal.pone.0190569. eCollection 2018.

28.

PharmGKB: A worldwide resource for pharmacogenomic information.

Barbarino JM, Whirl-Carrillo M, Altman RB, Klein TE.

Wiley Interdiscip Rev Syst Biol Med. 2018 Jul;10(4):e1417. doi: 10.1002/wsbm.1417. Epub 2018 Feb 23. Review.

29.

Mendelian Disease Associations Reveal Novel Insights into Inflammatory Bowel Disease.

Han L, Maciejewski M, Brockel C, Afzelius L, Altman RB.

Inflamm Bowel Dis. 2018 Feb 15;24(3):471-481. doi: 10.1093/ibd/izx087.

30.

Expanding a radiology lexicon using contextual patterns in radiology reports.

Percha B, Zhang Y, Bozkurt S, Rubin D, Altman RB, Langlotz CP.

J Am Med Inform Assoc. 2018 Jun 1;25(6):679-685. doi: 10.1093/jamia/ocx152.

31.

Systematic target function annotation of human transcription factors.

Li YF, Altman RB.

BMC Biol. 2018 Jan 10;16(1):4. doi: 10.1186/s12915-017-0469-0.

32.

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

Wagner JA, Dahlem AM, Hudson LD, Terry SF, Altman RB, Gilliland CT, DeFeo C, Austin CP.

Clin Transl Sci. 2018 Mar;11(2):166-174. doi: 10.1111/cts.12531. Epub 2017 Dec 22.

33.

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

Wagner J, Dahlem AM, Hudson LD, Terry SF, Altman RB, Gilliland CT, DeFeo C, Austin CP.

Nat Rev Drug Discov. 2018 Feb;17(2):150. doi: 10.1038/nrd.2017.217. Epub 2017 Dec 22. No abstract available.

PMID:
29269942
34.

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

Previde P, Thomas B, Wong M, Mallory EK, Petkovic D, Altman RB, Kulkarni A.

Pac Symp Biocomput. 2018;23:590-601.

35.

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

Mallory EK, Acharya A, Rensi SE, Turnbaugh PJ, Bright RA, Altman RB.

Pac Symp Biocomput. 2018;23:56-67.

36.

Aminoglycoside interactions and impacts on the eukaryotic ribosome.

Prokhorova I, Altman RB, Djumagulov M, Shrestha JP, Urzhumtsev A, Ferguson A, Chang CT, Yusupov M, Blanchard SC, Yusupova G.

Proc Natl Acad Sci U S A. 2017 Dec 19;114(51):E10899-E10908. doi: 10.1073/pnas.1715501114. Epub 2017 Dec 5.

37.

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

Wilson JL, Altman RB.

Exp Biol Med (Maywood). 2018 Feb;243(3):313-322. doi: 10.1177/1535370217744775. Epub 2017 Dec 3. Review.

38.

Cohort-specific imputation of gene expression improves prediction of warfarin dose for African Americans.

Gottlieb A, Daneshjou R, DeGorter M, Bourgeois S, Svensson PJ, Wadelius M, Deloukas P, Montgomery SB, Altman RB.

Genome Med. 2017 Nov 24;9(1):98. doi: 10.1186/s13073-017-0495-0.

39.

Association of Omics Features with Histopathology Patterns in Lung Adenocarcinoma.

Yu KH, Berry GJ, Rubin DL, Ré C, Altman RB, Snyder M.

Cell Syst. 2017 Dec 27;5(6):620-627.e3. doi: 10.1016/j.cels.2017.10.014. Epub 2017 Nov 15.

40.

Dynamics of P-type ATPase transport revealed by single-molecule FRET.

Dyla M, Terry DS, Kjaergaard M, Sørensen TL, Lauwring Andersen J, Andersen JP, Rohde Knudsen C, Altman RB, Nissen P, Blanchard SC.

Nature. 2017 Nov 16;551(7680):346-351. doi: 10.1038/nature24296. Epub 2017 Nov 8.

41.

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

Altman RB.

Clin Pharmacol Ther. 2018 Feb;103(2):171-173. doi: 10.1002/cpt.918. Epub 2017 Nov 14.

PMID:
29134624
42.

A probabilistic pathway score (PROPS) for classification with applications to inflammatory bowel disease.

Han L, Maciejewski M, Brockel C, Gordon W, Snapper SB, Korzenik JR, Afzelius L, Altman RB.

Bioinformatics. 2018 Mar 15;34(6):985-993. doi: 10.1093/bioinformatics/btx651.

43.

Biological and functional relevance of CASP predictions.

Liu T, Ish-Shalom S, Torng W, Lafita A, Bock C, Mort M, Cooper DN, Bliven S, Capitani G, Mooney SD, Altman RB.

Proteins. 2018 Mar;86 Suppl 1:374-386. doi: 10.1002/prot.25396. Epub 2017 Oct 17.

44.

PharmGKB summary: very important pharmacogene information for ABCG2.

Fohner AE, Brackman DJ, Giacomini KM, Altman RB, Klein TE.

Pharmacogenet Genomics. 2017 Nov;27(11):420-427. doi: 10.1097/FPC.0000000000000305. Review. No abstract available. Erratum in: Pharmacogenet Genomics. 2018 May;28(5):138.

45.

Shallow Representation Learning via Kernel PCA Improves QSAR Modelability.

Rensi SE, Altman RB.

J Chem Inf Model. 2017 Aug 28;57(8):1859-1867. doi: 10.1021/acs.jcim.6b00694. Epub 2017 Aug 7.

46.

PharmGKB summary: pazopanib pathway, pharmacokinetics.

Thorn CF, Sharma MR, Altman RB, Klein TE.

Pharmacogenet Genomics. 2017 Aug;27(8):307-312. doi: 10.1097/FPC.0000000000000292. Review. No abstract available.

47.

Working toward precision medicine: Predicting phenotypes from exomes in the Critical Assessment of Genome Interpretation (CAGI) challenges.

Daneshjou R, Wang Y, Bromberg Y, Bovo S, Martelli PL, Babbi G, Lena PD, Casadio R, Edwards M, Gifford D, Jones DT, Sundaram L, Bhat RR, Li X, Pal LR, Kundu K, Yin Y, Moult J, Jiang Y, Pejaver V, Pagel KA, Li B, Mooney SD, Radivojac P, Shah S, Carraro M, Gasparini A, Leonardi E, Giollo M, Ferrari C, Tosatto SCE, Bachar E, Azaria JR, Ofran Y, Unger R, Niroula A, Vihinen M, Chang B, Wang MH, Franke A, Petersen BS, Pirooznia M, Zandi P, McCombie R, Potash JB, Altman RB, Klein TE, Hoskins RA, Repo S, Brenner SE, Morgan AA.

Hum Mutat. 2017 Sep;38(9):1182-1192. doi: 10.1002/humu.23280. Epub 2017 Jul 7.

48.

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

Torng W, Altman RB.

BMC Bioinformatics. 2017 Jun 14;18(1):302. doi: 10.1186/s12859-017-1702-0.

49.

Pseudoknot Formation Seeds the Twister Ribozyme Cleavage Reaction Coordinate.

Vušurović N, Altman RB, Terry DS, Micura R, Blanchard SC.

J Am Chem Soc. 2017 Jun 21;139(24):8186-8193. doi: 10.1021/jacs.7b01549. Epub 2017 Jun 9.

50.

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

Chen JH, Alagappan M, Goldstein MK, Asch SM, Altman RB.

Int J Med Inform. 2017 Jun;102:71-79. doi: 10.1016/j.ijmedinf.2017.03.006. Epub 2017 Mar 18.

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