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Items: 1 to 20 of 83

1.

Transcriptomic variation of pharmacogenes in multiple human tissues and lymphoblastoid cell lines.

Chhibber A, French CE, Yee SW, Gamazon ER, Theusch E, Qin X, Webb A, Papp AC, Wang A, Simmons CQ, Konkashbaev A, Chaudhry AS, Mitchel K, Stryke D, Ferrin TE, Weiss ST, Kroetz DL, Sadee W, Nickerson DA, Krauss RM, George AL, Schuetz EG, Medina MW, Cox NJ, Scherer SE, Giacomini KM, Brenner SE.

Pharmacogenomics J. 2016 Feb 9. doi: 10.1038/tpj.2015.93. [Epub ahead of print]

PMID:
26856248
2.

Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop.

Sali A, Berman HM, Schwede T, Trewhella J, Kleywegt G, Burley SK, Markley J, Nakamura H, Adams P, Bonvin AM, Chiu W, Peraro MD, Di Maio F, Ferrin TE, Grünewald K, Gutmanas A, Henderson R, Hummer G, Iwasaki K, Johnson G, Lawson CL, Meiler J, Marti-Renom MA, Montelione GT, Nilges M, Nussinov R, Patwardhan A, Rappsilber J, Read RJ, Saibil H, Schröder GF, Schwieters CD, Seidel CA, Svergun D, Topf M, Ulrich EL, Velankar S, Westbrook JD.

Structure. 2015 Jul 7;23(7):1156-67. doi: 10.1016/j.str.2015.05.013. Epub 2015 Jun 18.

PMID:
26095030
3.

Multidomain Assembler (MDA) Generates Models of Large Multidomain Proteins.

Hertig S, Goddard TD, Johnson GT, Ferrin TE.

Biophys J. 2015 May 5;108(9):2097-102. doi: 10.1016/j.bpj.2015.03.051.

PMID:
25954868
4.

CyAnimator: Simple Animations of Cytoscape Networks.

Morris JH, Vijay D, Federowicz S, Pico AR, Ferrin TE.

Version 2. F1000Res. 2015 Aug 5 [revised 2015 Dec 30];4:482. doi: 10.12688/f1000research.6852.2. eCollection 2015.

5.

RRDistMaps: a UCSF Chimera tool for viewing and comparing protein distance maps.

Chen JE, Huang CC, Ferrin TE.

Bioinformatics. 2015 May 1;31(9):1484-6. doi: 10.1093/bioinformatics/btu841. Epub 2014 Dec 24.

PMID:
25540183
6.

setsApp for Cytoscape: Set operations for Cytoscape Nodes and Edges.

Morris JH, Lotia S, Wu A, Doncheva NT, Albrecht M, Pico AR, Ferrin TE.

Version 2. F1000Res. 2014 Jul 1 [revised 2015 Aug 5];3:149. doi: 10.12688/f1000research.4392.2. eCollection 2014.

7.

enhancedGraphics: a Cytoscape app for enhanced node graphics.

Morris JH, Kuchinsky A, Ferrin TE, Pico AR.

F1000Res. 2014 Jul 1;3:147. doi: 10.12688/f1000research.4460.1. eCollection 2014.

8.

cddApp: a Cytoscape app for accessing the NCBI conserved domain database.

Morris JH, Wu A, Yamashita RA, Marchler-Bauer A, Ferrin TE.

Bioinformatics. 2015 Jan 1;31(1):134-6. doi: 10.1093/bioinformatics/btu605. Epub 2014 Sep 10.

9.

Enhancing UCSF Chimera through web services.

Huang CC, Meng EC, Morris JH, Pettersen EF, Ferrin TE.

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W478-84. doi: 10.1093/nar/gku377. Epub 2014 May 26.

10.

The Structure-Function Linkage Database.

Akiva E, Brown S, Almonacid DE, Barber AE 2nd, Custer AF, Hicks MA, Huang CC, Lauck F, Mashiyama ST, Meng EC, Mischel D, Morris JH, Ojha S, Schnoes AM, Stryke D, Yunes JM, Ferrin TE, Holliday GL, Babbitt PC.

Nucleic Acids Res. 2014 Jan;42(Database issue):D521-30. doi: 10.1093/nar/gkt1130. Epub 2013 Nov 23.

11.

Macromolecular assembly structures by comparative modeling and electron microscopy.

Lasker K, Velázquez-Muriel JA, Webb BM, Yang Z, Ferrin TE, Sali A.

Methods Mol Biol. 2012;857:331-50. doi: 10.1007/978-1-61779-588-6_15.

PMID:
22323229
12.

Genetic and epigenetic regulation of the organic cation transporter 3, SLC22A3.

Chen L, Hong C, Chen EC, Yee SW, Xu L, Almof EU, Wen C, Fujii K, Johns SJ, Stryke D, Ferrin TE, Simko J, Chen X, Costello JF, Giacomini KM.

Pharmacogenomics J. 2013 Apr;13(2):110-20. doi: 10.1038/tpj.2011.60. Epub 2012 Jan 10.

13.

clusterMaker: a multi-algorithm clustering plugin for Cytoscape.

Morris JH, Apeltsin L, Newman AM, Baumbach J, Wittkop T, Su G, Bader GD, Ferrin TE.

BMC Bioinformatics. 2011 Nov 9;12:436. doi: 10.1186/1471-2105-12-436.

14.

UCSF Chimera, MODELLER, and IMP: an integrated modeling system.

Yang Z, Lasker K, Schneidman-Duhovny D, Webb B, Huang CC, Pettersen EF, Goddard TD, Meng EC, Sali A, Ferrin TE.

J Struct Biol. 2012 Sep;179(3):269-78. doi: 10.1016/j.jsb.2011.09.006. Epub 2011 Sep 22.

15.

A common 5'-UTR variant in MATE2-K is associated with poor response to metformin.

Choi JH, Yee SW, Ramirez AH, Morrissey KM, Jang GH, Joski PJ, Mefford JA, Hesselson SE, Schlessinger A, Jenkins G, Castro RA, Johns SJ, Stryke D, Sali A, Ferrin TE, Witte JS, Kwok PY, Roden DM, Wilke RA, McCarty CA, Davis RL, Giacomini KM.

Clin Pharmacol Ther. 2011 Nov;90(5):674-84. doi: 10.1038/clpt.2011.165. Epub 2011 Sep 28.

16.

Functional characterization of liver enhancers that regulate drug-associated transporters.

Kim MJ, Skewes-Cox P, Fukushima H, Hesselson S, Yee SW, Ramsey LB, Nguyen L, Eshragh JL, Castro RA, Wen CC, Stryke D, Johns SJ, Ferrin TE, Kwok PY, Relling MV, Giacomini KM, Kroetz DL, Ahituv N.

Clin Pharmacol Ther. 2011 Apr;89(4):571-8. doi: 10.1038/clpt.2010.353. Epub 2011 Mar 2.

17.

Improving the quality of protein similarity network clustering algorithms using the network edge weight distribution.

Apeltsin L, Morris JH, Babbitt PC, Ferrin TE.

Bioinformatics. 2011 Feb 1;27(3):326-33. doi: 10.1093/bioinformatics/btq655. Epub 2010 Nov 29.

18.

ModBase, a database of annotated comparative protein structure models, and associated resources.

Pieper U, Webb BM, Barkan DT, Schneidman-Duhovny D, Schlessinger A, Braberg H, Yang Z, Meng EC, Pettersen EF, Huang CC, Datta RS, Sampathkumar P, Madhusudhan MS, Sjölander K, Ferrin TE, Burley SK, Sali A.

Nucleic Acids Res. 2011 Jan;39(Database issue):D465-74. doi: 10.1093/nar/gkq1091. Epub 2010 Nov 19.

19.

Workshop on molecular animation.

Bromberg S, Chiu W, Ferrin TE.

Structure. 2010 Oct 13;18(10):1261-5. doi: 10.1016/j.str.2010.09.001.

20.

Role of organic cation transporter 3 (SLC22A3) and its missense variants in the pharmacologic action of metformin.

Chen L, Pawlikowski B, Schlessinger A, More SS, Stryke D, Johns SJ, Portman MA, Chen E, Ferrin TE, Sali A, Giacomini KM.

Pharmacogenet Genomics. 2010 Nov;20(11):687-99. doi: 10.1097/FPC.0b013e32833fe789.

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