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Results: 1 to 20 of 76

1.

cddApp: A Cytoscape App for Accessing the NCBI Conserved Domain Database.

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

Bioinformatics. 2014 Sep 10. pii: btu605. [Epub ahead of print]

PMID:
25212755
[PubMed - as supplied by publisher]
2.

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.

PMID:
24861624
[PubMed - indexed for MEDLINE]
Free Article
3.

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.

PMID:
24271399
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

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
[PubMed - indexed for MEDLINE]
5.

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.

PMID:
22231567
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

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.

PMID:
22070249
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

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.

PMID:
21963794
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

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.

PMID:
21956618
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

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.

PMID:
21368754
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

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.

PMID:
21118823
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

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.

PMID:
21097780
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

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.

PMID:
20947014
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

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.

PMID:
20859243
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Genetic variants of human organic anion transporter 4 demonstrate altered transport of endogenous substrates.

Shima JE, Komori T, Taylor TR, Stryke D, Kawamoto M, Johns SJ, Carlson EJ, Ferrin TE, Giacomini KM.

Am J Physiol Renal Physiol. 2010 Oct;299(4):F767-75. doi: 10.1152/ajprenal.00312.2010. Epub 2010 Jul 28.

PMID:
20668102
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Computational tools for the interactive exploration of proteomic and structural data.

Morris JH, Meng EC, Ferrin TE.

Mol Cell Proteomics. 2010 Aug;9(8):1703-15. doi: 10.1074/mcp.R000007-MCP201. Epub 2010 Jun 4.

PMID:
20525940
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Comparison of human solute carriers.

Schlessinger A, Matsson P, Shima JE, Pieper U, Yee SW, Kelly L, Apeltsin L, Stroud RM, Ferrin TE, Giacomini KM, Sali A.

Protein Sci. 2010 Mar;19(3):412-28. doi: 10.1002/pro.320.

PMID:
20052679
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Identification and characterization of novel polymorphisms in the basal promoter of the human transporter, MATE1.

Ha Choi J, Wah Yee S, Kim MJ, Nguyen L, Ho Lee J, Kang JO, Hesselson S, Castro RA, Stryke D, Johns SJ, Kwok PY, Ferrin TE, Goo Lee M, Black BL, Ahituv N, Giacomini KM.

Pharmacogenet Genomics. 2009 Oct;19(10):770-80. doi: 10.1097/FPC.0b013e328330eeca.

PMID:
19745787
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Genetic variation in the proximal promoter of ABC and SLC superfamilies: liver and kidney specific expression and promoter activity predict variation.

Hesselson SE, Matsson P, Shima JE, Fukushima H, Yee SW, Kobayashi Y, Gow JM, Ha C, Ma B, Poon A, Johns SJ, Stryke D, Castro RA, Tahara H, Choi JH, Chen L, Picard N, Sjödin E, Roelofs MJ, Ferrin TE, Myers R, Kroetz DL, Kwok PY, Giacomini KM.

PLoS One. 2009 Sep 9;4(9):e6942. doi: 10.1371/journal.pone.0006942.

PMID:
19742321
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Using sequence similarity networks for visualization of relationships across diverse protein superfamilies.

Atkinson HJ, Morris JH, Ferrin TE, Babbitt PC.

PLoS One. 2009;4(2):e4345. doi: 10.1371/journal.pone.0004345. Epub 2009 Feb 3.

PMID:
19190775
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Genetic variants in multidrug and toxic compound extrusion-1, hMATE1, alter transport function.

Chen Y, Teranishi K, Li S, Yee SW, Hesselson S, Stryke D, Johns SJ, Ferrin TE, Kwok P, Giacomini KM.

Pharmacogenomics J. 2009 Apr;9(2):127-36. doi: 10.1038/tpj.2008.19. Epub 2009 Jan 27.

PMID:
19172157
[PubMed - indexed for MEDLINE]
Free PMC Article

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