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Items: 1 to 20 of 287

1.

Structures of single-layer β-sheet proteins evolved from β-hairpin repeats.

Xu Q, Biancalana M, Grant JC, Chiu HJ, Jaroszewski L, Knuth MW, Lesley SA, Godzik A, Elsliger MA, Deacon AM, Wilson IA.

Protein Sci. 2019 Sep;28(9):1676-1689. doi: 10.1002/pro.3683. Epub 2019 Aug 2.

PMID:
31306512
2.

Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen.

Menden MP, Wang D, Mason MJ, Szalai B, Bulusu KC, Guan Y, Yu T, Kang J, Jeon M, Wolfinger R, Nguyen T, Zaslavskiy M; AstraZeneca-Sanger Drug Combination DREAM Consortium, Jang IS, Ghazoui Z, Ahsen ME, Vogel R, Neto EC, Norman T, Tang EKY, Garnett MJ, Veroli GYD, Fawell S, Stolovitzky G, Guinney J, Dry JR, Saez-Rodriguez J.

Nat Commun. 2019 Jun 17;10(1):2674. doi: 10.1038/s41467-019-09799-2.

3.

Stratification of amyotrophic lateral sclerosis patients: a crowdsourcing approach.

Kueffner R, Zach N, Bronfeld M, Norel R, Atassi N, Balagurusamy V, Di Camillo B, Chio A, Cudkowicz M, Dillenberger D, Garcia-Garcia J, Hardiman O, Hoff B, Knight J, Leitner ML, Li G, Mangravite L, Norman T, Wang L; ALS Stratification Consortium, Xiao J, Fang WC, Peng J, Yang C, Chang HJ, Stolovitzky G.

Sci Rep. 2019 Jan 24;9(1):690. doi: 10.1038/s41598-018-36873-4.

4.

Cancer3D 2.0: interactive analysis of 3D patterns of cancer mutations in cancer subsets.

Sedova M, Iyer M, Li Z, Jaroszewski L, Post KW, Hrabe T, Porta-Pardo E, Godzik A.

Nucleic Acids Res. 2019 Jan 8;47(D1):D895-D899. doi: 10.1093/nar/gky1098.

5.

Comprehensive Characterization of Cancer Driver Genes and Mutations.

Bailey MH, Tokheim C, Porta-Pardo E, Sengupta S, Bertrand D, Weerasinghe A, Colaprico A, Wendl MC, Kim J, Reardon B, Kwok-Shing Ng P, Jeong KJ, Cao S, Wang Z, Gao J, Gao Q, Wang F, Liu EM, Mularoni L, Rubio-Perez C, Nagarajan N, Cortés-Ciriano I, Zhou DC, Liang WW, Hess JM, Yellapantula VD, Tamborero D, Gonzalez-Perez A, Suphavilai C, Ko JY, Khurana E, Park PJ, Van Allen EM, Liang H; MC3 Working Group; Cancer Genome Atlas Research Network, Lawrence MS, Godzik A, Lopez-Bigas N, Stuart J, Wheeler D, Getz G, Chen K, Lazar AJ, Mills GB, Karchin R, Ding L.

Cell. 2018 Aug 9;174(4):1034-1035. doi: 10.1016/j.cell.2018.07.034. No abstract available.

6.

Comprehensive Characterization of Cancer Driver Genes and Mutations.

Bailey MH, Tokheim C, Porta-Pardo E, Sengupta S, Bertrand D, Weerasinghe A, Colaprico A, Wendl MC, Kim J, Reardon B, Ng PK, Jeong KJ, Cao S, Wang Z, Gao J, Gao Q, Wang F, Liu EM, Mularoni L, Rubio-Perez C, Nagarajan N, Cortés-Ciriano I, Zhou DC, Liang WW, Hess JM, Yellapantula VD, Tamborero D, Gonzalez-Perez A, Suphavilai C, Ko JY, Khurana E, Park PJ, Van Allen EM, Liang H; MC3 Working Group; Cancer Genome Atlas Research Network, Lawrence MS, Godzik A, Lopez-Bigas N, Stuart J, Wheeler D, Getz G, Chen K, Lazar AJ, Mills GB, Karchin R, Ding L.

Cell. 2018 Apr 5;173(2):371-385.e18. doi: 10.1016/j.cell.2018.02.060. Erratum in: Cell. 2018 Aug 9;174(4):1034-1035.

7.

Draft Genome Sequences of Two Vibrio parahaemolyticus Strains Associated with Gastroenteritis after Raw Seafood Ingestion in Colorado.

Trinh SA, Leyn SA, Rodionov ID, Godzik A, Satchell KJF.

Genome Announc. 2018 Jan 18;6(3). pii: e01387-17. doi: 10.1128/genomeA.01387-17.

8.

Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework.

Glusman G, Rose PW, Prlić A, Dougherty J, Duarte JM, Hoffman AS, Barton GJ, Bendixen E, Bergquist T, Bock C, Brunk E, Buljan M, Burley SK, Cai B, Carter H, Gao J, Godzik A, Heuer M, Hicks M, Hrabe T, Karchin R, Leman JK, Lane L, Masica DL, Mooney SD, Moult J, Omenn GS, Pearl F, Pejaver V, Reynolds SM, Rokem A, Schwede T, Song S, Tilgner H, Valasatava Y, Zhang Y, Deutsch EW.

Genome Med. 2017 Dec 18;9(1):113. doi: 10.1186/s13073-017-0509-y. Review.

9.

The Functional Impact of Alternative Splicing in Cancer.

Climente-González H, Porta-Pardo E, Godzik A, Eyras E.

Cell Rep. 2017 Aug 29;20(9):2215-2226. doi: 10.1016/j.celrep.2017.08.012.

10.

Comparison of algorithms for the detection of cancer drivers at subgene resolution.

Porta-Pardo E, Kamburov A, Tamborero D, Pons T, Grases D, Valencia A, Lopez-Bigas N, Getz G, Godzik A.

Nat Methods. 2017 Aug;14(8):782-788. doi: 10.1038/nmeth.4364. Epub 2017 Jul 17.

11.

The "Sticky Patch" Model of Crystallization and Modification of Proteins for Enhanced Crystallizability.

Derewenda ZS, Godzik A.

Methods Mol Biol. 2017;1607:77-115. doi: 10.1007/978-1-4939-7000-1_4. Review.

12.

Mutation Drivers of Immunological Responses to Cancer.

Porta-Pardo E, Godzik A.

Cancer Immunol Res. 2016 Sep 2;4(9):789-98. doi: 10.1158/2326-6066.CIR-15-0233. Epub 2016 Jul 11.

13.

Numerous proteins with unique characteristics are degraded by the 26S proteasome following monoubiquitination.

Braten O, Livneh I, Ziv T, Admon A, Kehat I, Caspi LH, Gonen H, Bercovich B, Godzik A, Jahandideh S, Jaroszewski L, Sommer T, Kwon YT, Guharoy M, Tompa P, Ciechanover A.

Proc Natl Acad Sci U S A. 2016 Aug 9;113(32):E4639-47. doi: 10.1073/pnas.1608644113. Epub 2016 Jul 6.

14.

Revealing aperiodic aspects of solenoid proteins from sequence information.

Hrabe T, Jaroszewski L, Godzik A.

Bioinformatics. 2016 Sep 15;32(18):2776-82. doi: 10.1093/bioinformatics/btw319. Epub 2016 Jun 9.

15.

Neutralizing antibody affords comparable protection against vaginal and rectal simian/human immunodeficiency virus challenge in macaques.

Moldt B, Le KM, Carnathan DG, Whitney JB, Schultz N, Lewis MG, Borducchi EN, Smith KM, Mackel JJ, Sweat SL, Hodges AP, Godzik A, Parren PW, Silvestri G, Barouch DH, Burton DR.

AIDS. 2016 Jun 19;30(10):1543-51. doi: 10.1097/QAD.0000000000001102.

16.

NMR in structural genomics to increase structural coverage of the protein universe: Delivered by Prof. Kurt Wüthrich on 7 July 2013 at the 38th FEBS Congress in St. Petersburg, Russia.

Serrano P, Dutta SK, Proudfoot A, Mohanty B, Susac L, Martin B, Geralt M, Jaroszewski L, Godzik A, Elsliger M, Wilson IA, Wüthrich K.

FEBS J. 2016 Nov;283(21):3870-3881. doi: 10.1111/febs.13751. Epub 2016 Jun 9.

17.

A Distinct Type of Pilus from the Human Microbiome.

Xu Q, Shoji M, Shibata S, Naito M, Sato K, Elsliger MA, Grant JC, Axelrod HL, Chiu HJ, Farr CL, Jaroszewski L, Knuth MW, Deacon AM, Godzik A, Lesley SA, Curtis MA, Nakayama K, Wilson IA.

Cell. 2016 Apr 21;165(3):690-703. doi: 10.1016/j.cell.2016.03.016. Epub 2016 Apr 7.

18.

UHM-ULM interactions in the RBM39-U2AF65 splicing-factor complex.

Stepanyuk GA, Serrano P, Peralta E, Farr CL, Axelrod HL, Geralt M, Das D, Chiu HJ, Jaroszewski L, Deacon AM, Lesley SA, Elsliger MA, Godzik A, Wilson IA, Wüthrich K, Salomon DR, Williamson JR.

Acta Crystallogr D Struct Biol. 2016 Apr;72(Pt 4):497-511. doi: 10.1107/S2059798316001248. Epub 2016 Mar 24.

19.

Crystal Structure and Activity Studies of the C11 Cysteine Peptidase from Parabacteroides merdae in the Human Gut Microbiome.

McLuskey K, Grewal JS, Das D, Godzik A, Lesley SA, Deacon AM, Coombs GH, Elsliger MA, Wilson IA, Mottram JC.

J Biol Chem. 2016 Apr 29;291(18):9482-91. doi: 10.1074/jbc.M115.706143. Epub 2016 Mar 3.

20.

Broadly Neutralizing Antibody Responses in a Large Longitudinal Sub-Saharan HIV Primary Infection Cohort.

Landais E, Huang X, Havenar-Daughton C, Murrell B, Price MA, Wickramasinghe L, Ramos A, Bian CB, Simek M, Allen S, Karita E, Kilembe W, Lakhi S, Inambao M, Kamali A, Sanders EJ, Anzala O, Edward V, Bekker LG, Tang J, Gilmour J, Kosakovsky-Pond SL, Phung P, Wrin T, Crotty S, Godzik A, Poignard P.

PLoS Pathog. 2016 Jan 14;12(1):e1005369. doi: 10.1371/journal.ppat.1005369. eCollection 2016 Jan.

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