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Items: 1 to 20 of 226

1.

ePlant: Visualizing and Exploring Multiple Levels of Data for Hypothesis Generation in Plant Biology.

Waese J, Fan J, Pasha A, Yu H, Fucile G, Shi R, Cumming M, Kelley LA, Sternberg MJ, Krishnakumar V, Ferlanti E, Miller J, Town C, Stuerzlinger W, Provart NJ.

Plant Cell. 2017 Aug;29(8):1806-1821. doi: 10.1105/tpc.17.00073. Epub 2017 Aug 14.

2.

Search for rare protein altering variants influencing susceptibility to multiple myeloma.

Scales M, Chubb D, Dobbins SE, Johnson DC, Li N, Sternberg MJ, Weinhold N, Stein C, Jackson G, Davies FE, Walker BA, Wardell CP, Houlston RS, Morgan GJ.

Oncotarget. 2017 May 30;8(22):36203-36210. doi: 10.18632/oncotarget.15874.

3.

Predicting Protein Dynamics and Allostery Using Multi-Protein Atomic Distance Constraints.

Greener JG, Filippis I, Sternberg MJ.

Structure. 2017 Mar 7;25(3):546-558. doi: 10.1016/j.str.2017.01.008. Epub 2017 Feb 9.

4.

Thienopyrimidinone Based Sirtuin-2 (SIRT2)-Selective Inhibitors Bind in the Ligand Induced Selectivity Pocket.

Sundriyal S, Moniot S, Mahmud Z, Yao S, Di Fruscia P, Reynolds CR, Dexter DT, Sternberg MJ, Lam EW, Steegborn C, Fuchter MJ.

J Med Chem. 2017 Mar 9;60(5):1928-1945. doi: 10.1021/acs.jmedchem.6b01690. Epub 2017 Feb 15.

5.

Computation Resources for Molecular Biology: Special Issue 2017.

Ostankovitch MI, Sternberg MJ.

J Mol Biol. 2017 Feb 3;429(3):345-347. doi: 10.1016/j.jmb.2016.12.018. Epub 2016 Dec 23. No abstract available.

PMID:
28025039
6.

k-SLAM: accurate and ultra-fast taxonomic classification and gene identification for large metagenomic data sets.

Ainsworth D, Sternberg MJE, Raczy C, Butcher SA.

Nucleic Acids Res. 2017 Feb 28;45(4):1649-1656. doi: 10.1093/nar/gkw1248.

7.

Landscape of Pleiotropic Proteins Causing Human Disease: Structural and System Biology Insights.

Ittisoponpisan S, Alhuzimi E, Sternberg MJ, David A.

Hum Mutat. 2017 Mar;38(3):289-296. doi: 10.1002/humu.23155. Epub 2017 Jan 11.

PMID:
27957775
8.

An expanded evaluation of protein function prediction methods shows an improvement in accuracy.

Jiang Y, Oron TR, Clark WT, Bankapur AR, D'Andrea D, Lepore R, Funk CS, Kahanda I, Verspoor KM, Ben-Hur A, Koo da CE, Penfold-Brown D, Shasha D, Youngs N, Bonneau R, Lin A, Sahraeian SM, Martelli PL, Profiti G, Casadio R, Cao R, Zhong Z, Cheng J, Altenhoff A, Skunca N, Dessimoz C, Dogan T, Hakala K, Kaewphan S, Mehryary F, Salakoski T, Ginter F, Fang H, Smithers B, Oates M, Gough J, Törönen P, Koskinen P, Holm L, Chen CT, Hsu WL, Bryson K, Cozzetto D, Minneci F, Jones DT, Chapman S, Bkc D, Khan IK, Kihara D, Ofer D, Rappoport N, Stern A, Cibrian-Uhalte E, Denny P, Foulger RE, Hieta R, Legge D, Lovering RC, Magrane M, Melidoni AN, Mutowo-Meullenet P, Pichler K, Shypitsyna A, Li B, Zakeri P, ElShal S, Tranchevent LC, Das S, Dawson NL, Lee D, Lees JG, Sillitoe I, Bhat P, Nepusz T, Romero AE, Sasidharan R, Yang H, Paccanaro A, Gillis J, Sedeño-Cortés AE, Pavlidis P, Feng S, Cejuela JM, Goldberg T, Hamp T, Richter L, Salamov A, Gabaldon T, Marcet-Houben M, Supek F, Gong Q, Ning W, Zhou Y, Tian W, Falda M, Fontana P, Lavezzo E, Toppo S, Ferrari C, Giollo M, Piovesan D, Tosatto SC, Del Pozo A, Fernández JM, Maietta P, Valencia A, Tress ML, Benso A, Di Carlo S, Politano G, Savino A, Rehman HU, Re M, Mesiti M, Valentini G, Bargsten JW, van Dijk AD, Gemovic B, Glisic S, Perovic V, Veljkovic V, Veljkovic N, Almeida-E-Silva DC, Vencio RZ, Sharan M, Vogel J, Kansakar L, Zhang S, Vucetic S, Wang Z, Sternberg MJ, Wass MN, Huntley RP, Martin MJ, O'Donovan C, Robinson PN, Moreau Y, Tramontano A, Babbitt PC, Brenner SE, Linial M, Orengo CA, Rost B, Greene CS, Mooney SD, Friedberg I, Radivojac P.

Genome Biol. 2016 Sep 7;17(1):184. doi: 10.1186/s13059-016-1037-6.

9.

Three-Dimensional Model of Human Nicotinamide Nucleotide Transhydrogenase (NNT) and Sequence-Structure Analysis of its Disease-Causing Variations.

Metherell LA, Guerra-Assunção JA, Sternberg MJ, David A.

Hum Mutat. 2016 Oct;37(10):1074-84. doi: 10.1002/humu.23046. Epub 2016 Aug 8.

10.

IGSF10 mutations dysregulate gonadotropin-releasing hormone neuronal migration resulting in delayed puberty.

Howard SR, Guasti L, Ruiz-Babot G, Mancini A, David A, Storr HL, Metherell LA, Sternberg MJ, Cabrera CP, Warren HR, Barnes MR, Quinton R, de Roux N, Young J, Guiochon-Mantel A, Wehkalampi K, André V, Gothilf Y, Cariboni A, Dunkel L.

EMBO Mol Med. 2016 Jun 1;8(6):626-42. doi: 10.15252/emmm.201606250. Print 2016 Jun.

11.

Computation Resources for Molecular Biology: A Special Issue.

Sternberg MJE, Ostankovitch MI.

J Mol Biol. 2016 Feb 22;428(4):669-670. doi: 10.1016/j.jmb.2016.02.001. Epub 2016 Feb 3. No abstract available.

12.

Incorporating Virtual Reactions into a Logic-based Ligand-based Virtual Screening Method to Discover New Leads.

Reynolds CR, Muggleton SH, Sternberg MJ.

Mol Inform. 2015 Sep;34(9):615-625. Epub 2015 Mar 20.

13.

PhyreStorm: A Web Server for Fast Structural Searches Against the PDB.

Mezulis S, Sternberg MJE, Kelley LA.

J Mol Biol. 2016 Feb 22;428(4):702-708. doi: 10.1016/j.jmb.2015.10.017. Epub 2015 Oct 27.

14.

AlloPred: prediction of allosteric pockets on proteins using normal mode perturbation analysis.

Greener JG, Sternberg MJ.

BMC Bioinformatics. 2015 Oct 23;16:335. doi: 10.1186/s12859-015-0771-1.

15.

Exploring the cellular basis of human disease through a large-scale mapping of deleterious genes to cell types.

Cornish AJ, Filippis I, David A, Sternberg MJ.

Genome Med. 2015 Sep 1;7:95. doi: 10.1186/s13073-015-0212-9.

16.

The Contribution of Missense Mutations in Core and Rim Residues of Protein-Protein Interfaces to Human Disease.

David A, Sternberg MJ.

J Mol Biol. 2015 Aug 28;427(17):2886-98. doi: 10.1016/j.jmb.2015.07.004. Epub 2015 Jul 11.

17.

Partial protein domains: evolutionary insights and bioinformatics challenges.

Kelley LA, Sternberg MJ.

Genome Biol. 2015 May 19;16:100. doi: 10.1186/s13059-015-0663-8.

18.

The Phyre2 web portal for protein modeling, prediction and analysis.

Kelley LA, Mezulis S, Yates CM, Wass MN, Sternberg MJ.

Nat Protoc. 2015 Jun;10(6):845-58. doi: 10.1038/nprot.2015.053. Epub 2015 May 7.

19.

A highly conserved program of neuronal microexons is misregulated in autistic brains.

Irimia M, Weatheritt RJ, Ellis JD, Parikshak NN, Gonatopoulos-Pournatzis T, Babor M, Quesnel-Vallières M, Tapial J, Raj B, O'Hanlon D, Barrios-Rodiles M, Sternberg MJ, Cordes SP, Roth FP, Wrana JL, Geschwind DH, Blencowe BJ.

Cell. 2014 Dec 18;159(7):1511-23. doi: 10.1016/j.cell.2014.11.035.

20.

The discovery of a highly selective 5,6,7,8-tetrahydrobenzo[4,5]thieno[2,3-d]pyrimidin-4(3H)-one SIRT2 inhibitor that is neuroprotective in an in vitro Parkinson's disease model.

Di Fruscia P, Zacharioudakis E, Liu C, Moniot S, Laohasinnarong S, Khongkow M, Harrison IF, Koltsida K, Reynolds CR, Schmidtkunz K, Jung M, Chapman KL, Steegborn C, Dexter DT, Sternberg MJ, Lam EW, Fuchter MJ.

ChemMedChem. 2015 Jan;10(1):69-82. doi: 10.1002/cmdc.201402431. Epub 2014 Nov 13.

PMID:
25395356

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