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Phylotranscriptomic insights into the diversification of endothermic Thunnus tunas.

Ciezarek A, Osborne O, Shipley ON, Brooks EJ, Tracey S, McAllister J, Gardner L, Sternberg MJE, Block B, Savolainen V.

Mol Biol Evol. 2018 Oct 26. doi: 10.1093/molbev/msy198. [Epub ahead of print]


Computation Resources for Molecular Biology: Special Issue 2018.

Sternberg MJE, Yosef N.

J Mol Biol. 2018 Jul 20;430(15):2181-2183. doi: 10.1016/j.jmb.2018.05.041. Epub 2018 May 31. No abstract available.


EzMol: A Web Server Wizard for the Rapid Visualization and Image Production of Protein and Nucleic Acid Structures.

Reynolds CR, Islam SA, Sternberg MJE.

J Mol Biol. 2018 Jul 20;430(15):2244-2248. doi: 10.1016/j.jmb.2018.01.013. Epub 2018 Jan 31.


PhenoRank: reducing study bias in gene prioritization through simulation.

Cornish AJ, David A, Sternberg MJE.

Bioinformatics. 2018 Jun 15;34(12):2087-2095. doi: 10.1093/bioinformatics/bty028.


In Silico Analysis of the Small Molecule Content of Outer Membrane Vesicles Produced by Bacteroides thetaiotaomicron Indicates an Extensive Metabolic Link between Microbe and Host.

Bryant WA, Stentz R, Le Gall G, Sternberg MJE, Carding SR, Wilhelm T.

Front Microbiol. 2017 Dec 8;8:2440. doi: 10.3389/fmicb.2017.02440. eCollection 2017.


Properties of human genes guided by their enrichment in rare and common variants.

Alhuzimi E, Leal LG, Sternberg MJE, David A.

Hum Mutat. 2018 Mar;39(3):365-370. doi: 10.1002/humu.23377. Epub 2017 Dec 21.


Structure-based prediction of protein allostery.

Greener JG, Sternberg MJ.

Curr Opin Struct Biol. 2018 Jun;50:1-8. doi: 10.1016/ Epub 2017 Nov 5. Review.


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.


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.


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

Greener JG, Filippis I, Sternberg MJE.

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


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


Genome3D: exploiting structure to help users understand their sequences.

Lewis TE, Sillitoe I, Andreeva A, Blundell TL, Buchan DW, Chothia C, Cozzetto D, Dana JM, Filippis I, Gough J, Jones DT, Kelley LA, Kleywegt GJ, Minneci F, Mistry J, Murzin AG, Ochoa-Montaño B, Oates ME, Punta M, Rackham OJ, Stahlhacke J, Sternberg MJ, Velankar S, Orengo C.

Nucleic Acids Res. 2015 Jan;43(Database issue):D382-6. doi: 10.1093/nar/gku973. Epub 2014 Oct 27.


Proteomic analysis of the Plasmodium male gamete reveals the key role for glycolysis in flagellar motility.

Talman AM, Prieto JH, Marques S, Ubaida-Mohien C, Lawniczak M, Wass MN, Xu T, Frank R, Ecker A, Stanway RS, Krishna S, Sternberg MJ, Christophides GK, Graham DR, Dinglasan RR, Yates JR 3rd, Sinden RE.

Malar J. 2014 Aug 13;13:315. doi: 10.1186/1475-2875-13-315.


SuSPect: enhanced prediction of single amino acid variant (SAV) phenotype using network features.

Yates CM, Filippis I, Kelley LA, Sternberg MJ.

J Mol Biol. 2014 Jul 15;426(14):2692-701. doi: 10.1016/j.jmb.2014.04.026. Epub 2014 May 5.


The effects of non-synonymous single nucleotide polymorphisms (nsSNPs) on protein-protein interactions.

Yates CM, Sternberg MJ.

J Mol Biol. 2013 Nov 1;425(21):3949-63. doi: 10.1016/j.jmb.2013.07.012. Epub 2013 Jul 15. Review.


AMBIENT: Active Modules for Bipartite Networks--using high-throughput transcriptomic data to dissect metabolic response.

Bryant WA, Sternberg MJ, Pinney JW.

BMC Syst Biol. 2013 Mar 25;7:26. doi: 10.1186/1752-0509-7-26.


Polyproline-II helix in proteins: structure and function.

Adzhubei AA, Sternberg MJ, Makarov AA.

J Mol Biol. 2013 Jun 26;425(12):2100-32. doi: 10.1016/j.jmb.2013.03.018. Epub 2013 Mar 16. Review.


Protein flexibility, not disorder, is intrinsic to molecular recognition.

Janin J, Sternberg MJ.

F1000 Biol Rep. 2013;5:2. doi: 10.3410/B5-2. Epub 2013 Jan 11.


Proteins and domains vary in their tolerance of non-synonymous single nucleotide polymorphisms (nsSNPs).

Yates CM, Sternberg MJ.

J Mol Biol. 2013 Apr 26;425(8):1274-86. doi: 10.1016/j.jmb.2013.01.026. Epub 2013 Jan 25.


A large-scale evaluation of computational protein function prediction.

Radivojac P, Clark WT, Oron TR, Schnoes AM, Wittkop T, Sokolov A, Graim K, Funk C, Verspoor K, Ben-Hur A, Pandey G, Yunes JM, Talwalkar AS, Repo S, Souza ML, Piovesan D, Casadio R, Wang Z, Cheng J, Fang H, Gough J, Koskinen P, Törönen P, Nokso-Koivisto J, Holm L, Cozzetto D, Buchan DW, Bryson K, Jones DT, Limaye B, Inamdar H, Datta A, Manjari SK, Joshi R, Chitale M, Kihara D, Lisewski AM, Erdin S, Venner E, Lichtarge O, Rentzsch R, Yang H, Romero AE, Bhat P, Paccanaro A, Hamp T, Kaßner R, Seemayer S, Vicedo E, Schaefer C, Achten D, Auer F, Boehm A, Braun T, Hecht M, Heron M, Hönigschmid P, Hopf TA, Kaufmann S, Kiening M, Krompass D, Landerer C, Mahlich Y, Roos M, Björne J, Salakoski T, Wong A, Shatkay H, Gatzmann F, Sommer I, Wass MN, Sternberg MJ, Škunca N, Supek F, Bošnjak M, Panov P, Džeroski S, Šmuc T, Kourmpetis YA, van Dijk AD, ter Braak CJ, Zhou Y, Gong Q, Dong X, Tian W, Falda M, Fontana P, Lavezzo E, Di Camillo B, Toppo S, Lan L, Djuric N, Guo Y, Vucetic S, Bairoch A, Linial M, Babbitt PC, Brenner SE, Orengo C, Rost B, Mooney SD, Friedberg I.

Nat Methods. 2013 Mar;10(3):221-7. doi: 10.1038/nmeth.2340. Epub 2013 Jan 27.


Functional assignment of Mycobacterium tuberculosis proteome revealed by genome-scale fold-recognition.

Mao C, Shukla M, Larrouy-Maumus G, Dix FL, Kelley LA, Sternberg MJ, Sobral BW, de Carvalho LP.

Tuberculosis (Edinb). 2013 Jan;93(1):40-6. doi: 10.1016/ Epub 2013 Jan 1. Review.


Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains.

Lewis TE, Sillitoe I, Andreeva A, Blundell TL, Buchan DW, Chothia C, Cuff A, Dana JM, Filippis I, Gough J, Hunter S, Jones DT, Kelley LA, Kleywegt GJ, Minneci F, Mitchell A, Murzin AG, Ochoa-Montaño B, Rackham OJ, Smith J, Sternberg MJ, Velankar S, Yeats C, Orengo C.

Nucleic Acids Res. 2013 Jan;41(Database issue):D499-507. doi: 10.1093/nar/gks1266. Epub 2012 Nov 30.


Gene function hypotheses for the Campylobacter jejuni glycome generated by a logic-based approach.

Sternberg MJ, Tamaddoni-Nezhad A, Lesk VI, Kay E, Hitchen PG, Cootes A, van Alphen LB, Lamoureux MP, Jarrell HC, Rawlings CJ, Soo EC, Szymanski CM, Dell A, Wren BW, Muggleton SH.

J Mol Biol. 2013 Jan 9;425(1):186-97. doi: 10.1016/j.jmb.2012.10.014. Epub 2012 Oct 24.


A new structural model of the acid-labile subunit: pathogenetic mechanisms of short stature-causing mutations.

David A, Kelley LA, Sternberg MJ.

J Mol Endocrinol. 2012 Oct 12;49(3):213-20. doi: 10.1530/JME-12-0086. Print 2012 Dec.


CombFunc: predicting protein function using heterogeneous data sources.

Wass MN, Barton G, Sternberg MJ.

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W466-70. doi: 10.1093/nar/gks489. Epub 2012 May 27.


PINALOG: a novel approach to align protein interaction networks--implications for complex detection and function prediction.

Phan HT, Sternberg MJ.

Bioinformatics. 2012 May 1;28(9):1239-45. doi: 10.1093/bioinformatics/bts119. Epub 2012 Mar 13.


Assessment of a rule-based virtual screening technology (INDDEx) on a benchmark data set.

Reynolds CR, Amini AC, Muggleton SH, Sternberg MJ.

J Phys Chem B. 2012 Jun 14;116(23):6732-9. doi: 10.1021/jp212084f. Epub 2012 Mar 28.


The Discovery of Novel 10,11-Dihydro-5H-dibenz[b,f]azepine SIRT2 Inhibitors.

Di Fruscia P, Ho KK, Laohasinnarong S, Khongkow M, Kroll SH, Islam SA, Sternberg MJ, Schmidtkunz K, Jung M, Lam EW, Fuchter MJ.

Medchemcomm. 2012 Mar 1;(3). doi: 10.1039/C2MD00290F.


Proteomic analysis of Plasmodium in the mosquito: progress and pitfalls.

Wass MN, Stanway R, Blagborough AM, Lal K, Prieto JH, Raine D, Sternberg MJ, Talman AM, Tomley F, Yates J 3rd, Sinden RE.

Parasitology. 2012 Aug;139(9):1131-45. doi: 10.1017/S0031182012000133. Epub 2012 Feb 16.


Protein-protein interaction sites are hot spots for disease-associated nonsynonymous SNPs.

David A, Razali R, Wass MN, Sternberg MJ.

Hum Mutat. 2012 Feb;33(2):359-63. doi: 10.1002/humu.21656. Epub 2011 Dec 27.


Genome-wide association study identifies loci influencing concentrations of liver enzymes in plasma.

Chambers JC, Zhang W, Sehmi J, Li X, Wass MN, Van der Harst P, Holm H, Sanna S, Kavousi M, Baumeister SE, Coin LJ, Deng G, Gieger C, Heard-Costa NL, Hottenga JJ, Kühnel B, Kumar V, Lagou V, Liang L, Luan J, Vidal PM, Mateo Leach I, O'Reilly PF, Peden JF, Rahmioglu N, Soininen P, Speliotes EK, Yuan X, Thorleifsson G, Alizadeh BZ, Atwood LD, Borecki IB, Brown MJ, Charoen P, Cucca F, Das D, de Geus EJ, Dixon AL, Döring A, Ehret G, Eyjolfsson GI, Farrall M, Forouhi NG, Friedrich N, Goessling W, Gudbjartsson DF, Harris TB, Hartikainen AL, Heath S, Hirschfield GM, Hofman A, Homuth G, Hyppönen E, Janssen HL, Johnson T, Kangas AJ, Kema IP, Kühn JP, Lai S, Lathrop M, Lerch MM, Li Y, Liang TJ, Lin JP, Loos RJ, Martin NG, Moffatt MF, Montgomery GW, Munroe PB, Musunuru K, Nakamura Y, O'Donnell CJ, Olafsson I, Penninx BW, Pouta A, Prins BP, Prokopenko I, Puls R, Ruokonen A, Savolainen MJ, Schlessinger D, Schouten JN, Seedorf U, Sen-Chowdhry S, Siminovitch KA, Smit JH, Spector TD, Tan W, Teslovich TM, Tukiainen T, Uitterlinden AG, Van der Klauw MM, Vasan RS, Wallace C, Wallaschofski H, Wichmann HE, Willemsen G, Würtz P, Xu C, Yerges-Armstrong LM; Alcohol Genome-wide Association (AlcGen) Consortium; Diabetes Genetics Replication and Meta-analyses (DIAGRAM+) Study; Genetic Investigation of Anthropometric Traits (GIANT) Consortium; Global Lipids Genetics Consortium; Genetics of Liver Disease (GOLD) Consortium; International Consortium for Blood Pressure (ICBP-GWAS); Meta-analyses of Glucose and Insulin-Related Traits Consortium (MAGIC), Abecasis GR, Ahmadi KR, Boomsma DI, Caulfield M, Cookson WO, van Duijn CM, Froguel P, Matsuda K, McCarthy MI, Meisinger C, Mooser V, Pietiläinen KH, Schumann G, Snieder H, Sternberg MJ, Stolk RP, Thomas HC, Thorsteinsdottir U, Uda M, Waeber G, Wareham NJ, Waterworth DM, Watkins H, Whitfield JB, Witteman JC, Wolffenbuttel BH, Fox CS, Ala-Korpela M, Stefansson K, Vollenweider P, Völzke H, Schadt EE, Scott J, Järvelin MR, Elliott P, Kooner JS.

Nat Genet. 2011 Oct 16;43(11):1131-8. doi: 10.1038/ng.970.


Functional significance of mutations in the Snf2 domain of ATRX.

Mitson M, Kelley LA, Sternberg MJ, Higgs DR, Gibbons RJ.

Hum Mol Genet. 2011 Jul 1;20(13):2603-10. doi: 10.1093/hmg/ddr163. Epub 2011 Apr 19.


Challenges for the prediction of macromolecular interactions.

Wass MN, David A, Sternberg MJ.

Curr Opin Struct Biol. 2011 Jun;21(3):382-90. doi: 10.1016/ Epub 2011 Apr 14. Review.


Systems analysis of bacterial glycomes.

Kay E, Lesk VI, Tamaddoni-Nezhad A, Hitchen PG, Dell A, Sternberg MJ, Muggleton S, Wren BW.

Biochem Soc Trans. 2010 Oct;38(5):1290-3. doi: 10.1042/BST0381290.


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