Imperial College London

ProfessorMichaelSternberg

Faculty of Natural SciencesDepartment of Life Sciences

Director Centre for Bioinformatics
 
 
 
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Contact

 

+44 (0)20 7594 5212m.sternberg Website

 
 
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Location

 

306Sir Ernst Chain BuildingSouth Kensington Campus

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Summary

 

Publications

Publication Type
Year
to

343 results found

Wass MN, Barton G, Sternberg MJE, 2012, CombFunc: predicting protein function using heterogeneous data sources, NUCLEIC ACIDS RESEARCH, Vol: 40, Pages: W466-W470, ISSN: 0305-1048

Journal article

Reynolds CR, Amini AC, Muggleton SH, Sternberg MJEet al., 2012, Assessment of a Rule-Based Virtual Screening Technology (INDDEx) on a Benchmark Data Set, JOURNAL OF PHYSICAL CHEMISTRY B, Vol: 116, Pages: 6732-6739, ISSN: 1520-6106

Journal article

Phan HTT, Sternberg MJE, 2012, PINALOG: a novel approach to align protein interaction networks-implications for complex detection and function prediction, BIOINFORMATICS, Vol: 28, Pages: 1239-1245, ISSN: 1367-4803

Journal article

David A, Razali R, Wass MN, Sternberg MJEet al., 2012, Protein-Protein Interaction Sites are Hot Spots for Disease-Associated Nonsynonymous SNPs, HUMAN MUTATION, Vol: 33, Pages: 359-363, ISSN: 1059-7794

Journal article

Di Fruscia P, Ho K-K, Laohasinnarong S, Khonghow M, Kroll SHB, Islam SA, Sternberg MJE, Schmidtkunz K, Jung M, Lam EW-F, Fuchter MJet al., 2012, The discovery of novel 10,11-dihydro-5H-dibenz[b,f]azepine SIRT2 inhibitors, MedChemComm

Journal article

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 J-J, Kuehnel B, Kumar V, Lagou V, Liang L, Luan J, Vidal PM, Leach IM, 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 EJC, Dixon AL, Doering A, Ehret G, Eyjolfsson GI, Farrall M, Forouhi NG, Friedrich N, Goessling W, Gudbjartsson DF, Harris TB, Hartikainen A-L, Heath S, Hirschfield GM, Hofman A, Homuth G, Hyppoenen E, Janssen HLA, Johnson T, Kangas AJ, Kema IP, Kuehn JP, Lai S, Lathrop M, Lerch MM, Li Y, Liang TJ, Lin J-P, Loos RJF, 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 JNL, 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 H-E, Willemsen G, Wuertz P, Xu C, Yerges-Armstrong LM, Abecasis GR, Ahmadi KR, Boomsma DI, Caulfield M, Cookson WO, van Duijn CM, Froguel P, Matsuda K, McCarthy MI, Meisinger C, Mooser V, Pietilainen KH, Schumann G, Snieder H, Sternberg MJE, Stolk RP, Thomas HC, Thorsteinsdottir U, Uda M, Waeber G, Wareham NJ, Waterworth DM, Watkins H, Whitfield JB, Witteman JCM, Wolffenbuttel BHR, Fox CS, Ala-Korpela M, Stefansson K, Vollenweider P, Voelzke H, Schadt EE, Scott J, Jarvelin M-R, Elliott P, Kooner JSet al., 2011, Genome-wide association study identifies loci influencing concentrations of liver enzymes in plasma, NATURE GENETICS, Vol: 43, Pages: 1131-1138, ISSN: 1061-4036

Journal article

Ehret GB, Munroe PB, Rice KM, Bochud M, Johnson AD, Chasman DI, Smith AV, Tobin MD, Verwoert GC, Hwang S-J, Pihur V, Vollenweider P, O'Reilly PF, Amin N, Bragg-Gresham JL, Teumer A, Glazer NL, Launer L, Zhao JH, Aulchenko Y, Heath S, Sober S, Parsa A, Luan J, Arora P, Dehghan A, Zhang F, Lucas G, Hicks AA, Jackson AU, Peden JF, Tanaka T, Wild SH, Rudan I, Igl W, Milaneschi Y, Parker AN, Fava C, Chambers JC, Fox ER, Kumari M, Go MJ, van der Harst P, Kao WHL, Sjogren M, Vinay DG, Alexander M, Tabara Y, Shaw-Hawkins S, Whincup PH, Liu Y, Shi G, Kuusisto J, Tayo B, Seielstad M, Sim X, Khanh-Dung HN, Lehtimaki T, Matullo G, Wu Y, Gaunt TR, Onland-Moret NC, Cooper MN, Platou CGP, Org E, Hardy R, Dahgam S, Palmen J, Vitart V, Braund PS, Kuznetsova T, Uiterwaal CSPM, Adeyemo A, Palmas W, Campbell H, Ludwig B, Tomaszewski M, Tzoulaki I, Palmer ND, Aspelund T, Garcia M, Chang Y-PC, O'Connell JR, Steinle NI, Grobbee DE, Arking DE, Kardia SL, Morrison AC, Hernandez D, Najjar S, McArdle WL, Hadley D, Brown MJ, Connell JM, Hingorani AD, Day INM, Lawlor DA, Beilby JP, Lawrence RW, Clarke R, Hopewell JC, Ongen H, Dreisbach AW, Li Y, Young JH, Bis JC, Kahonen M, Viikari J, Adair LS, Lee NR, Chen M-H, Olden M, Pattaro C, Bolton JAH, Koettgen A, Bergmann S, Mooser V, Chaturvedi N, Frayling TM, Islam M, Jafar TH, Erdmann J, Kulkarni SR, Bornstein SR, Graessler J, Groop L, Voight BF, Kettunen J, Howard P, Taylor A, Guarrera S, Ricceri F, Emilsson V, Plump A, Barroso IS, Khaw K-T, Weder AB, Hunt SC, Sun YV, Bergman RN, Collins FS, Bonnycastle LL, Scott LJ, Stringham HM, Peltonen L, Perola M, Vartiainen E, Brand S-M, Staessen JA, Wang TJ, Burton PR, Artigas MS, Dong Y, Snieder H, Wang X, Zhu H, Lohman KK, Rudock ME, Heckbert SR, Smith NL, Wiggins KL, Doumatey A, Shriner D, Veldre G, Viigimaa M, Kinra S, Prabhakaran D, Tripathy V, Langefeld CD, Rosengren A, Thelle DS, Corsi AM, Singleton A, Forrester T, Hilton G, McKenzie CA, Salako T, Iwai N, Kita Y, Ogihara T, Ohkubo T, Okamura T, Ueshimet al., 2011, Genetic variants in novel pathways influence blood pressure and cardiovascular disease risk, NATURE, Vol: 478, Pages: 103-109, ISSN: 0028-0836

Journal article

Mitson M, Kelley LA, Sternberg MJE, Higgs DR, Gibbons RJet al., 2011, Functional significance of mutations in the Snf2 domain of ATRX, HUMAN MOLECULAR GENETICS, Vol: 20, Pages: 2603-2610, ISSN: 0964-6906

Journal article

Wass MN, David A, Sternberg MJE, 2011, Challenges for the prediction of macromolecular interactions, CURRENT OPINION IN STRUCTURAL BIOLOGY, Vol: 21, Pages: 382-390, ISSN: 0959-440X

Journal article

Muggleton SH, Chen J, Watanabe H, Dunbar SJ, Baxter C, Currie R, Salazar JD, Taubert J, Sternberg MJEet al., 2011, Variation of Background Knowledge in an Industrial Application of ILP, 20th International Conference on Inductive Logic Programming (ILP), Publisher: SPRINGER-VERLAG BERLIN, Pages: 158-170, ISSN: 0302-9743

Conference paper

, 2010, Proceedings of the 4th Meeting on the Critical Assessment of Predicted Interaction (CAPRI), Barcelona, Spain., Proteins, Vol: 78, Pages: 3065-3249

Journal article

Fernandez-Recio J, Sternberg MJE, 2010, The 4th meeting on the Critical Assessment of PRedicted Interaction (CAPRI) held at the Mare Nostrum, Barcelona, PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, Vol: 78, Pages: 3065-3066, ISSN: 0887-3585

Journal article

Chubb D, Jefferys BR, Sternberg MJE, Kelley LAet al., 2010, Sequencing delivers diminishing returns for homology detection: implications for mapping the protein universe, BIOINFORMATICS, Vol: 26, Pages: 2664-2671, ISSN: 1367-4803

Journal article

Kay E, Lesk VI, Tamaddoni-Nezhad A, Hitchen PG, Dell A, Sternberg MJ, Muggleton S, Wren BWet al., 2010, Systems analysis of bacterial glycomes, BIOCHEMICAL SOCIETY TRANSACTIONS, Vol: 38, Pages: 1290-1293, ISSN: 0300-5127

Journal article

Lodhi H, Muggleton S, Sternberg MJE, 2010, Multi-class Mode of Action Classification of Toxic Compounds Using Logic Based Kernel Methods, MOLECULAR INFORMATICS, Vol: 29, Pages: 655-664, ISSN: 1868-1743

Journal article

Sinden RE, Talman A, Marques SR, Wass MN, Sternberg MJEet al., 2010, The flagellum in malarial parasites, CURRENT OPINION IN MICROBIOLOGY, Vol: 13, Pages: 491-500, ISSN: 1369-5274

Journal article

Wass MN, Kelley LA, Sternberg MJE, 2010, 3DLigandSite: predicting ligand-binding sites using similar structures, NUCLEIC ACIDS RESEARCH, Vol: 38, Pages: W469-W473, ISSN: 0305-1048

Journal article

Chambers JC, Zhang W, Lord GM, van der Harst P, Lawlor DA, Sehmi JS, Gale DP, Wass MN, Ahmadi KR, Bakker SJL, Beckmann J, Bilo HJG, Bochud M, Brown MJ, Caulfield MJ, Connell JMC, Cook HT, Cotlarciuc I, Smith GD, de Silva R, Deng G, Devuyst O, Dikkeschei LD, Dimkovic N, Dockrell M, Dominiczak A, Ebrahim S, Eggermann T, Farrall M, Ferrucci L, Floege J, Forouhi NG, Gansevoort RT, Han X, Hedblad B, van der Heide JJH, Hepkema BG, Hernandez-Fuentes M, Hypponen E, Johnson T, de Jong PE, Kleefstra N, Lagou V, Lapsley M, Li Y, Loos RJF, Luan J, Luttropp K, Marechal C, Melander O, Munroe PB, Nordfors L, Parsa A, Peltonen L, Penninx BW, Perucha E, Pouta A, Prokopenko I, Roderick PJ, Ruokonen A, Samani NJ, Sanna S, Schalling M, Schlessinger D, Schlieper G, Seelen MAJ, Shuldiner AR, Sjogren M, Smit JH, Snieder H, Soranzo N, Spector TD, Stenvinkel P, Sternberg MJE, Swaminathan R, Tanaka T, Ubink-Veltmaat LJ, Uda M, Vollenweider P, Wallace C, Waterworth D, Zerres K, Waeber G, Wareham NJ, Maxwell PH, McCarthy MI, Jarvelin M-R, Mooser V, Abecasis GR, Lightstone L, Scott J, Navis G, Elliott P, Kooner JSet al., 2010, Genetic loci influencing kidney function and chronic kidney disease, NATURE GENETICS, Vol: 42, Pages: 373-375, ISSN: 1061-4036

Journal article

Jefferys BR, Kelley LA, Sternberg MJE, 2010, Protein Folding Requires Crowd Control in a Simulated Cell, JOURNAL OF MOLECULAR BIOLOGY, Vol: 397, Pages: 1329-1338, ISSN: 0022-2836

Journal article

Chambers JC, Zhao J, Terracciano CMN, Bezzina CR, Zhang W, Kaba R, Navaratnarajah M, Lotlikar A, Sehmi JS, Kooner MK, Deng G, Siedlecka U, Parasramka S, El-Hamamsy I, Wass MN, Dekker LRC, de Jong JSSG, Sternberg MJE, McKenna W, Severs NJ, de Silva R, Wilde AAM, Anand P, Yacoub M, Scott J, Elliott P, Wood JN, Kooner JSet al., 2010, Genetic variation in SCN10A influences cardiac conduction, NATURE GENETICS, Vol: 42, Pages: 149-U80, ISSN: 1061-4036

Journal article

Hermoso A, Espadaler J, Enrique Querol E, Aviles FX, Sternberg MJE, Oliva B, Fernandez-Fuentes Net al., 2009, Including Functional Annotations and Extending the Collection of Structural Classifications of Protein Loops (ArchDB)., Bioinform Biol Insights, Vol: 1, Pages: 77-90

Loops represent an important part of protein structures. The study of loop is critical for two main reasons: First, loops are often involved in protein function, stability and folding. Second, despite improvements in experimental and computational structure prediction methods, modeling the conformation of loops remains problematic. Here, we present a structural classification of loops, ArchDB, a mine of information with application in both mentioned fields: loop structure prediction and function prediction. ArchDB (http://sbi.imim.es/archdb) is a database of classified protein loop motifs. The current database provides four different classification sets tailored for different purposes. ArchDB-40, a loop classification derived from SCOP40, well suited for modeling common loop motifs. Since features relevant to loop structure or function can be more easily determined on well-populated clusters, we have developed ArchDB-95, a loop classification derived from SCOP95. This new classification set shows a ~40% increase in the number of subclasses, and a large 7-fold increase in the number of putative structure/function-related subclasses. We also present ArchDB-EC, a classification of loop motifs from enzymes, and ArchDB-KI, a manually annotated classification of loop motifs from kinases. Information about ligand contacts and PDB sites has been included in all classification sets. Improvements in our classification scheme are described, as well as several new database features, such as the ability to query by conserved annotations, sequence similarity, or uploading 3D coordinates of a protein. The lengths of classified loops range between 0 and 36 residues long. ArchDB offers an exhaustive sampling of loop structures. Functional information about loops and links with related biological databases are also provided. All this information and the possibility to browse/query the database through a web-server outline an useful tool with application in the comparative study of lo

Journal article

Lodhi H, Muggleton S, Sternberg MJE, 2009, Multi-class protein fold recognition using large margin logic based divide and conquer learning, Pages: 22-26

Inductive Logic Programming (ILP) systems have been successfully applied to solve complex biological problem by viewing them as binary classification tasks. It remains an open question how an accurate solution to a multi-class problem can be obtained by using a logic based learning method. In this paper we present a novel logic based approach to solve complex and challenging multi-class classification problems in bioinformatics by focusing on a particular task, namely protein fold recognition. Our technique is based on the use of large margin kernel-based methods in conjunction with first order rules induced by an ILP system. The proposed approach learns a multi-class classifier by using a divide and conquer reduction strategy that splits multi-classes into binary groups and solves each individual problem recursively hence generating an underlying decision list structure. The method is applied to assigning protein domains to folds. Experimental evaluation of the method demonstrates the efficacy of the proposed approach to solving complex multi-class classification problems in bioinformatics. © 2009 ACM.

Conference paper

Chambers JC, Zhang W, Li Y, Sehmi J, Wass MN, Zabaneh D, Hoggart C, Bayele H, McCarthy MI, Peltonen L, Freimer NB, Srai SK, Maxwell PH, Sternberg MJE, Ruokonen A, Abecasis G, Jarvelin M-R, Scott J, Elliott P, Kooner JSet al., 2009, Genome-wide association study identifies variants in TMPRSS6 associated with hemoglobin levels, NATURE GENETICS, Vol: 41, Pages: 1170-1172, ISSN: 1061-4036

Journal article

Kelley LA, Shrimpton PJ, Muggleton SH, Sternberg MJEet al., 2009, Discovering rules for protein-ligand specificity using support vector inductive logic programming, PROTEIN ENGINEERING DESIGN & SELECTION, Vol: 22, Pages: 561-567, ISSN: 1741-0126

Journal article

Laskowski RA, Thornton JM, Sternberg MJE, 2009, The fine details of evolution, BIOCHEMICAL SOCIETY TRANSACTIONS, Vol: 37, Pages: 723-726, ISSN: 0300-5127

Journal article

Sternberg M, Thornton J, Laskowski R, 2009, Protein evolution - Sequence, structure and systems, Pages: 52-52, ISSN: 0954-982X

Conference paper

Kelley LA, Sternberg MJE, 2009, Protein structure prediction on the Web: a case study using the Phyre server, NATURE PROTOCOLS, Vol: 4, Pages: 363-371, ISSN: 1754-2189

Journal article

Lodhi H, Muggleton S, Sternberg MJE, 2009, Learning Large Margin First Order Decision Lists for Multi-Class Classification, 12th International Conference on Discovery Science, Publisher: SPRINGER-VERLAG BERLIN, Pages: 168-+, ISSN: 0302-9743

Conference paper

Wass MN, Sternberg MJE, 2009, Prediction of ligand binding sites using homologous structures and conservation at CASP8, PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, Vol: 77, Pages: 147-151, ISSN: 0887-3585

Journal article

Barton G, Abbott J, Chiba N, Huang DW, Huang Y, Krznaric M, Mack Smith J, Saleem A, Sherman BT, Tiwari B, Tomlinson CD, Aitman T, Darlington J, Game L, Sternberg MJE, Butcher Set al., 2008, EMAAS: An extensible grid-based Rich Internet Application for microarray data analysis and management, BMC Bioinformatics, Vol: 9, ISSN: 1471-2105

BackgroundMicroarray experimentation requires the application of complex analysis methods as well as the use of non-trivial computer technologies to manage the resultant large data sets. This, together with the proliferation of tools and techniques for microarray data analysis, makes it very challenging for a laboratory scientist to keep up-to-date with the latest developments in this field. Our aim was to develop a distributed e-support system for microarray data analysis and management.ResultsEMAAS (Extensible MicroArray Analysis System) is a multi-user rich internet application (RIA) providing simple, robust access to up-to-date resources for microarray data storage and analysis, combined with integrated tools to optimise real time user support and training. The system leverages the power of distributed computing to perform microarray analyses, and provides seamless access to resources located at various remote facilities. The EMAAS framework allows users to import microarray data from several sources to an underlying database, to pre-process, quality assess and analyse the data, to perform functional analyses, and to track data analysis steps, all through a single easy to use web portal. This interface offers distance support to users both in the form of video tutorials and via live screen feeds using the web conferencing tool EVO. A number of analysis packages, including R-Bioconductor and Affymetrix Power Tools have been integrated on the server side and are available programmatically through the Postgres-PLR library or on grid compute clusters. Integrated distributed resources include the functional annotation tool DAVID, GeneCards and the microarray data repositories GEO, CELSIUS and MiMiR. EMAAS currently supports analysis of Affymetrix 3' and Exon expression arrays, and the system is extensible to cater for other microarray and transcriptomic platforms.ConclusionEMAAS enables users to track and perform microarray data management and analysis tasks through

Journal article

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