Publications for 2013

2013

Protein Data Resources
Furnham, Nicholas, Garavelli John S., and Thornton Janet M.
Encyclopedia of Biological Chemistry. Volume 3, (2013), p.611-617
The Ramachandran plot and protein structure validation
Laskowski, Roman A., Furnham Nicholas, and Thornton Janet M.
Biomolecular Forms and Functions, A Celebration of 50 years of the Ramachandran Map. (2013), p.62-75
IPD—the Immuno Polymorphism Database
Robinson, James, Halliwell Jason A., McWilliam Hamish, Lopez Rodrigo, and Marsh Steven G. E.
Nucleic acids research. Volume 41, Number D1, (2013), p.D1234–D1240 doi:
Detecting regulatory gene–environment interactions with unmeasured environmental factors
Fusi, Nicoló, Lippert Christoph, Borgwardt Karsten, Lawrence Neil D., and Stegle Oliver
Bioinformatics. (2013),
Proteomics data exchange and storage: the need for common standards and public repositories
Jimenez, R. C., and Vizcaino J. A.
Methods Mol Biol. Volume 1007, (2013), p.317-33
Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains
Lewis, T. E., Sillitoe I., Andreeva A., Blundell T. L., Buchan D. W. A., Chothia C., Cuff A., DANA J. M., Filippis I., Gough J., et al.
Nucleic Acids Research. Volume 41, Number D1, (2013), p.D499–D507
ArrayExpress update—trends in database growth and links to data analysis tools
RUSTICI, G., KOLESNIKOV N., BRANDIZI M., BURDETT T., DYLAG M., EMAM I., FARNE A., HASTINGS E., ISON J., KEAYS M., et al.
Nucleic acids research. Volume 41, Number D1, (2013), p.D987–D990
Bridging the layers: towards integration of signal transduction, regulation and metabolism into mathematical models
GONCALVES, E., Bucher J., Ryll A., Niklas J., Mauch K., Klamt S., Rocha M., and SAEZ-RODRIGUEZ J.
Molecular bioSystems. Mar 25, Volume Article in press, (2013),
The role of structural bioinformatics resources in the era of integrative structural biology
GUTMANAS, A., Oldfield T. J., PATWARDHAN A., SEN S., VELANKAR S., and KLEYWEGT G. J.
Acta Crystallographica Section D. Number D69, (2013), p.710-721 doi: 10.1107/S0907444913001157
Report of the wwPDB Small-Angle Scattering Task Force: Data Requirements for Biomolecular Modeling and the PDB
Trewhella, J., Henrickson W. A., KLEYWEGT G. J., Sali A., Sato M., Schwede T., Svergun D. I., Tainer J. A., Westbrook J., and Berman H. M.
Structure. Volume 21, Number Issue 6, (2013), p.875-881 doi: 10.1016/j.str.2013.04.020
Analysing variation in Drosophila aging across independent experimental studies: a meta-analysis of survival data
Ziehm, Matthias, Piper Matthew D., and Thornton Janet M.
Aging Cell. (2013), doi: 10.1111/acel.12123
Inferring hierarchical orthologous groups from orthologous gene pairs
Altenhoff, A. M., Gil M., Gonnet G. H., and Dessimoz C.
PLoS ONE. Volume 8, (2013), p.e53786
Use of Gene Ontology Annotation to understand the peroxisome proteome in humans
Mutowo-Meullenet, P., HUNTLEY R. P., DIMMER E. C., ALAM-FARUQUE Y., SAWFORD T., Martin M. J., O’DONOVAN C., and Apweiler R.
Database: The Journal of Biological Databases and Curation. Volume 2013, (2013), doi:
IPD—the Immuno Polymorphism Database
Robinson, J., Halliwell J. A., McWilliam H., Lopez R., and Marsh S. G. E.
Nucleic acids research. Volume 41, Number D1, (2013), p.D1234–D1240
ArrayExpress update - trends in database growth and links to data analysis tools
Rustici, G, Kolesnikov N, Brandizi M, Burdett T, Dylag M, Emam I, Farne A, Hastings E, Ison J, Keays M, et al.
Nucleic acids research. Volume 41, Number D1, (2013), p.D987–D990 doi:
Evaluation of methods for modeling transcription factor sequence specificity
Weirauch, M. T., Cote A., Norel R., Annala M., Zhao Y., Riley T. R., SAEZ-RODRIGUEZ J., COKELAER T., Vedenko A., Talukder S., et al.
Nature biotechnology. Jan 27, Volume 31, Number 2, (2013), p.126-134
The mzQuantML data standard for mass spectrometry-based quantitative studies in proteomics
Walzer, M., Qi D., Mayer G., Uszkoreit J., Eisenacher M., Sachsenberg T., Gonzalez-Galarza F. F., Fan J., Bessant C., Deutsch E. W., et al.
Mol Cell Proteomics. (2013),
Multiple Epigenetic Mechanisms and the piRNA Pathway Enforce LINE1 Silencing during Adult Spermatogenesis
Di Giacomo, Monica, Comazzetto Stefano, Saini Harpreet, De Fazio Serena, Carrieri Claudia, Morgan Marcos, Vasiliauskaite Lina, Benes Vladimir, Enright Anton J., and O’Carroll Dónal
Molecular cell. Volume 50, (2013), p.601–608 doi:
The MetaboLights repository: curation challenges in metabolomics
Salek, Reza M., Haug Kenneth, Conesa Pablo, Hastings Janna, Williams Mark, Mahendraker Tejasvi, Maguire Eamonn, Gonzalez-Beltran Alejandra N., Rocca-Sera Phillippe, Sansone Susanna-Assunta, et al.
Database: The Journal of Biological Databases and Curation. Volume 2013, (2013), doi: 10.1093/database/bat029
Enhanced susceptibility to Citrobacter rodentium infection in miR-155-deficient mice
Clare, S., John V., Walker A. W., Hill J. L., ABREU-GOODGER C., Hale C., Goulding D., Lawley T. D., Mastroeni P., Frankel G., et al.
Infection and Immunity. (2013), doi:
Ensembl 2013.
Flicek, Paul, Ahmed Ikhlak, Amode Ridwan M., Barrell Daniel, Beal Kathryn, Brent Simon, Carvalho-Silva Denise, Clapham Peter, Coates Guy, Fairley Susan, et al.
Nucleic Acids Res. 1, Volume 41, Number D1, (2013), England, p.D48-55 doi: 10.1093/nar/gks1236
Facing growth in the European Nucleotide Archive
Cochrane, Guy, Alako Blaise, Amid Clara, Bower Lawrence, Cerdeño-Tárraga Ana, Cleland Iain, Gibson Richard, Goodgame Neil, Jang Mikyung, Kay Simon, et al.
Nucleic acids research. Volume 41, Number D1, (2013), p.D30–D35
Accurate detection of differential RNA processing
Drewe, Philipp, Stegle Oliver, Hartmann Lisa, Kahles André, Bohnert Regina, Wachter Andreas, Borgwardt Karsten, and Rätsch Gunnar
Nucleic acids research. (2013),
Shorthand notation for lipid structures derived from mass spectrometry
Liebisch, G., Vizcaino J. A., Kofeler H., Trotzmuller M., Griffiths W. J., Schmitz G., Spener F., and Wakelam M. J.
J Lipid Res. Volume 54, Number 6, (2013), p.1523-30
The EBI enzyme portal.
Alcántara, Rafael, Onwubiko Joseph, Cao Hong, de Matos Paula, Cham Jennifer A., Jacobsen Jules, Holliday Gemma L., Fischer Julia D., Rahman Syed Asad, Jassal Bijay, et al.
Nucleic Acids Res. Jan, Volume 41, Number Database issue, (2013), p.D773–D780 doi: 10.1093/nar/gks1112
Accounting for technical noise in single-cell RNA-seq experiments
Brennecke, P, Anders S, Kim JK, Kołodziejczyk AA, Zhang X, Proserpio V, Baying B, Benes V, Teichmann SA, Marioni JC, et al.
Nature Methods. (2013), p.- doi: 10.1038/nmeth.2645
The International Nucleotide Sequence Database Collaboration
Nakamura, Y., Cochrane G., Karsch-mizrachi I., and on behalf of the Collaboration International Nucleotide Sequence Database
Nucleic Acids Res. Volume 41, Number D1, (2013), p.D21-D24 doi:
Vivaldi: visualisation and validation of biomacromolecular NMR structures from the PDB
Hendrickx, P. M. S., GUTMANAS A., and KLEYWEGT G. J.
Proteins. Volume 81, (2013), p.583-591 doi: 10.1002/prot.24213
Critical assessment of automated flow cytometry data analysis techniques
Aghaeepour, N., Finak G., Consortium FlowCAP, Dougall D., Khodabakhshi A. H., Mah P., Obermoser G., Spidlen J., Taylor I., Wuensch S. A., et al.
Nature methods. Mar, Volume 10, Number 3, (2013), p.228-238
BioJS: an open source JavaScript framework for biological data visualization
Gómez, J., García L. J., Salazar G. A., Villaveces J., GORE S., Garcia A., Martin M. J., Launay G., ALCANTARA R., del-Toro N., et al.
Bioinformatics. Volume 29, Issue 8, (2013), p.1103-1104 doi: 10.1093/bioinformatics/btt100
From Peptidome to PRIDE: Public proteomics data migration at a large scale
Csordas, A., Wang R., Rios D., Reisinger F., Foster J. M., Slotta D. J., Vizcaino J. A., and Hermjakob H.
Proteomics. Volume 13, Number 10-11, (2013), p.1692-5 doi:
New functional families (FunFams) in CATH to improve the mapping of conserved functional sites to 3D structures.
Sillitoe, Ian, Cuff Alison L., Dessailly Benoit H., Dawson Natalie L., Furnham Nicholas, Lee David, Lees Jonathan G., Lewis Tony E., Studer Romain A., Rentzsch Robert, et al.
Nucleic Acids Res. Jan, Volume 41, Number Database issue, (2013), p.D490–D498 doi: 10.1093/nar/gks1211
The EBI enzyme portal
Alcántara, R., ONWUBIKO J., CAO H., De Matos P., Cham J. A., JACOBSEN J., HOLLIDAY G. L., FISCHER J. D., RAHMAN S. A., Jassal B., et al.
Nucleic Acids Research. Volume 41, Number D1, (2013), p.D773–D780
A Palaeolithic-type diet causes strong tissue-specific effects on ectopic fat deposition in obese postmenopausal women
Ryberg, M., Sandberg S., Mellberg C., Stegle O., Lindahl B., Larsson C., Hauksson J., and Olsson T.
Journal of Internal Medicine. (2013),
The EBI enzyme portal
Alcántara, R., ONWUBIKO J., CAO H., De Matos P., Cham J. A., JACOBSEN J., HOLLIDAY G. L., FISCHER J. D., RAHMAN S. A., Jassal B., et al.
Nucleic acids research. Volume 41, Number D1, (2013), p.D773–D780 doi:
HAMAP in 2013, new developments in the protein family classification and annotation system
Pedruzzi, I., Rivoire C., Auchincloss A. H., Coudert E., Keller G., de Castro E., Baratin D., Cuche B. A., Bougueleret L., Poux S., et al.
Nucleic Acids Research. Volume 41, Number D1, (2013), p.D584–D589
DvD: An R/Cytoscape pipeline for drug repurposing using public repositories of gene expression data
PACINI, C., IORIO F., GONCALVES E., Iskar M., Klabunde T., Bork P., and SAEZ-RODRIGUEZ J.
Bioinformatics (Oxford, England). Nov 4, Volume 29, Number 1, (2013), p.132-134
Analysis Tool Web Services from the EMBL-EBI
McWilliam, Hamish, Li Weizhong, Uludag Mahmut, Squizzato Silvano, Park Young Mi, Buso Nicola, Cowley Andrew Peter, and Lopez Rodrigo
Nucleic acids research. (2013), doi: 10.1093/nar/gkt376
LIN28 expression in malignant germ cell tumors down-regulates let-7 and increases oncogene levels.
Murray, Matthew J., Saini Harpreet K., Siegler Charlotte A., Hanning Jennifer E., Barker Emily M., van Dongen Stijn, Ward Dawn M., Raby Katie L., Groves Ian J., Scarpini Cinzia G., et al.
Cancer research. Volume 73, Issue 14, (2013), doi: 10.1158/0008-5472.CAN-12-2085
Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology.
Hill, David P., Adams Nico, Bada Mike, Batchelor Colin, Berardini Tanya Z., Dietze Heiko, Drabkin Harold J., Ennis Marcus, Foulger Rebecca E., Harris Midori A., et al.
BMC Genomics. Volume 14, (2013), p.513 doi: 10.1186/1471-2164-14-513
Ensembl 2013
Flicek, P., AHMED I., Amode M. R., Barrell D., Beal K., Brent S., Carvalho-Silva D., Clapham P., Coates G., Fairley S., et al.
Nucleic Acids Research. Volume 41, Number D1, (2013), p.D48–D55
Latent Regulatory Potential of Human-Specific Repetitive Elements
Ward, Michelle C, Wilson Michael D, Barbosa-Morais Nuno L, Schmidt Dominic, Stark Rory, Pan Qun, Schwalie Petra C, Menon Suraj, Lukk Margus, Watt Stephen, et al.
Molecular Cell. Volume 49, Number 2, (2013), p.262 - 272 doi: 10.1016/j.molcel.2012.11.013
The EBI enzyme portal
Alcantara, Rafael, Onwubiko Joseph, Cao Hong, De Matos Paula, Cham Jennifer A., Jacobsen Jules, Holliday Gemma L., Fischer Julia D., Rahman Syed Asad, Jassal Bijay, et al.
Nucleic acids research. Volume 41, Number D1, (2013), p.D773–D780
The zebrafish reference genome sequence and its relationship to the human genome
Howe, K., Clark M. D., Torroja C. F., Torrance J., Berthelot C., Muffato M., Collins J. E., Humphray S., McLaren K., Matthews L., et al.
Nature. Apr, Volume 496, (2013), p.498–503 doi:
Controlled vocabularies and ontologies in proteomics: Overview, principles and practice
Mayer, G., Jones A. R., Binz P. A., Deutsch E. W., Orchard S., Montecchi-Palazzi L., Vizcaino J. A., Hermjakob H., Oveillero D., Julian R., et al.
Biochim Biophys Acta. (2013),
bioWeb3D: an online webGL 3D data visualisation tool
Pettit, JB, and Marioni JC
BMC Bioinformatics. Volume 14, (2013), p.185 doi: 10.1186/1471-2105-14-185
Transcriptome and genome sequencing uncovers functional variation in humans
Lappalainen, Tuuli, Sammeth Michael, Friedländer Marc R., Hoen Peter A. C. ‘t, Monlong Jean, Rivas Manuel A., Gonzàlez-Porta Mar, Kurbatova Natalja, Griebel Thasso, Ferreira Pedro G., et al.
Nature. (2013),
Facing growth in the European Nucleotide Archive
Cochrane, G., Alako B., Amid C., Bower L., Cerdeno-Tárraga A., Cleland I., Gibson R., Goodgame N., Jang M., Kay S., et al.
Nucleic Acids Res. Volume 41, Number D1, (2013), p.D30-5 doi:
The Future of the Protein Data Bank
Berman, H. M., KLEYWEGT G. J., Nakamura H., and Markley J. L.
Biopolymers. Volume 99, Issue Number 3, (2013), p.218-222 doi: 10.1002/bip.22132
EDAM: An ontology of bioinformatics operations, types of data and identifiers, topics, and formats
Ison, Jon, Kalaš Matúš, Jonassen Inge, Bolser Dan, Uludag Mahmut, McWilliam Hamish, Malone James, Lopez Rodrigo, Pettifer Steve, and Rice Peter
Bioinformatics. (2013), doi:
UniChem: a unified chemical structure cross-referencing and identifier tracking system
CHAMBERS, J., DAVIES M., GAULTON A., HERSEY A., VELANKAR S., Petryszak R., HASTINGS J., Bellis L., MCGLINCHEY S., and OVERINGTON J. P.
Journal of Cheminformatics. Volume 5, (2013), p.3 doi: 10.1186/1758-2946-5-3
LipidHome: A Database of Theoretical Lipids Optimized for High Throughput Mass Spectrometry Lipidomics
Foster, J. M., Moreno P., Fabregat A., Hermjakob H., Steinbeck C., Apweiler R., Wakelam M. J., and Vizcaino J. A.
PLoS One. Volume 8, Number 5, (2013), p.e61951
Genome of Acanthamoeba castellanii highlights extensive lateral gene transfer and early evolution of tyrosine kinase signaling
Clarke, M., Lohan A. J., Liu B., Lagkouvardos I., Roy S., Zafar N., Bertelli C., Schilde C., Kianianmomeni A., Burglin T. R., et al.
Genome Biology. Volume 14, Number 2, (2013), p.R11
A Lasso multi-marker mixed model for association mapping with population structure correction
Rakitsch, B., Lippert C., Stegle O., and Borgwardt K.
Bioinformatics. Volume 29, Number 2, (2013), p.206–214
Metingear: A development environment for annotating genome-scale metabolic models
May, J. W., G James, and Steinbeck C.
Bioinformatics. Volume 29, Issue 17, (2013), p.2215 doi:
The EBI enzyme portal
Alcántara, R., Onwubiko J., Cao H., De Matos P., Cham J.A., Jacobsen J., Holliday G.L., Fischer J.D., Rahman S.A., Jassal B., et al.
Nucleic Acids Research. Volume 41, Number D1, (2013), p.D773–D780 doi:
Construction of cell type-specific logic models of signaling networks using CellNOpt
Morris, M. K., MELAS I., and SAEZ-RODRIGUEZ J.
Methods in molecular biology (Clifton, N.J.). Volume 930, (2013), p.179-214
SIFTS: Structure Integration with Function, Taxonomy and Sequences resource
VELANKAR, S., DANA J. M., JACOBSEN J., GINKEL VAN G., Gane P. J., LUO J., Oldfield T. J., O'Donovan C., Martin M. J., and KLEYWEGT G. J.
Nucleic Acids Research. Volume 41, Number D1, (2013), p.D483-D489 doi: 10.1093/nar/gks1258
Kraken: A set of tools for quality control and analysis of high-throughput sequence data
Davis, Matthew, van Dongen Stijn, Abreu-Goodger Cei, Bartonicek Nenad, and Enright Anton J.
Methods. (2013), doi:
Dissemination of metabolomics results: role of MetaboLights and COSMOS.
Salek, Reza M., Haug Kenneth, and Steinbeck Christoph
GigaScience. Volume 2, Number 1, (2013), p.8 doi: 10.1186/2047-217X-2-8
Factorbook. org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium
Wang, J., Zhuang J., Iyer S., Lin X. Y., Greven M. C., Kim B. H., Moore J., Pierce B. G., Dong X., Virgil D., et al.
Nucleic Acids Research. Volume 41, Number D1, (2013), p.D171–D176
Structural and Evolutionary Dynamics Facilitate Ordered Protein Complex Assembly
Marsh, J. A., Hernández H., Hall Z., Ahnert S. E., Perica T., Robinson C. V., and Teichmann S. A.
Biophysical Journal. Volume 104, Number 2, (2013), p.391a
The Enzyme Portal: A case study in applying user-centred design methods in bioinformatics
De Matos, Paula, Cham Jennifer A., Cao Hong, Alcantara Rafael, Rowland Francis, Lopez Rodrigo, and Steinbeck Christoph
BMC Bioinformatics. Volume 14, Number 1, (2013), p.103 doi: 10.1186/1471-2105-14-103
Lack of correlation between predicted and actual off-target effects of short-interfering RNAs targeting the human papillomavirus type 16 E7 oncogene
Hanning, JE, Saini HK, Murray MJ, van Dongen S, Davis MPA, Barker EM, Ward DM, Scarpini CG, Enright AJ, Pett MR, et al.
British journal of cancer. Volume 108, (2013), p.450–460 doi:
HI-bone: a scoring system for identifying phenylisothiocyanate-derivatized peptides based on precursor mass and high intensity fragment ions
Perez-Riverol, Y., Sanchez A., Noda J., Borges D., Carvalho P. C., Wang R., Vizcaino J. A., Betancourt L., Ramos Y., Duarte G., et al.
Anal Chem. Volume 85, Number 7, (2013), p.3515-20
Peroxiredoxin-3 is overexpressed in prostate cancer and promotes cancer cell survival by protecting cells from oxidative stress
Whitaker, HC, Patel D, Howat WJ, Warren AY, Kay JD, Sangan T, Marioni JC, Mitchell J, Aldridge S, Luxton HJ, et al.
British Journal of Cancer. (2013), doi: 10.1038/bjc.2013.396
Genotype-Environment Interactions Reveal Causal Pathways That Mediate Genetic Effects on Phenotype
Gagneur, Julien, Stegle Oliver, Zhu Chenchen, Jakob Petra, Tekkedil Manu M., Aiyar Raeka S., Schuon Ann-Kathrin, Pe'er Dana, and Steinmetz Lars M.
PLOS Genetics. Volume 9, Number 9, (2013), p.e1003803
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
Bradnam, K. R., Fass J. N., Alexandrov A., Baranay P., Bechner M., Birol İ., Boisvert10 S., Chapman J. A., Chapuis G., Chikhi R., et al.
arXiv preprint arXiv:1301.5406. (2013), doi:
dbVar and DGVa: public archives for genomic structural variation.
Lappalainen, Ilkka, Lopez John, Skipper Lisa, Hefferon Timothy, Spalding Dylan J., Garner John, Chen Chao, Maguire Michael, Corbett Matt, Zhou George, et al.
Nucleic Acids Res. 1, Volume 41, Number D1, (2013), England, p.D936-41 doi: 10.1093/nar/gks1213
The Annotation-enriched non-redundant patent sequence databases
Li, Weizhong, Kondratowicz Bartosz, McWilliam Hamish, Nauche Stephane, and Lopez Rodrigo
Database: the journal of biological databases and curation. Volume 2013, (2013),
Crystal structure of the entire respiratory complex I
Baradaran, R., Berrisford J. M., Minhas G. S., and Sazanov L. A.
Nature. Volume 494, Number Issue 7438, (2013), p.443-448 doi: 10.1038/nature11871
PRIDE Cluster: building a consensus of proteomics data
Griss, J., Foster J. M., Hermjakob H., and Vizcaino J. A.
Nat Methods. Volume 10, Number 2, (2013), p.95-6
Transcriptional feedback in the Insulin Signalling Pathway modulates ageing in both Caenorhabditis elegans and Drosophila melanogaster
Ivanov, Dobril K., Papatheodorou Irene, Ziehm Matthias, and Thornton Janet M.
Mol. BioSyst.. (2013), p.1756–1764 doi: 10.1039/C3MB25485B
Rfam 11.0: 10 years of RNA families
Burge, S. W., Daub J., EBERHARDT R., Tate J., Barquist L., Nawrocki E. P., Eddy S. R., Gardner P. P., and Bateman A.
Nucleic Acids Research. Volume 41, Number D1, (2013), p.D226–D232
Inferring the kinetics of stochastic gene expression from single-cell RNA-sequencing data.
Kim, JK, and Marioni JC
Genome Biology. Volume 14, Number 1, (2013), p.R7 doi: doi:10.1186/gb-2013-14-1-r7
LipidHome: A Database of Theoretical Lipids Optimized for High Throughput Mass Spectrometry Lipidomics
Foster, Joseph M., Moreno Pablo, Fabregat Antonio, Hermjakob Henning, Steinbeck Christoph, Apweiler Rolf, Wakelam Michael J. O., and Vizcano Juan Antonio
PLoS ONE. Volume 8, Issue 5, (2013), doi:
SIFTS: Structure Integration with Function, Taxonomy and Sequences resource
Velankar, S., Dana J.M., Jacobsen J., van Ginkel G., Gane P. J., Luo J., Oldfield T. J., O’Donovan C., Martin M. J., and Kleywegt G.J.
Nucleic Acids Research. Volume 41, Number D1, (2013), p.D483–D489 doi:
Transcriptional data: a new gateway to drug repositioning?
IORIO, F., Rittman T., Ge H., MENDEN M., and SAEZ-RODRIGUEZ J.
Drug discovery today. Aug 7, Volume 18, Number 7-8, (2013), p.350-357
Cryo-electron microscopy: a primer for the non-microscopist
Milne, J. L., Borgnia M. J., Bartesaghi A., Tran E. E., Earl L. A., Schauder D. M., Lengyel J., Pierson J., PATWARDHAN A., and Subramaniam S.
FEBS Journal. Volume 280, Number 1, (2013), p.28-45 doi: 10.1111/febs.12078
Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation
Swaney, Danielle L., Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J., and Villén Judit
Nature Methods. (2013), doi: 10.1038/nmeth.2519
BioJS: an open source JavaScript framework for biological data visualization.
Gómez, John, García Leyla J., Salazar Gustavo A., Villaveces Jose, Gore Swanand, García Alexander, Martín Maria J., Launay Guillaume, Alcantara Rafael, Del-Toro Noemi, et al.
Bioinformatics. Volume 29, Number 8, (2013), p.1103–1104 doi: 10.1093/bioinformatics/btt100
Approximate Bayesian computation
Sunnåker, M., Busetto A. G., Numminen E., Corander J., Foll M., and Dessimoz C.
PLoS Computational Biology. Volume 9, (2013), p.e1002803
Gene Expression Genomics
Teichmann, S. A.
Biophysical Journal. Volume 104, Number 2, (2013), p.534a
Towards practical, high-capacity, low-maintenance information storage in synthesized DNA
Goldman, N., Bertone P., Chen S., Dessimoz C., LeProust E.M., Sipos B., and Birney E.
Nature. Jan, Volume 494, Number 7435, (2013), p.77–80
A decadal view of biodiversity informatics: challenges and priorities
A., Hardisty, D. Roberts, and Biodiversity Informatics Community
BMC Ecology. Volume 13, (2013), doi:
Open source libraries and frameworks for mass spectrometry based proteomics: A developer's perspective
Perez-Riverol, Y., Wang R., Hermjakob H., Müller M., Vesada V., and Vizcaino J. A.
Biochim Biophys Acta. (2013),
Cooperativity and Rapid Evolution of Cobound Transcription Factors in Closely Related Mammals
Stefflova, K, Thybert D, Wilson MD, Streeter I, Aleksic J, Karagianni P, Brazma A, Adams DJ, Talianidis I, Marioni JC, et al.
Cell. Volume 154, (2013), p.530 doi: 10.1016/j.cell.2013.07.007
Machine learning prediction of cancer cell sensitivity to drugs based on genomic and chemical properties
MENDEN, M. P., IORIO F., Garnett M., Mcdermott U., Benes C. H., BALLESTER P. J., and SAEZ-RODRIGUEZ J.
PloS one. Apr 30, Volume 8, Number 4, (2013), p.e61318
The Annotation-enriched non-redundant patent sequence databases
Li, W., Kondratowicz B., McWilliam H., Nauche S., and Lopez R.
Database: The Journal of Biological Databases and Curation. Volume 2013, (2013), doi:
Genomicus: five genome browsers for comparative genomics in eukaryota.
Louis, Alexandra, Muffato Matthieu, and Roest Crollius Hugues
Nucleic Acids Res. 1, Volume 41, Number D1, (2013), England, p.D700-5 doi: 10.1093/nar/gks1156
The IMGT/HLA database
Robinson, James, Halliwell Jason A., McWilliam Hamish, Lopez Rodrigo, Parham Peter, and Marsh Steven G. E.
Nucleic acids research. Volume 41, Number D1, (2013), p.D1222–D1227 doi:
The EBI enzyme portal
ALCANTARA, R., ONWUBIKO J., CAO H., MATOS DE P., Cham J. A., JACOBSEN J., HOLLIDAY G. L., FISCHER J. D., RAHMAN S. A., Jassal B., et al.
Nucleic Acids Research. Volume 41, Number D1, (2013), p.D773-D780 doi: 10.1093/nar/gks1112
Pride-asap: Automatic fragment ion annotation of identified PRIDE spectra
Hulstaert, N., Reisinger F., Rameseder J., Barsnes H., Vizcaino J. A., and Martens L.
J Proteomics. (2013),
Abstracting knowledge from the protein data bank.
Furnham, Nicholas, Laskowski Roman A., and Thornton Janet M.
Biopolymers. Mar, Volume 99, Number 3, (2013), p.183–188 doi: 10.1002/bip.22107
Intratumor heterogeneity in human glioblastoma reflects cancer evolutionary dynamics
Sottoriva, A, Spiteri I, Piccirillo SGM, Touloumis A, Collins VP, Marioni JC, Curtis C, Watts C, and Tavaré S
Proceedings of the National Academy of Sciences. Volume 109, (2013), p.1204 doi: 10.1073/pnas.1115761109
KNIME-CDK: Workflow-driven Cheminformatics
Beisken, Stephan, Meinl Thorsten, Wiswedel Bernd, de Figueiredo Luis F., Berthold Michael, and Steinbeck Christoph
BMC Bioinformatics. Volume 14, (2013), doi:
CySBGN: A Cytoscape plug-in to integrate SBGN maps
GONCALVES, E., IERSEL MV, and SAEZ-RODRIGUEZ J.
BMC bioinformatics. Jan 16, Volume 14, (2013), p.17-2105-14-17
Genome 3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains
Lewis, T. E., Sillitoe I., Andreeva A., Blundell T. L., Buchan D. W. A., Chothia C., Cuff A., DANA J. M., Filippis I., Gough J., et al.
Nucleic Acids Research. Volume 41, Number D1, (2013), p.D499-D507 doi: 10.1093/nar/gks1266
Update on activities at the Universal Protein Resource (UniProt) in 2013
Apweiler, Rolf, Martin Maria Jesus, O'Donovan Claire, Magrane Michele, Alam-Faruque Yasmin, Alpi Emanuele, Antunes Ricardo, Arganiska Joanna, Casanova Elisabet Barrera, Bely Benoit, et al.
NUCLEIC ACIDS RESEARCH. Volume 41, Number D 1, (2013), p.D43–D47 doi:
Unlocking the potential of survival data for model organisms through a new database and online analysis platform: SurvCurv
Ziehm, Matthias, and Thornton Janet M.
Aging Cell. (2013), doi: 10.1111/acel.12121
Towards practical, high-capacity, low-maintenance information storage in synthesized DNA
Goldman, N., Bertone P., Chen S., Dessimoz C., LeProust E. M., Sipos B., and Birney E.
Nature. Volume 494, (2013), p.77-80
Regulation of protein–protein binding by coupling between phosphorylation and intrinsic disorder: analysis of human protein complexes
Nishi, H., Fong J. H., Chang C., Teichmann S. A., and Panchenko A. R.
Mol. BioSyst.. (2013),
The Annotation-enriched non-redundant patent sequence databases
Li, W., Kondratowicz B., McWilliam H., Nauche S., and Lopez R.
Database: the journal of biological databases and curation. Volume 2013, (2013),
Widespread resetting of DNA methylation in glioblastoma-initiating cells suppresses malignant cellular behavior in a lineage-dependent manner
Stricker, S. H., Feber A., Engström P. G., Carén H., Kurian K.M., Takashima Y., Watts C., Way M., Dirks P., Bertone P., et al.
Genes Dev. Mar, Volume 27, Number 6, (2013), p.654–669
SMIM1 underlies the Vel blood group and influences red blood cell traits
Cvejic, A., Haer-Wigman L., Stephens J.C., Kostadima M., Smethurst P.A., Frontini M., van den Akker E., Bertone P., Bielczyk-Maczyńska E., Farrow S., et al.
Nat Genet. May, Volume 45, (2013), p.542–545 doi:
The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013
Vizcaino, J. A., Cote R. G., Csordas A., Dianes J. A., Fabregat A., Foster J. M., Griss J., Alpi E., Birim M., Contell J., et al.
Nucleic Acids Res. Volume 41, Number Database issue, (2013), p.D1063-9
miR-221 affects multiple cancer pathways by modulating the level of hundreds messenger RNAs
Lupini, Laura, Bassi Cristian, Ferracin Manuela, Bartonicek Nenad, D'Abundo Lucilla, Zagatti Barbara, Callegari Elisa, Musa Gentian, Moshiri Farzaneh, Gramantieri Laura, et al.
Frontiers in genetics. Volume 4, Issue 64, (2013), doi:
Modeling signaling networks with different formalisms: a preview
MACNAMARA, A., HENRIQUES D., and SAEZ-RODRIGUEZ J.
Methods in molecular biology (Clifton, N.J.). Volume 1021, (2013), p.89-105 doi:
Facing growth in the European Nucleotide Archive
Cochrane, G., ALAKO B., Amid C., Bower L., Cerdeño-Tárraga A., Cleland I., Gibson R., Goodgame N., JANG M., Kay S., et al.
Nucleic Acids Research. Volume 41, Number D1, (2013), p.D30–D35
ENCODE Data in the UCSC Genome Browser: year 5 update.
Rosenbloom, Kate R., Sloan Cricket A., Malladi Venkat S., Dreszer Timothy R., Learned Katrina, Kirkup Vanessa M., Wong Matthew C., Maddren Morgan, Fang Ruihua, Heitner Steven G., et al.
Nucleic Acids Res. 1, Volume 41, Number D1, (2013), England, p.D56-63 doi: 10.1093/nar/gks1172