Publications

Below you will find a list of all publications resultant from the EMBRACE project.
If you feel an article is unjustly missing, please contact us to let us know and we'll be sure to add it to the list.

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Publications in 2006
Bar-Even A, Paulsson J, Maheshri N, Carmi M, O'Shea E, Pilpel Y, Barkai N.
Noise in protein expression scales with natural protein abundance (2006) Nature Genetics, 38(6):636-43
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Article website
DOI: 10.1038/ng1807
Pubmed: 16715097
Christophe Blanchet, Lefort V, Christophe Combet, Gilbert Delèage.
GPS@ Bioinformatics Portal: from Network to EGEE Grid. (2006) Stud. Health Technol. Inform., 120:187-93
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Article website
Pubmed: 16823137
ISBN: 978-1-58603-617-1
Lee H-C, Jean Salzemann, Nicolas Jacq, Chen H-Y, Ho L-Y, Merelli I, Milanesi L, Vincent Breton, Lin SC, Wu Y-T.
Grid enabled high throughput in silico screening against Influenza A neuraminidase. (2006) IEEE Trans. Nanobioscience., 5(4):288-95
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Article website
DOI: 10.1109/TNB.2006.887943
Pubmed: 17181029
Man O, Pilpel Y.
Differential translation efficiency of orthologous genes is involved in phenotypic divergence of yeast species. (2006) Nature Genetics, 39(3):415-21
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Article website
DOI: 10.1038/ng1967
Pubmed: 17277776
P. McDermott, J. Sinnott, D. Thorne, S. Pettifer, T. Attwood.
An Architecture for Visualisation and Interactive Analysis of Proteins (2006) In: Proceedings of the Fourth International Conference on Coordinated Multiple Views in Exploratory Visualization (CMV'06), pp. 55-68, London, UK
Article website
DOI: 10.1109/CMV.2006.3
Heinz Stockinger, Marco Pagni, Cerutti L, Falquet L.
Grid Approach to Embarrassingly Parallel CPU-Intensive Bioinformatics Problems. (2006) In: Proceedings of the 2nd IEEE International Conference one-Science and Grid Computing (e-Science 2006), Amsterdam, The Netherlands
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Article website
DOI: 10.1109/E-SCIENCE.2006.70
ISBN: 0-7695-2734-5
Heinz Stockinger.
Grid Computing in Physics and Life Sciences (2006) Third International Conference on Communication Technology, ICCT´06, 16 December 2006, Vienna, Austria
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Podvinec, M, Maffioletti, S, Kunszt, P, Arnold, K, Cerutti, L, Nyffeler, B, Schlapbach, R, Türker, C, Heinz Stockinger, Thomas, AJ, Peitsch, MC, Schwede, T.
The SwissBioGrid Project: Objectives, Preliminary Results and Lessons Learned. (2006) 2nd IEEE International Conference on e-Science and Grid Computing, - Workshop on Production Grids, IEEE Computer Society Press, Amsterdam, The Netherlands, Dec. 4-6, 2006
Article website
DOI: 10.1109/E-SCIENCE.2006.261081
ISBN: 0-7695-2734-5
Christophe Blanchet, Christophe Combet, Daric V, Gilbert Delèage.
Web Services Interface to Run Protein Sequence Tools on Grid, Testcase of Protein Sequence Alignment. (2006) In: Lecture Notes in Computer Science: Biological and Medical Data Analysis, 4345:240:249
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Article website
DOI: 10.1007/11946465_22
Publications in 2007
Sander B Nabuurs, Chris A Spronk, Geerten W Vuister, Gert Vriend.
Traditional Biomolecular Structure Determination by NMR Spectroscopy Allows for Major Errors (2007) PLoS Comput. Biol., 2(2):e9
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Article website
DOI: 10.1371/journal.pcbi.0020009
Pubmed: 16462939
Lopez G, Valencia A, Tress M.
FireDB - a database of functionally important residues from proteins of knownstructure. (2007) Nucleic Acids Research, 35(Database issue):D219-23
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Article website
DOI: 10.1093/nar/gkl897
Pubmed: 17132832
Hau J, Muller M, Marco Pagni.
HitKeeper, a Generic Software Package for Hit List Management. (2007) Source Code for Biology and Medicine, 2:2
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Article website
DOI: 10.1186/1751-0473-2-2
Pubmed: 17391514
Macías JR, Jiménez-Lozano N, Carazo JM.
Integrating electron microscopy information into existing Distributed Annotation Systems (2007) Journal of Structural Biology, 158(2):205-213
DOI: 10.1016/j.jsb.2007.02.004
Pubmed: 17400476
K. Lagesen, P.Hallin, E. A. Rodland, H.-H. Stærfeldt, T. Rognes, D. W. Ussery.
RNAmmer: consistent and rapid annotation of ribosomal RNA genes (2007) Nucleic Acids Res., 35(9):3100-3108
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Article website
DOI: 10.1093/nar/gkm160
Pubmed: 17452365
Jean Salzemann, Vinod Kumar Kasam, Nicolas Jacq, Astrid Maaß, Horst Schwichtenberg and Vincent Breton.
Grid Enabled High Throughput Virtual Screening Against Four Different Targets Implicated in Malaria (2007) Proceedings of Healthgrid conference 2007, Studies in Health Technology and Informatics, 126:47-54
Article website
Pubmed: 17476047
ISBN: 978-1-58603-738-3
Cases I, Pisano DG, Andres E, Carro A, Fernández JM, Gómez-López G, Rodriguez JM, Vera JF, Valencia A, Rojas AM.
CARGO: a web portal to integrate customized biological information. (2007) Nucleic Acids Research, 35(Web Server issue):W16-20
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Article website
DOI: 10.1093/nar/gkm280
Pubmed: 17483515
Barrio A M, Soeria-Atmadja D, Nister A, Gustafsson M G, Hammerling U, Erik Bongcam-Rudloff.
EVALLER: a web server for in silico assessment of potential protein allergenicity (2007) Nucleic Acids Research, 35(Web Server issue):694-700
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Article website
DOI: 10.1093/nar/gkm370
Pubmed: 17537818
Marco Pagni, Ioannidis, V, Cerutti, L, Zahn-Zabal, M, Jongeneel, CV, Hau, J, Martin, O, Kuznetsov, D, Falquet, L.
MyHits: improvements to an interactive resource for analyzing protein sequences. (2007) Nucleic Acids Research, 35(Web Server issue):W433-W437
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Article website
DOI: 10.1093/nar/gkm352
Pubmed: 17545200
Linding, R, Jensen, LJ, Ostheimer, GJ, van Vugt, MA, Jorgensen, C, Miron, IM, Diella, F, Colwill, K, Taylor, L, Elder, K, Metalnikov, P, Nguyen, V, Pasculescu, ., Jin, J, Park, JG, Samson, LD, Woodgett, JR, Russell, RB, Peer Bork, Yaffe, MB, Pawson, T.
Systematic Discovery of In Vivo Phosphorylation Networks. (2007) Cell, 129(7):1415-1426
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Article website
DOI: 10.1016/j.cell.2007.05.052
Pubmed: 17570479
Arne Elofsson, Gunnar von Heijne.
Membrane Protein Structure: Prediction vs Reality (2007) Annu. Rev. Biochemistry, 76:125-40
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Article website
DOI: 10.1146/annurev.biochem.76.052705.163539
Pubmed: 17579561
B. Wallner P. Larsson, Arne Elofsson.
Pcons.net: protein structure prediction meta server (2007) Nucleic Acids Research, 35(Web server issue):W369-W374.
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Article website
DOI: 10.1093/nar/gkm319
Pubmed: 17584798
Lopez G, Valencia A, Tress M.
firestar: prediction of functionally important residues using structural templates and alignment reliability (2007) Nucleic Acids Research, 35(Web server issue):W573-W577
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Article website
DOI: 10.1093/nar/gkm297
Pubmed: 17584799
Robbie P. Joosten, Gert Vriend.
PDB improvement starts with data deposition (2007) Science, 317:195-196
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Article website
DOI: 10.1126/science.317.5835.195
Pubmed: 17626865
Jean Salzemann, Nicolas Jacq, Vincent Breton.
Replication and Update of Molecular Biology Databases (2007) IEEE Transactions on NanoBiosciences, 6(2):131-135
Article website
DOI: 10.1109/TNB.2007.897468
Pubmed: 17695747
Björn Wallner, Arne Elofsson.
Prediction of global and local model quality in CASP7 using Pcons and ProQ (2007) Proteins: Structure, Function, and Bioinformatics, 69(S8):184-193
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Article website
DOI: 10.1002/prot.21774
Pubmed: 17894353
Vincent Breton, Nicolas Jacq, Vinod Kumar Kasam, M Hofmann-Apitius.
Grid added value to address malaria. (2007) IEEE Trans. Inf. Technol. Biomed. 12(2):173-81
Article website
DOI: 10.1109/TITB.2007.895930
Pubmed: 18348947
Heinz Stockinger.
Defining the Grid: A Snapshot on the Current View (2007) Journal of Supercomputing, 42(1):3-17
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Article website
DOI: 10.1007/s11227-006-0037-9
Christophe Blanchet, Christophe Combet, Gilbert Delèage.
Integrating Bioinformatics Resources on the EGEE Grid Platform. (2007) In: Proceedings of the Sixth IEEE International Symposium on Cluster Computing and the Grid Workshops (CCGRIDW'06), p. 48
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Article website
DOI: 10.1109/CCGRID.2006.147
ISBN: 0-7695-2585-7
Steve R Pettifer, Wolstencroft, K, Alper, P, Theresa K Attwood, Coletta, A, Carol Goble, Li, P, Philip Mcdermott, James Marsh, Oinn, T, Sinnott, J, David Thorne.
mygrid and UTOPIA: an integrated approach to enacting and visualising in silico experiments in the life sciences. (2007) In: Data Integration in the Life Sciences, Springer, 4544:59-70
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Article website
DOI: 10.1007/978-3-540-73255-6_8
Theresa K Attwood, Steve R Pettifer.
UTOPIA: User-friendly Tools for OPerating Informatics Applications. (2007) EMBNet News, 13(2):19-24
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Article website
Robbie P. Joosten, Glay Chinea, Gerard J. Kleywegt and Gert Vriend.
Protein Three-Dimensional Structure Validation (2007) Comprehensive Medical Chemistry II, 3:507-530
DOI: 10.1016/B0-08-045044-X/00096-1
Nicolas Jacq, Vincent Breton, Hsin-Yen Chen, Li-Yung Ho, Martin Hofmann, Vinod Kumar Kasam, Hurng-Chun Lee, Yannick Legré, Simon C Lin, Astrid Maaß, Emmanuel Medernach, Ivan Merelli, Luciano Milanesi, Giulio Rastelli, Matthieu Reichstadt, Jean Salzemann, Horst Schwichtenberg, Ying-Ta Wu, Marc Zimmermann.
Virtual Screening on Large Scale Grids. (2007) Parallel Computing, 33(4-5):289-301
Article website
DOI: 10.1016/j.parco.2007.02.010
Vinod Kumar Kasam, Jean Salzemann, Vincent Breton, Nicolas Jacq.
WISDOM-II: a large in silico docking effort for finding novel hits against malaria using computational grid infrastructure (2007) In: Proceedings of the 5th IEEE workshop on Challenges of large applications in distributed environments (CLADE'07) ACM, New York Pages: 27-34, 2007
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Article website
DOI: 10.1145/1273404.1273407
Vinod Kumar Kasam, Jean Salzemann, Nicolas Jacq, Astrid Maaß, Vincent Breton.
Large Scale Deployment of Molecular Docking Application on Computational Grid infrastructures for Combating Malaria (2007) in: Proceedings of Cluster Computing and the Grid 2007 (CCGRID 2007). Seventh IEEE International Symposium on Cluster Computing and the Grid
Article website
DOI: 10.1109/CCGRID.2007.66
ISBN: 0-7695-2833-3
Publications in 2008
Diella, F, Gould, CM, Chica, C, Via, A, Gibson, TJ.
Phospho.ELM: a database of phosphorylation sites - update 2008. (2008) Nucleic Acids Research, 36(Database issue):D240-D244
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Article website
DOI: 10.1093/nar/gkm772
Pubmed: 17962309
Heger A, Elja Korpelainen, Hupponen T, Mattila K, Ollikainen V, Holm L.
PairsDB atlas of protein sequence space (2008) Nucleic Acids Research, 36(Database issue):D276-D280
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Article website
DOI: 10.1093/nar/gkm879
Pubmed: 17986464
Bryne JC, Valen E, Tang MH, Marstrand T, Winther O, da Piedade I, Krogh A, Lenhard B, Sandelin A.
JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update (2008) Nucleic Acids Research, 36(Database issue):D102-D106
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Article website
DOI: 10.1093/nar/gkm955
Pubmed: 18006571
Andreas Bernsel, Håkan Viklund, Arne Elofsson
Remote homology detection of integral membrane proteins using conserved sequence features. (2008) Proteins: Structure, Function, and Bioinformatics, 71(3):1387-1399
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Article website
DOI: 10.1002/prot.21825
Pubmed: 18076048
Jose MG Izarzugaza, David Juan, Carles Pons, Florencio Pazos, Alfonso Valencia.
Enhancing the prediction of protein pairings between interacting families using orthology information (2008) BMC Bioinformatics, 9:35
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Article website
DOI: 10.1186/1471-2105-9-35
Pubmed: 18215279
Michal Lapidot, Orna Mizrahi-Man, Yitzhak Pilpel.
Functional Characterization of Variations on Regulatory Motifs. (2008) PLoS Genetics 4(3):e1000018
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Article website
DOI: 10.1371/journal.pgen.1000018
Pubmed: 18369443
Hallin, PF, Binnewies, TT, Ussery, DW.
The genome BLASTatlas-a GeneWiz extension for visualization of whole-genome homology. (2008) Mol Biosyst., 4(5):363-71
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Article website
DOI: 10.1039/B717118H
Pubmed: 18414733
Larsson, P, Wallner, B, Lindahl, E, Arne Elofsson.
Using multiple templates to improve quality of homology models in automated homology modeling (2008) Protein Science, 17(6):990-1002
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Article website
DOI: 10.1110/ps.073344908
Pubmed: 18441233
Claudia Chica, Alberto Labarga, Cathryn M Gould, Rodrigo López, Toby J Gibson.
A tree-based conservation scoring method for short linear motifs in multiple alignments of protein sequences. (2008) BMC Bioinformatics., 9:229
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Article website
DOI: 10.1186/1471-2105-9-229
Pubmed: 18460207
Håkan Viklund, Arne Elofsson.
OCTOPUS: improving topology prediction by two-track ANN-based preference scores and an extended topological grammar. (2008) Bioinformatics, 24(15):1662-1668
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Article website
DOI: 10.1093/bioinformatics/btn221
Pubmed: 18474507
Diella, F, Haslam, N, Chica, C, Budd, A, Michael, S., Brown, NP, Trave, G, Gibson, TJ.
Understanding eukaryotic linear motifs and their role in cell signaling and regulation. (2008) Frontiers in Bioscience, 13(17):6580-6603
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Article website
DOI: 10.2741/3175
Pubmed: 18508681
Anni Kauko, Kristoffer Illergård, Arne Elofsson.
Coils in the membrane core are conserved and functionally important. (2008) J. Mol. Biol., 380(1):170-180
DOI: 10.1016/j.jmb.2008.04.052
Pubmed: 18511074
von Grotthuss, M, Plewczynski, D, Gert Vriend, Rychlewski, L.
3D-Fun: predicting enzyme function from structure. (2008) Nucleic Acids Res., 36(Web Server issue), W303-W307
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Article website
DOI: 10.1093/nar/gkn308
Pubmed: 18515349
Heinz Stockinger, Theresa K Attwood, Nadeem Chohan, S, Côté, R, Cudré-Mauroux, P, Falquet, L, Fernandes, P, Finn, RD, Hupponen, T, Elja Korpelainen, Labarga, A, Laugraud, A, Lima, T, Pafilis, E, Marco Pagni, Steve R Pettifer, Phan, I, Rahman, N.
Experience Using Web Services for Biological Sequence Analysis, (2008) Briefings in Bioinformatics, 9(6):493-505
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Article website
DOI: 10.1093/bib/bbn029
Pubmed: 18621748
Miller, ML, Jensen, J, Diella, F, Jorgensen, C, Tinti, M, Li, Hsiung, M, Parker, SA, Bordeaux, J, Sicheritz-Ponten, Olhovsky, M, Pasculescu, A, Alexander, J, Knapp, S, Blom, N, Peer Bork, Li, S, Cesareni, G, Pawson, T, Turk, BE, Yaffe, MB, Brunak, S, inding, R.
Linear motif atlas for phosphorylation-dependent signaling. (2008) Sci. Signal., 1(35):ra2
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Article website
DOI: 10.1126/scisignal.1159433
Pubmed: 18765831
Shalem, O, Dahan, O, Levo, M, Martinez, MR, Furman, I, Segal, E, Pilpel Y.
Transient transcriptional responses to stress are generated by opposing effects of mRNA production and degradation. (2008) Mol. Sys. Biol., 4:4
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Article website
DOI: 10.1038/msb.2008.59
Pubmed: 18854817
Håkan Viklund, Andreas Bernsel, Skwark, M, Arne Elofsson.
SPOCTOPUS: a combined predictor of signal peptides and membrane protein topology. (2008) Bioinformatics, 24(24):2928-2929
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Article website
DOI: 10.1093/bioinformatics/btn550
Pubmed: 18945683
Marco Pagni, Hau, J, Heinz Stockinger.
A Multi-Protocol Bioinformatics Web Service: Use SOAP, Take a REST or Go With HTML. (2008) International Workshop of Modern Computer Tools for the Biosciences - a Grid Perspective (MBIO08), IEEE Computer Society Press, Lyon, France, May 19-22, 2008
Article website
DOI: 10.1109/CCGRID.2008.28
ISBN: 978-0-7695-3156-4
Heinz Stockinger.
Applying Scientific Applications to the Grid (2008) In: Grid Computing Research Progress, Nova Publishers, 2nd Quarter 2008
ISBN: 978-1-60456-404-4
Vincent Breton, Nicolas Jacq, Vinod Kumar Kasam, Salzeman J.
Deployment of Grid life sciences applications (2008) In: Grid Computing for Bioinformatics and Computational Biology, ch.9, Wiley 2008
Article website
ISBN: 978-0-471-78409-8
Nicolas Lebreton, Olivier Dameron, Christophe Blanchet, Julie Chabalier.
Semi-automatic composition of bioinformatics Web services based on task and domain ontologies. (2008) Data Integration in the Life Sciences 2008, Evry, France (Poster and oral "short"-presentation)
no additional information available
Nicolas Lebreton, Olivier Dameron, Christophe Blanchet, Julie Chabalier.
Utilisation d´ontologies de tâches et de domaine pour la composition semi-automatique de services Web bioinformatiques. (2008) In: Proceedings of the French Symposium JOBIM 2008, Lille, France
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Xosè M. Fernàndez-Suàrez, Ewan Birney.
Advanced Genomic Data Mining (2008) PLoS Computational Biology 4(9):e1000121
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Article website
DOI: 10.1371/journal.pcbi.1000121
Pubmed: 18818719
M. Diarena, S. Nowak, J.Y. Boire, Vincent Bloch, D. Donnarieix, A. Fessy, B, Grenier, B. Irrthum, Yannick Legrè, L. Maigne, Jean Salzemann, C. Thiam, N. Spalinger, N. Verhaeghe, P. de Vlieger, Vincent Breton.
HOPE, an open platform for medical data management on the grid (2008) In: Review of HealthGrid 2008: Global HealthGrid: eScience meets Biomedical Informatics
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Article website
Pubmed: 18560106
Publications in 2009
Costas Papaloukas, Erik Granseth, Håkan Viklund, Arne Elofsson.
Estimating the Length of Transmembrane Helices Using Z-coordinate Predictions (2009) Protein Science, 17:271-278
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Article website
DOI: 10.1110/ps.073036108
Pubmed: 18096645
Kamburov A, Wierling C, Lehrach H, Herwig R.
ConsensusPathDB - a database for integrating human functional interaction networks (2009) Nucleic Acids Research, 37(Database issue):D623-D628
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Article website
DOI: 10.1093/nar/gkn698
Pubmed: 18940869
Diella, F, Chabanis, S, Luck, K, Chica, C, Ramu, C, Nerlov, C, Gibson, TJ.
KEPE--a motif frequently superimposed on sumoylation sites in metazoan chromatin proteins and transcription factors. (2009) Bioinformatics, 25(1):1-5
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Article website
DOI: 10.1093/bioinformatics/btn594
Pubmed: 19033273
Hache, H, Wierling, C, Lehrach, H, Herwig, R.
GeNGe: systematic generation of gene regulatory networks. (2009) Bioinformatics, 25(9):1205-1207
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Article website
DOI: 10.1093/bioinformatics/btp115
Pubmed: 19251773
Lee, C, Erik Bongcam-Rudloff, Sollner, C, Jahnen-Dechent, W, Claesson-Welsh, L.
Type 3 cystatins; fetuins, kininogen and histidine-rich glycoprotein. (2009) Frontiers in Bioscience, 14:2911-2922
Article website
DOI: 10.2741/3422
Pubmed: 19273244
Vinod Kumar Kasam, Jean Salzemann, Botha, M, Dacosta, A, Degliesposti, G, Isea, R, Kim, D, Astrid Maaß, Kenyon, C, Giulio Rastelli, Hofmann-Apitius, M, Vincent Breton.
WISDOM-II: Screening against multiple targets implicated in malaria using computational grid infrastructures. (2009) Malaria Journal, 8:88
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Article website
DOI: 10.1186/1475-2875-8-88
Pubmed: 19409081
Degliesposti, G, Vinod Kumar Kasam, Ana L. da Costa, Kang, HK, Kim, N, Kim, DW, Vincent Breton, Kim, D, Rastelli, G.
Design and discovery of plasmepsin II inhibitors using an automated workflow on large-scale grids. (2009) Chem. Med. Chem., 4(7):1164-73
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Article website
DOI: 10.1002/cmdc.200900111
Pubmed: 19437467
Steve R Pettifer, David Thorne, Philip McDermott, Theresa K Attwood, Baran J, Bryne JC, Hupponen T, Mowbray D, Gert Vriend.
An active registry for bioinformatics web services. (2009) Bioinformatics, 25(16):2090-2091
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Article website
DOI: 10.1093/bioinformatics/btp329
Pubmed: 19460889
Kristoffer Illergård, Ardell, DH, Arne Elofsson.
Structure is three to ten times more conserved than sequence - A study of structural response in protein cores. (2009) Proteins: Structure, Function, and Bioinformatics, (3):499-508
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Article website
DOI: 10.1002/prot.22458
Pubmed: 19507241
Vincent Breton, Ana L. da Costa, de Vlieger, P, Kim, YM, Maigne, L, Reuillon, R, Sarramia, D, Truong, NH, Nguyen, HQ, Kim, D, Wu, YT.
Innovative in silico approaches to address avian flu using grid technology. (2009) Infectious Disorders - Drug Targets, 9(3):358-365
Article website
Pubmed: 19519488
Martínez Barrio, A, Lagercrantz, E, Sperber, GO, Blomberg, J, Erik Bongcam-Rudloff.
Annotation and visualization of endogenous retroviral sequences using the Distributed Annotation System (DAS) and eBioX. (2009) BMC Bioinformatics, 10(Suppl 6):S18
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Article website
DOI: 10.1186/1471-2105-10-S6-S18
Pubmed: 19534743
Steve R Pettifer, David Thorne, Philip Mcdermott, James Marsh, Villéger, A, Douglas B Kell, Theresa K Attwood.
Visualising biological data: a semantic approach to tool and database integration. (2009) BMC Bioinformatics, 10(Suppl 6):S19
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Article website
DOI: 10.1186/1471-2105-10-S6-S19
Pubmed: 19534744
Larsson, P, Skwark, MJ, Wallner, B, Arne Elofsson.
Assessment of global and local model quality in CASP8 using Pcons and ProQ. (2009) Proteins: Structure, Function, and Bioinformatics, 77(S9):167-172
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Article website
DOI: 10.1002/prot.22476
Pubmed: 19544566
Gouttenoire, J, Montserret, R, Kennel, A, Penin, F, Moradpour, D.
An Amphipathic alpha-Helix at the C Terminus of Hepatitis C Virus Nonstructural Protein 4B Mediates Membrane Association. (2009) J. Virol., 83(21):11378-84
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Article website
DOI: 10.1128/JVI.01122-09
Pubmed: 19692468
Quantin, C, Coatrieux, G, Allaert, FA, Fassa, M, Bourquard, K, Boire, J-Y, de Vlieger, P, Maigne, L, Vincent Breton.
New Advanced Technologies to Provide Decentralised and Secure Access to Medical Records: Case Studies in Oncology. (2009) Cancer Informatics, 7:217-229
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Article website
Pubmed: 19718446
Izarzugaza, JMG, Baresic, A, McMillan, LEM, Yeats, C, Andrew B Clegg, Orengo, CA, Martin, ACR, Valencia, A.
An integrated approach to the interpretation of Single Amino Acid Polymorphisms within the framework of CATH and Gene3D. (2009) BMC Bioinformatics, 10(Suppl 8):S5
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Article website
DOI: 10.1186/1471-2105-10-S8-S5
Pubmed: 19758469
Jurgen F Doreleijers, Wim F Vranken, Christopher Schulte, Jundong Lin, Jonathan R Wedell, Christopher J Penkett, Geerten W Vuister, Gert Vriend, John L Markley, Eldon L Ulrich.
The NMR restraints grid at BMRB for 5,266 protein and nucleic acid PDB entries. (2009) J Biomol NMR, 45(4):389-396
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Article website
DOI: 10.1007/s10858-009-9378-z
Pubmed: 19809795
Via A, Gould CM, Gemünd C, Gibson TJ, Helmer-Citterich M.
A structure filter for the Eukaryotic Linear Motif Resource. (2009) BMC Bioinformatics., 10:351
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Article website
DOI: 10.1186/1471-2105-10-351
Pubmed: 19852836
Yeats, C, Lees, J, Redfern, O, Clegg, A, Orengo, C.
Gene3D: Merging Structure and Function For a Thousand Genomes. (2009) Nucleic Acids Research, 38(Database issue):D296-D300;
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Article website
DOI: 10.1093/nar/gkp987
Pubmed: 19906693
Kahlem, P, Clegg, A, Reisinger, F, Xenarios, I, Hermjakob, H, Orengo, C, Birney, E.
ENFIN - A European network for integrative systems biology. (2009) Comptes Rendus Biologies, 332(11):1050-1058
DOI: 10.1016/j.crvi.2009.09.003
Pubmed: 19909926
Theresa K Attwood, Douglas B Kell, Philip Mcdermott, James Marsh, Steve R Pettifer, David Thorne.
Calling international rescue: knowledge lost in literature and data landslide! (2009) Biochem. J., 424:317-333
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Article website
DOI: 10.1042/BJ20091474
Pubmed: 19929850
Zakrzewska, K, Bouvier, B, Michon, A, Christophe Blanchet, Lavery, R.
Protein-DNA binding specificity: a grid-enabled computational approach applied to single and multiple protein assemblies. (2009) Phys. Chem. Chem. Phys., 11:10712-10721
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Article website
DOI: 10.1039/B910888M
Pubmed: 20145815
Klipp, E, Liebermeister, W, Wierling, C, Kowald, A, Lehrach, H, Herwig, R.
Systems Biology: A Textbook., Wiley-Blackwell. (2009)
Article website
ISBN: 978-3-527-31874-2
Martínez Barrio, A, Ekjerlund, M, Sperber, GO, Blomberg, J, Erik Bongcam-Rudloff, Andersson, G.
In silico analysis of the dog genome identifies Canine Endogenous Retroviruses (CfERVs) (2009) Retrovirology, 6(Suppl2):P7
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DOI: doi:10.1186/1742-4690-6-S2-P7
Theresa K Attwood, Douglas B Kell, Philip Mcdermott, James Marsh, Steve R Pettifer, David Thorne.
Calling international rescue: knowledge lost in literature and data landslide! (2009) The Biochemist, 31(6):23-38
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Heinz Stockinger, Auch, AF, Göker, M, Meier-Kolthoff, J, Stamatakis, A.
Large-Scale Co-Phylogenetic Analysis on the Grid. (2009) International Journal of Grid and High Performance Computing, 1(1):39-54
Article website
DOI: 10.4018/978-1-60566-374-6.ch035
ISBN: 978-1-60566-374-6
Robbie P Joosten, Jean Salzemann, Vincent Bloch, Heinz Stockinger, Ann-Charlott Berglund, Christophe Blanchet, Erik Bongcam-Rudloff, Christophe Combet, Ana L. da Costa, Gilbert Delèage, Matteo Diarena, Roberto Fabbretti, Géraldine Fettahi, Volker Flegel, Andreas Gisel, Vinod Kumar Kasam, Timo Kervinen, Elja Korpelainen, Kimmo Mattila, Marco Pagni, Matthieu Reichstadt, Vincent Breton, Ian J Tickle, Gert Vriend.
PDB_REDO: automated re-refinement of X-ray structure models in the PDB. (2009) J. Appl. Cryst., 42:376-384
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DOI: 10.1107/S0021889809008784
Hache, H, Lehrach, H, Herwig, R.
Reverse Engineering of Gene Regulatory Networks: A Comparative Study. (2009) EURASIP Journal on Bioinformatics and Systems Biology, Volume 2009, Article ID 617281
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DOI: 10.1155/2009/617281
Meinel, T, Herwig, R.
SOAP/WSDL-based Web Services for Biomedicine. (2009) In: Web-Based Applications in Healthcare and Biomedicine, Athina Lazakidou (Ed.): - Springer Press
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DOI: 10.1007/978-1-4419-1274-9_7
ISBN: 978-1-4419-1273-2.
Steve R Pettifer, David Thorne, Philip Mcdermott, Theresa K Attwood, Baran, J, Bryne, JC, Hupponen, T, Gert Vriend.
The EMBRACE registry. (2009) EMBNet News, 14(4):58-62
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Nicolas Lebreton, Christophe Blanchet, Julie Chabalier, Olivier Dameron.
Utilisation d´ontologies de tâches et de domaine pour la composition semi-automatique de services Web bioinformatiques. (2009) In: Proceedings of the French Symposium JOBIM 2009, Nantes, France
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Paul De Vlieger, Jean-Yves Boire, Vincent Breton, Yannick Legrè, David Manset, Jèrôme Revillard, David Sarramia and Lydia Maigne
Grid-enabled sentinel network for cancer surveillance (2009) In: Proceedings of HealthGrid 2009, Studies in Health Technology and Informatics, Berlin, Germany
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DOI: 10.3233/978-1-60750-027-8-289
Pubmed: 19593069
ISBN: 978-1-60750-027-8
Syed Haider, Benoit Ballester, Damian Smedley, Junjun Zhang, Peter Rice, Arek Kasprzyk.
BioMart Central Portal - unified access to biological data (2009) Nucleic Acids Research, 37(Web Server issue):W23-W27
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DOI: 10.1093/nar/gkp265
Pubmed: 19420058
Domenica D'Elia, Andreas Gisel, Nils-Einar Eriksson, Sophia Kossida, Kimmo Mattila, Lubos Klucar, Erik Bongcam-Rudloff.
The 20th anniversary of EMBnet: 20 years of bioinformatics for the Life Sciences community (2009) BMC Bioinformatics, 10(Suppl 6):S1
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DOI: 10.1186/1471-2105-10-S6-S1
Pubmed: 19534734
Natalia Jimènez-Lozano, Joan Segura, Josè Ramòn Macìas, Juanjo Vega, Josè Marìa Carazo.
aGEM: an integrative system for analyzing spatial-temporal gene-expression information (2009) Bioinformatics 25(19):2566-2572
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Article website
DOI: 10.1093/bioinformatics/btp422
Pubmed: 19592395
Damian Smedley, Syed Haider, Benoit Ballester, Richard Holland, Darin London, Gudmundur Thorisson, Arek Kasprzyk.
BioMart - biological queries made easy (2009) BMC Genomics, 10:22
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DOI: 10.1186/1471-2164-10-22
Pubmed: 19144180
Clemens Kühn, Christoph Wierling, Alexander Kühn, Edda Klipp, Georgia Panopoulou, Hans Lehrach, Albert J Poustka.
Monte Carlo analysis of an ODE Model of the Sea Urchin Endomesoderm Network (2009) BMC Systems Biology, 3:38
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DOI: 10.1186/1752-0509-3-83
Pubmed: 19698179
Helena Strömbergsson, Gerard J Kleywegt.
A chemogenomics view on protein-ligand spaces (2009) BMC Bioinformatics, 10(Suppl 6):S13
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DOI: 10.1186/1471-2105-10-S6-S13
Pubmed: 19534738
Àlvaro Martìnez Barrio, Oskar Eriksson, Jitendra Badhai, Anne-Sophie Frojmark, Erik Bongcam-Rudloff, Niklas Dahl, Jens Schuster
Targeted Resequencing and Analysis of the Diamond-Blackfan Anemia Disease Locus RPS19 (2009) PLoS ONE 4(7):e6172.
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DOI: 10.1371/journal.pone.0006172
Pubmed: 19587786
Publications in 2010
Hanka Venselaar, Robbie P Joosten, Bas Vroling, Coos A baakman, Maarten L Hekkelman, Elmar Krieger, Gert Vriend.
Homology modelling and spectroscopy, a never-ending love story. (2010) Eur Biophys J., 39(4):551-63
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DOI: 10.1007/s00249-009-0531-0
Pubmed: 19718498
Schuemie, MJ, Kang, N, Maarten L Hekkelman, Kors JA.
GeneE: gene and protein query expansion with disambiguation. (2010) Bioinformatics, 26(1),147-8
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DOI: 10.1093/bioinformatics/btp597
Pubmed: 19837720
Gould CM, Diella F, Via A, Puntervoll P, Gemünd C, Chabanis-Davidson S, Michael S, Sayadi A, Bryne JC, Chica C, Seiler M, Davey NE, Haslam N, Weatheritt RJ, Budd A, Hughes T, Pas J, Rychlewski L, Travé G, Aasland R, Helmer-Citterich M, Linding R, Gibson TJ.
ELM: the status of the 2010 eukaryotic linear motif resource. (2010) Nucleic Acids Research, 38(Database issue): D167-D180
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DOI: 10.1093/nar/gkp1016
Pubmed: 19920119
Tuller, T, Carmi, A, Vestsigian, K, Navon, S, Dorfan, Y, Zaborske, J, Pan, T, Dahan, O, Furman, I, Pilpel, Y.
An Evolutionarily Conserved Mechanism for Controlling the Efficiency of Protein Translation. (2010) Cell, 141:344-354
DOI: 10.1016/j.cell.2010.03.031
Pubmed: 20403328
Bhagat, J, Tanoh, F, Nzuobontane, E, Laurent, T, Orlowski, J, Roos, M, Wolstencroft, K, Stevens, R, Aleksejevs, S, Steve R Pettifer, Lopez, R, Carol Goble.
BioCatalogue : A universal catalogue of web services for the life sciences. (2010) Nucleic Acids Research, 38(Web Server issue):W689-W694
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DOI: 10.1093/nar/gkq394
Pubmed: 20484378
Haslam NJ, Gibson TJ.
EpiC: an open resource for exploring epitopes to aid antibody-based experiments. (2010) J. Proteome Res., 9(7):3759-63
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DOI: 10.1021/pr100029f
Pubmed: 20496950
Maarten L Hekkelman, Tim AH te Beek, Steve R Pettifer, David Thorne, Theresa K Attwood, Gert Vriend.
WIWS: a protein structure bioinformatics web service collection. (2010) Nucleic Acids Research, 38(Webserver issue):W719-W723
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DOI: 10.1093/nar/gkq453
Pubmed: 20501602
Reid, AJ, Ranea, JAG, Andrew B Clegg, Orengo, CA.
CODA: Accurate Detection of Functional Associations between Proteins in Eukaryotic Genomes Using Domain Fusion. (2010) PLoS ONE, 5(6):e10908
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DOI: 10.1371/journal.pone.0010908
Pubmed: 20532224
Trung-Tung Doan, Aurélien Bernard, Ana Lucia Da-Costa, Vincent Bloch, Thanh-Hoa Le, Yannick Legré, Lydia Maigne, Jean Salzemann, David Sarramia, Hong-Quang Nguyen, Vincent Breton.
Grid-based International Network for Flu Observation (g-INFO), Proceedings of Healthgrid conference 2010, (2010) Proceedings of Healthgrid conference 2010, Studies in Health Technology and Informatics, 159:215-226
Article website
DOI: 10.3233/978-1-60750-583-9-215
Pubmed: 20543440
ISBN: 978-1-60750-582-2
Kristoffer Illergård, Callegari, S, lofsson, A.
MPRAP: An accessibility predictor for a-helical transmem-brane proteins that performs well inside and outside the membrane (2010) BMC Bioinformatics, 11(1):333
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DOI: 10.1186/1471-2105-11-333
Pubmed: 20565847
Leitner F, Krallinger M, Cesareni G, Valencia A.
The FEBS Letters SDA corpus: A collection of protein interaction articles with high quality annotations for the BioCreative II.5 online challenge and the text mining community. (2010) FEBS Lett., 584(19):4129-4130
DOI: 10.1016/j.febslet.2010.08.026
Pubmed: 20728446
Kalas M, Puntervoll P, Joseph A, Edita Bartaseviciute, Töpfer A, Venkataraman P, Steve R Pettifer, Bryne JC, Ison J, Christophe Blanchet, Kristoffer Rapacki, Jonassen I.
BioXSD: the common data-exchange format for everyday bioinformatics Web services. (2010) Bioinformatics, 26(18):i540-i546
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DOI: 10.1093/bioinformatics/btq391
Pubmed: 20823319
Theresa K Attwood, Douglas B Kell, Philip Mcdermott, James Marsh, Steve R Pettifer, David Thorne.
Utopia Documents: linking scholarly literature with research data. (2010) In: Proceedings of 9th European Conference on Computational Biology (ECCB10), Ghent, Belgium, September 2010
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DOI: 10.1093/bioinformatics/btq383
Pubmed: 20823323
Leitner F, Chatr-Aryamontri A, Mardis SA, Ceol A, Krallinger M, Licata L, Hirschman L, Cesareni G, Valencia A.
The FEBS Letters/BioCreative II.5 experiment: making biological information accessible. (2010) Nature Biotechnol., 28(9):897-899
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DOI: 10.1038/nbt0910-897
Pubmed: 20829821
Ranea, JAG, Morilla, I, Lees, JG, Reid, AJ, Yeats, C, Andrew B Clegg, Sánchez Jiménez, F, Orengo, C.
Finding the 'Dark Matter' in Human and Yeast Protein Network Prediction and Modelling. (2010) PLoS Computational Biology, 6(9):e1000945
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DOI: 10.1371/journal.pcbi.1000945
Pubmed: 20885791
Leitner, F, Mardis, SA, Krallinger, M, Cesareni, G, Hirschman, LA, Valencia, A.
An Overview of BioCreative II.5 (2010) IEEE/ACM Trans Comput Biol Bioinform., 7(3):385-399
Article website
DOI: 10.1109/TCBB.2010.61
Meinel, T, Mueller, MS, Ahmed, J, Yildirimman, R, Dunkel, M, Herwig, R, Preissner, R.
SOAP/WSDL-Based Web Services for Biomedicine: Demonstrating the Technique with the Cancer Resource. (2010) Proceedings of the MEDICON 2010, Springer Press, 29(5):835-838
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Article website
DOI: 10.1007/978-3-642-13039-7_211
Steve R Pettifer, Ison J, Kalas M, David Thorne, Philip McDermott, Jonassen I, Liaquat A, Fernández JM, Rodriguez JM, INB-Partners, Pisano DG, Christophe Blanchet, Mahmut Uludag, Peter M Rice, Edita Bartaseviciute, Kristoffer Rapacki, Maarten L Hekkelman, Olivier Sand, Heinz Stockinger, Andrew B Clegg, Erik Bongcam-Rudloff, Jean Salzemann, Vincent Breton, Theresa K Attwood, Graham Cameron, Gert Vriend.
The EMBRACE web service collection. (2010) Nucleic Acids Research, 38(Web Server issue):W683-W688
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Article website
DOI: 10.1093/nar/gkq297
Theresa K Attwood, Douglas B Kell, Philip Mcdermott, James Marsh, Steve R Pettifer, David Thorne.
Utopia Documents and The Semantic Biochemical Journal experiment. (2010) EMBNet News, 15(4):3-6
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Bas Vroling, Marijn Sanders, Coos A Baakman, Annika Borrmann, Stefan Verhoeven, Jan Klomp, Laerte Oliveira, Jacob de Vlieg, Gert Vriend.
GPCRDB: information system for G protein-coupled receptors (2010) Nucleic Acids Research 39(Database issue):D309-D319.
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DOI: 10.1093/nar/gkq1009
Pubmed: 21045054
Hanka Venselaar, Tim AH te Beek, Remko KP Kuipers, Maarten L Hekkelman, Gert Vriend.
Protein structure analysis of mutations causing inheritable diseases. An e-Science approach with life scientist friendly interfaces (2010) BMC Bioinformatics 11:548
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DOI: 10.1186/1471-2105-11-548
Pubmed: 21059217
Àlvaro Martìnez Barrio
Thesis: Novel Bioinformatics Applications for Protein Allergology, Genome-Wide Association and Retrovirology Studies (2010) Digital Comprehensive Summaries of Uppsale Dissertantions from the Faculty of Science and Technology, 703, 103 pp. Uppsala
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ISBN: 978-91-554-7694-6
Publications in 2011
Àlvaro Martìnez Barrio, Marie Ekerljung, Patric Jern, Farid Benachenhou, Göran O. Sperber, Erik Bongcam-Rudloff, Jonas Blomberg, Göran Andersson
The First Sequenced Carnivore Genome Shows Complex Host-Endogenous Retrovirus Relationships. (2010) PLoS ONE, 6(5):e19832
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DOI: 10.1371/journal.pone.0019832
Pubmed: 21589882
Katarina Truvè, Oscar Eriksson, Martin Norling, Maria Wilbe, Evan Mauceli, Kerstin Lindblad-Toh, Erik Bongcam-Rudloff
SEQscoring: a tool to facilitate the interpretation of data generated with next generation sequencing technologies. (2011) EMBnet.journal, 17(1), pp. 38-45
Article website
Bas Vroling, David Thorne, Philip McDermott, Henk-Jan Joosten, Teresa K. Attwood, Steve Pettifer and Gert Vriend
NucleaRDB: information system for nuclear receptors. (2011) Nucleic Acids Research, 40(Database issue):D377-D380
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Article website
DOI: 10.1093/nar/gkr960
Pubmed: 22064856
Jurgen F. Doreleijers, Wim F. Vranken, Christopher Schulte, John L. Markley, Eldon L. Ulrich, Gert Vriend and Geerten W. Vuister
NRG-CING: integrated validation reports of remediated experimental biomolecular NMR data and coordinates in wwPDB (2011) Nucleic Acids Research, 40(Database issue):D519-D524
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Article website
DOI: 10.1093/nar/gkr1134
Pubmed: 22139937
Publications in 2012
José M. Fernández, Robert Hoffman and Alfonso Valencia
iHOP Web Services Family. (2012) Bioinformatics for Personalized Medicine: Lecture Notes in Computer Science, 6620/2012 102-107
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DOI: 10.1007/978-3-642-28062-7_12
José M. Fernández and Alfonso Valencia
Bioinformatic Software Developments in Spain. (2012) Bioinformatics for Personalized Medicine: Lecture Notes in Computer Science, 6620/2012 108-120
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Article website
DOI: 10.1007/978-3-642-28062-7_13
Teresa K. Attwood, Alain Coletta, Gareth Muirhead, Athanasia Pavlopoulou, Peter B. Philippou, Ivan Popov, Carlos Romá-Mateo, Athina Theodosiou, and Alex L. Mitchell
The PRINTS database: a fine-grained protein sequence annotation and analysis resource - its status in 2012. (2012) Database, vol. 2012, (online publication)
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Article website
DOI: 10.1093/database/bas019
Pubmed: 22508994