Publication overview
Autocorrelated logistic ridge regression for prediction based on proteomics spectra
Goeman, J. J.Stat.Appl.Genet.Mol.Biol. 2008, 7
http://www.ncbi.nlm.nih.gov/pubmed/18312215
Metabolic pathway alignment (M-Pal) reveals diversity and alternatives in conserved networks
Li, Y.de Ridder, D.de Groot, M. J. L.Reinders, M. J. T.Series on Advanced in Bioinformatics & Computational Biology 2008(6): 273
Discovering Relational Item Sets Efficiently
Koopman, A.Siebes, A.SDM 2008 2008
http://www.cs.uu.nl/groups/ADA/people/siebes/
The Emerging World of Wikis
Hu, James C.Aramayo, RodolfoBolser, DanConway, TyrrellElsik, Christine G.Gribskov, Mi...Science 2008, 320(5881): 1289
http://www.sciencemag.org/cgi/content/abstract/320/5881/1289b
The Emerging World of Wikis
Hu, JamesAramayo, RodolfoBolser, DanConway, TyrrellElsik, ChristineGribskov, MichaelK...Science 2008, 320(5881): 1289
http://dx.doi.org/10.1126/science.320.5881.1289b
Data Lineage Model for Taverna Workflows with Lightweight Annotation Requirements
Missier, P.Belhajjame, K.Zhao, K.Roos, M.Goble, C. A.Provenance and Annotation of Data and Processes 2008: 17
A versatile peptide pI calculator for phosphorylated and N-terminal acetylated peptides experimentally tested using peptide isoelectric focusing
Gauci, S.van, Breukelen B.Lemeer, S. M.Krijgsveld, J.Heck, A. J.Proteomics. 2008, 8(23): 4898
http://www.ncbi.nlm.nih.gov/pubmed/19003858
Multiple sclerosis-related proteins identified in cerebrospinal fluid by advanced mass spectrometry
Stoop, M. P.Dekker, L. J.Titulaer, M. K.Burgers, P. C.Sillevis Smitt, P. A.Luider, T....Proteomics 2008, 8(8): 1576
http://www.ncbi.nlm.nih.gov/pubmed/18351689
On defining the dynamics of hydrophobic patches on protein surfaces
Lijnzaad, P.Feenstra, K. A.Heringa, J.Holstege, F. C.Proteins 2008
http://www.ncbi.nlm.nih.gov/pubmed/18186474
Modelling of the ventricular conduction system
ten Tusscher, K. H.Panfilov, A. V.Prog.Biophys.Mol.Biol. 2008, 96(1): 152
http://www.ncbi.nlm.nih.gov/pubmed/17910889
Cross Language Information Retrieval for biomedical literature
Trieschnigg, D.Schuemie, M.Kraaij, W.Proceedings of TREC 16 2008
Aualia Structures and their Impact on the Concrete Noun Categorization Task
Katrenko, S.Adriaans, P. W.Proceedings of the Bridging the gap between semantic theory and computational simulations 2008
A novel approach to subtype tumors by association with single gene perturbation fingerprints
van Vliet, M. H.Wessels, L. F. A.Reinders, M. J. T.Proceedings of the 14th Annual conference of the Advanced school for computing and imaging 2008
M-PAS: a comprehensive and flexible metabolic pathway alignment and scoring method
Li, Y.de Ridder, D.de Groot, M. J. L.Reinders, M. J. T.Proceedings of the 14th Annual conference of the Advanced school for computing and imaging 2008
Inference of logic networks from insertion and expression data
de Ridder, J.Reinders, M.Wessels, L.Proceedings of the 14th Annual conference of the Advanced school for computing and imaging 2008
Predicting metabolic flow-routes based on gene expression data
van Berlo, R.de Ridder, D.Reinders, M. J. T.Proceedings of the 13th Annual conference of the Advanced school for computing and imaging 2008
Comparing human and automatic thesaurus mapping approaches in the agricultural domain
Lauser, B.Johannsen, G.Caracciolo, C.Keizer, J.van Hage, W. R.Mayr, P.Proceedings of DC 2008 2008
Measuring concept relatedness using language models
Trieschnigg, D.Meij, E.de Rijke, M.Kraaij, W.Proceedings ACM SIGIR 2008 2008: 823
Biomedical cross-language information retrieval
Trieschnigg, D.Proceedings ACM SIGIR 2008 2008
Parsimonious concept modeling
Meij, E.Trieschnigg, D.de Rijke, M.Kraaij, W.Proceedings ACM SIGIR 2008 2008: 815
Semantic Types of Some Generic Rlation Arguments: Detection and Evaluation
Katrenko, S.Adriaans, P. W.Proc.of the 46th Annual Meeting of the Association for Computational Linguistics 2008
A Local Alignment kernel in the Context of NLP
Katrenko, S.Adriaans, P. W.Proc.of the 22nd International Conference on Computational Linguistics 2008
Divide, Align and Full-Search for Discovering Conserved Protein Complexes
Jancura, P.Heringa, J.Marchiori, E.Proc of the 6th European Conference on Evolutionary Computation, Machine Learning and Datamining in Bioinformatics 2008: 73
SARS-coronavirus replication/transcription complexes are membrane-protected and need a host factor for activity in vitro
van Hemert, M. J.van den Worm, S. H.Knoops, K.Mommaas, A. M.Gorbalenya, A. E.Snijder,...PLoS Pathog. 2008, 4(5)
http://www.ncbi.nlm.nih.gov/pubmed/18451981
Proteomic profiling of Plasmodium sporozoite maturation identifies new proteins essential for parasite development and infectivity
Lasonder, E.Janse, C. J.van Gemert, G. J.Mair, G. R.Vermunt, A. M.Douradinha, B. G.va...PLoS Pathog. 2008, 4(10)
http://www.ncbi.nlm.nih.gov/pubmed/18974882
Simplicity, ideas and first results
Hageman, J. A.Hendriks, M. M. W. B.Westerhuis, J. A.van der Werf, M. J.Berger, R.Smil...PloS ONE 2008, 3(9)
Genetical genomics: spotlight on QTL hotspots
Breitling, R.Li, Y.Tesson, B. M.Fu, J.Wu, C.Wiltshire, T.Gerrits, A.Bystrykh, L. V.de...PLoS Genet. 2008, 4(10)
http://www.ncbi.nlm.nih.gov/pubmed/18949031
Protein complex evolution does not involve extensive network rewiring
van Dam, T. J.Snel, B.PLoS Comput.Biol. 2008, 4(7)
http://www.ncbi.nlm.nih.gov/pubmed/18711636
Functional rather than topological properties explain gene co-regulation in metabolic networks
Notebaart, R. A.Teusink, B.Siezen, R. J.Papp, B.PLoS Comput Biol 2008(4): 157
Co-regulation of metabolic genes is better explained by flux coupling than by network distance
Notebaart, R. A.Teusink, B.Siezen, R. J.Papp, B.PLoS Comput Biol 2008, 4(1)
http://www.ncbi.nlm.nih.gov/pubmed/18225949
Prediction of human disease genes by human-mouse conserved coexpression analysis
Ala, U.Piro, R. M.Grassi, E.Damasco, C.Silengo, L.Oti, M.Provero, P.Di, Cunto F.PLoS Comput Biol 2008, 4(3)
http://www.ncbi.nlm.nih.gov/pubmed/18369433
WikiPathways: Pathway Editing for the People
Pico, AlexanderKelder, Thomasvan Iersel, MartijnHanspers, KristinaConklin, BruceEvelo...PLoS Biology 2008, 6(7)
http://dx.doi.org/10.1371/journal.pbio.0060184
The Cladosporium fulvum virulence protein Avr2 inhibits host proteases required for basal defense
van Esse, H. P.Van't Klooster, J. W.Bolton, M. D.Yadeta, K. A.van, Baarlen P.Boeren, ...Plant Cell 2008, 20(7): 1948
http://www.ncbi.nlm.nih.gov/pubmed/18660430
Identification of Nipsnap1 as a novel auxiliary protein inhibiting TRPV6 activity
Schoeber, J. P.Topala, C. N.Lee, K. P.Lambers, T. T.Ricard, G.van der Kemp, A. W.Huyn...Pflugers Arch. 2008, 457(1): 91
http://www.ncbi.nlm.nih.gov/pubmed/18392847
On an elementary definition of visual saliency
Loog, M.Perception 2008, 37: 4
Maximizing the area under the ROC curve by pairwise feature combination
Marrocco, C.Duin, R. P. W.Tortorella, F.Pattern Recognition 2008, 41: 1961
Growing a multi-class classifier with a reject option
Tax, D. M.Duin, R. P. W.Pattern Recogn.Lett. 2008, 29: 1565
Integration of prior knowledge of measurement noise in kernel density classification
Li, Y.de Ridder, D.Duin, R. P. W.Reinders, M. J. T.Pattern Recogn. 2008, 41(1): 320
Distance measurements by combined method based on a femtosecond pulse laser
Joo, K. N.Kim, Y.Kim, S. W.Opt.Express 2008, 16(24): 19799
http://www.ncbi.nlm.nih.gov/pubmed/19030065
Similarities and Differences in Lipidomics Profiles among Healthy Monozygotic Twin Pairs
Draisma, H. H.Reijmers, T. H.Bobeldijk-Pastorova, I.Meulman, J. J.Estourgie-Van Burk,...OMICS. 2008, 12(1): 17
http://www.ncbi.nlm.nih.gov/pubmed/18266560
Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms
t Hoen, Peter A. C.Ariyurek, YavuzThygesen, Helene H.Vreugdenhil, ErnoVossen, Rolf H....Nucleic Acids Research 2008, 36(21)
http://www.ncbi.nlm.nih.gov/pubmed/18927111
PhyloPat: an updated version of the phylogenetic pattern database contains gene neighborhood
Hulsen, T.Groenen, P. M.de, Vlieg J.Alkema, W.Nucleic Acids Res. 2008
http://www.ncbi.nlm.nih.gov/pubmed/18832367
CoPub: a literature-based keyword enrichment tool for microarray data analysis
Frijters, R.Heupers, B.van, Beek P.Bouwhuis, M.van, Schaik R.de, Vlieg J.Polman, J.Al...Nucleic Acids Res. 2008, 36
http://www.ncbi.nlm.nih.gov/pubmed/18442992
Signature, a web server for taxonomic characterization of sequence samples using signature genes
Dutilh, B. E.He, Y.Hekkelman, M. L.Huynen, M. A.Nucleic Acids Res. 2008, 36
http://www.ncbi.nlm.nih.gov/pubmed/18487625
SEQATOMS: a web tool for identifying missing regions in PDB in sequence context
Brandt, B. W.Heringa, J.Leunissen, J. A.Nucleic Acids Res. 2008, 36
http://www.ncbi.nlm.nih.gov/pubmed/18463137
3D-Fun: predicting enzyme function from structure
Von Grotthuss, M.Plewczynski, D.Vriend, G.Rychlewski, L.Nucleic Acids Res 2008, 36
http://www.ncbi.nlm.nih.gov/pubmed/18515349
BioMagResBank
Ulrich, E. L.Akutsu, H.Doreleijers, J. F.Harano, Y.Ioannidis, Y. E.Lin, J.Livny, M.Ma...Nucleic Acids Res 2008, 36
http://www.ncbi.nlm.nih.gov/pubmed/17984079
Remediation of the protein data bank archive
Henrick, K.Feng, Z.Bluhm, W. F.Dimitropoulos, D.Doreleijers, J. F.Dutta, S.Flippen-An...Nucleic Acids Res 2008, 36
http://www.ncbi.nlm.nih.gov/pubmed/18073189
Identification of cancer genes using a statistical framework for multiexperiment analysis of nondiscretized array CGH data
Klijn, C. N.Holstege, H.de Ridder, J.Liu, X.Reinders, M. J. T.Jonkers, J.Wessels, L.Nucl.Acids Res. 2008
http://dx.doi.org/10.1093/nar/gkm1143
Gas chimney detection based on improving the performance of combined multilayer perception and support vector classifier
Hashemi, H.Tax, D. M.Duin, R. P.Javaherian, A.Groot, P. deNonlinear processes in geophysics 2008, 15(6): 863