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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. de

Nonlinear processes in geophysics 2008, 15(6): 863