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Publication overview

Papain-like protease 1 from transmissible gastroenteritis virus: crystal structure and enzymatic activity toward viral and cellular substrates

Wojdyla, J. A.Manolaridis, I.van Kasteren, P. B.Kikkert, M.Snijder, E. J.Gorbalenya, ...

J Virol, 84(19): 10063

Multidimensional chromatography coupled to mass spectrometry in analysing complex proteomics samples

Horvatovich, P.Hoekman, B.Govorukhina, N.Bischoff, R.

J Sep Sci, 33(10): 1421

APECS: A new strategy for selecting precursors in 2D-LC-MALDI-TOF/TOF experiments on complex biological samples

Gandhi, T.Fusetti, F.Wiederhold, E.Breitling, R.Poolman, B.Permentier, H. P.

J Proteome Res

Electron Density Fingerprints (EDprints): Virtual Screening Using Assembled Information of Electron Density

Kooistra, A. J.Binsl, T. W.van Beek, J. Graaf, C.Heringa, J.

J Chem Inf Model

HSPVdb-the Human Short Peptide Variation Database for improved mass spectrometry-based detection of polymorphic HLA-ligands

Nijveen, H.Kester, M. G.Hassan, C.Viars, Ru, A. Jager, M.Falkenburg, J. H.L...

Immunogenetics, 63(3): 143

The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance

Atanur, S. S.Birol, I.Guryev, V.Hirst, M.Hummel, O.Morrissey, C.Behmoaras, J.Fernande...

Genome Res, 20(6): 791

The Micronutrient Genomics Project: a community-driven knowledge base for micronutrient research

van Ommen, B.El-Sohemy, A.Hesketh, J.Kaput, J.Fenech, M.Evelo, C. T.McArdle, H. J.Bou...

Genes Nutr, 5(4): 285

Homology modelling and spectroscopy, a never-ending love story

Venselaar, H.Joosten, R. P.Vroling, B.Baakman, C. A.Hekkelman, M. L.Krieger, E.Vriend...

Eur Biophys J, 39(4): 551

Biotransformation pathway maps in WikiPathways enable direct visualization of drug metabolism related expression changes

Jennen, D. G.Gaj, S.Giesbertz, P. J.van Delft, J. H.Evelo, C. T.Kleinjans, J. C.

Drug Discov Today, 15(19): 851

The impact of delayed storage on the proteome and metabolome of human cerebrospinal fluid (CSF)

Rosenling, T.Stoop, M. P.Smolinska, A.Muilwijk, B.Coulier, L.Shi, S.Dane, A.Christin,...

Clinical Chemistry

Systems microscopy approaches to understand cancer cell migration and metastasis

Le Devedec, S. E.Yan, Bont, H.Ghotra, V.Truong, H.Danen, E. H.Verbeek, F.van de ...

Cell Mol Life Sci, 67(19): 3219

Functional overlap and regulatory links shape genetic interactions between signaling pathways

van Wageningen, S.Kemmeren, P.Lijnzaad, P.Margaritis, T.Benschop, J. Castro, I. ...

Cell, 143(6): 991

Modeling Gradients with Petri Nets

Bertens, L.M.F.Kleijn,J.Koutny, M.Verbeek, F.J.


GPCR-OKB: the G Protein Coupled Receptor Oligomer Knowledge Base

Khelashvili, G.Dorff, K.Shan, J.Camacho-Artacho, M.Skrabanek, L.Vroling, B.Bouvier, M...

Bioinformatics, 26(14): 1804

Comparing genome-wide chromatin profiles using ChIP-chip or ChIP-seq

Johannes, F.Wardenaar, R.Colome-Tatche, M.Mousson, Graaf, P.Mokry, M.Guryev, V.T...

Bioinformatics, 26(8): 1000

PanCGHweb: a web tool for genotype calling in pangenome CGH data

Bayjanov, J. R.Siezen, R. J.van Hijum, S. A.

Bioinformatics, 26(9): 1256

R/qtl: high-throughput multiple QTL mapping

Arends, D.Prins, P.Jansen, R. C.Broman, K. W.

Bioinformatics, 26(23): 2990

A high-throughput, user-friendly processing service for retention time alignment of complex proteomics and metabolomics LC-MS data

Ahmad, I.Suits, F.Swertz, M.Dijkstra, M.Hooft, R.Katsubo, D.van Breukelen, B.Bischoff...


Practical application of bioinformatics by the multidisciplinary VIZIER consortium

Gorbalenya, A. E.Lieutaud, P.Harris, M. R.Coutard, B.Canard, B.Kleywegt, G. J.Kravche...

Antiviral Res, 87(2): 95

Genomics and structure/function studies of Rhabdoviridae proteins involved in replication and transcription

Assenberg, R.Delmas, O.Morin, B.Graham, S. C.De Lamballerie, X.Laubert, C.Coutard, B....

Antiviral Res, 87(2): 149

Analysis of cardiac development in the turtle Emys orbicularis (Testudines: Emidydae) using 3-D computer modeling from histological sections

Bertens, L. M.Richardson, M. K.Verbeek, F. J.

Anat Rec (Hoboken), 293(7): 1101

The 2C putative helicase of echovirus 30 adopts a hexameric ring-shaped structure

Papageorgiou, N.Coutard, B.Lantez, V.Gautron, E.Chauvet, O.Baronti, C.Norder, La...

Acta Crystallogr D Biol Crystallogr, 66: 1116

Fully automatic registration and segmentation of first-pass myocardial perfusion MR image sequences

Gupta, V.Hendriks, E. A.Milles, J.van der Geest, R. J.Jerosch-Herold, M.Reiber, J. H....

Acad Radiol, 17(11): 1375

A comparison of database systems for XML-type data

Risse, J.Leunissen, J.

Interface Residues Contribute Dominantly to the Interaction Between Proteins – An in silico Mutagenesis Study

Pool, R.May, A.Feenstra, K.A.Heringa, J.

A Coarse-Grained Approach for Modeling Interactions Between Proteins

Pool, R.May, A.Feenstra, K.A.Heringa, J.

Enabling Grand-Canonical Monte Carlo with the GROMACS molecular simulation package – An Extension of GromPy

Pool, R.Keenstra, K.A.Heringa, J.

Micro-RNA during bacterial Infections in Zebrafish

Ordas, A.Zakrzewska, A.Stockhammer, O.W.Carvalho, R.van der Sar, A.M.Zhang, Y.Verbeek...

Liver tumor-related miRNA expression is conserved between Zebrafish and Human

Ordas, A.He, S.Gong, Z.Zhang, Y.Verbeek, F.J.Mink, M.Spaink, H.P.Snaar-Jagalska, B.E....

ProRepeat: an integrated repository for studying amino acid tandem repeats in proteins

Luo, H.Nijveen, HarmLin, K.Leunissen, J.

REGENT: Reverse engineering of gene regulation networks using thresholds on correlation and p-values

Ligtenberg, W.P.A.Bosnacki, D.Moerland, P.D.Hilbers, P.A.J.

ReConn: A Cytoscape plug-in for exploring and visualizing Reactome

Ligtenberg, W.P.A.Bosnacki, D.Hilbers, P.A.J.