Publication overview
PanCGH: a genotype-calling algorithm for pangenome CGH data
Bayjanov, J. R.Wels, M.Starrenburg, M.van, Hylckama V.Siezen, R. J.Molenaar, D.Bioinformatics 2009, 25(3): 309
http://www.ncbi.nlm.nih.gov/pubmed/19129208
Zebrafish development and regeneration: new tools for biomedical research
Brittijn, S. A.Duivesteijn, S. J.Belmamoune, M.Bertens, L. F.Bitter, W.de Bruijn, J. ...Int J Dev.Biol. 2009, 53(5): 835
http://www.ncbi.nlm.nih.gov/pubmed/19557689
MINOMICS: visualizing prokaryote transcriptomics and proteomics data in a genomic context
Brouwer, R. W.van Hijum, S. A.Kuipers, O. P.Bioinformatics 2009, 25(1): 139
http://www.ncbi.nlm.nih.gov/pubmed/19008250
Metabolite and reaction inference based on enzyme specificities
de Groot, M. J.van Berlo, R. J.van Winden, W. A.Verheijen, P. J.Reinders, M. J.de, Ri...Bioinformatics 2009
http://www.ncbi.nlm.nih.gov/pubmed/19696044
SigWinR; the SigWin-detector updated and ported to R
de Leeuw, W. C.Rauwerda, H.Inda, M.Bruning, O.Breit, T.BMC Res.Notes 2009
Optimal analysis of complex protein mass spectra
Dijkstra, M.Jansen, R. C.Proteomics. 2009, 9(15): 3869
http://www.ncbi.nlm.nih.gov/pubmed/19639597
Multi-view Ontology Visualization
Dmitrieva, J.Verbeeek, F. J.Proceedings 11th International Protege Conference 2009
http://protege.stanford.edu/conference/2009/abstracts/S9P3Dmitrieva.pd...
Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly
Dutilh, B. E.Huynen, M. A.Strous, M.Bioinformatics 2009
http://www.ncbi.nlm.nih.gov/pubmed/19542148
Correlating MALDI and SIMS imaging mass spectrometric datasets of biological tissue surfaces
Eijkel, G. B.Kukrer Kaleta, B.van der Wiel, I. M.Kros, J. M.Luider, T. M.Heeren, R. M...Interface Anal. 2009, 41(8): 675
http://www3.interscience.wiley.com/cgi-bin/fulltext/122512410/PDFSTART
Identification of two new serum protein profiles for renal cell carcinoma
Engwegen, J. Y.Mehra, N.Haanen, J. B.Schellens, J. H.Voest, E. E.Beijnen, J. H.Oncol.Rep. 2009, 22(2): 401
http://www.ncbi.nlm.nih.gov/pubmed/19578783
Gestures to Intuitively Control Large Displays
Fikkert, W.van der Vet, P. E.Rauwerda, H.Breit, T.Nijholt, A.Sales Dias, M.Gibet, S.W...Advances in Gesture-Based Human-Computer Interaction and Simulation 2009: 199
Cohesive versus flexible evolution of functional modules in eukaryotes
Fokkens, L.Snel, B.PLoS Comput.Biol. 2009, 5(1)
http://www.ncbi.nlm.nih.gov/pubmed/19180181
System-wide molecular evidence for phenotypic buffering in Arabidopsis
Fu, J.Keurentjes, J. J.Bouwmeester, H.America, T.Verstappen, F. W.Ward, J. L.Beale, M...Nat Genet. 2009, 41(2): 166
http://www.ncbi.nlm.nih.gov/pubmed/19169256
Clinical proteomics in breast cancer: a review
Gast, M. C.Schellens, J. H.Beijnen, J. H.Breast Cancer Res.Treat. 2009, 116(1): 17
http://www.ncbi.nlm.nih.gov/pubmed/19082706
Serum protein profiling for diagnosis of breast cancer using SELDI-TOF MS
Gast, M. C.Van Gils, C. H.Wessels, L. F.Harris, N.Bonfrer, J. M.Rutgers, E. J.Schelle...Oncol.Rep. 2009, 22(1): 205
http://www.ncbi.nlm.nih.gov/pubmed/19513525
Influence of sample storage duration on serum protein profiles assessed by surface-enhanced laser desorption/ionisation time-of-flight mass spectrometry (SELDI-TOF MS)
Gast, M. C.Van Gils, C. H.Wessels, L. F.Harris, N.Bonfrer, J. M.Rutgers, E. J.Schelle...Clin.Chem.Lab Med. 2009, 47(6): 694
http://www.ncbi.nlm.nih.gov/pubmed/19416081
Constraint-based probabilistic learning of metabolic pathways from tomato volatiles
Gavai, A. K.Tikunov, Y.Ursem, R.Bovy, A.van Eeuwijk, F.Nijveen, H.Lucas, P. J. F.Leun...Metabolomics 2009
http://www.springerlink.com/content/p4x6t8362321h85h/fulltext.pdf
Understanding the alphaviruses: Recent research on important emerging pathogens and progress towards their control
Gould, E. A.Coutard, B.Malet, H.Morin, B.Jamal, S.Weaver, S.Gorbalenya, A.Moureau, G....Antiviral Res. 2009
http://www.ncbi.nlm.nih.gov/pubmed/19616028
Influence of clotting time on the protein composition of serum samples based on LC-MS data
Govorukhina, N. I.de, Vries M.Reijmers, T. H.Horvatovich, P.van der Zee, A. G.Bischof...J Chromatogr.B Analyt.Technol.Biomed Life Sci. 2009, 877(13): 1281
http://www.ncbi.nlm.nih.gov/pubmed/18996063
Gene expression profiling of the forming atrioventricular node using a novel tbx3-based node-specific transgenic reporter
Horsthuis, T.Buermans, H. P.Brons, J. F.Verkerk, A. O.Bakker, M. L.Wakker, V.Clout, D...Circ.Res. 2009, 105(1): 61
http://www.ncbi.nlm.nih.gov/pubmed/19498200
Mitochondrial proteome evolution and genetic disease
Huynen, M. A.de, Hollander M.Szklarczyk, R.Biochim.Biophys Acta 2009
http://www.ncbi.nlm.nih.gov/pubmed/19328849
2-DE and MS analysis of key proteins in the adhesion of Lactobacillus plantarum, a first step toward early selection of probiotics based on bacterial biomarkers
Izquierdo, E.Horvatovich, P.Marchioni, E.oude-Werner, D.Sanz, Y.Ennahar, S.Electrophoresis 2009, 30(6): 949
http://www.ncbi.nlm.nih.gov/pubmed/19309013
Defining gene and QTL networks
Jansen, R. C.Tesson, B. M.Fu, J.Yang, Y.McIntyre, L. M.Curr.Opin.Plant Biol. 2009
http://www.ncbi.nlm.nih.gov/pubmed/19196544
Finding transcriptomics biomarkers for in vivo identification of (non-)genotoxic carcinogens using wild-type and Xpa/p53 mutant mouse models
Jonker, M. J.Bruning, O.van, Iterson M.Schaap, M. M.van der Hoeven, T. V.Vrieling, H....Carcinogenesis 2009
http://www.ncbi.nlm.nih.gov/pubmed/19696161
PDB_REDO: automated re-refinement of X-ray structure models in the PDB
Joosten, R. P.Salzemann, J.Bloch, V.Stockinger, H.Berglund, A. C.Blanchet, C.Bongcam-...J.Appl.Cryst. 2009, 42: 376
Re-refinement from deposited X-ray data can deliver improved models for most PDB entries
Joosten, R. P.Womack, T.Vriend, G.Bricogne, G.Acta Crystallogr.D.Biol.Crystallogr. 2009, 65: 176
http://www.ncbi.nlm.nih.gov/pubmed/19171973
Cyttron: A Virtualized Microscope supporting image integration and knowledge discovery
Kallergi, A.Bei, Y.Kok, P.Dijkstra, J.Abrahams, J. P.Verbeeek, F. J.Cell Death and Disease Series 2009
Correlated mutation analyses on super-family alignments reveal functionally important residues
Kuipers, R. K.Joosten, H. J.Verwiel, E.Paans, S.Akerboom, J.van der, Oost J.Leferink,...Proteins 2009, 76(3): 608
http://www.ncbi.nlm.nih.gov/pubmed/19274741
Situational awareness support to enhance teamwork in collaborative working environments
Kulyk, O.van Dijk, E. M. A. G.van der Vet, P. E.Nijholt, A.Whitworth, B.de Moor, A.Handbook on Socio-Technical Design and Social Networking Systems 2009: 635
A pathway approach to align regulatory-metabolic networks
Li, Y.Bot, J.Reinders, M.de Ridder, D.8th CSB2009 2009
http://ict.ewi.tudelft.nl/pub/yunlei/055Li.pdf
designGG: an R-package and web tool for the optimal design of genetical genomics experiments
Li, Y.Swertz, M. A.Vera, G.Fu, J.Breitling, R.Jansen, R. C.BMC Bioinformatics 2009, 10: 188
http://www.ncbi.nlm.nih.gov/pubmed/19538731
Limitations and possibilities of small RNA digital gene expression profiling
Linsen, S. E.de, Wit E.Janssens, G.Heater, S.Chapman, L.Parkin, R. K.Fritz, B.Wyman, ...Nat Methods 2009, 6(7): 474
http://www.ncbi.nlm.nih.gov/pubmed/19564845
The crystal structures of Chikungunya and Venezuelan equine encephalitis virus nsP3 macro domains define a conserved adenosine binding pocket
Malet, H.Coutard, B.Jamal, S.Dutartre, H.Papageorgiou, N.Neuvonen, M.Ahola, T.Forrest...J Virol. 2009, 83(13): 6534
http://www.ncbi.nlm.nih.gov/pubmed/19386706
Structure of the C-terminal domain of nsp4 from feline coronavirus
Manolaridis, I.Wojdyla, J. A.Panjikar, S.Snijder, E. J.Gorbalenya, A. E.Berglind, H.N...Acta Crystallogr.D.Biol.Crystallogr. 2009, 65: 839
http://www.ncbi.nlm.nih.gov/pubmed/19622868
De AIDA toolbox: Een gecombineerde aanpak voor het beheren van kennis
Marshall, M. S.Roos, M.Meij, E.Katrenko, S.van Hage, W. R.Adriaans, P. W.Agro Informatica 2009, 21(4): 5
Integrated analysis of DNA copy number and gene expression microarray data using gene sets
Menezes, R. X.Boetzer, M.Sieswerda, M.van Ommen, G. J.Boer, J. M.BMC Bioinformatics 2009, 10: 203
http://www.ncbi.nlm.nih.gov/pubmed/19563656
Analysis of mass spectrometry data using sub-spectra
Meuleman, W.Engwegen, J. Y.Gast, M. C.Wessels, L. F.Reinders, M. J.BMC Bioinformatics 2009, 10
http://www.ncbi.nlm.nih.gov/pubmed/19208154
Structure and function of 2,3-dimethylmalate lyase, a PEP mutase/isocitrate lyase superfamily member
Narayanan, B.Niu, W.Joosten, H. J.Li, Z.Kuipers, R. K.Schaap, P. J.Dunaway-Mariano, D...J Mol.Biol. 2009, 386(2): 486
http://www.ncbi.nlm.nih.gov/pubmed/19133276
Biochemical characterization of arterivirus nonstructural protein 11 reveals the nidovirus-wide conservation of a replicative endoribonuclease
Nedialkova, D. D.Ulferts, R.van den, Born E.Lauber, C.Gorbalenya, A. E.Ziebuhr, J.Sni...J Virol. 2009, 83(11): 5671
http://www.ncbi.nlm.nih.gov/pubmed/19297500
OligoRAP - an Oligo Re-Annotation Pipeline to improve annotation and estimate target specificity
Neerincx, P. B.Rauwerda, H.Nie, H.Groenen, M. A.Breit, T.Leunissen, J. A.BMC Proceedings 2009, 16(3)
Asymmetric relationships between proteins shape genome evolution
Notebaart, R. A.Kensche, P. R.Huynen, M. A.Dutilh, B. E.Genome Biol. 2009, 10(2)
http://www.ncbi.nlm.nih.gov/pubmed/19216750
A critical view of metabolic network adaptations
Papp, B.Teusink, B.Notebaart, R. A.HFSP J 2009, 3(1): 24
http://www.ncbi.nlm.nih.gov/pubmed/19492021
Clustering of codons with rare cognate tRNAs in human genes suggests an extra level of expression regulation
Parmley, J. L.Huynen, M. A.PLoS Genet. 2009, 5(7)
http://www.ncbi.nlm.nih.gov/pubmed/19578405
Crystal structures of the X-domains of a Group-1 and a Group-3 coronavirus reveal that ADP-ribose-binding may not be a conserved property
Piotrowski, Y.Hansen, G.Boomaars-van der Zanden, A. L.Snijder, E. J.Gorbalenya, A. E....Protein Sci. 2009, 18(1): 6
http://www.ncbi.nlm.nih.gov/pubmed/19177346
Lef1 plays a role in patterning the mesoderm and ectoderm in Xenopus tropicalis
Roel, G.Gent, Y.Peterson-Maduro, J.Verbeek, F.Destree, O.Int.Journal of Developmental Biology 2009
http://www.ncbi.nlm.nih.gov/pubmed/19123129
Comparison of isotope-labeled amino acid incorporation rates (CILAIR) provides a quantitative method to study tissue secretomes
Roelofsen, H.Dijkstra, M.Weening, D.de Vries, M. P.Hoek, A.Vonk, R. J.Mol.Cell Proteomics. 2009, 8(2): 316
http://www.ncbi.nlm.nih.gov/pubmed/18840871
Organ-specific attenuation of murine hepatitis virus strain A59 by replacement of catalytic residues in the putative viral cyclic phosphodiesterase ns2
Roth-Cross, J. K.Stokes, H.Chang, G.Chua, M. M.Thiel, V.Weiss, S. R.Gorbalenya, A. E....J Virol. 2009, 83(8): 3743
http://www.ncbi.nlm.nih.gov/pubmed/19176619
Life Sciences on the semantic web: the nerocommons and beyond
Ruttenberg, A.Rees, J.Samwald, M.Marshall, M. S.Brief Bioinform 2009
Mutations in NDUFAF3 (C3ORF60), encoding an NDUFAF4 (C6ORF66)-interacting complex I assembly protein, cause fatal neonatal mitochondrial disease
Saada, A.Vogel, R. O.Hoefs, S. J.van den Brand, M. A.Wessels, H. J.Willems, P. H.Vens...Am.J Hum.Genet. 2009, 84(6): 718
http://www.ncbi.nlm.nih.gov/pubmed/19463981
Suppression of inflammatory signaling in monocytes from patients with coronary artery disease
Schirmer, S. H.Fledderus, J. O.van der Laan, A. M.van der Pouw-Kraan, T. C.Moerland, ...J.Mol.Cell Cardiol. 2009, 46(2): 177
