Publication overview

Multiple testing on the directed acyclic graph of gene ontology

Goeman, J. J.Mansmann, U.

Bioinformatics. 2008, 24(4): 537

http://www.ncbi.nlm.nih.gov/pubmed/18203773

Finding Frequent Subgraphs in Biological Networks via Maximal Itemsets

Zantema, H.Wagemans, S.Bosnacki, D. Elloumi, M.ng, J.Linial, M.Murphy, R.Schneider, K.Toma, C.

Bioinformatics Research and Development. Second International Conference, BIRD 2008 Vienna, Austria, July 7-9, 2008 Proceedings 2008

Multi-RELIEF: a method to recognize specificity determining residues from multiple sequence alignments using a Machine-Learning approach for feature weighting

Ye, K.Anton, Feenstra K.Heringa, J.Ijzerman, A. P.Marchiori, E.

Bioinformatics 2008, 24(1): 18

http://www.ncbi.nlm.nih.gov/pubmed/18024975

Organization and integration of biomedical knowledge with concept maps for key peroxisomal pathways

Willemsen, A. M.Jansen, G. A.Komen, J. C.van, Hooff S.Waterham, H. R.Brites, P. M.Wan...

Bioinformatics 2008, 24(16)

http://www.ncbi.nlm.nih.gov/pubmed/18689827

Predicting and understanding transcription factor interactions based on sequence level determinants of combinatorial control

van Dijk, A. D.ter Braak, C. J.Immink, R. G.Angenent, G. C.van Ham, R. C.

Bioinformatics 2008, 24(1): 26

http://www.ncbi.nlm.nih.gov/pubmed/18024974

Predicting sub-Golgi localization of type II membrane proteins

van Dijk, A. D.Bosch, D.ter Braak, C. J.van der Krol, A. R.van Ham, R. C.

Bioinformatics 2008, 24(16): 1779

http://www.ncbi.nlm.nih.gov/pubmed/18562268

Jane: suggesting journals, finding experts

Schuemie, M. J.Kors, J. A.

Bioinformatics 2008, 24(5): 727

http://www.ncbi.nlm.nih.gov/pubmed/18227119

PRALINETM: a strategy for improved multiple alignment of transmembrane proteins

Pirovano, W.Feenstra, K. A.Heringa, J.

Bioinformatics 2008, 24(4): 492

http://www.ncbi.nlm.nih.gov/pubmed/18174178

Automated procedure for candidate compound selection in GC-MS metabolomics based on prediction of Kovats retention index

Mihaleva, V. V.Verhoeven, H. A.de Vos, R. C. H.Hall, R. D.van Ham, R. C. H. J.

Bioinformatics 2008

Combinatorial influence of environmental parameters on transcription factor activity

Knijnenburg, T. A.Wessels, L. F.Reinders, M. J.

Bioinformatics 2008, 24(13)

http://www.ncbi.nlm.nih.gov/pubmed/18586711

A noise model for mass spectrometry based proteomics

Du, P.Stolovitzky, G.Horvatovich, P.Bischoff, R.Lim, J.Suits, F.

Bioinformatics 2008, 24(8): 1070

http://www.ncbi.nlm.nih.gov/pubmed/18353791

High HDL cholesterol does not protect against coronary artery disease when associated with combined cholesteryl ester transfer protein and hepatic lipase gene variants

van Acker, B. A.Botma, G. J.Zwinderman, A. H.Kuivenhoven, J. A.linga-Thie, G. M.Sijbr...

Atherosclerosis 2008, 200(1): 161

http://www.ncbi.nlm.nih.gov/pubmed/18164013

Picornavirales, a proposed order of positive-sense single-stranded RNA viruses with a pseudo-T = 3 virion architecture

Le, Gall O.Christian, P.Fauquet, C. M.King, A. M.Knowles, N. J.Nakashima, N.Stanway, ...

Arch.Virol. 2008, 153(4): 715

http://www.ncbi.nlm.nih.gov/pubmed/18293057

A discriminating messenger RNA signature for bipolar disorder formed by an aberrant expression of inflammatory genes in monocytes

Padmos, R. C.Hillegers, M. H.Knijff, E. M.Vonk, R.Bouvy, A.Staal, F. J.de, Ridder D.K...

Arch.Gen.Psychiatry 2008, 65(4): 395

http://www.ncbi.nlm.nih.gov/pubmed/18391128

Genome-scale genotype-phenotype matching of two Lactococcus lactis isolates from plants identifies mechanisms of adaptation to the plant niche

Siezen, R. J.Starrenburg, M. J.Boekhorst, J.Renckens, B.Molenaar, D.van, Hylckama V.

Appl Environ Microbiol 2008, 74(2): 424

http://www.ncbi.nlm.nih.gov/pubmed/18039825

The VIZIER project: Preparedness against pathogenic RNA viruses

Coutard, B.Gorbalenya, A. E.Snijder, E. J.Leontovich, A. M.Poupon, A.De, Lamballerie ...

Antiviral Res. 2008, 78(1): 37

http://www.ncbi.nlm.nih.gov/pubmed/18083241

Analysis of gene expression identifies differentially expressed genes and pathways associated with lymphatic dissemination in patients with adenocarcinoma of the esophagus

Lagarde, S. M.Ver Loren van Themaat, P. E.Moerland, P. D.Gilhuijs-Pederson, L. A.Ten ...

Ann.Surg.Oncol. 2008, 15(12): 3459

http://www.ncbi.nlm.nih.gov/pubmed/18825457

Synovial tissue response to rituximab: mechanism of action and identification of biomarkers of response

Thurlings, R. M.Vos, K.Wijbrandts, C. A.Zwinderman, A. H.Gerlag, D. M.Tak, P. P.

Ann Rheum Dis 2008, 67(7): 917

http://www.ncbi.nlm.nih.gov/pubmed/17965121

Multiscale and modular analysis of cardiac energy metabolism. Repairing the broken interfaces of isolated system components

van Beek, J. H. G. M.

Ann NY Acad Sci 2008

A new two-dimensional method for time aligning liquid chromatography-mass spectrometry data

Suits, F.Lepre, J.Du, R.Bischoff, P.Horvatovich, P.

Analytical Chemistry 2008, 80(9): 3095

Optimized Time Alignment Algorithm for LC-MS Data: Correlation Optimized Warping Using Component Detection Algorithm-Selected Mass Chromatograms

Christin, C.Smilde, A. K.Hoefsloot, H. C.Suits, F.Bischoff, R.Horvatovich, P. L.

Anal.Chem. 2008

http://www.ncbi.nlm.nih.gov/pubmed/18715018

Multiplexed proteomics mapping of yeast RNA polymerase II and III allows near-complete sequence coverage and reveals several novel phosphorylation sites

Mohammed, S.Lorenzen, K.Kerkhoven, R.van, Breukelen B.Vannini, A.Cramer, P.Heck, A. J...

Anal Chem. 2008, 80(10): 3584

http://www.ncbi.nlm.nih.gov/pubmed/18416563

Gross deletions involving IGHM, BTK, or Artemis: a model for genomic lesions mediated by transposable elements

van Zelm, M. C.Geertsema, C.Nieuwenhuis, N.de, Ridder D.Conley, M. E.Schiff, C.Tezcan...

Am.J Hum.Genet. 2008, 82(2): 320

http://www.ncbi.nlm.nih.gov/pubmed/18252213

Mutations of ESRRB encoding estrogen-related receptor beta cause autosomal-recessive nonsyndromic hearing impairment DFNB35

Collin, R. W.Kalay, E.Tariq, M.Peters, T.van der, Zwaag B.Venselaar, H.Oostrik, J.Lee...

Am J Hum Genet 2008, 82(1): 125

http://www.ncbi.nlm.nih.gov/pubmed/18179891

A critical view of metbolic network adaptations

Papp, B.Teusink, B.Notebaart, R. A.

Adv.Online Publications HFSP Journal 2008

http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=H...

Biomarkers for lysosomal storage disorders: identification and application as exemplified by chitotriosidase in Gaucher disease

Aerts, J. M.van Breemen, M. J.Bussink, A. P.Ghauharali, K.Sprenger, R.Boot, R. G.Groe...

Acta Paediatr.Suppl 2008, 97(457): 7

http://www.ncbi.nlm.nih.gov/pubmed/18339181

Unified relevance models for rating prediction in coolborative filtering

Wang, J.de Vries, A. P.Reinders, M. J. T.

ACM Transactions on information systems 2008, 26(3): 16

Parsimonious Relevance Models

Meij, E.Weerkamp, W.Balog, K.de Rijke, M.

31st Annual International ACM SIGRI Conference on Research & Development on Information Retrieval 2008

Towards a combined model for search and navigation of annotated documents

Meij, E.

31st Annual International ACM SIGRI Conference on Research & Development on Information Retrieval 2008

Temporal Extrapolation within a Static Clustering

Cocx, T. K.Kosters, W.Laros, J. F. J. An, A.Matwin, S.Ras, Z. W.Slezak, D.

17th International Symposium on Methodologies for Intelligent Systems (ISMIS'08) 2008: 189

Bootstrapping Language Associated with Biomedical Entities

Meij, E.Katrenko, S.

16th text retrieval conference (TREC) proceedings 2008

The role of molecular structures in scientists' work

Vyas, D. M.Kulyk, O.van der Vet, P. E.Nijholt, A.

15th European Conference on Cognitive Ergonomics 2008: 1

Situational awareness support to enhance teamwork in collaborative working environments

Kulyk, O.van der Veer, G. C.van Dijk, E. M. A. G.

15th European Conference on Cognitive Ergonomics 2008: 18

Online segmentation of continuous gesturing in interfaces

Fikkert, W.van der Vet, P. E.Nijholt, A.

6th International Conference on Methods and Techniques in Behavorial Research 2008

Measuring behavior using motion capture symposium (editorial)

Fikkert, W.van der Kooij, H.Ruttkay, Zsvan Welbergen, H.

6th International Conference on Methods and Techniques in Behavorial Research 2008

Information visualization from ontology

Dmitrieva, J.Verbeek, F.

5th International Conference on formal ontology in information systems 2008

Enable data transport between web services through alternative protocols and streaming

Koulouzis, S.Meij, E.Marshall, M. S.Belloum, A.

4th IEEE International Conference on Escience 2008

Dividing Protein Interacction Networks by Growing Orthologous Articulations

Jancura, P.Heringa, J.Marchiori, E.

3rd IAPR in Bioinformatics 2008

miRNA Target Prediction through Mining of miRNA Relationships

Zhang, Y.de Bruin, J.verbeek, F. J.

 2008

System reduction and abstraction of biochemical reaction systems for a genetic network of Escherichia coli - Report 1

van Schuppen, J. H.

 2008

Problems of control and system theory motivated by biochemical reaction systems

van Schuppen, J. H.

 2008

Dynamic software infrastructures for the life sciences

Swertz, M.A.

 2008

Realization theory for rational systems: Minimal rational realizations

Nemcova, J.van Schuppen, J. H.

 2008

Realization theory for rational systems

Nemcova, J.van Schuppen, J. H.

 2008

Sticks, balls or a ribbon? results of a formative user study with bioinformaticians

Kulyk, O.Wassink, I.van der Vet, P. E.van der Veer, G. C.van Dijk, E. M. A. G.

 2008

On The Design of Knowledge Discovery Services: Design Patterns and Their Application In A Use Case Implementation

de Bruin, J.Kok, J.Lavrac, N.Trajkovski, I.

 2008

Towards Service-Oriented Knowledge Discovery: A Case Study

de Bruin, J.Kok, J.Lavrac, N.Trajkovski, I.

 2008

Stability of Clusters for Different Time Adjustments in Complex Disease Research

Colas, F.Meulenbelt, I.Houwing-Duistermaat, J.Kloppenburg, M.Watt, I.van Rooden, S. M...

 2008

A Scenario Implementation in R for Subtype Discovery Examplified on Chemoinformatics Data

Colas, F.Meulenbelt, I.Houwing-Duistermaat, J.Kloppenburg, M.Watt, I.van Rooden, S. M...

 2008

Enhancing the Automated Analysis of Criminal Careers

Cocx, T. K.Kosters, W. A.Laros, J. F. J.

 2008