PhD Thesis
 1 |
Pharmacophylogenomics - Explaining interspecies differences in drug discovery T. Hulsen Radboud University Nijmegen 2007 |
Scientific papers - Authorships
 1 |
Heavier-than-air flying machines are impossible L. Oliveira, T. Hulsen, D. Lutje Hulsik, A.C.M. Paiva and G. Vriend FEBS Letters 2004, 564 (3): 269-273 PubMed: 15111108 (Final submitted version) (Earlier, more extended version) |
 2 |
Benchmarking ortholog identification methods using functional genomics data T. Hulsen, M.A. Huynen, J. de Vlieg and P.M.A. Groenen Genome Biology 2006, 7 (4): R31 PubMed: 16613613 (Supplementary information) |
| 3 |
PhyloPat: phylogenetic pattern analysis of genes T. Hulsen, J. de Vlieg and P.M.A. Groenen BMC Bioinformatics 2006, 7 (1): 398 PubMed: 16948844 (Web application) |
| 4 |
Testing statistical significance scores of sequence comparison methods using structure similarity T. Hulsen, J. de Vlieg, J.A.M. Leunissen and P.M.A. Groenen BMC Bioinformatics 2006, 7 (1): 444 PubMed: 17038163 (Supplementary information) |
 5 |
Identification of novel functional TBP-binding sites and general factor repertoires S. Denissov, M.A. van Driel, R. Voit, M.L. Hekkelman, T. Hulsen, N. Hernandez, I. Grummt, R. Wehrens and H.G. Stunnenberg EMBO J. 2007, 26 (4): 944-954 PubMed: 17268553 |
 6 |
Evolution of closely linked gene pairs in vertebrate genomes E. Franck, T. Hulsen, M.A. Huynen, W.W. de Jong, N.H. Lubsen and O. Madsen Mol. Biol. Evol. 2008, 25 (9): 1909-1921 PubMed: 18566020 |
| 7 |
PhyloPat: an updated version of the phylogenetic pattern database contains gene neighborhood T. Hulsen, P.M.A. Groenen, J. de Vlieg and W. Alkema Nucleic Acids Res. 2009, 37 (Database issue): D731-D737 PubMed: 18832367 (Web application) |
| 8 |
BioVenn - a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams T. Hulsen, J. de Vlieg and W. Alkema BMC Genomics 2008, 9 (1): 488 PubMed: 18925949 (Web application) |
 9 |
The construction of genome-based transcriptional units S.R. van Hooff, J. Koster, T. Hulsen, B.D.C. van Schaik, M. Roos, M.F. van Batenburg, R. Versteeg and A.H.C. van Kampen OMICS: A Journal of Integrative Biology 2009, 13 (2): 105-114 PubMed: 19320556 |
| 10 |
Identification of new biomarkers for glucocorticoid induced insulin resistance using literature mining W.W.M. Fleuren, E. Toonen, S. Verhoeven, R. Frijters, T. Hulsen, T. Rullmann, R. van Schaik, J. de Vlieg and W. Alkema BioData Mining 2012, 6: 2 PubMed: 23379763 |
 11 |
From Big Data to Precision Medicine T. Hulsen, S.S. Jamuar, A.R. Moody, J.H. Karnes, V. Orsolya, S. Hedensted, R. Spreafico, D.A. Hafler and E.F. McKinney Frontiers in Medicine 2019, 6: 34 PubMed: 30881956 |
 12 |
An overview of publicly available patient-centered prostate cancer datasets T. Hulsen Translational Andrology and Urology 2019, 8 (Suppl 1): S64-S77 PubMed: 31143673 |
 13 |
The Ten Commandments of Translational Research Informatics T. Hulsen Data Science 2019, 2: 341-352 |
Scientific papers - Book chapters
 1 |
International AS Registry: The Movember Foundation's Global Action Plan Prostate Cancer Active Surveillance Initiative S.M. Bruinsma, D. Nieboer, T. Hulsen, L. Zhang, R. Kirk-Burnnand, S. Gledhill, M. Buzza Active Surveillance for Localized Prostate Cancer. Current Clinical Urology 2018, 135-147 |
Scientific papers - Collaborations
| 1 |
Expert consensus document: Semantics in active surveillance for men with localized prostate cancer - results of a modified Delphi consensus procedure S.M. Bruinsma, M.J. Roobol, P.R. Carroll, L. Klotz, T. Pickles, C.M. Moore, V.J. Gnanapragasam, A. Villers, A. Rannikko, R. Valdagni, M. Frydenberg, Y. Kakehi, C.P. Filson, C.H. Bangma, Movember Foundation's Global Action Plan Prostate Cancer Active Surveillance (GAP3) consortium Nature Reviews Urology 2017, 14 (5): 312-322 PubMed: 28290462 |
 2 |
The Movember Foundation's GAP3 cohort: A profile of the largest global prostate cancer active surveillance database to date S.M. Bruinsma, L. Zhang, M.J. Roobol, C.H. Bangma, E.W. Steyerberg, D. Nieboer, M. Van Hemelrijck, Movember Foundation's Global Action Plan Prostate Cancer Active Surveillance (GAP3) consortium BJU International 2018, 121 (5): 737-744 PubMed: 29247473 |
| 3 |
Consistent Biopsy Quality and Gleason Grading Within the Global Active Surveillance Global Action Plan 3 Initiative: A Prerequisite for Future Studies T.H. van der Kwast, J. Helleman, D. Nieboer, S.M. Bruinsma, M.J. Roobol, Movember Foundation's Global Action Plan Prostate Cancer Active Surveillance (GAP3) consortium European Urology Oncology 2019, 2 (3) PubMed: 31200849 |
| 4 |
Reasons for Discontinuing Active Surveillance: Assessment of 21 Centres in 12 Countries in the Movember GAP3 Consortium M. van Hemelrijck, X. Ji, J. Helleman, M.J. Roobol, W. van der Linden, D. Nieboer, C.H. Bangma, M. Frydenberg, A. Rannikko, L.S. Lee, V.J. Gnanapragasami, M.W. Kattan, Movember Foundation's Global Action Plan Prostate Cancer Active Surveillance (GAP3) consortium European Urology 2019, 75 (3): 523-531 PubMed: 30385049 |
| 5 |
Predicting Biopsy Outcomes During Active Surveillance for Prostate Cancer: External Validation of the Canary Prostate Active Surveillance Study Risk Calculators in Five Large Active Surveillance Cohorts F.-J. H. Drost, D. Nieboer, T.M. Morgan, P.R. Carroll, M.J. Roobol, Movember Foundation's Global Action Plan Prostate Cancer Active Surveillance (GAP3) consortium European Urology 2019, 76 (5): 693-702 PubMed: 31451332 |
| 6 |
Adherence to Active Surveillance Protocols for Low-risk Prostate Cancer: Results of the Movember Foundation’s Global Action Plan Prostate Cancer Active Surveillance Initiative A.A. Kalaparaa, J.F.M. Verbeek, D. Nieboer, M. Fahey, V. Gnanapragasam, M. Van Hemelrijck, L.S. Lee, C.H. Bangma, E.W. Steyerberg, T. Harkin, J. Helleman, M.J. Roobol, M. Frydenberg, Movember Foundation`s Global Action Plan Prostate Cancer Active Surveillance (GAP3) Consortium European Urology Oncology 2019, ?? (?): ???-??? PubMed: 31564531 |
Scientific papers - Acknowledgements
 1 |
Gene Array Analysis of Bone Morphogenetic Protein Type I Receptor-induced Osteoblast Differentiation O. Korchynskyi, K.J. Dechering, A. Sijbers, W. Olijve and P. ten Dijke Journal of Bone and Mineral Research (JBMR) 2003, 18 (7): 1177-1185 PubMed: 12854827 |
| 2 |
A text-mining analysis of the human phenome M.A. van Driel, J. Bruggeman, G. Vriend, H.G. Brunner, J.A. Leunissen Eur J Hum Genet. 2006, 14 (5): 535-542 PubMed: 16493445 |
| 3 |
The human phylome J. Huerta-Cepas, H. Dopazo, J. Dopazo, T. Gabaldon Genome Biology 2007, 8: R109 PubMed: 17567924 |
 4 |
Commercial harvest of logging residue in clear-cuts affects the diversity and community composition of ground beetles (Coleoptera: Carabidae) K. Nitterus, M. Astrom, B. Gunnarsson Scandinavian Journal of Forest Research 2007, 22 (3): 231-240 |
| 5 |
Plasma Membrane Proteomics E. Alexandersson, N. Gustavsson, K. Bernfur, P. Kjellbom, C. Larsson Plant Proteomics 2007, 186-206 |
 6 |
Multiple Ionization Mass Spectrometry Strategy Used To Reveal the Complexity of Metabolomics A. Nordstrom, E. Want, T. Northen, J. Lehtio, G. Siuzdak Analytical Chemistry 2008, 80 (2): 421-429 PubMed: 18085752 |
| 7 |
LocateP: Genome-scale subcellular-location predictor for bacterial proteins M. Zhou, J. Boekhorst, C. Francke, R.J. Siezen BMC Bioinformatics 2008, 9 (1): 173 PubMed: 18371216 |
 8 |
Genome-Wide Transcript Profiling of Endosperm without Paternal Contribution Identifies Parent-of-Origin–Dependent Regulation of AGAMOUS-LIKE36 R. Shirzadi, E.D. Andersen, K.N. Bjerkan, B.M. Gloeckle, M. Heese, A. Ungru, P. Winge, C. Koncz, R.B. Aalen, A. Schnittger, P.E. Grini PLOS Genetics 2011, 7 (2): e1001303 PubMed: 21379330 |
| 9 |
Polycomb Repressive Complex 2 Controls the Embryo-to-Seedling Phase Transition D. Bouyer, F. Roudier, M. Heese, E.D. Andersen, D. Gey, M.K. Nowack, J. Goodrich, J.P. Renou, P.E. Grini, V. Colot, A. Schnittger PLOS Genetics 2011, 7 (3): e1002014 PubMed: 21423668 |
| 10 |
Algorithmic and User Study of an Autocompletion Algorithm on a Large Medical Vocabulary M. Sevenster, R. van Ommering, Y. Qian Journal of Biomedical Informatics 2012, 45 (1): 107-119 PubMed: 22019376 |
| 11 |
Comparative transcriptomics of early dipteran development E. Jiménez-Guri, J. Huerta-Cepas, L. Cozzuto, K.R. Wotton, H. Kang, H. Himmelbauer, G. Roma, T. Gabaldón, J. Jaeger BMC Genomics 2013; 14: 123 PubMed: 23432914 |
| 12 |
Cell Reprogramming Requires Silencing of a Core Subset of Polycomb Targets G. Fragola, P.-L. Germain, P. Laise, A. Cuomo, A. Blasimme, F. Gross, E. Signaroldi, G. Bucci, C. Sommer, G. Pruneri, G. Mazzarol, T. Bonaldi, G. Mostoslavsky, S. Casola, G. Testa PLOS Genetics 2013; 9 (2): e1003292 PubMed: 23468641 |
| 13 |
PortionControl@HOME: results of a randomized controlled trial evaluating the effect of a multi-component portion size intervention on portion control behavior and body mass index M.P. Poelman, E. de Vet, E. Velema, M.R. de Boer, J.C. Seidell, I.H. Steenhuis Ann Behav Med. 2015; 49(1): 18–289 PubMed: 25142041 |
 14 |
Evaluation of Dispersion MRI for Improved Prostate Cancer Diagnosis in a Multicenter Study S. Turco, C. Lavini, S. Heijmink, J. Barentsz, H. Wijkstra, M. Mischi AJR Am J Roentgenol. 2018; 211(5): W242-W251 PubMed: 30346837 |
Scientific papers - Briefings
| 1 |
Abstracts I.K. Jordan Brief Bioinform 2006, 7 (4): 407-412 |
Conference Proceedings
| 1 |
958 Integrating large datasets for the Movember Global Action Plan on Active Surveillance for low risk Prostate Cancer T. Hulsen, J.H. Obbink, W. van der Linden, C. de Jonge, D. Nieboer, S.M. Bruinsma, M.J. Roobol, C.H. Bangma European Urology Supplements 2016, 15 (3): e958 |
 2 |
MP70-02 An Overview of Publicly Available Patient-Centered Prostate Cancer Datasets T. Hulsen, C.H. Bangma Journal of Urology 2018, 199 (4S): e934 |
| 3 |
PT073 - Developing a future-proof database for the European randomized study of screening for prostate cancer (ERSPC) T. Hulsen, W. van der Linden, C. de Jonge, J. Hugosson, A. Auvinen, M.J. Roobol European Urology Supplements 2019, 18 (1): e1766 |
Booklets
 1 |
Prostate Cancer Molecular Medicine - Molecular diagnosis, prognosis and imaging for tailored treatment of prostate cancer. C.H. Bangma, E. Schenk, G. Jenster, I.J. de Jong, H. Obbink, T. Hulsen and E. Caldenhoven CTMM, 2016-05-30 |
Posters
| 1 |
Connecting the proteomes of model organisms: Classification of the protein universe T. Hulsen, P.M.A. Groenen and M.A. Huynen ICS PhD Two-Day Conference Arnhem, 2003-05-08 Bioinformatics 2003: Bioinformatics at the Interface Utrecht, 2003-06-20 |
| 2 |
Protein World: Connecting the proteomes of model organisms T. Hulsen, P.M.A. Groenen and M.A. Huynen ECCB 2003 Paris (France), 2003-09-27 - 2003-09-30 SC2003 Phoenix (USA), 2003-11-15 - 2003-11-21 |
| 3 |
Conservation of chromosomal distance, relative orientation and co-expression of eukaryotic gene pairs T. Hulsen, P.M.A. Groenen and M.A. Huynen CMBI Conference Ravenstein, 2003-10-29 NVBMB Najaarssymposium 2003 Oss, 2003-11-05 |
| 4 |
Benchmarking ortholog identification methods using function similarity T. Hulsen, P.M.A. Groenen and M.A. Huynen ICS PhD Two-Day Conference Arnhem, 2004-04-19 |
| 5 |
Protein World & Orthology Benchmarking T. Hulsen, P.M.A. Groenen, W. Fleuren and M.A. Huynen ISMB/ECCB 2004 Glasgow (UK), 2004-08-01 |
| 6 |
Benchmarking ortholog identification methods using functional genomics data T. Hulsen, P.M.A. Groenen, J. de Vlieg and M.A. Huynen GeNeYouS Symposium Oss, 2005-04-27 ICS PhD Two-Day Conference Arnhem, 2005-04-28 |
| 7 |
Testing statistical significance scores of sequence comparison methods with structure similarity T. Hulsen, J.A.M. Leunissen, J. de Vlieg and P.M.A. Groenen NBIC Conference Ede, 2006-04-24 |
| 8 |
Dynamics of bidirectional gene pairs in vertebrate genomes E. Franck, T. Hulsen, M.A. Huynen, L. Lubsen, W. de Jong, O. Madsen Bioinformatics 2006 �hus(Denmark), 2006-06-17 |
| 9 |
PhyloPat: phylogenetic pattern analysis of genes T. Hulsen, J. de Vlieg and P.M.A. Groenen CMBI @ NCMLS Opening Nijmegen, 2006-10-09 BeNeLux Bioinformatics Conference 2006 Wageningen, 2006-10-17 |
| 10 |
Evolution of the immune system from model organism to man T. Hulsen, W.W.M. Fleuren and P.M.A. Groenen NBIC-ISNB 2007 Amsterdam, 2007-04-16 Organon MDI Retreat Heeze, 2007-06-11 |
| 11 |
BioRange SP 3.2.2.: Translational Medicine through Comparative Genomics and data integration W.W.M. Fleuren, R. Frijters, T. Hulsen, P.M.A. Groenen, J. de Vlieg and W. Alkema NBIC 2008 Lunteren, 2008-03-05 |
| 12 |
PhyloPat version 49 - An updated version contains gene neighborhood T. Hulsen, P.M.A. Groenen, W. Alkema, J. de Vlieg ISMB 2008 Toronto (Canada), 2008-07-19 |
| 13 |
Prostate Cancer Molecular Medicine - WP3 T. Hulsen, H. Obbink, H. van der Poel, I. van Oort, I.J. de Jong, E. Buskens, M. Wildhagen, E. Steyerberg, C. Bangma CTMM Annual meeting 2010 Utrecht, 2010-09-30 |
| 14 |
PCMM Biobank, IT-infrastructure and decision support T. Hulsen, H. Obbink, M. Wildhagen, C. Bangma CTMM Annual meeting 2011 Utrecht, 2011-09-29 |
| 15 |
PCMM Biobank, IT-infrastructure and decision support T. Hulsen, H. Obbink, E. Schenk, M. Wildhagen, C. Bangma CTMM Annual meeting 2012 Utrecht, 2012-09-14 |
| 16 |
PCMM Biobank, IT-infrastructure and decision support T. Hulsen, H. Obbink, E. Schenk, M. Wildhagen, C. Bangma CTMM Annual meeting 2013 Utrecht, 2013-09-12 |
| 17 |
Data Download Portal for The Maastricht Study Project P. Zakrzewski, T. Hulsen, W. Weistra, S. van Hagen, R. Jansen, R. van der Meulen, C. van der Kallen, P. Dagnelie tranSMART Annual meeting 2015 Amsterdam, 2015-10-19 |
| 18 |
Integrating large datasets for the Movember Global Action Plan on Active Surveillance for low risk Prostate Cancer T. Hulsen, J.H. Obbink, W. van der Linden, C. de Jonge, D. Nieboer, S.M. Bruinsma, M.J. Roobol, C.H. Bangma EAU 2016 Munich (Germany), 2016-03-14 |
| 19 |
Data Management and Data Curation Services for Translational Research T. Hulsen, W. van der Linden, C. de Jonge, D. Pletea Health RI meeting 2017 Utrecht, 2017-12-08 |
| 20 |
Developing a future-proof database for the European Randomized Study of Screening for Prostate Cancer (ERSPC) T. Hulsen, W. van der Linden, C. de Jonge, J. Hugosson, A. Auvinen, M.J. Roobol, on behalf of the ERSPC consortium DTL Communities@Work 2018 Utrecht, 2018-10-02 |
| 21 |
Translational Research IT at Philips Research T. Hulsen, W. van der Linden, P. van Hooft, D. Pletea Health RI meeting 2019 Utrecht, 2019-01-17 |
| 20 |
Developing a future-proof database for the European Randomized Study of Screening for Prostate Cancer (ERSPC) T. Hulsen, W. van der Linden, C. de Jonge, J. Hugosson, A. Auvinen, M.J. Roobol, on behalf of the ERSPC consortium EAU 2019 Barcelona (Spain), 2019-03-15 |
Reports
| 1 |
Generation of GST-p24 fusion proteins for antisera production and p24/COP binding studies T. Hulsen Molecular Animal Physiology Nijmegen, 2000-08-31 |
| 2 |
The cAMP response element binding protein (CREB) and its role in the nervous system T. Hulsen Molecular Animal Physiology Nijmegen, 2000-09-30 |
| 3 |
GPCR Website T. Hulsen and D. Lutje Hulsik CMBI Nijmegen, 2001-05-31 |
Kennislink
 1 |
Identificatie van genen en eiwitten Kennislink, 2003-08-28 |
| 2 |
De evolutie van genen Kennislink, 2004-02-23 |
| 3 |
Biologische databanken Kennislink, 2005-05-20 |
Others
| 1 |
PromScan, a promoter detection and analysis tool T. Hulsen and S. Denissov De Verbinding, 2003-06-27 |
 2 |
Academia or Industry: Making a Conscious Decision Science Next Wave / Science Careers, 2003-07-11 (Science TOC) (Spanish) (Portuguese) |
| 3 |
Werken in de bioinformatica G-mi, 2004-02-23 |
| 4 |
Tim Hulsen (24) en zijn twee linkerhanden - Voetballen met eiwitten Myrna Tinbergen Jaarverslag KUN, 2004-07-01 |
| 5 |
Bioinformatics in the Netherlands: Thriving and Exciting Science Next Wave / Science Careers, 2004-09-24 (Science TOC) |
| 6 |
Eiwittendatabank kan medicijnontwikkeling helpen Wetenschapsagenda Radboud Universiteit Nijmegen, 2007-08-15 (Index) (PDF) |
