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

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: xxxxxxxx
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

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

Website papers

1 http://www.eredivisiestats.nl
EredivisieStats, 2002 (PDF)
2 http://www.ourtravelpics.com
OurTravelPics, 2010 (PDF)

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)