Publication overview
Aspects of Ontology Visualization and Integration
Dmitrieva, JLIACS 2011
Fluxes of Life - Bioinformatics for Metabolic Flux Quantification in Isotopic Non-Steady-State
Binsl, T. W.IBIVU 2011
Genome scale prediction of protein subcellular location in bacteria, with focus on extracellular and surface-associated proteins
Zhou, M.2011
Evolution of Ras-like GTPase signaling pathways
Van Dam, T.J.P.2011
Computational approaches for dissecting cancer pathways from insertional mutagenesis data
De Ridder, J.2011
Proteomics screening of cerebrospinal fluid: Candidate proteomics biomarkers for sample stability and experimental autoimmune encephalomyelitis
Rosenling, A.T.I.Wiskunde en Natuurwetenschappen 2010
http://irs.ub.rug.nl/ppn/330611496
Different geometries in ontology visualization.
Dmitrieva, JVerbeek, F. J.VDA 2010 2010
Improving breast cancer outcome prediction by combining multiple data sources
Van Vliet, M. H.Tu/Delft 2010
http://www.narcis.info/publication/RecordID/oai%3Atudelft.nl%3Auuid%3A...
Creating a new Ontology: a Modular Approach
Dmitrieva, JVerbeek, F. J.SWAT4LS (2010) 2010
Multiple alignment of membrane protein sequences Structural Bioinformatics of Membrane Proteins
Pirovano, W.Ablen S.Feenstra, K.A.Heringa, J. Frishman, DmitrijStructural Bioinformatics of Membrane Proteins 2010
Frishman, DmitrijPirovano, WalterAbeln, SanneFeenstra, K. AntonHeringa, JaapStructural bioinformatics of membrane proteins 2010
Three-sided hypothesis testing: simultaneous testing of superiority, equivalence and inferiority
Goeman, Jelle J.Solari, AldoStijnen, TheoStatistics in Medicine 2010, 29(20): 2117
http://www.ncbi.nlm.nih.gov/pubmed/20658478
Different Geometries in Ontology Visualization. Visualization and Data Analysis
Dmitrieva, JVerbeek, F. J. Park, J.Hao, Ming.C.Wong, Pak.C.Chen, C.SPIE EI2010 2010
Texton-based analysis of paintings
Van der Maaten, L. J. P.Postema, E.O.SPIE 2010
Correspondence free 3D statistical shape model fitting to sparse X-ray projections
Baka, N.Niessen, W. J.Kaptein, B. L.van Walsum, T.Ferarrini, L.Reiber, J. H. C.Leliev...SPIE 2010, 11: 1
http://spiedl.aip.org/getpdf/servlet/GetPDFServlet?filetype=pdf&id=PSI...
LysNDeNovo: An algorithm enabling de novo sequencing of Lys-N generated peptides fragmented by electron transfer dissociation
van Breukelen, B.Georgiou, A.Drugan, M. M.Taouatas, N.Mohammed, S.Heck, A. J.Proteomics 2010
http://www.ncbi.nlm.nih.gov/pubmed/20077410
Early diagnosis of dementia based on intersubject whole-brain dissimilarities
Klein, S.Loog, M.van der Lijn, F.den Heijer, T.Hammers, A.Bruijne, M.van der Lugt, A....Proceedings of the 2010 IEEE International Symposium on Biomedical Imaging: From Nano to Macro 2010: 249
http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=5490366
Atlas-based organ & bone approximation for ex-vivo ÃŽ1/4MRI mouse data: A pilot study
Khmelinskii, A.Baiker, M.Chen, X. J.Reiber, J. H. C.Henkelman, R. M.Lelieveldt, B. P....Proceedings of the 2010 IEEE International Symposium on Biomedical Imaging: From Nano to Macro 2010: 1197
http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=5490209
Database guided detection of anatomical landmark points in 3D images of the heart
Karavides, T.Leung, K. Y. E.Paclik, P.Hendriks, E. A.Bosch, J. G.Proceedings of the 2010 IEEE International Symposium on Biomedical Imaging: From Nano to Macro 2010: 1089
http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=5490182
Confidence of model based shape reconstruction from sparse data
Baka, N.Bruijne, M.Reiber, J. H. C.Niessen, W.Lelieveldt, B. P. F.Proceedings of the 2010 IEEE International Symposium on Biomedical Imaging: From Nano to Macro 2010: 1077
http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=5490179
Using flickr geotags to predict user behaviour
Clements, M.Serdyukov, P.de Vries, A. P.Reinders, M. J. T.Proceedings of the 33rd international ACM SIGIR conference on Research and development in information retrieval 2010: 851
http://delivery.acm.org/10.1145/1840000/1835648/p851-clements.pdf?key1...
Deep Supervised t-Distributed Embedding
Min, R.van der Maaten, L. J. P.Yuan, Z.Bonner, A.Zhang, Z.Proceedings of the 27th International Conference on Machine Learning (ICML) 2010: 1
http://www.icml2010.org/papers/149.pdf
Capturing Appearance Variation in Active Appearance Models
van der Maaten, L. J. P.Hendriks, E. A.Proceedings of the 23rd IEEE Conference on Computer Vision and Pattern Recognition 2010: 34
the 23rd IEEE Conference on Computer Vision and Pattern Recognition
The detection of concept frames using Clustering Multi-Instance Learning
Tax, D. M. J.Hendriks, E. A.Valstar, M. F.Pantic, M.The proceedings of the 20th international conference for pattern recognition 2010: 2917
ftp://ftp.computer.org/press/outgoing/proceedings/juan/icpr10b/data/41...
Video Games for Collection Exploration: Games for and out of Data Repositories.
Kallergi, A.Verbeek, F. J. Lugmayr, A.Franssila, H.Sotamaa, O.Safran, C.Aaltonen, T.Proceedings of the 14th International Academic MindTrek Conference 2010
Onto-Frogger: The Making Of
Kallergi, A.Verbeek, F. J. Blandford, A.Gulliksen, J.Hvannberg, E.T.Larusdottir M.K.L-C Law, E.Vilhjalmsson, H.H...Proceedings of the 6th Nordic Conference on Human-Computer Interaction (Oct.16–20, 2010) 2010
Pattern Recognition for High Throughput Zebrafish Imaging Using Genetic Algorithm Optimization
Nezhinsky, A.E.Verbeek, F. J.PRIB 2010 2010
Frequent Episode Mining to Support Pattern Analysis in Developmental Biology
Bathoorn, R.Welten, M.C.Richardson, M.Siebes, A.Verbeek, F. J.PRIB 2010 2010
Discovery of a new human polyomavirus associated with trichodysplasia spinulosa in an immunocompromized patient
van der Meijden, E.Janssens, R. W.Lauber, C.Bouwes Bavinck, J. N.Gorbalenya, A. E.Fel...PLoS Pathog 2010, 6(7)
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&d...
Gene expression in chicken reveals correlation with structural genomic features and conserved patterns of transcription in the terrestrial vertebrates
Nie, H.Crooijmans, R. P.Lammers, A.van Schothorst, E. M.Keijer, J.Neerincx, P. B.Leun...PLoS One 2010, 5(8)
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&d...
Gene regulatory networks from multifactorial perturbations using Graphical Lasso: application to the DREAM4 challenge
Menendez, P.Kourmpetis, Y. A.ter Braak, C. J.van Eeuwijk, F. A.PLoS One 2010, 5(12)
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&d...
Bayesian Markov Random Field analysis for protein function prediction based on network data
Kourmpetis, Y. A.van Dijk, A. D.Bink, M. C.van Ham, R. C.ter Braak, C. J.PloS ONE 2010, 5(2)
http://www.ncbi.nlm.nih.gov/pubmed/20195360
Time-resolved and tissue-specific systems analysis of the pathogenesis of insulin resistance
Kleemann, Robertvan Erk, MarjanVerschuren, Larsvan den Hoek, Anita M.Koek, MaudWielin...PLoS ONE 2010, 5(1)
http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2809107&tool...
A Combined Transcriptomics and Lipidomics Analysis of Subcutaneous, Epididymal and Mesenteric Adipose Tissue Reveals Marked Functional Differences
Caesar, RobertManieri, MoniaKelder, ThomasBoekschoten, MarkEvelo, ChrisMüller, Micha...PLoS ONE 2010, 5(7)
http://dx.plos.org/10.1371/journal.pone.0011525
Identificaton of networks of co-occurring, tumor-related DNA copy number changes using a genome-wide scoring approach
Klijn, C. N.Bot, J. J.Adams, D. J.Reinders, M. J. T.Wessels, L. F. A.Jonkers, J.Plos computational biology 2010, 6(1): 1
http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcb...
Finding the right questions: exploratory pathway analysis to enhance biological discovery in large datasets
Kelder, T.Conklin, B. R.Evelo, C. T.Pico, A. R.PLoS Biol 2010, 8(8)
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&d...
The influence of micelle formation on the stability of colloid surfactant mixtures
Pool, RenéBolhuis, Peter G.Physical Chemistry Chemical Physics 2010, 12(44): 14789
http://xlink.rsc.org/?DOI=c0cp00912a
A multi-classifier for grading knee osteoarthritis using gait analysis
Koktas, N.S.Yalabik, N.Yavuzer, G.Duin, R.P.W.Pattern Recognition Letters 2010
Clinical subtypes of Parkinson's disease The identification of Parkinson's disease subtypes using cluster analysis: a systematic review
van Rooden, S. M.Heiser, W. J.Kok, J. N.Verbaan, D.van Hilten, J. J.Marinus, J.Mov Disord 2010
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&d...
Reliable application of SNPs from EST databases to high throughput genotyping in potato
Anithakumari, A.M.Tang, J.van Eck, H.J.Visser, R.G.F.Leunissen, J.A.M.Vosman, B.van d...Mol. Breeding 2010: 65
Breast density changes associated with postmenopausal hormone therapy: post hoc radiologist- and computer-based analyses
Nielsen, M.Pettersen, P. C.Alexandersen, P. M. D.Karemore, G.Raundahl, J.Loog, M.Chri...Menopause-the journal of the north american menopause society 2010, 17(4): 772
http://www.ncbi.nlm.nih.gov/pubmed/20386343
A framework for optimizing measurement weight maps to minimize
Qazi, A. A.Jørgensen, D. R.Lillholm, M.Loog, M.Nielsen, M.Dam, E. B.Medical image analysis 2010, 14(3): 255
http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B6W6Y-4Y95V7F-...
Model driven quantification of left ventricular function from sparse single-beat 3D echocardiography
Ma, M.van Stralen, M.Reiber, J. H. C.Bosch, J. G.Lelieveldt, B. P. F.Medical image analysis 2010, 14(4): 582
http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B6W6Y-5017HVF-...
Using Data Fusion to Enrich Customer Databases with Survey Data for Database Marketing
van der Putten, P.W.H.Kok, J.N. In Casillas, J.Martinez Lopez, F.J.Marketing Intelligent Systems Using Soft Computing. Studies in Fuzziness and Soft Computing 2010
Hypermethylation of specific microRNA genes in MLL-rearranged infant acute lymphoblastic leukemia: major matters at a micro scale
Stumpel, D. J. P. M.Schotte, D.Lange-Turenhout, E. A. M.Schneider, P.Seslija, L.de Me...Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K 2010
http://www.ncbi.nlm.nih.gov/pubmed/21116279
Genome-wide expression analysis of paired diagnosis-relapse samples in ALL indicates involvement of pathways related to DNA replication, cell cycle and DNA repair, independent of immune phenotype
Staal, F. J. T.de Ridder, D.Szczepanski, T.Schonewille, T.van der Linden, E. C. E.van...Leukemia 2010, 24(3): 491
http://www.nature.com/leu/journal/v24/n3/abs/leu2009286a.html
Sequence-based prediction of protein secretion success in Aspergillus niger
Van den Berg, B.A.Nijkamp, J.F.Reinders, M.J.T.Wu, L.Pel, H.J.Roubos, J.A.de Ridder, ...Lecture notes in computer science 2010
Dissimilarity-based multiple instance learning
Sorensen, L.Loog, M.Tax, D.M.J.Lee, W.J.Bruijne, M.Duin, R.P.W.Lecture notes in computer science 2010
Image dissimilarity-based quantification of lung disease from CT
Sorensen, L.Loog, M.Lo, P.Ashraf, H.Dirksen, A.Duin, R.P.W.de Bruijne, M.Lecture notes in computer science 2010
The dissimilarity representation as a tool for tree-way data classification: a 2D measure
Porro-Muñoz, D.Duin, R.P.W.Orozco Alzate, M.Talavera, I.London-Bonilla,J.M.Lecture notes in computer science 2010