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Publication overview

Aspects of Ontology Visualization and Integration

Dmitrieva, J

LIACS 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, Dmitrij

Structural Bioinformatics of Membrane Proteins 2010

Frishman, DmitrijPirovano, WalterAbeln, SanneFeenstra, K. AntonHeringa, Jaap

Structural bioinformatics of membrane proteins 2010

Three-sided hypothesis testing: simultaneous testing of superiority, equivalence and inferiority

Goeman, Jelle J.Solari, AldoStijnen, Theo

Statistics 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