Research Output 1996 2020

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Conference contribution
2015

Explaining disease using big data: How valid is your pathway?

Stringer, B., Dijkstra, M., Feenstra, A., Abeln, S. & Heringa, J., 2 Sep 2015, Proceedings of the 2015 International Conference on High Performance Computing and Simulation, HPCS 2015. Institute of Electrical and Electronics Engineers, Inc., p. 662-664 3 p. 7237114

Research output: Chapter in Book / Report / Conference proceedingConference contributionAcademicpeer-review

Life sciences
Pathway
Health
Valid
Sector

Genome sequence analysis with MonetDB: a case study on Ebola virus diversity

Klau, G. W., Cijvat, R., Manegold, S., Kersten, M., Schönhuth, A., Marschall, T. & Zhang, Y., 2015, Workshop on Data Management for Life Sciences at BTW 2015. Hamburg, Germany: Gesellschaft für Informatik (GI)

Research output: Chapter in Book / Report / Conference proceedingConference contributionAcademicpeer-review

2014

Petri nets are a biologist's best friend

Bonzanni, N., Feenstra, K. A., Fokkink, W. J. & Heringa, J., 2014, Formal Methods in Macro-Biology: First International Conference, FMMB 2014, Nouméa, New Caledonia, September 22-24, 2014. Proceedings. Springer/Verlag, p. 102-116 15 p. (Lecture Notes in Computer Science; vol. 8738)( Lecture Notes in Bioinformatics book sub series (LNBI); vol. 8738).

Research output: Chapter in Book / Report / Conference proceedingConference contributionAcademicpeer-review

File
Concurrency
Petri nets
Petri Nets
Cell Differentiation
Stem Cells
2013

Building Exceutable Biological Pathway Models Automatically from BioPAX

Willemsen, T., Feenstra, K. A. & Groth, P. T., 2013, 3rd International Workshop on Linked Science 2013—Supporting Reproducibility, Scientific Investigations and Experiments (LISC2013). Sydney

Research output: Chapter in Book / Report / Conference proceedingConference contributionAcademicpeer-review

Reconstructing consensus Bayesian network structures with application to learning molecular interaction networks

Fröhlich, H. & Klau, G. W., 2013, German Conference on Bioinformatics. Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik, p. 46-55

Research output: Chapter in Book / Report / Conference proceedingConference contributionAcademic

Molecular interactions
Bayesian networks
Cutoff frequency
Linear programming
Availability
2011

A Mathematical Programming Approach to marker-Assisted Gene Pyramiding

Canzar, S. & El-Kebir, M., 2011, Proceedings of the 11th Workshop on Algorithms in Bioinformatics (WABI). Springer

Research output: Chapter in Book / Report / Conference proceedingConference contributionAcademicpeer-review

Lagrangian Relaxation Applied to Sparse Global Network Alignment

El-Kebir, M., Heringa, J. & Klau, G. W., 2011, Pattern Recognition in Bioinformatics: 6th IAPR International Conference on PRIB 2011, Delft, The Netherlands, November 2-4, 2011, Proceedings. Loog, M., Wessels, L., Reinders, M. J. T. & de Ridder, D. (eds.). Berlin: Springer, p. 225-236 12 p. (Lecture Notes in Computer Science; vol. 7036).

Research output: Chapter in Book / Report / Conference proceedingConference contributionAcademicpeer-review

Open Access
File
Topology
Molecular interactions
Electric network analysis
Linear programming
Proteins
2006

Feature Selection Algorithm for Detecting Subtype Specific Sites for Smad Receptor Binding

Marchiori, E., Pirovano, W. A., Heringa, J. & Feenstra, K. A., 2006, International Conference on Machine Learning and Applications (ICMLA'06). Los Alamitos, CA, USA: IEEE Computer Society, p. 168-173

Research output: Chapter in Book / Report / Conference proceedingConference contributionAcademicpeer-review

2004

Analysis of proteomic pattern data for cancer detection

Jong, C., Marchiori, E. & van der Vaart, A. W., 2004, Applications of Evolutionary Computing. p. 41-51

Research output: Chapter in Book / Report / Conference proceedingConference contributionAcademicpeer-review

Feature selection based on support sector machines for proteomic pattern data

Jong, C., Marchiori, E., Sebag, M. & van der Vaart, A. W., 2004, 2004 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, San Diego. IEEE

Research output: Chapter in Book / Report / Conference proceedingConference contributionAcademicpeer-review

2003

A Million-Fold Speed Improvement in Genomic Repeats Detection.

Romein, J. W., Heringa, J. & Bal, H. E., 2003, SC. ACM, p. 20

Research output: Chapter in Book / Report / Conference proceedingConference contributionAcademicpeer-review

Chromosomal breakpoint detection in human cancer

Jong, C., Marchiori, E., van der Vaart, A. W., Ylstra, B., Weiss, M. & Meijer, G. J., 2003, Applications of Evolutionary Computing. p. 54-65

Research output: Chapter in Book / Report / Conference proceedingConference contributionAcademicpeer-review

Finding clusters using suppport classifiers

Jong, C., Marchiori, E. & van der Vaart, A. W., 2003, Proceedings. European Symposium on Artificial Neural Networks. p. 223-228

Research output: Chapter in Book / Report / Conference proceedingConference contributionAcademicpeer-review

1998

The domain decomposition of a single-domain protein

Feenstra, K. A. & Berendsen, H. J. C., 1998, Monte Carlo approach to biopolymers and protein folding. Grassberger, P., Nadler, W. & Barkema, W. (eds.). Singapore: World Scientific Publishing Co., p. 255-267

Research output: Chapter in Book / Report / Conference proceedingConference contributionAcademic