Machine learning

My research involves the development and application of computational methods with the ultimate goal to understand plant development. In particular, I am interested in the question how to analyze the large amount of genome sequences and other -omics data that are available nowadays. A lot of data is gathered nowadays, but it is far from trivial to obtain biological insights from these data. To do so, I use machine learning; starting from available knowledge, these methods deliver novel predictions which are subsequently tested by colleagues working in the lab.

Typical examples of projects include:
- Prediction of functional sites in protein sequences
- Analysis of transcription factor binding sites
- Modelling of regulatory networks
- Prediction of functions of genes
- Analysis of alternative splicing

Publications

Smart search for traits

Testerink, Christa , Ridder, Dick de , Dijk, Aalt-Jan van (2021) Slim zoeken naar eigenschappen, Resource jrg. 16 nr. 3 p. 7-7, 2021-09-30, https://edepot.wur.nl/555024;Smart search for traits, Resource jrg. 16 nr. 3 p. 7-7, 2021-09-29, https://edepot.wur.nl/555087
A THP-1 Cell Line-Based Exploration of Immune Responses Toward Heat-Treated BLG

Deng, Ying , Govers, Coen , Beest, Ellen ter , Dijk, Aalt Jan van , Hettinga, Kasper , Wichers, Harry J. (2021) Frontiers in Nutrition 7 (2021). - ISSN 2296-861X
Similarities between plant traits based on their connection to underlying gene functions

Nap, Jan Peter , Sanchez-Perez, Gabino F. , Dijk, Aalt-Jan van (2017) PLoS ONE 12 (2017)8. - ISSN 1932-6203
Sequence-based analysis of protein degradation rates

Correa Marrero, Miguel , Dijk, Aalt-Jan van , Ridder, Dick de (2017) Proteins : Structure, Function, and Bioinformatics 85 (2017)9. - ISSN 0887-3585 - p. 1593 - 1601.
An interactomics overview of the human and bovine milk proteome over lactation

Zhang, Lina , Dijk, Aalt-Jan van , Hettinga, Kasper (2017) Proteome Science 15 (2017). - ISSN 1477-5956
Species-specific genome sequence databases : A practical review

Dijk, Aalt-Jan van (2017) In: Plant genomics databases / , van Dijk, Aalt D.J.. - : Humana Press Inc. (Methods in Molecular Biology ) - ISBN 9781493966561 - p. 173 - 181.
Cross-Family Transcription Factor Interactions : An Additional Layer of Gene Regulation

Bemer, Marian , Dijk, Aalt-Jan van , Immink, Richard G.H. , Angenent, Gerco C. (2017) Trends in Plant Science 22 (2017)1. - ISSN 1360-1385 - p. 66 - 80.
Selected proceedings of Machine Learning in Systems Biology: MLSB 2016

Dijk, Aalt-Jan van , Lähdesmäki, Harri , Ridder, Dick de , Rousu, Juho (2016) BMC Bioinformatics 17 (2016)suppl. 16. - ISSN 1471-2105
An expanded evaluation of protein function prediction methods shows an improvement in accuracy

Jiang, Yuxiang , Oron, Tal Ronnen , Clark, Wyatt T. , Bankapur, Asma R. , Andrea, Daniel D' , Lepore, Rosalba , Funk, Christopher S. , Kahanda, Indika , Verspoor, Karin M. , Ben-Hur, Asa , Koo, Da Chen Emily , Penfold-Brown, Duncan , Shasha, Dennis , Youngs, Noah , Bonneau, Richard , Lin, Alexandra , Sahraeian, Sayed M.E. , Martelli, Pier Luigi , Profiti, Giuseppe , Casadio, Rita , Cao, Renzhi , Zhong, Zhaolong , Cheng, Jianlin , Altenhoff, Adrian , Skunca, Nives , Dessimoz, Christophe , Dogan, Tunca , Hakala, Kai , Kaewphan, Suwisa , Mehryary, Farrokh , Salakoski, Tapio , Ginter, Filip , Fang, Hai , Smithers, Ben , Oates, Matt , Gough, Julian , Törönen, Petri , Koskinen, Patrik , Holm, Liisa , Chen, Ching Tai , Hsu, Wen Lian , Bryson, Kevin , Cozzetto, Domenico , Minneci, Federico , Jones, David T. , Chapman, Samuel , BKC, Dukka , Khan, Ishita K. , Kihara, Daisuke , Ofer, Dan , Rappoport, Nadav , Stern, Amos , Cibrian-Uhalte, Elena , Denny, Paul , Foulger, Rebecca E. , Hieta, Reija , Legge, Duncan , Lovering, Ruth C. , Magrane, Michele , Melidoni, Anna N. , Mutowo-Meullenet, Prudence , Pichler, Klemens , Shypitsyna, Aleksandra , Li, Biao , Zakeri, Pooya , ElShal, Sarah , Tranchevent, Léon Charles , Das, Sayoni , Dawson, Natalie L. , Lee, David , Lees, Jonathan G. , Sillitoe, Ian , Bhat, Prajwal , Nepusz, Tamás , Romero, Alfonso E. , Sasidharan, Rajkumar , Yang, Haixuan , Paccanaro, Alberto , Gillis, Jesse , Sedeño-Cortés, Adriana E. , Pavlidis, Paul , Feng, Shou , Cejuela, Juan M. , Goldberg, Tatyana , Hamp, Tobias , Richter, Lothar , Salamov, Asaf , Gabaldon, Toni , Marcet-Houben, Marina , Supek, Fran , Gong, Qingtian , Ning, Wei , Zhou, Yuanpeng , Tian, Weidong , Falda, Marco , Fontana, Paolo , Lavezzo, Enrico , Toppo, Stefano , Ferrari, Carlo , Giollo, Manuel , Piovesan, Damiano , Tosatto, Silvio C.E. , Pozo, Angela del , Fernández, José M. , Maietta, Paolo , Valencia, Alfonso , Tress, Michael L. , Benso, Alfredo , Carlo, Stefano Di , Politano, Gianfranco , Savino, Alessandro , Rehman, Hafeez Ur , Re, Matteo , Mesiti, Marco , Valentini, Giorgio , Bargsten, Joachim W. , Dijk, Aalt-Jan van , Gemovic, Branislava , Glisic, Sanja , Perovic, Vladmir , Veljkovic, Veljko , Veljkovic, Nevena , Almeida-e-Silva, Danillo C. , Vencio, Ricardo Z.N. , Sharan, Malvika , Vogel, Jörg , Kansakar, Lakesh , Zhang, Shanshan , Vucetic, Slobodan , Wang, Zheng , Sternberg, Michael J.E. , Wass, Mark N. , Huntley, Rachael P. , Martin, Maria J. , O'Donovan, Claire , Robinson, Peter N. , Moreau, Yves , Tramontano, Anna , Babbitt, Patricia C. , Brenner, Steven E. , Linial, Michal , Orengo, Christine A. , Rost, Burkhard , Greene, Casey S. , Mooney, Sean D. , Friedberg, Iddo , Radivojac, Predrag (2016) Genome Biology 17 (2016)1. - ISSN 1474-7596
Mutational robustness of gene regulatory networks: interpay between transcription factor - target gene and protein-protein interactions

Dijk, Aalt-Jan van (2010)

Publications

Smart search for traits

A THP-1 Cell Line-Based Exploration of Immune Responses Toward Heat-Treated BLG

Similarities between plant traits based on their connection to underlying gene functions

Sequence-based analysis of protein degradation rates

An interactomics overview of the human and bovine milk proteome over lactation

Species-specific genome sequence databases : A practical review

Cross-Family Transcription Factor Interactions : An Additional Layer of Gene Regulation

Selected proceedings of Machine Learning in Systems Biology: MLSB 2016

An expanded evaluation of protein function prediction methods shows an improvement in accuracy

Mutational robustness of gene regulatory networks: interpay between transcription factor - target gene and protein-protein interactions