Bioinformatics

dr. Sanne Abeln
- s.abelnvunl
- Faculty of Science, Bioinformatics - Visiting Fellow
- AIMMS - Visiting Fellow
- Integrative Bioinformatics - Visiting Fellow
Person: Academic
dr. Evert Bosdriesz
- e.bosdrieszvunl
- Faculty of Science, Bioinformatics - Assistant Professor
- AIMMS - Assistant Professor
- Bio Informatics (IBIVU) - Assistant Professor
Person: Academic
dr. ir. Anton Feenstra
- k.a.feenstravunl
- Faculty of Science, Bioinformatics - Associate Professor
- AIMMS - Associate Professor
- Integrative Bioinformatics - Associate Professor
Person: Academic
Dea Gogishvili
- d.gogishvilivunl
- Faculty of Science, Bioinformatics - External PhD Candidate
- AIMMS - External PhD Candidate
- Bio Informatics (IBIVU) - External PhD Candidate
Person: Academic
Victor Kyllesbech
- v.kyllesbechvunl
- Faculty of Science, Bioinformatics - PhD Candidate
- AIMMS - PhD Candidate
Person: Academic

7 Finished

Targeting chromosomal breakpoint structural variants in colorectal cancer
Abeln, S. (Principal Investigator) & Lakbir, S. (Project Researcher)
1/10/21 → 31/10/24
Project: Research
Multi-omics Interdisciplinary Research Integration to Address DEmentia diagnosis.
Abeln, S. (Principal Investigator), Gogishvili, D. (Project Researcher), Waury, K. (Project Researcher) & Heringa, J. (Principal Investigator)
1/11/19 → 31/08/24
Project: Research
ELIXIR-NL Digital Research Infrastructure for Life Sciences.
Feenstra, A. (Project Researcher) & Donkervliet, J. (Project Researcher)
1/09/18 → 31/08/20
Project: Research
Delineating entropic contributions in beta-strand formation.
Abeln, S. (Principal Investigator), Hashemi Shabestari, M. (Project Researcher) & van Gils, J. (Project Researcher)
1/08/18 → 30/09/23
Project: Research
BIOEXE
Jacobsen, A. (Project Researcher) & Feenstra, A. (Principal Investigator)
1/12/12 → 1/07/17
Project: Research

Systems approaches to the infant gut microbiota: From temporal dynamics to metabolic interventions
Kort, R. & Li, S., 7 Jul 2026, 240 p.
Research output: PhD Thesis › PhD-Thesis – Research and graduation external

File
CycleVI: isolating cell cycle variation with an interpretable deep generative model
Mozdzanowski, P., Tarbier, M. & Jeuken, G. S., 1 Jun 2026, In: Bioinformatics. 42, 6, btag372.
Research output: Contribution to Journal › Article › Academic › peer-review

Open Access
Minimizing the minimizers via alphabet reordering
Verbeek, H., Ayad, L. A. K., Loukides, G. & Pissis, S. P., Jun 2026, In: Theoretical Computer Science. 1076, p. 1-13 13 p., 115932.
Research output: Contribution to Journal › Article › Academic › peer-review
Gap Analysis of Metabolic Conversions of Off‐Flavors and Antinutrients in Plant‐Based Substrates
Kuijpers, R. I., Clark, I. O. D. M., Cavaco, T., Nemanič, V., Tagliabue, B., Valero, A. A., Wennekers, W. M., Zhang, M., Zwet, K. V., Abeln, S., Moco, S., Paul, C. E., Mouhib, H., Notebaart, R. A., Smid, E. J., Teusink, B. & Bachmann, H., May 2026, In: Comprehensive Reviews in Food Science and Food Safety. 25, 3, p. 1-40 40 p., e70449.
Research output: Contribution to Journal › Article › Academic › peer-review

Open Access
A suite of macrocyclic peptide inhibitors and substrate probes for arginine methyltransferases
Yoshisada, R., Zhang, Y., Janssen, E., Bouchard, C., Poole, D. A., Wan, T., Soares, L. R., Houtkamp, I. M., Abeln, S., Mouhib, H., van Haren, M. J., Marechal, N., Troffer-Charlier, N., Cura, V., Cavarelli, J., van Ingen, H., Bauer, U. M., Martin, N. I. & Jongkees, S. A. K., 29 Apr 2026, In: Chemical Science. 17, 16, p. 7986-7996 11 p.
Research output: Contribution to Journal › Article › Academic › peer-review

Open Access

Algorithms in Sequence Analysis
Kumar, R.
1/09/25 → 31/08/26
Course
Basic Models of Biological Networks
Bruggeman, F.
1/09/25 → 31/08/26
Course
Basics of Bioinformatics and Systems Biology
Gralka, M.
1/09/25 → 31/08/26
Course
Bioinformatics for Translational Medicine
Urtasun Elizari, J.
1/09/25 → 31/08/26
Course
Biosystems Data Analysis
Westerhuis, J.
1/09/25 → 31/08/26
Course

13 Lecture / Presentation

Ensemble net and Protein Embeddings generalise Protein Interface Prediction beyond Homology
Feenstra, A. (Keynote speaker)
4 Nov 2024
Activity: Lecture / Presentation › Academic
PIPENN-EMB: Ensemble net and Protein Embeddings generalise Protein Interface Prediction beyond Homology
Feenstra, A. (Speaker) & Thomas, D. P. G. (Speaker)
18 Jun 2024
Activity: Lecture / Presentation › Academic
PIPENN: Protein Interface Prediction from sequence with an Ensemble of Neural Nets
Feenstra, A. (Invited speaker)
3 Nov 2022
Activity: Lecture / Presentation › Academic
Mapping the Protein-protein Interaction Free Energy Landscape
Feenstra, A. (Invited speaker)
12 May 2017
Activity: Lecture / Presentation › Academic
Seeing the Trees through the Forest: Sequence-based Homo- and Heteromeric Protein-protein Interaction sites prediction using Random Forest
Feenstra, K. A. (Speaker), Heringa, J. (Speaker), Hou, Q. (Speaker) & Vranken, W. F. (Speaker)
5 Apr 2017
Activity: Lecture / Presentation › Academic

NWO Veni
Abeln, S. (Recipient), 2011
Prize / Grant: Grant › Academic

Additional file 2 of INFLECT: an R-package for cytometry cluster evaluation using marker modality
Verhoeff, J. (Creator), Abeln, S. (Creator) & Garcia-Vallejo, J. J. (Creator), Figshare, 2022
DOI: 10.6084/m9.figshare.21582071, https://springernature.figshare.com/articles/dataset/Additional_file_2_of_INFLECT_an_R-package_for_cytometry_cluster_evaluation_using_marker_modality/21582071
Dataset / Software: Dataset
Additional file 4 of INFLECT: an R-package for cytometry cluster evaluation using marker modality
Verhoeff, J. (Creator), Abeln, S. (Creator) & Garcia-Vallejo, J. J. (Creator), Figshare, 2022
DOI: 10.6084/m9.figshare.21582077, https://springernature.figshare.com/articles/dataset/Additional_file_4_of_INFLECT_an_R-package_for_cytometry_cluster_evaluation_using_marker_modality/21582077
Dataset / Software: Dataset
Additional file 5 of INFLECT: an R-package for cytometry cluster evaluation using marker modality
Verhoeff, J. (Creator), Abeln, S. (Creator) & Garcia-Vallejo, J. J. (Creator), Figshare, 2022
DOI: 10.6084/m9.figshare.21582080, https://springernature.figshare.com/articles/dataset/Additional_file_5_of_INFLECT_an_R-package_for_cytometry_cluster_evaluation_using_marker_modality/21582080
Dataset / Software: Dataset
Additional file 2 of INFLECT: an R-package for cytometry cluster evaluation using marker modality
Verhoeff, J. (Creator), Abeln, S. (Creator) & Garcia-Vallejo, J. J. (Creator), Figshare, 2022
DOI: 10.6084/m9.figshare.21582071.v1, https://springernature.figshare.com/articles/dataset/Additional_file_2_of_INFLECT_an_R-package_for_cytometry_cluster_evaluation_using_marker_modality/21582071/1
Dataset / Software: Dataset
Additional file 3 of INFLECT: an R-package for cytometry cluster evaluation using marker modality
Verhoeff, J. (Creator), Abeln, S. (Creator) & Garcia-Vallejo, J. J. (Creator), Figshare, 2022
DOI: 10.6084/m9.figshare.21582074, https://springernature.figshare.com/articles/dataset/Additional_file_3_of_INFLECT_an_R-package_for_cytometry_cluster_evaluation_using_marker_modality/21582074
Dataset / Software: Dataset

Bioinformatics

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Collaborations and top research areas from the last five years

Dive into details

dr. Sanne Abeln

dr. Evert Bosdriesz

dr. ir. Anton Feenstra

Dea Gogishvili

Victor Kyllesbech

Targeting chromosomal breakpoint structural variants in colorectal cancer

Multi-omics Interdisciplinary Research Integration to Address DEmentia diagnosis.

ELIXIR-NL Digital Research Infrastructure for Life Sciences.

Delineating entropic contributions in beta-strand formation.

BIOEXE

Systems approaches to the infant gut microbiota: From temporal dynamics to metabolic interventions

CycleVI: isolating cell cycle variation with an interpretable deep generative model

Minimizing the minimizers via alphabet reordering

Gap Analysis of Metabolic Conversions of Off‐Flavors and Antinutrients in Plant‐Based Substrates

A suite of macrocyclic peptide inhibitors and substrate probes for arginine methyltransferases

Algorithms in Sequence Analysis

Basic Models of Biological Networks

Basics of Bioinformatics and Systems Biology

Bioinformatics for Translational Medicine

Biosystems Data Analysis

Ensemble net and Protein Embeddings generalise Protein Interface Prediction beyond Homology

PIPENN-EMB: Ensemble net and Protein Embeddings generalise Protein Interface Prediction beyond Homology

PIPENN: Protein Interface Prediction from sequence with an Ensemble of Neural Nets

Mapping the Protein-protein Interaction Free Energy Landscape

Seeing the Trees through the Forest: Sequence-based Homo- and Heteromeric Protein-protein Interaction sites prediction using Random Forest

NWO Veni

Additional file 2 of INFLECT: an R-package for cytometry cluster evaluation using marker modality

Additional file 4 of INFLECT: an R-package for cytometry cluster evaluation using marker modality

Additional file 5 of INFLECT: an R-package for cytometry cluster evaluation using marker modality

Additional file 2 of INFLECT: an R-package for cytometry cluster evaluation using marker modality

Additional file 3 of INFLECT: an R-package for cytometry cluster evaluation using marker modality

Bioinformatics

Fingerprint

Collaborations and top research areas from the last five years

Profiles

Projects

Research output

Courses

Activities

Prizes

Datasets