Generated by All in One SEO v5.0.1.1, this is an llms.txt file, used by LLMs to index the site.

# Bioinformatics Group

Vrije Universiteit Amsterdam

## Sitemaps

- [XML Sitemap](https://www.vubioinformatics.com/sitemap.xml): Contains all public & indexable URLs for this website.

## Posts

- [About Us](https://www.vubioinformatics.com/about-us/)
- [Poster session at Computational Structural Immunology - Nijmegen 2-4 September 2025](https://www.vubioinformatics.com/2025/09/18/poster-session-at-computational-structural-immunology-nijmegen-2-4-september-2025/) - Poster session featuring PIPENN-EMB poster at Computational Structural Immunology - Nijmegen 2-4 September 2025
- [Poster session at Flavors & Fragrances 2025 July 22 - 24, Göttingen](https://www.vubioinformatics.com/2025/08/25/poster-session-at-flavors-fragrances-2025-july-22-24-gottingen/) - Akshay Sajan, Nina Peters, and Mifen Chen, with Halima Mouhib, make odorants meet machine learning
- [At the end of our intense and productive group retreat!](https://www.vubioinformatics.com/2025/06/16/at-the-end-of-our-intense-and-productive-group-retreat/) - We spent three long and crowded days getting to know each other -- which is really nice since more than half the group is new -- as well as discussing #science, #funding, #collaborations (and the website).
- [Olga presenting on alternative splicing and protein-protein interactions at BioSB 2025](https://www.vubioinformatics.com/2025/06/12/821/) - Olga presenting on alternative splicing and protein-protein interactions at BioSB 2025
- [BioSB 2025 at Kasteel de Berckt](https://www.vubioinformatics.com/2025/06/12/biosb-2025-at-kasteel-de-berckt/) - Great location and vibrant atmosphere. Anton Feenstra presented PIPENN-EMB, Halima Mouhib - a new TDCC-LSH project.
- [Poster presentations at ISMB/ECCB](https://www.vubioinformatics.com/2023/07/26/poster-presentations-at-ismb-eccb/)
- [Juami van Gils presenting how peptide disordered flanks slow fibril growth at ISMB/ECCB](https://www.vubioinformatics.com/2023/07/25/juami-van-gils-presenting-how-peptide-disordered-flanks-slow-fibril-growth-at-ismb-eccb/) - Disordered flanks slow down the growth of amyloid fibrils in neurodegenerative disease, while hydrophobic surfaces accelerate growth
- [Dea Gogishvili presenting about novel dementia biomarker discovery at ISMB/ECCB](https://www.vubioinformatics.com/2023/07/25/dea-gogishvili/) - Discovery of novel CSF biomarkers to predict progression in dementia using machine learning
- [Renske de Wit presenting about metadata provenance at ISMB/ECCB](https://www.vubioinformatics.com/2023/07/25/renske-de-wit-presenting-about-metadata-provenance-at-ismb-eccb/) - From 2023 to a FAIR Future; bridging the provenance metadata gap by centering the bioinformatics practitioner perspective
- [Soufyan Lakbir presenting CIBRA at ISMB/ECCB Transmed](https://www.vubioinformatics.com/2023/07/25/soufyan-lakbir-presenting-cibra-at-ismb-eccb-transmed/) - Title "CIBRA identifies genomic alterations with a system-wide impact"
- [Victor and team win project prize at AIMMS festival](https://www.vubioinformatics.com/2023/07/06/victor-dea-and-team-win-project-prize-at-aimms-festival/) - In the future AIMMS projects category, Victor Kyllesbech, Sita Coenraads, Lackson Kashobwe and Tuğçe Çobanoğlu from AIMMS, won for their project on drug repurposing and considering toxic effects that may occur through the gut microbiome. aimmsfestival.nl/
- [Dea wins poster prize at AIMMS festival](https://www.vubioinformatics.com/2023/07/06/dea-wins-poster-prize-at-aimms-festival/) - Dea Gogishvili wins the AIMMS poster prize for her poster on "Discovery of novel CSF biomarkers to predict progression in dementia using machine learning". aimmsfestival.nl/
- [presenting at AIMMS festival](https://www.vubioinformatics.com/2023/07/06/presenting-at-aimms-festival/) - Halima Mouhib and Evert Bosdriesz gave an introduction of our group at the AIMMS fashionshow, highlighting the key topics of our research. aimmsfestival.nl/
- [Tumour break load is a biologically relevant feature of genomic instability with prognostic value in colorectal cancer](https://www.vubioinformatics.com/2023/06/21/tumour-break-load-is-a-biologically-relevant-feature-of-genomic-instability-with-prognostic-value-in-colorectal-cancer/) - We are pleased to share our recent publication by Soufyan Lakbir and Sanne Abeln in collaboration with Remond Fijneman, showing that the Tumor Break Load (TBL) is a distinct feature of genomic instability with prognostic value for patients with resected stage II and III microsatellite stable colorectal cancer. Highlights Tumour break load (TBL) is a
- [AIMMS Festival 2023](https://www.vubioinformatics.com/2023/06/21/aimms-festival-2023/) - Join us this July for our inaugural AIMMS Festival — an unforgettable event spanning two inspiring days and one night at Hotel ZuiderDuin in Egmond aan Zee. An exhilarating program that brings together cutting-edge research from our esteemed institute (that means you!) and addresses the innovation challenges of our valued industrial partners. During the festival,
- [Clusters of co-abundant proteins in the brain cortex associated with frontotemporal lobar degeneration](https://www.vubioinformatics.com/2023/06/21/paper-alert-clusters-of-co-abundant-proteins-in-the-brain-cortex-associated-with-frontotemporal-lobar-degeneration/) - New article out in collaboration with Charlotte Teunissen from the AUMC! We combined existing tools with a novel validation method to identify clusters of co-abundant proteins related to frontotemporal dementia. Read all about it here.
- [Discovery of novel CSF biomarkers to predict progression in dementia using machine learning](https://www.vubioinformatics.com/2023/06/21/discovery-of-novel-csf-biomarkers-to-predict-progression-in-dementia-using-machine-learning/) - We are excited to share our latest publication by Dea Gogishvili. The paper is a part of a special collection - artificial intelligence for personalised medicine. Here we explore the rate of cognitive decline in dementia patients to identify CSF biomarkers. Thanks to the co-authors for their valuable insights and dedication in bringing this project to life.
- [Ten quick tips for sequence-based prediction of protein properties using machine learning](https://www.vubioinformatics.com/2023/06/21/ten-quick-tips-for-sequence-based-prediction-of-protein-properties-using-machine-learning/) - We are happy to share our latest publication about protein property prediction using machine learning by Qingzhen Hou, Katharina Waury, Dea Gogishvili, Anton Feenstra. Abstract The ubiquitous availability of genome sequencing data explains the popularity of machine learning-based methods for the prediction of protein properties from their amino acid sequences. Over the years, while revising
- [How sticky are our proteins? Quantifying hydrophobicity of the human proteome](https://www.vubioinformatics.com/2022/06/23/how-sticky-are-our-proteins-quantifying-hydrophobicity-of-the-human-proteome/) - We are happy to share our recent publication by Juami Hermine Mariama van Gils, Dea Gogishvili, Jan van Eck, Robbin Bouwmeester, Erik van Dijk, and Sanne Abeln. Check out the ISMB-ECCB talk by Juami van Gils and Dea Gogishvili on our YouTube channel. Abstract: Proteins tend to bury hydrophobic residues inside their core during the folding process to provide stability to

## Pages

- [Home](https://www.vubioinformatics.com/) - Welcome to the VU bioinformatics group! Here we strive to understand biological processes across different levels of molecular and cellular organisation. With our expertise in advanced computational analysis and cutting-edge modelling techniques, we navigate through complex datasets and networks, striving to unlock the secrets hidden within. Our research primarily focuses on the following areas: Cancer
- [Tools](https://www.vubioinformatics.com/tools/) - Multiple Sequence Analysis CAO Contact-based substitution matrices LinkerDB Database for searching and visualising protein inter-domain linkers Next Generation Sequencing FluxEs 1.0 FluxEs 2.0 FluxEs is a program for metabolic flux analysis using NMR spectra of tracer experiments. FluxEs 1.0 is freely available via a web interface. FluxEs 2.0 is a development version and is available
- [Contact Us](https://www.vubioinformatics.com/15c42-web-agency-gb-contact-us/) - Email h.mouhib@vu.nl Offices 12th floor NU building, De Boelelaan 1111, 1081 HV, Amsterdam
- [Publications](https://www.vubioinformatics.com/publications/) - A selection of our most recent publications. 2025 Stohn, T., van Eijl, R., Mulder, K. W., Wessels, L. F. A., Bosdriesz, E. (2025). Reconstructing and comparing signal transduction networks from single cell protein quantification data. bioRxiv. https://doi.org/10.1101/2024.03.29.587331 Krämer, N., van Eijl, R., Stohn, T., Tanis, S., Wessels, L., Bosdriesz, E., Mulder, K. W. (2025). Cell-state
- [Members](https://www.vubioinformatics.com/members/) - Alumni
- [Join the group](https://www.vubioinformatics.com/join-the-group/) - Open Positions If interested, please reach out to us. Applications for PhD and Postdoc positions Are you passionate about tackling exciting challenges related to protein properties, cancer biology, and neurodegenerative diseases? Are you intrigued by the integration of machine learning and molecular simulations? We invite you to get in touch with us to explore various opportunities
- [User](https://www.vubioinformatics.com/user/)
- [Login](https://www.vubioinformatics.com/login/)
- [Register](https://www.vubioinformatics.com/register/)
- [Logout](https://www.vubioinformatics.com/logout/)
- [Account](https://www.vubioinformatics.com/account/)
- [Password Reset](https://www.vubioinformatics.com/password-reset/)
- [News](https://www.vubioinformatics.com/15c42-web-agency-gb-news/) - This is an example page. It's different from a blog post because it will stay in one place and will show up in your site navigation (in most themes). Most people start with an About page that introduces them to potential site visitors. It might say something like this: Hi there! I'm a bike messenger

## Categories

- [Uncategorized](https://www.vubioinformatics.com/category/uncategorized/)
- [Publications](https://www.vubioinformatics.com/category/publications/)

## Tags

- [Publications](https://www.vubioinformatics.com/tag/publications/)
- [Research](https://www.vubioinformatics.com/tag/research/)
- [protein hydrophobicity](https://www.vubioinformatics.com/tag/protein-hydrophobicity/)
- [MolPatch](https://www.vubioinformatics.com/tag/molpatch/)
- [Hydrophobic patches](https://www.vubioinformatics.com/tag/hydrophobic-patches/)
- [Dementia](https://www.vubioinformatics.com/tag/dementia/)
- [Neurodegenerative diseases](https://www.vubioinformatics.com/tag/neurodegenerative-diseases/)
- [Tumour](https://www.vubioinformatics.com/tag/tumour/)
- [genomic instability](https://www.vubioinformatics.com/tag/genomic-instability/)
- [tumour break load](https://www.vubioinformatics.com/tag/tumour-break-load/)
- [Sequence-based predictions](https://www.vubioinformatics.com/tag/sequence-based-predictions/)
- [protein properties](https://www.vubioinformatics.com/tag/protein-properties/)
- [machine learning](https://www.vubioinformatics.com/tag/machine-learning/)
- [CSF](https://www.vubioinformatics.com/tag/csf/)
- [Biomarkers](https://www.vubioinformatics.com/tag/biomarkers/)
- [Olink](https://www.vubioinformatics.com/tag/olink/)
- [FTD](https://www.vubioinformatics.com/tag/ftd/)
- [Frontotemporal dementia](https://www.vubioinformatics.com/tag/frontotemporal-dementia/)
- [conferences](https://www.vubioinformatics.com/tag/conferences/)