2018-2019 Academic Year : first semester

IB2 SEMINARS are held Fridays from 3pm to 4pm, at ULB-VUB Campus La Plaine, FORUM auditorium F


Nov 16 - IB2 research day - Green room (VUB) - 9am-5pm


Nov 30 - Laurent Gatto (UCL) - Probabilistic modelling of protein sub-cellular localisation

Feb 8 - Karoline Faust (KUL)

Feb 15 - Genevière Dupont (ULB)

Feb 22 - Rob Jelier (KUL)

Mar  8 - Journal Club : Charlotte

Mar 15, Zeynep Kalender Atak, Heterogeneity of melanoma genomes and cell states (KUL)

Mar 22 - Journal Club : Nathaniel, Rudy

Apr 5 - Journal Club : Sofia

April 26 - Journal Club : Alex

May 10 - Journal Club : Simon

May 24 - Journal Club : Sylvie


2017-2018 Academic Year : second semester


9/02 - Antointe Limasset ULB - Heterozygous assembly


23/02 - Sasha Panfilov UGent - Multiple mechanisms of cardiac arrhythmias studied using anatomically accurate modeling.

Forum OF2080

Cardiac arrhythmias account for about 1 death in 10 in industrialized countries. Although cardiac arrhythmias has been studied for well over a century, their underlying mechanisms remain largely unknown. Over the years, several factors that favor arrhythmias initiation were established. Among them are ionic and dynamical heterogeneity, remodeling and fibrosis of cardiac tissue. In addition a lot of attention was given to the arrhythmias which occur due to channelopathies which result in the long QT syndrome. In my talk I will present our recent studies on role of these arrhythmogenic factors performed using anatomically accurate model of ventricles of the human heart developed in our group.


2/03 - Lendert Gelens KUL - Coordination of cellular and developmental processes by biochemical waves 

Solvay room (NO building 5th floor) 
Biochemical waves are a recurring biological phenomenon involved in transmitting information quickly and reliably over large distances. Well-characterized examples include action potentials propagating along the axon of a neuron and calcium waves in various tissues. While in some biological systems information can be propagated efficiently through simple diffusion of molecules or through active transport, various recent findings indicate that traveling waves of biochemical activities are needed to coordinate cellular and developmental processes. Here, I will first discuss the theoretical principles that underlie such traveling waves. Next, in combination with experimental data, these principles will be used to illustrate how biochemical waves play a crucial role in coordinating cell division in the early frog embryo. Finally, I will discuss some of our ongoing research on this topic and highlight other recent work where biochemical waves have been observed. 


20/04 - PhD seminars session 1 with Rudy, Svitlana and Nicolas


27/04 - Fabrizio Pucci ULB - New insights in protein structure, stability and interactions: from the residue level to the structurome 

Forum OF2080

The understanding of the molecular mechanisms used by proteins to modulate their stability and interactions remains a challenging open problem. In this talk, I will review the current state of knowledge in this topic and present some of our last results about protein thermal stability, protein-protein binding mechanisms and the deleterious impact of non-synonymous variants. I will show how a multi-scale approach, from the amino acid interaction level up to the structurome level, can help gaining biophysical insights into these phenomena, identifying the molecular cause of diseases and improving rational protein optimization approaches. 

01/06 - PhD seminars session 2 with Lana, Stefan and Nathaniel

08/06 - Marnix Faes xpertSea - Detection and size-estimation of aquatic organisms using a machine learning approach - IB2 seminar room

Even though it's one of the fastest growing markets in the food industry, aquaculture barely has any supporting technology. Repetitive monitoring tasks such as counting and measuring aquatic organisms are traditionally done by hand, which is slow and error-prone. By using machine learning and computer vision, xpertSea powers shrimp farmers with technology aimed at improving the efficiency and quality of their monitoring operations. The focus of this talk will be on how to use image data to estimate the length of organisms, with an emphasis on whiteleg shrimp. After a brief introduction to convolutional neural networks, I will lay out the challenges of finding information about the length of an organism in an image. Next, the techniques we use to detect and measure shrimps will be explained and I'll conclude the seminar with our ongoing research.

15/06 - PhD seminars session 3 with Sofia, Youssef and Aziz





2017-2018 Academic Year : first semester

13-14th of December 2017 - Benelux Bioinformatics Conference -

8th of December 2017 - Dr. Alejandro Sifrim (CME, KU Leuven) --- title tba --- medical genomics

1st of December 2017 - TBA

24th of November 2017 - VUB & ULBPND & PGD conference  -

15-16th of November 2017 - Biotexcel - ULB & VUB - GENOMIC MEDICINE -

10th of November 2017 - TBA

20th of October 2017 - Prof. Uri Alon (Weizmann Institute, Israel) --- Multi-objective optimality in biology  --- systems biology

13th of October 2017 - 2nd ISCB Belgium Regional Student Group and (IB)2 Bioinformatics Student Day

Location: VUB U-residence Building, Etterbeek Campus, Bld Général Jacques 271, 1050 Brussels


9.00-9.10      Welcome and Introductions
9.10-9.30      Sarah Duerinckx A search for digenic inheritance of primary microcephaly using patients’exome data and zebrafish mutants
9.30-9.50      Rudy Pelicaen The reconstruction of a genome-scale metabolic model (GSMM) of the carbon core metabolism of Acetobacter pasteurianus 386B
9.50-10.10     Francois Ancien Deleteriousness prediction of coding variants from protein stability changes
10.10-10.30    Taushif Khan Traversing protein topology landscape from sequence information
10.30-11.00    Coffee break
11.00-12.00    Keynote speaker: Prof. Gert Vriend  (CMBI, Radboudumc, Nijmegen, Netherlands)
               Harvesting sequence information for GPCR structures
12.00-12.30    Poster flash presentations
12.30 - 2 pm   Lunch and Poster session
2.00-3.00 pm   Keynote speaker: Prof. Elfride De Baere (CMGG, UGent, Belgium)
               Why exome sequencing fails: lessons from mendelian blinding diseases
3.00-3.20 pm   Amin Ardeshirdavina A development framework for data analytics in genomics
3.20-3.40 pm   Dries Decap Scalable analysis of genomic and transcriptomic data
3.40-4.00 pm   Nicolas Dierckxsens NOVOLoci: Targeted assembly and variance calling from whole genome data
4.00-4.20 pm   Coffee break
4.20-4.40 pm   Julie Soblet Activating TIE2 mutations with distinct features cause a spectrum of venous malformations
4.40-5.00 pm   Andrea Gazzo Understanding mutational effects in digenic diseases
5.00-6.00 pm   Keynote speaker: Prof. Axel Cleeremans (UNI, ULB, Brussels, Belgium)
               Computational principles for consciousness
6.00-7.00 pm   Closing and drinks


2016-2017 Academic Year



19th of May       IB2 SPRING Student Day

2-3 pm              Prof. Renaud Lambiotte (UNamur) --- The many facets of community detection --- data science 

3.00-3.20           Gabriele Orlando --- Predicting beta-aggregation with AgMATa --- proteins

3.20-3.40           Lana Descheemaeker --- The Ss-LrpB system : a search for the natural behavior and development of the first synthetic oscillator in Archea --- systems biology

3.40-4.00           Nathaniel Mon Père --- From normal epithelial cells to distant tumors: mathematically exploring a novel hypothesis for late metastasis in breast cancer --- cancer

4.00-4.20           Coffee

4.20-4.40           Sofia Papadimitriou --- Predicting disease-causing variant combinations for digenic diseases --- oligogenic diseases

4.40-5.00           Nicolas Lufin --- Convader, the targeted enrichment exonic deletions viewer --- medical genetics

5-6 pm              Prof. Guy Van Camp (CMG UA, Antwerp) --- Genetics of deafness: from fundamental research to diagnostic applications --- medical genetics

6-7 pm              Drinks


12th of May - Prof. Anton Feenstra (IBIVU, Amsterdam, Netherlands) --- Mapping the protein-protein interaction free energy landscape --- protein bioinformatics

5th of May - Prof. Lieven Clement (BIG-N2N, UGent) --- Statistical methods for label-free quantitative MS-based proteomics --- statistical omics


17th of March - Prof. Niel Hens (I-BioStat, UHasselt) --- A biostatistical perspective on mathematical epidemiology --- biostatistics 

10th of March - Prof. Tias Guns (MOBI, VUB) --- Constraint-based pattern mining with an application to cis-regulatory module detection --- data science 

24th of February - Dr Christian Edlich-Muth (Max Planck Institute of Molecular Plant Physiology, Germany) --- Improving Plant Yield with computational methods --- plant genomics

17th of February - BeSHG Meeting, "Human Genetics Goes Somatic", Louvain-La-Neuve, Aula Magna, see

3rd of  February - Drs Xavier Tordoir and Andy Petrella (Data Fellas, Liège) --- Distributed genomic data analysis --- data science


21st of October - Prof. Vera Van Noort (KUL, CMPG) --- Role of kinase signaling in Ebola Virus Disease --- computational systems biology

25th of  November - REPORTED to 2017 - Drs Xavier Tordoir and Andy Petrella (Data Fellas) --- Distributed genomic data analysis --- big data

2nd of December - Prof. Elena Papaleo (CBL, DCRC, Copenhagen, Danemark) --- A multi-scale approach to cancer bioinformatics: from -omics signature to bimolecular structures --- cancer computational biology

9th of December - Prof. Patrick Meyer (ULg, BioSys) --- Study of Meta-Analysis Strategies for Network Inference using Information-Theoretic Approaches  --- computational systems biology

16th of December - Dr Jiajia Xu (ULB, LPGMP) --- Deciphering genetic control of root architecture in Arabidopsis thaliana and crop species Brassica napus --- plants genomics



7th of October 2016 - SPECIAL EVENT : ISCB Belgium Regional Student Group and  (IB)2 Bioinformatics Student Day

Location: VUB U-residence Building, Etterbeek Campus, Bld Général Jacques 271, 1050 Brussels

meeting will be held in the Green Room; coffee/reception will be held in the Polyvalente Room

9.30     Start
9.40     Daniele Parisi (KUL) - Data fusion in drug target interaction prediction and drug repositioning
10.00   Claudio Reggiani (IB2) - Intronic Promoters linked to Developmental Disorders and Intellectual Disability
10.20   Charlie Beirnaert (UA) - Speaq 2.0: Large scale NMR analysis made easy
10.40   Antonio Colaprico (IB2) - MoonlightR: An R/bioconductor package for the identification of dual-role cancer driver genes
11.00   Coffee
11.30   Keynote: Prof. Richard Redon (INSERM, Nantes, France) - Deciphering the genetic architecture of complex disorders: experience on the Brugada Syndrome
12.30   Flash presentations of posters
12.45   Lunch - poster session
14.00   Keynote: Prof. Antonio Rausell (IMAGINE, Paris, France) - Bioinformatics and functional genomics of human immune diseases: from genome analysis to single-cell transcriptomics
15.00   Andrea Gazzo (IB2) - Understanding mutational effects between combinations of variants in digenic diseases
15.20   Sarah Elshal (KUL) - Beegle: from literature mining to disease-gene discovery
15.40   Coffee
16.10   IB2 director’s address + Elixir European network Presentation by Dr Kim De Ruyck + WIV-ISP Bioinformatics Presentation by Dr Kevin Vanneste
16.40   Ashley Conard (Brown University, Providence, RI, USA) - Subclonal Driver Events Across 9 Cancer Types
17.00   Keynote: Prof. Jacques Beckmann (Swiss Bioinformatics Institute, Lausanne, Switzerland) - Evidence-based precision medicine in the context of big data
18.00   Drinks
19:00   End





2015-2016 Academic Year

4th and 5th of February (Thu-Fri) - Belgium BeSHG and Netherlands NVHG Genetics Societies 2016 Special Conference, held in Leuven, "Genetics and Society",
19th of February - seminar reported at an ulterior date 
26th of February - Dr. Celine Vens (KULAK, Kortrijk) --- Decision tree-based methods in gene function prediction
4th of March - Dr. Ibrahim Tanyalcin (VUB, UZ Brussel) --- I-PV: a Circos module for interactive protein sequence visualization
11th of March - Dr. Gerben Menschaert (UGent, BioBix) --- The forces of proteome complexity, measure you must!
17th and 18th of March (Thu-Fri) - VIB Conference - Applied Bioinformatics in Life Sciences, held in Leuven,
13th of April (Wed) - BeMGI annual meeting - 12 to 6 pm - UCL Saint-Luc Campus
13th to 15th of April - Genomics Disorders, Wellcome Trust Meeting - Cambridge, UK
22nd of April - Dr Daniele Catanzaro (UCL Mons, CORE, LSM) --- Classifying the Progression of Ductal Carcinoma from Single-Cell Sampled Data via Integer Linear Programming: A Case Study
29th of April - Prof Pierre Rouzé (UGent, PSB) --- How a monocot plant managed to live in the sea ? Mining the genome of the seagrass Zostera marina to figure it out
13th of May - Michael Crusoe (CWLproject, USA) --- Laptop, cluster, cloud: portable data analysis workflows with the Common Workflow Language
20th of May - (IB)2 Spring Student Day - Opening Keynote : Prof. Yves Van de Peer (BIG-N2N, PSB, UGent) --- The significance of gene and genome duplications for (plant) evolution --- Closing Keynote : Prof. Tom Lenaerts (IB2, MLG, AI Lab, ULB, VUB) --- Game theory, evolution and their synergy in computational biology and medicine
4th of September - M.Eng. Miguel Gaspar Lopes (ULB, MLG) --- PhD Public Defense (at 4pm) : Inference of gene networks from time series expression data and application to Type 1 Diabetes 
9th of October - (IB)2 Autumn Student Day - Opening Keynote 2-2.45 pm and Closing Keynote 5-5.45 pm, both by Prof. Jacques van Helden (Université d'Aix-Marseille, France) --- Opening Keynote: A motif perspective on genomic regulation with Next Generation Sequencing data; Closing Keynote: Taming that fickle p-value
16th of October - Dr. Raphael Leplae (ULB-VUB Computing Center) --- High Performance Computing : available resources at the ULB-VUB Computing Center and trends for the coming years.
23rd of October - Dr. Tom Druet (GiGa, ULg) --- Higher male than female recombination rate in cattle is controlled by genetic variants effective in both sexes
13th of November - Prof. Marianne Rooman (IB2, 3BIO, ULB) --- Knowledge-driven prediction of protein stability and rational design
2nd of December - BRIGHTcore VUB-ULB Inauguration Meeting (UZ Jette, Auditorium Kiekens, Brussels) --- 2-6 pm --- Opening address by Belgian Minister of Health, Dr Maggie De Block and Keynotes by Prof. J. Veltman (Nijmegen, Netherlands), Prof. C. Sotiriou (ULB), Prof. J. Degrève (VUB), see
4th of December - Dr. Frederik Hendrickx (Natural Sciences Museum, Brussels) --- Integrating genomics to understand the evolutionary history of adaptations
7th and 8th of December (Mon-Tue) - Benelux Bioinformatics Conference, held in Antwerp,
11th of December - Prof. Silvio Tosatto (Padova, Italy) --- Cataloguing and annotating flavors of intrinsic disorder in proteins with ModiDB

2014-2015 Academic Year

9th of January - Prof. Ann Nowe (VUB, AI Lab, COMO) --- Stochastic Optimization based on Reinforcement Learning
15th and 16th of January - VIB NGS Conference (held in Leuven) --- Revolutionizing Next-Generation Sequencing: Tools and Technologies
6th of February - (IB)Student Day --- Keynotes by Prof. Yvan Saeys (UGent, DAMBI, IRC, VIB) - Flow Cytometry Bioinformatics: machine learning challenges for systems immunology, Dr. Jean-François Flot (UCLondonUK) - From read tags to genomic riches: turning garbage into gold using bioinformatics
27th of February - Dr. David Venet (ULB, BCTL, Bordet institute) --- RNA sequencing of HER+ breast cancers
6th of March - 2015 BeSHG annual meeting (held in Charleroi) --- Behaviour: Is it genetically determined ?
20th of March - Dr. Charlotte Herzeel (IMEC, ExaScience lab) --- elPrep: high-performance preparation of sequence alignment/map files for variant calling
27th of March - Prof. Dr. Stefan Weckx (VUB, IMDO, (IB)2) --- Unravelling food fermentation processes in the next generation sequencing era
8th of May - (IB)Student Day --- Keynotes by Prof. Pierre Dupont (ICTEAM, INGI, UCL) - A balanced hazard ratio to evaluate survival risk groups and by Prof. Dr. Albena Jordanova (VIB, UAntwerpen) - Genetic studies in the Roma/Gypsy population – opportunities and challenges
29th of May - Dr. Neta Zach (Prize4Life, Israel) --- Crowdsourced analysis of clinical trial data to predict amyotrophic lateral sclerosis progression
5th of June - Prof. Geert Molenberghs (I-BioStat, UHasselt and KULeuven) --- Clusters with Random Size: Maximum Likelihood versus Weighted Split-sample Pseudo-likelihood
26th of September - Prof. Kris Laukens (UA, ADReM, Biomina) --- Making pattern discovery simple, intuitive, and useful for biology
3rd of October - Prof. Kathleen Marchal (UGent, PSB, INTEC, iMinds, N2N; KUL, M2S) --- Network-based data-integration: application to clonal systems
10th of October - (IB)Student Day - Keynotes by Dr Pieter Mestdagh (UGent) --- Decoding Non-Coding RNAs in Cancer and Prof. Rita Casadio (Biocomputing Group, Bologna, Italy) --- The Effects of Disease Related Variations on Protein Stability; A Large Scale Investigation
17th of October - Prof. Kristel Van Steen (ULg, Montefiore Institute, GiGA) --- Methodological aspects in Integromics : integrating multiple omics datasets
7th of November - Dr. Matthieu Defrance (ULB, Laboratory of Cancer Epigenetics, (IB)2) --- Computational challenges in methylome analysis
14th of November - Prof. Jean-Charles Delvenne (UCL, ICTEAM) --- Structure and dynamics of networks
28th of November - Prof. Jan Fostier (UGent, INTEC, IBCN, N2N) --- Halvade : a framework for variant calling in the cloud 
5th of December - Prof. Jan Aerts (KUL, Datavislab, ESAT-STADIUS, iMinds) --- Visual Data Analysis in Biology : Putting the human back into the loop
2013-2014 Academic Year

10th of January - Prof. Joris Vermeesch (KUL - CME) --- Cleavage stage embryos are the cradle of chromosomal disorders
17th of January - Prof. Lennart Martens (UGent - CompOmics) --- Taking high-throughput data to the metascale: management and integrated processing of datasets
24th of January  - Prof. Vincent Detours (ULB, IRIBHM) --- Principles governing A-to-I editing in the cancer transcriptome

31st of january - Prof. Thierry Voet (KULeuven - Sanger) --- Single-cell genomics to study DNA-mutation, genetic heterogeneity and disease


7th of February - 2014 BeSHG meeting (held in Antwerp) --- Translational Genetics: From cage over bench to bed

14th of February - Dr Francesc Peris-Bondia (ULB, IBMM, Bacterial Genetics and Physiology) --- Complete Genome Sequence of the Escherichia coli PMV-1 Strain, a Model Extraintestinal Pathogenic E. coli Strain Used for Host-Pathogen Interaction Studies

21st of Feb - (IB)² Student Day --- Student presentations


14th of March - Prof. Stein Aerts (KULeuven, CME, LCB) --- Identification of master regulators and cis-regulatory interactions in human and Drosophila gene networks
21st of March - Prof. Tom Lenaerts (ULB-VUB, IB2 and MLG) --- Proteins as communication devices
28th of March - Prof. Patrick Mardulyn (ULB, EBE) --- A geographically-explicit model of coalescence to study the impact of past climate changes on the range of organisms
25th of April - no seminar (replaced by BeMGI meeting in Liège on the 24th of April)


9th of May - Dr Steven Maere (UGent, ESB, PSB, VIB) --- Using uncontrolled expression variations among individual Arabidopsis plants to reverse engineer gene networks
16th of May - Dr Bart Jansen (VUB, ETRO, IB2) --- title to be determined
23rd of May - Dr Pierre Geurts (ULg, Institute Montefiore) --- Gene regulatory network inference using tree-based ensemble methods
6th of June - postponed to 26th of september Prof. Kris Laukens (UA, ADReM, Biomina) --- Making pattern discovery simple, intuitive, and useful for biology

18th of October - Dr Sonia Van Dooren and Dorien Daneels (VUB - UZ Brussel CMG) --- Challenges in Cardiogenetics and research
08th of November - Prof. Yves Moreau, (KUL - Bioinformatics) --- eXtasy: variant prioritization by genomic data fusion
15th of November - Dr Wim Vranken (VUB - (IB)) --- Dynamine: from protein sequence to dynamics and disorder
22nd of November - Dr Karoline Faust (VUB - (IB)2 ) --- Inference of microbial association networks from metagenomic data - challenges, tools and results
29th of November - Dr Raphael Helaers (UCL - De Duve Institute) --- Highlander: variant filtering made easy

6th of December - Dr Tarik Roukny Ornia (ULB, IRIDIA) --- Default Cascades in Complex Networks: Topology and Systemic Risk

13th of December - Dr Bjorn Menten (UGent - CMGG) --- Mate pair/Paired End sequencing for the detection of chromosomal aberrations in patients with intellectual disability and congenital malformations