BEGIN:VCALENDAR VERSION:2.0 PRODID:-//IBsquare - ECPv6.15.20//NONSGML v1.0//EN CALSCALE:GREGORIAN METHOD:PUBLISH X-ORIGINAL-URL:https://ibsquare.be X-WR-CALDESC:Events for IBsquare REFRESH-INTERVAL;VALUE=DURATION:PT1H X-Robots-Tag:noindex X-PUBLISHED-TTL:PT1H BEGIN:VTIMEZONE TZID:Europe/Brussels BEGIN:DAYLIGHT TZOFFSETFROM:+0100 TZOFFSETTO:+0200 TZNAME:CEST DTSTART:20200329T010000 END:DAYLIGHT BEGIN:STANDARD TZOFFSETFROM:+0200 TZOFFSETTO:+0100 TZNAME:CET DTSTART:20201025T010000 END:STANDARD BEGIN:DAYLIGHT TZOFFSETFROM:+0100 TZOFFSETTO:+0200 TZNAME:CEST DTSTART:20210328T010000 END:DAYLIGHT BEGIN:STANDARD TZOFFSETFROM:+0200 TZOFFSETTO:+0100 TZNAME:CET DTSTART:20211031T010000 END:STANDARD BEGIN:DAYLIGHT TZOFFSETFROM:+0100 TZOFFSETTO:+0200 TZNAME:CEST DTSTART:20220327T010000 END:DAYLIGHT BEGIN:STANDARD TZOFFSETFROM:+0200 TZOFFSETTO:+0100 TZNAME:CET DTSTART:20221030T010000 END:STANDARD END:VTIMEZONE BEGIN:VTIMEZONE TZID:Europe/Paris BEGIN:DAYLIGHT TZOFFSETFROM:+0100 TZOFFSETTO:+0200 TZNAME:CEST DTSTART:20170326T010000 END:DAYLIGHT BEGIN:STANDARD TZOFFSETFROM:+0200 TZOFFSETTO:+0100 TZNAME:CET DTSTART:20171029T010000 END:STANDARD BEGIN:DAYLIGHT TZOFFSETFROM:+0100 TZOFFSETTO:+0200 TZNAME:CEST DTSTART:20180325T010000 END:DAYLIGHT BEGIN:STANDARD TZOFFSETFROM:+0200 TZOFFSETTO:+0100 TZNAME:CET DTSTART:20181028T010000 END:STANDARD BEGIN:DAYLIGHT TZOFFSETFROM:+0100 TZOFFSETTO:+0200 TZNAME:CEST DTSTART:20190331T010000 END:DAYLIGHT BEGIN:STANDARD TZOFFSETFROM:+0200 TZOFFSETTO:+0100 TZNAME:CET DTSTART:20191027T010000 END:STANDARD BEGIN:DAYLIGHT TZOFFSETFROM:+0100 TZOFFSETTO:+0200 TZNAME:CEST DTSTART:20200329T010000 END:DAYLIGHT BEGIN:STANDARD TZOFFSETFROM:+0200 TZOFFSETTO:+0100 TZNAME:CET DTSTART:20201025T010000 END:STANDARD BEGIN:DAYLIGHT TZOFFSETFROM:+0100 TZOFFSETTO:+0200 TZNAME:CEST DTSTART:20210328T010000 END:DAYLIGHT BEGIN:STANDARD TZOFFSETFROM:+0200 TZOFFSETTO:+0100 TZNAME:CET DTSTART:20211031T010000 END:STANDARD END:VTIMEZONE BEGIN:VEVENT DTSTART;TZID=Europe/Brussels:20211203T093000 DTEND;TZID=Europe/Brussels:20211203T172000 DTSTAMP:20260422T205112 CREATED:20211115T132738Z LAST-MODIFIED:20211129T203801Z UID:1436-1638523800-1638552000@ibsquare.be SUMMARY:IB2 Research Day 2021 DESCRIPTION:IB2 Research Day\n# in view of the sanitary situation\, we simplified the schedule of the day & the conference will be held in hybrid format in the morning and online in the afternoon – the zoom link has been sent the participants # \nMorning session – Solvay room\n\n9:30 Plasticity in Regenerative Biology: Immediate and Long-term impact of cellular stress \nSumeet Pal Singh\, ULB \n10:30 Understanding liver morphogenesis and differentiation in health and disease: impact of computational modeling \nFrédéric Lemaigre\, Institut de Duve \n11h30 Computational challenges in mass spectrometry-based single-cell proteomics\, Christophe Vanderaa (UCL) \n11h50 Modelling neural induction in Ascidian embryogenesis\, Rossana Bettoni (ULB/VUB) \nLunch – La Mirabelle\n\n12h10 – 2h30 : We will go “La Mirabelle” in the cimetière d’Ixelles. \nAfternoon session – Online only\n\n2:30 Policy optimisation in epidemiological models \nPieter Libin\, VUB \n3:30 From DIDA to OLIDA: the oligogenic disease database\, Barbara Gravel (ULB) \n3:50 A panoramic perspective of Human phosphorylation\, Pathmanaban Ramasamy (UGent/VUB) \n4:20 Assembling genomes of non-vertebrate animals \nNadège Guiglielmoni (Universität zu Köln) \n### Covid Safe Ticket Plus required (CST + mask) ###\nRegistration\nRegister here (no longer possible to submit a title for a short presentation) https://framaforms.org/registration-ib2-research-day-1635245542 URL:https://ibsquare.be/event/ib2-research-day-2021/ LOCATION:Solvay Room (ULB\, NO building 5th floor)\, Campus Plaine\, Bvd du Triomphe\, Brussels\, 1050 CATEGORIES:Other END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Brussels:20211126T120000 DTEND;TZID=Europe/Brussels:20211126T130000 DTSTAMP:20260422T205112 CREATED:20211117T164500Z LAST-MODIFIED:20211117T164500Z UID:1457-1637928000-1637931600@ibsquare.be SUMMARY:Journal Club - Barbara Gravel DESCRIPTION:TBA by Barbara Gravel\, ULB-VUB URL:https://ibsquare.be/event/journal-club-barbara-gravel/ LOCATION:(IB)² common room\, 1C6.111 - Building B/C\, 6th floor\, La Plaine Campus\, ULB END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Brussels:20211112T120000 DTEND;TZID=Europe/Brussels:20211112T130000 DTSTAMP:20260422T205112 CREATED:20211117T164355Z LAST-MODIFIED:20211117T164355Z UID:1455-1636718400-1636722000@ibsquare.be SUMMARY:Journal Club - Charlotte Nachtegael DESCRIPTION:https://www.nature.com/articles/s41746-021-00520-6 \nby Charlotte Nachtegael\, ULB URL:https://ibsquare.be/event/journal-club-charlotte-nachtegael/ LOCATION:(IB)² common room\, 1C6.111 - Building B/C\, 6th floor\, La Plaine Campus\, ULB END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Brussels:20211029T120000 DTEND;TZID=Europe/Brussels:20211029T130000 DTSTAMP:20260422T205112 CREATED:20211117T164238Z LAST-MODIFIED:20211117T164238Z UID:1453-1635508800-1635512400@ibsquare.be SUMMARY:Journal Club - Antony Piron DESCRIPTION:TIGER: The gene expression regulatory variation landscape of human pancreatic islets\n \nby Anthony Piron \n  \n  URL:https://ibsquare.be/event/journal-club-antony-piron/ LOCATION:(IB)² common room\, 1C6.111 - Building B/C\, 6th floor\, La Plaine Campus\, ULB END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Paris:20200306T150000 DTEND;TZID=Europe/Paris:20200306T160000 DTSTAMP:20260422T205112 CREATED:20200207T145953Z LAST-MODIFIED:20200228T084347Z UID:1058-1583506800-1583510400@ibsquare.be SUMMARY:Seminar: Understanding of Plant Adaptation to Different Environment Conditions DESCRIPTION:Understanding of Plant Adaptation to Different Environment Conditions \nBing CHENG \nAbstract: \nClimate change is threatening many agricultural regions around the globe. Plants are sessile organisms and migrate to more prosperous habitat. How do they approach this is an open question in plant science. This presentation will cover our recent studies exploiting plant phenotypic and genomic information\, to demonstrate how their deployment can help agriculture withstands climate change responsibly and sustainably. Results from these studies will provide insights into the genetic adaptation of plants in a wider range of available future environments. \nShort Bio: \nIn 2019\, Bing gained her PhD degree from The University of Queensland\, Australia under the supervision of Prof. R. Henry. She focused on the genetic improvement of coffee quality through comparative genomics and transcriptomics. She has published the first long-read reference transcriptome for Arabica coffee bean and identified candidate genes regulating essential chemical accumulation during bean ripening. Currently\, Bing Cheng is a postdoctoral fellow from the Crop Production and Biostimulation Laboratory (CPBL) at the Interfaculatry School of Bioengineers\, ULB\, under the guidance of Prof C. Hermans. She is exploiting the natural variability of the model (Arabidopsis) and crop (oilseed rape) species to decipher genetic bases of resource use efficiency\, using genome-wide association studies and global transcriptome analysis. \nAbout CPBL: \nThe Crop Nutrition unit at CPBL focuses on improving resource use efficiency of crops to ensure food security and environmental quality. A considerable fraction of fertilizer to sustain plant biomass production gets lost as runoffs with detrimental consequences to the environment and human health. Faced with those pressing societal costs\, modern agriculture must make a step change to produce biomass with less input. The unit develops synergistic activities in the laboratory\, natural habitat and field environments to identify plant characteristics for improving the resilience of agricultural production. \nThe core research theme developed at CPBL is on the environmentally sustainable intensification of the agricultural system. Research developed by the host group is interdisciplinary and aims at (i) identifying crop characteristics for improving resilience of agricultural production while limiting the environmental footprint\, (ii) providing breeders with selection criteria (including molecular and genomic tools) to develop new crop varieties\, (iii) developing and evaluating methods (in lab and field environments) for performance testing of these varieties. URL:https://ibsquare.be/event/seminar-bing-cheng/ LOCATION:VUB I.1.05 CATEGORIES:Seminar END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Paris:20200221T153000 DTEND;TZID=Europe/Paris:20200221T163000 DTSTAMP:20260422T205112 CREATED:20200207T145846Z LAST-MODIFIED:20200212T161954Z UID:1054-1582299000-1582302600@ibsquare.be SUMMARY:Seminar Predicting Protein and RNA Structures via data inference DESCRIPTION:Alexander Schug\nJohn von Neumann Institute for Computing\, Jülich Supercomputer Centre\, Forschungszentrum Jülich\nFaculty of Biology\, University of Duisburg-Essen \nPredicting Protein and RNA Structures via data inference \nOn the molecular level\, life is orchestrated through an interplay of many biomolecules. To gain any detailed understanding of biomolecular function\, one needs to know their structure. Yet the structural characterization of many important biomolecules and their complexes – typically preceding any detailed mechanistic exploration of their function- remains experimentally challenging. Tools rooted in statistical physics such as Direct Coupling Analysis (DCA) but also increasingly Machine Learning driven approaches take advantage of the explosive growth of sequence databases and infer residue co-evolution to guide structure prediction methods via spatial constraints. Going beyond anecdotal cases of a few protein families\, systematic large-scale studies of >1000 protein families are now possible and other information\, such as low-resolution experimental information from\, e.g. SAXS or FRET \, can be used as further constraints in simulations. URL:https://ibsquare.be/event/seminar-alex-schug/ LOCATION:VUB I.1.05 CATEGORIES:Seminar END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Paris:20191213T150000 DTEND;TZID=Europe/Paris:20191213T150000 DTSTAMP:20260422T205112 CREATED:20191121T084616Z LAST-MODIFIED:20191202T122859Z UID:1036-1576249200-1576249200@ibsquare.be SUMMARY:Seminar Tomas Brazdil - Pushing the limits in automated NMR structure determination DESCRIPTION:Pushing the limits in automated NMR structure determination \nTomas Brazdil (Masaryk University) \nNuclear Magnetic Resonance (NMR) spectroscopy is a technique for determining the structural and dynamic properties of molecules. NMR spectroscopy generates complex data whose analysis is a laborious task and the road to NMR structure is generally a long one. Our starting point is the 4D-CHAINS algorithm that performs a fully automated assignment of chemical shifts based on 4D TOCSY and 4D NOESY spectra. We propose to perform the assignment task using solely the 4D NOESY spectrum. Since Rosetta software can deliver accurate structures from a sparse network of distance constraints extracted from the NOESY spectrum\, our approach promises to crack the atomic structures of large proteins in a single step. To solve the assignment problem\, we utilize both machine learning as well as elementary graph theoretic methods. Machine learning techniques are used to train models for the amino acid and atom type prediction from a given set of chemical shifts. To overcome relative scarcity of 4D-NOESY data\, we employ large amounts of chemical shifts deposited in Biological Magnetic Resonance Bank by human experts. The trained models are subsequently incorporated into an algorithm that assigns the corresponding sets of chemical shifts to amino acid residues of a given protein. In my talk\, I will describe the core pipeline\, explain the main difficulties and demonstrate the functionality of the current version which is still under development. URL:https://ibsquare.be/event/seminar-tomas-pushing-the-limits-in-automated-nmr-structure-determination/ LOCATION:VUB\, Building I\, I.0.01 END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Paris:20191206T150000 DTEND;TZID=Europe/Paris:20191206T150000 DTSTAMP:20260422T205112 CREATED:20191121T085000Z LAST-MODIFIED:20191202T123045Z UID:1042-1575644400-1575644400@ibsquare.be SUMMARY:Seminar Isel Grau - An interpretable semi-supervised classifier with bioinformatics applications DESCRIPTION:An interpretable semi-supervised classifier with bioinformatics applications. \nIsel Grau (VUB) \nIn the context of medical or bioinformatic applications of machine learning\, obtaining data instances is a relatively easy process but labeling them could become quite expensive or tedious. Such scenarios lead to datasets with few labeled instances and a larger number of unlabeled ones. Semi-supervised classification techniques combine labeled and unlabeled data during the learning phase in order to increase classifier’s generalization capability. Regrettably\, most successful semi-supervised classifiers do not allow explaining their outcome\, thus behaving like black boxes. However\, experts in the bioinformatics and medical domains demand a clear understanding of the decision process in order to trust the results of the machine learning algorithms. We present an interpretable self-labeling grey-box classifier that uses a black box to estimate the missing class labels and a white box to make the final predictions. We propose two different approaches for amending the self-labeling process: a first one based on the confidence of the black box and the latter one based on measures from Rough Set Theory. With this approach we aim to achieve interpretability by means of transparency and simplicity\, while attaining superior prediction rates when compared with most prominent self-labeling classifiers reported in the literature. We will show our preliminary results on two case studies: the prediction of early folding in proteins and the classification of pathogenicity of Brugada Syndrome variants. URL:https://ibsquare.be/event/seminar-isel-grau-an-interpretable-semi-supervised-classifier-with-bioinformatics-applications/ LOCATION:VUB\, Building I\, I.0.01 END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Paris:20191122T150000 DTEND;TZID=Europe/Paris:20191122T160000 DTSTAMP:20260422T205112 CREATED:20191024T190144Z LAST-MODIFIED:20191108T130544Z UID:967-1574434800-1574438400@ibsquare.be SUMMARY:Seminar Simon Dellicour\, ULB DESCRIPTION:Simon Dellicour\, ULB \nLandscape phylogeography – Using viral gene sequences to compare and explain the heterogeneous spatial dynamics of virus epidemics URL:https://ibsquare.be/event/seminar-simon-dellicour-ulb/ LOCATION:VUB\, Building I\, I.0.01 CATEGORIES:Seminar END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Paris:20191025T090000 DTEND;TZID=Europe/Paris:20191025T173000 DTSTAMP:20260422T205112 CREATED:20190920T110044Z LAST-MODIFIED:20191023T192814Z UID:958-1571994000-1572024600@ibsquare.be SUMMARY:(IB)2 Research Day 2019 DESCRIPTION:Event Timing: October 25th\, 2019 from 9am to 5.30pm\nEvent Address:  Bozar\, Koningsstraat 10\, 1000 Brussels (Entrance in front of the Parc Royal)\nContact: Sophie de Buyl \nMatthieu Defrance \n\n9:00 – 9:25 Welcome Coffee \n9:25 – 9:30 Introduction\n9:30 – 10:30 Keynote 1 Benjamin Werner\, Centre for Cancer Genomics\nA brief history of somatic evolution and a briefer tour trough modern cancer genomics\n10:30 – 11:00 Daniele Parisi\, KULeuven\nNetflix&Chill: fusing ligand-based and structure-based information in drug repositioning with artificial intelligence \n11:00 – 11:30 Coffee break \n11:00 – 11:30 Pathmanaban Ramasamy\, U Gent\, VUB\nScop3P: a comprehensive resource of human phosphosites within their full context\n11:30 – 12:30 Keynote 2 Laurent Bréhélin\, CNRS LIRMM Montpellier\, France\nStatistical modelling for regulatory genomics \n12:30 – 14:00 Lunch Break & Poster session \n14:00 – 14:30 Natália Araujo\, ULB\nTranscriptomics of heat adaptation in ants\n14:30 – 15:00 Stefan Vet\, VUB\nManipulation of bistability in mutualistic microbial systems via prebiotics \n15:00 – 16:00 Keynote 3 Pierre Peterlongo\, INRIA Rennes\, France\nAlgorithms for analyzing large metagenomics data\n16:00 – 16:10 Présentation of the RSG regional group\n16:10 – 16:30 Closing remarks by the (IB)2 directors\n16:30 – 17:30 Drink & Music by the (IB)2 band URL:https://ibsquare.be/event/ib2-research-day-2019/ LOCATION:ozar\, Koningsstraat 10\, 1000 Brussels\, Belgium END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Paris:20190524T150000 DTEND;TZID=Europe/Paris:20190524T160000 DTSTAMP:20260422T205112 CREATED:20190118T141236Z LAST-MODIFIED:20190522T125909Z UID:883-1558710000-1558713600@ibsquare.be SUMMARY:Journal Club: Sylvie DESCRIPTION:Inverse problem : an application in brain imaging and in cancerology\nInverse problem is a class of models in which we try to determine the causes of a phenomenon from the experimental observations of its effects. During my presentation\, I will speak about two inverse problems that show similarities in their resolution. The first one is in magnetoencephalography where the goal is to find the activated brain regions thanks to measures of the magnetic field outside the skull. The second one is in cancerology where the goal is try to find the percentage of all cell types present in a tumor thanks to sequencing data. URL:https://ibsquare.be/event/journal-club-sylvie/ LOCATION:(IB)² common room\, 1C6.111 - Building B/C\, 6th floor\, La Plaine Campus\, ULB CATEGORIES:Seminar END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Paris:20190517T080000 DTEND;TZID=Europe/Paris:20190517T170000 DTSTAMP:20260422T205112 CREATED:20190510T140236Z LAST-MODIFIED:20190510T140236Z UID:947-1558080000-1558112400@ibsquare.be SUMMARY:Journal Club - Simon DESCRIPTION:pBRIT: gene prioritization by correlating functional and phenotypic annotations through integrative data fusion. URL:https://ibsquare.be/event/journal-club-simon/ LOCATION:(IB)² common room\, 1C6.111 - Building B/C\, 6th floor\, La Plaine Campus\, ULB END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Paris:20190510T150000 DTEND;TZID=Europe/Paris:20190510T160000 DTSTAMP:20260422T205112 CREATED:20190118T141101Z LAST-MODIFIED:20190508T150100Z UID:879-1557500400-1557504000@ibsquare.be SUMMARY:Journal Club: Alex - Knowledge representations for contextualising disease associated molecular signatures DESCRIPTION: URL:https://ibsquare.be/event/journal-club-alex/ LOCATION:(IB)² common room\, 1C6.111 - Building B/C\, 6th floor\, La Plaine Campus\, ULB CATEGORIES:Seminar END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Paris:20190503T150000 DTEND;TZID=Europe/Paris:20190503T160000 DTSTAMP:20260422T205112 CREATED:20190327T155000Z LAST-MODIFIED:20190329T124410Z UID:935-1556895600-1556899200@ibsquare.be SUMMARY:Seminar Thierry Mora (ENS\, Paris) - Diversity and response in immune repertoires DESCRIPTION:The diversity of repertoires of B-cell and T-cell receptors is\ngenerated by a stochastic process of gene rearrangement called VDJ\nrecombination\, and is later sculpted by selection\, clonal\nproliferation\, and somatic hypermutations. I will show how these\nprocesses can be learned quantitatively from high-throughput\nrepertoire sequencing data. The resulting models can then be used to\nestimate the diversity of repertoires and their overlap between\nindividuals\, to identify condition-specific immune receptors from\npatient cohort data\, and to detect signatures of immune responses in\nsingle patients\, opening the way for novel sequencing-based diagnostic\nand prognostic tools. URL:https://ibsquare.be/event/seminar-thierry-mora-ens-paris/ LOCATION:Solvay Room (ULB\, NO building 5th floor)\, Campus Plaine\, Bvd du Triomphe\, Brussels\, 1050 CATEGORIES:Seminar END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Paris:20190405T150000 DTEND;TZID=Europe/Paris:20190405T160000 DTSTAMP:20260422T205112 CREATED:20190118T141021Z LAST-MODIFIED:20190425T104521Z UID:877-1554476400-1554480000@ibsquare.be SUMMARY:Journal Club: Sofia DESCRIPTION:In the era of the rise against statistical significance: what have we (not) learnt from millions of scientific papers with P-values URL:https://ibsquare.be/event/journal-club-sofia/ LOCATION:(IB)² common room\, 1C6.111 - Building B/C\, 6th floor\, La Plaine Campus\, ULB CATEGORIES:Seminar END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Paris:20190322T150000 DTEND;TZID=Europe/Paris:20190322T160000 DTSTAMP:20260422T205112 CREATED:20190118T140938Z LAST-MODIFIED:20190320T102816Z UID:875-1553266800-1553270400@ibsquare.be SUMMARY:Journal Club: Nathaniel and Rudy - "Cell movement\, chemotaxis\, and statistical physics" DESCRIPTION: URL:https://ibsquare.be/event/journal-club-nathaniel-rudy/ LOCATION:(IB)² common room\, 1C6.111 - Building B/C\, 6th floor\, La Plaine Campus\, ULB CATEGORIES:Seminar END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Paris:20190315T150000 DTEND;TZID=Europe/Paris:20190315T160000 DTSTAMP:20260422T205112 CREATED:20190118T140757Z LAST-MODIFIED:20190313T095253Z UID:871-1552662000-1552665600@ibsquare.be SUMMARY:Seminar Zeynep Kalender Atak\, Heterogeneity of melanoma genomes and cell states (KUL) DESCRIPTION:Heterogeneity in cancer is a consequence of both irreversible genetic changes and reversible transcriptional changes. Melanoma is prime example for this since on the genomic level melanomas have a high mutational burden leading to inter and intra-tumor heterogeneity while on the transcriptomic level they can be classified into two distinct but highly plastic transcriptional states (termed as proliferative and invasive) leading to intra-tumor heterogeneity. These states potentially play a role in metastasis\, therapy resistance and immune evasion\, thus understanding the mechanisms of this transcriptional plasticity is crucial. In my talk\, I will present our efforts for identifying molecular characteristics of these states using multi-omics approaches ranging from whole genome sequencing to bulk & single-cell transcriptome sequencing. URL:https://ibsquare.be/event/seminar-zeynep-kalender-atak-heterogeneity-of-melanoma-genomes-and-cell-states-kul/ LOCATION:Forum F\, ULB CATEGORIES:Seminar END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Paris:20190308T150000 DTEND;TZID=Europe/Paris:20190308T160000 DTSTAMP:20260422T205112 CREATED:20190118T140856Z LAST-MODIFIED:20190118T140856Z UID:873-1552057200-1552060800@ibsquare.be SUMMARY:Journal Club: Charlotte DESCRIPTION: URL:https://ibsquare.be/event/journal-club-charlotte/ CATEGORIES:Seminar END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Paris:20190222T150000 DTEND;TZID=Europe/Paris:20190222T160000 DTSTAMP:20260422T205112 CREATED:20190118T140638Z LAST-MODIFIED:20190219T104918Z UID:868-1550847600-1550851200@ibsquare.be SUMMARY:Seminar Rob Jelier (KUL) : Simulating Cellular Movements in Early C. elegans Embryogenesis DESCRIPTION:Abstract: Understanding how cells position themselves correctly in multicellular environments is a fundamental challenge in developmental biology. We use the invariable embryogenesis of C. elegans and a modelling approach to better understand the underlying mechanisms driving cellular movements. We developed a simulator to model the physical interactions among cells that influence cell motion\, including physical constraints\, cell division\, adhesion\, and active forces. To inform and evaluate simulations we use a dataset of real embryos with microscopy tracked nuclei positions. In the model cells are represented as soft spheres that can repulse and adhere to each other\, and also move and divide. Cell division timings and movement directions are taken from the dataset. The egg shell repulses the cells and is modelled as a convex hull whose shape is derived from the embryo dataset. We use the model to unravel the contribution of purely physical processes in early embryogenesis\, such as the spatial constraints\, egg shape\, and shape changes due to divisions\, and active biological phenomena such as differential adhesion and active movements. The problem is framed as a machine learning approach to find the correct cellular positioning\, where hypotheses are evaluated by learning optimal parameter values on a training set and testing how much they improved cellular positioning. To optimize the model parameters we used evolutionary algorithms. Differential evolution is used for continuous variables and a novel molecule-based evolution scheme optimizes the differential cellular adhesion. At the 8-cell stage our simulations highlight previously described phenomena\, such as a weak basal adhesion force among all cells and active movements for the ABpl and ABpr cells. Also adhesion between E and P3 is suggested\, which matches published results of how descendants of both cells adhere during gastrulation. Our main goal however is to reproduce the complex movements during the AB64 stage. We are currently evaluating our predictions for this phase with experimens\, by visualizing e-cadherin molecules\, cell shapes and the actomyosin network. As a perspective\, we are expanding our simulator with a signaling model. Cell signaling is represented as a network of reactions expressed as logic rules\, where signals trigger cascades and determine cell fate. By modelling how signals affect fate\, linking fate to cell behavior\, we can predict the effects of perturbations on cell fates and positions. URL:https://ibsquare.be/event/seminar-rob-jelier-kul/ LOCATION:Forum F\, ULB CATEGORIES:Seminar END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Paris:20190215T150000 DTEND;TZID=Europe/Paris:20190215T160000 DTSTAMP:20260422T205112 CREATED:20190118T140515Z LAST-MODIFIED:20190208T110533Z UID:866-1550242800-1550246400@ibsquare.be SUMMARY:Seminar Genevière Dupont (ULB) - Intracellular calcium dynamics: from modeling to physiology DESCRIPTION: URL:https://ibsquare.be/event/seminar-geneviere-dupont-ulb/ LOCATION:Forum F\, ULB CATEGORIES:Seminar END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Paris:20190208T150000 DTEND;TZID=Europe/Paris:20190208T160000 DTSTAMP:20260422T205112 CREATED:20190118T140421Z LAST-MODIFIED:20190128T094433Z UID:864-1549638000-1549641600@ibsquare.be SUMMARY:Seminar Karoline Faust (KUL) : Emergent behaviour in a synthetic gut community DESCRIPTION:Due to its complexity and the impact of the human host\, it is hard to obtain a mechanistic understanding of the gut microbial community from sequencing data alone. Synthetic communities are an excellent tool to complement in vivo studies. Their dynamics can be accurately monitored while exerting a degree of control that is impossible to achieve in vivo.\nHere\, I will present an in vitro study of a synthetic microbial community consisting of three human gut bacterial strains. We monitored each community member growing in isolation and in co-culture and developed a kinetic model to describe their dynamics.\nThe experiments validate cross-feeding interactions and highlight the special role of Blautia hydrogenotrophica as an interaction partner. When parameterized on mono- and bi-culture data\, our model describes well the observed community dynamics\, but fails to predict community dynamics from mono-cultures alone. RNA-seq applied to mono- and tri-culture samples confirmed a change in behavior. In conclusion\, we showed that gut bacteria respond to their interaction partners\, giving rise to emergent behaviour. URL:https://ibsquare.be/event/seminar-karoline-faust-kul/ LOCATION:Forum F\, ULB CATEGORIES:Seminar END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/Paris:20181219T123000 DTEND;TZID=Europe/Paris:20181219T140000 DTSTAMP:20260422T205112 CREATED:20181219T094315Z LAST-MODIFIED:20190118T131411Z UID:770-1545222600-1545228000@ibsquare.be SUMMARY:IB2 Xmas lunch DESCRIPTION:All members are invited to participate in the IB2 Xmas lunch\, 19 December 2018\, at 12:30. Don’t forget to bring something edible for the gang! URL:https://ibsquare.be/event/ib2-xmas-lunch/ LOCATION:(IB)² common room\, 1C6.111 - Building B/C\, 6th floor\, La Plaine Campus\, ULB CATEGORIES:Other END:VEVENT BEGIN:VEVENT DTSTART;VALUE=DATE:20181116 DTEND;VALUE=DATE:20181117 DTSTAMP:20260422T205112 CREATED:20181104T123949Z LAST-MODIFIED:20190118T131417Z UID:596-1542326400-1542412799@ibsquare.be SUMMARY:(IB)2 Research Day 2018 DESCRIPTION:9.30 – 9.35 Welcome \n  \n9.35 – 10.35 Keynote 1 – Carl Herrmann\, University of Heidelberg \nMulti-omics data integration for single-cell genomics \n  \n10.35 – 11.05 Charlotte Nachtegael\, Unraveling the oligogenic potential \nof developmental disorders \nIB2\, ULB \n  \n11.05 – 11.30 Coffee Break \n  \n11.30 – 12.00 Youssef Bouysran\, Bioinformatic investigations of missense mutations \nin the FBN1 gene \nIB2\, ULB \n  \n12.00 – 12.30 Nathaniel Mon Père\, Quantitative Models for Cell Differentiation in Hematopoiesis \nIB2\, ULB \n  \n12.30 – 12.45 Flash presentations \n  \n12.45 – 14.00 Lunch break and poster session \n  \n14.00 – 15.00 Keynote 2 – Hervé Isambert\, Institut Curie Paris \nLearning causal and non-causal networks from large scale genomic and \nclinical data (Abstract below) \n  \n15.00 – 15.30 Gipsi Lima Mendez\, Ocean Eco-system biology through integration \nof heterogeneous data \nIB2\, ULB \n  \n15.30 – 16.00 Closing remarks / Future of the (IB)2 \n  \n16.00 17.00 Musical Coffee \n  \n(IB)² – Interuniversity Institute of Bioinformatics in Brussels http://ibsquare.be\nContact: Sophie de Buyl sophie.de.Buyl at vub.be\, Matthieu Defrance matthieu.dc.defrance at ulb.ac.be \nLearning causal and non-causal networks from large scale genomic and clinical data\, Hervé Issambert\, Curie Institute \nNetwork reconstruction aims at disentangling direct from indirect dependences in information-rich data and has become ubiquitous to analyze the rapidly expanding resources of genomic and clinical data. However\, most network inference methods are restricted to specific types of data and assume either causal or non-causal graphical models a priori. We have developed an information-based approach\, which reconstructs causal\, non-causal or mixed networks from large scale genomic or clinical data\, without the need for an a priori choice on the causal or non-causal nature of reconstructed networks. Starting from a fully connected graph\, it first removes dispensable edges by iteratively subtracting the most significant information contributions from indirect paths between each pair of nodes. The remaining edges are then filtered based on their confidence assessment or oriented based on the signature of causality in observational data. This computational approach outperforms or matches state-of-the-art methods for either causal (eg regulatory interaction) or non-causal (eg protein contact map) network reconstruction. In the talk\, I will present different applications on a broad range of biological and clinical data\, from single-cell transcriptomics and genomic alterations in tumor progression to long term evolution of vertebrates through whole genome duplication. URL:https://ibsquare.be/event/ib2-research-day-2018/ LOCATION:Groene Zaal\, Congrescentrum U-Residence\, VUB Campus\, Generaal Jacqueslaan 271\, Brussel\, 1050\, Belgique CATEGORIES:Seminar ATTACH;FMTTYPE=image/png:https://ibsquare.be/wp-content/uploads/2018/11/event_template.png END:VEVENT BEGIN:VEVENT DTSTART;VALUE=DATE:20180223 DTEND;VALUE=DATE:20180224 DTSTAMP:20260422T205112 CREATED:20181105T071601Z LAST-MODIFIED:20190118T131425Z UID:647-1519344000-1519430399@ibsquare.be SUMMARY:Multiple mechanisms of cardiac arrhythmias studied using anatomically accurate modeling. DESCRIPTION: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. URL:https://ibsquare.be/event/multiple-mechanisms-of-cardiac-arrhythmias-studied-using-anatomically-accurate-modeling/ LOCATION:UGent CATEGORIES:Seminar END:VEVENT END:VCALENDAR