Leiden Computation Biology Center http://www.lcbc.nl/ Wed, 28 Nov 2018 08:28:34 +0000 Wed, 28 Nov 2018 08:28:34 +0000 Jekyll v3.7.4 LCBC at SFN 2018 <p>Ahmed and Mandy attended the Society for Neuroscience Annual Meeting (<a href="https://www.sfn.org/Meetings/Neuroscience-2018">Neuroscience 2018</a>) in San Diego, California between 3 and 7 November. Mandy presented a poster on identifying gene expression signatures underlying stress resilience in the brain.</p> Fri, 09 Nov 2018 08:00:00 +0000 http://www.lcbc.nl/press/2018/11/09/sfn/ http://www.lcbc.nl/press/2018/11/09/sfn/ press LCBC at ECCB 2018 <p>LCBC was strongly present at <a href="http://eccb18.org/">ECCB2018</a>. Marcel, Ahmed, Arlin, and Tamim represented LCBC at <a href="http://eccb18.org/">ECCB2018</a>, taking place in Athens, Sep 8 to 12 this year. Arlin presented a poster on her work on identifying gene expression patterns correlated to Parkinson’s disease progression (unpublished work) and Tamim presented his method for automatic identification of cell types in mass cytometry single cell data (<a href="https://www.lcbc.nl/publications/2018_cytof_classification/">preprint</a>).</p> Fri, 14 Sep 2018 08:00:00 +0000 http://www.lcbc.nl/press/2018/09/14/eccb/ http://www.lcbc.nl/press/2018/09/14/eccb/ press LCBC proud to be partner in DC4Balance <p>On behalf of the LCBC, Dr. Erik van den Akker will be a partner in a recently <a href="https://www.health-holland.com/news/2018/07/topsector-lsh-en-sgf-onderzoek-afweer-in-balans">Health~Holland</a> funded project <a href="https://www.health-holland.com/public/news/2018/07/180724-immunologie-call-samenvattingen-onderzoeken.pdf">“DC4Balance”</a>. This project aims to develop vaccines that will restore the balance of disturbed immune systems typically observed in allergies or auto-immune diseases.</p> Thu, 26 Jul 2018 12:00:00 +0000 http://www.lcbc.nl/award/2018/07/26/DC4Balance/ http://www.lcbc.nl/award/2018/07/26/DC4Balance/ award Indu Khatri receives Marie-Sklodowska-Curie LEaDing Fellows <p>Indu Khatri has been awarded the prestiguous Marie-Sklodowska-Curie <a href="http://leadingfellows.eu/">LEaDing Fellows</a> Project. From August 20187 onward she will work for a 2-year period on “A computational model to assess vaccine efficacy based on the analysis of B-cell clonal lineages”.</p> Fri, 20 Jul 2018 12:00:00 +0000 http://www.lcbc.nl/award/2018/07/20/Indu_LeadingFellow/ http://www.lcbc.nl/award/2018/07/20/Indu_LeadingFellow/ award LCBC at ISMB 2018 <p>Marcel and Thomas will represent LCBC at <a href="https://www.iscb.org/ismb2018">ISMB</a> conference, taking place in Chicago, July 6 to 10 this year. Thomas will give a talk in the <a href="http://www.biovis.net">BioVis COSI</a> on July 9th in the first Session at 11:50 a.m. He will present an overview of the <a href="https://www.lcbc.nl/publications/2017_hsne_nature_communications/">Nature Communications paper</a> Visual Analysis of Mass Cytometry Data by Hierarchical Stochastic Neighbor Embedding Reveals Rare Cell Types, discussing HSNE and <a href="https://www.cytosplore.org">Cytosplore</a>. Please check the <a href="http://biovis.net/2018/program_ismb/">full BioVis program</a> for details.</p> <p>If you are an active <a href="https://www.cytosplore.org">Cytosplore</a> user Thomas would love to hear your feedback, so don’t hesitate to chat us up!</p> Wed, 27 Jun 2018 08:00:00 +0000 http://www.lcbc.nl/press/2018/06/27/ismb/ http://www.lcbc.nl/press/2018/06/27/ismb/ press Online Talk on Single Cell Analysis using Cytosplore <p>Last week, Thomas gave a remote talk at the <a href="https://www.jku.at/en/institute-of-computer-graphics/" target="_blank_">Institute of Computer Graphics </a> of the <a href="https://www.jku.at/" target="_blank_">Johannes Kepler University, Linz</a> on the work of the group on Exploration of Large Single-Cell data with Cytosplore and HSNE. The talk has been recorded and is available on <a href="https://www.youtube.com/watch?v=dQnj3PejG6w" target="_blank_">YouTube</a>.</p> <div class="embed-responsive embed-responsive-16by9"> <iframe src="https://www.youtube.com/embed/dQnj3PejG6w" frameborder="0" allowfullscreen=""></iframe> </div> Wed, 28 Mar 2018 12:00:00 +0000 http://www.lcbc.nl/press/2018/03/28/jku_talk/ http://www.lcbc.nl/press/2018/03/28/jku_talk/ press Paper on Duchenne muscular dystrophy receives prize from Prinses Beatrix Spierfonds <p>Nathalie Doorenweerd from the Radiology Department at LUMC has received the annual prize of neuromuscular disease research (<a href="https://www.prinsesbeatrixspierfonds.nl/wat-wij-doen/werkwijze/stimuleren-onderzoekstalent/">Jaarprijs Neuromusculaire Ziekten</a>) from the <a href="https://www.prinsesbeatrixspierfonds.nl/">Princes Beatrix Spierfonds</a>.</p> <p>Nathalie won the award for her paper together with Ahmed Mahfouz on mapping the expression of dystrophin isoforms in the developing human brain. The paper was published in 2017 in Scientific Reports.</p> <p>You can read more about the award on the <a href="https://www.prinsesbeatrixspierfonds.nl/nathalie-doorenweerd-wint-jaarprijs-neuromusculaire-ziekten/">website of the Princes Beatrix Spierfonds</a></p> <p>You can check the paper here: <a href="/publications/2017_sr_DMD/">Timing and localization of human dystrophin isoform expression provide insights into the cognitive phenotype of Duchenne muscular dystrophy</a></p> Fri, 12 Jan 2018 00:00:00 +0000 http://www.lcbc.nl/press/2018/01/12/SpierFonds/ http://www.lcbc.nl/press/2018/01/12/SpierFonds/ press Single cell HSNE paper published in Nature Communications <p>We are excited to announce that our paper <a href="/publications/2017_hsne_nature_communications/">Visual Analysis of Mass Cytometry Data by Hierarchical Stochastic Neighbor Embedding Reveals Rare Cell Types</a>, previously available on <a href="https://doi.org/10.1101/169888">BiorXiv</a> has been published in <a href="https://dx.doi.org/10.1038/s41467-017-01689-9">Nature Communications</a>. The paper describes the application of HSNE, a hierarchical SNE-based technique that allows the exploration of datasets too large for other SNE-based techniques (such as t-SNE) through a hierarchical representation, to single cell mass cytometry data. See the movie below for an exemplary exploration of a dataset consisting of 5 Million cells.</p> <p>Along with the paper we released a major update for our single cell analysis software <a href="https://www.cytosplore.org">Cytosplore</a> now featuring HSNE alongside A-tSNE and SPADE for single cell analysis. The software is available for free to download at <a href="https://www.cytosplore.org">https://www.cytosplore.org</a></p> <p>The paper is the result of a strong collaboration between multiple groups at LUMC and TU Delft. Press releases from <a href="https://www.lumc.nl/over-het-lumc/nieuws/2017/november/interactieve-technologie-zeldzame-celtypen/?setlanguage=English&amp;setcountry=en">LUMC</a> and <a href="https://www.tudelft.nl/en/2017/tu-delft/new-interactive-technology-makes-rare-cell-types-visible/">TU Delft</a> are available.</p> <div class="embed-responsive embed-responsive-16by9"> <iframe src="https://player.vimeo.com/video/205552113" frameborder="0" webkitallowfullscreen="" mozallowfullscreen="" allowfullscreen=""></iframe> </div> Mon, 27 Nov 2017 00:00:00 +0000 http://www.lcbc.nl/press/2017/11/27/NatComm/ http://www.lcbc.nl/press/2017/11/27/NatComm/ press Paper on Duchenne Muscular Dystrophy is out <p>Our paper on Duchenne muscular dystrophy is published in Scientific Reports. The paper provides a comprehensive analysis of the expression patterns of dystrophin isoforms across human brain development uisng data from the Allen Brain Atlas, the Roadmap Epigenomics Consortium, and the FANTOM5 project. The results provide new insights into the cognitive phenotype associated with Duchenne muscular dystrophy.</p> <p>There is a press-release from LUMC highlighting the paper and you can read the paper <a href="https://www.nature.com/articles/s41598-017-12981-5">here</a>.</p> <p>Nathalie Doorenweerd presented this work at the International Congress of the World Muscle Society. Nathalie’s poster won the Best Poster Award.</p> Tue, 17 Oct 2017 00:00:00 +0000 http://www.lcbc.nl/press/2017/10/17/DMD/ http://www.lcbc.nl/press/2017/10/17/DMD/ press Leiden CBC at IEEE VIS Conference <p>Thomas will be at the <a href="https://www.ieeevis.org" target="_blank_">IEEE VIS Conference</a>, taking place in Phoenix, AZ from October 1st to 6th this year. He will present his latest paper <a href="/publications/2017_vis_cyteguide/"><em>CyteGuide: Visual Guidance for Hierarchical Single-Cell Analysis</em></a> on Thursday, October 5th in the InfoVis Papers Session <em>Trees and Table Tennis</em> (10:30AM-12:10PM, room 301-D). The talk we start at approximately 11:45AM. Furthermore Nicola Pezzotti will present joint work on <a href="/publications/2017_vis_deepeyes/"><em>DeepEyes: Progressive Visual Analytics for Designing Deep Neural Networks</em></a> (Wed, Oct 4th, 11:45AM, room 301-C) For the full conference program check the official <a href="http://ieeevis.org/attachments/vis17-program-final.pdf" target="_blank_">program pdf</a>.</p> <p>Thomas will be around the whole week, if you have any questions or want to see a Cytosplore demo don’t hesitate to ask.</p> Tue, 19 Sep 2017 00:00:00 +0000 http://www.lcbc.nl/event/2017/09/19/Vis/ http://www.lcbc.nl/event/2017/09/19/Vis/ event