Leiden Computation Biology Center http://www.lcbc.nl/ Fri, 22 Feb 2019 10:54:37 +0000 Fri, 22 Feb 2019 10:54:37 +0000 Jekyll v3.7.4 Cover Image for Nature Immunology <p><img src="/assets/papers/2019_nature_immunology/cover.png" alt="Nature Immunology, March 2019, Cover Image" style="width:80%; max-width:500px; display: block; margin: 0.5em auto;" /></p> <p>We are very proud to announce that <a href="https://www.nature.com/ni">Nature Immunology</a> chose one of the results of our study on <a href="/publications/2019_nature_immunology/">CD4+ T cells in the human fetal intestine</a> for the cover of the <a href="https://www.nature.com/ni/volumes/20/issues/3">2019 March issue</a> shown above.</p> <p>Nature Immunology also published a <a href="https://doi.org/10.1038/s41590-019-0326-0">comment on the paper</a> in the same issue.</p> Tue, 19 Feb 2019 00:00:00 +0000 http://www.lcbc.nl/press/2019/02/19/NatImmuCover/ http://www.lcbc.nl/press/2019/02/19/NatImmuCover/ press Study on CD4+ T Cell Variety in the Human Fetal Intestine Published in Nature Immunology <p>Our collaborators from the <a href="https://www.lumc.nl/org/ihb/">Immunohematology and Blood Transfusion</a> department at LUMC published their study showing that memory CD4+ T cells are generated in the human fetal intestine in <a href="https://doi.org/10.1038/s41590-018-0294-9">Nature Immunology</a>. The extensive study integrates data from several sources, such as Suspension Mass Cytometry, Imaging Mass Cytometry, RNA sequencing and TCR sequencing to paint a wholistic picture of CD4+ T cells in the prenatal immune system. Particularly, the study identifies T cells with wide-ranging degrees of maturity. “The great thing is that whichever way we looked at them, all the results pointed in the same direction: the T cells are already fairly mature. They looked like mature cells and behaved that way too,” explains Van Unen.</p> <p>LCBC was involved in the study working on scRNA-seq data analysis (Tamim) and CyTOF data analysis was carried out with the <a href="\projects\cytosplore">Cytosplore</a> software, developed by Thomas.</p> <p>LUMC provides a complete <a href="https://www.lumc.nl/over-het-lumc/nieuws/2019/Januari/immuunsysteem-volwassen-geboorte/?setlanguage=English&amp;setcountry=en">press release</a>, the paper can be downloaded directly from <a href="https://rdcu.be/bh0Xm">Nature Immunology</a>.</p> Mon, 21 Jan 2019 00:00:00 +0000 http://www.lcbc.nl/press/2019/01/21/NatImmu/ http://www.lcbc.nl/press/2019/01/21/NatImmu/ press 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