Leiden Computation Biology Center http://www.lcbc.nl/ Mon, 02 Jul 2018 13:30:02 +0000 Mon, 02 Jul 2018 13:30:02 +0000 Jekyll v3.7.3 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 Ahmed featured in a Data Story from the Allen Institute <p>The <a href="http://www.alleninstitute.org/what-we-do/brain-science/" target="_blank_">Allen Institute for Brain Science</a> released a <a href="https://www.alleninstitute.org/what-we-do/brain-science/news-press/articles/data-stories-visualizing-human-brain" target="_blank_">Data Story</a> about the work of Ahmed Mahfouz, amongst others discussing how Ahmed and our colleagues at Delft University of Technology and Leiden University Medical Center developed the open-source data visualization tool BrainScope, which was built on publicly available human brain data from the Allen Institute.</p> <div class="embed-responsive embed-responsive-16by9"> <iframe src="https://www.youtube.com/embed/1eINLbIujkY" frameborder="0" webkitallowfullscreen="" mozallowfullscreen="" allowfullscreen=""></iframe> </div> Mon, 10 Jul 2017 12:00:00 +0000 http://www.lcbc.nl/press/2017/07/10/allen_data_story/ http://www.lcbc.nl/press/2017/07/10/allen_data_story/ press Leiden CBC organizes a Single Cell Analysis meeting <p>On September 21, we are organizing the <a href="https://sites.google.com/view/biosb-singlecell/home" target="_blank">BioSB HotTopics Meeting on Single Cell Analysis</a> at LUMC, with the aim of bringing together researchers with shared interest in single cell analysis. The meeting will feature presentations from the following speakers: <br /></p> <ul> <li>Lude Franke (UMC Groningen)</li> <li>Thomas Höllt (LUMC/TU Delft)</li> <li>Patrick van den Berg (Leiden University)</li> <li>Mauro Muraro (Hubrecht Institute) <br /> Check the full program and register <a href="http://tinyurl.com/biosb-singlecell" target="_blank">here</a></li> </ul> Tue, 04 Jul 2017 12:00:00 +0000 http://www.lcbc.nl/event/2017/07/04/HotTopics/ http://www.lcbc.nl/event/2017/07/04/HotTopics/ event Keynote and Highlight Talk at BioVis 2017 <p>We will present our work at <a href="https://www.iscb.org/ismbeccb2017" target="_blank">ISMB/ECCB</a> and <a href="http://biovis.net/2017/program_ismb/" target="_blank">BioVis</a> from 21st to 25th of July.<br /> On 24th of July, Boudewijn Lelieveldt will present some of our work, including <a href="https://www.cytosplore.org" target="_blank">Cytosplore</a>, in his keynote <em>Visual Analytics for Spatial Transcriptomics: From Single Cell to Tissue and Back</em>. Later on the same day, Sjoerd will give a Highlight Talk on his <a href="/publications/2017_nar_brainscope/" target="_blank">NAR paper</a>; <em>Brainscope: Interactive Visual Exploration of the Spatial and Temporal Human Brain Transcriptome</em>. Both talks are part of BioVis.</p> <p>Arlin will present her poster <em>Interaction Between Polyglutamine Genes ATN1 and ATXN2 Coincides with Regions Associated to Huntington’s Disease</em> in Session A on July 22nd and 23rd and Tamim will present his poster <em>Single Cell Mass Cytometry Marker Panel Extension</em> in Session B on July 24th and 25th.</p> <p>See the <a href="http://biovis.net/2017/program_ismb/" target="_blank">BioVis</a> and <a href="https://www.iscb.org/ismbeccb2017" target="_blank">ISCB ECCB</a> websites for more details.</p> Sat, 01 Jul 2017 12:00:00 +0000 http://www.lcbc.nl/event/2017/07/01/BioVis/ http://www.lcbc.nl/event/2017/07/01/BioVis/ event Leiden CBC at Keystone Single Cell Omics Meeting <p>We’ll be at the <a href="https://www.keystonesymposia.org/17E3">Keystone Single Cell Omics Meeting</a> in Stockholm from May 26 to May 30 this year. Tamim will present a poster about his work on combining CyTOF marker panels and Thomas will demo our latest advances in integrating HSNE into <a href="http://www.cytosplore.org">Cytosplore</a>.</p> Mon, 01 May 2017 12:00:00 +0000 http://www.lcbc.nl/event/2017/05/01/KSomics/ http://www.lcbc.nl/event/2017/05/01/KSomics/ event