From mahogny at areta.org Wed May 1 13:26:30 2019 From: mahogny at areta.org (mahogny at areta.org) Date: Wed, 01 May 2019 12:26:30 +0100 Subject: [SocBiN] Wanted: PhD and postdoc in T cell systems biology, MIMS Message-ID: <06f57265d1be7bb0c788cda44c7e891b@areta.org> Hi everyone, I am setting up shop in Umeå, MIMS (the swedish nordic partner of EMBL), and hope to soon be able to announce a PhD and postdoc position. http://www.henlab.org/what-we-do/ The goal is to build a quantitative model explaining all aspects of human CD4 T cells, using explainable machine learning methods on a plethora of omics datasets that we will generate (I also welcome groups specialized on different pathways who want to help curate/interpret the data, as a collaboration) In many ways this is a follow up on previous work on CRISPR and single-cell methods that I have developed at Sanger. See e.g. https://www.cell.com/cell/pdf/S0092-8674(18)31569-1.pdf While not set in stone, I could imagine the prospective PhD student having a physics/math/programming background, while the postdoc has a more mixed wet/dry profile (e.g. having produced and analyzed RNA/ChIP/single cell-seq data ideal) For more details, visit http://www.henlab.org/join-us/ Best wishes, Johan Henriksson -------------- next part -------------- An HTML attachment was scrubbed... URL: From albin at binf.ku.dk Thu May 2 12:06:35 2019 From: albin at binf.ku.dk (Albin Sandelin) Date: Thu, 2 May 2019 12:06:35 +0200 Subject: [SocBiN] Phd position in pancreatic cancer bioinformatics Message-ID: Dear all We have a PhD position in pancreatic cancer bioinformatics in my group, part of an ITN consortium. Please share! https://candidate.hr-manager.net/ApplicationForm/SinglePageApplicationForm.aspx?cid=1307&departmentId=18965&ProjectId=149457&MediaId=5 Best, Albin Albin Sandelin Professor, PhD Section for Computational and RNA Biology, Department of Biology & Biotech Research and Innovation Centre, Copenhagen University Ole Maaloes Vej 5, DK2200, Copenhagen N, Denmark tel +45 224 56668 albin at binf.ku.dk skype: albinsan twitter: @albin_san -------------- next part -------------- An HTML attachment was scrubbed... URL: From luca.bortolussi at gmail.com Fri May 3 17:04:44 2019 From: luca.bortolussi at gmail.com (Luca Bortolussi) Date: Fri, 3 May 2019 17:04:44 +0200 Subject: [SocBiN] CMSB 2019 - Call for Posters and Highlight talks Message-ID: CMSB 2019 - Call for Posters and Highlight talks The 17th conference on Computational Methods in Systems Biology (CMSB 2019) will take place from 18th to 20th September 2019 in Trieste, Italy. Its aim is to bring together researchers from across biological, mathematical, computational, and physical sciences who are interested in the study, modelling, simulation, advanced analysis, and design of biological systems. CMSB 2019 will be hosted at the University of Trieste, Italy. INVITED SPEAKERS Benenson Kobi, synthetic biology group, ETH Zurich, CH Adelinde Uhrmacher, Modelling and Simulation Group, Rostock University, DE Trevor Graham, Bart Cancer Institute, London, UK Gasper Tkačik, IST Austria, Klosterneuburg, Austria Manuel Zimmer, University of Vienna, Austria IMPORTANT DATES All deadlines are AOE (Anywhere on Earth). Highlight talks and poster abstract submission: 28.6.2019 Notification to authors 12.07.2019 TOPICS OF INTEREST CMSB 2019 solicits original research articles, tool papers, posters, and presentations on the modelling and analysis of biological systems and networks as well as the analysis of biological data. The conference brings together computer scientists, biologists, mathematicians, engineers, and physicists interested in a system-level understanding of biological processes. It covers the broad field of computational methods and tools in systems and synthetic biology and their applications. Topics of interest include, but are not limited to: - formalisms for modelling biological processes - models, methods, tools and their biological applications - frameworks for model verification, validation, analysis, and simulation of biological systems - high-performance methods for computational systems biology - parameter and model inference from experimental data - automated parameter and model synthesis - model integration and biological databases - multi-scale modelling and analysis methods - design, analysis, and verification methods for synthetic biology - methods for biomolecular computing and engineered molecular devices - theoretical systems biology - data-based approaches for systems and synthetic biology In general, the conference is open to new theoretical results with potential applications to systems and synthetic biology, as well as novel applications and case studies of existing methods, tools, or frameworks. The CMSB 2019 proceedings will be published in the Springer LNCS series and indexed by ISI Web of Science, Scopus, ACM Digital Library, DBLP, and Google Scholar. A selection of best papers will be invited to be extended and submitted to a special issue of a Bioinformatics journal. At this stage, we are still soliciting submissions for the two following categories of contributions: A) Posters B) Highlight talks A) CALL FOR POSTERS CMSB 2019 solicits poster abstracts presenting I) original unpublished work and II) recent outstanding results already accepted to a recognised journal or a high-quality conference during the last year. The abstracts should be submitted in Springer LNCS style and should not exceed 2 pages including references. Based on the abstracts the program committee will select posters to be presented at the CMSB 2018 poster session including flash presentations. B) CALL FOR HIGHLIGHT TALKS CMSB 2019 offers the track of oral presentations without full paper or poster submission. We welcome submissions of work that has been already published in a journal, or that is currently under review or will soon be submitted. The abstracts summarizing the results and their relevance should not exceed 2 pages including references. The document format must be single spaced and written in an 11 point type font. Selected talks will be presented during plenary sessions of the conference. We encourage authors to also bring along a poster on their contribution, to facilitate further discussions. SUBMISSION INFORMATION All poster/ highlight talk abstracts have to be written in English and submitted electronically using the EasyChair online submission system (https://easychair.org/conferences/?conf=cmsb2019) in the form of a PDF file. All accepted contributions must be presented at the conference by one of the authors. PROGRAM COMMITTEE CHAIRS Luca Bortolussi, University of Trieste, IT Guido Sanguinetti, University of Edinburgh, UK PROGRAM COMMITTEE Alessandro Abate, University of Oxford, UK Ezio Bartocci, Vienna University of Technology, AT Nikola Beneš, Masaryk University, CZ Luca Bortolussi, University of Trieste, IT (co-chair) Giulio Caravagna, Institute of Cancer Research London, UK Luca Cardelli, University of Oxford, UK Milan Češka, Brno University of Technology, CZ Claudine Chaouiya, Instituto Gulbenkian de Ciência, PT Eugenio Cinquemani, IBIS – INRIA, Grenoble, FR Thao Dang, VERIMAG/CNRS, Grenoble, FR Hidde de Jong, IBIS – INRIA, Grenoble FR François Fages, INRIA Saclay Île-de-France, FR Jérôme Feret, INRIA, Paris, FR Jasmin Fisher, Microsoft Research Cambridge, UK Christoph Flamm, University of Vienna, AT Elisa Franco, University of California at Riverside, USA Tomáš Gedeon, Montana State University, US Calin Guet – IST Austria (Austria) Monika Heiner, Brandenburg Technical University Cottbus-Senftenberg, DE Jane Hillston, The University of Edinburgh, UK Heinz Köppl, Technische Universität Darmstadt, DE Jean Krivine, IRIF, Paris Diderot University, FR Tommaso Mazza, RCCS Casa Sollievo della Sofferenza – Mendel, IT Laura Nenzi, Vienna University of Technology, AT Marco Nobile - University of Milano-Bicocca, IT Diego Oyarzún - Imperial College London, UK Nicola Paoletti, Stony Brook University, USA Loïc Paulevé, CNRS/LRI, FR Ion Petre, Åbo Akademi Turku, FI Tatjana Petrov, Universität Konstanz, DE Carla Piazza, University of Udine, IT Ovidiu Radulescu, University of Montpellier 2, FR Olivier Roux, Ecole Centrale Nantes, FR Jakob Ruess - Institute Pasteur Paris, FR Guido Sanguinetti, The University of Edinburgh, UK (co-chair) Thomas Sauter, University of Luxembourg, LU Abhyudai Singh, University of Delaware, US David Šafránek, Masaryk University, CZ Carolyn Talcott, SRI International, US Chris Thachuk – California Institute of Technology (USA) P.S. Thiagarajan, Harvard University, US Adelinde Uhrmacher, University of Rostock, DE Stefanie Winkelmann - Zuse Institut Berlin, DE Verena Wolf, Saarland University, DE Boyan Yordanov – Microsoft Research, UK Paolo Zuliani, Newcastle University, UK TOOL EVALUATION COMMITTEE Dimitrios Milios, Eurecom, FR (chair) Simone Silvetti, Esteco SpA, IT Daniel Trejo Banos, University of Lausanne, CH Michalis Michaelides, University of Edinburgh, UK Matej Hajnal, Masaryk University, CZ Chris Banks, University of Edinburgh, UK Anastasis Georgoulas, UCL London, UK LOCAL ORGANIZATION CHAIRS Luca Bortolussi - University of Trieste (Italy) Laura Nenzi - University of Trieste (Italy) LOCAL ORGANIZATION COMMITTEE Luca Bortolussi - University of Trieste (Italy) Francesca Cairoli - University of Trieste (Italy) Simone Silvetti - Esteco SpA (Trieste) Laura Nenzi - University of Trieste (Italy) STEERING COMMITTEE Finn Drablos, NTNU, NO François Fages, INRIA Saclay Île-de-France, FR David Harel, Weizmann Institute of Science, IL Monika Heiner, Brandenburg Technical University Cottbus-Senftenberg, DE Tommaso Mazza, RCCS Casa Sollievo della Sofferenza – Mendel, IT Satoru Miyano, The University of Tokyo, JP Gordon Plotkin, The University of Edinburgh, UK Corrado Priami, University of Pisa, IT Carolyn Talcott, SRI International, US Adelinde Uhrmacher, University of Rostock, DE From paolo.romano at hsanmartino.it Fri May 10 15:17:55 2019 From: paolo.romano at hsanmartino.it (Romano Paolo) Date: Fri, 10 May 2019 13:17:55 +0000 Subject: [SocBiN] NETTAB / BBCC 2019: Call for abstracts for oral communications Message-ID: Dear list members, I'm glad to announce the launch of the Call for abstracts for oral communications for the Joint NETTAB/BBCC 2019 Meeting. Abstracts of max four pages must be submitted within June 30, 2019 through EasyChair. Please find here below the text of the Call. The meeting will be held on November 11-13, 2019, at the Fisciano Campus, University of Salerno, Italy. You will find some information on the meeting at the end of this message. The meeting web site is available at http://www.nettab.org/2019/ . I'm looking forward to meeting many of you in Fisciano! All the best. Paolo Romano on behalf of the Chairs of the Joint NETTAB / BBCC 2019 Meeting ==**==**== Joint NETTAB/BBCC 2019 Meeting November 11-13, 2019 Fisciano Campus, University of Salerno, Italy http://www.nettab.org/2019/ CALL FOR ABSTRACTS FOR ORAL COMMUNICATIONS Topics A Special session of the meeting will be devoted to Computational Proteomics, but contributions on usual NETTAB and BBCC topics are also welcome. See the full list of topics at http://www.igst.it/nettab/2019/submissions/topics/ . Computational Proteomics topics (provisional list) Bioinformatics methods, tools and platforms for: * Standardization of data and methods * Annotation, visualization, integrated discovery * Protein identification and validation * Biomarker discovery * Quantitative proteomics * Single cell proteomics * Targeted proteomics * Molecular imaging by mass spectrometry * Microbial proteomics Authors' instructions Abstracts must be submitted through EasyChair at https://easychair.org/conferences/?conf=nettabbcc2019 . Submission deadline: Sunday June 30, 2019. Notification to authors: Monday September 2, 2019 Abstracts' length: max four A4 pages. Templates are available for MS Word and LaTeX. See detailed instructions at http://www.igst.it/nettab/2019/submissions/instructions-for-authors/ . ==**==**== Joint NETTAB/BBCC 2019 Meeting November 11-13, 2019 Fisciano Campus, University of Salerno, Italy http://www.nettab.org/2019/ CONFIRMED SPEAKERS * Davide Cacchiarelli, Telethon Institute of Genetics and Medicine, Naples, Italy. * Martin Eisenacher, Medizinisches Proteom-Center (MPC), Ruhr-Universität Bochum, Germany. * Lennart Martens, VIB, University of Gent, Belgium. * Juan Antonio Vizcaíno, EMBL-European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, United Kingdom. CONFIRMED TUTORIALS Tutorial 2, Thursday November 14, 09:00 - 17:00 Label-free quantification with OpenMS Oliver Kohlbacher, Julianus Pfeuffer and Timo Sachsenberg, University of Tuebingen, Germany Tutorial supported by the German Network for Bioinformatics Infrastructure (de.NBI). IMPORTANT DATES Abstract submission deadlines * Abstracts for oral communications: Sunday June 30, 2019 * Abstracts for posters: Friday September 20, 2019 Registration deadlines * Early registration: October 10, 2019 Meeting * Tutorials: November 11, 2019 and November 14, 2019 * Workshop: November 11-13, 2019 CONTACT INFORMATION For further information, please email to nettab.workshops at gmail.com or bbcc.meetings at gmail.com . ==**==**== Paolo Romano Ospedale Policlinico San Martino Genova, Italy Disclosure: despite any misleading formatting of my Institutional email address, please note that my name is Paolo, So, please, call me Paolo. Skype: p.romano Email: paolo.romano at hsanmartino.it - paolo.dm.romano at gmail.com [DEVOLVI IL TUO 5xmille AL SAN MARTINO! C.F. 02060250996] CON TE LA NOSTRA RICERCA PUO' DIVENTARE CURA DEVOLVI IL TUO 5xmille AL SAN MARTINO! FINANZIAMENTO DELLA RICERCA SANITARIA CODICE FISCALE 02060250996 5xmille.ospedalesanmartino.it -------------- next part -------------- An HTML attachment was scrubbed... URL: From Tanja.Slotte at scilifelab.se Wed May 22 09:27:58 2019 From: Tanja.Slotte at scilifelab.se (Tanja Slotte) Date: Wed, 22 May 2019 09:27:58 +0200 Subject: [SocBiN] Postdoc/researcher positions in ERC-funded project Message-ID: <9BB6CD24-DFA1-46FD-9752-DC9ADFA2F4DA@scilifelab.se> Open positions in Evolutionary Genomics at Stockholm University We have two open ERC-funded positions in evolutionary genomics at Stockholm University. The SuperGenE project focuses on genomic studies of a classic supergene, in a plant genus with lots of interesting mating system variation. The postdocs/researchers will be testing evolutionary hypotheses using new long-read genomes, population genomics and expression analyses. Proficiency in bioinformatics is a strong merit for these positions. Apply by June 7, 2019 Postdoctoral fellow in Evolutionary Genomics, 2-year position in ERC-funded project https://tinyurl.com/yygoqqln Researcher in Evolutionary Genomics, 2-year position in ERC-funded project https://tinyurl.com/y3t8fs6g In addition, we have a stipend-funded postdoc available on population genomics of plant mating system variation: https://tanjaslottelab.se/postdoctoral-fellowship-in-population-genomics-of-plant-mating-system-shifts/ Best regards, Tanja Slotte ---------------- Tanja Slotte PhD, Associate Professor SciLifeLab Fellow Department of Ecology, Environment and Plant Sciences (DEEP) Stockholm University 106 91 Stockholm E-mail: tanja.slotte at su.se Visiting address: Science for Life Laboratory Stockholm Tomtebodav. 23A, Solna -------------- next part -------------- An HTML attachment was scrubbed... URL: From thomas.svensson at scilifelab.se Mon May 27 15:15:52 2019 From: thomas.svensson at scilifelab.se (Thomas Svensson) Date: Mon, 27 May 2019 15:15:52 +0200 Subject: [SocBiN] Two open NBIS positions at Chalmers Message-ID: <9E746808-374A-4575-BFEA-10311B700E17@scilifelab.se> Dear all, The NBIS-node at Chalmers University of Technology is looking for staff scientists with extensive experience in an appropriate computational science and feel comfortable with several of the following "labels”; systems biology, integrative omics, data science, artificial intelligence, biostatistics, metagenomics, Big Data, single-cell biology or reproducible research. Link to the ad: https://www.chalmers.se/en/about-chalmers/Working-at-Chalmers/Vacancies/Pages/default.aspx?rmpage=job&rmjob=7569 Best regards, Thomas -------------------------------------------------------- Thomas Svensson, PhD Head of Facility, SciLifeLab Systems Biology support www.scilifelab.se/platforms/nbis/ Department of Biology and Biological Engineering Chalmers University of Technology Kemivägen 10, SE-412 96 Göteborg Sweden Phone: +46-31-7726812 Mobile: +46-73-305 17 30 -------------- next part -------------- An HTML attachment was scrubbed... URL: From mahogny at areta.org Mon May 27 20:28:34 2019 From: mahogny at areta.org (mahogny at areta.org) Date: Mon, 27 May 2019 19:28:34 +0100 Subject: [SocBiN] wanted: 2 postdocs and 1 phd, T cells // migraine Message-ID: Hi everyone, furthering to previous announcement, I am also looking for a postdoc who is interested in spearheading a new initiative that is likely to be done with in collaboration with FIMM. We believe there might be several good reasons to study migraine in T cells(!), and there are two grants in writing. Any interesting applicants should get in touch ASAP (especially if swedish, for one of the grants) I am also still looking for a phd and postdoc for our T cell atlas project For more details, visit http://www.henlab.org/join-us/ Best wishes, Johan Henriksson -------------- next part -------------- An HTML attachment was scrubbed... URL: From michaut.bioinfo at gmail.com Fri May 31 15:11:14 2019 From: michaut.bioinfo at gmail.com (Magali Michaut) Date: Fri, 31 May 2019 15:11:14 +0200 Subject: [SocBiN] Group leader positions, stem cell & development, Copenhagen Message-ID: <9DF69D63-E050-4F28-BC65-39E74A2E2615@gmail.com> Dear all, 2 group leader positions are open at DanStem in Copenhagen, Denmark. It would be great to recruit someone with computational expertise. https://www.nature.com/naturecareers/job/group-leaders-to-danstem-copenhagen-university-of-copenhagen-ucph-685411 Please share! Cheers, Magali -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: IMG_4219.jpeg Type: image/jpeg Size: 135285 bytes Desc: not available URL: