From erik.kristiansson at chalmers.se Tue May 3 13:38:24 2016 From: erik.kristiansson at chalmers.se (Erik Kristiansson) Date: Tue, 3 May 2016 13:38:24 +0200 Subject: [SocBiN] Post-doc position in mathematical statistics with focus on modelling of high-dimensional molecular data available at Chalmers University of Technology, Gothenburg, Sweden In-Reply-To: <56C9AED2.8050402@chalmers.se> References: <52264493.30404@chalmers.se> <56C9AED2.8050402@chalmers.se> Message-ID: <57288DB0.2000607@chalmers.se> Everyone, There is a two-year post-doc position in biostatistics available at Chalmers University of Technology, Göteborg, Sweden. Full details are available at http://www.chalmers.se/en/about-chalmers/vacancies/Pages/default.aspx?rmpage=job&rmjob=4002 Cheers, Erik -- -------------------------------------------------------------------------------- Erik Kristiansson, Associate Professor Department of Mathematical Statistics Chalmers University of Technology, Sweden Email: erik.kristiansson at chalmers.se, Phone: +46 (0)31 772 3521 -------------------------------------------------------------------------------- From Anagha.Joshi at roslin.ed.ac.uk Tue May 3 14:35:58 2016 From: Anagha.Joshi at roslin.ed.ac.uk (JOSHI Anagha) Date: Tue, 3 May 2016 12:35:58 +0000 Subject: [SocBiN] =?windows-1252?q?ECCB_2016_workshop_=96_Network_Inferenc?= =?windows-1252?q?e=3A_New_Methods_and_New_Data?= Message-ID: ECCB 2016 workshop – Network Inference: New Methods and New Data Submit an abstract for ECCB 2016 workshop - extended deadline 18th May http://www.eccb2016.org/programme/workshops/w2/ W2 – Network Inference: New Methods and New Data Workshop details Date: Saturday September 3, 2016 Time: 9:00 – 17:00 Venue: World Forum, room: t.b.c. Organisers •Dr. Anagha Joshi, Roslin Institute, University of Edinburgh, UK •Dr. Tom Michoel, Roslin Institute, University of Edinburgh, UK •Dr. Eric Bonnet, Centre National de Génotypage, CEA, Paris, France Summary Background Mammalian systems constitute over 200 cell types, each specialized to perform a distinct function, and yet all cell types share the same genome. This cell type specificity is achieved by a context-specific interpretation of the DNA sequence to produce a cell type specific transcription signature. Advances in sequencing techniques have accelerated the characterization of transcription landscapes across many normal and malignant cell types. The challenge now is to integrate these data to understand transcriptional control at a systems level. Over the years, powerful machine learning algorithms have been developed for inferring transcriptional networks from expression data, thereby revealing new aspects of complex biological systems. Aims and scope This one day SIG session will bring together experts from computational biology and machine learning to present recent advances in the development and application of gene regulatory network inference methods, as well as novel emerging single-cell and epigenomics data types suitable for network inference. The SIG will be split into two half day sessions. The first half will focus entirely on novel network inference methods, while the second half will focus on opportunities and challenges arising from new data types. Each session will feature an invited speaker and three short talks. Keynote speakers Prof. Sushmita Roy, University of Wisconsin-Madison. Website Prof. Klaas Vandepoele, Ghent University. Website Target audience The target audience is researchers working in the field of network inference or anyone who is working with large scale genome wide data. We expect typically 20 participants. Submissions Six talks will be selected by the organisers from submitted abstracts (max. 250 words). There will also be a ‘hands-on’ session with short pitches of new network inference tools or databases. Abstracts for both kinds of talks should be submitted online via the Easychair submission system. The deadline for submission is 1 May 2016. -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From Anagha.Joshi at roslin.ed.ac.uk Tue May 3 14:37:00 2016 From: Anagha.Joshi at roslin.ed.ac.uk (JOSHI Anagha) Date: Tue, 3 May 2016 12:37:00 +0000 Subject: [SocBiN] =?windows-1252?q?ECCB_2016_workshop_=96_Network_Inferenc?= =?windows-1252?q?e=3A_New_Methods_and_New_Data?= Message-ID: Submit an abstract for ECCB 2016 workshop - extended deadline 18th May http://www.eccb2016.org/programme/workshops/w2/ W2 – Network Inference: New Methods and New Data Workshop details Date: Saturday September 3, 2016 Time: 9:00 – 17:00 Venue: World Forum, room: t.b.c. Organisers •Dr. Anagha Joshi, Roslin Institute, University of Edinburgh, UK •Dr. Tom Michoel, Roslin Institute, University of Edinburgh, UK •Dr. Eric Bonnet, Centre National de Génotypage, CEA, Paris, France Summary Background Mammalian systems constitute over 200 cell types, each specialized to perform a distinct function, and yet all cell types share the same genome. This cell type specificity is achieved by a context-specific interpretation of the DNA sequence to produce a cell type specific transcription signature. Advances in sequencing techniques have accelerated the characterization of transcription landscapes across many normal and malignant cell types. The challenge now is to integrate these data to understand transcriptional control at a systems level. Over the years, powerful machine learning algorithms have been developed for inferring transcriptional networks from expression data, thereby revealing new aspects of complex biological systems. Aims and scope This one day SIG session will bring together experts from computational biology and machine learning to present recent advances in the development and application of gene regulatory network inference methods, as well as novel emerging single-cell and epigenomics data types suitable for network inference. The SIG will be split into two half day sessions. The first half will focus entirely on novel network inference methods, while the second half will focus on opportunities and challenges arising from new data types. Each session will feature an invited speaker and three short talks. Keynote speakers Prof. Sushmita Roy, University of Wisconsin-Madison. Website Prof. Klaas Vandepoele, Ghent University. Website Target audience The target audience is researchers working in the field of network inference or anyone who is working with large scale genome wide data. We expect typically 20 participants. Submissions Six talks will be selected by the organisers from submitted abstracts (max. 250 words). There will also be a ‘hands-on’ session with short pitches of new network inference tools or databases. Abstracts for both kinds of talks should be submitted online via the Easychair submission system. The deadline for submission is 1 May 2016. -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From iamb at genesilico.pl Wed May 4 09:01:29 2016 From: iamb at genesilico.pl (Janusz Bujnicki) Date: Wed, 4 May 2016 09:01:29 +0200 Subject: [SocBiN] A call for post-doctoral fellowships in Poland - an offer of a project in structural bioinformatics of RNA Message-ID: <57289DBC.1010804@genesilico.pl> Dear All, Polish funding agency NCN announced a new call for postdoctoral fellowships POLONEZ to be carried out in Poland, and I am looking for prospective candidates interested in applying to this funding scheme to carry out work in my lab. Please forward this announcement to anybody who may be interested. ### an opportunity for postdoctoral researchers ### ### interested in RNA structural bioinformatics ### I am looking for postdoctoral candidates interested in structural bioinformatics and RNA, either in developing new methods/programs (in particular for modeling and designing/engineering RNA structure and protein-RNA complexes) or in biological data analysis (with the focus on RNA evolution), and motivated to develop a career in an interdisciplinary team, in collaboration between theoreticians and experimentalists. I am particulaly interested in candidates willing to apply for the POLONEZ senior postoctoral fellowship (https://www.ncn.gov.pl/polonez?language=en) or to another similar funding scheme. The funding in POLONEZ is for incoming researchers (foreigners or Poles who spent at least 24 months outside Poland in the last 3 years), who may apply for 12- or 24-month fellowships in host institutions in Poland - in this case I am offering my lab and an opportunity to carry out a project aligned with the research in my group. A successful application will be considered as step towards independence: the POLONEZ grant holder will be supported towards an independent PI position in the next step of their career. Funding: - Salary (incl. mobility allowance): € 4350 gross/month (full time contract), - Family allowance: € 300 gross/month (for fellows whose families stay in Poland for at least 3 months), - Research grant, - Opportunity to participate in research and non-research training programs organized by the NCN. CALL DEADLINE: 15 June 2016 CALL RESULTS: November 2016 For more information about the grant program please see the NCN website: https://www.ncn.gov.pl/polonez?language=en About my group: • We combine basic science (to answer fundamental scientific questions) and applied science (to make the discoveries practically useful). In our team, software developers meet with experimental biologists, and high-throughput data analysis combines with sophisticated studies of individual biomacromolecules. Examples of our recent activities include the development of methods for RNA 3D structure modeling SimRNA and ModeRNA, and engineering of RNases that cleave RNA sequence-specifically. More information: http://genesilico.pl • We are hosted by IIMCB (http://iimcb.gov.pl), the top-ranked (A+) Polish research institute in biology. The institute provides cutting-edge equipment and facilities, in particular for bioinformatics (e.g. a computing cluster with >2000 cores), experimental molecular biology, and structural biology. Candidates accepted to apply to carry out their project in my lab in IIMCB will be supported by the grants office in IIMCB in all steps of the preparation of the POLONEZ grant proposal, and of course I would be very happy to work out a join scientific project. Prospective candidates interested in applying to POLONEZ (and maybe also other funding programs) are encouraged to make informal inquiries with me at iamb at genesilico.pl Best regards, Janusz Bujnicki -- __________________________________ Janusz M. Bujnicki, PhD, Professor Email: iamb at genesilico.pl Head, Laboratory of Bioinformatics and Protein Engineering International Institute of Molecular and Cell Biology Trojdena 4, 02-109 Warsaw, POLAND tel: +48-22 597 0750 fax: +48 22 597 0715 http://iimcb.genesilico.pl Laboratory of Bioinformatics Institute of Molecular Biology and Biotechnology Faculty of Biology Adam Mickiewicz University Umultowska 89, 61-614 Poznan, POLAND tel: +48 61 829 5839 http://bioinformatics.amu.edu.pl Executive Editor, Nucleic Acids Research 2014 impact factor: 9.112 All content is open access Journal website: http://nar.oxfordjournals.org Manuscript submission: http://mc.manuscriptcentral.com/nar From marcela.davila at gu.se Wed May 4 13:55:34 2016 From: marcela.davila at gu.se (Marcela Davila Lopez) Date: Wed, 4 May 2016 11:55:34 +0000 Subject: [SocBiN] Postdoctoral fellow in Bioinformatics Message-ID: <75c6275930514e53a5c84b8498a13786@gu.se> Bioinformatics analysis of data generated from translational stroke research focusing on hemostasis Type of employment: Fixed-term employment, 2 years Extent: 100 % Location: Institute of Biomedicine, Gothenburg Closing date 2016-05-25 http://www.gu.se/english/about_the_university/announcements-in-the-job-application-portal/?languageId=100001&disableRedirect=true&returnUrl=http%3A%2F%2Fwww.gu.se%2Fomuniversitetet%2Faktuellt%2Fledigaanstallningar%2F%3Fid%3D19144%26Dnr%3D763369%26Type%3DS&Dnr=763369&Type=E Marcela Dávila Bioinformatics Core Facility The Sahlgrenska Academy at the University of Gothenburg Visiting address: Medicinaregatan 3B www.bioinformatics.cf.gu.se -------------- next part -------------- An HTML attachment was scrubbed... URL: From Karin.Lagesen at vetinst.no Sun May 8 18:41:05 2016 From: Karin.Lagesen at vetinst.no (Lagesen, Karin) Date: Sun, 8 May 2016 16:41:05 +0000 Subject: [SocBiN] PhD position available focusing on the spread of antibiotics resistance In-Reply-To: <3AF7ADBEC1C9A4459D3CD3AA6BE8AA5139B9EF10@Bring.vetinst.no> References: <3AF7ADBEC1C9A4459D3CD3AA6BE8AA5139B9EF10@Bring.vetinst.no> Message-ID: <3AF7ADBEC1C9A4459D3CD3AA6BE8AA5139BA0F4B@Bring.vetinst.no> The Norwegian Veterinary Institute has a 3 year PhD position available which focuses on mechanisms behind how quinolone resistance spreads in Norwegian animal production, and also the sources of this resistance. The position will entail a mix between lab work and bioinformatics. The deadline for application is 18.05.2016. The full advertisement can be found here: http://vetinst.easycruit.com/vacancy/1628939/62784?iso=no Don't hesitate to contact me if you have any questions regarding the position. Karin -- Karin Lagesen, PhD Bioinformatician, Section for Epidemiology Norwegian Veterinary Institute -------------- next part -------------- An HTML attachment was scrubbed... URL: From jolepp at utu.fi Mon May 9 14:20:24 2016 From: jolepp at utu.fi (=?iso-8859-1?Q?Johanna_M=E4kel=E4?=) Date: Mon, 09 May 2016 12:20:24 +0000 Subject: [SocBiN] Postdoctoral Researcher position at Dr. Elo's Group In-Reply-To: <42AD353ABD93C148B60CE22D5E09BE8768BF2523@exch-mbx-03.utu.fi> References: <42AD353ABD93C148B60CE22D5E09BE8768BF2523@exch-mbx-03.utu.fi> Message-ID: <1462796424663.21989@utu.fi> Dear all, A postdoctoral researcher position is available in the project directed by Dr. Laura Elo, Research Director in Bioinformatics at Turku Centre for Biotechnology, University of Turku, Finland (http://www.btk.fi). More details can be found from the attachment. Sincerely, Johanna Mäkelä -- Johanna Mäkelä, PhD Research coordinator Computational biomedicine Turku Centre for Biotechnology University of Turku Tykistökatu 6 FI-20520 Turku Finland -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: postdoc_BTK_en.pdf Type: application/x-download Size: 234459 bytes Desc: postdoc_BTK_en.pdf URL: From Erik.Bongcam at slu.se Tue May 10 07:04:54 2016 From: Erik.Bongcam at slu.se (Erik Bongcam-Rudloff) Date: Tue, 10 May 2016 05:04:54 +0000 Subject: [SocBiN] courses at CSC in Finland Message-ID: Please note that registration is now open for the following two variant analysis courses at CSC in Finland: Variant analysis workshop 13.-15.6.2016 (www.csc.fi/web/training/-/variant-analysis) This ELIXIR EXCELERATE -funded course covers several aspects of variant analysis including variant annotation and prioritization. It consists of lectures and hands-on exercises which are suitable for everybody, as analysis is performed with easy-to-use graphical tools (the VEP hands-on tutorial on day 2 contains also an optional session for participants with coding experience). Participants can select and combine the following course days according to their needs: 13.6.2016 Introduction to variant analysis from sequencing data -Variant analysis with Chipster 14.6.2016 Variant annotation and effect prediction -Analysing variation data with the Variant Effect Predictor (VEP) -Genome variant annotation and interpretation in a clinical context using omnomicsQ -TBA 15.6.2016 Variant analysis and prioritization -European Genome-phenome Archive (EGA) -RD-Connect genomics analysis platform -Variant prioritization with UMD-Predictor, VarAFT and Human Splicing Finder Variant analysis with GATK 16.-17.6.2016 (www.csc.fi/web/training/-/gatk) This course covers the core steps involved in calling variants with the Broad's Genome Analysis Toolkit (GATK), using the Best Practices developed by the GATK team. It highlights key functionalities such as the GVCF workflow for joint variant discovery in cohorts, RNAseq specific processing, and somatic variant discovery using MuTect2. The trainers also preview capabilities of the upcoming GATK version 4, including a new workflow for CNV discovery. The course consists of a lecture day which is suitable for everybody, and an optional hands-on day for which you need to have basic familiarity with the command line environment. Best regards, Eija Eija Korpelainen, Ph.D Product Manager Application services, Bioinformatics CSC - IT Centre for Science P.O.Box 405 02101 Espoo, Finland Phone +358 50 381 9726 -------------- next part -------------- An HTML attachment was scrubbed... URL: From Inge.Jonassen at ii.uib.no Fri May 13 11:58:53 2016 From: Inge.Jonassen at ii.uib.no (Inge Jonassen) Date: Fri, 13 May 2016 11:58:53 +0200 Subject: [SocBiN] systems biology post-doc position in Bergen Message-ID: Dear all, Four-years post-doc position at the mathematics department at the University of Bergen The post-doc will work on using topology methods to analyze biological data. For full announcement, and to submit your application go to https://www.jobbnorge.no/en/available-jobs/job/121576/postdoctoral-fellow-in-mathematics For more information, contact Professor Morten Brun at morten.brun at uib.no Inge Inge Jonassen, Prof PhD Head of Node, Elixir Norway Computational Biology Unit Department of Informatics University of Bergen HiB N5020 Bergen Norway Inge.Jonassen at uib.no -------------- next part -------------- An HTML attachment was scrubbed... URL: From hiller at mpi-cbg.de Wed May 18 16:22:23 2016 From: hiller at mpi-cbg.de (Michael Hiller) Date: Wed, 18 May 2016 16:22:23 +0200 Subject: [SocBiN] Postdoc Position in Evolutionary Genomics at the Max Planck Institute Message-ID: The Research Group “Computational Biology and Evolutionary Genomics” at the Max Planck Institute in Dresden, Germany has a Postdoc opening. Job description We are hiring for a project to discover genomic differences underlying the evolution of morphological differences in mammals. The postdoc will use our computational methods and multiple-genome alignments to predict phenotype-genotype associations for numerous phenotypic differences that will be provided by our collaborators. The postdoc will analyze and interpret the results using enrichment tests, biomedical knowledge and functional genomics data. Promising genomic candidates will be tested experimentally. The Postdoc will work closely with other lab members on all computational aspects and with a group of collaborators on phenotypic data and experimental aspects. Funding according to the German TVöD scale is available for at least 3 years. Our group The mission of our group is to discover the differences in the genome that underlie phenotypic differences between species. Thus, we will contribute to our understanding how nature’s incredible diversity evolved. To this end, we are combining computational and experimental approaches. On the computational side, we build high-quality genome alignments, develop and apply comparative methods to discover functional genomic differences, and use statistical approaches to associate genomic to phenotypic differences. On the experimental side, we sequence and assemble genomes of species with interesting phenotypes, we use approaches like RNA-seq and ATAC-seq to annotate genes and regulatory regions, and we experimentally test discovered genomic loci. Our group is located at the Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG) and we are jointly affiliated with the Max Planck Institute for the Physics of Complex Systems (MPI-PKS), both in Dresden. Both institutes are highly interactive and interdisciplinary workplaces, provide an international atmosphere with English as working language and access to cutting-edge computational and experimental infrastructure and facilities. The MPI-CBG was awarded one of the “Best Places To Work for Postdocs” in 2011. Requirements Applicants should have a background in bioinformatics or computational biology and a strong publication record. Excellent programming skills (perl, python, or C/C++) in a Linux environment as well as experience with shell scripting and Unix tools are required. Previous experience in large-scale genomic data analysis is an advantage. Applicants should also have an interest in the molecular biology underlying species’ phenotypes. How to apply If interested, please email (i) your CV including publication list and contact information for at least two references and (ii) a summary of previous research experience (max 1 page) to Michael Hiller (hiller at mpi-cbg.de ). Further information: http://www.mpi-cbg.de/research/michael-hiller.html -- Michael Hiller, PhD Research Group Leader Max Planck Institute of Molecular Cell Biology and Genetics& Max Planck Institute for the Physics of Complex Systems Dresden, Germany http://www.mpi-cbg.de/research/michael-hiller.html -------------- next part -------------- An HTML attachment was scrubbed... URL: From jonathan.coquet at ki.se Wed May 18 17:32:32 2016 From: jonathan.coquet at ki.se (Jonathan Coquet) Date: Wed, 18 May 2016 15:32:32 +0000 Subject: [SocBiN] computational biologist - Karolinska Institute Message-ID: <2C5B97D6-DC02-48DE-BD80-C0F3B9D75E44@ki.se> Dear all, we are currently recruiting a post-doc (or equivalent) computational biologist to our team to help us to analyse the immune system in more detail. Please find a link below and a broad description of the lab, project and responsibilities. All application should proceed through the Karolinska Institute portal. Kind regards, Jonathan https://ki.mynetworkglobal.com/en/what:job/jobID:88719/where:4/ Research group Jonathan’s team is interested in lineage commitment and in particular in subset specification of a population of immune cells called T helper cells. T helper cells are central mediators of a range of inflammatory disorders including asthma, multiple sclerosis and inflammatory bowel disease and are known to acquire specialized functions. The team is interested in 2 aspects of their differentiation; 1) What functions do these cells acquire in different inflammatory diseases and can these functions be extrapolated using unbiased techniques? 2) Identifying novel factors and gene networks that may regulate the acquisition of functions over time, and to test their functions in physiological models of disease. To tackle these questions, Jonathan’s team is using Single Cell RNA-Sequencing among other array and sequencing based approaches to analyse T helper cells in diseased tissues. The lab’s goal is to more accurately define T helper cell functions in disease states and find novel regulators that may be the target of future therapies. The Karlsson Hedestam group studies B cell biology, with a focus on understanding the development of antigen-specific B cells in memory compartments. This is studied through the isolation of monoclonal antibodies and next generation sequencing (NGS) analysis of antibody repertoires for longitudinal lineage tracing. The candidate will provide computational support for a recently established pipeline for NGS antibody analysis techniques and other programs being developed by the group. These bioinformatics tools for antibody repertoire analysis can be used for a wide range of pre-clinical and clinical applications, related to infections, cancer and autoimmunity. Area of responsibilities/work description The successful applicant will work with a team of biologists to apply existing, or to develop novel, statistical and computational bioinformatics methods for analysis of various -omics data, with particular focus on NGS technologies, including RNA-Seq, and single-cell RNA-Seq. An interest in the application of machine learning approaches is also desirable. The duties also include: * Consulting researchers on the NGS experimental design * Data QC, data management and archival storage * Analysis of large datasets, preparation of codes, development of new methods/tools for advanced analysis of datasets * Support the ongoing research in the group, help write papers, grants and scientific meeting presentations * Shape, develop and maintain the current computing resources of the group Qualifications The successful candidate has a solid background in bioinformatics, statistics and computational biology, good expertise in statistical and bioinformatics software, and an ability to work in a multidisciplinary research environment. The individual should be highly driven and be able to work independently, while being able to communicate effectively with other members of the team. Preferably, the candidate should hold a PhD degree (or complete one within the next months) or have a track record of performing independent research over the past 4 years. Proven track record of publishing research results in high-ranked journals is appreciated. Experience with Python, R, Matlab or other software/programming languages is required. Jonathan Coquet Dept. of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet Nobels väg 16 Stockholm 171 77, SWEDEN +46 8 524 86952 http://ki.se/en/mtc/jonathan-coquet-project -------------- next part -------------- An HTML attachment was scrubbed... URL: From nicosia at dmi.unict.it Wed May 18 18:06:06 2016 From: nicosia at dmi.unict.it (Giuseppe Nicosia) Date: Wed, 18 May 2016 18:06:06 +0200 Subject: [SocBiN] SSBSS 2016: Call for Oral Presentations/Posters: 9-13 July 2016, Volterra (Pisa) Tuscany, Italy - 3rd Int. Synthetic & Systems Biology Summer School - Early Application: May 26, 2016 Message-ID: _________________________________________________________________________ Call for Participation (apologies for multiple copies) Please help forward it to other potentially interested attendees, thanks! _________________________________________________________________________ 3rd International Synthetic and Systems Biology Summer School - SSBSS 2016, 9-13 July 2016, Volterra (Pisa) - Tuscany, Italy ssbss.school at gmail.com http://www.taosciences.it/ssbss/ https://www.facebook.com/ssbss.school/ https://twitter.com/SchoolSsbss EARLY APPLICATION DEADLINE: May 26, 2016 http://www.taosciences.it/ssbss/#application-form The Synthetic and Systems Biology Summer School (SSBSS) is a full-immersion five-day residential summer school at the Volterra Learning Center (Pisa - Tuscany, Italy) on cutting-edge advances in systems and synthetic biology with lectures delivered by world-renowned experts. The school provides a stimulating environment for students (from Master students to PhD students), Post-Docs, early career researches, academics and industry leaders. Participants will also have the chance to present their results (with Oral Talks and Posters), and to interact with their peers, in a friendly and constructive environment. SSBSS 2016 DEADLINES: Early Application: May 26, 2016 Notification Acceptance: from April 2 to 28 May 2016 Late Application: from May 27, to July 4th 2016 Notification Acceptance: from May 28th 2016 according to registration time Early Short Talk/Poster Submission: May 26, 2016 Notification Acceptance: from 2 April to 28 May 2016 Late Short Talk/Poster Submission: from May 27, to July 4th 2016 Notification of Decision for Oral/Poster Presentation: from May 28, 2016 according to submission time http://www.taosciences.it/ssbss/#application-form FINAL LIST OF SPEAKERS * Yaakov (Kobi) Benenson, Synthetic Biology Group at Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland Lecture 1: The practice of mammalian synthetic biology Lecture 2: Mammalian cell classifiers * Leonidas Bleris, Bioengineering Department, The University of Texas at Dallas, USA Lecture 1: Genome Editing Technologies and Therapeutic Modalities Lecture 2: Benchmark Circuits and Topological Properties * Edoardo Boncinelli, Universita’ Vita-Salute San Raffaele, Milano, Italy Lecture: TBA * John Cumbers, Founder SynBioBeta, Mountain View, CA, USA Lecture: Synthetic Biology: new tools for an industry at an inflection point. * Domitilla Del Vecchio, Department of Mechanical Engineering, MIT, USA Lecture 1: Modularity in genetic circuits: Dream versus Reality Lecture 2: Engineering Modularity in Genetic Circuits * Diego Di Bernardo, Dept of Chemical Materials and Industrial Production Engineering University of Naples "Federico II", Naples, Italy Lecture 1: "Engineering and Control of Biological Circuits in Yeast" Lecture 2: "Engineering and Control of Biological Circuits in Mammalian Cells * Barbara Di Ventura, Synthetic Biology Group, BioQuant/DKFZ, Heidelberg, Germany Lecture 1: Using blue light to control protein localization in living mammalian cells Lecture 2: Using split inteins for protein engineering in living cells * Jonathan S. Gootenberg, Feng Zhang and Aviv Regev Groups, Department of Systems Biology, Harvard Medical School, Harvard University, USA Lecture 1: "Discovering and Characterizing CRISPR effectors" Lecture 2: "Probing Biology with CRISPR Screening" * Markus Herrgard, Technical University of Denmark - Biosustain, Novo Nordisk Foundation Center for Biosustainability, Denmark Lecture 1: "Developing an Integrated Cell Factory Design Tool" Lecture 2: "Using Automated Laboratory Evolution to Optimize Cell Factories” * Shalev Itzkovitz, Department of Molecular Cell Biology, Weizmann Institute of Science, Israel Lecture 1: "Single Molecule Approaches for Studying Gene Expression in Intact Mammalian Tissues" Lecture 2: "Systems Biology of Stem Cell-Maintained Tissues” * Francesco Ricci, Dipartimento di Scienze e Tecnologie Chimiche, University of Rome Tor Vergata, Rome, Italy Lecture 1: "DNA Nanotechnology Tools and Reactions for Synthetic Biology" Lecture 2: "Nature-inspired DNA-based Nanodevices Next Generation Sequencing Workshop – Afternoon July 12th, 2016 * “How fast can we align sequences?” Mario Guarracino, CNR, Italy * “Advanced Bioinformatics tools for NGS” – TBC Luca Zammataro, Yale University, USA Tutorials: * “Detection and analysis of contaminating sequences in NGS sequencing data” Ilaria Granata, CNR, Italy * “Detection and interpretation of circular RNAs in RNA-seq experiments” Parijat Tripathi, CNR, Italy SSBSS 2016 DIRECTORS Diego Di Bernardo, TeleThon Institute of Genetics & Medicine - TIGEM and University of Napoli "Federico II", Italy Giuseppe Nicosia, University of Catania, Italy Luca Zammataro, Yale University, USA MORE INFORMATION ssbss.school at gmail.com http://www.taosciences.it/ssbss/ https://www.facebook.com/ssbss.school/ https://twitter.com/SchoolSsbss Social event(s): social tour and dinner in Florence. Please help us distributing in your circles (emails, blogs, and social networks) the call for participation and call for oral talks/posters for SSBSS 2016. Together we will make SSBSS a great event! See you in Tuscany in July! More Info: ssbss.school at gmail.com http://www.taosciences.it/ssbss/ -- Giuseppe Nicosia, Ph.D. Associate Professor of Computer Engineering Dept of Mathematics & Computer Science University of Catania Viale A. Doria, 6 - 95125 Catania, Italy P +39 095 7383048 nicosia at dmi.unict.it http://www.dmi.unict.it/nicosia ================================================================== 3rd International Synthetic & Systems Biology Summer School - SSBSS 2016 * Biology meets Computer Science & Engineering * July 8-14, 2016 - Volterra (Pisa), Tuscany, Italy http://www.taosciences.it/ssbss/ ================================================================== 2nd International Workshop on Machine learning, Optimization & big Data - MOD 2016 August 26-29, 2016 - Volterra (Pisa), Tuscany, Italy http://www.taosciences.it/mod/ ================================================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: From etienne.ruppe at genomic.ch Thu May 19 08:20:35 2016 From: etienne.ruppe at genomic.ch (Etienne =?UTF-8?B?UnVwcMOp?=) Date: Thu, 19 May 2016 08:20:35 +0200 Subject: [SocBiN] International Conference on Clinical Metagenomics, Geneva, October 13-14 2016 Message-ID: <1463638835-043df57911832366acf2be0799afce37@genomic.ch> Dear all,  Pr Jacques Schrenzel and I from the genomic research laboratory (Geneva University Hospitals) are organizing the first International Conference on Clinical Metagenomics (ICCMg) here in Geneva next October 13-14. The program, call for abstracts (including a bio-informatic section) and registration are available from [www.clinicalmetagenomics.org](http://www.clinicalmetagenomics.org) Wishing to see a lot of you there, best etienne ** ********Etienne Ruppé****Hôpitaux Universitaires de Genève** Genomic Research Laboratory Rue Gabrielle-Perret-Gentil 4 CH-1211 Geneva 14 - Switzerland Tel: [+41 (0)22 372 93 16 ](tel:%2B41%20%280%2922%20372%2093%2022)Web: [http://www.genomic.ch](http://www.genomic.ch/)[etienne.ruppe at genomic.ch](mailto:etienne.ruppe at genomic.ch)[etienne.ruppe at hcuge.ch](mailto:etienne.ruppe at hcuge.ch)[etienne.ruppe at unige.ch](mailto:etienne.ruppe at hcuge.ch) @RuppeEtienne -------------- next part -------------- An HTML attachment was scrubbed... URL: From bioinforupesh2009.au at gmail.com Thu May 19 11:33:13 2016 From: bioinforupesh2009.au at gmail.com (Rupesh Kumar Kesharwani) Date: Thu, 19 May 2016 11:33:13 +0200 Subject: [SocBiN] International Conference on Clinical Metagenomics, Geneva, October 13-14 2016 In-Reply-To: <1463638835-043df57911832366acf2be0799afce37@genomic.ch> References: <1463638835-043df57911832366acf2be0799afce37@genomic.ch> Message-ID: Dear prof, could you please tell me what is the registration fee ??? i couldn't find in the website. Seems i need fill are requirements first to reach payment section. Thank you. On Thu, May 19, 2016 at 8:20 AM, Etienne Ruppé wrote: > Dear all, > Pr Jacques Schrenzel and I from the genomic research laboratory (Geneva > University Hospitals) are organizing the first International Conference on > Clinical Metagenomics (ICCMg) here in Geneva next October 13-14. The > program, call for abstracts (including a bio-informatic section) and > registration are available from www.clinicalmetagenomics.org > Wishing to see a lot of you there, > > best > > etienne > > *Etienne Ruppé* > *Hôpitaux Universitaires de Genève* > Genomic Research Laboratory > Rue Gabrielle-Perret-Gentil 4 > CH-1211 Geneva 14 - Switzerland > Tel: +41 (0)22 372 93 16 <%2B41%20%280%2922%20372%2093%2022> > Web: http://www.genomic.ch > etienne.ruppe at genomic.ch > etienne.ruppe at hcuge.ch > etienne.ruppe at unige.ch > @RuppeEtienne > > > _______________________________________________ > SocBiN mailing list > SocBiN at lists.su.se > https://lists.su.se/mailman/listinfo/socbin-at-sbc.su.se > > -- *RUPESH KUMAR KESHARWANI* *M.Sc. BioinformaticsPh.D. Bioengineering & BioinformaticsLaboratory of Biomedical InformaticsDept. of Computer Engineering and Systems ScienceUniversity of Pavia* *.Laboratory of Immunology and Functional GenomicsHospital Centre of Cardiology Monzino,Milan.ITALYMobile: +393319603860 * *Email : rupeshkumar.kesharwani01 at universitadipavia.it (official)* * rkesharwani at ccfm.it (official)* * bioinforupesh2009.au at gmail.com (private)* *P* *Save a tree. Do not print this e-mail the unless it's Necessary.* "Love all, Trust a few, Do wrong to none"- Shakespeare -------------- next part -------------- An HTML attachment was scrubbed... URL: From etienne.ruppe at genomic.ch Thu May 19 12:11:40 2016 From: etienne.ruppe at genomic.ch (Etienne =?UTF-8?B?UnVwcMOp?=) Date: Thu, 19 May 2016 12:11:40 +0200 Subject: [SocBiN] International Conference on Clinical Metagenomics, Geneva, October 13-14 2016 Message-ID: <1463652700-cf6b8bb248edf95dc4eff9b6a42c2f2b@genomic.ch> Dear Rupesh,  sorry for the missing information, please find the fees below.  best etienne       Fees in CHF **Regular Registration Fees (congress dinner included)**  250.00 **Regular Registration Fees (congress dinner not included)**  200.00 - - - - - - **Student Registration Fees (congress dinner not included)**  100.00 Please make sure to send a copy of your student ID to [ICCMG2016 at ch.kuoni.com](mailto:ICCMG2016 at ch.kuoni.com) (only ID under validity will be accepted). - - - - - - **One day registration (congress dinner not included)**  100.00 Dear prof, could you please tell me what is the registration fee ??? i couldn't find in the website. Seems i need fill are requirements first to reach payment section. Thank you. On Thu, May 19, 2016 at 8:20 AM, Etienne Ruppé wrote: Dear all,  Pr Jacques Schrenzel and I from the genomic research laboratory (Geneva University Hospitals) are organizing the first International Conference on Clinical Metagenomics (ICCMg) here in Geneva next October 13-14. The program, call for abstracts (including a bio-informatic section) and registration are available from www.clinicalmetagenomics.org Wishing to see a lot of you there, best etienne Etienne RuppéHôpitaux Universitaires de Genève Genomic Research Laboratory Rue Gabrielle-Perret-Gentil 4 CH-1211 Geneva 14 - Switzerland Tel: +41 (0)22 372 93 16 Web: http://www.genomic.chetienne.ruppe at genomic.chetienne.ruppe@hcuge.chetienne.ruppe at unige.ch @RuppeEtienne _______________________________________________ SocBiN mailing list SocBiN at lists.su.se https://lists.su.se/mailman/listinfo/socbin-at-sbc.su.se -- RUPESH KUMAR KESHARWANI M.Sc. Bioinformatics Ph.D. Bioengineering & Bioinformatics Laboratory of Biomedical Informatics Dept. of Computer Engineering and Systems Science University of Pavia. Laboratory of Immunology and Functional Genomics Hospital Centre of Cardiology Monzino,Milan. ITALY Mobile: +393319603860 Email : rupeshkumar.kesharwani01 at universitadipavia.it (official)            rkesharwani at ccfm.it (official)           bioinforupesh2009.au at gmail.com (private) PSave a tree. Do not print this e-mail the unless it's Necessary. "Love all,Trust a few,Do wrong to none"- Shakespeare -------------- next part -------------- An HTML attachment was scrubbed... URL: From claudio.altafini at liu.se Tue May 24 13:59:16 2016 From: claudio.altafini at liu.se (Claudio Altafini) Date: Tue, 24 May 2016 11:59:16 +0000 Subject: [SocBiN] =?utf-8?q?Post_doc_in_bioinformatics=2C_Link=C3=B6ping_U?= =?utf-8?q?niversity=2C_Sweden?= Message-ID: <975975EF-A234-4DC1-9C22-4FCE4D319A59@liu.se> Post doc in bioinformatics at the Centre for Personalised Medicine, Linköping University, Sweden The overall aim of the Centre for Personalised Medicine (CePMed) is clinical implementation of personalised medicine, based on combining omics, computational, functional and clinical studies (Bruhn et al. Science Translational Med 2014, Gustafsson et al. Science Translational Medicine 2015). We focus on T cells because they are involved in multiple diseases and are readily obtained from peripheral blood, and optimal for functional studies. Tasks: Bioinformatics analyses of T cells, public data and electronic medical records, in close collaboration with other bioinformaticians, experimental and clinical researchers. The position is a scholarship for two years with a monthly compensation of 2700 euro (tax free). Health insurance is covered by the university. Start as soon as possible. Career prospects: A career plan is made in collaboration with each CePMed member. Close collaborations between group members is encouraged and results in excellent publication records. This has resulted in national and international grants, as well as faculty positions for young researchers. Previous experiences: PhD in bioinformatics, ideally based on network- or omics related research. More Information: professor Mikael Benson Mikael.benson at liu.se Prof. Claudio Altafini Division of Automatic Control Dept. of Electrical Engineering Linkoping University, Sweden claudio.altafini at liu.se From Erik.Bongcam at slu.se Wed May 25 21:33:12 2016 From: Erik.Bongcam at slu.se (Erik Bongcam-Rudloff) Date: Wed, 25 May 2016 19:33:12 +0000 Subject: [SocBiN] =?iso-8859-1?q?_IMGT=AE_recruiting_Software_Developer_?= =?iso-8859-1?q?=26_Bioinformatician?= Message-ID: <94a3c96462184ce1ae586032d08b4fab@exch2-4.slu.se> Begin forwarded message: From: Domenica D'Elia Date: May 25, 2016 3:55:14 PM To: EMBnet-general list Subject: IMGT® recruiting Software Developer & Bioinformatician Dear EMBnet, below the announcement for a job opportunity at IMGT. Please, share this information about your contact. Best regards, Domenica ------------------------------------------- Name: Sofia Kossida e-mail: sofia.kossida at igh.cnrs.fr Subject: job opportunities Message: IMGT® recruiting Software Developer & Bioinformatician IMGT®, the international ImMunoGeneTics information system® http://www.imgt.org, is the global reference in immunogenetics and immunoinformatics, created in 1989 by Marie-Paule Lefranc (Université de Montpellier and CNRS). IMGT® is a high-quality integrated knowledge resource specialized in the immunoglobulins (IG) or antibodies, T cell receptors (TR), major histocompatibility (MH) of human and other vertebrate species, and in the immunoglobulin superfamily (IgSF), MH superfamily (MhSF) and related proteins of the immune system (RPI) of vertebrates and invertebrates. We are looking for a software developer and for a bioinformatician with an open and inquisitive mind, to join our team that develops software and analyzes data within the immunoinformatics field. The ultimate goal is to build on your strong background in scientific programming, to gradually learn the code base of the IMGT software and databases, and help improve the system architecture and its performance (optimization of the algorithms and results visualization). Knowledge of an object oriented language is highly desirable. If you understand the science field of Next Generation Sequencing, it will be a plus. You will work in a small operational team of a dozen bioinformaticians with different backgrounds (biologists, informaticians, pharmacists) and different nationalities. Montpellier with >45K students is a young city which enables you to enjoy a good work-life balance. The positions are open from 01/09/2016 and up until the right candidate has been recruited. It is a two year long contract with possibility of extension for another year. The recruitment is at the 'Engineer' level with approximately 2K Euros net salary per month. For more info, send an email to: Sofia.Kossida at igh.cnrs.fr (with cc to: Patrice.Duroux at igh.cnrs.fr and Marie-Paule.Lefranc at igh.cnrs.fr) ? -------------- next part -------------- An HTML attachment was scrubbed... URL: From albin at binf.ku.dk Fri May 27 05:49:56 2016 From: albin at binf.ku.dk (Albin Sandelin) Date: Fri, 27 May 2016 05:49:56 +0200 Subject: [SocBiN] Two postdocs in data-driven lncRNA bioinformatics in Copenhagen Message-ID: Dear all I would appreciate if you could spread this. Deadline is soon (30th may and 15th June) http://www.nature.com/naturejobs/science/jobs/579591-two-postdoc-positions-in-computational-transcriptomics The Marquardt group and the Sandelin group offer two positions for talented postdoctoral researchers to join our highly dynamic and collaborative research environment. Position: Postdoc in Computational Biology of Non-coding Transcription Dynamics, Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre Project description: Computational Biology of Non-coding Transcription Dynamics, to strengthen the interactions between the Sandelin lab located at the Department of Biology and BRIC and the Marquardt lab located at Copenhagen Plant Science Centre (CPSC), Department of Plant and Environmental Sciences. The Sandelin lab and the Marquardt lab are interested in the molecular events determining transcription of abundant non-coding genomic sequences into mysterious long non-coding RNA (lncRNA). We employ cutting edge experimental technologies in a range of experimental systems to identify the underlying mechanisms. lncRNA expression responds rapidly to environmental change. The Marquardt lab is generating maps of nascent RNAPolymerase Pol II (Pol II) transcription in a range of cellular environments with high-resolution. Local differences in Pol II transcription speed are likely central to the underlying response kinetics yet we understand little about the interplay between transcriptional plasticity and local Pol II speed control. Your will develop and implement bioinformatic approaches to detect and quantify local differences in nascent Pol II transcription dynamics. Bioinformatics expertise and support is provided by the Sandelin lab, the starting experimental data by the Marquardt lab. You will have the opportunity to assist or independently generate additional experimental data to address this question. A main focus will be on identifying plant genomic regions with dynamic non-coding transcription as a function of the cellular environment. Your identification of these regions for experimental follow-up analysis will require you to incorporate existing genomic datasets into your own analysis. You are working on the edge of current knowledge, and are expected to keep up to date with the relevant literature to drive this project into the most interesting direction. Your results will inform experiments of our lab and collaborators, we are therefore looking for a postdoc that stimulates productive and synergistic interactions with existing lab members. The employment period of the position is 3 years and the position is open from 15 July 2016 or as soon as possible thereafter. Please find the full job advertisement at http://employment.ku.dk/faculty/?show=823162 Deadline for applications is 30 May 2016, 23:59 GMT +1. Only electronic applications from the university Job Portal are accepted. Position: Postdoc in computational transcriptomics at Department of Biology and BRIC Project description: Computational Biology of Non-coding Transcription Stability and Function We have previously devised an approach to profile the susceptibility of lncRNA to rapid decay and in this way identify new functional candidates from the ‘sea’ of pervasive transcripts that our genomes constantly produce. We will now engage disease-relevant model systems in mouse and human coupled to high throughput biochemical and computational methods to further the identification and functional validation of new lncRNAs. Collectively, we will reveal new physiologically meaningful RNAs and gain a mechanistic understanding of their regulation and function. In doing so, we will also uncover new regulatory concepts created by the pervasive transcription of mammalian genomes. This will be done as a tight collaboration between experimental and computational biologists.The successful candidate will also be part of the international FANTOM6 project (http://fantom.gsc.riken.jp/6/ ), where lncRNAs are systematically knocked down followed by phenotypic screening. The employment period of the position is 2 years with the possibility of a 1-year extension. Starting time is tentatively August – October 2016. Please find the full job advertisement for the position at http://employment.ku.dk/faculty/?show=818716 Deadline for application is 15 June 2016, 23:59 GMT +1. Only electronic applications from the university Job Portal are accepted. … 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 arne at bioinfo.se Tue May 31 20:00:24 2016 From: arne at bioinfo.se (Arne Elofsson) Date: Tue, 31 May 2016 20:00:24 +0200 Subject: [SocBiN] Fwd: [NGP-Net CoreGroup] Belgrade meeting_pdf announcement In-Reply-To: References: <56cf8b22ec6f3c3af1ff23f0581a7f50@vin.bg.ac.rs> Message-ID: Dear All, Please find attached a pdf announcement for the Belgrade NGP-NET conference. -- Nevena Veljkovic, PhD Head of the Center for Multidisciplinary Research Institute of Nuclear Sciences VINCA P.O.Box522 11001 Belgrade Serbia Tel: +381 11 3408154 Fax: + 381 11 7440100nevenav at vinca.rs Dr Nevena Veljkovic Direktor Centar za multidisciplinarna istrazivanja Institut za nuklearne nauke VINCA Univerzitet u Beogradu P.O.Box522 11001 Belgrade Serbia Tel: +381 11 3408154 Fax: + 381 11 7440100nevenav at vinca.rs _______________________________________________ CoreGroup mailing list CoreGroup at ngp-net.bio.unipd.it http://ngp-net.bio.unipd.it/mailman/listinfo/coregroup -------------- next part -------------- An HTML attachment was scrubbed... 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