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RegGenSIG 2016 - Call for abstracts
by Stein Aerts 24 Feb '16

24 Feb '16

Regulatory Genomics Special Interest Group (RegGenSIG) <http://www.reggen.net/2016> RegGenSIG 2016 will take place in Orlando, Florida, on Saturday, July 9, as part of ISMB 2016 <https://www.iscb.org/ismb2016>. The RegGenSIG meeting focuses on bioinformatics for regulatory genomics, which involves the study of the genomic "control system", which determines how, when and where to activate the "blueprint" encoded in the genome. An important goal of the meeting is to foster a collaborative community wherein scientists convene to solve difficult research problems in all areas of computational regulatory genomics. Please check <http://www.reggen.net/2016> for more information. *Call for abstracts - Oral presentations and poster presentations* To make an oral presentation at RegGenSIG, a one-page abstract should be submitted by April 11, 2016, to Jason Ernst (jason.ernst(a)ucla.edu<mailto:jason.ernst@ucla.edu>), with Subject: "RegGenSIG 2016 - Abstract for oral presentation", using the template found on the RegGenSIG web page. Based on the submitted abstracts, selected authors will be invited for oral presentation. Authors will be notified by May 2, 2016. Abstracts submitted for oral presentation may also be considered for poster presentation. For poster presentations, authors should submit a one-page abstract no later than May 9, 2016, to Jason Ernst (jason.ernst(a)ucla.edu<mailto:jason.ernst@ucla.edu>), with Subject: "RegGenSIG 2016 - Abstract for poster presentation", using the same template as for oral presentations. Author notification will occur no later than May 23, 2016. Yours sincerely, Finn Drabløs -- Department of Cancer Research and Molecular Medicine, Faculty of Medicine, Norwegian University of Science and Technology (NTNU) POST : P.O. Box 8905, NO-7491 Trondheim, NORWAY VISIT: Laboratory Center, Erling Skjalgsons gt. 1 Web http://bigr.medisin.ntnu.no Phone +47 72573333

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Python for Life Scientists, 13-14 May 2016, Amsterdam
by Nicola Bonzanni 23 Feb '16

23 Feb '16

Dear all, I'm writing to announce the course "Python for Life Scientists". Tailored for life scientists with little or no prior programming experience, the course is driven by real-life use cases. Participants will learn by doing, completing snippets of code that they will be able to reuse in their everyday tasks. Extensive use of IPython Notebook (Jupyter) will encourage to annotate and document the code, building the basis for sound and reproducible data analysis. The course will run on May 13-14 2016 in Amsterdam. More information and the registration form are available from the Web site: http://www.enpicom.com/training/python Feel free to spread this information to people that might be interested. Kind Regards, Nicola Bonzanni ENPICOM | Science Park 402 | 1098 XH Amsterdam http://www.enpicom.com +31 (0)20 895 0964

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Fwd: Last chance to join 'Applied Bioinformatics in Life Sciences'
by Frederik Coppens 22 Feb '16

22 Feb '16

Email not displaying correctly? View it in your browser. <http://vib.cmail20.com/t/r-i-vuilyo-l-i/> Last chance to join 'Applied Bioinformatics in Life Sciences' Late registration deadline March 3, 2016! The conference is almost sold out. Dear colleague, We want to remind you that the final registration deadline for Applied Bioinformatics in Life Sciences approaches. Make use of this last chance to join over 180 colleagues & stay up to date on the latest developments in the field of Bioinformatics. Register here <http://vib.cmail20.com/t/r-i-vuilyo-l-d/>. 19 INTERNATIONALLY RENOWNED SPEAKERS The conference will bring together some of the most highly regarded academics in the world of bioinformatics in several sessions, with topics focused on: Data Integration and Modeling // Next Generation Sequencing // Protein Bioinformatics // Systems Biology. The speakers covering these topics include:Matthias Mann (MPI,DE), Peer Bork (EMBL,DE), Luis Serrano (CGR,ES), Nuria Lopez-Bigas (University of Pompeu Fabra, ES) Christine Orengo(UCL,UK), Eran Segal (Weizmann Institute, IL), and many more <http://vib.cmail20.com/t/r-i-vuilyo-l-h/>. OVER 70 POSTER PRESENTERS Junior researchers have sent in their research and will present it via posters and presentations during the conference. After the closing remarks on the second day, a poster prize will be awarded. MORE THAN JUST TALKS The first day we welcome all the attendees to network at our unique Begian beer reception. On day one you can also enjoy a relaxing dinner in The Faculty Club <http://vib.cmail20.com/t/r-i-vuilyo-l-k/> located in the ancient historical site of the Grand Beguinage which was included in the UNESCO World Heritage List. Aguided walk through the ancient city will get you there. Select the dinner when you register <http://vib.cmail20.com/t/r-i-vuilyo-l-u/> for the conference. <http://vib.cmail20.com/t/r-i-vuilyo-l-o/> We hope to have triggered your interest in our conference. In case you have questions or remarks, please feel free to contact us. With kind regards, Alexander Botzki VIB BioInformatics Training and Service facility, VIB HQ On behalf of the organizing committee <http://vib.cmail20.com/t/r-i-vuilyo-l-b/> You received this email based on your expertise in the field. In case this research area is not of your interests, we apologize for any inconvenience. Please unsubscribe here <http://vib.cmail20.com/t/r-u-vuilyo-l-r/> | subscription preferences <http://vib.updatemyprofile.com/r-l-2AD73FFF-l-y> ================================================================== Frederik Coppens, Ph.D. Project Leader Applied Bioinformatics & Biostatistics IT manager Tel: 32 (0)9 3313812 Fax:32 (0)9 3313809 VIB DEPARTMENT OF PLANT SYSTEMS BIOLOGY, UGent Technologiepark 927, 9052 Gent, BELGIUM frcop(a)psb.ugent.be http://www.psb.ugent.be/abb ==================================================================

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Introduction to Python for Biologists 4-8 April 2016 - Few places left
by Bert Overduin 22 Feb '16

22 Feb '16

Dear all, This is to let you know that we have a few places left on our Introduction to Python for Biologists course from 4-8 April 2016. As Python is an ideal first language for beginning programmers, this course is extremely well suited for those working in biology / genomics without any previous programming experience. The course will be taught by Martin Jones, founder of Python for Biologists (http://pythonforbiologists.com) and a very experienced Python teacher, assisted by myself. Having two instructors for around 20 students will guarantee lots of one-on-one time. For more information and to register, please have a look at: https://genomics.ed.ac.uk/introduction-python-biologists-april-2016 Note that the course will be repeated from 11-15 July 2016: https://genomics.ed.ac.uk/introduction-python-biologists-july-2016 Finally, I don't want to withhold from you some of the feedback we received for last week's course: *"Brilliantly well-run. From the book; to the USB stick with all the files we need; to the topics covered; to the system of helping us one-on-one, I cannot fault the course."* *"It was a great workshop full of amazing content and great people. Thank you!"* *"#Drawing upon 15 years of teaching experience at a University, I find: Num_faults == 0"* With kind regards, Bert -- Bert Overduin, PhD TRAINING AND OUTREACH BIOINFORMATICIAN Bert.Overduin(a)ed.ac.uk EDINBURGH GENOMICS The University of Edinburgh Ashworth Laboratories The King's Buildings Charlotte Auerbach Road Edinburgh EH9 3FL Scotland, United Kingdom tel. +44(0)1316507403 http://genomics.ed.ac.uk The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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call for abstracts - NBC-16 "Next Level Biotechnology"
by Roubos, Hans 19 Feb '16

19 Feb '16

Please be invited to participate in NBC-16 - a broad Biotech event in The Netherlands. NBC-16 "Next Level Biotechnology" On the 14th of April 2016 NBV organizes the 16th edition of the Netherlands Biotechnology Conference (NBC-16). NBC-16 "Next Level Biotechnology" will highlight some of the most promising developments in biotechnology. Scientists working at universities and research institutes are performing cutting edge science on biological systems and processes. Biotech entrepreneurs use this know how to develop all kinds of innovative products with immense economical and societal impacts. Please consider sending in an abstract for poster and/or talk! * Cell and Fermentation Biotechnology * Green Biotechnology * Societal Aspects * Microbial Systems Biology & Synthetic Biology * Microbial Physiology * Product Isolation & Purification * Applied Biocatalysis http://nbv.kncv.nl/nbc-16-biotechnology-the-next-level/speakers.184255.lynkx Keynotes John van der Oost John van der Oost (1958) is molecular microbiologist/biochemist. He is group leader of Bacterial Genetics group at Wageningen University since 1995, currently consisting of 20 scientists, and on average 10 MSc students. He is (co-)author of >250 scientific publications, with an H-factor >50. John is (co-) inventor of 13 patents. He has obtained an EMBO long-term fellowship, an EMBL fellowship, a KNAW fellowship, and is laureate of a NWO-VICI grant, and a NWO TOP grant. He has been coordinator of two European networks. He participated in 3 STW projects. In 2005 John was appointed Full Professor, and in 2013 he was elected as EMBO member. Apart from metabolic engineering and synthetic biology projects, he works on CRISPR-Cas since 2005. Alex Patist Alex has over 15 years of experience in directing new product, process technology & optimization and scale-up in the food, nutraceutical, biochemical & biofuel industries. Since 2013, he has been at Genomatica, a leading biotech innovator for the chemical industry. At Genomatica, he has led several teams responsible for technology transfer to customers worldwide; development of high precision scale-up/scale-down methodologies; and selection and preparation of tolling facilities. In addition, he has been a catalyst in 'mainstreaming' a whole-process approach to deliver advantaged bioprocesses. A multi-cultural heritage - and perhaps a Dutch sense of humor - help him bring together project teams across different countries, languages, core capabilities, company sizes and time zones. Previously, Alex was at Cargill R&D in Minneapolis, MN. During his tenure as Director of Technology, he worked with major partners such as PepsiCo, Kraft and Nestle, taking ideas from concept, through patents, to rollout in areas such as natural sweeteners (e.g., Stevia) and improved line operations. Alex has a BS from Hogeschool Utrecht, MS from TU Eindhoven and a Ph.D. from the University of Florida, all in Chemical Engineering. Marc Robillard Dr. Robillard initiated and led the team working on Tagworks' In Vivo Chemistry within Philips Research from 2006 until the spinout end of 2011. In 2003, he joined Philips Research to define and initiate their molecular medicine program in conjunction with the building of the corresponding laboratory facilities. As senior scientist and project leader he was involved in several imaging and drug delivery projects before creating the In Vivo Chemistry technology. Prior to Philips he worked at Kreatech Diagnostics on the development of a portfolio of probes for drug targeting and microarray-based detection of DNA, RNA and proteins. In addition he was a visiting scientist at the School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, and he worked at the CRO Syncom as a synthetic chemist. Dr. Robillard obtained his MSc and PhD in bio(in)organic chemistry at, respectively, the University of Groningen and the Leiden Institute of Chemistry, The Netherlands. He has published 19 peer-reviewed papers and is a co-inventor on 18 patents. Hans Roubos | Principal Scientist Bioinformatics & Modeling | DSM Food Specialties B.V. | Alexander Fleminglaan 1 | 2613 AX Delft | Netherlands | T +31 (0)15 2792147 | Trade Register Number 27235314 | Stay connected: [http://static.dsm.com/content/dam/dsm/images/twitter.png] <https://twitter.com/DSM> [http://static.dsm.com/content/dam/dsm/images/linkedin.png] <https://www.linkedin.com/company/3108> [http://static.dsm.com/content/dam/dsm/images/youtube.png] <https://www.youtube.com/user/dsmcompany> [http://static.dsm.com/content/dam/dsm/images/googleplus.png] <https://plus.google.com/117689312065000346895#117689312065000346895/posts> [http://static.dsm.com/content/dam/dsm/images/facebook.png] <https://www.facebook.com/DSMcompany> [http://static.dsm.com/content/dam/dsm/images/DSM_Email_EN.jpg] ________________________________ DISCLAIMER: This e-mail is for the intended recipient only. If you have received it by mistake please let us know by reply and then delete it from your system; access, disclosure, copying, distribution or reliance on any of it by anyone else is prohibited. If you as intended recipient have received this e-mail incorrectly, please notify the sender (via e-mail) immediately.

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PhD position available
by Jennen Danyel (TGX) 17 Feb '16

17 Feb '16

The department of Toxicogenomics is looking for a PhD candidate for the EUToxRisk21 project (An Integrated EUropean 'Flagship' Program Driving Mechanism-based Toxicity Testing and Risk Assessment for the 21st Century) with a strong basis in molecular biology and biomedical sciences and experienced in bioinformatics. Further details on how to apply can be found here: https://www.academictransfer.com/employer/UM/vacancy/32341/lang/en/ Kind regards Danyel Jennen [cid:964010910@27082013-01E6] Danyel Jennen Assistant Professor Toxico-informatics Department of Toxicogenomics danyel.jennen(a)maastrichtuniversity.nl <mailto:danyel.jennen@maastrichtuniversity.nl> www.toxicogenomics-um.nl <http://www.toxicogenomics-um.nl/> Room 5.578A, Universiteitssingel 40, 6229 ER Maastricht P.O. Box 616, 6200 MD Maastricht, The Netherlands T +31 (0)43-3883983 F +31 (0)43-3884146 [cid:964010910@27082013-01ED]Please consider your environmental responsibility before printing this e-mail.

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4th European Student Council Symposium 2016
by ISCBSC announcement 16 Feb '16

16 Feb '16

Dear colleague, We would like to invite you to the 4th European Student Council Symposium (ESCS) 2016 taking place on *Saturday 3 September* during ECCB 2016 in The Hague, Netherlands. The ESCS is a biennial interdisciplinary symposium that brings together students and young researchers from computational biology, bioinformatics, systems biology, and related fields. This symposium offers you a great opportunity to present your research to an international audience, get insights into hot topics and newly developed methods and build a network within the computational biology community of Europe. We are pleased to announce our confirmed keynote speakers *Kris Laukens* (University of Antwerp, Belgium), and *Nuria Lopez-Bigas* (Universitat Pompeu Fabra, Spain). The symposium includes ice-breaking, *oral presentations*, *keynote talks*, *poster presentations* and an *evening social event* that offer you the opportunity to get to know fellow young scientists from all over Europe in a casual setting. Abstract submission will open on Monday 25th April 2016. Please visit our website http://escs2016.iscbsc.org/ regularily as more information will be announced soon. For registration details, please visit http://www.eccb2016.org/registration/. We welcome students and young researchers from all areas of computational biology to join our community. Please help us spread the word by sharing the event flyer (please find it attached), and using the hashtag #ESCS16 on social media. We look forward to welcome you in The Hague! Annika Jacobsen and Kevin Schwahn, chair and co-chair, ESCS 2016

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PhD student Bioinformatics - New tools for genome annotation in unknown microeukaryote lineages
by Klaas Vandepoele 16 Feb '16

16 Feb '16

PhD student - New tools for genome annotation in unknown microeukaryote lineages In the framework of a H2020 Marie-Sk?odowska-Curie Innovative Training Network on Promoting Single Cell Genomics to explore the ecology and evolution of hidden microeukaryotes (SINGEK), we have a position open for a *PhD student in Bioinformatics*, with a strong focus on tool development and data visualization. Specifically, we are looking for: -Master in computational sciences, preferably with some experience in biological data analysis -Experience with Unix and command-line usage -Good programming skills (Python, or Java/C++) -Experience with relational databases (mySQL), PHP and webdesign/JavaScript is a plus -Excellent English communication skills -A passion for science and driven to decode the mysteries of life. Need more info? Contact Prof. K. Vandepoele (klaas.vandepoele AT psb.vib-ugent.be). Want to apply? Find the application form here: http://www.singek.eu/esr-10-new-tools-for-genome-annotation-in-unknown-micr…. - apologies for cross-posting - --- This email has been checked for viruses by Avast antivirus software. https://www.avast.com/antivirus

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EMS-ESMTB Summer School “Mathematical Biology of Tissue Mechanics”, 25-29 July 2016
by Roeland Merks 16 Feb '16

16 Feb '16

EMS-ESMTB Summer School “Mathematical Biology of Tissue Mechanics” Monday 25 through Friday 29 July 2016 Lorentz Center@Oort - Leiden Organizers: Andreas Deutsch, Roeland Merks and Vitaly Volpert Scientific Topic: This summer school will bring together 40 young researchers in the quantitative life sciences and teach them a range of mathematical approaches to analyse and model the biomechanics of tissues and the collective behaviour of cells. The workshop has been organized jointly with the European Mathematical Society (EMS) and the European Society for Mathematical and Theoretical Biology (ESMTB), and fits into a series of annual workshops on mathematical biology organized with the EMS (http://www.esmtb.org/schools <http://www.esmtb.org/schools>). The workshop is co-funded by the EMS, ESMTB, the Lorentz Center, and NDNS+ Workshop Format: The school will focus on hands-on group work, with participants focusing on one out of five biological problems. The mornings will start with plenary lectures that will showcase exemplary stories that have combined mathematical modeling and experimental biology, as well as discuss a number of mathematical methods in-depth. The lectures will cover a range of topics, including, but not limited to: vertex-based models, cellular automata models, cellular Potts modeling, partial-differential equations, and hybrid individual-based and continuum approaches. Projects: TEAM A: Spatial effects in the pathogenesis of blood cancers, including leukemia - Mentors: Vitaly Volpert and Anass Bouchnita, CNRS Lyon, France - Mathematical methods: Hybrid, cell-based models based on Lagrangian dynamics TEAM B: Modelling pigment cell interactions in zebrafish skin patterns - Mentors: Roeland Merks, CWI and U Leiden, The Netherlands - Mathematical Methods: modelling of tissues using the cellular Potts model, vertex-based models and using cellular automata. TEAM C: Modeling of cell-cell signaling in discrete cell lattices with reaction-diffusion systems - Mentors: Andreas Deutsch and Walter de Back, TU Dresden, Germany - Mathematical Methods: Cell-cell signaling in discrete cell lattices, reaction-diffusion systems Team D. Zebrafish epiboly and formation of compartments in 3D tissues: coupling mechanical behavior and gene regulation - Mentors: Dr. Nadine Peyriéras and Dr. René Doursat, BioEmergences, CNRS USR3695, Gif-sur-Yvette, France - Mathematical Methods: Modeling cross-talk between biomechanics and gene regulation Lorentz Center Facilities: The venue Lorentz Center@Oort, located at the Faculty of Science campus of Leiden University, the Netherlands. The Lorentz Center provides each participant with office space and wireless internet access. Lorentz Center also provides various practical services for the participants, such as arranging accommodations at the nearby hotel Van der Valk Hotel Leiden at a special rate (€ 84 including breakfast and taxes), visa assistance and bike rental. For further information, please refer to our website: www.lorentzcenter.nl <http://www.lorentzcenter.nl/>. Costs and Refunds: Lorentz Center does not charge registration fees. In addition, Lorentz Center hosts a welcome reception and a workshop dinner, both free of charge. Some budget is available for travel refunds and hotel accommodation. Please apply for this upon registration. Application: Motivated applications, including a poster abstract, can be submitted until the deadline of April 30th, 2016, via the workshop webpage at: http://www.lorentzcenter.nl/lc/web/2016/803/info.php3?wsid=803&venue=Oort <http://www.lorentzcenter.nl/lc/web/2016/803/info.php3?wsid=803&venue=Oort>. Decisions will be announced by May 17th, 2016. For further information, please do not hesitate to contact the coordinator of all practical matters of this Lorentz Center workshop, Ms. Tara Seeger, seeger(a)lorentzcenter.nl <mailto:seeger@lorentzcenter.nl>.

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PhD position - lncRNAs in cancer
by Pieter Mestdagh 15 Feb '16

15 Feb '16

Dear all, We’re looking for a PhD candidate to study long non-coding RNA expression data in cancer. The PhD candidate will work with high-dimensional (single-cell) RNA-sequencing datasets (pubic and in house generated) and apply various bio-informatics tools to delineate and characterize lncRNA transcript structures, study lncRNA expression regulation and integrate complementary data types (i.e. histone marks, CAGE-sequencing, DNA copy-number, …) in the context of cancer. The goal is to expand our knowledge on the role of lncRNAs in cancer, characterize lncRNA expression heterogeneity (between lineages and within lineages) and prioritize novel candidate biomarkers and therapeutic targets. More information can be found here: https://edit.ugent.be/en/work/vacancies/scientific/phd-student-ev784/ Best regards, Pieter Mestdagh -- prof. dr. ir. Pieter Mestdagh Center for Medical Genetics Ghent (CMGG) Ghent University Hospital Medical Research Building (MRB), 2nd floor, room 120.055 De Pintelaan 185, B-9000 Ghent, Belgium +32 9 332 6979 (phone) | +32 9 332 6549 (fax) http://cmgg.be<http://medgen.ugent.be/> Pieter.Mestdagh(a)UGent.be<mailto:Pieter.Mestdagh@UGent.be>

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