February 2016 - BBClist - maillist.psb.ugent.be

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. 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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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Bioinformatics position @ Bayer, NL
by Joan Wong 15 Feb '16

15 Feb '16

Dear all, We are looking for a motivated and enthusiastic bioinformatician to join our growing team at Bayer based in Nunhem, the Netherlands. The posting can be viewed here: http://career.bayer.nl/nl/job/Bioinformatics-Researcher--0000156142.html. Best regards, Joan Wong Bioinformatics Scientist [cid:C15DEDD5-288E-4312-857A-B6E1A5E2692F] Nunhems Netherlands B.V. Vegetable Seeds Napoleonsweg 152 6083 AB Nunhem, the Netherlands Tel: +31 475 599 545 Mobile: +31 634 959 061 E-mail: joan.wong(a)bayer.com<mailto:joan.wong@bayer.com> Web: http://www.bayer.com<http://www.bayer.com/> ________________________________________________________________________ The information contained in this e-mail is for the exclusive use of the intended recipient(s) and may be confidential, proprietary, and/or legally privileged. Inadvertent disclosure of this message does not constitute a waiver of any privilege. If you receive this message in error, please do not directly or indirectly use, print, copy, forward, or disclose any part of this message. Please also delete this e-mail and all copies and notify the sender. Thank you. For alternate languages please go to http://bayerdisclaimer.bayerweb.com ________________________________________________________________________

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PhD Candidate - Single Cell Transcriptomics of the Early Stages of Alzheimer’s Disease
by Mark Fiers 12 Feb '16

12 Feb '16

Dear all, We are looking for a PhD candidate to explore single-cell transcriptome data of the early stages of Alzheimer's Disease. The early stages of Alzheimer's disease are still poorly understood. It is unknown how the different cell types react to early amyloid stress and how these changes propagate through the different brain regions (in particular the hippocampus). In this project we will apply single cell transcriptomics to an Alzheimer's mouse model. Combining this data with a number of different technologies, such as in-situ hybridization and electrophysiology, will allow us to build a detailed spatio-temporal model, distinguishing different cell types, of the earliest steps in the progression of Alzheimer's disease. The candidate will work on the analysis of transcriptomics data and integrate this data with data from other sources, both locally generated, as well as public data. The ultimate goal is to generate a spatial and temporal model of the transcriptional changes at the onset of AD. More information: http://www.vib.be/en/jobs/Pages/PhD-Candidate---Single-Cell-Transcriptomics… With best regards Mark Fiers

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Postdoc position in the Archie lab
by Karoline Faust 11 Feb '16

11 Feb '16

POSTDOC POSITION Post-doctoral position in the ecology and evolution of baboon gut microbiomes A postdoctoral position applying ecological and evolutionary frameworks to understand the causes and consequences of gut microbial dynamics is available in the lab of Elizabeth Archie (University of Notre Dame, Department of Biological Sciences; http://blogs.nd.edu/archielab/) The postdoc will have access to an unprecedented data set of 20,000 microbiome samples, collected from 600+ individual baboons and spanning over 15 years. These samples are currently being sequenced at the 16S rRNA v4 region in collaboration with the Earth Microbiome Project (http://www.earthmicrobiome.org/) data will be available in the spring of 2016. Samples were collected from the well-studied Amboseli baboon population in Kenya (http://amboselibaboons.nd.edu/) which has long-term data on the baboons ecology, social interactions, health, and fitness. Some relevant recent publications include: Tung et al. (2015) eLife and Archie & Tung (2015) Curr Opin Behav Sci. Postdoctoral applicants should have a strong background two or more of the following areas: microbial ecology, community ecology, evolution, behavior, bioinformatics, and genomics. Strong data analysis skills, including programming and statistical modeling experience, are preferred. Familiarity or experience with primates is a plus, but is not essential. Several projects are available; applicants will have the freedom to choose their own projects as long as they fit within the general interests of the collaborative research. The Archie lab offers congenial research environments that foster strong interdisciplinary training and collaborative exchange. Collaborators on this project include Jenny Tung (http://www.tung-lab.org/) Ran Blekhman (http://blekhmanlab.org/) Luis Barreiro (http://luis-barreirolab.org/) Stuart Jones (http://www3.nd.edu/~sjones20/) and David Boone (IU School of Medicine), all of whom are available for advice and interaction. The postdoc is funded by the Eck Institute for Global Health, and the Environmental Change Initiative at Notre Dame. To apply for the position please send an email to Elizabeth Archie (earchie(a)nd.edu) including a cover letter, current CV, and contact information for at least two references. The anticipated start date is in late spring or summer 2016. Applicants should submit their materials by March 1 to ensure full consideration.

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GATK Best Practices for Variant Discovery workshop 14-15 April 2016 (second announcement)
by Bert Overduin 10 Feb '16

10 Feb '16

Dear all, I am very happy to announce that, after the success of the GATK workshop last year, Edinburgh Genomics again has been able to get a 3-person-strong team from the Broad Institute in Boston over to Edinburgh to deliver a two-day workshop on 14 and 15 April 2016. This workshop will focus on the core steps involved in calling variants with the Broad’s Genome Analysis Toolkit ( https://www.broadinstitute.org/gatk/) using the “Best Practices” developed by the GATK team. The workshop is composed of one day of lectures (including many opportunities for Q&A) and one optional day of hands-on training. For more information and to register, please visit https://genomics.ed.ac.uk/gatk-best-practices-variant- <https://genomics.ed.ac.uk/gatk-best-practices-variant-discovery>discovery <https://genomics.ed.ac.uk/gatk-best-practices-variant-discovery>. Note that for the hands-on part places are limited and allocated on a first come, first served basis. Also note that a similar workshop will be given on Monday 18 and Tuesday 19 April 2016 at the University of Oxford. For more information about this, please contact David Sims (david.sims(a)dpag.ox.ac.uk) Please feel free to forward this mail to anyone else potentially interested and/or to print out the attached flyer for further distribution. Hope to see many of you in April! 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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