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

Job opening - Programmer/Bioinformatician for SILVA
by Katrijn Vannerum 28 Jan '16

28 Jan '16

-------- Doorgestuurd bericht -------- Onderwerp: [straininfo] Job opening - Programmer/Bioinformatician for SILVA wanted! Datum: Thu, 28 Jan 2016 08:59:24 +0100 Van: Frank Oliver Glöckner <f.gloeckner(a)jacobs-university.de><mailto:f.gloeckner@jacobs-university.de> Antwoord-naar: straininfo(a)lists.ugent.be<mailto:straininfo@lists.ugent.be>, Frank Oliver Glöckner <f.gloeckner(a)jacobs-university.de><mailto:f.gloeckner@jacobs-university.de> Organisatie: Jacobs University Bremen gGmbH Dear Colleagues, the SILVA Team is searching for a full time Programmer/Bioinformatician for 3 years funded by the DFG. More information can be found at www.arb-silva.de/jobs/<http://www.arb-silva.de/jobs/> Please forward this information to anyone who might be interested. Many thanks Frank Oliver Glöckner -- Prof. Dr. Frank Oliver Glöckner Head of the Microbial Genomics and Bioinformatics Research Group Max Planck Institute for Marine Microbiology Jacobs University Bremen gGmbH E-mail: fog(a)mpi-bremen.de<mailto:fog@mpi-bremen.de> Address: MPI for Marine Microbiology Celsiusstrasse 1 28359 Bremen MPI: +49 (0) 421 2028 970 Jacobs: +49 (0) 421 200 3167 Fax: +49 (0) 421 2028 580 Mobile: +49 (0) 172 82 70 191 WWW: http://www.microbial-genomics.de http://www.ribocon.com http://www.microb3.eu Submit your next paper to: http://www.journals.elsevier.com/marine-genomics/

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EMBO courses on computational biology and biological interactions
by Roland KRAUSE 26 Jan '16

26 Jan '16

There are two EMBO courses nteresting to early stage bioinformaticians. EMBO Practical Course on computational analysis of protein-protein interactions: sequences, networks and diseases 30 May-4th June 2016<http://airmail.calendar/2016-05-30%2012:00:00%20GMT+2> in Budapest, Hungary organized by Zsuzsanna Dosztányi with a strong support from the EMBL as well. http://events.embo.org/16-protein-protein/ EMBO Practical Course on Computational Biology, ran at the EMBL by in Heidelberg by a group around Peer Bork (EMBL) 19 - 23 Jun 2016 http://www.embl.de/training/events/2016/COM16-01/ (I am an organizer of the second course) Best regards, Roland -- Roland Krause Luxembourg Centre for Systems Biomedicine University of Luxembourg Campus Belval 7, avenue des Hauts-Fourneaux L-4362 Esch-sur-Alzette roland.krause(a)uni.lu<mailto:roland.krause@uni.lu> +352 466644<tel://+352%20466644> 6267

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postdoc in Computational structure based drug design
by Martijn.Huijnen＠radboudumc.nl 26 Jan '16

26 Jan '16

Postdoctoral position in Computational structure based drug design at the CMBI, Radboud University Medical Centre Job description Project title: 3D-e-Chem: Integrated eScience workflow to translate biological and chemical data into structure-based protein-ligand polypharmacology prediction. Efficient exploitation of the massive amount of modern-day life science data requires a integrative approach that only eScience technologies can provide. The 3D-e-Chem project<https://www.esciencecenter.nl/project/3d-e-chem> will design a KNIME-based workflow for the integration of chemical and biological data for the prediction of polypharmacological action of drug molecules (ligands) on multiple proteins.This project will combine the strengths of the CMBI<http://www.cmbi.ru.nl> on protein structures together with the knowledge on ligand screening data and its interpretation from the department of Division of Medicinal Chemistry at VU University<http://www.chem.vu.nl/en/research/division-of-medicinal-chemistry/index.aspx> to develop novel chem- and bioinformatic workflows together with the Netherlands eScience Center in Amsterdam<https://www.esciencecenter.nl/> that improve the interpretation and prediction of polypharmacological effects. Key words: Chem- and Bioinformatics, protein structures, polypharmacology, workflow development. Postdoc 'Computational structure based drug design' * Center for Molecular and Biomolecular Informatics * Scale 10.4: max. € 43570 gross income per year at full employment (incl. vacation bonus and end of year payments) * 36 - 36 hours per week * Published: 26-01-2016 * Closing date: 08-02-2016 * Contract: Temporary, 1 year with possible extension Profile candidate * PhD in Molecular Sciences, Bioinformatics, Computer Science, Pharmacy or equivalent * Experience in Linux, Python, Java * Expertise in computational structure based drug design * Experience with KNIME or Pipeline pilot are a plus * Affinity with fundamental research related to human disease * Good communication skills * Ambition * Ability to work in an interdisciplinary team Organization The Computational Discovery and Design group is part of the Center for Molecular and Biomolecular Informatics (www.cmbi.ru.nl) and located within the Radboud Institute for Molecular Life Sciences<http://www.rimls.nl/>. Working at Radboudumc Radboudumc aims to be at the forefront of the development of innovative, sustainable and affordable healthcare. Our mission is 'to have a significant impact on healthcare'. We believe we can achieve that by providing excellent quality, participatory and personalized healthcare, operational excellence and by working together in sustainable networks. The starting point for this is patients and their quality of life. Throughout all this, patient care, research and education go hand in hand. To realize our mission, we are searching for colleagues who want to take on this challenge with us; employees who are excellent in their field of expertise and give it their all by pushing boundaries and providing 'that little bit more'. At Radboudumc, you gain the confidence, receive and take responsibility to successfully make these changes. For the best patient care and the best future of healthcare. Comments and contact information Conditions of employment * Employment will initially be for one year, with possible extension * Salary starts in scale 10.4: € 3122 gross per month, up to a maximum of € 4111 gross per year, depending on experience. You will also receive an additional vacation bonus (8% per year) and end of year payments (8.3% per year). Application Include your curriculum vitae, description of research experience and names and addresses of 2 references in your application. Information Additional information about the vacancy can be obtained from dr. Tina Ritschel, Tina.Ritschel(a)radboudumc.nl<mailto:Tina.Ritschel@radboudumc.nl>. (This e-mail address is to be used for information purposes only. Use the ‘Apply’ button to apply for the position.) Please apply before February 9, 2016. Het Radboudumc staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629. The Radboud university medical center is listed in the Commercial Register of the Chamber of Commerce under file number 41055629.

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Cytomine open-source software for collaborative analysis of multi-gigapixel bioimages
by Raphael.Maree. 26 Jan '16

26 Jan '16

Dear colleagues, After five years of research and development at the University of Liège, Belgium, I would like to draw your attention to the release under an open source licence of our Cytomine software (http://www.cytomine.be/) for collaborative analysis of multi-gigapixel imaging data. Although our initial focus was on biomedical research with cytology and histology whole-slide images, this is a generic software that might be useful for other types of imaging data from various fields (e.g. botany, geology, astronomy, environmental biology, ...). Based on modern web, database, and machine learning algorithms, it has been designed to foster active and distributed collaboration between computer vision/machine learning researchers and other scientists dealing with very large images. Among other functionalities, it implements: - a web user interface to explore (à la Google Maps) very large images using pyramidal formats; - web user interfaces to efficiently and collaboratively build large semantic ground-truth datasets from multi-gigapixel images; - a multi-thread implementation of our tree-based learning recognition algorithms (for content-based image retrieval [MIR2010], object classification [PatternRecognitionLetters2016], image segmentation [VISAPP2009], and landmark detection; - web proofreading tools to edit (ours or yours) algorithm predictions; - a RESTful API and software templating mechanisms to easily import/export data with your own software and extend it to your own purposes; - Python and Java clients to easily access and extend the system. Our paper in Bioinformatics (open access): http://bioinformatics.oxfordjournals.org/content/early/2016/01/09/bioinform… Other related papers: http://www.cytomine.be/#publications Read more (documentation, source code, etc.) on: http://www.cytomine.be/ Best regards, Raphaël. -- Raphaël Marée (PhD) http://www.montefiore.ulg.ac.be/~maree/ http://www.cytomine.be/ Tél.: +32 4 366 26 44 | Fax: +32 4 366 29 84

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Fwd: vacancy at Bayer, Ghent
by Lieven Sterck 26 Jan '16

26 Jan '16

FYI. apologies for cross posting. Lieven > From: "Antje Rohde" <antje.rohde(a)bayer.com> > We hebben een vacature voor een programmer om genetica-gerelateerde workflows in > scripts te gieten. > Mag ik jullie verzoeken om deze vacature onder de aandacht van mogelijk > geïnteresseerde kandidaten te brengen. > Antje > Antje Rohde > Group Leader Crop Genetics > Crop Science Division > Bayer CropScience SA-NV > Breeding & Trait development > Technologiepark 38 > 9052 Gent (Zwijnaarde), Belgium > Tel: +32 9 243 0471 > Mobile: +32 471 983 401 > Fax: +32 9 224 0694 > E-mail: antje.rohde(a)bayer.com > Web: http://www.bayer.be > 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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job opportunity: Project coordinator ELIXIR, Belgium
by Lieven Sterck 26 Jan '16

26 Jan '16

Dear, We would like to bring the following position at the VIB-UGent department of Plant Systems Biology to your notice: to strengthen the Belgian Elixir node we are looking for a dedicated individual to join us as a project coordinator. For more information and for applying, please visit : http://www.vib.be/en/jobs/Pages/Project-coordinator-ELIXIR-Belgium.aspx We would also appreciate if this could be circulated to any potential candidates in your wider network. With kind regards, lieven -- Lieven Sterck, PhD Senior Postdoctoral fellow Tel:+32 (0)9 331 38 21 Department of Plant Systems Biology Bioinformatics and Evolutionary Genomics VIB, Ghent University Technologiepark 927 9052 Ghent, Belgium http://www.psb.ugent.be http://bioinformatics.psb.ugent.be "Facts are meaningless. You could use facts to prove anything that's even remotely true" - H. Simpson

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Job opening at Janssen Pharmaceutica
by Joke Reumers 25 Jan '16

25 Jan '16

Janssen Discovery Sciences is a center of excellence focused on small-molecule drug discovery at Janssed collaborators, perform cutting-edge research from target & lead discovery through pre-clinical safety assessment to discover and develop transformational medicines. Every day we use our deep scientific expertise in drug discovery and development and our integrated suite of enabling technologies, platforms and tools to advance the research portfolio of Janssen’s five Therapeutic Areas: Cardiovascular & Metabolism, Immunology, Infectious Diseases & Vaccines, Neuroscience and Oncology. Within Discovery Sciences, the department of Computational Sciences provides expertise in computational/systems biology and big data analytics to support all aspects of drug discovery and development. The team provides a variety of complementary computational methodologies to extract meaningful and actionable information from biomedical data to facilitate the identification and validation of new targets in partnership with disease area experts in the therapeutic area discovery groups. The team is heavily engaged in deploying bioinformatics, machine learning and cutting-edge computational modeling and simulations techniques to advance our understanding of disease. The in silico activities are complemented and experimentally validated by wet lab capabilities within the team, utilizing stem cell, molecular genetics, gene editing, next generation sequencing and a variety of ‘-omics’ technologies We are looking for an enthusiastic candidate to join the European Computational Sciences team. The successful candidate will have a broad bioinformatics experience with a good working knowledge of genetics / pathway biology and deep scientific expertise in a number of disciplines including high-dimensional omics technologies and data analysis, methodologies for drug discovery and reverse translation coupled with the ability to work collaboratively with internal and external partners. Whereas the position will be based in Beerse (Belgium), it will support global teams in the different therapeutic areas and its Disease Area Strongholds. Furthermore, as the immune system plays a pivotal role in the progression of many diseases, we are searching for a candidate with a background in immunology. Description of the function • Work closely with therapeutic area teams to understand where bioinformatics approaches can best impact their scientific and technical challenges. • Steer application of bioinformatics/genomics to benefit projects in therapeutic area projects. • Work collaboratively with wet lab, IT and statistical specialists to deliver processes, tools and techniques to solve scientific problems. • Application of a wide range of genomic technologies (RNAseq, WES, WGS) to target identification, validation and biomarker discovery. • Development and application of approaches combining multi-omic data sets (including next-generation-sequencing) with phenotypic annotation to reveal actionable insights surrounding complex biological problems. • Written and verbal communication of study results to project teams, including proposals for further experiments to validate key findings. • Build and steer further development of small prototype tools for bench scientists to access and visualize project data. • Play a key role in the interactions with other omics experts in functional areas such as Toxicology and Quantitative Sciences. • Collaborate with industry and academia, and exploit external resources, to find the most effective solutions to complex biological problems. Qualifications • PhD in bioinformatics, biostatistics, computational biology or similar. Alternately, a PhD in molecular biology, immunology, etc. combined with a very strong record of high-throughput data analysis, supported by publication in this area. • Post-doctoral experience as well as exposure to wet lab activities in an academic or industrial setting is a plus. • Ability to analyze and interpret complex omics datasets (e.g. microarrays, next-generation sequencing, flow cytometry, mass spectrometry proteomics, etc.). • Proficiency in appropriate programming languages and software (e.g., R /Python/Perl/ Spotfire) and data management. • Strong written and oral presentation capabilities, with a convincing record of peer-reviewed publications and presentations at scientific conferences. Ability to clearly articulate scientific and operational concepts of biomarker research across functions, levels, and disciplines. • High intrinsic motivation in combination with strong scientific curiosity and a high level of autonomy. • Strong interpersonal skills and ability to work productively in a highly dynamic environment. • Strong team orientation, highly collaborative and results-oriented. • Good planning, prioritization, problem solving, and organizational skills. • Knowledge and understanding of the regulatory, legal and operational requirements of sample collection and data handling for omics analyses in clinical studies is a plus.

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REMINDER: ALPHY 2016
by Denis BAURAIN 24 Jan '16

24 Jan '16

ALPHY 2016: French-Belgian meeting on Bioinformatics and Evolutionary Genomics March 17-18 2016, Lille (France) EXTENDED DEADLINE for abstract submission, travel grant application and registration: February 15 2016 ALPHY is an annual meeting, organized in France since 1995, dedicated to the field of Bioinformatics and Comparative Genomics (ALPHY = ALignments and PHYlogeny). The main goal of this meeting is to promote informal communication in this highly multidisciplinary field, and to encourage young scientists to present their work. This year, ALPHY is co-organized by Belgian and French scientists in Lille, with the hope of enhancing scientific exchanges between research groups of these two countries. There will be two invited speakers (Karine Van Doninck and Christian Parisod), and the program will be open for around 20 contributions of 20' talks. ALPHY is funded by the GdR BiM (working group in Molecular Bioinformatics). Registration to the meeting is free, but mandatory. Please use the link below to register. If you wish to present your work, please submit an abstract in the registration form. Some budget will be available for supporting the travel expenses of young speakers. Please indicate whether you are asking for such a travel grant when registering. Tot straks ! A bientôt ! See you in Lille ! Alphy 2016 web site: http://lbbe.univ-lyon1.fr/alphy/ Contact: celine.poux(a)univ-lille1.fr The organizing committee: Denis Baurain Céline Brochier-Armanet Laurent Duret Nicolas Galtier Philippe Lemey Céline Poux Xavier Vekemans

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Two Postdoctoral Fellowships in Statistics at BIG N2N
by Katrijn Vannerum 22 Jan '16

22 Jan '16

For the first position, funded by the Fund for Scientific Research (Flanders, Belgium), we are looking for candidates with a strong mathematical foundation who have conducted methodological research in statistics with the aim to advance data analysis, to work on the project entitled `Bias-reduced Double-robust estimation' (Principal Investigator: Prof. Dr. Stijn Vansteelandt, project description given below). We particularly welcome promising candidates who have expertise in regularisation, model selection, semi-parametric inference and/or empirical processes. Pre-doctoral candidates with a strong mathematical foundation who are interested to work towards a PhD on this research project are also invited to express their interest. For the second position, funded by the Ghent University Hospital, we are looking for candidates with a strong methodological interest and experience with collaborative research, to work on the project entitled `Causal analysis of large electronic health registers' in collaboration with Prof. Dr. Stijn Vansteelandt from the Statistics research group in the Department of Applied Mathematics, Computer Science and Statistics, and Prof. Dr. Johan Decruyenaere, from the Intensive Care Outcomes Research Group at the Ghent University Hospital. We particularly welcome promising candidates who have expertise in causal inference, the analysis of electronic health records, or large-scale data analysis. The research group on Statistics in the Department of Applied Mathematics, Computer Science and Statistics at Ghent University is internationally well known for its research in biostatistics, in particular, on causal inference, missing data, survival analysis and statistical genomics. The successful candidate for this position is expected to pursue innovating research at the highest international level, and to participate in limited teaching activities and student guidance. Both fellowships will start in 2016, but the starting date can be negotiated. Applicants should have a Ph.D. in Statistics or a degree recognized as equivalent; they are expected to have a strong background in the mathematical foundations of statistics and show evidence of high-level research. To receive full consideration, applicants must submit their curriculum vitae, a brief (approximately 1/2 page) research statement (in English) and up to three selected publications or preprints electronically or by regular mail as soon as possible and preferably before March 1 to: Stijn Vansteelandt Ghent University Department of Applied Mathematics, Computer Science and Statistics Krijgslaan 281, S9 9000 Gent, Belgium email: Stijn.Vansteelandt(a)UGent.be tel: ++32 9 2644776 Project description `Bias-reduced Double-robust estimation': Most data analyses rely on statistical working models, which are not of primary scientific interest, but are needed to accommodate sparseness in the data. For instance, the estimation of treatment effects typically requires modelling the dependence of either outcome or treatment decisions on covariates. Misspecification of these models can be difficult to detect, yet seriously bias the treatment effect estimate. This is a major concern in practice, which has encouraged the growing popularity of double-robust data analyses. These rely on two working models, but demand only one of them to be correct, thereby giving the data analyst two chances of a valid analysis result. Bias- reduced double-robust (BR-DR) data analyses expand this double-protection property even further to realistic settings where both working models are misspecified. This is accomplished by fitting these working models in such a way that it minimises the (large sample) bias of the double-robust estimator of, e.g. the treatment effect. The theory on BR-DR estimation is novel and promising, especially considering the lack of statistical theories to control bias under model misspecification. In this project, we will develop greater insight into the properties of this method and of hybrid strategies that target bias-reduction in specific directions. We will extend it to make it widely applicable to all double-robust analyses, and we will develop its assimilation into regularisation and model selection methods. For Stijn Vansteelandt, Katrijn Vannerum PhD Project manager BIG N2N (Bioinformatics Institute Ghent From Nucleotides to Networks) Ghent University http://www.bign2n.ugent.be/ twitter: @N2N_UGent Katrijn.Vannerum(a)UGent.be<mailto:Katrijn.Vannerum@UGent.be> Technologiepark 927 9052 Gent, Belgium +32 (0)9 331 36 85 [logo_BIG N2N_signature]

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Two postdoctoral positions at the Clinical Bioinformatics lab - Imagine Institute, Paris
by Antonio Rausell 21 Jan '16

21 Jan '16

Dear all, Two postdoctoral positions are available at the new Clinical Bioinformatics lab at Imagine Institute for Genetic diseases, headed by Dr. Antonio Rausell: JOB DESCRIPTION Imagine is an interdisciplinary research center focused on human genetic diseases located at the Necker Hospital campus in the heart of Paris. Imagine is affiliated with the Université Paris Descartes (Sorbonne Paris Cité), the INSERM French National Institute for Medical Research and the Paris Public Hospitals Group (Assistance Publique-Hôpitaux de Paris). Coming in March 2016 Imagine will launch a new research Laboratory in Clinical Bioinformatics under the direction of Dr. Antonio Rausell. The laboratory will develop statistical methods and bioinformatics pipelines with a clinical focus on the following two main research lines: 1) Computational assessment and prioritization of human rare genetic variants with a potential clinical impact and application to disease-specific sequencing projects. Both coding and non-coding variants will be considered. The work will integrate large-scale genome/exome sequencing, transcriptomes (RNA-seq), high-throughput proteomics (mass spectrometry), immune phenotyping and clinical datasets both from public and in-house sources. Development of predictive tools will include machine-learning techniques such as Bayesian classifiers and SVMs. The goal is implementing software to help decision-making at the clinic. 2) Statistical analyses of high-dimensional single-cell data of human cells (mainly single-cell RNA-seq) with a focus on immune disorders and susceptibility to infectious diseases. Computational methods will be developed to cope with different noise sources and complex experimental designs: e.g. multiple conditions/stimuli and time points, simultaneous analyses of host and intracellular pathogens and several read-outs from the same cells, e.g.: genome and transcriptome, transcriptome and proteome, etc. The goal is the identification of cell markers with clinical value for diagnosis and treatment. In this context, the Clinical Bioinformatics lab is hiring two postdocs with complementary expertise in order to i) take the lead in one of the two previous research lines, ii) being able to assist the other line with specific skills if needed, and iii) set up the suite of common data and pipelines to build the core’s lab. As someone said before: “we hire smart people so they can tell us what to do”. PROFILE REQUIREMENTS Applicants should have a PhD in Bioinformatics, Computational Biology, Computer Science, Biostatistics, Statistical Genetics or Medical Informatics and at least one first author paper in a peer-reviewed journal. Demonstrated experience in NGS and large-scale ‘omics’ data analyses and strong data analyses skills are required. Experience in the research topics described above is preferable. Knowledge/interest in human innate immunity, infectious diseases, population genetics or structural biology will be appreciated. We are looking for knowledgeable candidates with versatile skills, with an eye on basic science and another on translational applications in the clinic. Flexibility to move across different projects, curiosity to enter into new topics and a team-building spirit are required. The position will require a constant interaction with experimental labs and clinicians. HOW TO APPLY Interested candidates should submit a single pdf application file to recruitment011.clinicalbioinfo(a)institutimagine.org with the following items: - Detailed CV (maximum 4 pages) with list of publications - A 3-page summary of past research, describing your specific contributions to your papers. - A 3-page statement of research interests, indicating which of the above described lines you would like to lead, the skills that you could contribute to our lab and your career development plans. - BSc/MSc/PhD official transcripts. - Contact information of three references. The desired starting date is March-June 2016. However, the positions could remain open beyond this date until suitable candidates are found. Informal inquiries can be addressed to Dr. Antonio Rausell to: recruitment011.clinicalbioinfo(a)institutimagine.org

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