- BBClist - maillist.psb.ugent.be

Looking for Post-doc scientist to apply for MSCA IF fellowship at VIB
by Alexander Botzki 11 Jun '18

11 Jun '18

Dear All, The Vandenbroucke lab<http://www.vib.be/en/research/scientists/Pages/Roos-Vandenbroucke-Lab.aspx> (Barriers in Inflammation) in collaboration with the VIB Bioinformatics Core is looking for an energetic and motivated post-doctoral scientist to work on '-omics' data integration at VIB & Ghent University and who is willing to apply for a MSCA IF fellowship. VIB greatly values diverse standpoints and promotes an inclusive environment in which everyone is respected. More info at: https://vibvzw.jobsoid.com/j/13426/post-doctoral-scientist Thank you very much for your consideration. Best regards, Alex Alexander Botzki - Head of VIB Bioinformatics Core | Training Coordinator ELIXIR-BE VIB Bioinformatics Core Rijvisschestraat 126, 9052 GENT, Belgium | +32 9 248 16 00 www.bits.vib.be<http://www.bits.vib.be/> | @vibbioinfocore | https://corefacilities.vib.be<https://corefacilities.vib.be/> [MAIL SIGNATURE - CTLS2018] [signatureFooter (002)]

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Bioinformatics Engineer and Genetics data analysis in Lille (France)
by SAND Olivier 11 Jun '18

11 Jun '18

Bioinformatics Engineer and Genetics data analysis (12 months renewable) CNRS unit UMR 8199 (http://www.good.cnrs.fr) based in Lille (France), is a research lab of 50 people led by Pr Philippe Froguel. It is part of the European Genomics Institute of Diabetes (http://www.egid.fr) Research activities are mainly focused on characterization of genetic variants associated to metabolic diseases like diabetes and obesity, and use modern approaches of genomics, bioinformatics, biostatistics, molecular biology and animal models. As a member of the bioinformatics team, the engineer will participate in Next Generation Sequencing data analysis. He/She will develop and install data analysis techniques for research projects and services. She/He will also take care of maintenance and follow up of the evolution in that area. Main activities: - collect, manage and analyse data from NGS sequencers (Illumina) - develop variant annotation and selection tools - develop bioinformatics tools and deploy them on our intranet - develop, manage and maintain databases - organise data storage Profile and skills: - Master degree or higher in bioinformatics, preferably with experience, but beginners can apply - practice knowledge of scripting languages (Python, Perl, shell, R…) - knowledge of variant annotation and selection procedures - knowledge in genetics would be an asset - knowledge of SQL and - oral and written English - organisation skills (autonomy, deadlines, anticipate delay sources…) If interested, please contact: Amelie Bonnefond (amelie.bonnefond(a)cnrs.fr) or Stefan Gaget (stefan.gaget(a)cnrs.fr)

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Bioinformatics PhD position at the NIOZ
by Julia Engelmann 11 Jun '18

11 Jun '18

Dear all, I am looking for a PhD student in bioinformatics, modeling marine microbial interactions at the NIOZ on Texel. *What is it about?* The project is concerned with elucidating marine microbial inter-species interactions based on high-throughput genomic data by applying network modeling. Microbes in the oceans, sediment and in microbiomes of higher organisms, form communities which keep the element and nutrient cycles in the seas and on land running. Different microorganisms have different metabolic capabilities. The product of one species can be the substrate for another. Besides dependencies based on individual nutrients, more complex interactions, such as symbiosis, predator-prey and competition for limited resources among marine microbes, will be elucidated in this project. Moreover, the impact of changing environmental conditions due to climate change on microbial communities will be assessed. To do so, causal network modelling will be applied to microbial abundance data and measurements of environmental parameters such as temperature and salinity to predict causal effects of species and environmental parameters on other species. The PhD student will then perform follow-up experiments in the lab to validate predicted interactions. *Who are we looking for? * We like to get into contact with a PhD student holding an MSc degree in Bioinformatics, Computational Biology, Computer Science, Mathematics, (Bio-)Statistics, Physics, Microbiology, Molecular Biology, Microbial Ecology or related fields. You are highly organized, motivated, and fluent in oral and written English. Experience with Unix is mandatory. Candidates need to have a proven record of their bioinformatics and programming skills. Candidates with good command of R, Bash and Python are preferred. If your background is in Biology-related fields, you will need to catch up with some mathematics and statistics. The ideal candidate also has experience in the analysis of high-throughput genomic data, including metagenomic data. *For more information and to apply, see:* https://www.workingatnioz.com/our-jobs/phd-student-%E2%80%9Cmodelling-causa… Please apply before July 15, 2018. Thanks and kind regards, Julia -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Julia C. Engelmann Tenure-track scientist Department of Marine Microbiology and Biogeochemistry NIOZ Royal Netherlands Institute for Sea Research and Utrecht University Landsdiep 4, 1797 SZ ‘t Horntje Texel, The Netherlands Phone: +31 (0) 222 369 388 Email: julia.engelmann(a)nioz.nl

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Post-doc in applied mathematics at CEA (Paris)
by SAND Olivier 08 Jun '18

08 Jun '18

Post-doc in applied mathematics: Innovative mathematical methods for the integration of proteomics and metabolomics data Context Proteomics and metabolomics provide unique and complementary information to decipher gene function and pathways, elucidate phenotypes, and robustly discover new biomarkers for disease treatments. Integration of both approaches is a mathematical challenge because of the heterogeneity and the complexity of the proteomics and metabolomics data, and the partial annotation (i.e. metabolite identification) provided by the metabolomics mass spectrometry technologies. The national infrastructures in bioinformatics (IFB), metabolomics (MetaboHUB), proteomics (ProFI), genomics (France Génomique), and mouse phenogenomics (PHENOMIN) have decided to join forces and develop new biostatistics and bioinformatics methods and tools for high-throughput and combined proteomics and metabolomics data analysis. Project First, statistical modeling will be used to explore the specific and common information from each type of omics data, and to determine how their combination as molecular signatures can optimally be used to interpret and predict the phenotypes. Such approaches will include linear and nonlinear methods for multivariate analysis. Second, network integration will be used to facilitate interpretation and annotation of the data. Proteins and metabolites will be mapped on the metabolic networks to facilitate chemical annotation and biological interpretation, and to suggest new biomarkers and metabolic functions. The mathematical approaches and tools will be validated on two use cases: 1) the high-throughput molecular phenotyping of comprehensive collections of mouse models and 2) the discovery of new gene functions in a bacterial model of interest for environmental and biotechnological applications. Profile Interested applicants should have a PhD in applied statistics (data analysis, network analysis), and be motivated by multidisciplinary applications (chemistry, biology). Contact Etienne Thévenot (CEA Saclay, Laboratory for Data Analysis and Systems’ Intelligence) Email: etienne.thevenot(a)cea.fr<mailto:etienne.thevenot@cea.fr> Web: http://etiennethevenot.pagesperso-orange.fr/index.html David Vallenet (CEA Evry, Laboratory of Bioinformatics Analyses for Genomics and Metabolism) Email: vallenet(a)genoscope.cns.fr<mailto:vallenet@genoscope.cns.fr> Web: http://orcid.org/0000-0001-6648-0332

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Tenure-track position at the Maastricht Centre for Systems Biology
by Adriaens, Michiel (MACSBIO) 08 Jun '18

08 Jun '18

Dear all, To strengthen MaCSBio's ongoing research and teaching activities in the field of metabolic modelling, we are looking for an ambitious Assistant or Associate Professor (tenure-track) with experience in dynamic (ODE) models, model fitting and parameter estimation, genome-scale metabolic models (GEMs), and/or integration of omics data into GEMs: https://www.academictransfer.com/en/47652/assistantassociate-professor-in-s…. Please feel free to share this information on relevant media or forward it to potential candidates. Kind regards, Michiel Adriaens -- Michiel E. Adriaens, PhD Assistant Professor Maastricht Centre for Systems Biology - MaCSBio Universiteitssingel 60, 6229 ER Maastricht, The Netherlands

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Software engineer position in the area of clinical and translational medicine domain
by Venkata Pardhasaradhi SATAGOPAM 06 Jun '18

06 Jun '18

Dear all We are looking for a "software engineer for web-based translational medicine knowledge management and analysis tools” at Luxembourg Centre For Systems Biomedicine (LCSB), University of Luxembourg. Please refer the below URL for more details: http://recruitment.uni.lu/en/details.html?id=QMUFK026203F3VBQB7V7VV4S8&nPos… Best regards, Venkata -- Venkata P. Satagopam Bioinformatics Core Luxembourg Centre For Systems Biomedicine (LCSB) University of Luxembourg Campus Belval, House of Biomedicine II 6, avenue du Swing L-4367 Belvaux T +352-466-644-6421 F +352-466-644-36421 venkata.satagopam(a)uni.lu http://lcsb.uni.lu ----- This message is confidential and may contain privileged information. It is intended for the named recipient only. If you receive it in error please notify me and permanently delete the original message and any copies. -----

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AlCoB 2018: call for participation
by IRDTA 04 Jun '18

04 Jun '18

AlCoB 2018: call for participation********************************************************************************** 5th INTERNATIONAL CONFERENCE ON ALGORITHMS FOR COMPUTATIONAL BIOLOGY AlCoB 2018 Hong Kong June 25-26, 2018 Co-organized by: The Hong Kong Polytechnic University Department of Computing Research Group on Mathematical Linguistics (GRLMC) Rovira i Virgili University http://grammars.grlmc.com/AlCoB2018/ ********************************************************************************** PROGRAM Monday, June 25 09:00 - 09:30 Registration 09:30 - 09:40 Opening 09:40 - 10:30 Tatsuya Akutsu. Algorithms for Analysis and Control of Boolean Networks - Invited lecture 10:30 - 11:00 Coffee break 11:00 - 12:15 Ricson Cheng, Matthew Dohlen, Chen Pekker, Gabriel Quiroz, Jincheng Wang, Ran Libeskind-Hadas and Yi-Chieh Wu. Reconciliation Feasibility of Non-binary Gene Trees under a Duplication-Loss-Coalescence Model Andreas Dwi Maryanto Gunawan. Solving the Tree Containment Problem for Reticulation-visible Networks in Linear Time Leo van Iersel, Remie Janssen, Mark Jones, Yukihiro Murakami and Norbert Zeh. Polynomial-time Algorithms for Phylogenetic Inference Problems 12:15 - 13:45 Lunch 13:45 - 14:35 Ben Raphael. Algorithms for Cancer Evolution - Invited lecture 14:35 - 14:50 Break and Group photo 14:50 - 16:05 Alexsandro Alexandrino, Carla Lintzmayer and Zanoni Dias. Approximation Algorithms for Sorting Permutations by Fragmentation-weighted Operations Klairton Brito, Andre Rodrigues Oliveira, Ulisses Dias and Zanoni Dias. Heuristics for the Sorting Signed Permutations by Reversals and Transpositions Problem Guilherme Miranda, Carla Negri Lintzmayer and Zanoni Dias. Sorting Permutations by Limited-size Operations 16:05 - 16:20 Coffee break 16:20 - 17:10 Poster presentations 17:15 - 19:15 Touristic visit --- Tuesday, June 26 09:00 - 09:50 Bin Ma. De Novo Protein Sequencing with Mass Spectrometry and Its Medical Applications - Invited lecture 09:50 - 10:20 Coffee break 10:20 - 11:35 Michael Sadovsky, Sergey Tsarev and Maria Senashova. Fast Algorithm for Vernier Search of Long Repeats in DNA Sequences with Bounded Error Density Eugen Czeizler, Alexandru Popa and Victor Popescu. Fixed Parameter Algorithms and Hardness of Approximation Results for the Structural Target Controllability Problem Chenqi Mou. Symbolic Detection of Steady States of Autonomous Differential Biological Systems by Transformation into Block Triangular Form 11:35 - 11:50 Break 11:50 - 12:40 Jordi Silvestre-Ryan and Ian Holmes. Consensus Decoding of Recurrent Neural Network Basecallers Ezra B. Wijaya, Erwandy Lim, David Agustriawan, Chien-Hung Huang, Jeffrey J.P. Tsai and Ka-Lok Ng. Utilizing Imputation and Meta-analysis to Identify DNA-methylation-mediated MicroRNAs in Ovarian Cancer 12:40 - 12:50 Closing 12:50 - Lunch

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Bioinformatician position at UCL (Brussels)
by Benoît Van den Eynde 04 Jun '18

04 Jun '18

Dear All, The de Duve Institute at the Université catholique de Louvain (Brussels) is looking for a highly motivated post-doctoral bioinformatician with hybrid-expertise, able to integrate bioinformatics/computational biology/systems biology/biostatistics, and data from different omics-approaches in the context of biological questions. The suitable candidate would be working within the context of the ‘DECODE’ consortium, whose research aims are at the interface of the immunobiology of cell death processes and cancer immunotherapy. For more details, please refer to the attached job offer. Do not hesitate to forward this email to anyone who might be interested. Best regards, Auriane Sibille Assistant to Professor Benoît Van den Eynde Ludwig Institute for Cancer Research Ltd de Duve Institute, Université catholique de Louvain Av. Hippocrate, 75 Bte B1.74.03 B - 1200 Brussels BELGIUM Phone: +32 2 764 75 80 Fax: +32 2 764 75 90 E-mail: auriane.sibille(a)bru.licr.org<mailto:auriane.sibille@bru.licr.org>

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[Gtpb] MSc level scholarship available
by GTPB Administration 02 Jun '18

02 Jun '18

Dear All A nice opportunity for someone wanting to have a fresh start at Bioinformatics Training provision. Biodata-PT, the Portuguese national infrastructure for biomedical data, is selecting a Training Assistant to scale-up from the GTPB training model, and lay-out the plans to reproduce training at the country level. International connections, substantial learning in Bioinformatics and practice in training provision. Training Assistant for Biodata.pt (recruiting) http://www.eracareers.pt/opportunities/index.aspx?task=global&jobId=100246 Please help us to find the right person. Open for applications from June 4th to June 15th Thank you Pedro Fernandes -- The Gulbenkian Training Programme in Bioinformatics Pedro L. Fernandes, Organiser Instituto Gulbenkian de Ciência Rua da Quinta Grande, 6 2780-156 OEIRAS Portugal _______________________________________________ GTPB mailing list GTPB(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb Click here to unsubscribe: https://lists.igc.gulbenkian.pt/mailman/options/gtpb/bbclist%40psb.vib-ugen…

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Course Data management and computational workflows, 25 June 2018, Amsterdam
by Celia van Gelder 02 Jun '18

02 Jun '18

Dear all Please find below the information about the course Data Management and Computational Workflows that will take place June 25 in Amsterdam. Registration is free of charge. There are ca. 20 places. First come, first serve. It is a course from the regular SURFsara portfolio but for this edition there is a focus on life sciences examples. The weblink for the course is here: https://www.surf.nl/en/agenda/2018/06/course-data-management-and-computatio… Please spread this announcement in your organization as you see fit. Best Celia SURFsara, ELIXIR-nl and ELIXIR introduce how data management based on iRODS can be incorporated into computational workflows. Date: 25 Jun 2018 Time: 09:30-16:30 Location: <https://www.surf.nl/en/about-surf/contact/directions-to-surfsara/index.html> SURFsara Science Park 140 VK1/2 Prior knowledge needed? No Description With the advance of new technologies, data volumes and numbers of files are constantly increasing. Good datamanagement is therefore an essential part of data-driven research. In response to the need of researchers and new regulations (e.g. GDPR) for better data management tools, we are currently developing a data management platform at SURFsara on the basis of iRODS. For whom? Bioinformaticians, computational biologists, data stewards in the field Life Sciences. Training objectives Learn about the concept of iRODS’s resource abstraction Gain hands on experience with managing data with iRODS Steer data flows across different iRODS administrative domains Work with metadata attached to data managed by iRODS and how to query for data using this metadata. After an introduction the training will purely be hands-on and will be taught in the style of software and data carpentry, i.e. live-coding sessions with exercises. Topics in this course will include: Data Life Cycle and FAIR principles * iRODS concepts * Metadata and searching for data in iRODS * Building a computational pipeline that draws on data managed in iRODS Requirements (or pair up with someone familiar with): Bash commands and basic python You need to be able to connect with ssh, bring your own client

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