From arne at bioinfo.se Wed Feb 8 17:22:21 2017 From: arne at bioinfo.se (Arne Elofsson) Date: Wed, 8 Feb 2017 17:22:21 +0100 Subject: [SocBiN] Postdoc Positions Available in Stockholm Message-ID: Postdoc Protein Bioinformatics Arne Elofsson, Stockholm University. http://bioinfo.se/ *Theme: *We are developing state of the art method to predict protein features, including membrane protein topology, protein structure and protein model quality. In addition we have a general interest in protein evolution. *Location: *We are located at Science for Life Laboratory, Stockholm Sweden. *Group: *Friendly environment with significant freedom. *Positions: *Tax Free postdoc scholarships for two years, medical insurance etc. *Contact: *arne at bioinfo.se *Position 1: *Deep learning in protein bioinformatics. We apply modern machine learning methods for various protein structure prediction problems. *Position 2: *Ab-Initio Structure Prediction using PconsC3. We have recently developed an ab-initio method to predict the structure of more than 2000 Pfam families. Here we will both improve this method and use it to gain biological insights in these proteins. *Position 3: *Evolution of transporters and channels. We are studying the evolution of protein transporters and channels both to understand their function and predict their structures. Here, we are closely collaborating with experimental colleagues. Selected Publications · Uziela, K., Menendez Hurtado, D., Shu, N., Wallner, B. and Elofsson, A. (Epub 2017) ProQ3D: improved model quality assessments using deep learning. *Bioinformatics* · Hayat, S., Peters, C., Shu, N., Tsirigos, K.D. and Elofsson, A. (2016) Inclusion of dyad-repeat pattern improves topology prediction of transmembrane beta-barrel proteins. *Bioinformatics* *32* (10) : 1571-1573. · Shiota, T., Imai, K., Qiu, J., Hewitt, V.L., Tan, K., Shen, H.H., Sakiyama, N., Fukasawa, Y., Hayat, S., Kamiya, M., Elofsson, A., Tomii, K., Horton, P., Wiedemann, N., Pfanner, N., Lithgow, T. and Endo, T. (2015) Molecular architecture of the active mitochondrial protein gate. *Science* *349* (6255) : 1544-1548. · Tsirigos, K.D., Peters, C., Shu, N., Kall, L. and Elofsson, A. (2015) The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides. *Nucleic Acids Res* *43* (W1) : W401-W407. · Hayat, S., Sander, C., Marks, D.S. and Elofsson, A. (2015) All-atom 3D structure prediction of transmembrane beta-barrel proteins from sequences. *Proc Natl Acad Sci U S A* *112* (17) : 5413-5418. Yours Arne ----------------------------------------- Arne Elofsson Science for Life Laboratory Tel:+46-(0)70 695 1045 Stockholm University http://bioinfo.se/ Box 1031, Email: arne at bioinfo.se 17121 Solna, Sweden Twitter: https://twitter.com/arneelof Scholar: http://scholar.google.se/citations?user=s3OCM3AAAAAJ ORCID: 0000-0002-7115-9751 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: postdocs-2017.pdf Type: application/pdf Size: 78281 bytes Desc: not available URL: From Inge.Jonassen at ii.uib.no Wed Feb 15 16:29:54 2017 From: Inge.Jonassen at ii.uib.no (Inge Jonassen) Date: Wed, 15 Feb 2017 16:29:54 +0100 Subject: [SocBiN] Five bioinformatics group leader positions open in Bergen, Norway Message-ID: Please help us and forward this announcement to candidates you think might be interested! CBU is seeking five talented young researchers for group leader / associate professor positions For more information about the positions, and also to apply, see https://www.jobbnorge.no/en/available-jobs/job/134177/associate-professors-in-bioinformatics-up-to-five-positions For more information about CBU, see http://www.cbu.uib.no/ or contact me. All the best, 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 Inge.Jonassen at ii.uib.no Wed Feb 15 16:37:52 2017 From: Inge.Jonassen at ii.uib.no (Inge Jonassen) Date: Wed, 15 Feb 2017 16:37:52 +0100 Subject: [SocBiN] senior engineer position at CBU in Bergen Message-ID: <366511F2-FB5C-4DAB-911D-4198790DBE59@ii.uib.no> Do you want to work with systems for running cutting-edge e-infrastructures for life sciences? Here is an excellent opportunity: https://www.jobbnorge.no/en/available-jobs/job/134286/senior-engineer-chief-engineer-system-administrator-at-the-department-of-informatics All the best, 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 coordinator at rth.dk Thu Feb 16 14:04:17 2017 From: coordinator at rth.dk (Betina Wingreen Jensen) Date: Thu, 16 Feb 2017 14:04:17 +0100 Subject: [SocBiN] Deadline extended for PhD fellowship in RNA Bioinformatics in Bacillus and related Organisms - RTH, University of Copenhagen Message-ID: <000f01d28855$2e6c8fb0$8b45af10$@rth.dk> Dear Colleague, Center for non-coding RNA in Technology and Health (RTH), http://rth.dk, Department of Veterinary and Animal Sciences, Faculty Health and Medical Sciences at University of Copenhagen has an open PhD fellowship in RNA Bioinformatics in Bacillus and related Organisms. We are looking for an enthusiastic person to join our team for three years starting 1st April 2017 or as soon as possible thereafter. You will be a hardworking team player and a key person in the project group essential for obtaining successful results. The application deadline has been extended to: 2017-03-05 Background Cell factories are based on organisms, which have been carefully optimized to produce protein-based products such as enzymes and pharmaceutical proteins with the highest possible yield. However, current technology is saturated with respect to yield improvement although the theoretical maximum has not been reached yet. Within the NextProd project, the goal is to improve the yield by manipulating ncRNAs. See more at http://nextprod.dk. Specific Job description Comprehensive annotation for noncoding and structured RNA on the bacillus gene is to be made from transcriptome data as well as from genomic data. In addition the include RNA interaction predictions and data when relevant. Pipeline that encompass known tools will be made. The pipeline will further include developing tools for integrating RNA structure probing data in the RNA structure annotation. Furthermore, the work will involve transcriptome and expression analyses. ncRNA RNA annotation and transcriptome analysis. The full posting and online application procedure, can be found on: http://employment.ku.dk/phd/?show=884209 Please forward this posting to all suitable candidates in your network. Thank you in advance for your assistance. With best wishes, Betina Betina Wingreen Jensen Project Coordinator Københavns Universitet IHV Center for non-coding RNA in Technology and Health Grønnegårdsvej 3 1870 Frederiksberg C DIR 35334704 MOB 21510932 coordinator at rth.dk -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.gif Type: image/gif Size: 5975 bytes Desc: not available URL: From olivier.colliot at upmc.fr Tue Feb 21 16:38:33 2017 From: olivier.colliot at upmc.fr (Olivier Colliot) Date: Tue, 21 Feb 2017 16:38:33 +0100 Subject: [SocBiN] Postdoc position - Knowledge models for analysis and interpretation of genetic data - Paris (France) Message-ID: Dear colleagues, We have a postdoc position on Knowledge models for analysis and interpretation of genetic data. The profile is available at: http://aramislab.prod.lamp.cnrs.fr/wp-content/ uploads/2017/02/Post-doc-2017_IPL_Neuromarkers_For_diffusion-2.pdf Could you please help us circulate this announce? Best regards Olivier Colliot -------------- JOB OFFER - Postdoctoral fellow - Knowledge models for analysis and interpretation of genetic data in neurodegenerative diseases Keywords: computational biology, bioinformatics, knowledge models, ontologies, genomic data LABORATORY: Brain and Spinal Cord Institute (ICM), Paris, France PROJECT Neurodegenerative diseases (such as Alzheimer’s disease and Parkinson’s disease) are major public health concerns. To develop new treatments for these diseases, it is crucial to identify at the earliest stage (ideally presymptomatic) the patients that will develop the disease. Genetic factors play an important role in these diseases. A major goal is to identify genetic variants and their combination that can influence disease evolution. To that aim, knowledge models of biological processes at play appear essential. First, such knowledge models could be used to inform the analysis of genetic variants (identified through sequencing and microarray technologies), for instance by constraining statistical learning approaches. These models are also essential for the biological interpretation of the discovered variants. The objective of this post-doctoral project is to design approaches to integrate knowledge models of biological processes in neurodegenerative diseases in the analysis of genetic variants. These will include both healthy and pathological metabolic and signaling pathway models. Pathways models can formalize the relationships between different gene activations in a given biological process or cellular cycle. The building of such models and their use with patient-specific data relies on approaches from the domains of ontologies, semantic web and graph-based representations. Different knowledge bases, such as that of the Gene Ontology (www.geneontology.org) for describing gene products, Reactome (www.reactome.org) for describing pathways, or OMIM and the Disease Ontology for describing pathologies have been developed by the scientific community. However, many of these models are either relatively generic or developed for other types of diseases (mainly cancer). Specific models of neurodegenerative disease have been proposed but the tools to automatically use these models for analysis of genetic data are still underdeveloped. Furthermore, knowledge about regional effects (such as effect on specific brain structures) needs to be added for better integration with imaging data. The present project will thus aim to propose knowledge models which are better adapted to these pathologies. These knowledge models will be based upon the increasing interoperability between specialized data repositories enabled by the Linked Open Data Initiative. Another important element is the ability to create a mapping between the knowledge model and the genetic data to be analyzed (such as for instance sets of Single Nucleotide Polymorphisms or structural variants). Such a mapping is non-trivial, in particular in non-coding regions and because of distant regulations. The second aim of the project will thus be to develop mapping strategies that can map knowledge models to genetic data. To address both issues, we propose to use query building tools such as the Askomics (https://github.com/askomics/askomics) tool in development by Dyliss. Askomics supports both the integration of tabulated data into an RDF triplestore, and an intuitive interface for generating SPARQL queries in order to analyze them in combination with domain ontologies. Based on this approach, the first step of the project will be to integrate and standardize all genomic data produced in the project, and to link these datasets with external disease and pathway databases. The next step will be to extract for the local RDF database suitable gene-dependencies networks that will be used as a-priori knowledge for statistical methods. As a final step, the post-doc will represent the mapping between variants and regulated genes by taking into account additional genomic information. YOUR PROFILE PhD in Computer Science, Bioinformatics, Computational Biology or a related field Previous work on ontologies or semantic web technologies for genomic data would be a plus. Alternatively, an expertise in genomic sequence analysis (SNP, variants) would be highly appreciated. Strong relational skills to interact with professionals from various backgrounds. Ability to synthesize informations from different sources Excellent written and oral communication skills Starting date: Around November 2017 Duration: 18 months CONTACTS Olivier Colliot - Olivier.Colliot at upmc.fr Ivan Moszer – i.moszer-ihu at icm-institute.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From geirksa at ifi.uio.no Mon Feb 27 10:04:16 2017 From: geirksa at ifi.uio.no (Geir Kjetil Sandve) Date: Mon, 27 Feb 2017 10:04:16 +0100 Subject: [SocBiN] Postdoc position in Oslo: methodology for integrative epigenomics Message-ID: <7F1B885A-30F0-40B2-AF53-190063D3EA54@ifi.uio.no> Postdoc position in Oslo on development of computational methodology for integrative epigenomics: https://www.jobbnorge.no/en/available-jobs/job/134291/postdoctoral-research-fellowship-in-bioinformatics The position is associated with both the department of biology and computer science at the university of Oslo, allowing a suited candidate to interact with strong environments in both fields when developing her/his unique competence and contributions. Application deadline is March 7. best regards, .. Geir Kjetil Sandve From gemma.atkinson at gmail.com Tue Feb 28 09:05:08 2017 From: gemma.atkinson at gmail.com (Gem Atkinson) Date: Tue, 28 Feb 2017 09:05:08 +0100 Subject: [SocBiN] =?utf-8?q?Post_doc_position_in_Ume=C3=A5_University=2C_S?= =?utf-8?q?weden?= Message-ID: <59EF1DA3-665F-4AC7-A270-775BFDEAA05C@gmail.com> There is a post doc position available in the lab of Vasili Hauryliuk, MIMS Nordic EMBL, Umeå University, Sweden: http://www.ucmr.umu.se/images/postdoc2017/Hauryliuk.pdf http://www.mims.umu.se/groups/vasili-hauryliuk.html The project is on small alarmone ((p)ppGpp) syntetase enzymes in bacteria, and their recently discovered regulation by RNA (Beljantseva et al. PNAS, in press). These enzymes are important for many aspects of bacterial physiology, and response to stress including antibiotic challenges. The project is open ended, and can be either web lab based, or computer based (including comparative genomics and phylogenetics). Bioinformatic investigations would be co-supervised by me (http://www.molbiol.umu.se/english/research/researchers/gemma-atkinson/ ). Contact: vasili.hauryliuk at umu.se Please spread the word! Best wishes, Gemma C. Atkinson Umeå Centre for Microbial Research (UCMR) Department of Molecular Biology Umeå University, Sweden -------------- next part -------------- An HTML attachment was scrubbed... URL: