From biotop at boku.ac.at Fri Oct 9 10:58:49 2015 From: biotop at boku.ac.at (Office BioTop) Date: Fri, 09 Oct 2015 10:58:49 +0200 Subject: [SocBiN] PhD student position in Bioinformatics (BOKU Vienna, Austria) Message-ID: <56179DE9020000C6000158A3@gwia2.boku.ac.at> PhD student position: Genomic and epigenomic analysis of a plant-based expression platform for recombinant glycoproteins This project is offered within the framework of the International PhD Program „Biomolecular Technology of Proteins – BioToP” at BOKU - University of Natural Resources and Life Sciences, Vienna, Austria. Project description The tobacco-related plant species Nicotiana benthamiana is emerging as a promising host for the rapid, versatile and safe production of biopharmaceuticals. Furthermore, N. benthamiana lines have been established which permit the production of recombinant glycoproteins with customized N- and O-glycan structures and thus superior biological activities. The project will focus on a detailed genomic and epigenomic analysis of a glycoengineered N. benthamiana line optimized for the production of recombinant proteins and its comparison with wild-type plants. NGS libraries will be generated from genomic DNA and mRNA isolated from leaves and other organs. Computational analysis of the data obtained with these sequencing libraries will then involve mapping of read-pairs against the Nb-1 draft genome, with the aim of assessing the genetic differences existing between Nb-1 and glycoengineered N. benthamiana, as well as its progenitor line. For once, this information can be used to reconstruct the genome sequence of glycoengineered N. benthamiana. Secondly, these studies will yield a comprehensive assessment of the genomic status of the currently most frequently used N. benthamiana production line and reveal any genetic or epigenetic alterations incurred during its generation. Special attention will be paid to the identification and transcriptional activity of genes encoding cysteine and serine proteinases, since degradation of recombinant proteins in planta is largely due to members of these protease families. Particular emphasis will be also placed on the characterization of the N. benthamiana complement of glycosyltransferases, glycosidases and prolyl hydroxylases whose activities could potentially lead to the formation of non-human N- and O-glycan structures or other protein modifications on biotherapeutics. Altogether, the outcomes of this project will provide a powerful resource for the further development of this attractive new expression platform. Required skills and qualifications We are looking for a graduate student with a Master´s degree in bioinformatics or in a related field, solid programming skills (e.g. developing sequence analysis tools), experience with the analysis of NGS data sets, understanding of lab methods and knowledge of genomics/transcriptomics. For more detailed information about the project and the PhD program BioToP please visit http://biotop.boku.ac.at Application The PhD Program BioToP will only consider applications that are submitted using the official BioToP application forms. No other forms of applications will be accepted. For application guidelines and download of forms please visit http://biotop.boku.ac.at. Application Deadline: 31.10.2015 PhD Programme BioToP "Biomolecular Technology of Proteins" BOKU - University of Natural Resources and Applied Life Sciences Muthgasse 18 A-1190 Vienna Email:biotop at boku.ac.at Web: http://biotop.boku.ac.at -------------- next part -------------- An HTML attachment was scrubbed... URL: From rune.linding at gmail.com Fri Oct 9 11:31:47 2015 From: rune.linding at gmail.com (Rune Linding) Date: Fri, 9 Oct 2015 11:31:47 +0200 Subject: [SocBiN] Fwd: uli stelzl: post doc position to announce In-Reply-To: <1444207065043.44923@uni-graz.at> References: <1444207065043.44923@uni-graz.at> Message-ID: ---------- Forwarded message ---------- From: Stelzl, Ulrich (ulrich.stelzl at uni-graz.at) Date: Wed, Oct 7, 2015 at 10:37 AM Subject: uli stelzl: post doc position to announce To: "stelzl at molgen.mpg.de" Dear colleagues and friends, I am starting to set up a new lab in Graz, Austria, and have a postdoc position to announce. Maybe you can post the advertisement, distribute it otherwise or target it towards potential candidates. My apologies for abusing my “collected emails” folder. Best regards Uli ---------------------------------------------------------------------------------------------- Ulrich STELZL University of Graz Institute of Pharmaceutical Sciences (IPW) Pharmaceutical Chemistry Universitätsplatz 1/I A-8010 Graz, Austria phone: +43(0)316380-5397 e-mail: ulrich.stelzl at uni-graz.at http://pharmazie.uni-graz.at/en/research/pharmaceutical-chemistry/network-pharmacology-stelzl/ ---------------------------------------------------------------------------------------------- -- Best wishes, Prof Dr Rune Linding Slotsvej 84B - DK-2920 Charlottenlund, Denmark Mobile: +45 2365 1941 Phone: +45 3940 1941 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: PostdocPosition-Graz-AT.pdf Type: application/pdf Size: 31341 bytes Desc: not available URL: From Carsten.Daub at ki.se Mon Oct 12 20:50:00 2015 From: Carsten.Daub at ki.se (Carsten Daub) Date: Mon, 12 Oct 2015 18:50:00 +0000 Subject: [SocBiN] Fwd: ZENCODE-ITN PhD position In-Reply-To: References: Message-ID: Begin forwarded message: From: Juanma Vaquerizas > Date: 12 October 2015 at 17:41:50 CEST To: Juanma Vaquerizas > Subject: ZENCODE-ITN PhD position Reply-To: > Dear friends and colleagues (apologies for multiple posting), I'd be grateful if you could please distribute the following PhD position opening in my lab: http://www.mpi-muenster.mpg.de/186318/job_full_offer_9665647?c=78621 We are looking for an outstanding fellow to work on mobile genetic elements and zebrafish development using genomic approaches. Please feel free to distribute to anyone that you think might be interested. Thank you in advance. Best wishes, Juanma -- Dr Juan M Vaquerizas Max Planck Research Group Leader Max Planck Institute for Molecular Biomedicine Röntgenstraße 20 48149 Münster Germany http://www.vaquerizaslab.org Phone: +49 251 70365-580 Fax: +49 251 70365-599 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 15-2015_ZENCODE-ITN_PhD_Vaquerizas.pdf Type: application/pdf Size: 111012 bytes Desc: 15-2015_ZENCODE-ITN_PhD_Vaquerizas.pdf URL: -------------- next part -------------- An HTML attachment was scrubbed... URL: From henrik.lantz at bils.se Wed Oct 14 13:45:02 2015 From: henrik.lantz at bils.se (Henrik Lantz) Date: Wed, 14 Oct 2015 13:45:02 +0200 Subject: [SocBiN] Genome Assembly and Metagenomics courses in Uppsala, Sweden Message-ID: <88CE398F-5C98-4B4A-ACD5-A7EA0CBFD994@bils.se> Dear all, SciLifeLab in Sweden offers two courses in November that also are open to non-Swedish participants. Both courses are aimed at PhD-students, post docs, or other researchers that already have experience working in Linux command line but have no experience in the specific fields. Both courses include lectures as well as computer exercises. The first course is on Genome Assembly 16-17 Nov, deadline Oct 19. Please see https://www.scilifelab.se/events/assembly-ht2015/ for details. The second course is on Metagenomics 24-25 Nov, deadline Oct 27. Please see https://www.scilifelab.se/events/metagenomics-1-hp-2/ for details. The number of positions are limited and will be offered on a first-come first-serve basis. Best regards, Henrik Henrik Lantz NGS-coordinator, BILS Uppsala, Sweden From rune.linding at gmail.com Sat Oct 17 10:46:20 2015 From: rune.linding at gmail.com (Rune Linding) Date: Sat, 17 Oct 2015 10:46:20 +0200 Subject: [SocBiN] Fwd: PhD positions within ITN Marie Curie Training Network at RWTH Aachen In-Reply-To: <694EA15B-76BF-4836-A719-889B77064F0B@combine.rwth-aachen.de> References: <694EA15B-76BF-4836-A719-889B77064F0B@combine.rwth-aachen.de> Message-ID: ---------- Forwarded message ---------- From: Saez Rodriguez, Julio Dear Friends and Colleagues, As part of the just launched Interdisciplinary Training Network SymBioSys, we have two MARIE-CURIE Early Stage Researcher positions at the Joint Research Center for Computational Biomedicine, RWTH Aachen University. These fellows will have excellent salaries according to EU regulations and will be involved in a Marie-Curie network with excellent opportunities for scientific and personal development, including funding for short stays at top-class research groups and regular training events and meetings across Europe. Candidates should a strong background in mathematical modeling and/or scientific computing. Previous experience in applications to biology will be appreciated. Candidates with a background in engineering, bioinformatics, applied mathematics or physics are especially encouraged to apply. Candidates should (i have) less than 4 years of experience, (ii) should not have a PhD, (iii) any nationality, but must not have resided or carried out their main activity in the country of the host institution (Germany) for more than 12 months in the 3 years prior to their recruitment. One fellow will work on hybrid networks combining signaling, regulatory, and metabolic networks, and the other on the identification of both structure and parameters of large signalling models. More information here: http://www.combine.rwth-aachen.de/index.php/news/12.html I would be very grateful if you could forward this message to people that might be interested and post it within your institutions. Many thanks in advance. Best, Julio Joint Research Centre for Computational Biomedicine (JRC-COMBINE) RWTH Aachen University, Faculty of Medicine MTI2 Wendlingweg 2 D-52074 Aachen | Tel: +49 2418089347 saezrodriguez at combine.rwth-aachen.de | www.combine.rwth-aachen.de Admin: Gabi Lützeler- gluetzeler at ukaachen.de | Tel: +49 2418089-337 -- Best wishes, Prof Dr Rune Linding Slotsvej 84B - DK-2920 Charlottenlund, Denmark Mobile: +45 2365 1941 Phone: +45 3940 1941 -------------- next part -------------- An HTML attachment was scrubbed... URL: From mikael.borg at bils.se Wed Oct 21 14:57:38 2015 From: mikael.borg at bils.se (mikael borg) Date: Wed, 21 Oct 2015 14:57:38 +0200 Subject: [SocBiN] BILS Annual Symposium and User Meeting in Stockholm 12 Nov 2015 Message-ID: <56278BC2.7020300@bils.se> BILS (Bioinformatics Infrastructure for Life Sciences) is a distributed national research infrastructure supported by the Swedish Research Council (Vetenskapsrådet) providing bioinformatics support to life science researchers in Sweden. The fourth annual BILS symposium and user meeting will take place Nov 12 in Stockholm. Theme: Big Data / Data Integration / Data Access Time: Thursday 12 November from 10h00 to 16h00 Location: Gardaulan at Folkhälsomyndigheten, Nobels väg 18, Stockholm Keynote speakers: Mauno Vihinen, Lund University Samuli Ripatti, Institute for Molecular Medicine Finland (FIMM) Jens Nielsen, Chalmers The symposium is free of charge. Please register before Friday Nov 6 at: https://bils.se/div/symposium-2015.html Welcome! -- Mikael Borg, PhD technical coordinator BILS - Bioinformatics Infrastructure for Life Sciences - https://bils.se ORCiD: 0000-0002-0646-4231 e-mail: mikael.borg at bils.se phone: +46-(0)76-306 50 80 address: SciLifeLab, Box 1031, 171 21 Solna, Sweden -------------- next part -------------- A non-text attachment was scrubbed... Name: BILS Annual Symposium 2015.pdf Type: application/pdf Size: 99332 bytes Desc: not available URL: From jolepp at utu.fi Fri Oct 23 10:00:22 2015 From: jolepp at utu.fi (=?iso-8859-1?Q?Johanna_M=E4kel=E4?=) Date: Fri, 23 Oct 2015 08:00:22 +0000 Subject: [SocBiN] Open Early stage researcher position in ENLIGHT-TEN consortium Message-ID: <42AD353ABD93C148B60CE22D5E09BE87564531DE@exch-mbx-03.utu.fi> Dear members of SocBiN, We are looking for a talented early stage researcher with strong computational background for a fixed 3-year position. Feel free to distribute the announcement to potential candidates. Thank you! Sincerely, Johanna Mäkelä -- Johanna Mäkelä, PhD Research coordinator Computational biomedicine Turku Centre for Biotechnology University of Turku Tykistökatu 6 FI-20520 Turku Finland -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Open_PhD_student_position.pdf Type: application/pdf Size: 103142 bytes Desc: Open_PhD_student_position.pdf URL: From jolepp at utu.fi Fri Oct 23 10:02:31 2015 From: jolepp at utu.fi (=?iso-8859-1?Q?Johanna_M=E4kel=E4?=) Date: Fri, 23 Oct 2015 08:02:31 +0000 Subject: [SocBiN] Open Early stage researcher position in ENLIGHT-TEN consortium Message-ID: <42AD353ABD93C148B60CE22D5E09BE87564531F7@exch-mbx-03.utu.fi> Dear members of SocBiN, We are looking for a talented early stage researcher with strong computational background for a fixed 3-year position. Feel free to distribute the announcement to potential candidates. Thank you! Sincerely, Johanna Mäkelä -- Johanna Mäkelä, PhD Research coordinator Computational biomedicine Turku Centre for Biotechnology University of Turku Tykistökatu 6 FI-20520 Turku Finland -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Open_PhD_student_position.pdf Type: application/pdf Size: 103142 bytes Desc: Open_PhD_student_position.pdf URL: From arne at bioinfo.se Mon Oct 26 06:27:55 2015 From: arne at bioinfo.se (Arne Elofsson) Date: Sun, 25 Oct 2015 22:27:55 -0700 Subject: [SocBiN] Fwd: Post Doc Position - Structural Bioinformatics In-Reply-To: References: Message-ID: From: Charlotte Deane Dear all, I am writing to let you know that I am currently advertising for a Postdoctoral Researcher in Structural Bioinformatics. The project will focus on how protein structure prediction could benefit from incorporating information about the biological environment and process of production of proteins in the cell. We aim to both increase our understanding of the natural process of protein folding and identify which parts of the process can most easily and most beneficially be incorporated into protein structure prediction. Further particulars, containing details of the application procedure and duties, may be obtained from https://www.stats.ox.ac.uk/vacancies/?a=13654 Please feel free to send this onto colleagues or associates who may be interested in the post. The closing date for applications is 12:00 noon (UK time) Monday 20th November 2015. Should you have any questions please do not hesitate to contact me. Best wishes Charlotte Professor Charlotte Deane Professor of Structural Bioinformatics & Head of Department, Department of Statistics University of Oxford, 1 South Parks Road, Oxford, OX1 3TG Head of the Oxford Protein Informatics group Website: http://opig.stats.ox.ac.uk/ PA Madeline Mitchell: mitchell at stats.ox.ac.uk (email)| +44 1865 282857 (tel) -------------- next part -------------- An HTML attachment was scrubbed... URL: