From coordinator at rth.dk Wed Aug 14 15:01:08 2013 From: coordinator at rth.dk (Betina Wingreen Jensen) Date: Wed, 14 Aug 2013 15:01:08 +0200 Subject: [SocBiN] Available Phd Position in RNA Bioinformatics at the RTH Center Message-ID: <002201ce98ee$58011f30$08035d90$@rth.dk> Dear Colleague, The RTH center in Copenhagen is inviting applications for a PhD position in Bioinformatics, and we are looking for a person to join our team from September, or soon thereafter. The position is for three years. Application deadline is 25th August 2013. For more information about the RTH center visit http://rth.dk. For full posting and online application procedure visit http://jobbank.ku.dk/job/395276/koebenhavns-universitet/phd-fellowship-in-rn a-bioinformatics. Please pass the mail on to qualified students or people you think could be otherwise interested. Background: Non-coding RNAs (ncRNAs) have been established as a highly abundant class of genes which play numerous important roles in the cell and in disease. These ncRNAs often contain RNA structure either for the entire sequence or sometimes as minor "domains". In RTH we have developed a range of computational tools for the analysis of both structured RNAs and high-throughput data. Job description: Within RTH material has been collected for a range of diseases and will be combined with in silico generated information of structured RNA and a range of information such as expression and (protein and RNA) binding generated from predictions and experiments. A key goal of the project is to filter and rank selected candidates for detailed molecular functional analysis with respect to the disease samples. Pipelines for expression analysis, data integration and statistical analysis will be developed within the project. Qualification and requirements: The applicant should hold professional as well as personal skills and qualifications as stated below: . A master degree in bioinformatics, computational biology, computer science or similar. . Very strong experience with script languages such as Perl or Python (or similar). . Strong experience with the linux/unix environment, command lines and shell scripting. . Experience with statistical analysis. . Differential expression analysis (with background correction / multiple testing). . Possess good interpersonal skills. . Be excellent in English, writing and speech. In addition to the above, weight will be given to applicants meeting one or more of the following requirements: . General knowledge about RNA structure folding algorithms. . C or C++. On behalf of Professor Jan Gorodkin ( gorodkin at rth.dk). With best wishes, Betina -- Betina Wingreen Jensen Scientific and Administrative Coordinator Center for non-coding RNA in Technology and Health Department of Veterinary Clinical and Medical Sciences Faculty of Health and Medical Sciences University of Copenhagen Groennegaardsvej 3 1870 Frederiksberg Denmark Phone: +45 353 34704 -------------- next part -------------- An HTML attachment was scrubbed... URL: From rune.linding at gmail.com Tue Aug 13 09:55:43 2013 From: rune.linding at gmail.com (Rune Linding) Date: Tue, 13 Aug 2013 09:55:43 +0200 Subject: [SocBiN] FINAL ANNOUNCEMENT - REGISTER NOW - ICSB 2013 - OUTSTANDING PROGRAM Message-ID: ICSB 2013 - FANTASTIC PROGRAM - REGISTER NOW - Please FWD [image: Inline image 1] *The 14th International Conference on Systems Biology* *Copenhagen, Denmark* *30 August - 3 September, 2013* *Sponsored by* The International Conference on Systems Biology (ICSB) is the main event for the systems biology community. The 14th International Conference on Systems Biology continues an annual series of conferences launched by the International Society of Systems Biology (ISSB) in Tokyo in 2000. It attracts scientists from all over the world. The conference brings together interdisciplinary researchers in order to advance biomedical research, health care, and drug development: http://icsb2013.dk/ The programme features an outstanding lineup of confirmed high-profile speakers and includes plenary lectures, parallel sessions, poster display, and workshops. The programme can be downloaded here: http://icsb2013.dk/images/Media/pdf/icsb2013_programme.pdf * Keynote speakers* Gene Myers, DE (confirmed) ? Stuart Kauffman, USA (confirmed) ? Kim Sneppen, DK (confirmed) ? Jennifer Lippincott-Schwartz, USA (confirmed) ? Wendell Lim, USA (confirmed) ? Bernhard Palsson, DK (confirmed) ? Anne-Claude Gavin, DE (confirmed) ? Lars Steinmetz, DE (confirmed) ? Doug Lauffenburger, USA (confirmed) ? Ruedi Aebersold, CH (confirmed) ? Marc Vidal, USA (confirmed) ? Chris Voigt, USA (confirmed) ? Matthias Mann, DE (confirmed) ? Peer Bork, DE (confirmed) ? Philippe Bastiaens, DE (confirmed) ? Alexander van Oudenaarden, NL (confirmed) ? Rama Ranganathan, USA (confirmed) ? Dana Pe'er, USA (confirmed) ? Levi Garraway, USA (confirmed) ? Ben Neel, CA (confirmed) ? Elaine Mardis, USA (confirmed) ? -------------- next part -------------- An HTML attachment was scrubbed... URL: From Erik.Bongcam at slu.se Thu Aug 22 11:13:12 2013 From: Erik.Bongcam at slu.se (Erik Bongcam-Rudloff) Date: Thu, 22 Aug 2013 09:13:12 +0000 Subject: [SocBiN] EMBnet.journal: new issue Message-ID: <30E84EF44125A849BFC3A59CF1CBD79128D8B8E2@exchange2-1> Readers: EMBnet.journal has just published its latest issue at http://journal.embnet.org/index.php/embnetjournal/issue/view/74. We invite you to visit the journal site to review articles and items of interest. Thanks for the continuing interest in our work, Erik Bongcam-Rudloff Swedish University of Agricultural Sciences, Uppsala Phone +4618672121 erik.bongcam at slu.se -------------------------------------------------------------------------------------------------------------- EMBnet.journal Vol 19, No 1 ARTICLES Letters to the Editor -ISBE ? set out for a Systems Biology Infrastructure for Europe , Susanne Hollmann, Vitor AP Martins dos Santos, Babette Regierer -MIRRI - The Microbial Resource Research Infrastructure: managing resources for the bio-economy, Manuela Sch?ngel, Erko Stackebrandt, Chantal Bizet,David Smith Technical Notes -Quick Direct-method Controlled (QDC): a simulator of metabolic experiments . Davide Cangelosi, Salvatore Fabbiano, Claudio Felicioli, Luca Freschi, Roberto Marangoni REPORTS, -The Global Organisation for Bioinformatics Learning, Education & Training (GOBLET), GOBLET Consortium -Sino-Swiss Workshop on Bioinformatics, Jingchu Luo -ICT needs and challenges for Big Data in the Life Sciences. A workshop report - SeqAhead/ISBE Workshop in Pula, Sardinia, Italy, 6 June 2013, Babette Regierer, Luca Pireddu, Martijn Mon?, Andreas Gisel ISB Spotlight Spring 2013, Protein Spotlight 149 and more. From arne at bioinfo.se Fri Aug 23 13:06:50 2013 From: arne at bioinfo.se (Arne Elofsson) Date: Fri, 23 Aug 2013 13:06:50 +0200 Subject: [SocBiN] Fwd: SciLifeLab is recruiting 8 leading positions In-Reply-To: <855B3C9A-9110-465D-875E-9AC66A3C296B@scilifelab.se> References: <855B3C9A-9110-465D-875E-9AC66A3C296B@scilifelab.se> Message-ID: Dear colleagues please help spreading this information. These are very well funded positions, so we would very much ask you best posdocs/young PIs to apply. Please note that the deadline for the positions at Stockholm University (RNA biology and Ecological Genomics) is Sept 10. Yours Arne * *----------------------------------------- Arne Elofsson Science for Life Laboratory Tel:+46-(0)852481531 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 ---------- Forwarded message ---------- From: Mikaela Friedman Date: Fri, Aug 23, 2013 at 12:54 PM Subject: SciLifeLab is recruiting 8 leading positions To: Adnane Achours , Afshin Ahmadian < afshin.ahmadian at scilifelab.se>, Anders Andersson < Anders.andersson at scilifelab.se>, Bj?rn Andersson < bjorn.andersson at scilifelab.se>, Helene Andersson Svahn < helene.andersson-svahn at biotech.kth.se>, Lars Arvestad < lars.arvestad at scilifelab.se>, Helena Berglund , Hjalmar Brismar , Jens Carlsson < jens.carlsson at scilifelab.se>, Arne Elofsson , Olof Emanuelsson , Lars Engstrand < lars.engstrand at scilifelab.se>, Thomas Helleday < thomas.helleday at scilifelab.se>, Berk Hess , Lukasz Huminiecki , Annika Jenmalm Jensen < Annika.Jenmalm-Jensen at ki.se>, Lukas K?ll , Juha Kere , Jens Lagergren , Janne Lehti? , Erik Lindahl < erik.lindahl at scilifelab.se>, Emma Lundberg , Joakim Lundeberg , Jan Mulder < jan.mulder at scilifelab.se>, Mats Nilsson , Peter Nilsson , Jacob Odeberg < jacob.odeberg at scilifelab.se>, Bj?rn ?nfelt , Bengt Persson , Aman Russom , Peter Savolainen , Jochen Schwenk < jochen.schwenk at scilifelab.se>, Erik Sonnhammer < erik.sonnhammer at scilifelab.se>, Jussi Taipale , Mathias Uhl?n , Gunnar von Heijne < gvheijne at mac.com>, Anna Wedell , Roman Zubarev < Roman.Zubarev at ki.se>, Sara Light , H?kan J?nsson < hakan.jonsson at scilifelab.se> Cc: Fredrik Sterky Dear SciLifeLab PIs As you might have seen and heard already, SciLifeLab is looking to recruit 8 research group leaders, two at each of the host universities. We would be grateful if you can spread this information to your colleagues and network in Sweden and abroad. See below a text and ad that you can forward. With Kind Regards, Mikaela --------- I wish to inform you that SciLifeLab, a center for molecular biosciences with the focus on health and environmental research in Sweden, now is looking to recruit 8 excellent research group leaders. The positions are within the fields; Biomedical Sciences, Microbial Bioenergy Production, Applied Physics, Ecological Genomics, RNA biology, Molecular Medicine and Molecular Biosciences. Last day of application is September 10. To find out more about the research group leader positions please visit: http://www.scilifelab.se/index.php?content=research_group_leader_positions Please spread this information to your colleagues. ---------------------------------------------------------------------------- Mikaela Friedman, PhD Head of scientific communications and external relations Science for Life Laboratory (SciLifeLab Stockholm) Box 1031 171 21 Solna Phone: +46-8-52481510 Email: mikaela.friedman at scilifelab.se Visiting address: Tomtebodav?gen 23 171 65 Solna ---------------------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: SciLifeLab_AD_254x178_low_res_FINAL (2).pdf Type: application/pdf Size: 547926 bytes Desc: not available URL: From repsilber at fbn-dummerstorf.de Wed Aug 28 17:23:43 2013 From: repsilber at fbn-dummerstorf.de (Dirk Repsilber) Date: Wed, 28 Aug 2013 17:23:43 +0200 Subject: [SocBiN] PhD position, Dept of Bioinformatics and Biomathematics, Leibniz-Institute for Farm Animal Biology (near Rostock, Germany) [Scanned] Message-ID: <13a37b6e-e96f-4bba-9ef3-c75aa5aedf47@URANUS3.fbn-dummerstorf.de> Dear Bioinformaticians, at the Department forBiomathematics and Bioinformatics at the Leibniz Institute for Farm Animal Biology inDummerstorf (nearRostock), Germany, a *three-year PhD position* with focus on statistical genetics, quantitative genetics, biomathematics and statistical modelingis available -> http://www.fbn-dummerstorf.de/images/Stellen/en/2013-21_FB%2020_Doc_NG-Wittenburg_engl%20VfG.pdf please forward to the interested candidates! Thanks for your consideration, sincerely Dirk. -- ______________________________________________________ Dr. Dirk Repsilber Functional Bioinformatics School of Health and Medical Sciences University of ?rebro S - 701 82 ?rebro Sweden phone: +46 19 30 1256 mobil: +46 72 0131547 ______________________________________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: From andre.juffer at oulu.fi Thu Aug 29 10:19:03 2013 From: andre.juffer at oulu.fi (Andre Juffer) Date: Thu, 29 Aug 2013 08:19:03 +0000 Subject: [SocBiN] (no subject) Message-ID: <8747F2213126EF46887B3D6FB0F7B72F581767@nippu1.univ.yo.oulu.fi> Dear All, there are a number of PhD student positions available in Oulu, Finland: http://www.oulu.fi/uniogs/dppositionscall http://www.oulu.fi/biocenter/open-call-bco-dp I would like to draw attention specifically to a PhD student position in the biocomputing group: http://www.oulu.fi/biocenter/bco-dp-call-b/b1 The area of research is structural bioinformatics with a touch of system biology and also molecular simulations. To apply, please follow the guideline at Best regards, Andr? ------------------------------------------------------------------------------------------------------------------------------ Andre H. Juffer Biocenter Oulu and Department of Biochemistry University of Oulu, Finland Phone: +358-294-481161 Email: andre.juffer at oulu.fi WWW: www.biochem.oulu.fi/Biocomputing/ www.oulu.fi/biocenter/biocomputing-and-bioinformatics www.oulu.fi/biocenter/groups/juffer StrucBioCat, www.strucbiocat.oulu.fi Triacle Biocomputing, www.triacle-bc.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From ola.spjuth at farmbio.uu.se Thu Aug 29 13:20:54 2013 From: ola.spjuth at farmbio.uu.se (Ola Spjuth) Date: Thu, 29 Aug 2013 13:20:54 +0200 Subject: [SocBiN] Open position: Chemoinformatics Scientist at Karolinska Institutet, Stockholm Message-ID: Link to ad: https://ki.mynetworkglobal.com/what:job/jobID:24447/where:4/ Chemoinformatics Scientist Karolinska Institutet, Institutionen f?r medicinsk biokemi och biofysik (MBB) Division Chemical Biology Consortium Sweden (CBCS) are looking for a highly motivated and talented Cheminformatics Scientist to support and coordinate a wide scope of research informatics applications and data analysis at our Stockholm facilities. Duties The desired candidate will have a demonstrated track record in managing large volumes of scientific data in support of basic research and/or drug discovery projects and should have significant experience with in-house and commercial software solutions that facilitate data capture, analysis and visualization in small molecule research and drug design. Responsibilities include: Evaluation and implementation of a nationally encompassing chemoinformatics system for the SciLifeLab community. Maintainance, configuration, monitoring, and/or troubleshooting scientific applications and underlying software. Partnering and interaction with software vendors and external professional service staff to resolve issues and implement enhancements. Assist scientists from multiple disciplines with data capture, analysis, visualization. Entry requirements The credentials required for a position as a senior research fellow/assistant professor include a PhD or equivalent scientific competence, as well as documented postdoc research work. Pedagogical competence or some other form of professional competence that is relevant to the duties associated with the position may also be required. Eligible applicants will have a strong, documented background in chemoinformatics management and/or computational chemistry. Desired qualifications: An MS or PhD in a relevant scientific/technical discipline (Chemistry, Biology or Computer Science), working in the biotech/pharmaceutical industry or relevant academic research. Familiar with relational database management, chemistry registration, microtiterplate-based data generation and capture and electronic lab notebooks. Knowledge and experience with the latest cheminformatics tools, including commercial software packages, eg Dotmatics, ChemAxon, Spotfire, Pipeline Pilot, PE Ensemble, CDD etc. Experience in managing Oracle/SQL relational database schemas. Capable in script-based programming (eg Python) Working knowledge of modern aspects of computational chemistry in basic research. Excellent written and oral communication skills in Swedish and English are required, as is the desire and ability to work in a multidisciplinary, fast-paced environment and contribute to team-based decisions with a distinct quality- and results-focus. -- Ola Spjuth, PhD Department of Pharmaceutical Biosciences and Science for Life Laboratory Box 541, Uppsala University Sweden Email: ola.spjuth at farmbio.uu.se Ph: +46 (0)70 425 06 28 Web: http://www.farmbio.uu.se/research/researchgroups/pb/olaspjuth/ SciLifeLab: http://www.scilifelab.se UPPMAX: http://www.uppmax.uu.se UPPNEX: https://www.uppnex.uu.se -------------- next part -------------- An HTML attachment was scrubbed... URL: From arne at bioinfo.se Fri Aug 30 10:01:54 2013 From: arne at bioinfo.se (Arne Elofsson) Date: Fri, 30 Aug 2013 10:01:54 +0200 Subject: [SocBiN] Well funded Assistant professor Positions at SciLifeLab in Stockholm/Uppsal Message-ID: Dear friends please spread the news about the following positions assistant professor positions. For a long time there have been too many internal candidates recruited in Sweden, let us try to change this. These are (for Swedish standards) extremely well funded and tenure-track. Applicants must have obtained their PhD within the last seven years. At *Karolinska Institutet*: two positions in "*Biomedical Sciences*" (i.e. anything): https://ki.mynetworkglobal.com/en/what:job/jobID:24298/where:4/ at *KTH*: One position in *Mirobial Energy production* http://www.kth.se/en/om/work-at-kth/vacancies/assistant-professor-in-microbial-bioenergy-production-1.397383 One position in * Applied Physics* (e.g bioimaging) http://www.kth.se/en/om/work-at-kth/vacancies/assistant-professor-in-applied-physics-1.397367 at *Stockholm University:* One position in *RNA Biology * http://www.su.se/english/about/vacancies/lecturers-researchers/assistant-professor-in-rna-biology-1.139360 One position in *Ecological Genomics * http://www.su.se/english/about/vacancies/lecturers-researchers/assistant-professor-in-ecological-genomics-1.139344 at *Uppsala University* One position in *Molecular Biosciences* http://www.uu.se/jobb/?languageId=1b/teacher/annonsvisning?languageId=1&tarContentId=249912 One position in *Molecular Medicine * http://www.uu.se/jobb/?languageId=1b/teacher/annonsvisning?languageId=1&tarContentId=249912 All deadlines are Sept 10, I think Yours Arne * *----------------------------------------- Arne Elofsson Science for Life Laboratory Tel:+46-(0)852481531 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: From arne at bioinfo.se Fri Aug 30 15:11:47 2013 From: arne at bioinfo.se (Arne Elofsson) Date: Fri, 30 Aug 2013 15:11:47 +0200 Subject: [SocBiN] Fwd: Post-doctoral candidate wanted CNRS Lille In-Reply-To: <20130830114623.GA20019@lensink.iri.univ-lille1.fr> References: <20130830114623.GA20019@lensink.iri.univ-lille1.fr> Message-ID: Yours Arne * *----------------------------------------- Arne Elofsson Science for Life Laboratory Tel:+46-(0)852481531 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 ---------- Forwarded message ---------- From: Marc Lensink Date: Fri, Aug 30, 2013 at 1:46 PM Subject: Fwd: Post-doctoral candidate wanted CNRS Lille To: marc.lensink at iri.univ-lille1.fr Cc: marc.aumercier at iri.univ-lille1.fr Dear colleagues, please be advised that this call is still open and will remain so until the third week of September. Please make suitable candidates aware of this excellent opportunity! Thanks, Marc Lensink ----- Forwarded message ----- Subject: post-doctoral candidate wanted dear Friends and Colleagues, I would appreciate if you could make suitable candidates aware of the following call. We are looking for an excellence-level post-doctoral candidate with at least 18 months of post-doctoral experience coming October. many thanks in advance! Marc CALL FOR POST-DOCTORAL CANDIDATE We are looking for a post-doctoral candidate to work on a computational project in cancer research. The successful candidate will participate in a regional grant proposal of which the deadline is October 22nd, 2013. The targeted starting date is March/April 2014, at which date the candidate must be no older than 35 years and have at least two years of post-doctoral experience, preferably outside of France. Scientific excellence is sought and the successful candidate will be offered a 18- or 24-month contract with a highly competitive salary. The project evolves around the Ets-1 oncoprotein, a transciption factor that regulates many genes involved in cancer progression and tumor invastion. We identified and purified novel interaction partners, including two DNA repair enzymes. Our work highlights that the interaction between Ets-1 and both DNA repair enzymes is important for the cancer cell. The three-dimensional structures of the interacting partner domains are known and we aim at using protein docking and molecular modeling to sketch a molecular picture in order to increase our understanding of these important biological interactions and design mutagenesis experiments. If granted, the candidate will join my team of Computational and Theoretical Molecular Biology at the French CNRS Interdisciplinary Research Institute in the Lille area (north of France), and work in close collaboration with the experimental team of Marc Aumercier. Lille is a vibrant and dynamic region, with 35% of the population under 25, and the heart of the Eurometropole Lille-Kortrijk-Tournai, counting close to 2 million inhabitants. It features high-speed train connections to Brussels, Paris and London. The call will remain open until end of August, 2013, or when a suitable candidate has been identified. Informal questions may be directed to dr. Marc Aumercier (marc.aumercier at iri.univ-lille1.fr), or dr. Marc Lensink (marc.lensink at iri.univ-lille1.fr). ----- End forwarded message ----- -- Marc F. Lensink, CR1, PhD Interdisciplinary Research Institute (IRI) - USR3078 CNRS Computational Biology marc.lensink at iri.univ-lille1.fr Parc de la Haute Borne, 50 Avenue de Halley, BP 70478 F-59658 Villeneuve d'Ascq, France tel: +33 3 62 53 17 28 fax: +33 3 62 53 17 01 -------------- next part -------------- An HTML attachment was scrubbed... URL: