From lisa.klasson at icm.uu.se Thu Jun 5 09:17:57 2014 From: lisa.klasson at icm.uu.se (Lisa Klasson) Date: Thu, 5 Jun 2014 09:17:57 +0200 Subject: [SocBiN] 2 open PhD positions in genomics at Uppsala University Message-ID: <77B1EDA8-D05E-4691-BB57-403336663A5E@icm.uu.se> 2 PhD-positions in genomics are available in the program of Molecular Evolution, Department of Cell and Molecular Biology, Uppsala University: 1. Functional and evolutionary genomics of symbiotic bacteria and their animal hosts - in the group of Lisa Klasson see add for more information: http://www.uu.se/en/jobs/jobs-detail-page/?positionId=38849 2. Evolutionary genomics of microbial eukaryotes - in the group of Jan Andersson see add for more information: http://www.uu.se/en/jobs/jobs-detail-page/?positionId=38851 Application deadline: 27 June ================================== Lisa Klasson, Ph.D. Molecular Evolution Department of Cell and Molecular Biology Uppsala University Box 596 SE-751 24 Uppsala Sweden phone: +46 (0)18 471 6403 website: http://www.icm.uu.se/forskning/molekylar-evolution/personal/lisa-klasson/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From ovidiu.radulescu at univ-montp2.fr Thu Jun 5 17:10:01 2014 From: ovidiu.radulescu at univ-montp2.fr (Ovidiu Radulescu) Date: Thu, 05 Jun 2014 17:10:01 +0200 Subject: [SocBiN] Postdoctoral position in cancer computational systems biology Message-ID: <53908849.2050807@univ-montp2.fr> Postdoctoral position in computational systems biology with applications to signaling pathways involved in breast cancer suppression A 2-year post-doctoral position in systems biology is offered jointly by the "Biological Physics and Systems Biology" team (O. Radulescu) at the DIMNP CNRS 5235 / University of Montpellier 2 and the "Signaling, Invasion and Cancer" team (P. Coopman) at the Montpellier Cancer Research Institute (IRCM, INSERM U896/ University of Montpellier 1), in the South of France, starting at earliest on October 1st, 2014. The post-doctoral fellow will have a PhD. degree in computational systems biology, in computer science, or applied mathematics. Knowledge on cell biology, signaling, logical and/or differential equations modeling will be a benefit. He/she will be involved in data processing, dynamical modeling of signaling networks, large scale formal model reconstruction and analysis. The computational challenge of the project will be to create predictive models of complex signaling crosstalk based on the signaling networks identified using quantitative (phospho)proteomics as well as biochemical and /in cellulo/in vivo/ experimental models. The methodology developed will be used to process a large body of data on signaling via the anti-oncogenic Syk kinase and PTPL1 phosphatase in breast cancer and to elucidate the mechanisms by which these proteins inhibit tumor development and malignant progression. Montpellier is offering a unique environment for interdisciplinary and biomedical research, with excellent laboratories and technical facilities working in a tight collaboration and within a close geographical perimeter. The city is ideally situated between the Mediterranean sea and the magnificent landscapes of the Cevennes mountains. Applications, including a CV, a motivation letter and the contact information of at least two referees, should be sent by email to Ovidiu Radulescu (ovidiu.radulescu at univ-montp2.fr) with as subject "Cancer systems biology postdoc application'' before August 31st, 2014. -- Prof. Ovidiu Radulescu Universit? de Montpellier 2 ------------------------------------------------------------------- DIMNP - UMR 5235 CNRS/UM1/UM2 Phone: +33-(0)4-6714-9221 Pl. E. Bataillon - Bat. 24 Fax: +33-(0)4-6714-4286 Universit? Montpellier 2 email: ovidiu.radulescu at univ-montp2.fr CP 107 34095 Montpellier Cedex 5 FRANCE -------------- next part -------------- An HTML attachment was scrubbed... URL: From mimi.deprez at esat.kuleuven.be Fri Jun 6 10:36:05 2014 From: mimi.deprez at esat.kuleuven.be (mimi deprez) Date: Fri, 6 Jun 2014 10:36:05 +0200 Subject: [SocBiN] =?windows-1252?q?KU_Leuven_-_Postdoctoral_computer_scien?= =?windows-1252?q?tist_=96_Kernel_methods_and_network_analysis_for_data_fu?= =?windows-1252?q?sion_in_chemobioinformatics?= In-Reply-To: References: <77B1EDA8-D05E-4691-BB57-403336663A5E@icm.uu.se> Message-ID: Dear On behalf of prof Moreau would it be possible to send out our jobopening to all your list members? please find the details of the position below : -------- ========= Postdoctoral computer scientist ? Kernel methods and network analysis for data fusion in chemobioinformatics University of Leuven ESAT-STADIUS SymBioSys Center for Computational Systems Biology Keywords: machine learning, bioinformatics, chemoinformatics In the framework of a collaboration with Janssen Pharmaceuticals, we are looking for a talented postdoctoral researcher to develop kernel methods that link drug targets, disease phenotypes, and pharmaceutical compounds. Leveraging large-scale public and in-house data sets, you will develop kernel methods and/or network-based methods to predict potential links between targets, diseases, or candidate drugs. This research builds upon the expertise of Janssen Pharma and previous work of our team on genomic data fusion. The research will be also carried out with a team of the University of Linz, Austria (Prof. Sepp Hochreiter) specialized in kernel learning and chemoinformatics. Methodological research results will be published as academic research articles. Genomic data fusion (Moreau and Tranchevent, 2012; Aerts et al., 2006) offers a range of approaches to tackle the challenge described above. Among such methods, the University of Leuven has pioneered the use of kernel methods to integrate heterogeneous omics data (De Bie et al., 2007; Yu et al., 2009). The key advantage of kernel methods for mining heterogeneous data is that when multiple data sets are available, they all lead to kernel similarity matrices independently of the original type of data. Those kernels can then be efficiently integrated using Multiple Kernel Learning (De Bie et al., 2007; Yu et al., 2009). Similarly, our team has developed network analysis methods using kernel diffusion to identify potential targets of a drug. The goal of the project is to refine and generalize these methods to the complex and large-scale data sets available at a major pharmaceutical company. The STADIUS Center for Dynamical Systems, Signal Processing, and Data Analytics at KU Leuven is an academic research center, with a research focus on mathematical engineering, where mathematical tools from numerical linear and multi-linear algebra, statistics and optimization are used for applications of dynamical systems and control, signal processing, data modeling and analytics. The project is embedded within the SymBioSys Center for Computational Systems Biology, a universitywide center aiming at linking genomic variation to disease, and within the Exascience Life Lab, a major collaboration on scaling up genomic data analysis methods at exaflop scale. The University of Leuven is one of Europe?s leading research universities, with English as the working language for research. Leuven lies just east of Brussels, at the heart of Europe. PROFILE The ideal candidate holds a PhD degree in computer science or computational biology. Experience with machine learning, in particular kernel methods, is a core asset. Ability to develop powerful machine learning algorithms and scale them up to large data sets is essential. Capacity to plan and deliver on time, as well as strong communication skills, are important to manage a successful collaboration with our pharmaceutical and academic partners. A two-year commitment is expected from the candidate. RELEVANT PUBLICATIONS Moreau Y, Tranchevent LC. Computational tools for prioritizing candidate genes: boosting disease gene discovery. Nat Rev Genet. 2012 Jul 3;13(8):523-36. Yu S, Falck T, Daemen A, Tranchevent LC, Suykens JA, De Moor B, Moreau Y. L2-norm multiple kernel learning and its application to biomedical data fusion. BMC Bioinformatics. 2010 Jun 8;11:309. De Bie T, Tranchevent LC, van Oeffelen LM, Moreau Y. Kernel-based data fusion for gene prioritization. Bioinformatics. 2007 Jul 1;23(13):i125-32. Aerts S, Lambrechts D, Maity S, Van Loo P, Coessens B, De Smet F, Tranchevent LC, De Moor B, Marynen P, Hassan B, Carmeliet P, Moreau Y. Gene prioritization through genomic data fusion. Nat Biotechnol. 2006 May;24(5):537-44. Laenen G, Thorrez L, B?rnigen D, Moreau Y. Finding the targets of a drug by integration of gene expression data with a protein interaction network. Mol Biosyst. 2013 Jul;9(7):1676-85. HOW TO APPLY (Publication date of the vacancy: May 15, 2014) Please send in PDF at your earliest convenience: 1. CV including education, research experience, and bibliography 2. Three references (with phone and email) 3. A statement of purpose describing why you are qualified for the position and what your contribution could be to Ms. Mimi Deprez (mimi.deprez at esat.kuleuven.be), cc Prof. Yves Moreau (yves.moreau at esat.kuleuven.be), and Ms. Ida Tassens (ida.tassens at esat.kuleuven.be). Pre-application inquiries can be sent to Yves.Moreau at esat.kuleuven.be. URL: http://www.kuleuven.be/bioinformatics ---------- Mimi Deprez Project Coordinator KU Leuven - University of Leuven Dept. Elektrotechniek-ESAT-STADIUS (STADIUS Center for Dynamical Systems, Signal Processing and Data Analytics) iMinds Department Medical Information Technologies t:+ 32 (0) 16 32 85 55 m: + 32 476 72 68 59 Kasteelpark Arenberg 10, bus 2446 B-3001 Leuven http://www.esat.kuleuven.be http://www.kuleuven.be/iMinds/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From andrej.alekseenko at scilifelab.se Tue Jun 17 15:01:14 2014 From: andrej.alekseenko at scilifelab.se (Andrey Alexeyenko) Date: Tue, 17 Jun 2014 15:01:14 +0200 Subject: [SocBiN] Summer School in Computational and Systems Biology of Cancer Message-ID: <53A03C1A.3070702@scilifelab.se> Dear colleagues! Please find here our message about the StratCan - Kicancer - BILS Summer School that will happen in a Stockholm suburb in 2.5 months. PhD students and postdocs are warmly welcome! Please spread this information further. (Note that there is just 4 weeks to the application deadline). Best regards, Andrey Alexeyenko BILS - Bioinformatics Infrastructure for Life Sciences http://bils.se Science For Life Laboratory http://www.scilifelab.se/ Department of Microbiology, Tumor and Cell Biology, Karolinska Institute http://www.mtc.ki.se/ e-mail: andrej.alekseenko at scilifelab.se phone: +46-(0)8 5248 1513 address: SciLifeLab, Box 1031, 171 21 Solna, Sweden From Inge.Jonassen at ii.uib.no Tue Jun 17 15:27:57 2014 From: Inge.Jonassen at ii.uib.no (Inge Jonassen) Date: Tue, 17 Jun 2014 15:27:57 +0200 Subject: [SocBiN] senior bioinformatics engineer position in Bergen Message-ID: <69DA10D1-7532-4204-91BC-62D1C5A596BA@ii.uib.no> We are recruiting a senior engineer to work on a project on sensitive data linked with the Norwegian ELIXIR Node and with the Tryggve project supported by NeIC. For more information, see http://www.jobbnorge.no/en/available-jobs/job/103252/senior-engineer-chief-engineer-temporary-employment Inge Jonassen Inge Jonassen, Prof PhD Computational Biology Unit Department of Informatics University of Bergen HiB N5020 Bergen Norway inge at ii.uib.no From andrej.alekseenko at scilifelab.se Tue Jun 17 15:27:50 2014 From: andrej.alekseenko at scilifelab.se (Andrey Alexeyenko) Date: Tue, 17 Jun 2014 15:27:50 +0200 Subject: [SocBiN] Summer School in Computational and Systems Biology of Cancer In-Reply-To: <53A03C1A.3070702@scilifelab.se> References: <53A03C1A.3070702@scilifelab.se> Message-ID: <53A04256.6040300@scilifelab.se> Really sorry - please find the attached poster here. Regards, Andrey On 2014-06-17 15:01, Andrey Alexeyenko wrote: > Dear colleagues! > Please find here our message about the > StratCan - Kicancer - BILS > Summer School that will happen in a Stockholm suburb in 2.5 months. > > PhD students and postdocs are warmly welcome! > Please spread this information further. > (Note that there is just 4 weeks to the application deadline). > > Best regards, > Andrey Alexeyenko > BILS - Bioinformatics Infrastructure for Life Sciences http://bils.se > Science For Life Laboratory http://www.scilifelab.se/ > Department of Microbiology, Tumor and Cell Biology, Karolinska Institute > http://www.mtc.ki.se/ > > e-mail: andrej.alekseenko at scilifelab.se > phone: +46-(0)8 5248 1513 > address: SciLifeLab, Box 1031, 171 21 Solna, Sweden > -------------- next part -------------- A non-text attachment was scrubbed... Name: PosterStratCanSummarSchool2014.pdf Type: application/pdf Size: 502490 bytes Desc: not available URL: From lex.nederbragt at ibv.uio.no Wed Jun 18 14:38:20 2014 From: lex.nederbragt at ibv.uio.no (Lex Nederbragt) Date: Wed, 18 Jun 2014 12:38:20 +0000 Subject: [SocBiN] Bioinformatician position at the Norwegian Sequencing Centre, Oslo Message-ID: <08017225-2A43-409D-ACFE-F97510D583A2@ibv.uio.no> Hi, We have an opening for a Senior engineer in computational biology/bioinformatics at the The Norwegian Sequencing Centre (NSC) hosted by the Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo. See the full announcement at http://uio.easycruit.com/vacancy/1200955/96871?iso=no By the way, we also have an opening for 'wet lab' Staff engineer/head engineer at the NSC: http://uio.easycruit.com/vacancy/1200977/96871?iso=no Application deadline for both positions: July 4th, 2014. Best, Lex Nederbragt -- Lex Nederbragt Norwegian High-Throughput Sequencing Centre (NSC) Centre for Ecological and Evolutionary Synthesis (CEES) Dept. of Biosciences, University of Oslo P.O. Box 1066 Blindern 0316 Oslo, Norway Ph. +47 22844132 +47 48028722 Fax. +47 22854001 Email lex.nederbragt at ibv.uio.no http://www.sequencing.uio.no http://flavors.me/flxlex -------------- next part -------------- An HTML attachment was scrubbed... URL: From per.stenberg at molbiol.umu.se Mon Jun 23 17:05:03 2014 From: per.stenberg at molbiol.umu.se (Per Stenberg) Date: Mon, 23 Jun 2014 17:05:03 +0200 Subject: [SocBiN] 2 year Post-Doc position in Bioinformatics With Focus on Comparative/Evolutionary Genomics Message-ID: I have an open Post-Doc position in my lab (Ume? University). I have attached the announcement. Please, spread to anyone you might think would be interested. Cheers, \Per ------------------------------------------------------------ Per Stenberg, PhD, Ass. Prof. Molecular Biology Computational Life Science Cluster (CLiC) Ume? University SE-901 87 Ume? Sweden +46(0)90 7856777 WWW -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: PostDocComparativeGenomics_2014.pdf Type: application/pdf Size: 131943 bytes Desc: PostDocComparativeGenomics_2014.pdf URL: From arne at bioinfo.se Tue Jun 24 16:08:15 2014 From: arne at bioinfo.se (Arne Elofsson) Date: Tue, 24 Jun 2014 16:08:15 +0200 Subject: [SocBiN] Two Tenure track assistant professorships at SciLifeLab in Stockholm Message-ID: Tenure track assistant professorships at SciLifeLab in Stockholm We are happy to announce two tenure track assistant professorships at SciLifeLab in Stockholm, Sweden. Both positions are tenure track and well funded (at least twice what Harvard would give you). The research environment is excellent with large access to genomics (Lundeberg), proteomics (Uhlen), biotechnology (Gromacs is developed here), structural bioinformatics (Elofsson), membrane proteins (von Heijne). SciLifeLab is a joint research institute between three universities in Stockholm and located at the Karolinska Institute campus next to worl class biomedical research labs. The first position (at Stockhoolm University) is in "High-resolution biomolecular single-particle cryo-electron microscopy". Funding for a K2 detector (and microscope) is secured. The second position is in Computational Biophysics. Here all computational approaches to study biomolecules are of interest. Both positions will have deadline at Sep 15 2014 For more information see: Cryo-EM: http://www.su.se/english/about/vacancies Computational biophysics: http://www.kth.se/om/work-at-kth/lediga-anstallningar/Assignmentview.aspx?guid=4955947E-9F40-4950-916E-F8B3669CCD9C&templateid=0 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 lindfors at lifeglimmer.com Thu Jun 26 14:11:22 2014 From: lindfors at lifeglimmer.com (Erno Lindfors) Date: Thu, 26 Jun 2014 14:11:22 +0200 (CEST) Subject: [SocBiN] Marie Curie Experienced Researcher/post-doc position in metabolic network analysis (Berlin, Germany) Message-ID: <198462330.294826.1403784682946.open-xchange@patina.store> LifeGlimmer (http://www.lifeglimmer.com/) is a start up founded in 2012 with the goal of providing to the Biotechnological, Biomedical and Environmental Research Communities an efficient way to outsource Scientific Computing needs. Our office is located in Berlin, Germany. We have an open post-doc position in the systems medicine EU project PerFuMe (http://www.itn-perfume.eu) which aims to unravel principles of peroxisome biology. The candidate will be embedded in a computational team and his/her major tasks are on data integration and visualisation, and on the reconstruction of peroxisomal metabolic networks in mammalian cells and yeast based on heterogeneous ?omics? data (e.g. transcriptomics, proteomics, metabolomics, genomics). The candidate should have an MSc/PhD degree and fluent English language skills. Ideally he/she has a strong background from molecular biology, biochemistry, genetics or related field. Basic knowledge of of computational systems biology is appreciated. Due to administrative requirements of EU the candidate must have: * 4 to 5 years full-time research experience (e.g. PhD training) since finishing an MSc/Diploma degree; * Not worked or studied in Germany for more than 12 months in the last 3 years. We offer: * 18 months full-time position; * Good salary plus mobility allowance; * Training in complementary skills and techniques via courses and visits to other labs in the Network. Please apply electronically to info at lifeglimmer.com until July 13th 2014 with your CV, cover letter and supporting information in a single document (max. 3MB). -------------- next part -------------- An HTML attachment was scrubbed... URL: From arne at bioinfo.se Thu Jun 26 14:57:03 2014 From: arne at bioinfo.se (Arne Elofsson) Date: Thu, 26 Jun 2014 14:57:03 +0200 Subject: [SocBiN] Bioinformatics position in Uppsala Message-ID: See http://www.uu.se/jobb/detaljsida/?positionId=39909 (unfortunately only in Swedish, use automatic translation) 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 namrata.tomar at gmail.com Thu Jun 26 19:17:56 2014 From: namrata.tomar at gmail.com (Namrata) Date: Thu, 26 Jun 2014 22:47:56 +0530 Subject: [SocBiN] Bioinformatics position in Uppsala Message-ID: <53ac5612.0168440a.30da.ffffefa1@mx.google.com> Namrata -----Original Message----- From: "Arne Elofsson" Sent: ?26-?06-?2014 06:27 PM To: "socbin at socbin.org" Subject: [SocBiN] Bioinformatics position in Uppsala See http://www.uu.se/jobb/detaljsida/?positionId=39909 (unfortunately only in Swedish, use automatic translation) 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: