From Ola.Spjuth at farmbio.uu.se Mon Dec 1 15:14:44 2014 From: Ola.Spjuth at farmbio.uu.se (Ola Spjuth) Date: Mon, 1 Dec 2014 14:14:44 +0000 Subject: [SocBiN] Workshop: e-Infrastructures for Massively Parallel Sequencing, Uppsala, 2015 Message-ID: <77F3B455-03C8-4799-AB40-7925541FCB25@farmbio.uu.se> [cid:6C6A475B-1821-4293-B446-F6CCB3CEC4DC at bmc.uu.se] Workshop: e-Infrastructures for Massively Parallel Sequencing This workshop will bring together scientists sharing their experiences on how to build efficient and sustainable e-infrastructures for massively parallel sequencing data management and storage, as well as setting up and maintaining an associated ecosystem of workflows, pipelines, and bioinformatics software. Dates: Jan 19-20, 2015 Venue: Science for Life Laboratory, Uppsala University, Sweden Website: http://www.uppnex.se/events/eInfraMPS2015 Sessions: 1) e-infrastructures for NGS 2) NGS pipelines in action 3) Clinical data management 4) Workflow systems 5) Virtual machines for NGS The workshop will also include a knowledge cafe with round-table discussions, and a set of short-tutorials. The workshop is free of charge and includes coffee, lunch and dinner but requires registration. The number of participants is limited to 36 on a first come, first served basis. The event is funded by SeqAhead, SciLifeLab, eSSENCE, SeRC, NeIC and BILS. Welcome! Ola Spjuth UPPMAX and Science for Life Laboratory Uppsala University, Sweden -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: banner.png Type: image/png Size: 103015 bytes Desc: banner.png URL: From vang at ki.au.dk Wed Dec 3 00:21:56 2014 From: vang at ki.au.dk (=?UTF-8?Q?S=C3=B8ren_Vang?=) Date: Wed, 3 Dec 2014 00:21:56 +0100 Subject: [SocBiN] open associate professorship at MOMA, Department of Clinical Medicine, Aarhus University, Denmark Message-ID: Dear all, We have an open associate professorship at MOMA, Department of Clinical Medicine, Aarhus University, Denmark: http://health.au.dk/en/currently/vacant-positions/scientific-positions/stillinger/Vacancy/show/700562/5283/ Deadline is Dec. 17. Please forward to anybody who might be interested. S?ren Vang, Ph.D. Department of Molecular Medicine (MOMA) Aarhus University Hospital, Skejby Brendstrupgaardsvej 100 DK-8200 Aarhus N, Denmark Phone: +45 784 55362 (local 55362) Fax: +45 8678 2108 email: vang at ki.au.dk From bpn at ifm.liu.se Mon Dec 8 11:48:49 2014 From: bpn at ifm.liu.se (Bengt Persson) Date: Mon, 08 Dec 2014 11:48:49 +0100 Subject: [SocBiN] Associate Professor in Bioinformatics, Aarhus, Denmark In-Reply-To: <50C87650.2060909@ifm.liu.se> References: <50C87650.2060909@ifm.liu.se> Message-ID: <54858211.7020401@ifm.liu.se> Associate professor in bionformatics, deadline 17 Dec 2014. Best wishes, Yours, Bengt -------------- next part -------------- A non-text attachment was scrubbed... Name: momaAssociateProfessorshipBioinf.pdf Type: application/pdf Size: 72122 bytes Desc: not available URL: From Inge.Jonassen at ii.uib.no Tue Dec 9 11:22:23 2014 From: Inge.Jonassen at ii.uib.no (Inge Jonassen) Date: Tue, 9 Dec 2014 11:22:23 +0100 Subject: [SocBiN] Professor / associate professor positions in Bergen Message-ID: <4F137151-6A74-428D-8359-C06C0984B4A8@ii.uib.no> We are recruiting up to two full professors (alternatively associate professors) in bioinformatics. Do you want to be my colleague - or know somebody who might be looking for opportunities? Please spread the word! www.jobbnorge.no/en/available-jobs/job/108238/professor-associate-professor-in-bioinformatics-up-to-2-positions Inge Jonassen Inge Jonassen, Prof PhD, head of unit Computational Biology Unit Department of Informatics University of Bergen HiB N5020 Bergen Norway inge at ii.uib.no -------------- next part -------------- An HTML attachment was scrubbed... URL: From bpn at ifm.liu.se Tue Dec 9 14:19:34 2014 From: bpn at ifm.liu.se (Bengt Persson) Date: Tue, 09 Dec 2014 14:19:34 +0100 Subject: [SocBiN] Bioinformatics professorship(s) in Bergen Message-ID: <5486F6E6.9070908@ifm.liu.se> Dear all, Forwarded message from Prof. Inge Jonassen regarding bioinformatics professorship(s) in Bergen. Best wishes, Yours, Bengt -- Dear colleague, I would be very grateful if you could pass on the following link to potential applicants for a professorship/associate professorship in bioinformatics at the University of Bergen. Thank you very much for your help. All the best, Inge www.jobbnorge.no/en/available-jobs/job/108238/professor-associate-professor-in-bioinformatics-up-to-2-positions -- Bengt Persson, M.D., Ph.D. Professor of Bioinformatics Director of BILS (Bioinformatics Infrastructure for Life Sciences) Science for Life Laboratory Uppsala University & Karolinska Institutet Telephone: +46 18 471 4422 Mobile phone: +46 70 425 0230 <== Please note new number! Facsimile: +46 18 530 396 E-mail: bpn at icm.uu.se, bpn at bils.se, bengt.persson at ki.se Addresses: Uppsala University | Karolinska Institutet SciLifeLab | SciLifeLab ICM -- Department of | CMB -- Department of Cell and Molecular Biology | Cell and Molecular Biology BMC, room C10:308c | House Gamma, level 6, G6613 Box 596 | Box 1031 S-751 24 Uppsala, SWEDEN | S-171 21 Stockholm, SWEDEN From lukas.kall at scilifelab.se Thu Dec 11 11:59:06 2014 From: lukas.kall at scilifelab.se (=?UTF-8?Q?Lukas_K=C3=A4ll?=) Date: Thu, 11 Dec 2014 11:59:06 +0100 Subject: [SocBiN] Course announcement - Analysis of data from high-throughput molecular biology experiments Message-ID: Dear SocBiN, Dear SciLifeLab, We, Lars Arvestad, Olof Emanuelsson, and Lukas K?ll at KTH, will give two colocalized courses at advanced level named "Analysis of data from high-throughput molecular biology experiments" 7.5hp and "Omic Data and Systems Biology", KTH course codes BB2490/DD2399 starting 20 January 2015 and finishing 20 March. The courses are identical in format and content, but have separate course codes for historical reasons. The courses will cover how to analyze (i) next/now generation sequencing data (e.g., assembly, RNA-seq, ChIP-seq) and (ii) mass spectrometry data (e.g., peptide identification and quantification, post-translational modifications). There are 11 lectures, 4 computer exercises, 3 seminars, and one project. The project is done in groups of 2 or 3 students, with real data and will be presented in poster format at a "poster session" towards the end of the course. The official course plans are available here: http://www.kth.se/student/kurser/kurs/BB2490?l=en_UK http://www.kth.se/student/kurser/kurs/DD2399 If you're interested in taking this course, first talk to your supervisor to find out if it fits into your course package, and then email a short motivation (1/2 A4 page) of why you would like to participate. Please note that the number of participants is limited. Also, note that we need your application at the very latest by noon, Monday 12 January. The course is given in collaboration with Science for Life Laboratory and the national infrastructure in next-generation sequencing, NGI. Lectures and computer exercises are held at the AlbaNova and SciLifeLab Stockholm campuses. Welcome with your application! Lars Arvestad (lars.arvestad at scilifelab.se), Olof Emanuelsson (olof.emanuelsson at scilifelab.se), Lukas K?ll (lukas.kall at scilifelab.se) -- ======================== Lukas K?ll http://kaell.org Royal Institute of Technology - KTH Science for Life Laboratory School of Biotechnology Box 1031, 171 65 Solna, Sweden +46 8 52481196 or +46 76 9425179 From Orjan.Carlborg at slu.se Tue Dec 16 12:52:11 2014 From: Orjan.Carlborg at slu.se (=?utf-8?B?w5ZyamFuIENhcmxib3Jn?=) Date: Tue, 16 Dec 2014 11:52:11 +0000 Subject: [SocBiN] Post-doc: The genetic mechanisms of adaptation Message-ID: <39398BD8-7F6A-4103-8B65-69B28C82D203@slu.se> The genetic mechanisms of adaptation Post-doc position in the Division of Computational Genetics, Department of Clinical Sciences, SLU, Uppsala, Sweden A Post-doc position is available in a project where we study the genetic mechanisms of adaptation. In the project we do in-depth analyses of data from mainly two model systems: i) A long-term selection experiment in domestic chicken and ii) Large collections of natural Arabidopsis thaliana accessions. The focus in the project is to develop and use new quantitative-, population-, and evolutionary genetics approaches to analyze already available data. Depending on the background, competence and interests of the applicant, the project can be focused either on the development of new genetics theory, statistical methods, computational algorithms and bioinformatics tools, analyses of empirical data using methods developed by others working on the project, or a combination of the two. Examples of earlier work in this project include: Opinion articles 1. Carlborg, ?. and Haley, C. Epistasis: too often neglected in complex traits studies? Nature Reviews Genetics 2004 5: 618-625. 2. Le Rouzic, A. and Carlborg, ?. Evolutionary potential of hidden genetic variation. Trends in Ecology and Evolution 2008 23:33-37. 3. Nelson, R.M., Pettersson, M.E., Carlborg, ?. A century after Fisher: time for a new paradigm in quantitative genetics. Trends Genet. 2013 29:669-76. Original publications 1. Carlborg, ?., Jacobsson, L., ?hgren, P., Siegel, P., Andersson, L. Epistasis and the release of genetic variation during long-term selection. Nature Genetics 2006 38:418-20. 2. Alvarez-Castro, J. and Carlborg, ?. A general model for functional and statistical epistasis and its application in QTL analysis. Genetics 2007 176: 1151-1167 3. Alvarez-Castro, J., le Rouzic, A. and Carlborg, ?. How to perform meaningful estimates of genetic effects. PLOS Genetics 2008 May 2; 4(5):e1000062 4. Le Rouzic, A., Alvarez-Castro, J. and Carlborg, ?. Dissection of the genetic architecture of body weight in chicken reveals the impact of epistasis on domestication traits. Genetics 2008 179:1591-1599. 5. Johansson, A.M., Pettersson, M.E., Siegel, P.B. and Carlborg, ?. Genome-wide effects of long-term divergent selection. PLoS Genet. 2010 6(11):e1001188. 6. Pettersson, M.E., Besnier, F., Siegel, P. and Carlborg, ?. 2011. Replication and explorations of high-order epistasis using a large Advanced Intercross Line pedigree. PLOS Genetics, Jul;7(7):e1002180. 7. Shen, X., Pettersson, M., R?nneg?rd, L. and Carlborg, ?. Inheritance beyond plain heritability: variance-controlling genes in Arabidopsis thaliana. PLoS Genetics 2012 8(8):e1002839. Epub 2012 Aug 2. 8. Nelson, R.M., Pettersson, M.P., LI, X., Carlborg, ?. 2013. Variance heterogeneity in Saccharomyces cerevisiae expression data: trans-regulation and epistasis. PLoS One. 2013 8:e79507. 9. Shen, X., De Jonge, J., Forsberg, S., Pettersson, M., Sheng, Z., Hennig, L., and Carlborg, ?. Natural CMT2 variation is associated with genome-wide methylation changes and temperature seasonality. PLoS Genet. 2014 10(12): e1004842 10. Lachowiec, J., Shen, X., Queitsch, C. and Carlborg, ?. Highly epistatic genetic architecture of root length in Arabidopsis thaliana. BIORXIV/2014/008789 To be suitable for the post, we believe that you have a thorough theoretical background in quantitative-, population- or evolutionary genetics and an interest in using this knowledge to improve our understanding of the genetic mechanisms contributing to adaptation via analyses of empirical data. You have probably also have experience in performing quantitative-, population- or evolutionary genetics analyses in empirical data. As we use R as a common platform for all our work, previous experience in R-programming is an advantage. The post is available immediately and we are now looking for candidates are available to start the post by April 1, 2015 at the latest. Forms for funding or employment Employment as Post-doctoral researcher student for 1 year with possibility of extension 1+2 years. If you have questions about the post, us or our work, please contact ?rjan Carlborg (Orjan.Carlborg at slu.se We are looking forward to hearing from you! -------------- next part -------------- An HTML attachment was scrubbed... URL: From doubleanders at gmail.com Sun Dec 21 20:38:48 2014 From: doubleanders at gmail.com (Anders Andersson) Date: Sun, 21 Dec 2014 20:38:48 +0100 Subject: [SocBiN] Post Doctor in Marine Metagenomics at SciLifeLab, Stockholm Message-ID: Dear All, We have an opening for a postdoc in our group in the field of marine metagenomics: https://www.kth.se/en/om/work-at-kth/lediga-jobb/what:job/jobID:49042/where:4/ The application deadline is Februari 15. Kind regards, Anders Andersson -- Associate Professor SciLifeLab School of Biotechnology KTH Royal Institute of Technology Stockholm, Sweden Webpage: http://envgen.github.io/ Email: anders.andersson at scilifelab.se Phone: +46-8-5248-1414; +46-73-9838962 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jensl at csc.kth.se Sun Dec 28 17:22:52 2014 From: jensl at csc.kth.se (Jens Lagergren) Date: Sun, 28 Dec 2014 17:22:52 +0100 Subject: [SocBiN] 2-year Postdoc in Computational Cancer Resarch/Machine Learning, deadline Jan 31 Message-ID: Postdoc position in computational biology at SciLifeLab/CSC, KTH, Stockholm. The project is concerned with Machine Learning and probabilistic modeling applied to cancer, in particular somatic evolution in cancer and cancer heterogeneity. Methodologically, this project will be focused on Machine Learning and advanced methods for computational inference as well as implementation of such methods on modern high performance computers and clusters. We expect to collaborate with Swedish groups developing new experimental methods and data at SciLifeLab as well as with international collaborators. This is a 2 year time-limited position. The starting date is open for discussion, though ideally we would like the successful candidate to start as soon as possible. The position is located at Science for Life Laboratory (SciLifeLab) together with a part of the Computational Biology department, CSC, KTH. SciLifeLab is a national center for molecular biosciences with focus on health and environmental research. It combines frontline technical expertise with advanced knowledge of translational medicine and molecular bioscience. Application deadline January 31 2015. For details on how to apply see https://www.kth.se/en/om/work-at-kth/lediga-jobb/what:job/jobID:49115/where:4/ For enquiries about the project, please contact Professor Jens Lagergren, jensl at csc.kth.se , 08-524 814 96 Best, Jens csc.kth.se/~jensl/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From Timo.Lassmann at telethonkids.org.au Mon Dec 29 05:20:11 2014 From: Timo.Lassmann at telethonkids.org.au (Timo Lassmann) Date: Mon, 29 Dec 2014 04:20:11 +0000 Subject: [SocBiN] Postdoc in Translational Bioinformatics: Perth, Australia Message-ID: <9DFD9A95-A40E-48C5-8D60-4CDDBA8DAA2D@telethonkids.org.au> Dear Friends and Colleagues, We have an opening for a postdoc in the field of translational bioinformatics: " The laboratories of Timo Lassmann and Jenefer Blackwell at the Telethon Kids Institute have a joint opening for a postdoctoral position in translational bioinformatics. The postdoc will be involved in creating and applying state of the art computational approaches to clinical sequencing data. The overarching theme is to place unique datasets from the SeqNextGen project, aimed at sequencing DNA from children suffering from rare diseases, into the context of publicly available data to improve data interpretation and ultimately child healthcare. The position represents an exciting opportunity to work at the crossroads between basic science and clinical practise. The successful candidate will have the unique opportunity to be part of a truly inter-disciplinary team composed of molecular biologists, statisticians, computational biologists and clinicians. The successful candidate should have a PhD in a relevant subject area (e.g Computational Biology, Bioinformatics, Genomics, Computer Science) and a strong background in programming (C/C++, R, Python) and be proficient in UNIX/Linux environments. In addition all candidates should have at least two first author publications in reputed journals and demonstrated their ability to work well in a team. We expect all our lab members to be strongly self-motivated and ambitious. All applications should include a cover letter addressing the requirements along with two (2) academic references. Submit your application along with a covering letter to applications at telethonkids.org.au. Please quote the position title in the subject heading of your email application. For further information about this position please contact: timo.lassmann at telethonkids.org.au ? The ad can be found here: http://www.nature.com/naturejobs/science/jobs/484581-postdoc-in-translational-bioinformatics Please forward this to anyone that you might think would be interested and feel free to contact me with further questions about the job opening. Best regards, Timo ------------------------------------ Dr Timo Lassmann, PhD Academic Head of Computational Biology, Telethon Kids Institute 100 Roberts Road, Subiaco, Western Australia, 6008 PO Box 855, West Perth, Western Australia, 6872 www.telethonkids.org.au -------------- next part -------------- An HTML attachment was scrubbed... URL: From ali.shariati.b at gmail.com Mon Dec 29 07:57:48 2014 From: ali.shariati.b at gmail.com (Ali Shariati) Date: Mon, 29 Dec 2014 10:27:48 +0330 Subject: [SocBiN] ali.shariati.b@gmail.com Message-ID: -------------- next part -------------- An HTML attachment was scrubbed... URL: From arne at bioinfo.se Tue Dec 30 12:42:45 2014 From: arne at bioinfo.se (Arne Elofsson) Date: Tue, 30 Dec 2014 12:42:45 +0100 Subject: [SocBiN] Postdoc position in protein structure prediction in Stockholm Message-ID: Postdoc position in computational biology at SciLifeLab/CSC, KTH, Stockholm. The project is concerned with protein protein structure prediction using predicted contacts (see http://dx.doi.org/10.1371/journal.pcbi.1003889) and in combination with experimental data (in particular Cryo-EM data in collaboration with the infrastructure for single particle Cryo-EM under construction at SciLifeLab). This is a 2 year time-limited position, finances with a scholarship. The starting date is open for discussion, though ideally we would like the successful candidate to start as soon as possible and at the latest April 1 2015. The position is located at Science for Life Laboratory (SciLifeLab). SciLifeLab is a national center for molecular biosciences with focus on health and environmental research. It combines frontline technical expertise with advanced knowledge of translational medicine and molecular bioscience. Applications are accepted until January 31 by an email to arne at bioinfo.se including a CV and the name of two scientists who can write recommendation letters. Arne -------------- next part -------------- An HTML attachment was scrubbed... URL: From jacob-michaelson at uiowa.edu Tue Dec 30 16:16:57 2014 From: jacob-michaelson at uiowa.edu (Michaelson, Jacob J) Date: Tue, 30 Dec 2014 15:16:57 +0000 Subject: [SocBiN] postdoc position (Iowa, USA): bioinformatics/computational biology in psychiatry References: <03DFC838BC06EA4284C4947651974F9A29AD8B5E@HC-MAILBOXC1-N5.healthcare.uiowa.edu> Message-ID: <03DFC838BC06EA4284C4947651974F9A29AD8BAD@HC-MAILBOXC1-N5.healthcare.uiowa.edu> Dear all, I am looking for talented and driven individuals to join my new lab at the University of Iowa, where we combine computational and experimental approaches to study the genetic contributions to neuropsychiatric conditions, in particular autism spectrum disorders. The open position emphasizes quantitative and computational skills. Check out the posting at: http://www.nature.com/naturejobs/science/jobs/481815-postdoctoral-researcher-genome-informatics-in-psychiatry ...and feel free to contact me directly with any questions you have. Thanks and have a happy new year! Jake ___ Jacob Michaelson, PhD Assistant Professor Systems Biology and Genomics Department of Psychiatry Department of Biomedical Engineering University of Iowa ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ________________________________