From awe at signatur.dk Mon Oct 3 11:03:12 2016 From: awe at signatur.dk (Alan Wervick) Date: Mon, 3 Oct 2016 11:03:12 +0200 Subject: [SocBiN] Postdoc position on computational proteomics at the Novo Nordisk Foundation Center for Protein Research Message-ID: *Postdoc position on computational proteomics at the Novo Nordisk Foundation Center for Protein Research* A postdoc position is available in the Cellular Network Biology group at The Novo Nordisk Foundation Center for Protein Research (CPR – www.cpr.ku.dk). The Center has been established at the Faculty of Health and Medical Sciences, University of Copenhagen, to promote basic and applied discovery research on human proteins of medical relevance. The Center comprises a wide range of expertise and resources including proteomics, protein production, bioinformatics and general characterization of disease mechanisms. The Programme for Disease Systems Biology consists of two research groups covering many systems level aspects of biology and medicine, including the integration of molecular-level data and healthcare data, including biomedical texts. *Responsibilities and tasks* The Cellular Network Biology group ( www.cpr.ku.dk/research/disease-systems-biology/jensen/) led by Lars Juhl Jensen focuses on network-based analysis of proteins and their posttranslational modifications in the context of cellular signaling and disease. The postdoc will work on developing novel computational methods for analysis of proteomics data and apply them to unpublished state-of-the-art mass-spectrometry data in close collaboration with the proteomics groups at CPR. Projected start date: Early 2017. *Qualifications* Candidates for the postdoctoral positions must hold a PhD degree (or equivalent) within a relevant discipline and have experience with programming and large-scale data analysis. The successful candidates will have strong qualifications or experience within several of the following areas: - Bioinformatics / computational biology - Statistical data analysis - Mass spectrometry / proteomics - Programming in Python and/or R The cellular network biology group is highly multidisciplinary and international. Members are expected to collaborate both within the group, within the center, nationally, and internationally; strong networking and team player skills are therefore valued. *Place of employment and work* The employment is at CPR, University of Copenhagen, located in central Copenhagen. The research environment at CPR is ambitious and international, with approx. 30 different nationalities currently represented. The Center comprises modern laboratories, supercomputer resources and state-of-the-art facilities within protein science. Seminars with high-profile international speakers and regular internal research seminars are organized at the Center. The selected candidate should expect some travel activity. For more information on working and living in Denmark visit www.ism.ku.dk (International staff mobility) and www.workingconditions.ku.dk. *Terms of salary and employment* Salary, pension and terms of employment will be in accordance with the agreement between the Ministry of Finance and The Academics Central organization. Currently, the monthly salary is around 32,000-33,700 DKK (around 4,200-4,500 €) plus 17.1 % in pension contribution. The Danish Ministry of Finance and the Danish Confederation of Professional Associations (AC) have agreed on a protocol that makes it possible for all international researchers employed by the University to achieve a pension exemption, where the pension will be paid as salary. For more information about the different pension schemes: http://ism.ku.dk/onarrival/pension/ *Duration*: 2 or 3 years *Application procedure* Your application should be submitted electronically to: http://employment.ku.dk/faculty/ Only applications sent through this link will be accepted. Your application should include the following documents: 1. Motivated letter of application 2. Curriculum vitae, incl. education and experience 3. Copy of diplomas/degree certificate(s) 4. List of publications *Deadline for application: November 1, 2016* After the expiry of the deadline for applications, the authorized recruitment manager selects applicants for assessment on the advice of the Appointments Committee. All applicants are then immediately notified whether their application has been passed for assessment by an expert assessment committee. Selected applicants are notified of the composition of the committee and each applicant has the opportunity to comment on the part of the assessment that relates to the applicant him/herself. You can read about the recruitment process at http://employment.ku.dk For further information about the position or the process, please contact CPR: jobs at cpr.ku.dk CPR and the University of Copenhagen wish to reflect the diversity of society and welcome applications from all qualified candidates regardless of personal background. *APPLY NOW * *Part of the International Alliance of Research Universities (IARU), and among Europe’s top-ranking universities, the University of Copenhagen promotes research and teaching of the highest international standard. Rich in tradition and modern in outlook, the University gives students and staff the opportunity to cultivate their talent in an ambitious and informal environment. An effective organisation – with good working conditions and a collaborative work culture – creates the ideal framework for a successful academic career.* -------------- next part -------------- An HTML attachment was scrubbed... URL: From awe at signatur.dk Mon Oct 3 11:04:38 2016 From: awe at signatur.dk (Alan Wervick) Date: Mon, 3 Oct 2016 11:04:38 +0200 Subject: [SocBiN] Postdoc position on biomedical text mining at the Novo Nordisk Foundation Center for Protein Research Message-ID: *Postdoc position on biomedical text mining at the Novo Nordisk Foundation Center for Protein Research* A postdoc position is available in the Cellular Network Biology group at The Novo Nordisk Foundation Center for Protein Research (CPR – www.cpr.ku.dk). The Center has been established at the Faculty of Health and Medical Sciences, University of Copenhagen, to promote basic and applied discovery research on human proteins of medical relevance. The Center comprises a wide range of expertise and resources including proteomics, protein production, bioinformatics and general characterization of disease mechanisms. The Programme for Disease Systems Biology consists of two research groups covering many systems level aspects of biology and medicine, including the integration of molecular-level data and healthcare data, including biomedical texts. *Responsibilities and tasks* The Cellular Network Biology group ( www.cpr.ku.dk/research/disease-systems-biology/jensen/) led by Lars Juhl Jensen focuses on network-based analysis of proteins and their posttranslational modifications in the context of cellular signaling and disease. The postdoc will work on development of advanced methods for protein-centric text mining of large corpora, including combining efficient dictionary-based named entity-recognition with conditional random fields and classification based on word embedding. The resulting improved methods will in collaboration with other group members be integrated into STRING ( http://string-db.org) and related databases/tools, and the software will be made available under open licenses. Projected start date: Early 2017. *Qualifications* Candidates for the postdoctoral positions must hold a PhD degree (or equivalent) within a relevant discipline and have strong programming experience. The successful candidates will have strong qualifications or experience within several of the following areas: - Text mining - Bioinformatics / computational biology - Machine learning - Statistical data mining - Biomedical ontologies - Programming in Python and/or C++ The cellular network biology group is highly multidisciplinary and international. Members are expected to collaborate both within the group, within the center, nationally, and internationally; strong networking and team player skills are therefore valued. *Place of employment and work* The employment is at CPR, University of Copenhagen, located in central Copenhagen. The research environment at CPR is ambitious and international, with approx. 30 different nationalities currently represented. The Center comprises modern laboratories, supercomputer resources and state-of-the-art facilities within protein science. Seminars with high-profile international speakers and regular internal research seminars are organized at the Center. The selected candidate should expect some travel activity. For more information on working and living in Denmark visit www.ism.ku.dk (International staff mobility) and www.workingconditions.ku.dk. *Terms of salary and employment* Salary, pension and terms of employment will be in accordance with the agreement between the Ministry of Finance and The Academics Central organization. Currently, the monthly salary is around 32,000-33,700 DKK (around 4,200-4,500 €) plus 17.1 % in pension contribution. The Danish Ministry of Finance and the Danish Confederation of Professional Associations (AC) have agreed on a protocol that makes it possible for all international researchers employed by the University to achieve a pension exemption, where the pension will be paid as salary. For more information about the different pension schemes: http://ism.ku.dk/onarrival/pension/ *Duration*: 2 or 3 years *Application procedure* Your application should be submitted electronically to: http://employment.ku.dk/faculty/ Only applications sent through this link will be accepted. Your application should include the following documents: 1. Motivated letter of application 2. Curriculum vitae, incl. education and experience 3. Copy of diplomas/degree certificate(s) 4. List of publications *Deadline for application: November 1, 2016* After the expiry of the deadline for applications, the authorized recruitment manager selects applicants for assessment on the advice of the Appointments Committee. All applicants are then immediately notified whether their application has been passed for assessment by an expert assessment committee. Selected applicants are notified of the composition of the committee and each applicant has the opportunity to comment on the part of the assessment that relates to the applicant him/herself. You can read about the recruitment process at http://employment.ku.dk For further information about the position or the process, please contact CPR: jobs at cpr.ku.dk CPR and the University of Copenhagen wish to reflect the diversity of society and welcome applications from all qualified candidates regardless of personal background. *APPLY NOW * *Part of the International Alliance of Research Universities (IARU), and among Europe’s top-ranking universities, the University of Copenhagen promotes research and teaching of the highest international standard. Rich in tradition and modern in outlook, the University gives students and staff the opportunity to cultivate their talent in an ambitious and informal environment. An effective organisation – with good working conditions and a collaborative work culture – creates the ideal framework for a successful academic career.* -------------- next part -------------- An HTML attachment was scrubbed... URL: From albin at binf.ku.dk Thu Oct 6 14:44:33 2016 From: albin at binf.ku.dk (Albin Sandelin) Date: Thu, 6 Oct 2016 14:44:33 +0200 Subject: [SocBiN] Postdoc in single cell analysis of neutrons in development and regeneration Message-ID: Dear all (apologies for multiple postings). My colleague Konstantin Khodasevich has a computational postdoc position in single cell transcriptomics here at BRIC i Copenhagen. Please forward to great candidates! http://employment.ku.dk/faculty/?show=856464 Best regards, Albin Albin Sandelin Professor, PhD Section for Computational and RNA Biology, Department of Biology & Biotech Research and Innovation Centre, Copenhagen University Ole Maaloes Vej 5, DK2200, Copenhagen N, Denmark tel +45 224 56668 albin at binf.ku.dk skype: albinsan twitter: @albin_san -------------- next part -------------- An HTML attachment was scrubbed... URL: From Carsten.Daub at ki.se Fri Oct 7 11:30:40 2016 From: Carsten.Daub at ki.se (Carsten Daub) Date: Fri, 7 Oct 2016 09:30:40 +0000 Subject: [SocBiN] Postdoctoral researcher with a background in the analysis of genomic and epigenomic data Message-ID: <6B0FC268-881E-4DB4-A95D-6FAD3B22F342@ki.se> Open position: Postdoctoral researcher with a background in the analysis of genomic and epigenetic data Professor Boris Lenhard: b.lenhard at imperial.ac.uk. Imperial College London Call closing Date: 6 November 2016 https://www4.ad.ic.ac.uk/OA_HTML/OA.jsp?page=/oracle/apps/irc/candidateSelfService/webui/VisVacDispPG&akRegionApplicationId=821&transactionid=1096675663&retainAM=Y&addBreadCrumb=S&p_svid=49997&p_spid=1806300&oapc=7&oas=vJypGn5K9xtKREbmRkFvpg We are looking for a talented and highly skilled postdoctoral researcher with a background in the analysis of genomic and epigenomic data or a related field. The candidate should have a record of accomplishments indicating the ability to perform analysis, visualisation and dissemination of data produced by high-throughput sequencing, as well as in-depth knowledge of molecular biology. The candidate is expected to have proficiency in programming and analysis of genomics data and the design of analysis pipelines. The knowledge of UNIX administration is a plus. The post is funded by BBSRC for the project entitled “DanioPeaks: A Central Resource for Standardised Annotation and Re-annotation of Whole-Genome Data for the Model Vertebrate Zebrafish”. Its aim is to develop the processing pipeline for analysis of all published NGS sequencing datasets available for zebrafish by using the established standardised protocols of ENCODE and modENCODE. It will make the growing amount of zebrafish NGS data directly comparable and available for meta-analysis to the wider scientific community. Besides resulting in a resource of broad interest and associated publication, the project will give opportunity to the postdoctoral researcher to demonstrate the utility of the integrated data produced on the project for discovering new biology. Within the latter part of the project there is ample opportunity for taking initiative and choosing one’s own direction, which will be strongly encouraged. The post is a unique opportunity to work on developing and applying cutting-edge approaches for genome-wide data processing and integration for a model organism of rapidly growing importance, in one of the leading research environments in Europe and the world. The post holder will have the opportunity to work with a worldwide network of collaborators, attend scientific conferences, and publish the results of their work in top journals. You should have a PhD in Computational Biology, Bioinformatics or a related discipline. Knowledge of programming, molecular biology and genomics is expected, as well as prior experience with processing and management of next-generation sequencing data. Informal enquiries may be directed to Professor Boris Lenhard at b.lenhard at imperial.ac.uk. -------------- next part -------------- An HTML attachment was scrubbed... URL: From henrik.lantz at bils.se Mon Oct 10 15:56:43 2016 From: henrik.lantz at bils.se (Henrik Lantz) Date: Mon, 10 Oct 2016 15:56:43 +0200 Subject: [SocBiN] 2xPost doc in bee genomics/bioinformatics (Uppsala University, Sweden) Message-ID: <9FE00C77-AC4C-43D7-8C2D-5F7C1271AB77@bils.se> Dear all, please see below for two post doc positions in Matt Webster’s group at Uppsala University, Sweden. ------------------- We are looking for two postdocs to join Matthew Webster’s group working on evolutionary genomics and population genomics. Research in this group currently focuses on two main areas: 1) the genetic basis of local adaptation and 2) the evolution of recombination. We use multiple species of bees to study these questions. The research primarily involves population-scale genome sequencing and bioinformatic/statistical analyses, but there are also opportunities for field/apiary work and molecular genetics lab work. A good summary of the research focus can be gained from the following publications: *Wallberg A, Han F, Wellhagen G, Dahle B, Kawata M, Haddad N, Simões ZL, Allsopp MH, Kandemir I, De la Rúa P, Pirk CW, Webster MT. (2014). A worldwide survey of genome sequence variation provides insight into the evolutionary history of the honeybee Apis mellifera. Nat Genet. 46(10):1081-8. *Wallberg A, Glémin S, Webster MT. (2015). Extreme recombination frequencies shape genome variation and evolution in the honeybee, Apis mellifera. PLoS Genet. 11(4):e1005189. *Wallberg A, Pirk CW, Allsopp MH, Webster MT. (2016). Identification of multiple loci associated with social parasitism in honeybees. PLoS Genet. 12(6):e1006097. The successful candidates will to work on new and ongoing projects under the two main research focuses. The main duties involve analysis of next-generation sequencing data, including processing of raw data, and statistical analysis using population/evolutionary genetics methods. Involvement in sample collection, molecular genetics and teaching/supervision of students is also possible depending on requirements of the projects and interests of the candidate. Successful candidates should be proficient in bioinformatics and statistics, ideally including perl scripting, analysis of next-gen sequencing data and population genetics. A strong interest in evolution and social insects is also desirable. Excellent communication skills and high level of motivation are required. Good spoken and written English is required. Employment will be initially for one year with possibility of extension. If you are interested in the position, you are encouraged to make an informal enquiry to Matthew Webster, matthew.webster at imbim.uu.se. A full job description and details of how to apply can be found here: http://www.uu.se/en/about-uu/join-us/details/?positionId=115841 You are welcome to submit your application no later than November 4, 2016 -------------- next part -------------- An HTML attachment was scrubbed... URL: From besenbacher at clin.au.dk Mon Oct 10 22:41:59 2016 From: besenbacher at clin.au.dk (=?iso-8859-1?Q?S=F8ren_Besenbacher?=) Date: Mon, 10 Oct 2016 20:41:59 +0000 Subject: [SocBiN] Postdoc position in bioinformatics / population genetics Message-ID: <615AA572-9A3A-42F4-A2EC-CEFA747A9DD3@clin.au.dk> A two-year post-doctoral position is available in the bioinformatics group at the Department of Molecular Medicine at Aarhus University: http://www.au.dk/en/about/vacant-positions/scientific-positions/stillinger/Vacancy/show/859855/5283/ The application deadline is 30 October. From lukas.kall at scilifelab.se Wed Oct 12 15:28:17 2016 From: lukas.kall at scilifelab.se (=?UTF-8?Q?Lukas_K=C3=A4ll?=) Date: Wed, 12 Oct 2016 15:28:17 +0200 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 Käll at KTH, will give a course named "Analysis of data from high-throughput molecular biology experiments" 7.0hp, course code BB2491, starting 2 November 2016 and finishing 16 January 2017 (with a break over Christmas and New Year's). Although this is a course at the master's level, it is also suitable for phd students with basic knowledge of bioinformatics and programming. The course starts soon, but we have some seats left! The course will cover how to analyze (i) massively parallel 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 3 students, with real data and the results will be presented in poster format at a "poster session" towards the end of the course. We require student presence and active participation at most events. Most of the activities will take place at the KTH-AlbaNova campus. The official course plan is available here: http://www.kth.se/student/kurs er/kurs/BB2491?l=en_UK 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 (absolutely max 1/2 A4 page) of why you would like to participate. Please note that the number of participants is limited. Please email your application to lukas.kall at scilifelab.se as soon as possible (and at the very latest by noon Tuesday 25 October). This is the seventh time this course is given, and you may very well have a course alumnus in your vicinity. The course is given by School of Biotechnology at KTH in collaboration with Science for Life Laboratory and NGI, National Genomics Infrastructure. Welcome with your application! Lars Arvestad (lars.arvestad at scilifelab.se), Olof Emanuelsson (olofem at kth.se), Lukas Käll (lukas.kall at scilifelab.se) -- ======================== Lukas Käll 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From sajan.raju at helsinki.fi Wed Oct 26 16:22:38 2016 From: sajan.raju at helsinki.fi (Raju, Sajan) Date: Wed, 26 Oct 2016 14:22:38 +0000 Subject: [SocBiN] Vacancy -PostDoc and Database manager Message-ID: Dear all, Our group is looking for a post-doctoral fellow with interest in obesity and/or microbiota research and Database manager in a large adolescents' health study (expert in MySQL). Details attached as PDFs or can view from below links https://drive.google.com/open?id=0B0qqzreQnr-pVUJEQm5xcEpqM3c https://drive.google.com/open?id=0B0qqzreQnr-pQks4XzkzZk51cjA Br, Sajan Raju Bioinformatician Folkhälsan Research Center Biomedicum 1, Helsinki P.O 63, Haartmaninkaatu 8 00014, Helsinki University, Finland [finhit-logo] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... 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Details attached as PDFs or can view from below links https://drive.google.com/open?id=0B0qqzreQnr-pVUJEQm5xcEpqM3c https://drive.google.com/open?id=0B0qqzreQnr-pQks4XzkzZk51cjA Br, Sajan Raju Bioinformatician Folkhälsan Research Center Biomedicum 1, Helsinki P.O 63, Haartmaninkaatu 8 00014, Helsinki University, Finland [finhit-logo] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.jpg Type: image/jpeg Size: 15884 bytes Desc: image001.jpg URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Database_manager_announcement_Fin-HIT-study.pdf Type: application/pdf Size: 156020 bytes Desc: Database_manager_announcement_Fin-HIT-study.pdf URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Post-doc_announcement_Fin-HIT-study (002).pdf Type: application/pdf Size: 169884 bytes Desc: Post-doc_announcement_Fin-HIT-study (002).pdf URL: From arne at bioinfo.se Wed Oct 26 18:49:57 2016 From: arne at bioinfo.se (Arne Elofsson) Date: Wed, 26 Oct 2016 18:49:57 +0200 Subject: [SocBiN] Fwd: Postdoc in genome data integration/computational biology - Lenhard group, Imperial College London In-Reply-To: <683F7DC8-0EBB-41E3-9D18-8170D478421B@ic.ac.uk> References: <683F7DC8-0EBB-41E3-9D18-8170D478421B@ic.ac.uk> Message-ID: ---------- Forwarded message ---------- From: "Lenhard, Boris" Date: 26 Oct 2016 6:39 p.m. Subject: Postdoc in genome data integration/computational biology - Lenhard group, Imperial College London To: "Lenhard, Boris" Cc: Dear colleagues, My group is looking for a talented and highly skilled postdoctoral researcher with a background in the analysis of genomic and epigenomic data or a related field. The post is funded by BBSRC for the project entitled “*DanioPeaks: A Central Resource for Standardised Annotation and Re-annotation of Whole-Genome Data for the Model Vertebrate Zebrafish*”. I would be very grateful if you could help me spread the word. The position is ideally suited for a person with interest in genomic data integration and database development. Due to the nature of the project that provides the initial funding, the initial contract is for one year, but it can be extended to three years in total. The position is announced at http://www.jobs.ac.uk/job/ AUT089/research-associate The closing date for applications is *06 November 2016 (Midnight BST)*. More information about my group can be found at http://group.genereg.net Many thanks, Boris _____________________________________ Boris Lenhard, Ph.D. Professor of Computational Biology Department of Molecular Sciences Institute of Clinical Sciences Faculty of Medicine Imperial College London and MRC Clinical Sciences Centre, London, UK Hammersmith Hospital Campus Du Cane Rd. London W12 0NN United Kingdom E-mail: b.lenhard at imperial.ac.uk Tel.: +44 (0)20 838 38353 _____________________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: From bjorn.nystedt at scilifelab.se Fri Oct 28 09:56:37 2016 From: bjorn.nystedt at scilifelab.se (=?iso-8859-1?Q?Bj=F6rn_Nystedt?=) Date: Fri, 28 Oct 2016 09:56:37 +0200 Subject: [SocBiN] Job: Permanent position for advanced national bioinformatics support in Sweden (WABI) Message-ID: <7D089417-8D82-4001-909D-CD441A4B5EF3@scilifelab.se> 1 permanent position providing advanced bioinformatics support, located at the SciLifeLab Bioinformatics Platform, Uppsala, Sweden. Science for Life Laboratory (SciLifeLab, www.scilifelab.se) in Sweden serves as a national infrastructure to support advanced high-throughput life science research, and is currently one of the fastest-growing life science research establishments in Europe. The SciLifeLab bioinformatics platform (www.nbis.se) is a national infrastructure in rapid development, now looking for a permanent staff member to join the Bioinformatics Long-term Support team (WABI), placed in Uppsala. The Bioinformatics Long-term Support team provides advanced bioinformatics analyses to some of the most scientifically exciting projects across Sweden, and with 24 full-time senior bioinformaticians, the team is one of the strongest units for analysis of large-scale genomics and integrative omics in Sweden. We are looking forward to your application at the latest November 21, 2016 http://www.uu.se/en/about-uu/join-us/details/?positionId=120221 Björn Nystedt, bjorn.nystedt at scilifelab.se Pär Engström, par.engstrom at scilifelab.se Head of SciLifeLab Bioinformatics Long-term Support www.nbis.se/support/longtermsupport.html www.scilifelab.se/platforms/bioinformatics/ ------------------------------------------------ Bjorn Nystedt, PhD Manager, SciLifeLab Bioinformatics Long-term Support (WABI) www.scilifelab.se/facilities/wabi/ BMC E10:3206, entrance C11 Husargatan 3, SE-752 37 Uppsala Phone: 018 - 471 4413 E-mail: bjorn.nystedt at scilifelab.se ------------------------------------------------ -------------- next part -------------- An HTML attachment was scrubbed... URL: