From tony.handstad at medisin.uio.no Wed Jan 3 10:07:22 2018 From: tony.handstad at medisin.uio.no (=?UTF-8?Q?Tony_H=c3=a5ndstad?=) Date: Wed, 3 Jan 2018 10:07:22 +0100 Subject: [SocBiN] Open position at Department of Medical Genetics, Oslo University Hospital In-Reply-To: References: Message-ID: A bioinformatics position is available at Department of Medical Genetics, Oslo University Hospital. The position is part of the BigMed project, a collaboration between multiple commercial and academic partners who aim to develop solutions for some of the key barriers for precision medicine in Norway. See https://www.finn.no/job/fulltime/ad.html?finnkode=110478706 Kind regards Tony Håndstad Department of Medical Genetics, Ullevål Sykehus, Oslo University Hospital, Norway -------------- next part -------------- An HTML attachment was scrubbed... URL: From ilakya.selvarajan at gmail.com Thu Jan 4 13:49:43 2018 From: ilakya.selvarajan at gmail.com (Ilakya Selvarajan) Date: Thu, 4 Jan 2018 14:49:43 +0200 Subject: [SocBiN] Open positions at GenomMed Doctoral program (Marie Curie Actions Cofund) Message-ID: Hello! The EU funded GenomMed (Genetics and Mechanisms in Translational Medicine) doctoral program has a 2nd call open for doctoral student positions at the University of Eastern Finland (Kuopio, Finland). Our group ( https://www.uef.fi/en/web/aivi/group-leader-minna-kaikkonen-maatta) is looking for candidates for Early Stage Researcher Positions in GenomMed Doctoral programme. We do cool research in identifying gene regulatory mechanisms governing atherogenesis ( https://www.uef.fi/en/web/aivi/minna-kaikkonen-maatta-science). More details about the projects can be discussed with our group leader. * Application process: * i) How to apply: http://www.uef.fi/en/web/genommed/how-to-apply ii) More detailed information about the research topics can be found at: http://www.uef.fi/en/web/genommed/research-topics iii) Template for the research proposal & evaluation criteria available at: http://www.uef.fi/en/web/genommed/documents *Eligibility requirements :* i) Should not have resided in Finland for more than 12 months in the 3 years immediately prior to recruitment, and should not possess a doctoral degree/and should not have over 4 years of research experience since master’s degree. ii) Detailed information about the doctoral program can be found at: http://www.uef.fi/en/web/genommed Interested candidates please email *Dr. Minna Kaikkonen-Määttä*, minna.kaikkonen at uef.fi Thanks and best regards, Ilakya Selvarajan -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: GenomMed 2nd Call.pdf Type: application/pdf Size: 223878 bytes Desc: not available URL: From mauno.vihinen at med.lu.se Thu Jan 4 14:40:20 2018 From: mauno.vihinen at med.lu.se (Mauno Vihinen) Date: Thu, 4 Jan 2018 14:40:20 +0100 Subject: [SocBiN] Position in systems biology at Lund University Message-ID: <566ab251-625a-7cbf-7d19-fea9bb4a4522@med.lu.se> We have an opening for an Assistant Researcher (Biträdande forskare) at postdoc level at the Protein Structure and Bioinformatics Group at Lund University. For further requirements and description see https://lu.mynetworkglobal.com/en/what:job/jobID:185890/iframeEmbedded:0/where:4 Note that the application portal is accessed by pressing the button "Login and apply". The position is originally filled for one year with a possible extension for another. The deadline for submissions in on the January 17th. Only applications submitted via the electronic system will be considered. For further information, contact: -- Mauno Vihinen Professor of Medical Structural Biology Department of Experimental Medical Science Lund University BMC B13 SE-22184 Lund Sweden http://structure.bmc.lu.se tel +46 72 526 0022 ORCID iD 0000-0002-9614-7976 From mauno.vihinen at med.lu.se Thu Jan 4 14:49:15 2018 From: mauno.vihinen at med.lu.se (Mauno Vihinen) Date: Thu, 4 Jan 2018 14:49:15 +0100 Subject: [SocBiN] Postdoc position, machine learning for variant interpreation, at Lund Unversity Message-ID: <60bb1cda-a85b-51e5-108f-495de1aed325@med.lu.se> We are seeking for a compentent candidates to a position of post doctoral fellow at Lund University. The position is for two years with an immediate opening. Requirements and details are at available at https://lu.mynetworkglobal.com/en/what:job/jobID:181799/type:job/where:4/apply:1 Applications submitted only by the electronic system at university will be considered. This position is for a person to continue development of our highly accurate variation prediction methods including PON-P2, PON-MMR2, PON-mt-tRNA, PON-Sol and others. For further information, contact: -- Mauno Vihinen Professor of Medical Structural Biology Department of Experimental Medical Science Lund University BMC B13 SE-22184 Lund Sweden http://structure.bmc.lu.se tel +46 72 526 0022 ORCID iD 0000-0002-9614-7976 From ilakya.selvarajan at gmail.com Thu Jan 4 15:01:43 2018 From: ilakya.selvarajan at gmail.com (Ilakya Selvarajan) Date: Thu, 4 Jan 2018 16:01:43 +0200 Subject: [SocBiN] Open positions at GenomMed Doctoral program (Marie Curie Actions Cofund) Message-ID: Hello! The EU funded GenomMed (Genetics and Mechanisms in Translational Medicine) doctoral program has a 2nd call open for doctoral student positions at the University of Eastern Finland (Kuopio, Finland). Our group (https://www.uef.fi/en/web/aivi/group-leader-minna-kaikkonen -maatta) is looking for candidates for Early Stage Researcher Positions in GenomMed Doctoral programme. We do cool research in identifying gene regulatory mechanisms governing atherogenesis (https://www.uef.fi/en/web/aiv i/minna-kaikkonen-maatta-science). More details about the projects can be discussed with our group leader. * Application process: * i) How to apply: http://www.uef.fi/en/web/genommed/how-to-apply ii) More detailed information about the research topics can be found at: http://www.uef.fi/en/web/genommed/research-topics iii) Template for the research proposal & evaluation criteria available at: http://www.uef.fi/en/web/genommed/documents *Eligibility requirements :* i) Should not have resided in Finland for more than 12 months in the 3 years immediately prior to recruitment, and should not possess a doctoral degree/and should not have over 4 years of research experience since master’s degree. ii) Detailed information about the doctoral program can be found at: http://www.uef.fi/en/web/genommed Interested candidates please email *Dr. Minna Kaikkonen-Määttä*, minna.kaikkonen at uef.fi Thanks and best regards, Ilakya Selvarajan -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: GenomMed 2nd Call.pdf Type: application/pdf Size: 223878 bytes Desc: not available URL: From prash at bioclues.org Wed Jan 3 02:32:42 2018 From: prash at bioclues.org (Prash) Date: Wed, 03 Jan 2018 01:32:42 +0000 Subject: [SocBiN] Fwd: FW: Post-doc at UCL, London In-Reply-To: References: Message-ID: Courtesy of Richard and Rajeev Varshney -- Sent from iPad Mini -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Research Associate in Statistical Genetics and Bioinformatics.docx Type: application/vnd.openxmlformats-officedocument.wordprocessingml.document Size: 105789 bytes Desc: not available URL: From arne at bioinfo.se Tue Jan 9 13:08:11 2018 From: arne at bioinfo.se (Arne Elofsson) Date: Tue, 9 Jan 2018 13:08:11 +0100 Subject: [SocBiN] Fwd: Applications are now invited for the FIMM-EMBL International PhD program Message-ID: *Applications are now invited for the FIMM-EMBL International PhD program.* In collaboration with the Nordic EMBL Partnership in Molecular Medicine and the Helsinki Institute for Information Technology, FIMM announces the opening of the 2018 call for applications for Doctoral Students in Molecular Medicine, Bioinformatics, and Data Science as part of the FIMM-EMBL International PhD recruitment and training program . In this program, outstanding doctoral students are recruited to the institute-level rotation program where they will work with two to three different research groups during a six to nine month period prior to matching to a research group in which they remain for their doctoral studies. The program provides an exciting opportunity to explore different research areas and working environments as well as to learn a variety of science and technologies, making connections within and beyond the institutes. We hope that you will share these call announcements with your international and national networks. The detailed call announcement can be found on the FIMM Open Positions page. The deadline for applications is 8 February 2018, and application instructions are available within the announcement. Questions are welcome to FIMM’s Doctoral Training Coordinator, William Hennah (william.hennah at helsinki.fi). -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Nordic EMBL call image.jpeg Type: image/jpeg Size: 129874 bytes Desc: not available URL: From coordinator at rth.dk Thu Jan 11 14:58:31 2018 From: coordinator at rth.dk (Betina Wingreen Jensen) Date: Thu, 11 Jan 2018 14:58:31 +0100 Subject: [SocBiN] Job Opp: Postdoc in Bioinformatics and Neurotranscriptomics Message-ID: <004b01d38ae4$43f4f560$cbdee020$@rth.dk> Dear Colleague, A two-year Postdoc position is available in the bioinformatics group (http://ivh.ku.dk/bioinformatics), Center for non-coding RNA in Technology and Health (RTH), (http://rth.dk ) at Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences at University of Copenhagen. The Postdoc position in Bioinformatics and Neurotranscriptomics is available from 1 March 2018 or as soon as possible thereafter. Application deadline is: Feb 8th 2018 Background The NeuroStem project aims at identifying and manipulating non-coding RNA to obtain novel functional insight in Alzheimer´s and Parkinson’s diseases that can enable improved treatment. The non-coding RNAs will be extracted from expression experiments of patient-specific neuronal cells derived from induced pluripotent stem cells obtained from skin fibroblasts. Further details can be found at http://neurostem.dk. Job description The project involves detection and analysis of non-coding and structured RNA and their correlation of transcriptomic data in regards to the neurodegenerative diseases. Relevant methods will be employed for the transcriptome analysis and methods for detecting structured RNA and RNA-RNA interactions will be developed and incorporated in the integrated pipelines. There will be close synergy to the experimental side in e.g. the set up for mechanistic experiments to further verify RNA functions in relation to neurodegeneration. For more information about the center, please go to http://rth.dk and to see the full posting and online application procedure visit: http://jobportal.ku.dk/videnskabelige-stillinger/?show=146536 Please forward this message to possible candidates in your network. With best wishes, Betina Betina Wingreen Jensen Scientific and administrative Coordinator Københavns Universitet Det Sundhedsvidenskabelige Fakultet Grønnegårdsvej 3 DIR 35334704 MOB 20510932 bwj at sund.ku.dk -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.gif Type: image/gif Size: 5975 bytes Desc: not available URL: From henrik.lantz at nbis.se Thu Jan 11 15:19:41 2018 From: henrik.lantz at nbis.se (Henrik Lantz) Date: Thu, 11 Jan 2018 15:19:41 +0100 Subject: [SocBiN] System development positions at NBIS/SciLifeLab in Uppsala (Sweden) Message-ID: <97B212D7-1B35-4FD8-8C99-2CA52FA17534@nbis.se> Dear all, please see the following link for 1-3 system development positions currently available at National Bioinformatics Infrastructure Sweden (a part of SciLifeLab): http://uu.se/en/about-uu/join-us/details/?positionId=181081 Please contact manager Jonas Hagberg (address available at linked page) if you have any questions. Best regards, Henrik From coordinator at rth.dk Mon Jan 15 11:16:09 2018 From: coordinator at rth.dk (Betina Wingreen Jensen) Date: Mon, 15 Jan 2018 11:16:09 +0100 Subject: [SocBiN] Job Opp: Postdoc in RNA Bioinformatics and Systems Biology Message-ID: <002001d38de9$dd053a00$970fae00$@rth.dk> Dear Colleague, A two-year Postdoc position in RNA Bioinformatics and Systems Biology is available in the bioinformatics group ( http://ivh.ku.dk/bioinformatics), Center for non-coding RNA in Technology and Health (RTH), ( http://rth.dk ) at Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences at University of Copenhagen. The Postdoc position in RNA Bioinformatics and Systems Biology is available from 1st March 2018 or as soon as possible thereafter. Application deadline is: 2018-02-08 Background Cell factories are based on organisms, which have been carefully optimised to produce protein-based products such as enzymes and pharmaceutical proteins with the highest possible yield. However, current technology is saturated with respect to yield improvement although the theoretical maximum has not yet been reached. Within the NextProd project, the goal is to improve the yield by manipulating ncRNAs. See more at http://nextprod.dk. Job description Transcriptomic data sets from relevant strains of the model cell-factory Bacillus subtilis will be used as outset for identification of ncRNAs and their pathways through integrative analysis. This will also include in silico analysis of expression data, RNA structure and RNA-RNA interactions. An integrated workflow will be established including both known tools and tools developed on demand when relevant. The workflow will be employed directly within the context of the data generated in the project and is expected to give rise to further experimental analysis.For more information about the center, please go to http://rth.dk or http://nextprod.dk . To see the full posting and online application procedure visit: http://jobportal.ku.dk/videnskabelige-stillinger/?show=146544 Please forward this message to possible candidates in your network. With best wishes, Betina Betina Wingreen Jensen Scientific and administrative Coordinator Københavns Universitet Det Sundhedsvidenskabelige Fakultet Grønnegårdsvej 3 DIR 35334704 MOB 20510932 bwj at sund.ku.dk -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.gif Type: image/gif Size: 5975 bytes Desc: not available URL: From torognes at ifi.uio.no Tue Jan 16 13:06:49 2018 From: torognes at ifi.uio.no (=?utf-8?Q?Torbj=C3=B8rn_Rognes?=) Date: Tue, 16 Jan 2018 13:06:49 +0100 Subject: [SocBiN] Fwd: Permanent position as bioinformatician/researcher at Newborn Screening, Oslo University Hospital References: Message-ID: <4F59A425-E788-4A50-8199-E48F153639C7@ifi.uio.no> > Begin forwarded message: > > From: "Alexander D. Rowe" > Subject: [cbo-all] Permanent position as bioinformatician/researcher at Newborn Screening, Oslo University Hospital > Date: 16 January 2018 at 13:02:15 CET > To: "cbo-all at usit.uio.no" > Resent-From: > Reply-To: "Alexander D. Rowe" > > We have a permanent position available for a bioinformatician/researcher at the Department of Newborn Screening, Oslo University Hospital. > > Screening for 25 rare treatable disorders is offered to all of the ~60,000 children born in Norway annually. > > We are looking for a dynamic, capable, and enthusiastic colleague to assist us with the implementation of robust best-practice pipelines for quality control and interpretation of our next-generation sequencing data, and to contribute scientifically to the future development of newborn screening - both nationally and through our extensive international collaborations. > > More information about newborn screening is available on our website > https://oslo-universitetssykehus.no/avdelinger/barne-og-ungdomsklinikken/nyfodtscreeningen/nyfodtscreening > > and the job advertisement can be found below. > https://tjenester.nav.no/stillinger/stilling?p=0&q=0316+2017+12+643&rpp=50&rv=al&sort=akt&ID=9694124 > > Please also feel free to forward this announcement to anybody who may be interested in the position, and to make contact if you require further information. > > > Regards, > > Alex Rowe > > > -- > Dr Alexander D. Rowe > Research Scientist > Department of Newborn Screening > Division of Child and Adolescent Medicine > Oslo University Hospital > Norway -------------- next part -------------- An HTML attachment was scrubbed... URL: From iwona.zielinska at mimuw.edu.pl Wed Jan 17 15:20:44 2018 From: iwona.zielinska at mimuw.edu.pl (=?UTF-8?Q?Iwona_Zieli=c5=84ska?=) Date: Wed, 17 Jan 2018 15:20:44 +0100 Subject: [SocBiN] ad for PhD students - MSCE project Message-ID: <9f8d4f41-178c-e9f0-a618-914a4647563a@mimuw.edu.pl> Dear All, I am project manager related to project “CONTRA – Computational Oncology Training Alliance” for Marie Skłodowska-Curie European Training Network. We are going to employ 15 PhD students close to the following fields : bioinformatics, statistics, mathematics, computer science or evolutionary biology. All info you may find at attached advertisement. best regards, Iwona Zielinska -- Iwona Zielińska project manager Horizon 2020 - CONTRA University of Warsaw www.uw.edu.pl www.mimuw.edu.pl -------------- next part -------------- A non-text attachment was scrubbed... Name: 15 PHD - with logos v.2.pdf Type: application/pdf Size: 240102 bytes Desc: not available URL: From lionel.guy at imbim.uu.se Thu Jan 18 13:44:14 2018 From: lionel.guy at imbim.uu.se (Lionel Guy) Date: Thu, 18 Jan 2018 12:44:14 +0000 Subject: [SocBiN] Two post-doc fellowships available Message-ID: <210A7737-21EF-4B0D-B3E2-9960ECE1A316@imbim.uu.se> I have two post-doc fellowships available for two exciting projects: 1. Evolvability of antibiotic resistance genes, collaboration with Diarmaid Hughes. 2. Evolution of host-adaptation in the intracellular bacteria Legionellales. Deadline for applications February 18th, 2018. See full description below or on my website (http://www.imbim.uu.se/Research/Microbiology-immunology/guy-lionel/). Best regards, Lionel ======= 1 ======= EVOLVABILITY OF ANTIBIOTIC RESISTANCE GENES, POST-DOC Lionel Guy and Diarmaid Hughes are looking for a post-doctoral fellow with, ideally, experience of both bacterial genetics and molecular evolution to tackle a collaborative project on the evolvability of ancestral antibiotics resistance genes. PROJECT The mains goals are (i) to better understand how different antibiotic resistance genes evolved before the clinical use of antibiotics, and to assess (ii) their evolutionary potential and (iii) the predictability of the mutations providing antibiotic resistance. We will focus on four classes of genes providing resistance to four classes of antibiotics: beta-lactams, aminoglycosides, tetracycline and the last-resort antibiotic colistin. First, the successful candidate will reconstruct the evolutionary history of each class of genes, trying to infer what they are derived from. Second, they will evaluate the resistance potential of ancestors, by reconstructing them, cloning them into E. coli MG1655 and assessing their minimal inhibitory concentrations (MIC). Third, the reconstructed ancestors will be evolved in sub-MIC conditions, to examine evolutionary paths and time necessary to reach present-day MICs. By comparing the mutations obtained in experimental evolution to the ones found in actual modern sequences we’ll be watching how “replaying the tape of life” mimics the actual evolutionary pressures experienced by sequences in vivo, and may predict the potential emergence of antibiotics resistance in clinical settings. FORM Two-years post-doctoral fellowship (SEK 276 000, circa USD 32 400, per annum), free of tax. Fellowship rules exclude candidates with a PhD from the host institution (Uppsala University). The candidate has to be approved by the funder. Starting date: to be discussed BASIC SKILLS AND QUALIFICATIONS - A PhD in molecular evolutionary biology, microbial genetics or a related topic. - Experience with microbiology and bacterial genetics. - Experience of bioinformatics, ability to run basic molecular evolution software. - A documented experience of team work and collaborative projects. DESIRED QUALIFICATIONS - Extended experience of molecular evolution tools. - Programming experience. - Skills in molecular genetic tools in E. coli and Salmonella. APPLICATIONS To be sent by email to lionel.guy at imbim.uu.se, latest on February 18th, 2018. Applications (in one single document) should include: - Letter of motivation. - Resume. - Publication list. - Names and contact information of two references or two letters of reference. HOST INSTITUTION The project is a collaboration between the research groups of Lionel Guy and Diarmaid Hughes, Department of Medical Biochemistry Microbiology, Uppsala University. The host department is a very strong and stimulating research environment, counting over 250 researchers in over 30 groups, and is conducting world-leading research in antibiotic resistance. Uppsala University is a comprehensive research-intensive university with a strong international standing. Our mission is to pursue top-quality research and education and to interact constructively with society. Our most important assets are all the individuals whose curiosity and dedication make Uppsala University one of Sweden’s most exciting workplaces. Uppsala University has 40,000 students, 7,000 employees and a turnover of SEK 6.5 billion. CONTACT Lionel Guy, M: lionel.guy at imbim.uu.se, P: +46 18 471 42 46, W: http://www.imbim.uu.se/Research/Microbiology-immunology/guy-lionel/ ======= 2 ======= POSTDOCTORAL FELLOW IN EVOLUTIONARY MICROBIOLOGY, BIOINFORMATICS We are recruiting a new postdoctoral fellow to Lionel Guy’s research group at Uppsala University. PROJECT Our group is studying the evolution of host-adaptation in bacteria. We are currently focusing on the Legionellales order, which contains representatives at several stages of host adaptation. We are gathering a number of novel genomes through extended sampling, metagenomics and data mining. The goal of this project is to extend the current dataset, analyze it, to shed light on the evolution of Legionellales in particular, and on the evolutionary transitions in host adaptation in general. FORM One-year post-doctoral fellowship (SEK 288 000, circa USD 34 000, per annum); extension for a second year possible. Candidates who are employees of Uppsala University, or have been in the two years before the start of the fellowship, are not eligible. Starting date: to be discussed. BASIC SKILLS AND QUALIFICATIONS - A PhD in evolutionary biology, molecular evolution, microbiology or related topic. - Experience with high-throughput sequencing data, metagenomics, comparative genomics, and molecular evolution tools. - A documented experience of team work and collaborative projects. DESIRED QUALIFICATIONS - Programming experience. APPLICATIONS To be sent by email to lionel.guy at imbim.uu.se, latest on January 18th, 2018. Applications (in one single document) should include: - Letter of motivation. - Resume. - Publication list. - Names and contact information of two references or two letters of reference. HOST INSTITUTION The group is located at the Department of Medical Biochemistry Microbiology, Uppsala University. The host department is a very strong and stimulating research environment, counting over 250 researchers in over 30 groups, and is conducting world-leading research in antibiotic resistance. Uppsala University is a comprehensive research-intensive university with a strong international standing. Our mission is to pursue top-quality research and education and to interact constructively with society. Our most important assets are all the individuals whose curiosity and dedication make Uppsala University one of Sweden’s most exciting workplaces. Uppsala University has 40,000 students, 7,000 employees and a turnover of SEK 6.5 billion. CONTACT Lionel Guy, M: lionel.guy at imbim.uu.se, P: +46 18 471 42 46, W: http://www.imbim.uu.se/Research/Microbiology-immunology/guy-lionel/ -- Lionel Guy, PhD Assistant Professor (forskarassistent), Docent in Evolutionary Microbiology Department for Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden lionel.guy at imbim.uu.se From par.engstrom at scilifelab.se Fri Jan 19 10:19:46 2018 From: par.engstrom at scilifelab.se (=?utf-8?B?UMOkciBFbmdzdHLDtm0=?=) Date: Fri, 19 Jan 2018 10:19:46 +0100 Subject: [SocBiN] Job: Advanced national bioinformatics support, SciLifeLab Stockholm Message-ID: <476AD1E3-24FB-47A1-8440-59AA825F6ADC@scilifelab.se> We have several openings for bioinformatics experts at SciLifeLab Stockholm. SciLifeLab (www.scilifelab.se ) is a Swedish national center for molecular biosciences with focus on health and environmental research. The SciLifeLab bioinformatics platform, National Bioinformatics Infrastructure Sweden (www.nbis.se ), is a large national infrastructure in rapid development, now looking for several experts to join the Bioinformatics Long-term Support team (a.k.a. WABI). The Bioinformatics Long-term Support team provides advanced bioinformatics analyses to some of the most scientifically exciting projects across Sweden, and with more than 20 full-time senior bioinformaticians, the team is one of the strongest units in Sweden for analysis of large-scale genomics and related “omics” data. The experts will carry out advanced analyses within nationally prioritized projects, develop tools and workflows for such analyses and educate other scientists in bioinformatics. The new staff members will be employed at Stockholm university, with placement at SciLifeLab Stockholm. More information: http://www.su.se/english/about/working-at-SU/jobs?rmpage=job&rmjob=4680&rmlang=UK We are looking forward to your application, at the latest February 13, 2018! Pär Engström, par.engstrom at scilifelab.se Björn Nystedt, bjorn.nystedt at scilifelab.se Joint Heads of SciLifeLab Bioinformatics Long-term Support --- Pär Engström, PhD Joint Head of Bioinformatics Long-term Support (WABI) National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory Department of Biochemistry and Biophysics, Stockholm University Tel. +46 (0)8 16 22 44 http://www.nbis.se , http://www.scilifelab.se/platforms/nbis -------------- next part -------------- An HTML attachment was scrubbed... URL: From arne at bioinfo.se Fri Jan 19 10:43:48 2018 From: arne at bioinfo.se (Arne Elofsson) Date: Fri, 19 Jan 2018 10:43:48 +0100 Subject: [SocBiN] Job: Advanced national bioinformatics support, SciLifeLab Stockholm In-Reply-To: References: <476AD1E3-24FB-47A1-8440-59AA825F6ADC@scilifelab.se> Message-ID: Det är rätt adres och mailet godkänt nu... Jag brukar vara snabb på att godkänna mail, men förfrågan hade inte ens kommit fram till mig så det var inte gjort ännu. Möjigen finns det någon sorts fördröjning på list-sidan så att man ska ha chans att ta bort sitt mail... Yours Arne ----------------------------------------- Arne Elofsson Science for Life Laboratory Tel:+46-(0)70 695 1045 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 On Fri, Jan 19, 2018 at 10:29 AM, Pär Engström wrote: > Hej Arne, > > Skickade jag nedanstående mail till rätt SocBiN adress? > > Jag har märkt att jag haft svårt att få genom mina mail tidigare när jag > använt denna adress, trots att det är den som anges på listans hemsida ( > https://lists.su.se/mailman/listinfo/socbin-at-sbc.su.se). Just mailet > nedan skickade jag för bara en liten stund sedan och fick ett svar att det > står i kö för godkännande av moderator. Jag förstår att ni inte hunnit > godkänna detta mail än, men vill ändå kolla att adressen är rätt så att det > inte blir fördröjt i onödan. > > Mvh > Pär > > Begin forwarded message: > > *From: *Pär Engström > *Subject: **Job: Advanced national bioinformatics support, SciLifeLab > Stockholm* > *Date: *19 January 2018 at 10:19:46 GMT+1 > *To: *socbin-at-sbc.su.se at lists.su.se > > We have several openings for bioinformatics experts at SciLifeLab > Stockholm. > > SciLifeLab (www.scilifelab.se) is a Swedish national center for molecular > biosciences with focus on health and environmental research. The SciLifeLab > bioinformatics platform, National Bioinformatics Infrastructure Sweden ( > www.nbis.se), is a large national infrastructure in rapid development, > now looking for several experts to join the Bioinformatics Long-term > Support team (a.k.a. WABI). The Bioinformatics Long-term Support team > provides advanced bioinformatics analyses to some of the most > scientifically exciting projects across Sweden, and with more than 20 > full-time senior bioinformaticians, the team is one of the strongest units > in Sweden for analysis of large-scale genomics and related “omics” data. > The experts will carry out advanced analyses within nationally prioritized > projects, develop tools and workflows for such analyses and educate other > scientists in bioinformatics. > > The new staff members will be employed at Stockholm university, with > placement at SciLifeLab Stockholm. > > More information: > http://www.su.se/english/about/working-at-SU/jobs? > rmpage=job&rmjob=4680&rmlang=UK > > We are looking forward to your application, at the latest February 13, > 2018! > > Pär Engström, par.engstrom at scilifelab.se > Björn Nystedt, bjorn.nystedt at scilifelab.se > Joint Heads of SciLifeLab Bioinformatics Long-term Support > > --- > Pär Engström, PhD > Joint Head of Bioinformatics Long-term Support (WABI) > National Bioinformatics Infrastructure Sweden (NBIS), Science for Life > Laboratory > Department of Biochemistry and Biophysics, Stockholm University > Tel. +46 (0)8 16 22 44 <08-16%2022%2044> > http://www.nbis.se, http://www.scilifelab.se/platforms/nbis > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From iwona.zielinska at mimuw.edu.pl Thu Jan 25 14:20:55 2018 From: iwona.zielinska at mimuw.edu.pl (=?UTF-8?Q?Iwona_Zieli=c5=84ska?=) Date: Thu, 25 Jan 2018 14:20:55 +0100 Subject: [SocBiN] Jobs for PhD students Message-ID: Dear Colleagues, *Project “CONTRA – Computational Oncology Training Alliance”*for Marie Skłodowska-Curie European Training Network - *invites 15 PhD students to cooperation* – in the field of *CANCER GENOMIC EVOLUTION* https://itn-contra.org *Application deadline: 23:59 CET on the 15 February 2018 * CONTRA (https://itn-contra.org) is a H2020 Marie-Sklodowska-Curie Innovative Training Network aimed at providing a structured training programme to 15 Early Stage Researchers (ESRs) *to study tumor evolution using computational techniques* upon novel experimental data including, but not limited to, single-cell genomic data. See the list of projects at the end of this message. The training structure of CONTRA will include local and network-wide activities and secondments to other labs in the network. *Most positions are for 3 years and some for 4 years*, contracts starting approximately July 1, 2018, but all of  them lead to a PhD degree. Specific conditions may apply to individual positions depending on local regulations. Top-level graduates (master degree or equivalent) in bioinformatics, statistics, mathematics, computer science or evolutionary biology are encouraged to apply. No discrimination will be made on the basis of nationality, gender, race, religion or disability. H2020 EU funding imposes strict eligibility criteria. At the time of recruitment the researcher must not have resided or carried out his/her main activity (work, studies, etc…) in the country of the host institute for more than 12 months in the three years immediately prior to his/her recruitment. The researcher should also be in the first four years of their research careers at the time of recruitment by the host organisation and have not been awarded a doctoral degree. The successful candidate will receive a very generous financial package. The exact conditions varies across the universities, but the gross amounts of *EU funding for an ESR is in the range 3710€-4210€.* The net salary will result from deducting all compulsory (employer/employee) social security contributions as well as direct taxes from the gross amounts, according to the law applicable to the agreement concluded with the ESR.  Some universities will also supplement the EU funding. EU Guide for applicants: https://goo.gl/d6LtsE Candidates may apply for the positions through the KTH application system https://goo.gl/yTThgg *The application should include the following documents: * 1.1. Curriculum vitae with at most 3 pages 2.2. Transcripts from University / University College 3.3. Contact details for three references 4.4. Brief description of why the applicant wishes to become a PhD student within this network 5.5. Ranking of 3 ESR projects based on the applicant’s preference Each project supervisor will revise the candidates’ documentation and, on the basis of the completeness and adequacy of the requested material and eligibility, will score candidates based on: (1) academic profile; (2) personal motivation; (3) scientific skills and relevant experience; and (4) English proficiency. Shortlisted candidates will be invited to teleconference interviews with the relevant project supervisor(s). Application deadline: 23:59 CET on 15 February 2018. Candidates are invited to contact the supervisors for more details. For individual descriptions of the 15 projects, please use the following link: https://itn-contra.org/esr-projects/. *List of projects, including supervisor and host institution:* - *ESR1*: Comparing tumour phylogenies from single cell data versus bulk sequencing data. Florian Markowetz, University of Cambridge, Cambridge, UK. - *ESR2*: The mechanisms of coding and non-coding oncogenic alterations. Nuria Lopez-Bigas, IRB, Barcelona, Spain. - *ESR3*: Identification of drivers of relapse and metastasis. Nuria Lopez-Bigas, IRB, Barcelona, Spain. - *ESR4:* Estimating tumour phylogenies from single-cell SNV and CNA data. Niko Beerenwinkel, ETH Zurich, Basel, Switzerland. - *ESR5*: Evolutionary history of circulating tumour cells and distant metastases. Ewa Szczurek, University of Warsaw, Warsaw, Poland. - *ESR6*: Identification and impact of clonal and subclonal driver alterations on cancer progression. Francesca Ciccarelli, KCL/Crick Institute, London, UK. - *ESR7*: Inferring tumour evolution and migration. Niko Beerenwinkel, ETH Zurich, Basel, Switzerland. - *ESR8*: Models and inference for Single-cell sequencing and tumour evolution. Jens Lagergren, KTH, Stockholm, Sweden. - *ESR9*: Evolution of drug resistance on genetic and phenotypic levels. Ewa Szczurek, University of Warsaw, Warsaw, Poland. - *ESR10*: Driver events, evolutionary dynamics and interplay with the external environment across cancer types. Francesca Ciccarelli, KCL/Crick Institute, London, UK. - *ESR11*: Estimation of tumour growth rates from NGS data. David Posada, University of Vigo, Vigo, Spain. - *ESR12*: Mutational patterns and models within tumours. David Posada, University of Vigo, Vigo, Spain. - *ESR13*: Integrated image and genomics. Yinyin Yuan, ICR, London, UK. - *ESR14*: Spatial genetics and transcriptomics of pancreatic and ovarian cancer. Florian Markowetz, University of Cambridge, Cambridge, UK. - *ESR15*: Reconciling tumour trees and multiple tumour progression models. Jens Lagergren, KTH, Stockholm, Sweden. Please forward this message to possible candidates in your network. Best regards, Iwona Zielińska -- Iwona Zielińska project manager Horizon 2020 - CONTRA University of Warsaw www.uw.edu.pl www.mimuw.edu.pl -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: iwona_zielinska.vcf Type: text/x-vcard Size: 195 bytes Desc: not available URL: From peter.norberg at microbio.gu.se Thu Jan 25 12:10:46 2018 From: peter.norberg at microbio.gu.se (Peter Norberg) Date: Thu, 25 Jan 2018 11:10:46 +0000 Subject: [SocBiN] Postdoctoral research position Message-ID: <6A858E7E-BA3D-49C7-9CAC-44354B6030BA@microbio.gu.se> Dear colleagues, There is an open postdoc position in my lab at Sahlgrenska, Gothenburg. Please forward to anyone that might be interested. Best Peter -------------------------------------------- Peter Norberg Associate Professor MD, PhD, MSc (CompSc) The Institute of Biomedicine Dept. of Infectious Diseases University of Gothenburg Guldhedsgatan 10 B SE 413 46 Gothenburg Sweden phone: +46 735 316166 email: peter.norberg at gu.se -------------------------------------------- OPEN POSITIONSPostdoctoral fellow in bioinformatics and medical microbiology Diary id: PAR 2018/86 Employment level: Time limited employment (temporary) Location: Institute of Biomedicine Apply by: 2018-02-23 The Institute of Biomedicine is involved in both research and education. In both of these areas, we focus on fundamental knowledge of the living cell – what it consists of, how it works, how its function is directed by the genetic material, and how it interacts with various kinds of micro-organisms. Using this knowledge, we try to elucidate the causes of diseases, and find new ways to diagnose and treat them. The Institute is composed of the following five departments: * The Department of Infectious Diseases * The Department of Microbiology and Immunology * The Department of Pathology and Genetics * The Department of Clinical Chemistry and Transfusion Medicine * The Department of Medical Biochemistry and Cell Biology At present, the institute has about 360 employees and approximately 400 million SEK in total assets. The institution now seeks a postdoc fellow with focus on bioinformatics and pathogenic genetics. Subject area Bioinformatics and medical microbiology Subject area description The research group has recently found that the vast majority of viruses have highly optimized genomes. This optimization is very species-specific and is called genomic signatures. The aim of the group is to take advantage of these genomic signatures to develop new methods for the optimization of viral vectors, and attenuation of viruses. Another aim is to develop a platform for non-homologue classification of pathogens. The research group has close collaboration with pre-clinical and clinical researchers at Sahlgrenska Hospital, and with computer scientists at Chalmers University of Technology. Job assignments The applicant will analyze and map genomic signatures in various pathogens, such as viruses, bacteria, and fungi. The project also includes development of computational algorithms for analysis and modification of genomic signatures. Eligibility An achieved doctoral degree is compulsory for a position as postdoctor at Göteborg University. The doctoral thesis shall be in a relevant area according to the specific position stated here. Since a position as postdoctor aims to give new holders of the doctorate the opportunity mainly to strengthen and develop their scholarly proficiency, we aim for those who have a doctoral degree not older than 3 years counting from last date of application. The qualifications for academic positions are given in Chapter 4, Section 3 - 4 of the Higher Education Ordinance. Assessment The applicant should have a strong background in bioinformatics and microbiology. PhD in related area is compulsory. Degree in computer science is a merit. Other merits are expertise in viral and bacterial genomics, genomic signatures, vectors, and algorithmic development. Regulations for the evaluation of qualifications for academic positions are given in Chapter 4, Section 3 - 4 of the Higher Education Ordinance. Employment The employment is temorary, two years, full time with placement at the Institute of Biomedicine. For further information: Please contact Peter Norberg, docent, phone: +46 (0)735 316 166, e-mail: peter.norberg at gu.se Unions Union representatives at the University of Gothenburg: http://www.gu.se/english/about_the_university/job-opportunities/union-representatives How to apply In order to apply for a position at the University of Gothenburg, you have to register an account in our online recruitment system. It is the responsibility of the applicant to ensure that the application is complete in accordance with the instructions in the job advertisement, and that it is submitted before the deadline. The selection of candidates is made on the basis of the qualifications registered in the application. The application should contain: - A cover letter giving a brief description of previous research experience, and a motivation to why you are applying - A CV including a list of publications - Proof of completed PhD - Contact details of two references Closing date: February 23, 2018 The University of Gothenburg promotes equal opportunities, equality and diversity. Salary is determined on an individual basis. Applications will be destroyed or returned (upon request) two years after the decision of employment has become final. Applications from the employed and from those who appeal the decision will not be returned. -------------- next part -------------- An HTML attachment was scrubbed... URL: From lex.nederbragt at ibv.uio.no Fri Jan 26 12:56:39 2018 From: lex.nederbragt at ibv.uio.no (Lex Nederbragt) Date: Fri, 26 Jan 2018 12:56:39 +0100 Subject: [SocBiN] Call for new Software Carpentry workshop locations in the Nordic countries Message-ID: Hi, We are looking for universities in the Nordic countries (Denmark, Finland, Iceland, Norway, Sweden) that are interested in hosting their first (!) Software Carpentry workshop in the spring of 2018. We will apply for funds from the Nordic e-Infrastructure Collaboration (NeIC) available from their open call for course mobility proposals. We will apply for funds that cover these costs for four workshops: Costs for the travel and lodging for two instructors, these will be recruited from the Nordic countries The Software Carpentry workshop fee What are we looking for: Universities that have not yet hosted a Software Carpentry workshop (check out the maps of past and upcoming workshops) A person willing to be the local contact person taking care of Finding a suitable room Finding 3 or 4 helpers (local helpers to assist the learners, answer questions etc) Announcing the workshop through appropriate channels Helping the instructors with arranging travel and lodging Software Carpentry will take care of workshop registration and instructor recruitment. Interested in hosting a workshop? Please fill out this form: https://goo.gl/forms/h2RLzV5a4vgRw6AM2 . Questions? Contact me at lex.nederbragt at ibv.uio.no Regards, Lex Nederbragt (University of Oslo) Disclaimer: I am a member of The Carpentries Executive Committee, but I am not writing this proposal in that capacity. -- Lex Nederbragt 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://flxlex.flavors.me/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From torgeir.r.hvidsten at nmbu.no Wed Jan 31 08:25:02 2018 From: torgeir.r.hvidsten at nmbu.no (Torgeir Rhoden Hvidsten) Date: Wed, 31 Jan 2018 08:25:02 +0100 Subject: [SocBiN] Associate Professor in Computational and Statistical Genomics In-Reply-To: References: Message-ID: <0f12c2f5-e051-30d8-817b-95b0eca33c78@nmbu.no> Position as Associate Professor in Computational and Statistical Genomics at NMBU, Norway: The Department of Animal- and Aquacultural Sciences, Faculty of Biosciences, at the Norwegian University of Life Sciences (NMBU) invites applications for a permanent, full time position as an Associate Professor in Computational and Statistical Genomics. The successful candidate will join the multidisciplinary Genome Biology research group, which possess expertise in genetics, evolutionary and comparative genomics, bioinformatics and systems biology. This group includes two full-time professors, one associate professor, twelve researchers, seven PhD students and nine research technicians, teaming up within Centre for Integrative Genetics (CIGENE; www.cigene.no ). CIGENE has a strong aqua- and agri- research profile, with key strengths in application of ‘omics’ data to understand the genetic architecture of complex traits. The group has a track-record in high-impact publishing and development of invaluable genomic resources for agricultural and marine species. CIGENE has also established excellent wet lab facilities for automated high-throughput omics, as well as a connected dry-lab with bioinformatics specialists. *The position* The successful candidate will play a key role in developing the group’s research portfolio and teaching within computational and statistical genomics. The person will be central for implementation of computing, analysis and software development essential to meet the challenges arising from the rapid growth and complexity of omics data. Abilities to critically assimilate information across disciplines (molecular genomics, systems genetics and statistics), talent for structuring and analysing data, and interest in teamwork and interdisciplinary cooperation are essential for the position. The successful candidate will be required to make a major contribution to the development of genome biology research and teaching at the Faculty of Biosciences. This include teaching and developing study programs, writing of grant applications and publishing in peer reviewed journals. Communicating key results and new methodologies to industry, and engaging with industry partners will also be a part of the position. The appointed candidate will take part in the Department’s teaching and supervision of BSc, MSc and PhD students and participate in administrative work at the department, faculty and university level. *Application deadline: 15^th March 2018.* More information about the position at: https://www.jobbnorge.no/ledige-stillinger/stilling/147496/associate-professor-in-computational-and-statistical-genomics-refno-18-00595 Best regards, Sig /Sigbjørn Lien / // /Centre for Integrative Genetics (CIGENE) and/ // /Department of Animal and Aquacultural Sciences,/ // /Faculty of Biosciences,/ // /Norwegian University of Life Sciences/ // // Cigenecid:image001.jpg at 01D387EB.5B3487F0 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.jpg Type: image/jpeg Size: 4805 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image002.jpg Type: image/jpeg Size: 2277 bytes Desc: not available URL: From arne at bioinfo.se Wed Jan 31 17:34:44 2018 From: arne at bioinfo.se (Arne Elofsson) Date: Wed, 31 Jan 2018 17:34:44 +0100 Subject: [SocBiN] Call for applications to the National Graduate School in Medical Bioinformatics Message-ID: Dear Colleague, MedBioInfo is the Swedish National Graduate School in Medical Bioinformatics, providing advanced bioinformatics training to the next generation of life science researchers in Sweden. The application deadline for the MedBioInfo incoming class of 2018 is now quite close -- February 28. MedBioInfo has had a great start, with two successful courses completed in 2017, a productive Annual Meeting, a new collaboration with our Norwegian sister school NORBIS, and several excellent courses planned for 2018. The faculty have put a lot of effort into providing the highest quality PhD-level bioinformatics training possible -- more than is available in most places in the world. However for us to deliver a high quality program, we have to attract the best students possible. So we kindly request that you forward this announcement to people that you think may be interested, as well as to your departmental or other relevant email groups. To all current and prospective 1st year PhD students in Bioinformatics, You are invited to apply to MedBioInfo, the National Graduate School in Medical Bioinformatics, established to provide advanced training in bioinformatics to the next generation of world-class life-science researchers. Our 36 affiliated faculty members include most of the leading bioinformaticians in Sweden, and we also draw on the faculty of NORBIS, our Norwegian sister school. Alongside your peers, this will form a key part of your future scientific network. Our courses are short (1-2 weeks), and offered 2-3 times per year, totalling about 30 HP over the course of 3 years. The courses are more specialised than can be provided by your home university. You will be matched with a faculty mentor, providing a perspective and advice complementary to that of your advisor. We also have an annual meeting where you will attend faculty talks and soft-skills workshops (this year featuring scientific graphics and data management, law, and ethics), present your research, network, and get feedback. You will be granted a yearly travel budget. Best of all, this should be fun. You are eligible to apply if you began or will begin your PhD between January 2017 and April 2018, though there is some flexibility in this. Target groups include PhD students in Life Science doing primarily computational research. The deadline is *February 28, *2018. Enrollment is limited to 20 incoming students per year. You should sign up using this form , also linked to from medbioinfo.se. Feel free to email me with any questions. We look forward to reading your application. With kind regards, Sam *Samuel Coulbourn Flores, Docent *Dean of the Swedish National Graduate School in Medical Bioinformatics *Studierektor för den nationella forskarskolan inom medicinsk bioinformatik* SciLifeLab A6220 (Alpha Floor 6) Tomtebodavägen 26a Department of Biochemistry and Biophysics Stockholm University Mobil: +46.706000464 <070-600%2004%2064> Mexank: 0816-3949 samuel.flores at dbb.su.se skype: samuelfloresc -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: poster-forskarskola.A4.pdf Type: application/pdf Size: 5604599 bytes Desc: not available URL: From Inge.Jonassen at ii.uib.no Wed Jan 31 18:25:48 2018 From: Inge.Jonassen at ii.uib.no (Inge Jonassen) Date: Wed, 31 Jan 2018 18:25:48 +0100 Subject: [SocBiN] bioinformatics service scientist (researcher) - permanent job - in Bergen Message-ID: Exciting job with many opportunities for the right candidate! The job is part of the help desk of ELIXIR Norway For more information (and to apply), see https://www.jobbnorge.no/en/available-jobs/job/147545/service-scientist-researcher-at-the-computational-biology-unit-department-of-informatics-university-of-bergen Or send me an email. All the best, Inge Inge Jonassen, Prof PhD Head of Node, Elixir Norway Director, Computational Biology Unit Department of Informatics University of Bergen HiB N5020 Bergen Norway Inge.Jonassen at uib.no -------------- next part -------------- An HTML attachment was scrubbed... URL: