From Carsten.Daub at ki.se Fri Jun 8 09:55:43 2018 From: Carsten.Daub at ki.se (Carsten Daub) Date: Fri, 8 Jun 2018 07:55:43 +0000 Subject: [SocBiN] Recruiting a bioinformatics technician to annotate genomes as part of an international consortium effort Message-ID: <08A525AA-C0E2-4923-9BE2-51B672D12FC5@ki.se> We are recruiting a bioinformatics technician to annotate genomes as part of an international consortium effort. Twitter: https://twitter.com/zencodeITN https://twitter.com/daublab Place: Karolinska Institutet, Stockholm Starting date: ASAP Latest application date: June 28, 2018 (but sooner is better) A laboratory technician position is available until December 31, 2018. A one year extension might be possible depending on the funding situation. To be eligible, potential candidates must not have resided or carried out their main activity (work, studies, etc.) in Sweden for more than 12 months in the 3 years immediately prior to the recruitment, and have no more than 4 years of research experience. This is great fun and you will learn lots! Please email me if you have questions! Best, Carsten --- Carsten O. Daub, PhD Associate Professor, Group Leader Department of Biosciences and Nutrition & Science for Life Laboratory Karolinska Institutet Stockholm, Sweden https://www.daublab.org/ http://ki.se/bionut/daub/ Phone +46 (0) 8-524-81224 Mobile: +46 (0) 72-250-6890 -------------- next part -------------- An HTML attachment was scrubbed... URL: From dirk.repsilber at oru.se Fri Jun 8 11:19:43 2018 From: dirk.repsilber at oru.se (Dirk Repsilber) Date: Fri, 8 Jun 2018 11:19:43 +0200 Subject: [SocBiN] =?utf-8?q?The_Swedish_Bioinformatics_Workshop_=28SBW2018?= =?utf-8?q?=29_in_=C3=96rebro=3A_Oct_25/26th=2C_registration_opens_Mon=2C_?= =?utf-8?q?June_11th_=28free_for_early-bird_PhD_students_registrations=29?= Message-ID: <5B1A4A2F.40802@oru.se> Dear bioinformaticians, this year The Swedish Bioinformatics Workshop (SBW2018) will be held in Örebro (Oct 25/26th): https://www.oru.se/sbw2018 We have an exciting program, with an introductory tutorial on genome-scale metabolomic modelling, invited speakers covering a broad collection of bioinformatics approaches (also from Germany), and a career path discussion in the end. PhD students' early-bird registration will be free of charge. Registration will open coming week Monday, June 11th. Please advertise to all of bioinformaticians in Sweden. Welcome to Örebro in October! Sincerely Dirk. -- _________________________________________________________ Dirk Repsilber Professor Functional Bioinformatics School of Medical Sciences (MV) University of Örebro S - 701 82 Örebro Sweden phone: +46 19 30 1256 web: http://www.oru.se/English/Employee/dirk_repsilber/ _________________________________________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: From eduardo.villablanca at ki.se Fri Jun 8 17:20:09 2018 From: eduardo.villablanca at ki.se (Eduardo Villablanca) Date: Fri, 8 Jun 2018 15:20:09 +0000 Subject: [SocBiN] Postdoctoral position available Message-ID: <46C8B9DF-A460-4E7E-A947-BE802EF6F01B@ki.se> Dear colleagues, We open today the call for a postdoctoral researcher to work in our Lab at the Karolinska Institute (Stockholm, Sweden) as bioinformatician. The candidate will try to understand the molecular and cellular mechanisms underlying intestinal immune homeostasis and how breakdown of these mechanism may lead to immune-mediated inflammatory diseases (IMIDs). The successful candidate will investigate intestinal cell composition and function at the single cell level by combining flow citometry and single cell RNA-sequencing (scRNA-seq) approaches. This position is an exciting opportunity to work on the cutting-edge of mucosal immunology field utilizing computational biology and data visualization tools. The candidate will be part of a multidisciplinary team actively working with renowned collaborators around the globe. I thank you in advance and please feel free to spread the enclosed advertisement in your respective lab/institution. Deadline to apply July 15, 2018 All the best, Eduardo *************************************** Eduardo J. Villablanca, Ph.D., PI Assistant Professor & Wallenberg Academy Fellow in Medicine Department of Medicine, Immunology and Allergy Unit, Karolinska Institute Faculty member, SciLifeLab Karolinska Sjukhuset, L2:04 | 171 76 Stockholm, Sweden Office: +46 8 517 759 34 Website: at KI | CMM -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: V22018_postdoc_Flyer.pdf Type: application/pdf Size: 296425 bytes Desc: V22018_postdoc_Flyer.pdf URL: From Margus.Lukk at cruk.cam.ac.uk Thu Jun 14 15:21:45 2018 From: Margus.Lukk at cruk.cam.ac.uk (Margus Lukk) Date: Thu, 14 Jun 2018 13:21:45 +0000 Subject: [SocBiN] Advert for bioinformatician at DKFZ, Heidelberg, Germany Message-ID: <7BE4259EED9CFF458979146EEE79DD9DAF338DA7@SRV12-0033.cri.camres.org> Dear all, We are looking for a staff bioinformatician to work at Odom lab at DKFZ, Heidelberg, Germany. The job advert can be found here: https://www.dkfz.de/de/stellenangebote/index.php?id=134/2018 Best regards, Margus ---- Margus Lukk, PhD Senior Staff Scientist, University of Cambridge -------------- next part -------------- An HTML attachment was scrubbed... URL: From lionel.guy at imbim.uu.se Fri Jun 15 09:48:50 2018 From: lionel.guy at imbim.uu.se (Lionel Guy) Date: Fri, 15 Jun 2018 07:48:50 +0000 Subject: [SocBiN] Postdoc fellow@UppsalaU: Host Adaptation in Bacteria / Metagenomics Message-ID: <49888F61-A336-417E-9838-EEEFF9C400FC@imbim.uu.se> I am recruiting a new postdoc fellow: POSTDOCTORAL FELLOW IN EVOLUTIONARY MICROBIOLOGY, BIOINFORMATICS 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 available. 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. APPLICATION To be sent by email to lionel.guy at imbim.uu.se, latest on June 30th, 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-groups/infections-and-defences/guy-lionel/ -- Lionel Guy Department for Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden phone: +46 18 471 4246; postal address: Box 582, SE-751 23 Uppsala lionel.guy at imbim.uu.se -- Lionel Guy Department for Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden phone: +46 18 471 4246; mobile +46 73 976 0618; Skype: lionelguy; postal address: Box 582, SE-751 23 Uppsala; visiting address: BMC D7:308b, Husargatan 3, SE-752 37 Uppsala lionel.guy at imbim.uu.se När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/om-uu/dataskydd-personuppgifter/ From anders.andersson at scilifelab.se Fri Jun 15 12:47:42 2018 From: anders.andersson at scilifelab.se (Anders Andersson) Date: Fri, 15 Jun 2018 12:47:42 +0200 Subject: [SocBiN] Research Engineer in Biodiversity Informatics at Scilifelab Message-ID: We are recruiting a Research Engineer in Biodiversity Informatics within the Biodiversity Atlas Sweden project. The position will be located mainly at SciLifeLab in Stockholm. Read more here: https://www.scilifelab.se/vacancies/research-engineer-in-biodiversity-informatics/ /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 michaut.bioinfo at gmail.com Mon Jun 18 08:36:46 2018 From: michaut.bioinfo at gmail.com (Magali Michaut) Date: Mon, 18 Jun 2018 08:36:46 +0200 Subject: [SocBiN] REMINDER: Exciting postdoc opportunity in Copenhagen Message-ID: <437825B1-DAEB-4EDA-9D8F-44D718746A20@gmail.com> One more week to apply to this computational postdoc position in cancer stem cell research with exciting single cell data and more ! Check it out and/or spread the word: http://jobportal.ku.dk/alle-opslag/?show=147220 If you have questions about our group, please contact me. Looking forward to hearing from you, Magali ======= An exciting position in cancer bioinformatics with focus on normal and malignant hematopoiesis as well as cancer stem cell models is available in the Porse Group, at the Biotech Research and Innovation Centre (BRIC)/DanStem in Copenhagen. We are seeking a PhD level computational biologist with an expertise in analysis and interpretation of complex biological data. In our group, we generate omics data using the latest technologies (RNA-seq, single cell RNA-seq, ChIP-seq, proteomics) and have expertise in integrated analysis of gene expression and epigenetic data using cutting edge machine learning approaches. The Research Centre The Biotech Research and Innovation Centre (BRIC) is a research centre of excellence for biomedical research, focusing on disease-oriented basic research, at the Faculty of Health and Medical Sciences, University of Copenhagen. BRIC hosts 24 independent research groups that perform basic and translational research aimed to understand diseases like cancer, neurological and metabolic disorders. For further information about the Porse group and BRIC: http://www.bric.ku.dk/ Our research Several cancers, including acute myeloid leukemias (AML), are maintained by Cancer Stem Cells (CSCs). Similar to normal stem cells, CSCs are able to self-renew and are thus the cells that need to be targeted in order to efficiently eradicate the disease. The focus of the Porse group is therefore to study cancer from a stem-cell centric viewpoint. Specifically, we address the gene regulatory mechanisms governing both normal and malignant hematopoiesis with the aim to identify novel targets for future therapeutic intervention in patients suffering from AML. Additionally, we use single-cell technologies to unravel cellular heterogeneity in normal and malignant stem cells. Key publications relevant for computational biologists: Paul F et al., Cell 2015, 163, 1663-77 Pundhir S, Nucleic Acids Research 2016, 44, 4037-51 Bagger FO et al., Nucleic Acids Research (2016), 44, D917-24 Rapin N. et al., Blood 2014, 123, 894-904 Vitting-Seerup K et al., BMC Bioinformatics 2014, 15, 81 Jakobsen JS et al., Genome Research 2013, 23, 592-603 Weischenfeldt J. et al, Genome Biology 2012, 13, R35 Your job The successful candidate will join our bioinformatics team, currently consisting of two people. Your time will be shared between involvement/support in projects originating from our wet lab, and your own projects, on which you can dedicate 20-30% of your time. You will have the opportunity to develop your own research ideas, which can potentially be supported by experiments from our wet lab. Profile We are looking for a highly motivated and enthusiastic scientist with the following competences and experience: 〈 Essential: PhD in Computer Science, Bioinformatics, or Computational Biology 〈 Strong experience in Python or R and in Linux/UNIX computing environment. 〈 Documented experience with NGS data analysis (ChIP-seq, ATAC-seq, or RNA-seq) 〈 Experience in integrated analysis of large-scale biological data sets 〈 Strong communication and collaboration skills, including the ability to work well in a diverse academic setting, and to balance scientific and day-to-day needs 〈 Ability to work in a team of multidisciplinary scientists, and independently with minimal direction 〈 Excellent written and oral communication skills in English Desirable but not required: 〈 Experience with analysis of single cell RNA-seq data 〈 Experience with applying supervised and unsupervised statistical learning and mathematical methods to biological problems 〈 Experience with system administration 〈 Interest in modern visualisation tools (e.g. plotly, dash, tableau, shiny) 〈 Background in molecular biology and genetics, especially related to disease and drug development will be considered an advantage. We offer - A two-year (possibly extendable) with a competitive salary and social benefits (e.g. social security, health coverage, parental leave) - Access to state-of-the art tools and infrastructure - Tailored support in raising competitive funds and communicate your research - A stimulating and supportive international research environment We have weekly internal seminars with PhD students and postdocs presenting their work as well as external seminars with international speakers. BRIC also hosts several research clubs; hematology club, Chromosome Biology club, Stem cell club and single cell transcriptomics seminar series. The institute has an association for students and postdocs (ASAP), a PhD programme (MoMeD) and a Postdoc Career Programme (PCP). BRIC has extensive international collaborations and actively participates in the European alliance, EU-LIFE consisting of 13 excellent life science research institutions and is part of the EU-funded LIBRA initiative to obtain gender balance in life science research. BRIC has a highly international profile (>60% international researchers) and English as working language. An International Staff Mobility Office at UCPH supports and guides international researchers through your initial steps in Denmark (e.g. residence and work permits, tax and pension, banking, medical care, childcare). They also offer a dual career network open for spouses of our researchers. Start date: preferably Sep 1 or after agreement For further information regarding the position, please contact Bo Porse on e-mail: bo.porse at bric.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 starts at 33,224.48 DKK / 4.456 Euro. An additional 17.1 % monthly contribution to pension will be paid by the employer. Depending on qualifications, a higher salary may be negotiated. Non-Danish and Danish applicants may be eligible for tax reductions, if they hold a PhD degree and have not lived in Denmark the last 10 years. The position is covered by the “Memorandum on Job Structure for Academic Staff at the Universities” of June 28, 2013. Application Your application must be submitted electronically by clicking ‘Apply now’ below or via BRIC’s website on http://www.bric.ku.dk/jobs/. The application must include the following documents/attachments – all in PDF format: 1. Motivated letter of application (max. one page). 2. CV incl. education, work/research experience, language skills and other skills relevant for the position. 3. A certified/signed copy of a) PhD certificate and b) Master of Science certificate. If the PhD is not completed, a written statement from the supervisor will do. 4. List of publications. Letters of recommendation Furthermore, the shortlisted applicant should provide two letters of recommendation. To be taken into consideration, the letter must be signed by the supporting person on paper with institutional letter head and in PDF-format and send to bo.porse at bric.ku.dk with subject “name candidate-postdoc-year”; preferably by the supporting person. The letters should be received 1 week after being notified about shortlisting. Please make sure that an easy match between the recommendation letter and the individual applicant is possible. Application deadline: July 1, 2018 We reserve the right not to consider material received after the deadline, and not to consider applications or letters of recommendation that do not live up to the abovementioned requirements. Application procedure 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/faculty/ BRIC and University of Copenhagen wish to reflect the diversity of society and welcome applications from all qualified candidates regardless of age, disability, gender, nationality, race, religion or sexual orientation. Appointment will be based on merit alone. From Karin.Lagesen at vetinst.no Mon Jun 18 14:40:20 2018 From: Karin.Lagesen at vetinst.no (Lagesen, Karin) Date: Mon, 18 Jun 2018 12:40:20 +0000 Subject: [SocBiN] bioinformatics developer position available at the Norwegian Veterinary Institute and the Norwegian Institute for PUblic Health Message-ID: <74ff0e6a9b684ffc94d7ba87b372ce06@vetinst.no> Hi! In connection with EU projects focusing on sequencing and surveillance of foodborne zoonoses, we now have a 2 year position available shared between the the Norwegian Veterinary and the Norwegian Institute for Public Health. The position focuses on bioinformatics infrastructure and pipeline development, and the person hired will work closely with other international partners involved in the project. For a the full ad, please see here: https://euraxess.ec.europa.eu/jobs/316453 Deadline is 3rd of July. Feel free to ask me any questions that you might have. Karin -- Karin Lagesen, PhD Bioinformatician, Section for Epidemiology Norwegian Veterinary Institute From Inge.Jonassen at ii.uib.no Wed Jun 20 19:44:44 2018 From: Inge.Jonassen at ii.uib.no (Inge Jonassen) Date: Wed, 20 Jun 2018 19:44:44 +0200 Subject: [SocBiN] Bioinformatics researcher position in Bergen Message-ID: A researcher position is available to work on integromics analysis aimed to improve the understanding of Parkinson disease. The position is within the Translational Science in Neurodegeneration and Aging group at the department of clinical medicine and linked with the Jonassen group at the Computational Biology Unit For more information see https://www.nature.com/naturejobs/science/jobs/646715-full-time-permanent-position-as-researcher-at-the-department-of-clinical-medicine 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: From erik.larsson at gu.se Fri Jun 29 13:52:14 2018 From: erik.larsson at gu.se (Erik Larsson Lekholm) Date: Fri, 29 Jun 2018 11:52:14 +0000 Subject: [SocBiN] Postdoc in Gothenburg Message-ID: Hi, There is an opening for a postdoc in computational cancer genomics in my lab in Göteborg - see below: https://www.gu.se/english/about_the_university/job-opportunities/vacancies-details/?id=2775 Please spread the word! Best wishes, Erik Larsson Lekholm