From kimleeng at gmail.com Mon Feb 1 10:10:11 2021 From: kimleeng at gmail.com (Kim Ng) Date: Mon, 1 Feb 2021 10:10:11 +0100 Subject: [SocBiN] Bioinformaticians permanent job positions (SSI, Copenhagen, Denmark) Deadline 07-02-2021 Message-ID: Hello, I'm doing this on behalf of Marc Stegger (MTG at ssi.dk), who is looking for multiple people interested in microbial surveillance including work related to the current national covid-19 surveillance in Denmark. Work would be related to public health infrastructure related to microbials including pipeline development and software infrastructure. Deadline is 07-02-2021 https://candidate.hr-manager.net/ApplicationInit.aspx?cid=5001&ProjectId=138971&DepartmentId=9178&MediaId=5&SkipAdvertisement=False Kind regards, -Kim Ng -------------- next part -------------- An HTML attachment was scrubbed... URL: From jonas.paulsen at ibv.uio.no Tue Feb 2 09:24:59 2021 From: jonas.paulsen at ibv.uio.no (Jonas Paulsen) Date: Tue, 2 Feb 2021 08:24:59 +0000 Subject: [SocBiN] PhD position in bioinformatics and genomics - University of Oslo Message-ID: <1612254299168.50882@ibv.uio.no> A fully funded bioinformatics/genomics PhD position is available at the Department of Biosciences, University of Oslo. The fellowship will be for a period of 3 years, or for a period of 4 years, with 25% teaching responsibilities at the department, contingent on the qualifications of the candidate and the teaching needs of the department. The candidate will be supervised within the recently established research group of Associate Professor Jonas Paulsen. Building on bioinformatics software developed in his research group [Nature Protoc. 2018; Nature Genetics 2019], Hi-C and RNA-seq data will be used to generate predictive computational models of 3D genome reorganization and gene expression changes during different types of induced nuclear deformations in cancer cells. Imaging techniques, including super-resolution imaging, will be used to validate the models. Relevant skills: Bioinformatics, high-throughput sequencing (or imaging) analyses, hands-on experience in general laboratory work Salary offered: 482 200 - 526 000 NOK / year (~48 000 EUR / year) Earliest starting date: April 1, 2021 Latest starting date: October 1, 2021. Read more about the group here: https://www.mn.uio.no/sbi/english/groups/paulsen-group/ Read more and apply here: https://www.jobbnorge.no/en/available-jobs/job/199984/phd-research-fellow-in-genomics-and-bioinformatics ? ________________________________ Jonas Paulsen, PhD Associate Professor Section for Genetics and Evolutionary Biology (EVOGENE) Department of Biosciences University of Oslo https://urlproxy.sunet.se/canit/urlproxy.php?_q=aHR0cHM6Ly93d3cucGF1bHNlbmxhYi5jb20v&_s=ZGVmYXVsdA%3D%3D&_c=2e66bf7f&_r=c3Utc2U%3D Tel: +47 41147241 ________________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: From phil.ewels at scilifelab.se Wed Feb 3 11:09:24 2021 From: phil.ewels at scilifelab.se (Phil Ewels) Date: Wed, 3 Feb 2021 02:09:24 -0800 Subject: [SocBiN] nf-core (Nextflow pipelines) seminar series + hackathon Message-ID: Hi all! Over at nf-core (Nextflow pipeline community) we are launching a series of short *15 minute* seminars covering a number of focussed training topics, called *nf-core/bytesize*. The seminars will be on Zoom at 13:00 European time each Tuesday, also live-streamed to YouTube and available on YouTube afterwards. You can find out more details and get the schedule here: https://nf-co.re/events We are also running a 3-day online hackathon March 22-24 - https://nf-co.re/events/2021/hackathon-march-2021 . We’re aiming to run 24-hrs for all time zones. Let me know if you have any questions (or hop on to the nf-core Slack for more). Everyone welcome! Phil Ewels -- Phil Ewels, Ph.D. Bioinformatics Lead, NGI Applications Development National Genomics Infrastructure (NGI), SciLifeLab Sweden phil.ewels at scilifelab.se - Twitter: @tallphil - GitHub: @ewels -------------- next part -------------- An HTML attachment was scrubbed... URL: From michaut.bioinfo at gmail.com Wed Feb 3 11:16:30 2021 From: michaut.bioinfo at gmail.com (Magali Michaut) Date: Wed, 3 Feb 2021 11:16:30 +0100 Subject: [SocBiN] Bioinformatics Specialist Position in Copenhagen, DK Message-ID: <28CA4A10-43AE-44D5-A509-81C60A6B8A30@gmail.com> Dear all, A permanent position is available on the Genomics Platform of DanStem & CPR at the University of Copenhagen. https://employment.ku.dk/staff/?show=153434 Apply before the end of February. Cheers, Magali -------------- next part -------------- An HTML attachment was scrubbed... URL: From phil.ewels at scilifelab.se Wed Feb 3 11:45:01 2021 From: phil.ewels at scilifelab.se (Phil Ewels) Date: Wed, 3 Feb 2021 02:45:01 -0800 Subject: [SocBiN] Open position: Bioinformatician at NGI SciLifeLab, Stockholm Message-ID: Hi all! We’re looking for a bioinformatician / software dev / systems engineer / jack-of-all-trades in Stockholm, Sweden: https://ngisweden.scilifelab.se/2021/01/bioinformatician-job-advert/ Examples of duties are: - Working in collaborative projects with users. - Analysing data from internal development projects. - Working with systems development and HPC deployments, (e.g. deploying Nextflow pipelines across multiple systems using Nextflow Tower ). - Developing new analysis pipelines as part of nf-core . - Software development, for example for quality control (eg. MultiQC ). - Automation of internal data / analysis flow. The exact work tasks for the candidate will depend on experience and individual interest. We are a curious and flexible team and aim to work on what we are most excited by. Let me know if you have any questions, Phil Ewels -- Phil Ewels, Ph.D. Bioinformatics Lead, NGI Applications Development National Genomics Infrastructure (NGI), SciLifeLab Sweden phil.ewels at scilifelab.se - Twitter: @tallphil - GitHub: @ewels -------------- next part -------------- An HTML attachment was scrubbed... URL: From arne at bioinfo.se Thu Feb 4 15:30:13 2021 From: arne at bioinfo.se (Arne Elofsson) Date: Thu, 4 Feb 2021 15:30:13 +0100 Subject: [SocBiN] Medbioinfo PhD school in medical bioinformatics Message-ID: Dear Colleague -- We would much appreciate it if you could forward the below message and attached flyer to Departmental and other relevant email lists. 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 43 affiliated faculty members include most of the leading bioinformaticians in Sweden, and we also draw on the faculty of NORBIS, our Norwegian sister school. In January 2020 we admitted 28 students, up from a target of 20, of which 43% were female, substantially higher than the field in general. The faculty and fellow students will form a key part of your future scientific network. Our courses are short, worth 3 or 5 HP(ECTS). Each course typically requires a one-week at-home pre-assignment, one week in residence (or, during the crisis, by zoom), and (often) a one-week take-home post-assignment. You would typically take two courses per year, for a total 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. Crisis permitting, we will hold an annual meeting where you will attend faculty talks and soft-skills workshops, 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 at any Swedish university between January 2020 and April 2021, though there is some flexibility in this. Target groups include PhD students in Life Science doing primarily computational research.Selection criteria include your CV, transcript, and the relevance of your research project. You will also need an endorsement letter from your advisor and a suitable laptop. We strive to have a broad distribution of home universities as well as a continued good gender balance. You will be expected to attend your first course, "Applied Bioinformatics," probably in June, as will be announced on MedBioInfo.se. Several of our core courses require programming in Python. If your Python background is weak, you will need to strengthen your skills before your first course. There are many online courses for this, and we also recommend Shaw's "Python 3 the hard way." For climate reasons we ask students (with the possible exception of those from Umeå) to avoid flying to MedBioInfo events. The deadline is February 28, 2021. Our enrollment target is approximately 20 incoming students per year, though we have admitted more in recent years. You should sign up following https://ec.europa.eu/eusurvey/runner/MedBioInfo-application-2021 , also linked to from medbioinfo.se . Feel free to email me with any questions. We look forward to reading your application. With kind regards, Samuel Coulbourn Flores (Dean of Students) and Arne Elofsson (Director) Department of Biochemistry and Biophysics Stockholm University Visiting: SciLifeLab A6220 (Alpha Tr. 6) Tomtebodavägen 23a (main entrance) Mobil: +46.706000464 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From sermarcue at gmail.com Mon Feb 8 20:28:43 2021 From: sermarcue at gmail.com (Sergio Martinez Cuesta) Date: Mon, 8 Feb 2021 19:28:43 +0000 Subject: [SocBiN] Two Senior Bioinformatics Scientist positions at AstraZeneca (Cambridge, UK) Message-ID: Hi everyone, This may be of interest for those of you reaching your end of contracts We are currently recruiting two Senior Bioinformatics Scientists to join our bioinformatics team in AstraZeneca (Cambridge, UK). Please feel free to distribute this among your contacts: - Senior Bioinformatician with a focus on enabling the implementation of our *DNA Encoded Library (DEL)* drug discovery infrastructure (application deadline *16th Feb 2021)* https://careers.astrazeneca.com/job/cambridge/senior-bioinformatician-data-engineer-data-scientist/7684/18216461 - Senior Bioinformatician to develop our *oncology **target identification and validation *strategy using data from CRISPR screens and related functional genomics technologies (*apply as soon as possible*) https://careers.astrazeneca.com/job/cambridge/senior-bioinformatician/7684/18547944 Thanks in advance, Sergio -------------- next part -------------- An HTML attachment was scrubbed... URL: From Erik.Bongcam at slu.se Fri Feb 12 17:23:09 2021 From: Erik.Bongcam at slu.se (Erik Bongcam Rudloff) Date: Fri, 12 Feb 2021 16:23:09 +0000 Subject: [SocBiN] Two new bioinformatics positions Message-ID: Dear all, We have to positions at the Swedish University for Agricultural Sciences Bioinformatics platform in Uppsala. www.slubi.se For more detailed information and where to apply: https://www.slu.se/en/about-slu/work-at-slu/jobs-vacancies/?rmpage=job&rmjob=4568&rmlang=UK https://www.slu.se/en/about-slu/work-at-slu/jobs-vacancies/?rmpage=job&rmjob=4575&rmlang=UK Have a nice weekend and be safe. Erik ----------------------------------- Dr. Erik Bongcam-Rudloff Professor of Bioinformatics Head of SLU Bioinformatics Infrastructure (SLUBI) Head of SGBC SLU-Uppsala +46-(0)72-535 55 87 +46 (0)18-67 21 21 --- N?r du skickar e-post till SLU s? inneb?r detta att SLU behandlar dina personuppgifter. F?r att l?sa mer om hur detta g?r till, klicka h?r E-mailing SLU will result in SLU processing your personal data. For more information on how this is done, click here -------------- next part -------------- An HTML attachment was scrubbed... URL: From arne at bioinfo.se Sun Feb 14 15:43:07 2021 From: arne at bioinfo.se (Arne Elofsson) Date: Sun, 14 Feb 2021 15:43:07 +0100 Subject: [SocBiN] Fwd: Two Senior Bioinformatics Scientist positions in AstraZeneca (Cambridge, UK) In-Reply-To: <398995ca5b0a4aa18a5c73d07bd7e5d0@ebox-prod-srv13.win.su.se> References: <398995ca5b0a4aa18a5c73d07bd7e5d0@ebox-prod-srv13.win.su.se> Message-ID: Dear Arne, I hope this finds you and the members of your lab well We currently have two exciting openings to join our bioinformatics dept. in AstraZeneca. I was wondering if you could please share the positions among bioinformatics colleagues who may be reaching their end of contracts in the Society of Bioinformatics in Nordic Countries Senior Bioinformatics Scientist to lead development and enable implementation of our *DNA Encoded Library (DEL) drug discovery infrastructure* – application deadline 16th Feb 2021 https://careers.astrazeneca.com/job/cambridge/senior-bioinformatician-data-engineer-data-scientist/7684/18216461 Senior Bioinformatics Scientist to lead our *oncology target identification and validation strategy* using data from CRISPR screens and functional genomics technology – apply as soon as possible https://careers.astrazeneca.com/job/cambridge/senior-bioinformatician/7684/18547944 For more details about the roles, please get in touch with sergio.martinezcuesta at astrazeneca.com Have a good weekend Thanks in advance, Sergio ------------------------------ AstraZeneca UK Limited is a company incorporated in England and Wales with registered number:03674842 and its registered office at 1 Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0AA. This e-mail and its attachments are intended for the above named recipient only and may contain confidential and privileged information. If they have come to you in error, you must not copy or show them to anyone; instead, please reply to this e-mail, highlighting the error to the sender and then immediately delete the message. For information about how AstraZeneca UK Limited and its affiliates may process information, personal data and monitor communications, please see our privacy notice at www.astrazeneca.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From mvitezic at gmail.com Tue Feb 16 09:25:06 2021 From: mvitezic at gmail.com (Morana Vitezic) Date: Tue, 16 Feb 2021 09:25:06 +0100 Subject: [SocBiN] Principal Bioinformatician position at Lundbeck Message-ID: Dear all, At Lundbeck we are looking for a new colleague to join our growing Bioinformatics Department. The position is located at our headquarters in the Copenhagen area. Our ideal candidate has a PhD, experience in neuroscience and is proficient in the standard bioinformatics tools. Please find the whole open call and details on how to apply here: https://jobs.lundbeck/job/Copenhagen-Principal-Bioinformatician-Hove/649866701/ I am also happy to reply to any questions regarding this position. Best, Morana -------------- next part -------------- An HTML attachment was scrubbed... URL: From henrik.lantz at nbis.se Thu Feb 18 10:56:09 2021 From: henrik.lantz at nbis.se (Henrik Lantz) Date: Thu, 18 Feb 2021 10:56:09 +0100 Subject: [SocBiN] Permanent Bioinformatician position at SciLifeLab in Uppsala, Sweden Message-ID: Dear all, The bioinformatics platform (NBIS) at SciLifeLab is looking for a new expert to join the organisation in Uppsala, Sweden. The position focuses on giving support to Swedish researchers in bioinformatics, and could dependent on the competences of the applicant involve many different types of analyses. We think experience with non-model organisms and areas such as genome annotation or population genomics will be beneficial for this position, but most of all we want to find the right person for the organisation. Solid experience in sequence-based bioinformatics and good technical competence is more important than experience from a specific type of analysis. NBIS is one of the larger bioinformatics infrastructures in Europe, with over 100 experts employed. To be a support expert in NBIS means being involved in exciting research projects together with researchers from all over Sweden. The variety of projects encountered will give you ample opportunity to learn and expand your competence into new areas, all with the support of your fellow experts. The position is permanent with a 6 month trial period, and deadline is Mar 22. Please see here for more information and how to register: https://www.uu.se/en/about-uu/join-us/details/?positionId=381399 You are very welcome to contact henrik.lantz at nbis.se if you have any questions! Best regards, Henrik ———————— Henrik Lantz Support manager, NBIS Uppsala, Sweden -------------- next part -------------- An HTML attachment was scrubbed... URL: From Kjell.Petersen at uib.no Thu Feb 18 08:55:39 2021 From: Kjell.Petersen at uib.no (Kjell Petersen) Date: Thu, 18 Feb 2021 08:55:39 +0100 Subject: [SocBiN] SystemDeveloper position Elixir Norway - University of Bergen Message-ID: Dear all, We have an open position as System Developer in Elixir Norway , at the Computational Biology Unit - University of Bergen . For more detailed information and where to apply: https://www.jobbnorge.no/en/available-jobs/job/200977/senior-engineer Stay safe, Kjell Kjell Petersen Group leader CBU Service Group University of Bergen Technical Coordinator Elixir Norway -------------- next part -------------- An HTML attachment was scrubbed... URL: From lars.juhl.jensen at gmail.com Mon Feb 22 13:24:04 2021 From: lars.juhl.jensen at gmail.com (Lars Juhl Jensen) Date: Mon, 22 Feb 2021 13:24:04 +0100 Subject: [SocBiN] Postdoc position on biomedical text mining at the Novo Nordisk Foundation Center for Protein Research Message-ID: A postdoc position is available jointly between the Cellular Network Biology (Lars Juhl Jensen) and the Translational Disease Systems Biology (Søren Brunak) groups at The Novo Nordisk Foundation Center for Protein Research (CPR – https://www.cpr.ku.dk). The Disease Systems Biology program consists of three research groups covering many systems level aspects of biology and medicine, including the integration of molecular-level data and healthcare data, including biomedical texts. To address the challenging task of extracting information on lifestyle from text, we have developed a prototype lifestyle-factor ontology. You will train state-of-the-art deep learning-based language models to identify lifestyle descriptors, such as diet, from one of the large biomedical text collections comprising millions of full-text articles. Subsequently you will use it in combination with existing pretrained models and vocabularies to resolve cases of ambiguity, extract associations between diseases and lifestyle factors, and construct an open publicly available knowledge graph from the results. In collaboration with other members of the groups, you will also use cross-lingual representation learning to identify lifestyle factors in text from Danish electronic health records. Furthermore, you will use the literature-based knowledge graph to interpret patient-level data on the progression from healthy to sick from electronic health records and registry data. Projected start date: Second quarter of 2021 Application deadline: March 15th, 2021. For more details please see https://jobportal.ku.dk/videnskabelige-stillinger/?show=153544 -- Lars Juhl Jensen Professor, Group Leader in Disease Systems Biology NNF Center for Protein Research Faculty of Health Sciences University of Copenhagen, Denmark http://jensenlab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From arne at bioinfo.se Wed Feb 24 09:08:42 2021 From: arne at bioinfo.se (Arne Elofsson) Date: Wed, 24 Feb 2021 09:08:42 +0100 Subject: [SocBiN] Fwd: Senior Bioinformatician for Oligonucleotide Therapeutics - Gothenburg (Sweden) In-Reply-To: References: Message-ID: Yours ---------- Forwarded message --------- From: Sergio Martinez Cuesta Date: Wed, Feb 24, 2021 at 12:33 AM Subject: Senior Bioinformatician for Oligonucleotide Therapeutics - Gothenburg (Sweden) We are concluding this recruitment campaign with a role closer to home as we are looking for a *Senior Bioinformatician for Oligonucleotide Therapeutics *in our team in Gothenburg - application *deadline February 28th* https://careers.astrazeneca.com/job/gothenburg/senior-bioinformatician-for-oligonucleotide-therapeutics/7684/18703113 Would you share it among colleagues in the Society of Bioinformatics in the Nordic Countries mailing list please? All the best, Sergio -------------- next part -------------- An HTML attachment was scrubbed... URL: From janina.bocksch at senckenberg.de Fri Feb 26 11:15:47 2021 From: janina.bocksch at senckenberg.de (Janina Bocksch) Date: Fri, 26 Feb 2021 11:15:47 +0100 (CET) Subject: [SocBiN] Postdoc Position in Comparative Genomics at Senckenberg Frankfurt / Application deadline March 15th 2021 Message-ID: <306065024.135858.1614334547107@office.mailbox.org> The Hiller Lab at the LOEWE Center for Translational Biodiversity Genomics (TBG) in Frankfurt, Germany is looking for an ambitious Postdoc to investigate the genomic basis of phenotypic differences between vertebrates. Project The project aims at linking phenotypic adaptations to genomic differences, which is a central goal in the genomics era. The postdoc is expected to capitalize on a powerful repertoire of genomic methods as well as genome alignments and comparative data for several hundred mammals and birds that the lab has generated. A large list of interesting adaptations including metabolic, physiological and morphological traits in bats, dolphins, other mammals and vertebrates is available to be studied, and choices can be influenced by the preference of the postdoc. Our lab The mission of our group is to understand how nature's fascinating phenotypic diversity has evolved and how it is encoded in the genome. Work in the lab includes genome sequencing and assembly, genome alignment and annotation, development and application of comparative genomic methods to discover differences in genes and cis-regulatory elements, and the use of statistical approaches to link phenotypic to genomic changes [1-8]. Our lab is part of TBG (https://tbg.senckenberg.de/) and Senckenberg Research Society, and is based near the city center of Frankfurt am Main, Germany. The TBG provides access to cutting-edge computational infrastructure (HPC, genome browser) and lab facilities to sequence genomes of diverse creatures. English is the working language in our lab. Frankfurt is a vibrant and highly-international city at the heart of Europe that combines a skyscraper skyline with ample park and green areas. Requirements Applicants should have a degree in bioinformatics/computational biology, genomics or a related area, and a strong publication record. Solid programming skills in a Linux environment and experience with shell scripting and Unix tools are required. Previous experience in large-scale comparative genomic data analysis is an advantage. How to apply If interested, please email (i) your CV including publication list and contact information for at least two references and (ii) a summary of previous research experience (max 1 page) to Michael Hiller (Michael.Hiller at sen­­­­ckenberg.de). Further information: https://tbg.senckenberg.de/personen/hiller/ The position is fully-funded. Salary and benefits are according to TV-H E13 100%. The position will be initially for 2 years, but funding is available to extend it further. The employer is the Senckenberg Society for Nature Research in Frankfurt am Main. Senckenberg supports equal opportunity of men and women and therefore strongly invites women to apply. Equally qualified handicapped applicants will be given preference. Application deadline is March 15th 2021. The position is available immediately and the search continues until the position has been filled. Recent publications [1] Jebb et al. Six reference-quality genomes reveal evolution of bat adaptations. Nature, 583, 578–584, 2020 [2] Huelsmann et al. Genes lost during the transition from land to water in cetaceans highlight genomic changes associated with aquatic adaptations. Science Adv, 5(9), eaaw6671, 2019 [3] Hecker et al. Convergent gene losses illuminate metabolic and physiological changes in herbivores and carnivores. PNAS, 116(8), 3036-3041, 2019 [4] Roscito et al. Phenotype loss is associated with widespread divergence of the gene regulatory landscape in evolution. Nature Communications, 9:4737, 2018 [5] Langer et al. REforge associates transcription factor binding site divergence in regulatory elements with phenotypic differences between species. MBE, 35(12), 3027–3040, 2018 [6] Lee et al. Molecular parallelism in fast-twitch muscle proteins in echolocating mammals. Science Adv, 4(9), eaat9660, 2018 [7] Sharma et al. A genomics approach reveals insights into the importance of gene losses for mammalian adaptations. Nature Communications, 9(1), 1215, 2018 [8] Nowoshilow et al. The axolotl genome and the evolution of key tissue formation regulators. -------------- next part -------------- An HTML attachment was scrubbed... URL: