From gemma.atkinson at gmail.com Tue Feb 6 09:28:49 2024 From: gemma.atkinson at gmail.com (Gemma Atkinson) Date: Tue, 6 Feb 2024 09:28:49 +0100 Subject: [SocBiN] Bioinformatics PhD position in the Atkinson lab, Lund University Message-ID: Dear colleagues, We have an open position for a PhD student in the Atkinson lab, Lund University. We are looking for a full-time bioinformatics PhD student to be involved in the Novo Nordisk funded project: ‘Development of phage biocontrol to overcome the antiphage defense system arsenal of phytopathogenic Ralstonia solanacearum bacterium’. This is a project led by Ville Friman in the University of Helsinki, with Vasili Hauryliuk and Gemma C. Atkinson in the University of Lund as co-investigators. This position will be based in the Atkinson lab in Lund. Due to a lack of efficient control methods, plant-pathogenic bacteria threaten safe and stable food production. This project will develop a novel biocontrol method against the plant-pathogenic bacterium Ralstonia solanacearum by employing its natural viral enemies, phages. While phages are highly pathogen-specific and safe to the environment, they can become inefficient due to the rapid development of phage resistance. This project will overcome this by identifying antiphage defence systems in R. solanacearum, and isolating phages that can counteract these defences by escaping their recognition or by deploying their own counter-defence systems. More information and application link here https://lnkd.in/dggfhJWY Deadline March 5th Read about the computational microbiology research we do in the Atkinson lab here: https://atkinson-lab.com/ Best wishes, Gemma Gemma C. Atkinson https://atkinson-lab.com/ Senior Lecturer Department of Experimental Medical Science (EMV) Lund University Sweden gemma.atkinson at med.lu.se -------------- next part -------------- An HTML attachment was scrubbed... URL: From coordinator at rth.dk Thu Feb 15 11:29:39 2024 From: coordinator at rth.dk (Betina Wingreen Jensen) Date: Thu, 15 Feb 2024 11:29:39 +0100 Subject: [SocBiN] Deadline extendend to Feb26 - PhD Fellowship in Bioinformatic analysis at University of Copenhagen, Denmark Message-ID: <003f01da5ff9$e19b07a0$a4d116e0$@rth.dk> Dear Colleagues, We have a super exciting open position for a PhD fellowship in bioinformatic analysis of host - pathogen interactions in the context of anti-microbial resistance in pigs here at the University of Copenhagen, Denmark. For more information about the position and on how to apply, please visit the UCPH website: https://employment.ku.dk/phd/?show=160788 Application deadline: Feb 26, 2024 Start date is May 1st, 2024, or as soon as possible thereafter. Best wishes, Betina Betina Wingreen Jensen Special Advisor/Project Manager University of Copenhagen Department of Veterinary and Animal Sciences 1870 Frederiksberg C DIR +45 35 33 47 04 MOB +45 21 51 09 32 bwj at sund.ku.dk How we protect personal data -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 5362 bytes Desc: not available URL: From erik.sonnhammer at scilifelab.se Thu Feb 15 15:01:10 2024 From: erik.sonnhammer at scilifelab.se (Erik Sonnhammer) Date: Thu, 15 Feb 2024 15:01:10 +0100 Subject: [SocBiN] Bioinformatics PhD position in Stockholm: "Gene regulatory network inference and systems biology" Message-ID: <1e522f98-14f1-4c46-8670-3b40d78b8b50@scilifelab.se> Dear colleagues, There is an open PhD student position in the Sonnhammer group at Science for Life Laboratory in Stockholm, Sweden The goal of the project is to develop computational algorithms and methods that use omics data to infer gene regulatory networks (GRNs), and apply these to understand regulatory mechanisms that lead to cancer formation. See ad at https://sonnhammer.org/download/ads/open.html Deadline 21 February Kind Regards ___________________________________ Erik Sonnhammer, Ph.D. Professor of Bioinformatics DBB, Stockholm University Science for Life Laboratory Stockholm, Sweden Email: Erik.Sonnhammer at scilifelab.se Web: http://sonnhammer.org Description: twitter (20x20) -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: WBsCxsIwz1aTYNUC.png Type: image/png Size: 885 bytes Desc: not available URL: From arne.elofsson at gmail.com Fri Feb 16 15:42:04 2024 From: arne.elofsson at gmail.com (Arne Elofsson) Date: Fri, 16 Feb 2024 15:42:04 +0100 Subject: [SocBiN] PhD position Message-ID: Please forward this add to any relevant students PhD student in Bioinformatics *Project description *Your studies in Bioinformatics will be in the project: *"Deep Learning for protein structure prediction”.* Protein structure is essential for understanding their function and developing drugs targeting proteins. Recently, a deep learning method that can predict the structure of most proteins was made freely available and released a database with predicted protein structures. However, proteins do not act alone - they work together with other proteins. Therefore, the next major challenge is using these methods for predicting protein-protein interactions. Our initial studies have shown that it is possible to predict accurate structures of a large part of dimeric proteins using either a modified version of AlphaFold2 or AlphaFold-multimer. However, many proteins cannot be built accurately, nor can we always distinguish interacting from non-interacting protein pairs and building larger complexes accurately is still an unsolved problem. In this project, we are recruiting additional Ph.D. student to leverage recent advances in machine learning to create better deep-learning models to predict protein-protein interactions and to apply these methods to biologically relevant problems. The Elofsson group is located at the Science for Life Laboratory. Elofsson has worked on protein structure predictions for more than two decades. He has worked on various techniques using machine learning and other computational techniques. Our most important contributions to this work are the methods he has developed to identify the quality of protein models, Pcons and various versions of ProQ. The group comprises 5 PhD students, two postdocs and one senior researcher. https://www.su.se/english/about-the-university/work-at-su/available-jobs/phd-student-positions-1.507588?rmpage=job&rmjob=22761&rmlang=UK 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: @arneelof Mastodon: @arneelof at fediscience.org Zoom: https://stockholmuniversity.zoom.us/my/arneelof/ Scholar: http://scholar.google.se/citations?user=s3OCM3AAAAAJ ORCID: 0000-0002-7115-9751 -------------- next part -------------- An HTML attachment was scrubbed... URL: From janina.bocksch at senckenberg.de Tue Feb 20 09:47:56 2024 From: janina.bocksch at senckenberg.de (Janina Bocksch) Date: Tue, 20 Feb 2024 09:47:56 +0100 (CET) Subject: [SocBiN] ERC-funded Bioinformatician Position / Senckenberg Frankfurt / Application Deadline 22.03.24 Message-ID: <1928282983.302714.1708418876306@office.mailbox.org> Job Announcement ref. #12-24001 ERC-funded Bioinformatician Position The Hiller Lab at the LOEWE Center for Translational Biodiversity Genomics (TBG) in Frankfurt, Germany is looking for a Bioinformatician to work on the BATPROTECT project to investigate the genomic basis of long healthspans, disease resistance and viral tolerance in bats. BATPROTECT is a 6-year funded ERC synergy grant project that will use bats as natural models of healthy aging and disease tolerance to elucidate the molecular mechanisms behind bat’s exceptional longevity and resistance to viral and age-related diseases. BATPROTECT brings together a team of global leaders in bat biology and ageing (Emma Teeling, Dublin), bat immunology and virology (Linfa Wang, Singapore), evolution and genomics (Michael Hiller, Frankfurt), and ageing model organisms (Bjoern Schumacher, Cologne) that will jointly investigate aging and immune responses in bats from the wild and captive colonies, discover genes with evolutionary importance for longevity and disease resistance, and functionally validate longevity and immune regulators in stem and differentiated cells of bats and model organisms, with the ultimate goal to uncover new directions to improve human healthspan and disease outcome. The Project The Bioinformatician will be responsible for the assembly of reference-quality genomes of more than one hundred bat species, for which we are generating PacBio HiFi and HiC data. For a few focal species, we also aim at generating a T2T assembly. The Bioinformatician will also work on analyzing transcriptomics data that we are sequencing in parallel for all target bat species, using this data and our homology-based methods (TOGA) to annotate the new genomes, generating whole genome alignments of bats and other mammals, and supporting the BATPROTECT project with other data processing and analysis tasks. The Bioinformatician will work closely with other Bioinformaticians at TBG, other members of the BATPROTECT team and the Hiller lab. We offer exchanges with the other BATPROTECT labs as well as yearly retreats with all project members. 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 sequencing and assembly of reference-quality genomes, genome alignment and gene annotation, development and application of comparative genomic methods to discover differences in genes and gene expression, and the use of statistical approaches to link phenotypic to genomic changes [1-10]. 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. TBG provides access to cutting-edge computational (large HPC clusters, genome browser) and lab infrastructure to sequence genomes. English is the working language in our lab. Senckenberg and TBG provide flexible working hours, an annual special payment, a company pension scheme, the Senckenberg badge for free entry in museums, the zoo, botanical garden and Palmengarten, and a leave of 30 days per year. Frankfurt is a vibrant and highly-international city at the heart of Europe that combines a skyscraper skyline with ample park and green areas. The Economist 2022 index ranked Frankfurt among the top 10 most livable cities worldwide. Your profile - A Master-level degree in bioinformatics / computational biology, genomics or a related area. A PhD degree is an advantage, but not strictly required. - Excellent programming skills in a Linux environment as well as experience with shell scripting and Unix tools. - Previous experience in genome assembly and ideally genome annotation. Place of employment: Frankfurt am Main Working hours: full time (40 hours/week) / part-time options are available Type of contract: initially limited for 2 years, but ERC funding is available for a total of 4 years Start date: flexible but should ideally be in late spring 2024. Salary and benefits: according to the collective agreement of the State of Hesse (pay grade E13) Senckenberg is committed to diversity. We benefit from the different expertise, perspectives and personalities of our staff and welcome every application from qualified candidates, irrespective of age, gender, ethnic or cultural origin, religion and ideology, sexual orientation and identity or disability. Women are particularly encouraged to apply, as they are underrepresented in the field of this position; in the case of equal qualifications and suitability they will be given preference. Applicants with disabilities (“Schwerbehinderung”) will be given preferential consideration in case of equal suitability. Senckenberg actively supports the compatibility of work and family and places great emphasis on an equal and inclusive work culture. How to apply Please send us your application documents containing - a CV with publication list and contact information for at least two references - a summary of previous research experience (max 1 page) - and copies of certificates, transcripts and grades) in electronic form (as a coherent PDF file) by March 22, 2024 to recruiting at senckenberg.de mailto:recruiting at senckenberg.de quoting the reference number #12-24001, or apply through the online application form on our homepage. Senckenberg Gesellschaft für Naturforschung Senckenberganlage 25 60325 Frankfurt a.M. E-Mail: recruiting at senckenberg.de mailto:recruiting at senckenberg.de For more information please contact Prof. Dr. Michael Hiller, michael.hiller at senckenberg.de mailto:michael.hiller at senckenberg.de or visit the lab webpage https://tbg.senckenberg.de/hillerlab/. For more information about the Senckenberg Gesellschaft für Naturforschung, please visithttp://www.senckenberg.de . Recent publications [1] Kirilenko BM, et al. Integrating gene annotation with orthology inference at scale. Science, 380(6643), 2023 [2] Osipova E, et al. Loss of a gluconeogenic muscle enzyme contributed to adaptive metabolic traits in hummingbirds. Science, 379(6628), 185-190, 2023 [3] Blumer et al. Gene losses in the common vampire bat illuminate molecular adaptations to blood feeding. Science Advances, 8(12), 2022 [4] Roscito et al. Convergent and lineage-specific genomic differences in limb regulatory elements in limbless reptile lineages. Cell Reports, 38(3):110280, 2022 [5] Jebb et al. Six reference-quality genomes reveal evolution of bat adaptations. Nature, 583, 578–584, 2020 [6] Huelsmann et al. Genes lost during the transition from land to water in cetaceans highlight genomic changes associated with aquatic adaptations. Science Advances, 5(9), 2019 [7] Hecker et al. Convergent gene losses illuminate metabolic and physiological changes in herbivores and carnivores. PNAS, 116(8), 3036-3041, 2019 [8] Roscito et al. Phenotype loss is associated with widespread divergence of the gene regulatory landscape in evolution. Nature Communications, 9:4737, 2018 [9] Sharma et al. A genomics approach reveals insights into the importance of gene losses for mammalian adaptations. Nature Communications, 9(1), 1215, 2018 [10] Nowoshilow et al. The axolotl genome and the evolution of key tissue formation regulators. Nature, 554(7690), 50-55, 2018 -------------- next part -------------- An HTML attachment was scrubbed... URL: From coordinator at rth.dk Tue Feb 20 13:13:29 2024 From: coordinator at rth.dk (Betina Wingreen Jensen) Date: Tue, 20 Feb 2024 13:13:29 +0100 Subject: [SocBiN] (Deadline March 5) Postdoc position in computational CRISPR guide RNA design at University of Copenhagen, Denmark In-Reply-To: <3176c9be4df54c76b53615763885b540@sund.ku.dk> References: <3719d2c0350748999460844143c98d77@sund.ku.dk> <3176c9be4df54c76b53615763885b540@sund.ku.dk> Message-ID: <000c01da63f6$37495b70$a5dc1250$@rth.dk> Dear Colleagues, We have a super exciting 3-year position for a Postdoc in computational CRISPR guide RNA design targeting network modules here at the University of Copenhagen, Denmark. For more information about the position and on how to apply, please visit the UCPH website: https://candidate.hr-manager.net/ApplicationInit.aspx/?cid=1307 &departmentId=19008&ProjectId=161190&MediaId=5&SkipAdvertisement=false Application deadline: March 5, 2024 Start date is May 15, 2024, or as soon as possible thereafter. Best wishes, Betina Betina Wingreen Jensen Special Advisor/Project Manager University of Copenhagen Department of Veterinary and Animal Sciences Grønnegårdsvej 3 & 7 & Ridebanevej 3 & 9 1870 Frederiksberg C DIR +45 35 33 47 04 MOB +45 21 51 09 32 bwj at sund.ku.dk How we protect personal data -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 5384 bytes Desc: not available URL: From l.a.meza-zepeda at ous-research.no Sat Feb 24 11:57:17 2024 From: l.a.meza-zepeda at ous-research.no (=?iso-8859-1?Q?Leonardo_Andr=E9s_Meza-Zepeda?=) Date: Sat, 24 Feb 2024 10:57:17 +0000 Subject: [SocBiN] Cancer Bioinformatics position at the Institute fro Cancer Research in Oslo Message-ID: Dear Colleague, We have an exciting postdoctoral position open to work with advanced cancer bioinformatics at the Insititute for Cancer Research in Oslo, Norway. The researcher will use advanced computational approaches to analyse molecular and clinical data of gastrointestinal stromal tumours associated with aggressive clinical behaviour. The analysis will include genome and transcriptome sequencing, single-cell sequencing, long-read sequencing and spatial transcriptomics of tumour samples. If you are interested, please find more infromation in the ad below. https://www.finn.no/job/fulltime/ad.html?finnkode=339556373 Kind regards, Leonardo A. Meza-Zepeda, Dr. philos. Department Head Head of Genomics Core Facility Department of Core Facilities Institute for Cancer Research Oslo University Hospital OSLO, Norway Mobile: +47-9903 5706 E-mail: L.A.Meza-Zepeda at ous-research.no www.ous-research.no/meza-zepeda Oslo.genomics.no @MezaZepeda @OSLOmicsCore Ikke sensitiv Not sensitive -------------- next part -------------- An HTML attachment was scrubbed... URL: From arne at bioinfo.se Mon Feb 26 21:39:50 2024 From: arne at bioinfo.se (Arne Elofsson) Date: Mon, 26 Feb 2024 21:39:50 +0100 Subject: [SocBiN] Fwd: Assistant Professorship at Biophysics, KTH In-Reply-To: <7905CF1E-C9EE-478C-AEBB-2DCF6F951798@scilifelab.se> References: <7905CF1E-C9EE-478C-AEBB-2DCF6F951798@scilifelab.se> Message-ID: Dear All, The department of Applied Physics, KTH is recruiting an Assistant Professor (Biträdande Lektor) in Biophysics with special focus on in vivo mimetic technologies. This SciLifeLab Fellowship comes with a great starting package that can be used to establish your own research group. If you are interested in applying follow the link below. Please forward to anyone who might be interested in applying. Feel free to contact me if you have any questions. Best regards, Björn Önfelt Biophysics, Department of Applied Physics KTH Royal Institute of Technology Center for Infectious Medicine, Department of Medicine Huddinge Karolinska Institutet Science for Life Laboratory Tomtebodavägen 23 A 171 65 Solna Tel. +46 730 766146 www.onfeltlab.com https://www.kth.se/lediga-jobb/681359?l=en -- This list has been created to share general news and updates about SciLifeLab Campus Solna activities. Everyone within the SciLifeLab Campus Solna community may sign up and use this group list to communicate information that concerns SciLifeLab Campus Solna operations or in other ways are of relevance to members of the community. Sign up or Unsubscribe on “My page”: https://staff.scilifelab.se -------------- next part -------------- An HTML attachment was scrubbed... URL: