From erik.larsson at gu.se Tue Oct 4 10:32:07 2022 From: erik.larsson at gu.se (Erik Lekholm) Date: Tue, 4 Oct 2022 08:32:07 +0000 Subject: [SocBiN] Postdoc in computational cancer genomics in Gothenburg Message-ID: <236B3511-28BA-435A-9A17-7DDC2B2B6FBC@gu.se> Hello everyone, There is an open postdoc position in my group in Göteborg, for anyone interested in computational cancer genomics: https://web103.reachmee.com/ext/I005/1035/job?site=7&lang=UK&validator=9b89bead79bb7258ad55c8d75228e5b7&job_id=27307 Our main web lab page is down at the moment (sorry) but here’s a bit of information about the group!: https://www.gu.se/en/research/erik-larsson With best wishes, Erik Larsson Lekholm Select papers: Elias E, Ardalan A, Lindberg M, Reinsbach SE, Muth A, Nilsson O, Arvidsson Y, Larsson E. Independent somatic evolution underlies clustered neuroendocrine tumors in the human small intestine. Nature Communications. 2021 Nov 4. Elliott K, Larsson E. Non-coding driver mutations in human cancer. Nature Reviews Cancer. 2021 Jul 6. Review. Basu S, Xie X, Uhler JP, Hedberg-Oldfors C, Milenkovic D, Baris OR, Kimoloi S, Matic S, Stewart JB, Larsson NG, Wiesner RJ, Oldfors A, Gustafsson CM, Falkenberg M, Larsson E. Accurate mapping of mitochondrial DNA deletions and duplications using deep sequencing. PLoS Genetics. 2020 Dec 14. Van den Eynden J, Jiménez-Sánchez A, Miller ML, Larsson E. Lack of detectable neoantigen depletion signals in the untreated cancer genome. Nature Genetics. 2019 Nov 25. Lindberg M, Boström M, Elliott K, Larsson E. Intragenomic variability and extended sequence patterns in the mutational signature of ultraviolet light. Proc Natl Acad Sci U S A. 2019 Sep 23. Persson Ö, Muthukumar Y, Basu S, Jenninger L, Uhler JP, Berglund AK, McFarland R, Taylor RW, Gustafsson CM, Larsson E*, Falkenberg M*. Copy-choice recombination during mitochondrial L-strand synthesis causes DNA deletions. Nature Communications. 2019 Feb 15. Elliott K, Boström M, Filges S, Lindberg M, Van den Eynden J, Ståhlberg A, Clausen AR, Larsson E. Elevated pyrimidine dimer formation at distinct genomic bases underlies promoter mutation hotspots in UV-exposed cancers. PLoS Genetics. 2018 Dec 26. Fredriksson NJ, Elliott K, Filges S, Van den Eynden J, Ståhlberg A, Larsson E. Recurrent promoter mutations in melanoma are defined by an extended context-specific mutational signature. PLoS Genetics. 2017 May 10. Van den Eynden J, Basu S, Larsson E. Somatic Mutation Patterns in Hemizygous Genomic Regions Unveil Purifying Selection during Tumor Evolution. PLoS Genetics. 2016 Dec 27. Alaei-Mahabadi B, Bhaduryb J, Karlsson JW, Nilsson JA, Larsson E. Global analysis of somatic structural genomic alterations and their impact on gene expression in diverse human cancers. Proc Natl Acad Sci U S A. 2016 Nov. Ashouri A, Sayin VI, Van den Eynden J, Singh SX, Papagiannakopoulos T, Larsson E. Pan-cancer transcriptomic analysis associates long non-coding RNAs with key mutational driver events. Nature Communications. 2016 Oct. FocalScan: Scanning for altered genes in cancer based on coordinated DNA and RNA change. Karlsson J, Larsson E. Nucleic Acids Res. 2016 Jul 29. Stewart JB, Alaei-Mahabadi B, Sabarinathan R, Samuelsson T, Gorodkin J, Gustafsson CM, Larsson E. Simultaneous DNA and RNA Mapping of Somatic Mitochondrial Mutations across Diverse Human Cancers. PLoS Genetics 2015 Jun 30. Fredriksson NJ, Ny L, Nilsson JA, Larsson E. Systematic analysis of noncoding somatic mutations and gene expression alterations across 14 tumor types. Nature Genetics. 2014 Dec. Tang K, Alaei-Mahabadi B, Samuelsson T, Lindh M, Larsson E. The landscape of viral expression and host gene fusion and adaptation in human cancer. Nature Communications. 2013 Oct 1. Ashwini J, Marks DS, Larsson E. miRcode: a map of putative microRNA target sites in the long non-coding transcriptome. Bioinformatics. 2012 Aug 1. -------------- next part -------------- An HTML attachment was scrubbed... URL: From laurent.guyon at cea.fr Thu Oct 6 10:56:55 2022 From: laurent.guyon at cea.fr (GUYON Laurent) Date: Thu, 6 Oct 2022 08:56:55 +0000 Subject: [SocBiN] Free web seminars on small non-coding RNAs Message-ID: <8e2b0888ce14481ab866dd8c8dbf61cc@cea.fr> Dear colleagues, This **upcoming Monday**, we propose a free web-seminar on identifying microRNA targets at the single cell level! In the framework of the small non-coding RNA bioinformatics club (https://smallrna-bioinformatics.eu/), we are happy to share with you the future freely available web seminars. The club will propose seminars every two months. Abstracts and links for the seminars are available here: https://smallrna-bioinformatics.eu/Pages/Seminars/Seminars.aspx Tweet for easy re-transmission: https://twitter.com/Laurent_Guyon/status/1575819982817984512 YouTube channel (most of the seminars are then shared through this channel): https://www.youtube.com/channel/UCTiHtqOKzneeqIqauQMgx3A Seminars are given at 4pm CET, except in rare cases. - 10th of October: 2 senior researchers - miRNA targets at the single-cell levels (Marc Friedländer) and small RNA-seq tools (flash talk, Matthias Zytnicki) - https://smallrna-bioinformatics.eu/Pages/Seminars/S22_09.aspx - 7th of November: Amy Buck, RNA communication in host-pathogen interactions (not recorded) - 28th of November: Cynthia Sharma, Regulatory RNAs in pathogenic Epsilonproteobacteria (not recorded) - 9th of January: Li Xuan Qin, Depth normalization of small RNA sequencing: using data and biology to select a suitable method 'hope to see you virtually in these seminars, Laurent Guyon, on behalf of all the organizers (Rolf Backofen, Ana Eulálio, Bastian Fromm, Laurent Guyon, Andreas Keller, Marie-France Sagot) ____________________________ Laurent GUYON, PhD, HDR - Bioinformatics CEA IRIG (Interdisciplinary Research Institute of Grenoble) BioHealth Department - BCI (Biology of Cancer and Infection laboratory) UMR 1292 CEA/Inserm/Université Grenoble Alpes CEA Grenoble - Bât C3 - Bureau 224 17 rue des Martyrs - 38054 GRENOBLE Cedex 9 - France Tél : (+33)4.38.78.04.53 - Fax : (+33)4 38 78 50 58 Email : laurent.guyon at cea.fr - http://laurent.guyon.phd.free.fr/ Interested by small non-coding RNA bioinformatics? Join the club! https://smallrna-bioinformatics.eu/ Special issue on small non-coding RNA bioinformatics, submit before the 15th of October (updated - contact me if you need delay): https://www.mdpi.com/journal/genes/special_issues/Small_RNA_Bioinformatics Happy to share miRViz (free to use website to analyze your microRNA datasets): http://mirviz.prabi.fr/ Article: https://doi.org/10.1093/nar/gkaa259 Messages of the paper: https://twitter.com/Laurent_Guyon/status/1255487510563651586 -------------- next part -------------- An HTML attachment was scrubbed... URL: From arne.elofsson at gmail.com Fri Oct 7 16:41:18 2022 From: arne.elofsson at gmail.com (Arne Elofsson) Date: Fri, 7 Oct 2022 16:41:18 +0200 Subject: [SocBiN] Postdoc openings in Stockholm at SciLifeLab Message-ID: *This is an unusual postdoc opening, where you as a postdoc applies and not so that the PI applies for a grant. Great opportunity to join great labs in Stockholm. For details see below.* *RED Postdoctoral Fellowships – SciLifeLab Campus Solna, Stockholm, Sweden * Three* R*esearch *E*nvironment and *D*evelopment (*RED*) Postdoctoral Fellowship grants are open for applications in 2022. RED Postdoc Fellows will receive a 2-year contract (1 MSEK/yr) to work on self-designed research projects. Successful candidates will be matched to an existing research group and embedded in the unique interdisciplinary and collaborative research environment at SciLifeLab Campus Solna. SciLifeLab is a research infrastructure in Sweden with unique technologies and broad expertise in molecular life sciences. Campus Solna is jointly operated by the Royal Institute of Technology (KTH), Karolinska Institutet (KI) and Stockholm University (SU), also known as Stockholm Trio. All activities at Campus Solna are aligned with its dual mission: hosting national research infrastructures, and being an internationally competitive research center. Technical innovations developed at Campus Solna, enhance SciLifeLab's reputation at the forefront of molecular life sciences. Research at Campus Solna is supported by expert staff scientists and state-of-the-art experimental facilities that together provide a unique environment for training scientists at all career stages. As a RED Postdoc Fellow at Campus Solna SciLifeLab you will: · be part of an internationally recognized research community with access to cutting edge technologies in molecular life sciences · have the opportunity to work on an ambitious research project in conjunction with competent interdisciplinary experimentalists and bioinformaticians · work in a supportive and collaborative research environment with a community that fosters scientific exchange and promotes scientific independence · be employed by one of the Stockholm Trio universities *Eligibility:* Applicants must have obtained a PhD within the past 3 years, or have completed their PhD by the starting date of the fellowship, and not already engaged as a postdoctoral researcher at SciLifeLab Campus Solna. *Application Deadline: December 19, 2022* *Application:* 1. *Curriculum vitae*, including publications (submit as a PDF file) 2. *Project Proposal* – organized as follows (5 page limit; submit as a single PDF file): I. Background and significance (approx. ¾ page) - specify the question/problem being addressed II. Project aims, (approx. ¼ page) III. Project description (maximum 3 pages, may include one figure) IV. Describe the involvement of the host group with emphasis on the relevance of the existing expertise provided. Indicate the skills you bring to the project and what new skills you anticipate to gain. (approx. ¾ pages) V. References (approx. ¼ page) 3. *Letter of Support from Campus Solna SciLifeLab Host*, and, if relevant, a letter of support from an external partner (submit as a PDF file) *Submit CV, Project Proposal and Letter of Support using the **Anubis Web* * portal* 4. *Two Reference Letters* – referees should send their reference letters to: RefLett-REDPOST22 at scilifelab.se It is the applicant’s responsibility to ensure that the letters are received by the deadline. *Contact:* Professor Per Ljungdahl, Director Campus Solna, SciLifeLab; e‑mail: cs.director at scilifelab.se RED Postdoc Call - Timeline: Application opens October 10, 2022 Submission deadline December 19, 2022 Review/Interviews January 2023 Decision January 2023 Start date negotiable; ambition latest fall 2023 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 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 arne at bioinfo.se Mon Oct 10 12:07:08 2022 From: arne at bioinfo.se (Arne Elofsson) Date: Mon, 10 Oct 2022 12:07:08 +0200 Subject: [SocBiN] RED postdoc grants Message-ID: https://www.scilifelab.se/career/red-postdoctoral-fellowships/ RED Postdoctoral Fellowships – SciLifeLab Campus Solna, Stockholm, Sweden Three* R*esearch *E*nvironment and *D*evelopment (*RED*) Postdoctoral Fellowship grants are open for applications in 2022. RED Postdoc Fellows will receive a 2-year contract (1 MSEK/yr) to work on self-designed research projects. Successful candidates will be matched to an existing research group and embedded in the unique interdisciplinary and collaborative research environment at SciLifeLab Campus Solna. SciLifeLab is a research infrastructure in Sweden with unique technologies and broad expertise in molecular life sciences. Campus Solna is jointly operated by the Royal Institute of Technology (KTH), Karolinska Institutet (KI) and Stockholm University (SU), also known as Stockholm Trio. All activities at Campus Solna are aligned with its dual mission: hosting national research infrastructures, and being an internationally competitive research center. Technical innovations developed at Campus Solna, enhance SciLifeLab’s reputation at the forefront of molecular life sciences. Research at Campus Solna is supported by expert staff scientists and state-of-the-art experimental facilities that together provide a unique environment for training scientists at all career stages. *As a RED Postdoc Fellow at Campus Solna SciLifeLab you will:* - be part of an internationally recognized research community with access to cutting-edge technologies in molecular life sciences - have the opportunity to work on an ambitious research project in conjunction with competent interdisciplinary experimentalists and bioinformaticians - work in a supportive and collaborative research environment with a community that fosters scientific exchange and promotes scientific independence - be employed by one of the Stockholm Trio universities *Eligibility:* Applicants must have obtained a PhD within the past 3 years, or have completed their PhD by the starting date of the fellowship, and *not already engaged* as a postdoctoral researcher at SciLifeLab Campus Solna. *Application Deadline: 17:00 CET, December 19, 2022* *Application:* 1. *Curriculum vitae*, including publications (submit as a PDF file) 2. *Project Proposal* – organized as follows (5 page limit; submit as a single PDF file): I. Background and significance (approx. ¾ page) – specify the question/problem being addressed II. Project aims, (approx. ¼ page) III. Project description (maximum 3 pages, may include one figure) IV. Describe the involvement of the host group with emphasis on the relevance of the existing expertise provided. Indicate the skills you bring to the project and what new skills you anticipate to gain. (approx. ¾ pages) V. References (approx. ¼ page) 3. *Letter of Support from Campus Solna SciLifeLab Host*, and, if relevant, a letter of support from an external partner (submit as a PDF file) *Submit CV, Project Proposal and Letter of Support using the **Anubis Web* * portal* 4. *Two Reference Letters* – referees should send their reference letters to: RefLett-REDPOST22 at scilifelab.se *It is the applicant’s responsibility to ensure that the letters are received by the deadline (17:00 CET, December 19, 2022).* Read more 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 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 Fredrik.Ronquist at nrm.se Mon Oct 10 15:46:19 2022 From: Fredrik.Ronquist at nrm.se (Fredrik Ronquist) Date: Mon, 10 Oct 2022 13:46:19 +0000 Subject: [SocBiN] Head, Department of Bioinformatics and Genetics at the Swedish Museum of Natural History Message-ID: <544AC8B1-DF12-4B93-87BD-33303D2DC36E@nrm.se> The Swedish Museum of Natural History is looking to fill a position as Head of the Department of Bioinformatics and Genetics. Among other things, the department is coordinating the Swedish Biodiversity Data Infrastructure (https://sbdi.se), a national research infrastructure backed by 11 universities and government agencies in Sweden. The department is also responsible for the museum's participation in the National Bioinformatics Infrastructure Sweden (https://nbis.se) and in the infrastructure part of the Data-Driven Life Science (DDLS) program of the Knut and Alice Wallenberg Foundation (https://www.scilifelab.se/data-driven/). For more information about the position, see: https://www.nrm.se/ommuseet/jobbahososs/ledigatjanster.9005019.html Application deadline is October 16, 2022. Fredrik Ronquist Professor Department of BIoinformatics and Genetics Swedish Museum of Natural History From arne.elofsson at gmail.com Mon Oct 17 09:22:05 2022 From: arne.elofsson at gmail.com (Arne Elofsson) Date: Mon, 17 Oct 2022 09:22:05 +0200 Subject: [SocBiN] Fwd: Job openings at biotech startup in Stockholm, computational biology/bioinformatics In-Reply-To: References: Message-ID: Pixelgen (biotech startup founded by former Scilifelab guy Alvaro Martinez-Barrio) is recruiting for a couple of interesting positions: https://careers.pixelgen.tech/jobs/2051282-computational-biologist-in-product-development https://careers.pixelgen.tech/jobs/2140974-field-bioinformatics-scientist-stockholm ************************************************************ Jakub Orzechowski Westholm, PhD SciLifeLab Bioinformatics Long-term Support https://www.scilifelab.se/platforms/nbis/ Science for Life Laboratory Stockholm Tomtebodavägen 23A SE17165 Solna Sweden -- 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: From arne.elofsson at gmail.com Mon Oct 17 19:57:30 2022 From: arne.elofsson at gmail.com (Arne Elofsson) Date: Mon, 17 Oct 2022 19:57:30 +0200 Subject: [SocBiN] Fwd: EMBL-EBI Postdoctoral Fellowship - Protein Science Machine Learning with Astra Zeneca In-Reply-To: <30c2d9106e924f85a15859c1e1355c32@ebox-prod-srv13.win.su.se> References: <7067068E-430F-4769-A66C-F6DE99EAB780@ebi.ac.uk> <34AD0097-6879-41E9-99B8-B497C306D6D5@ebi.ac.uk> <30c2d9106e924f85a15859c1e1355c32@ebox-prod-srv13.win.su.se> Message-ID: Postdoc for a recently graduated PhD in computational biology / structural bioinformatics. https://www.embl.org/jobs/position/EBI02081 The aim of the project, which is a collaboration between EMBL-EBI and AstraZeneca, will be to investigate the applications of machine learning and AI in predicting the results of protein expression experiments and to develop computational tools that can accurately address the following two key questions: • For a given sequence, will this lead to successful protein expression? • Given a protein, what sequence (or sequences) are most likely to lead to successful expression? On a separate note - most of the speakers have confirmed to be joining the workshop in-person: Jonas Adler, Mohammed AlQuraishi, Diego del Alamo, Christine Orengo, Gonzalo Parra, Randy Read, Sameer Velankar. I am just waiting to hear back from Lucy Colwell. Panos Kastritis will join on-line. Many thanks, Matt -------------- next part -------------- An HTML attachment was scrubbed... URL: From Tanja.Slotte at scilifelab.se Fri Oct 28 11:33:18 2022 From: Tanja.Slotte at scilifelab.se (Tanja Slotte) Date: Fri, 28 Oct 2022 11:33:18 +0200 Subject: [SocBiN] Postdoc in Evolutionary Genomics Message-ID: <2CD56E2F-C036-4DE0-BC78-68BB94B8D7EE@scilifelab.se> Dear colleagues, I have an opening for an evolutionary genomics postdoc (2 years) in my group at Stockholm University. The project concerns supergene evolution and would be ideal for a candidate with bioinformatics skills and an interest in evolutionary genetics, who wants to quickly get started analyzing genomic data. For a recent relevant paper, see: Gutiérrez-Valencia et al. 2022. Current Biology. https://doi.org/10.1016/j.cub.2022.08.042 For more information and how to apply, please see: https://tanjaslottelab.se/join-the-lab/ Evaluation of applications will begin November 17, 2022. Please forward to anyone who might be interested. All the best, Tanja Tanja Slotte Professor in Ecological Genomics Subject Representative for Ecology and Evolution Department of Ecology, Environment and Plant Sciences (DEEP) Stockholm University 106 91 Stockholm E-mail: tanja.slotte at su.se From Tanja.Slotte at su.se Fri Oct 28 16:00:26 2022 From: Tanja.Slotte at su.se (Tanja Slotte) Date: Fri, 28 Oct 2022 16:00:26 +0200 Subject: [SocBiN] Postdoc in Evolutionary Genomics Message-ID: <94672867-A54C-4428-9B33-5DE1ACB7467A@su.se> Dear colleagues, I have an opening for an evolutionary genomics postdoc (2 years) in my group at Stockholm University. The project concerns supergene evolution and would be ideal for a candidate with bioinformatics skills and an interest in evolutionary genetics, who wants to quickly get started analyzing genomic data produced in an ERC-funded project. For a recent relevant paper, see: Gutiérrez-Valencia et al. 2022. Current Biology. https://doi.org/10.1016/j.cub.2022.08.042 For more information and how to apply, please see: https://tanjaslottelab.se/join-the-lab/ Evaluation of applications will begin November 17, 2022. Please forward to anyone who might be interested. All the best, Tanja Tanja Slotte Professor in Ecological Genomics Subject Representative for Ecology and Evolution Department of Ecology, Environment and Plant Sciences (DEEP) Stockholm University 106 91 Stockholm E-mail: tanja.slotte at su.se