From ion.petre at utu.fi Fri Nov 4 19:09:05 2022 From: ion.petre at utu.fi (Ion Petre) Date: Fri, 4 Nov 2022 20:09:05 +0200 Subject: [SocBiN] Special issue of TCS/C on Foundational Methods in Systems Biology: call for papers References: Message-ID: ** Please distribute this call for papers also in your own groups/networks ** Special issue of Theoretical Computer Science (track C) on Foundational Methods in Systems Biology Submission: continuous, cut-off date May 15, 2023 ================================================================= Dear Colleague, With this email we would like to invite you to submit a paper to the special issue of the Theoretical Computer Science journal (series C: Natural Computing) on “Foundations of Systems Biology”. This special issue is aligned with the conference series on “Computational Methods in Systems Biology (CMSB)” and shares its topics of interests. We look for original research articles on foundational aspects of systems biology and their applications. Topics of interest include, but are not limited to: • formalisms for modelling biological processes; • methods and tools for biological system analysis, modelling and simulation; • frameworks for model verification, validation, analysis, and simulation of biological systems; • high-performance methods for computational systems biology; • identification of biological systems; • network modelling, analysis, inference; • automated parameter and model synthesis; • multi-scale modelling and analysis methods; • design, analysis, and verification methods for synthetic biology; • methods for biomolecular computing and engineered molecular devices; • data-based approaches for systems and synthetic biology; • optimality and control of biological systems; • machine learning for systems biology. Submitted papers should not be under consideration for publication elsewhere. Extended versions of manuscripts that have been published in conference proceedings (CMSB or other conferences) can be submitted to this special issue if they have been extended by at least 30% and the differences between the two versions are explained in the introduction. The manuscripts should include all content in the article, rather than in appendices or in supplementary information. Please prepare your article in LaTeX in the Elsevier journal paper format (https://www.elsevier.com/authors/author-schemas/latex-instructions) and submit it using the editorial manager (https://www.editorialmanager.com/TCS/default.aspx). The tile of the special issue is “Foundations of Systems Biology” (short title VSI: FoundSysBio). In order to properly assign your submission to the special issue we are preparing, it is crucial to select VSI: FoundSysBio twice, as Article Type (starting the submission procedure) and Requested Editor (in Review Preferences). All papers for the special issue will be reviewed following the standard refereeing procedure for Theoretical Computer Science. Submissions will be reviewed on a continuous basis, with a cut-off date set for May 15, 2023. We suggest an upper limit of 40 pages on the length of the paper in the LaTeX style of the journal; please contact us if you need more pages for your manuscript. To keep track of the papers, please inform us of after the submission with an email to ion.petre at utu.fi and apaun at fmi.unibuc.ro. With best wishes, Ion Petre and Andrei Paun Guest editors of the special issue of TCS/C on Foundations of Systems Biology -------------- next part -------------- An HTML attachment was scrubbed... URL: From laurent.guyon at cea.fr Mon Nov 7 09:52:42 2022 From: laurent.guyon at cea.fr (GUYON Laurent) Date: Mon, 7 Nov 2022 08:52:42 +0000 Subject: [SocBiN] Great virtual seminar today about small RNA communication & host-pathogen interactions Message-ID: Dear colleagues, In the framework of the small non-coding RNA bioinformatics club (https://smallrna-bioinformatics.eu/), here is a late announcement of the virtual seminars of Amy Buck and Jose Roberto Bermudez Barrientos about *RNA communication in host-pathogen interactions*. Caution: this seminar will not be recorded. The club will propose seminars ~ every two months. *Today, Monday, November 7, 2022 at 4pm Berlin/Paris time* More information here: https://smallrna-bioinformatics.eu/Pages/Seminars/S22_11.aspx Tweet for easy re-transmission: https://twitter.com/Laurent_Guyon/status/1589540248882941952 Links to join: Zoom: https://univ-grenoble-alpes-fr.zoom.us/j/91695622024?pwd=NjhjVXcrTGwrb3lIZThoRGd0WmsxZz09 Or YouTube: https://www.youtube.com/watch?v=tEErw2MK6lo9 See you virtually very soon! Laurent Guyon PS: 2 very interesting seminars to come soon, more details here: https://smallrna-bioinformatics.eu/Pages/Seminars/Seminars.aspx - 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 ____________________________ 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 mid-December (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 Mon Nov 7 16:52:59 2022 From: arne.elofsson at gmail.com (Arne Elofsson) Date: Mon, 7 Nov 2022 16:52:59 +0100 Subject: [SocBiN] Fwd: everyone@dbb.su.se Assistant Professor in integrative structural biology with focus on structural dynamics In-Reply-To: <4e07e4491be441578e0487bd330ac268@ebox-prod-srv13.win.su.se> References: <4e07e4491be441578e0487bd330ac268@ebox-prod-srv13.win.su.se> Message-ID: Dear all, DBB has an add out for an Assistant Professor in integrative structural biology with focus on structural dynamics. This position is part of the SciLife Fellows program and includes a generous startup package to establish a research group. The deadline is Dec 28 2022. English https://www.su.se/english/about-the-university/work-at-su/available-jobs?rmpage=job&rmjob=19334&rmlang=UK Swedish https://www.su.se/om-universitetet/jobba-p%C3%A5-su/lediga-jobb?rmpage=job&rmjob=19331&rmlang=SE About the program https://www.scilifelab.se/research/?filter=all#fellows Please spread in your networks and to suitable candidates. /Martin __ Prof. Martin Högbom Head of department Department of Biochemistry and Biophysics, Stockholm University -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ everybody-at-dbb.su.se mailing list everybody-at-dbb.su.se at lists.su.se https://lists.su.se/mailman/listinfo/everybody-at-dbb.su.se From skanduri at ifi.uio.no Wed Nov 9 15:02:43 2022 From: skanduri at ifi.uio.no (Chakravarthi Kanduri) Date: Wed, 9 Nov 2022 14:02:43 +0000 Subject: [SocBiN] 2 year postdoc position at the Centre for Bioinformatics, University of Oslo, Norway Message-ID: <69DF56CA-D0C6-4FB9-A811-1D7700577B63@uio.no> A 2-year postdoc position is available at the Centre for Bioinformatics, University of Oslo. The candidate will work at the intersection of bioinformatics, statistics and cancer research. Please see the job announcement for more information: https://www.jobbnorge.no/en/available-jobs/job/234939/postdoctoral-research-fellow-in-bioinformatics-statistics Please circulate the information to relevant candidates. -------------- next part -------------- An HTML attachment was scrubbed... URL: From janina.bocksch at senckenberg.de Thu Nov 17 16:57:39 2022 From: janina.bocksch at senckenberg.de (Janina Bocksch) Date: Thu, 17 Nov 2022 16:57:39 +0100 (CET) Subject: [SocBiN] PostDoc Position in Gene Annotation at Senckenberg Frankfurt / Application deadline December 15th 2022 Message-ID: <753604169.35369.1668700659406@office.mailbox.org> Job Announcement ref. #12-22014 PostDoc Position in Gene Annotation The Hiller Lab at the LOEWE Center for Translational Biodiversity Genomics (TBG) in Frankfurt, Germany is looking for an ambitious PostDoc (m/f/d) to apply and develop new gene annotation approaches. The Project Comprehensively annotating genes in newly-sequenced genomes remains a challenging task. Our lab recently developed TOGA [1], the first method that integrates gene annotation and orthology inference, and used it to provide comparative annotations for >1000 mammals and birds (http://genome.senckenberg.de/). The project aims at developing a new automated strategy to integrate TOGA annotations with transcriptomics (short read RNA-seq and long read Iso-seq) data to produce comprehensive, high-quality gene annotations. We also aim at further improving TOGA by incorporating deep learning predictions into the annotation process. The new strategy will be applied to assemblies of numerous species, including bats, cetaceans, birds, snakes and fish, sequenced by us and collaborators. This will form the basis to uncover key differences in genes and link phenotypic adaptations of these species to differences in their genomes. The postdoc is expected to work closely with other lab members and capitalize on a wealth of existing methods and comparative genomic data. 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 referencequality genomes, genome alignment and gene 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 [1-10].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 (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 index recently ranked Frankfurt among the top 10 most livable cities worldwide. Requirements Applicants should have a PhD degree in bioinformatics/computational biology, computer science, 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 gene annotation, comparative genomics or methods development is an advantage. Place of employment: Frankfurt am Main Working hours: full time (40 hours/week), optional: part-time (80%) Type of contract: initially limited for 2 years with the possibility of an extension Salary and benefits: according to the collective agreement of the State of Hesse (pay grade E 13 100%) The position is fully funded and should ideally start as soon as possible. The employer is the Senckenberg Gesellschaft für Naturforschung who supports equal opportunity of men and women and therefore strongly invites women to apply. Equally qualified handicapped applicants will be given preference. How to apply Please send your application, mentioning the reference of this job announcement (ref.#12-22014), by e-mail to Michael Hiller (michael.hiller at senckenberg.de mailto:michael.hiller at senckenberg.de) and recruiting at senckenberg.de mailto:recruiting at senckenberg.de. The application should include the reference number of this job announcement, 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. The application deadline is December 15th, 2022. For more information please contact Prof. Dr. Michael Hiller, michael.hiller at senckenberg.de mailto:michael.hiller at senckenberg.de or visit https://tbg.senckenberg.de/hillerlab/. Recent publications [1] Kirilenko BM, et al. Integrating gene annotation with orthology inference at scale. Science, in press, 2022 [2] Blumer et al. Gene losses in the common vampire bat illuminate molecular adaptations to blood feeding. Science Advances, 2022 [3] Roscito et al. Convergent and lineage-specific genomic differences in limb regulatory elements in limbless reptile lineages. Cell Reports, 38(3):110280, 2022 [4] Jebb et al. Six reference-quality genomes reveal evolution of bat adaptations. Nature, 583, 578–584, 2020 [5] 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), eaaw6671, 2019 [6] Hecker et al. Convergent gene losses illuminate metabolic and physiological changes in herbivores and carnivores. PNAS, 116(8), 3036-3041, 2019 [7] Roscito et al. Phenotype loss is associated with widespread divergence of the gene regulatory landscape in evolution. Nature Communications, 9:4737, 2018 [8] Lee et al. Molecular parallelism in fast-twitch muscle proteins in echolocating mammals. Science Advances, 4(9), eaat9660, 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 arne at bioinfo.se Sat Nov 19 12:37:34 2022 From: arne at bioinfo.se (Arne Elofsson) Date: Sat, 19 Nov 2022 12:37:34 +0100 Subject: [SocBiN] Fwd: Funding Opportunity for Postdocs: Branco Weiss Fellowship In-Reply-To: <146bc5ddf6cd4f40a507431632cb5e5c@ebox-prod-srv13.win.su.se> References: <146bc5ddf6cd4f40a507431632cb5e5c@ebox-prod-srv13.win.su.se> Message-ID: *The Branco Weiss Fellowship* The Branco Weiss Fellowship has just started its recruiting campaign *(deadline 15 January 2023)*. Over ten years ago, Branco Weiss, a Swiss entrepreneur and patron of the sciences, made a donation to support excellent, exceptional postdocs to follow their personal vision of a particular scientific project outside the mainstream ( https://brancoweissfellowship.org). *The fellowship is awarded to postdocs for up to five years and although it is hosted at ETH Zurich, fellows have the freedom to perform their project at the best fitting academic institution around the globe.* Over the last years, the Branco Weiss Fellowship - Society in Science has grown into a vibrant community of postdocs and former fellows who share a passion for exploring new avenues in research outside the mainstream. Researchers who have earned or will earn a PhD degree between 15 January 2018 and 15 January 2023 are eligible to apply for a Branco Weiss Fellowship. If they succeed during the selection process, they will receive financial support for up to five years. Applications from all disciplines, including social sciences and humanities, are encouraged. The selection committee is particularly eager to hear about research topics not yet represented in the fellowship. *_____________________________________________________________________________________________* *Viviana Stechina* Forskningssekreterare, Fil dr / Research Officer, PhD Avdelningen för forsknings- och samverkansstöd (FS) / Office for Research, Engagement and Innovation Services (REIS) *Stockholms universitet / Stockholm University* 106 91 Stockholm / SE-10691 Stockholm, SWEDEN Besöksadress: Bloms paviljong, Svante Arrhenius väg 26, 138 C. Tel: 08-16 22 57 / Phone: + 46 (0)8 16 22 57 E-post: viviana.stechina at su.se www.su.se/fs www.su.se/reis -------------- next part -------------- An HTML attachment was scrubbed... URL: From arne at bioinfo.se Sat Nov 19 12:36:04 2022 From: arne at bioinfo.se (Arne Elofsson) Date: Sat, 19 Nov 2022 12:36:04 +0100 Subject: [SocBiN] Fwd: Call for applications to the National Graduate School in Medical Bioinformatics (MedBioInfo) In-Reply-To: References: Message-ID: Dear Colleague, I would much appreciate it if you could forward the attached message to Departmental and other relevant email lists. Please print out the attached flyer and post on your physical bulletin board if applicable. *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. Thanks to a recently approved extension of time, we are admitting students again this year. If admitted you will join a competitively selected student community. We have in recent years attained a good gender balance. Our 42 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, worth 3 or 5 HP(ECTS). Each course typically requires a one-week at-home pre-assignment, one week in residence, and (often) a take-home one-week 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. We also have 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 between January 2022 and April 2023, though there is 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 will strive to have a broad distribution of Swedish home universities as well as a good gender balance. . Please be aware that, if admitted, you should expect to attend our Spring Meeting -- this will likely require 3-4 days sometime just before Easter. You should also plan to attend your first course, "Applied Bioinformatics" in Uppsala, most likely in June. Several of our core courses require programming in Python. If your Python background is weak, you will need to start strengthening your skills soon after admissions. There are many online courses, and we also recommend Shaw's "Python 3 the hard way." Considering the climate, we ask students to avoid flying to MedBioInfo events. The application deadline is *February 28, *2023. We aim to enroll 20-30 incoming students per year. You should apply following *https://ec.europa.eu/eusurvey/runner/MedBioInfo2023* also linked to from medbioinfo.se. Feel free to email Sam with any questions. We look forward to reading your application. With kind regards, Samuel Flores, Dean of Students Arne Elofsson, Director Petras Kundrotas, Course Coordinator -- *Samuel Coulbourn Flores, Docent* Universitetslektor i Bioinformatik / Associate Professor in Bioinformatics Sveriges Lantsbruksuniversitet / Swedish University of Agricultural Sciences Rum 54613, Inst. för Husdjursgenetik Ulls väg 26, Uppsala 75007 Studierektor för den nationella forskarskolan inom medicinsk bioinformatik / Dean of Students for the Swedish National Graduate School in Medical Bioinformatics Department of Biochemistry and Biophysics Stockholm University SciLifeLab A6220 (Alpha Tr. 6) Tomtebodavägen 23a (main entrance) Deliveries: Samuel Flores Stockholms Universitet, Org # 202100-3062 Tomtebodavägen 23b (loading dock) 171 65 Solna SWEDEN Mobil: +46.706000464 Mexank:0816-3949 skype: samuelfloresc. Zoom (subject to change): https://stockholmuniversity.zoom.us/j/2207537839 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: MedBioInfoIncoming2023.A4.pdf Type: application/pdf Size: 903983 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: MedBioInfo.light.A4.landscape.pdf Type: application/pdf Size: 902212 bytes Desc: not available URL: From sofia.kossida at igh.cnrs.fr Sun Nov 20 20:25:56 2022 From: sofia.kossida at igh.cnrs.fr (Sofia KOSSIDA) Date: Sun, 20 Nov 2022 19:25:56 +0000 Subject: [SocBiN] post-doc position in immunogenetics In-Reply-To: References: Message-ID: IMGT has opened a postdoc position in the field of Immunogenetics and bioinformatics. Fantastic environment for scrutinizing the adaptive immune response. If you live outside France and got your PhD recently (less than five years), contact us! sofia.kossida at igh.cnrs.fr -------------- next part -------------- An HTML attachment was scrubbed... URL: From sermarcue at gmail.com Mon Nov 21 09:00:00 2022 From: sermarcue at gmail.com (Sergio Martinez Cuesta) Date: Mon, 21 Nov 2022 08:00:00 +0000 Subject: [SocBiN] Machine learning approaches to predict recombinant protein expression Message-ID: Dear all, I hope this finds you well. If you happen to take part in the training/coaching part of a Masters programme in bioinformatics, computational biology or a related subject with students completing research internships e.g. in industry, I would very much appreciate if you could share the following opportunity in AstraZeneca Gothenburg with your student groups. https://www.randstad.se/jobb/thesis-work-curating-data-for-machine-learning-approaches_molndal-kommun_201412525/ Thanks in advance Sergio -------------- next part -------------- An HTML attachment was scrubbed... URL: From sermarcue at gmail.com Tue Nov 22 09:00:00 2022 From: sermarcue at gmail.com (Sergio Martinez Cuesta) Date: Tue, 22 Nov 2022 08:00:00 +0000 Subject: [SocBiN] R&D Data Sciences & AI Graduate Programme - AstraZeneca UK Message-ID: If you have a quantitative science focussed bachelor’s or master’s degree and a desire to explore and develop your skills in data science and artificial intelligence within a global biopharmaceutical organisation, our R&D Data Science & AI Graduate Programme could be the perfect start to your career. You’ll gain invaluable insight, exposure and opportunities across our diverse, Research and Development organisation. We’ll accelerate your learning and help you achieve your potential. To find out more, please check: https://careers.astrazeneca.com/job/cambridge/r-and-d-data-sciences-and-ai-graduate-programme-uk/7684/38281055280 Thanks, Sergio -------------- next part -------------- An HTML attachment was scrubbed... URL: From sermarcue at gmail.com Tue Nov 22 10:58:10 2022 From: sermarcue at gmail.com (Sergio Martinez Cuesta) Date: Tue, 22 Nov 2022 09:58:10 +0000 Subject: [SocBiN] Machine learning approaches to predict recombinant protein expression In-Reply-To: References: Message-ID: Now with the project description attached as the previous link has expired. There is no application deadline at the moment, for any questions please contact Lovisa Holmberg-Schiavone directly at: Lovisa.Holmberg.Schiavone at astrazeneca.com Thanks, Sergio On Mon, 21 Nov 2022 at 08:00, Sergio Martinez Cuesta wrote: > Dear all, > > I hope this finds you well. > > If you happen to take part in the training/coaching part of a Masters > programme in bioinformatics, computational biology or a related subject > with students completing research internships e.g. in industry, I would > very much appreciate if you could share the following opportunity in > AstraZeneca Gothenburg with your student groups. > > > https://www.randstad.se/jobb/thesis-work-curating-data-for-machine-learning-approaches_molndal-kommun_201412525/ > > Thanks in advance > Sergio > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: master_thesis_project_proteinproduction.docx Type: application/vnd.openxmlformats-officedocument.wordprocessingml.document Size: 18276 bytes Desc: not available URL: From bengt.persson at icm.uu.se Wed Nov 23 16:44:09 2022 From: bengt.persson at icm.uu.se (Bengt Persson) Date: Wed, 23 Nov 2022 16:44:09 +0100 Subject: [SocBiN] =?utf-8?q?Assistant_professor_position_=28Bitr=C3=A4dand?= =?utf-8?q?e_Universitetslektor=29_in_algorithmic_bioinformatics_at_Uppsal?= =?utf-8?q?a_University?= Message-ID: Dear all, There is an Assistant Professor position (Biträdande Universitetslektor) in algorithmic bioinformatics open at Uppsala University. The position is tenure track and can be converted to an Associate Professor after 6 years. More details at: https://www.uu.se/en/about-uu/join-us/details/?positionId=548045 Deadline 27 December 2022 All the best, Yours, Bengt -- Bengt Persson, M.D., Ph.D., Professor of Bioinformatics Head of department Department of Cell and Molecular Biology (ICM) Uppsala University Telephone: +46 18 471 4422 Mobile phone: +46 70 425 0230 Facsimile: +46 18 530 396 E-mail: bengt.persson at icm.uu.se Address: Uppsala University ICM -- Department of Cell and Molecular Biology BMC, room C10:308c Box 596 S-751 24 Uppsala, SWEDEN 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/en/about-uu/data-protection-policy -------------- next part -------------- An HTML attachment was scrubbed... URL: From coordinator at rth.dk Thu Nov 24 16:28:43 2022 From: coordinator at rth.dk (Betina Wingreen Jensen) Date: Thu, 24 Nov 2022 16:28:43 +0100 Subject: [SocBiN] Two CRISPR bioinformatics positions available Message-ID: <001701d90019$6ff65fa0$4fe31ee0$@rth.dk> Dear Colleagues, We have two super exciting open positions in CRISPR design here at the University of Copenhagen, Denmark. Check them out here: PhD: https://employment.ku.dk/faculty/?show=157954 Postdoc: https://employment.ku.dk/faculty/?show=157950 The work will take outset our on/off -target and post editing analysis strategies: https://doi.org/10.1038/s41467-021-23576-0 https://doi.org/10.1038/s41467-022-30515-0 https://doi.org/10.1093/nar/gkab1131 https://doi.org/10.1186/s13059-018-1534-x Best wishes, Betina Betina Wingreen Jensen Special Advisor/Project Manager University of Copenhagen Department of Veterinary and Animal Sciences Grønnegårdsvej 7 & Thorvaldsensvej 57 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 skanduri at ifi.uio.no Fri Nov 25 10:54:19 2022 From: skanduri at ifi.uio.no (Chakravarthi Kanduri) Date: Fri, 25 Nov 2022 09:54:19 +0000 Subject: [SocBiN] A permanent senior engineer position available in the bioinformatics ELIXIR Oslo team, University of Oslo, Norway Message-ID: A permanent position as a senior engineer is available in the bioinformatics ELIXIR team, part of the Centre for Bioinformatics, University of Oslo. The candidate will participate in the development and deployment of functionality for various national and international solutions provided by ELIXIR Norway. Please see the job announcement for more information: https://www.jobbnorge.no/en/available-jobs/job/235791/senior-engineer-for-python-java-systems-developer Please circulate the information to relevant candidates. -------------- next part -------------- An HTML attachment was scrubbed... URL: From skanduri at ifi.uio.no Fri Nov 25 11:22:53 2022 From: skanduri at ifi.uio.no (Chakravarthi Kanduri) Date: Fri, 25 Nov 2022 10:22:53 +0000 Subject: [SocBiN] 2 year postdoc position at the Centre for Bioinformatics, University of Oslo, Norway Message-ID: <8A7A139D-41FA-4561-B043-619A2A7D3406@uio.no> A 2-year postdoc position is available at the Centre for Bioinformatics, University of Oslo. The candidate will contribute to the European project EOSC4Cancer, specifically for the advancement of cancer data analysis platforms. Please see the job announcement for more information: https://www.jobbnorge.no/en/available-jobs/job/235672/postdoctoral-research-fellow-in-bioinformatics Please circulate the information to relevant candidates. -------------- next part -------------- An HTML attachment was scrubbed... URL: From laurent.guyon at cea.fr Fri Nov 25 18:36:44 2022 From: laurent.guyon at cea.fr (GUYON Laurent) Date: Fri, 25 Nov 2022 17:36:44 +0000 Subject: [SocBiN] Web-seminar on small RNAs in bacteria, this Monday 28th Message-ID: Dear colleagues, This **upcoming Monday 28th of November (4pm Berlin/Paris time)**, we propose a free web-seminar on small RNAs in bacteria! 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 Zoom link: https://univ-grenoble-alpes-fr.zoom.us/j/95796803415?pwd=UU50WEpEbTNXb1p1SmJPUitqbEcwQT09 YouTube stream: https://youtu.be/VYIKBJq_coM Tweet for easy re-transmission: https://twitter.com/Laurent_Guyon/status/1596193837348683776 YouTube channel (most of the seminars are then shared through this channel): https://www.youtube.com/channel/UCTiHtqOKzneeqIqauQMgx3A CAUTION: this upcoming seminar will not be recorded! Seminars are given a Monday at 4pm Berlin/Paris time, except in rare cases. - 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 mid-December (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 laurent.guyon at cea.fr Mon Nov 28 13:41:56 2022 From: laurent.guyon at cea.fr (GUYON Laurent) Date: Mon, 28 Nov 2022 12:41:56 +0000 Subject: [SocBiN] [small non-coding RNA bioinformatics club]: today's seminar with Cynthia Sharma **cancelled** Message-ID: <0a41fff0f8474a16b18f286c0250ec87@cea.fr> Dear all, The seminar planed today with Cynthia Sharma in the framework of the small non-coding RNA bioinformatics club (https://smallrna-bioinformatics.eu/) is cancelled. It will be re-postponed later on... Stay tuned (you can subscribe to the mailing list): https://smallrna-bioinformatics.eu/Pages/_PAGES/Mailing-List.aspx Sorry for the inconvenience. Best, Laurent Guyon on behalf of all the organizers (Rolf Backofen, Ana Eulálio, Bastian Fromm, Laurent Guyon, Andreas Keller, Marie-France Sagot) PS: other planned seminar: - 9th of January: Li Xuan Qin, Depth normalization of small RNA sequencing: using data and biology to select a suitable method, https://smallrna-bioinformatics.eu/Pages/Seminars/S23-01.aspx ____________________________ 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 mid-December (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 gemma.atkinson at gmail.com Mon Nov 28 14:38:13 2022 From: gemma.atkinson at gmail.com (Gemma Atkinson) Date: Mon, 28 Nov 2022 14:38:13 +0100 Subject: [SocBiN] Structural bioinformatics research engineer position, Lund University Message-ID: Dear all, We are looking to hire a Research engineer/Engineer who will establish a computational protein structure prediction facility in Lund University. The new facility, LU-Fold, will be a university-wide resource, focussed on helping researchers take advantage of deep learning structural prediction methods such as AlphaFold2 to reveal new aspects of function of their proteins of interest. Read more and apply here: https://lu.varbi.com/en/what:job/jobID:564808/ 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