From ion.petre at utu.fi Thu Mar 3 10:11:54 2022 From: ion.petre at utu.fi (Ion Petre) Date: Thu, 3 Mar 2022 09:11:54 +0000 Subject: [SocBiN] Computational Methods in Systems Biology (14-16.9, Bucharest): 2nd CfP References: Message-ID: <6ead84b4-6fec-4a6a-ac13-6f1f7824fb49@Spark> CMSB2022: International Conference on Computational Methods in Systems Biology University of Bucharest Bucharest, Romania, September 14-16, 2022 Conference website https://fmi.unibuc.ro/en/cmsb-2022/ Submission link https://easychair.org/conferences/?conf=cmsb2022 Call for papers https://easychair.org/cfp/CMSB2022 Abstract registration deadline April 27, 2022 Submission deadline May 4, 2022 CMSB 2022 - Second Call for Papers The 20th conference on Computational Methods in Systems Biology (CMSB 2022, https://fmi.unibuc.ro/en/cmsb-2022/) will take place on September 14-16, in Bucharest (Romania), on-site, hybrid, or online, depending on the evolution of the Covid-19 pandemic. CMSB is a well established conference series, whose aim is to bring together researchers from across the biological, mathematical, computational, and physical sciences, interested in the modelling, simulation, analysis, inference, design, and control of biological systems. NEW in the 2nd CfP * Invited speakers confirmed: * Alessandra Carbone (Sorbonne Université, France) * Gabriela Chiosis (Memorial Sloan Kettering Cancer Center, USA) * Loïc Paulevé (Laboratoire Bordelais de Recherche en Informatique, France) * Alfonso Rodríguez-Patón (Universidad Politécnica de Madrid, Spain) * Erik Sonnhammer (Stockholm University, Sweden) * Conference proceedings to be published in the LNBI series of Springer Nature. * Best paper award(s) sponsored by Springer Nature with 1000 EUR. List of Topics * 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; * applications of machine learning and data analytics in biology; * network modelling, analysis, inference; * automated parameter and model synthesis; * model integration and biological databases; * 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; * modelling, analysis and control of microbial communities. Types of contributions to CMSB 2022 * REGULAR papers should describe original work that has not been previously published and is not under review for publication elsewhere. Accepted regular papers will be published as part of the conference proceedings in the Springer LNBI series. Papers in this category should not exceed 15 pages in the Springer LNBI style (including main figures and tables, excluding references and possible appendices). * TOOL papers should present new tools or public websites, new tool components or novel extensions to existing tools or websites supporting biological system modelling, analysis, simulation, or similar. Submissions must include information on methods, tool availability, and selected application results. They should be original and not previously published in a similar form. Accepted tool papers will be published as part of the conference proceedings in the Springer LNBI series. Papers in this category should have 4-6 pages in the Springer LNBI style (including main figures and tables, excluding references and possible appendices). * POSTERS: Extended abstracts should be submitted to propose poster presentation of original unpublished work, or of major results published or accepted in the last year in a high-quality journal or conference. The abstracts should be submitted in Springer LNBI style and should not exceed 4 pages all included. Authors of accepted abstracts will be invited for presentation in a poster sessions and/or for flash presentations. Poster submissions will not be included in the Springer LNBI proceedings. * HIGHLIGHT TALKS: Highlight talk proposals should be submitted in the form of an extended abstract, for possible oral presentation without publication of related material in the conference proceedings. We particularly welcome submission of recently published work. Submitted abstracts summarising the results and their relevance should not exceed 2 pages including references. Extended abstracts will not be included in the Springer LNBI proceedings. The full information for authors on how to prepare and submit their contributions is available at https://fmi.unibuc.ro/en/cmsb-2022/cmsb-2022-call/. Committees Program Committee * Alessandro Abate – University of Oxford (UK) * Paolo Ballarini – Centrale Supélec (France) * Daniela Besozzi – University of Milan Bicocca (Italy) * Luca Cardelli – University of Oxford (UK) * Milan Češka – Brno University of Technology (Czech Republic) * Eugenio Cinquemani – Inria Grenoble-Rhône-Alpes (France) * Eugen Czeizler – University of Helsinki (Finland) * Franck Delaplace – Université Paris-Saclay (France) * Jerome Feret – Inria Paris (France) * Clémence Frioux – Inria Bordeaux (France) * Ashutosh Gupta – IIT Bombay (India) * Monika Heiner – Brandenburg Technical University Cottbus-Senftenberg (Germany) * Jane Hillston – University of Edinburgh (UK) * Tommaso Mazza – CSS Mendel (Italy) * Andrzej Mizera – University of Luxembourg (Luxembourg) * Jun Pang – University of Luxembourg (Luxembourg) * Nicola Paoletti – University of London (UK) * Loïc Paulevé – CNRS, LaBRI (France) * Andrei Paun – University of Bucharest, Romania, co-chair * Ion Petre – University of Turku, Finland, co-chair * Tatjana Petrov – University of Konstanz (Germany) * Ovidiu Radulescu – University of Montpellier France) * Andre Ribeiro – University of Tampere (Finland) * Maria Rodriguez Martinez – IBM Zürich Research Laboratory (Switzerland) * Olivier Roux – École Centrale de Nantes (France) * David Šafránek – Masaryk University (Czech Republic) * Carolyn Talcott – SRI International (USA) * Jing Tang – University of Helsinki (Finland) * Adelinde Uhrmacher – University of Rostock (Germany) * Andrea Vandin – Technical University of Denmark (Denmark) * Verena Wolf – Saarland University (Germany) * Christoph Zechner – Max Planck Institute of Molecular Cell Biology and Genetics (Germany) Organizing committee * David Pacioianu, University of Bucharest, Romania * Andrei Paun, University of Bucharest, Romania (co-chair) * Ion Petre, University of Turku, Romania (co-chair) * Nicoleta Siminea, University of Bucharest * Joel Sjöberg, University of Turku, Finland Publication The submissions to CMSB 2022 will be fully peer-reviewed. The accepted (regular and tool) articles will be published in the conference proceedings, in the Springer LNBI series. A special issue of a widely recognized international journal is expected to be organized later based on the conference, subject to separate peer-review. A selection of the best papers will be invited to be extended and submitted to this special issue. Important dates * May 4, 2022: regular and tool paper submission deadline (their abstracts submitted by April 27). * June 10, 2022: acceptance notifications. * June 17, 2021: poster and highlight talk abstract submission deadline. * September 14-16, 2021: conference. Venue The conference will be held in Bucharest (Romania), on-site, hybrid, or online, depending on the evolution of the Covid-19 pandemic. Contact All questions about submissions should be emailed to the conference organizers Ion Petre (ion.petre at utu.fi) and Andrei Paun (apaun at fmi.unibuc.ro). -- Prof. Ion Petre Department of Mathematics and Statistics University of Turku, Finland https://users.utu.fi/ionpet/ ion.petre at utu.fi -------------- next part -------------- An HTML attachment was scrubbed... URL: From nicosia at dmi.unict.it Fri Mar 4 09:28:30 2022 From: nicosia at dmi.unict.it (Giuseppe Nicosia) Date: Fri, 4 Mar 2022 09:28:30 +0100 Subject: [SocBiN] CfP ACAIN 2022, 2nd Int. Online & Onsite Advanced Course & Symposium on Artificial Intelligence & Neuroscience, Sept 18-22, Certosa di Pontignano, Tuscany - Italy Message-ID: _______________________________________________________________ Call for Participation & Call for Papers (apologies for cross-postings) Please distribute this call to interested parties, thanks _______________________________________________________________ The 2nd International Online & Onsite Advanced Course & Symposium on #ArtificialIntelligence & #Neuroscience - #ACAIN2022 September 18-22, 2022 Certosa di Pontignano, Castelnuovo Berardenga (Siena), #Tuscany - Italy LECTURERS: * Marvin M. Chun, Yale University, USA * Ila Fiete, MIT, USA * Karl Friston, University College London, UK & Wellcome Trust Centre for Neuroimaging * Wulfram Gerstner, EPFL, Switzerland * Máté Lengyel, Cambridge University, UK * Max Erik Tegmark, MIT, USA & Future of Life Institute * Michail Tsodyks, Institute for Advanced Study, USA More Lecturers and Speakers to be announced soon! W: https://acain2022.artificial-intelligence-sas.org E: acain at icas.cc NEWS: https://acain2022.artificial-intelligence-sas.org/category/news/ Past Edition: https://acain2021.artificial-intelligence-sas.org Early Registration (Course): by March 23, 2022 (AoE) https://acain2022.artificial-intelligence-sas.org/registration/ Paper Submission (Symposium) : by Saturday April 23, 2022 (AoE) https://acain2022.artificial-intelligence-sas.org/symposium-call-for-papers/ https://easychair.org/conferences/?conf=acain2022 SCOPE & MOTIVATION: The ACAIN 2022 symposium is an interdisciplinary event featuring leading scientists from AI and Neuroscience, providing a special opportunity to learn about cutting-edge research in the fields. While the Advanced Course and Symposium on Artificial Intelligence & Neuroscience (ACAIN) is a full-immersion residential (or online) Course and Symposium at the Certosa di Pontignano (Tuscany - Italy) on cutting-edge advances in Artificial Intelligence and Neuroscience with lectures delivered by world-renowned experts. The Course provides a stimulating environment for academics, early career researchers, Post-Docs, PhD students and industry leaders. Participants will also have the chance to present their results with oral talks or posters, and to interact with their peers, in a friendly and constructive environment. Two days of keynote talks and oral presentations, the ACAIN Symposium, (September 21-22), will be preceded by lectures of leading scientists, the ACAIN Course, (September 18-20). Bringing together AI and neuroscience promises to yield benefits for both fields. The future impact and progress in both AI and Neuroscience will strongly depend on continuous synergy and efficient cooperation between the two research communities. These are the goals of the International Course and Symposium – ACAIN 2022, which is aimed both at AI experts with interests in Neuroscience and at neuroscientists with an interest in AI. ACAIN 2022 accepts rigorous research that promotes and fosters multidisciplinary interactions between artificial intelligence and neuroscience. The Event (Course and Symposium) will involve a total of 36-40 hours of lectures. Academically, this will be equivalent to 8 ECTS points for the PhD Students and the Master Students attending the Event. COURSE DESCRIPTION: https://acain2022.artificial-intelligence-sas.org/course-description/ LECTURERS: https://acain2022.artificial-intelligence-sas.org/course-lecturers/ * Marvin M. Chun, Yale University, USA * Ila Fiete, MIT, USA * Karl Friston, University College London, UK & Wellcome Trust Centre for Neuroimaging * Wulfram Gerstner, EPFL, Switzerland * Máté Lengyel, Cambridge University, UK * Max Erik Tegmark, MIT, USA & Future of Life Institute * Michail Tsodyks, Institute for Advanced Study, USA More Lecturers and Speakers to be announced soon! ORGANIZING COMMITTEE: https://acain2022.artificial-intelligence-sas.org/organizing-committee/ VENUE & ACCOMMODATION: https://acain2022.artificial-intelligence-sas.org/venue/ https://acain2022.artificial-intelligence-sas.org/accommodation/ The venue of ACAIN 2022 will be The Certosa di Pontignano — Siena The Certosa di Pontignano Località Pontignano, 5 – 53019, Castelnuovo Berardenga (Siena) – Tuscany – Italy phone: +39-0577-1521104 fax: +39-0577-1521098 info at lacertosadipontignano.com https://www.lacertosadipontignano.com/en/index.php Contact person: Dr. Lorenzo Pasquinuzzi You need to book your accommodation at the venue and pay the amount for accommodation directly to the Certosa di Pontignano. ACTIVITIES: https://acain2022.artificial-intelligence-sas.org/activities/ REGISTRATION: https://acain2022.artificial-intelligence-sas.org/registration/ See you in 3D or 2D :) in Tuscany in September! ACAIN 2022 Directors. POSTER: https://acain2022.artificial-intelligence-sas.org/wp-content/uploads/sites/21/2022/02/poster-ACAIN-2022.png NEWS: https://acain2022.artificial-intelligence-sas.org/category/news/ E: acain at icas.cc W: https://acain2022.artificial-intelligence-sas.org Past Edition, ACAIN 2021: https://acain2021.artificial-intelligence-sas.org * Apologies for multiple copies. Please forward to anybody who might be interested * -------------- next part -------------- An HTML attachment was scrubbed... URL: From laurent.guyon at cea.fr Mon Mar 7 11:12:32 2022 From: laurent.guyon at cea.fr (GUYON Laurent 217719) Date: Mon, 7 Mar 2022 10:12:32 +0000 Subject: [SocBiN] Upcoming web-seminars related to small non-coding RNA bioinformatics club Message-ID: Dear colleagues, 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/1499789459696627716 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. - 21 March 2022 (new date) - Stefan Kirsch - Single Cell microRNA sequencing: Protocol Comparison, Automation and Application to Clinical Samples (+ 8 minute presentation of Sarah Hücker) - link - 2 May 2022 - Isana Veksler-Lublinsky - miRNA target prediction through a machine learning lens (+ 8 minute presentation of Shani cohen) - link - 4 July 2022 - Cynthia Sharma - mechanisms/functions of small RNAs in bacteria - 5 September 2022 - to come - 7 November 2022 - Amy Buck - Dr Buck is working in the field of microRNA-virus interactions '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 20th of April (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 janina.bocksch at senckenberg.de Tue Mar 8 09:51:11 2022 From: janina.bocksch at senckenberg.de (Janina Bocksch) Date: Tue, 8 Mar 2022 09:51:11 +0100 (CET) Subject: [SocBiN] PostDoc Position in Comparative Genomics at Senckenberg Frankfurt / Application deadline April 5th 2022 Message-ID: <1611112134.885091.1646729471108@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 apply and develop new comparative genomic methods. The Project The project combines the development of new comparative genomic methods to uncover key genomic differences with large-scale analyses to link phenotypic adaptations to genomic differences, which is a central goal in the genomics era. Powerful computational methods are fundamental to gain novel insights through comparative genomics and our lab has developed several approaches to address the phenotype – genotype question (https://github.com/hillerlab/). We aim at expanding our methods repertoire by detecting new “types” of relevant differences, such as genomic changes in non-coding RNAs and gene duplication events. New and existing approaches will then be applied to vertebrate genomes, including new assemblies generated in our lab, to reveal the genomic underpinnings of phenotypic differences. The postdoc is expected to work closely with other lab members and to capitalize on a wealth of comparative data for several hundred vertebrate genomes (http://genome.senckenberg.de/). 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 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 [1-9]. 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, a leave of 30 days per year, and a subsidy job ticket for public transport. 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 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 comparative genomics is an advantage. Place of employment: Frankfurt am Main Working hours: full time (40 hours/week) Type of contract: initially for 2 years, but funding is available to extend it further Salary and benefits: according to the collective agreement of the State of Hesse (pay grade E13 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.#12-22006), 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 initial application deadline is April 5th, 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/personen/hiller/. Recent publications [1] Blumer et al. Gene losses in the common vampire bat illuminate molecular adaptations to blood feeding. Science Advances, 2022 [2] Roscito et al. Convergent and lineage-specific genomic differences in limb regulatory elements in limbless reptile lineages. Cell Reports, 38(3):110280, 2022 [3] Jebb et al. Six reference-quality genomes reveal evolution of bat adaptations. Nature, 583, 578–584, 2020 [4] 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 [5] Hecker et al. Convergent gene losses illuminate metabolic and physiological changes in herbivores and carnivores. PNAS, 116(8), 3036-3041, 2019 [6] Roscito et al. Phenotype loss is associated with widespread divergence of the gene regulatory landscape in evolution. Nature Communications, 9:4737, 2018 [7] Lee et al. Molecular parallelism in fast-twitch muscle proteins in echolocating mammals. Science Advances, 4(9), eaat9660, 2018 [8] Sharma et al. A genomics approach reveals insights into the importance of gene losses for mammalian adaptations. Nature Communications, 9(1), 1215, 2018 [9] 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 janina.bocksch at senckenberg.de Tue Mar 8 09:56:10 2022 From: janina.bocksch at senckenberg.de (Janina Bocksch) Date: Tue, 8 Mar 2022 09:56:10 +0100 (CET) Subject: [SocBiN] PhD Position in Comparative Vertebrate Genomics at Senckenberg Frankfurt / Application deadline April 4th 2022 Message-ID: <1673735270.885682.1646729770603@office.mailbox.org> The Hiller Lab at the LOEWE Center for Translational Biodiversity Genomics (TBG) in Frankfurt, Germany is looking for an ambitious PhD student to investigate the genomic basis of phenotypic differences between vertebrates. The Project The project aims at linking phenotypic adaptations to genomic differences, which is a central goal in the genomics era. The PhD student will capitalize on a number of new long-read based genomes that we are sequencing in a collaborative project as well as a powerful repertoire of comparative methods to trace key genomic differences in genes and regulatory elements. We plan to investigate the genomic underpinnings of many interesting adaptations including metabolic, physiological and morphological traits in bats and other mammals, reptiles and fishes. The PhD student will work closely with other members of our lab, the TBG lab center and students from other collaborating institutes on all computational and experimental aspects. 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 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 [1-9]. 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, a leave of 30 days per year, and a subsidy job ticket for public transport. 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. Place of employment: Frankfurt am Main Type of contract: 3 years Salary and benefits: according to the collective agreement of the State of Hesse (pay grade E13 75% TV-H) 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 offer (ref.#12-22004), 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 of this job offer, a CV with a publication list and contact information for at least two references, and a summary of previous research experience (max 1 page), and copies of certificates, transcripts and grades. The application deadline is April 4th, 2022. For more information please contact Prof. Dr. Michael Hiller, michael.hiller at senckenberg.de mailto:michael.hiller at senckenberg.de or use the following link: https://tbg.senckenberg.de/personen/hiller/ Recent publications [1] Blumer et al. Gene losses in the common vampire bat illuminate molecular adaptations to blood feeding. Science Advances, 2022 [2] Roscito et al. Convergent and lineage-specific genomic differences in limb regulatory elements in limbless reptile lineages. Cell Reports, 38(3):110280, 2022 [3] Jebb et al. Six reference-quality genomes reveal evolution of bat adaptations. Nature, 583, 578–584, 2020 [4] 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 [5] Hecker et al. Convergent gene losses illuminate metabolic and physiological changes in herbivores and carnivores. PNAS, 116(8), 3036-3041, 2019 [6] Roscito et al. Phenotype loss is associated with widespread divergence of the gene regulatory landscape in evolution. Nature Communications, 9:4737, 2018 [7] Lee et al. Molecular parallelism in fast-twitch muscle proteins in echolocating mammals. Science Advances, 4(9), eaat9660, 2018 [8] Sharma et al. A genomics approach reveals insights into the importance of gene losses for mammalian adaptations. Nature Communications, 9(1), 1215, 2018 [9] 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 bjorn.wallner at liu.se Thu Mar 10 10:36:56 2022 From: bjorn.wallner at liu.se (=?utf-8?B?QmrDtnJuIFdhbGxuZXI=?=) Date: Thu, 10 Mar 2022 09:36:56 +0000 Subject: [SocBiN] Postdoc in ML, structural biology and cryo-EM Message-ID: <413A36A0-C417-46D1-8B5E-941B275FC93B@liu.se> Dear all, We have a postdoc position open in artificial intelligence for structural bioinformatics and cryo-EM. NOTE: It closes 11 March, if you are interested just upload your CV here (it system might ask for more, but CV is fine): https://liu.se/en/work-at-liu/vacancies?rmpage=job&rmjob=18192&rmlang=UK In this position you will be using and develop AI/ML methods to study protein-protein interactions. The methods will be applied to solve large molecular structures augmented by cryo-EM data. The project involves using existing methods, e.g, AlphaFold, and developing new AI methods that are specific tailored to the problem and the data available. We are seeking applicants who have a Ph.D. degree in a relevant area, such as bioinformatics, computer science or structural biology eager to learn new methodologies.. Previous experience with machine learning, artificial intelligence and/or structural biology is required. The applicant should also be experienced in programming, preferably Python or equivalent language. Strong communicative skills and fluency in written and spoken English are a requirement. Having worked with large data set in HPC environment is also a merit. The position is a joint interdisciplinary research project between professor Bjorn Wallner at Linkoping University (Bjorn Wallner – LiU) and associate professor Alexey Amunts at SciLifeLab (Alexey Amunts – SU) with aim of using and develop AI methods to understand protein-protein interactions and apply them to biologically relevant problems for which we have cryo-EM data. The position is based at the AI structural biology group at LiU, but it also includes collaborations with the cryo-EM groups at SciLifeLab. Environment The AI structural biology group, where the position will be based, at LiU consists of one PhD student, one senior AI expert, and one structural bioinformatics professor working on applying AI in structural biology. A new group leader has also been recruited that will join the team after the summer. The group is embedded together with experimental groups in structural biology at the department ensuring that the developed methods are relevant and can be readily applied. The current research focus is on how to incorporate protein dynamics and flexibility into the models to enable a deeper understanding on protein function. The group have access to the newly installed Berzelius GPU-cluster. Berzelius is an NVIDIA SuperPOD consisting of 60 NVIDIA DGX-A100 compute nodes supplied by Atos. Each DGX-A100 node is equipped with 8 NVIDIA A100 Tensor Core GPUs, 2 AMD Epyc 7742 CPUs, 1 TB RAM and 15 TB of local NVMe SSD storage. The A100 GPUs have 40 GB on-board HBM2 VRAM. The cryo-EM group at SU consists of three PhD students, and three postdocs. The group has access to the state-of-the-art cryo-EM facility equipped with Titan Krios microscopes with K3 direct electron detectors. The research focus is on large multi-protein complexes involved in bioenergetics. cheers Björn Wallner Professor Head of Bioinformatics Division [Linköping University] Institutionen för Fysik, Kemi och Biologi (IFM) 581 83 Linköping Telephone: 013-28 27 59 Mobile: 070-521 56 65 Visiting address: 2B:580 (B-huset) -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 17237 bytes Desc: image001.png URL: From erik.larsson at gu.se Fri Mar 11 09:00:56 2022 From: erik.larsson at gu.se (Erik Lekholm) Date: Fri, 11 Mar 2022 08:00:56 +0000 Subject: [SocBiN] Funding for Ukrainian scientists to conduct research in Sweden Message-ID: <096371E1-B3D9-4490-980F-FE2C4D9934EE@gu.se> Hi everyone, FYI: The Swedish Foundation for Strategic Research has announced about 3 million euros in funding dedicated to Ukrainian scientists who wish to conduct research in Sweden starting in 2022 - at all levels including postdoc. The funds are primarily to cover salary expenses during a period up to 3 years. More information: https://strategiska.se/en/ssf-supports-ukrainian-researchers-with-30-million-sek/ With best wishes, Erik Larsson Lekholm Professor in Bioinformatics Department of Biochemistry and Cell Biology University of Gothenburg P.O. Box 440 SE-405 30 Gothenburg Sweden Office: +46 31 786 6942 Mobile: +46 736 735 735 www.larssonlab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From awe at signatur.dk Fri Mar 11 15:09:53 2022 From: awe at signatur.dk (Alan Wervick) Date: Fri, 11 Mar 2022 14:09:53 +0000 Subject: [SocBiN] Associate/Full Professorship in Bioinformatics at Associate/Full Professorship in Bioinformatics at Department of Biology, Faculty of Science, University of Copenhagen Message-ID: Associate/Full Professorship in Bioinformatics Department of Biology, Faculty of Science University of Copenhagen The Department of Biology at the University of Copenhagen invites applications for a position as Associate or Full Professor in Bioinformatics. The position is to be filled by 1st November 2022 or as soon as possible thereafter, subject to negotiation. The Department of Biology employs about 450 academic and technical staff and hosts research programmes and teaching curricula that cover all major biological sub-disciplines. University rankings typically place the fields of Biology and Biochemistry at the University of Copenhagen first in Denmark and among the top 15-30 universities globally. In addition to a PhD-programme, three BSc study programmes (biology, biochemistry, molecular biomedicine) and four MSc study programmes (biology, biochemistry, molecular biomedicine, bioinformatics) engage close to 2000 students. A new Bioinformatics BSc programme, to be launched in the Fall of 2024, is under development as a cross-departmental collaboration anchored at the Department of Biology. The ambition is to make the Bioinformatics programme among the best world-wide. The department is committed to equality of opportunity and to creating an inclusive working environment that reflects the diversity of society. We highly value a safe, informal, trusting and collaborative working atmosphere. The Associate Professor/Full Professor will be embedded in the Section for Computational and RNA Biology (https://www1.bio.ku.dk/scarb/), which currently consists of twelve research groups working in the fields of computational biology, population and statistical genetics and RNA biology. The section has state-of-the-art computational infrastructure and laboratory facilities, and is currently responsible for teaching a 2-year Bioinformatics Master programme. The section will also play a leading role in the establishment of the new Bachelors programme. The vacant position is opened as part of this initiative. Description of the position The successful candidate is expected to take a leading role in the development of an externally funded research programme in biological data sciences/bioinformatics. She/he is expected to integrate with and strengthen the research environment of high-quality bioinformatics research. Complementarity to the current research focus of the section is essential, as is an interest in establishing interdisciplinary collaboration with the other sections at the department. A very important duty is to be Head of Studies for Bioinformatics and play a leading role in the development of the new BSc study programme and a reorganisation of the existing MSc programme. The appointment as Head of Studies will be for three years with likely 3-yr extensions. Obligations also include teaching and supervision of students at the undergraduate, graduate and PhD-levels. To a limited extent, the position may also include duties requested by the Department such as research dissemination of scientific results or participation in local committees. Qualifications/profile at the Associate Professor level Applicants should have a scientific background within computational biology/bioinformatics. The position requires a track-record of successful external research funding as well as a significant publication record in high-level, international, peer-reviewed ISI journals. Candidates are also required to have documented university level competencies in delivering high-quality undergraduate/graduate teaching and must be able to explain and reflect upon own teaching practice and portfolio. Formal pedagogical training or supervision equivalent to the University of Copenhagen teacher training programme is required. Finally, candidates are expected to have managerial and out-reach qualifications. Qualifications/profile at the Full Professor level Applicants should have a scientific background within computational biology/bioinformatics. A significant track-record of attracting external research funding as well as a significant publication record in high-level, international, peer-reviewed ISI journals is expected. Candidates are also required to have documented university level competencies in delivering high-quality undergraduate/graduate teaching and must be able to explain and reflect upon own teaching practice and portfolio. Formal pedagogical training or supervision equivalent to the University of Copenhagen Teaching and Learning in Higher Education programme is necessary. Finally, candidates are expected to possess managerial qualifications and experience in leading a competitive research group, as well as having out-reach qualifications. Assessment of applicants will primarily consider their level of documented, original scientific production at an international level, including contributions to developments in their field, scientific profile in relation to ongoing research at the section, as well as documented teaching qualifications. Ability to attract external funding will also be considered as will managerial and out-reach qualifications. Six overall criteria apply for Associate/ Full Professor appointments at the University of Copenhagen. The six criteria (research, teaching, societal impact, organizational contribution, external funding and leadership) are considered a framework for an overall assessment of the candidates. Furthermore, each candidate must be assessed according to the specific requirements stated in the job advertisement. Please read more at: https://www1.bio.ku.dk/english/about/jobs/criteria-for-recognising-merit/ where the local criteria applied at the Department of Biology can also be found. The Appointment Committee will prepare a short-list of applicants to be assessed by an Assessment Committee. Note that being on the short-list, is not equivalent to being assessed qualified for the position. Short-listed candidate may potentially be deemed “not qualified” by the Assessment Committee. A sub-set of the qualified short-listed candidates will be selected for a formal interview by the Appointment Committee. Invited candidates may also be given the opportunity to visit the department to meet with the faculty and the Head of Department, and to give a research presentation. The University wishes our staff to reflect the diversity of society and thus welcomes applications from all qualified candidates regardless of personal background. Terms of employment The position is open from 1st November 2022 or as soon as possible thereafter. The position is covered by the Memorandum on Job Structure for Academic Staff. Terms of appointment and payment accord to the agreement between the Ministry of Finance and The Danish Confederation of Professional Associations on Academics in the State. Negotiation for salary supplement is possible. Further information For more information about the Department of Biology, please visit our web-site https://www1.bio.ku.dk/english/. Inquiries about the position can be made to Head of Department, Professor Niels Kroer (nk at bio.ku.dk) and/or Head of Section, Associate Professor Jeppe Vinther (jvinther at bio.ku.dk). Copenhagen is one of the 10 most livable cities in the world with a rich culture within music, theater and associations. Life for families is made easy by a publicly supported daycare and health care system, dual career opportunities, maternity leave and six weeks of annual vacation. International candidates may find information on living and working in Denmark at www.workindenmark.dk. Useful information is also available at The International Staff Mobility office (ISM) at the University of Copenhagen (https://ism.ku.dk). ISM offers a variety of services to international researchers coming to and working at the University of Copenhagen. Filing of application The position may be applied for at the Associate Professor or Full Professor levels. Please note that it is possible to apply at more than one level. If applied at more than one level, separate applications must be submitted (see below). The application including all attachments must be in English and submitted electronically by clicking APPLY NOW below . Please include * Curriculum vitae including information about external funding * Diplomas (Master and PhD degree or equivalent) * Research plan – description of current and future research plans * Description and documentation of teaching experience and qualifications according to university guidelines * Complete publication list * Separate reprints of 5 particularly relevant papers Deadline for applications is 20th April 2022 at 23:59 GMT +2. After the expiry of the deadline for applications, the authorized recruitment manager selects applicants for assessment on the advice of the Appointment Committee. You can read about the recruitment process at http://employment.ku.dk/faculty/recruitment-process/. Interviews will be held on 2nd September 2022. Invited candidates may also be invited to visit the Department of Biology, to meet with the faculty and the Head of Department, and to give a research presentation. Please refer to the following no. in future communication in this case: Associate Professorship in Bioinformatics: 211-0381/22-2E Professorship in Bioinformatics: 211-0159/22-2K APPLY NOW Part of the International Alliance of Research Universities (IARU), and among Europe’s top-ranking universities, the University of Copenhagen promotes research and teaching of the highest international standard. Rich in tradition and modern in outlook, the University gives students and staff the opportunity to cultivate their talent in an ambitious and informal environment. An effective organisation – with good working conditions and a collaborative work culture – creates the ideal framework for a successful academic career. -------------- next part -------------- An HTML attachment was scrubbed... URL: From laurent.guyon at cea.fr Mon Mar 21 12:42:36 2022 From: laurent.guyon at cea.fr (GUYON Laurent) Date: Mon, 21 Mar 2022 11:42:36 +0000 Subject: [SocBiN] Virtual seminar about Single Cell microRNA sequencing, Today (Monday 21st) Message-ID: <542e6af55784479da149f9fb624d0662@cea.fr> Dear colleagues, As a late reminder, don't miss today at 4PM CET the virtual seminars of Stefan Kirsch and Sarah Hücker about #SingleCell #microRNA sequencing. They are provided in the framework of the small non-coding RNA bioinformatics club, https://smallrna-bioinformatics.eu/. YouTube streaming (if you don't ask question): https://www.youtube.com/watch?v=Zgxh5w9yvgM&list=PLCwWvQ5hkUsU_dpbVcSQHun5H5rh_kOse Zoom: https://univ-grenoble-alpes-fr.zoom.us/j/95557401151?pwd=ZEpobUNlWHpNNlFha2k2ZERGN09Vdz09 More information: https://smallrna-bioinformatics.eu/Pages/Seminars/Seminar-March.aspx Future seminars: https://smallrna-bioinformatics.eu/Pages/Seminars/Seminars.aspx 'hope to see you virtually there, Laurent Guyon (on behalf of the organizers of the club, Andreas Keller, Laurent Guyon, Marie-France Sagot, Bastian Fromm, Ana Eulálio and Rolf Backofen) ____________________________ 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 20th of April (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 nicosia at dmi.unict.it Mon Mar 21 15:44:19 2022 From: nicosia at dmi.unict.it (Giuseppe Nicosia) Date: Mon, 21 Mar 2022 15:44:19 +0100 Subject: [SocBiN] ACAIN 2022, 2nd International Advanced Course on Artificial Intelligence & Neuroscience, Sept 18-22, Tuscany Message-ID: _______________________________________________________________ Call for Participation (apologies for cross-postings) Please distribute this call to interested parties, thanks. _______________________________________________________________ The 2nd International Advanced Course on #ArtificialIntelligence & #Neuroscience - #ACAIN2022 September 18-22 Certosa di Pontignano, Castelnuovo Berardenga #Tuscany https://acain2022.artificial-intelligence-sas.org acain at icas.cc Past Edition: https://acain2021.artificial-intelligence-sas.org LECTURERS: * Marvin M. Chun, Yale University, USA * Ila Fiete, MIT, USA * Karl Friston, University College London, UK * Wulfram Gerstner, EPFL, Switzerland * Máté Lengyel, Cambridge University, UK * Max Erik Tegmark, MIT, USA & Future of Life Institute * Michail Tsodyks, Institute for Advanced Study (IAS) Princeton, USA More Lecturers and Speakers to be announced soon! https://acain2022.artificial-intelligence-sas.org/course-lecturers/ Early Registration (Course): by Thursday June 30, 2022 (AoE) https://acain2022.artificial-intelligence-sas.org/registration/ SCOPE & MOTIVATION: The ACAIN 2022 is an interdisciplinary event featuring leading scientists from AI and Neuroscience, providing a special opportunity to learn about cutting-edge research in the fields. The Advanced Course on Artificial Intelligence & Neuroscience (ACAIN) is a full-immersion residential (or online) Course and Symposium at the Certosa di Pontignano (Tuscany - Italy) on cutting-edge advances in Artificial Intelligence and Neuroscience with lectures delivered by world-renowned experts. The Course provides a stimulating environment for academics, early career researchers, Post-Docs, PhD students and industry leaders. Participants will also have the chance to present their results with oral talks or posters, and to interact with their peers, in a friendly and constructive environment. Bringing together AI and neuroscience promises to yield benefits for both fields. The future impact and progress in both AI and Neuroscience will strongly depend on continuous synergy and efficient cooperation between the two research communities. The Event will involve a total of 36-40 hours of lectures. Academically, this will be equivalent to 8 ECTS points for the PhD Students and the Master Students attending the Event. COURSE DESCRIPTION: https://acain2022.artificial-intelligence-sas.org/course-description/ VENUE & ACCOMMODATION: https://acain2022.artificial-intelligence-sas.org/venue/ https://acain2022.artificial-intelligence-sas.org/accommodation/ The Certosa di Pontignano Località Pontignano, 5 – 53019, Castelnuovo Berardenga (Siena) – Tuscany – Italy phone: +39-0577-1521104 fax: +39-0577-1521098 info at lacertosadipontignano.com https://www.lacertosadipontignano.com/en/index.php Contact person: Dr. Lorenzo Pasquinuzzi You need to book your accommodation at the venue and pay the amount for accommodation directly to the Certosa di Pontignano. ACTIVITIES: https://acain2022.artificial-intelligence-sas.org/activities/ REGISTRATION: https://acain2022.artificial-intelligence-sas.org/registration/ See you in 3D or 2D :) in Tuscany in September! ACAIN 2022 Directors. Past Edition: https://acain2021.artificial-intelligence-sas.org POSTER: https://acain2022.artificial-intelligence-sas.org/wp-content/uploads/sites/21/2022/02/poster-ACAIN-2022.png NEWS: https://acain2022.artificial-intelligence-sas.org/category/news/ E: acain at icas.cc W: https://acain2022.artificial-intelligence-sas.org * Apologies for multiple copies. Please forward to anybody who might be interested * -------------- next part -------------- An HTML attachment was scrubbed... URL: From trinro at ifi.uio.no Mon Mar 21 16:41:50 2022 From: trinro at ifi.uio.no (Trine Ballestad Rounge) Date: Mon, 21 Mar 2022 15:41:50 +0000 Subject: [SocBiN] Postdoc/researcher position in Oslo - omics and colorectal cancer screening In-Reply-To: <78B5A1D2-93B7-48FB-B1D7-9A22A7D27B2C@kreftregisteret.no> References: <78B5A1D2-93B7-48FB-B1D7-9A22A7D27B2C@kreftregisteret.no> Message-ID: <3AADD7EF-52B4-490A-9AC6-C44ACC7DF018@kreftregisteret.no> Dear all, We have a 3-year postdoc/researcher position available in our CRCbiome group. The postdoc/researcher will be analyzing our microbiome, epigenome, lifestyle and clinical data. Read more about the position here: https://www.finn.no/job/fulltime/ad.html?finnkode=251929873 And about the project here: https://www.kreftregisteret.no/en/CRC-biome Best regards, Trine B Rounge, PhD Researcher, Department of Research, Cancer Registry of Norway Associate Professor II, Centre for Bioinformatics, University of Oslo Address: Kreftregisteret | Ullernchausseen 64 | 0379 Oslo Office: +47 22 92 87 34 | Mobile: +47 99 604 304 Webpage, Researchgate, ORCID -------------- next part -------------- An HTML attachment was scrubbed... URL: From andersson.robin at gmail.com Wed Mar 23 08:53:54 2022 From: andersson.robin at gmail.com (Robin Andersson) Date: Wed, 23 Mar 2022 07:53:54 +0000 Subject: [SocBiN] Associate/Full Professorship in Bioinformatics at UCPH Message-ID: Dear colleagues, The Department of Biology at the University of Copenhagen invites applications for a position as Associate or Full Professor in Bioinformatics. We are seeking a new colleague to develop and lead research in Computational Biology / Bioinformatics and take the lead in the development of a new BSc programme in Bioinformatics. Read more and apply online at https://employment.ku.dk/faculty/?show=155972 Deadline for applications is 20th April, 2022. Best wishes, Robin -- Robin Andersson, PhD Associate professor The Bioinformatics Centre Department of Biology University of Copenhagen Ole Maaloes Vej 5 DK-2200 Copenhagen N Denmark http://anderssonlab.org Twitter: @robin_andersson -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Bioinformatics_Prof_UCPH.pdf Type: application/pdf Size: 184772 bytes Desc: Bioinformatics_Prof_UCPH.pdf URL: From Fredrik.Ronquist at nrm.se Mon Mar 28 12:05:52 2022 From: Fredrik.Ronquist at nrm.se (Fredrik Ronquist) Date: Mon, 28 Mar 2022 10:05:52 +0000 Subject: [SocBiN] Director of the Swedish Biodiversity Data Infrastructure (SBDI) Message-ID: <0630CE32-E33E-407B-8F4A-20FE3AC0C93A@nrm.se> Director of the Swedish Biodiversity Data Infrastructure The Swedish Biodiversity Data Infrastructure (SBDI) (see https://biodiversitydata.se) is one of two national research infrastructures hosted by the Swedish Museum of Natural History. SBDI is funded by the Swedish Research Council in collaboration with eleven Swedish universities and government agencies. SBDI is the informatics infrastructure for biodiversity and ecosystems research, providing data from multiple sources as well as powerful modeling and analysis tools to the scientific community. SBDI is a distributed infrastructure, with staff at all partner organizations and a secretariat based at the Museum. SBDI also includes the Swedish node of the Global Biodiversity Information Facility (GBIF), an extensive global network of similar infrastructures (see https://gbif.org). SBDI is now looking for a Director. This is a permanent full-time position. The SBDI tasks are not expected to be a full-time commitment, and there is some flexibility in customizing the position according to the background and preferences of the successful candidate. The successful candidate is expected to be proficient or develop proficiency in Swedish. Read more and apply here (application deadline April 25): https://www.nrm.se/ommuseet/jobbahososs/ledigatjanster.9005019.html. Some background to the position and the search on the SBDI web site here: https://biodiversitydata.se/news/sbdi-looking-for-a-director/ Fredrik Ronquist Professor, Acting Director of SBDI -------------- next part -------------- An HTML attachment was scrubbed... URL: From tony.handstad at usit.uio.no Tue Mar 29 09:39:30 2022 From: tony.handstad at usit.uio.no (Tony =?utf-8?Q?H=C3=A5ndstad?=) Date: Tue, 29 Mar 2022 09:39:30 +0200 Subject: [SocBiN] Three positions available at Oslo University Hospital Message-ID: Three positions are currently available at Department of Medical Genetics, Oslo University Hospital: System administrator / Bioinformatician: https://www.finn.no/job/fulltime/ad.html?finnkode=251434521 (deadline for this one is April 3rd) Frontend developer: https://www.finn.no/job/fulltime/ad.html?finnkode=252877777 Backend developer: https://www.finn.no/job/fulltime/ad.html?finnkode=252877874 We are the creators of ELLA https://allel.es, an open-source web-based application for identifying disease-causing variants. Please spread the word and apply if you are interested! Best regards Tony Håndstad