From sonja.lorenz at mpinat.mpg.de Mon Aug 8 10:40:23 2022 From: sonja.lorenz at mpinat.mpg.de (Sonja Lorenz) Date: Mon, 8 Aug 2022 10:40:23 +0200 Subject: [SocBiN] Job opportunity for a bioinformatician at the Max Planck Institute in Goettingen, Germany Message-ID: Job opportunity: Bioinformatician (f/m/d) @ the Max Planck Institute for Multidisciplinary Sciences, Goettingen, Germany Link to this job offer: https://www.mpinat.mpg.de/4179228/40-22?c=645962 BACKGROUND: The Max Planck Institute for Multidisciplinary Sciences is a leading international research institute of exceptional scientific breadth. With more than 40 research groups and some 1,000 employees from over 50 nations, it is the largest institute of the Max Planck Society. The department of Tissue Dynamics and Regeneration (Dr. Jochen Rink) invites applications for a position as Bioinformatician (f/m/d) RESPONSIBILITIES: We study the fascinating ability of some planarian species to regenerate complete animals from random tissue pieces and we carry out worldwide field expeditions to study the evolution of regenerative abilities. Our approach encompasses various next generation sequencing techniques, including RNAseq, ATACseq, CHIPseq, Hi-C and long-read sequencing and comparative genomics. The Bioinformatician supports department members in the analysis and mining of NGS data sets, maintains the departmental analysis pipelines and databases and integrates or develops new analysis tools. The bioinformatician further interfaces with the Institute IT services and the computational service provider at the local university (GWDG). Close collaborations with department members and external contacts are a core aspect of the position. In addition, the pursuit of personal research interests is possible, including the mentoring of Masters or PhD students. REQUIREMENTS: * You hold a Master's degree or Ph.D. in a relevant subject area, e.g., biology, computational biology or computer sciences. * You have extensive experience and a proven track record in one or more of the following: RNAseq and differential expression analysis, single cell seq, Chip or ATACseq, genome assembly and annotation, comparative genomics. * You have hands-on experience with high performance computing and/or cluster management. * You are passionate about big data analysis and the ongoing developments in the field. * You are self-motivated, organized and independent. * You enjoy team work and being an active part of a collaborative research environment. WHAT WE OFFER: * Competitive research in an inspiring, world-class environment * Professional training, networking and career-development opportunities; free language courses * On-site health management: free fitness and yoga room, sports groups, beach volleyball league, and courses for a "moving lunch break" * A wide range of opportunities to balance work and family life, including an on-campus kindergarten and vacation care * Spacious on-site cafeteria with diverse meals; espresso bar * Initiatives for sustainability and a green environment with an on-site biotope ABOUT US: We are a young department at the Max Planck Institute for Multidisciplinary sciences, part of one of Germany's premier research campuses. We represent the organismal end of the wide spectrum of research activities at the institute and investigate the mechanistic and evolutionary underpinnings of planarian regeneration. We are a thoroughly international and interdisciplinary department and our working language is English (knowledge of German is not required). Our department maintains its own state-of -the art high performance computing clusters and we have access to large computation resources elsewhere on Campus and in Germany. We enjoy generous funding by the Max Planck Society, the ERC and other funding programs. The historic town center of Göttingen in close proximity offers rich cultural opportunities and a vibrant student scene, while its green surroundings are ideal for running, hiking, cycling and other outdoor activities. POSITION DETAILS: * Payment and benefits are based on the German Public Service Payscale (TVöD Bund) guidelines. The positions should be filled as soon as possible; the exact start date is flexible. * The Positions are initially limited to two years with a possibility of extension. * The Max Planck Society is committed to increasing the number of individuals with disabilities in its workforce and therefore encourages applications from such qualified individuals. The Max Planck Society strives for gender and diversity equality. We welcome applications from all backgrounds. HOW TO APPLY: Please submit your application including a cover letter (explaining background and motivation), CV, transcripts and publication record (if applicable) and the contact addresses of 3 references (if possible) preferably as a single PDF file to: ausschreibung40-22 at mpinat.mpg.de DEADLINE: Review of applications will begin immediately and continue until the position is filled. Max Planck Institute for Multidisciplinary Sciences Department "Tissue Dynamics and Regeneration" Dr. Jochen Rink Am Fassberg 11 37077 Göttingen Germany www.mpinat.mpg.de/de/rink -------------- next part -------------- An HTML attachment was scrubbed... URL: From arne at bioinfo.se Mon Aug 8 17:08:14 2022 From: arne at bioinfo.se (Arne Elofsson) Date: Mon, 8 Aug 2022 17:08:14 +0200 Subject: [SocBiN] 3d bioinfo annual General meeting Message-ID: Submit your abstract for 3D BioInfo Community Annual General Meeting2-4 November 2022 | EMBL-EBI, UK (hybrid) The ELIXIR 3D BioInfo Community is inviting its Community members to participate in and contribute to the 3D BioInfo Community Annual General Meeting. This will be a hybrid meeting with F2F attendance at EMBL-EBI, Hinxton. Funding, including travel, accommodation and (food) expenses is available for a number of people. Selection will be based on submitted abstracts. Submit an abstract by 12 August 2022 » -------------- next part -------------- An HTML attachment was scrubbed... URL: From ion.petre at utu.fi Tue Aug 9 14:20:57 2022 From: ion.petre at utu.fi (Ion Petre) Date: Tue, 9 Aug 2022 15:20:57 +0300 Subject: [SocBiN] CMSB 2022: call for participation References: <3afdbced-c5a2-4a75-9a9a-08942f4d4fc9@Spark> Message-ID: <0be13112-cb95-4b51-8c59-be975f1d17b6@Spark> CMSB 2022: call for participation ====================================== September 14-16, 2022 at the University of Bucharest, Romania CMSB 2022 website: https://fmi.unibuc.ro/en/cmsb-2022/ Program: https://fmi.unibuc.ro/en/cmsb-2022/cmsb-2022-program/ Registration: https://fmi.unibuc.ro/en/cmsb-2022/cmsb-2022-registration/ CMSB series website: https://cmsb.sciencesconf.org/ CMSB, the conference on Computational Methods in Systems Biology, brings together researchers from across the biological, mathematical, computational, and physical sciences, interested in the modelling, simulation, analysis, inference, design, and control of biological systems. The 20th edition of the conference takes place at University of Bucharest, Romania, in the period September 14-16, 2022, as an in-person meeting with some support for online attendance. The early registration is open until August 15. INVITED SPEAKERS 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) ORGANIZATION COMMITTEE David Pacioianu, University of Bucharest, Romania Andrei Paun, University of Bucharest, Romania (co-chair) Ion Petre, University of Turku, Finland (co-chair) Nicoleta Siminea, University of Bucharest 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) François Fages – INRIA (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) TOOL EVALUATION COMMITTEE Georgios Argyris – Technical University of Denmark, Copenhagen (Denmark) Candan Çelik – Comenius University, Bratislava (Slovakia) Anastasis Georgoulas – University College London (UK) Lukrécia Mertová – Heidelberg Institute for Theoretical Studies (Germany) Samuel Pastva – IST Austria (Austria) Misbah Razzaq – INRAe, Tours (France) David Šafránek – Masaryk University (Czech Republic), chair Jakub Šalagovič – KU Leuven (Belgium) Matej Trojak – Masaryk University (Czech Republic) STEERING COMMITTEE Luca Cardelli – University of Oxford (UK) François Fages – INRIA (France) Monika Heiner – Brandenburg Technical University Cottbus-Senftenberg (Germany) Tomasso Mazza – CSS Mendel (Italy) Satoru Miyano – University of Tokyo (Japan) Ion Petre – University of Turku, Finland Gordon Plotkin – University of Edinburgh (UK) Corrado Priami – University of Pisa (Italy) Carolyn Talcott – SRI International (USA) Adelinde Uhrmacher – University of Rostock (Germany) Alessandro Abate – University of Oxford (UK) Eugenio Cinquemani – Inria Grenoble-Rhône-Alpes (France) Jun Pang – University of Luxembourg (Luxembourg) Loïc Paulevé – CNRS, LaBRI (France) Andrei Paun – University of Bucharest, Romania Tatjana Petrov – University of Konstanz (Germany) Verena Wolf – Saarland University (Germany) CONTACT All questions about the conference should be emailed to the organizers Ion Petre (ion.petre at utu.fi) and Andrei Paun (apaun at fmi.unibuc.ro). Prof. Dr. Ion Petre Department of Mathematics and Statistics University of Turku, Finland -------------- next part -------------- An HTML attachment was scrubbed... URL: From bjorn.wallner at liu.se Tue Aug 9 15:43:11 2022 From: bjorn.wallner at liu.se (=?utf-8?B?QmrDtnJuIFdhbGxuZXI=?=) Date: Tue, 9 Aug 2022 13:43:11 +0000 Subject: [SocBiN] Postdoc in machine learning for structural bioinformatics Message-ID: Dear all, We are looking for a Postdoc in machine learning for structural bioinformatics at Linköping University. 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. More details here: https://liu.se/en/work-at-liu/vacancies?rmpage=job&rmjob=19565&rmlang=UK If you are interested just upload your CV at the link above (the system might ask for more, but CV is fine): Deadline August 15. Please feel free to forward to anyone that might be interested. 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: 17238 bytes Desc: image001.png URL: From alexandru.tomescu at helsinki.fi Fri Aug 12 09:00:49 2022 From: alexandru.tomescu at helsinki.fi (Tomescu, Alexandru) Date: Fri, 12 Aug 2022 07:00:49 +0000 Subject: [SocBiN] PhD position in Graph Algorithms for Bioinformatics (University of Helsinki) Message-ID: <82721CC7-B198-465C-8B39-2662A11F29B8@helsinki.fi> Dear colleagues, I'm looking to recruit one PhD student (full-time employment, 3.5 - 4 years) for a Bioinformatics project at the University of Helsinki, involving graph algorithms (focusing on network flows and flow decompositions) for long-read RNA-seq assembly problems and possibly pan-genomics problems. Ideally, the candidate has a strong algorithmic and/or programming background, but also (strong) knowledge of Bioinformatics and an interest to apply graph algorithms in developing practical Bioinformatics tools. However, there is flexibility in adapting the project to the interests and expertise of the student. The student is expected to take an active role in leading the project, working with the team members and international collaborators, and doing possible research visits abroad. The person will join my Graph Algorithms team, which is part of the wider Algorithmic Bioinformatics group at the University of Helsinki. The team consists of 3 PhD Students, 2 Postdocs, and we are currently funded also by an ERC Starting Grant on Algorithmic Bioinformatics. For some key pointers related to this position, see: - Dias et al. "Fast, Flexible, and Exact Minimum Flow Decompositions via ILP" https://link.springer.com/chapter/10.1007/978-3-031-04749-7_14 (RECOMB 2022) - Khan et al. "Safety and Completeness in Flow Decompositions for RNA Assembly" https://arxiv.org/abs/2201.10372 (RECOMB 2022) - Prjibelski et al. "IsoQuant: a tool for accurate novel isoform discovery with long reads" https://www.researchsquare.com/article/rs-1571850/v1 - Cáceres et al. "Width Helps and Hinders Splitting Flows" https://arxiv.org/abs/2207.02136 (ESA 2022) The application deadline is August 28, and applications are done via our doctoral school https://hict.fi/admissions/ (mentioning the project "Graph Algorithms for Long-Read Sequencing Data"). After the deadline, the position will remain open until a suitable candidate is found. Applications after the deadline are possible by e-mail to alexandru.tomescu at helsinki.fi. If you are interested in applying shortly after the deadline, please send as soon as possible a notification to my e-mail address including at least your CV. Required documents: 1. Letter of motivation (max. one page) 2. A curriculum vitae and list of publications 3. A study transcript 4. A copy of the M.Sc. degree certificate 5. Contact details of two possible referees We are based at the Department of Computer Science, University of Helsinki, Finland, in a city that often ranks among the best places to live in the world. Despite being a capital, Helsinki is a very easy city to live in, with lots of green areas, an efficient public transport system and a housing market rather accessible. Helsinki offers easy access to national parks or islands within the metropolitan area: nature lovers, this is the place to be! Candidates from a minority background in our field are warmly encouraged to apply! For any inquiry, please do not hesitate to contact me. Best regards, Alexandru Tomescu Associate Professor of Algorithmic Bioinformatics and Academy of Finland Research Fellow alexandru.tomescu at helsinki.fi https://www.cs.helsinki.fi/u/tomescu/ https://www2.helsinki.fi/en/researchgroups/algorithmic-bioinformatics/teams/graph-algorithms https://www2.helsinki.fi/en/researchgroups/algorithmic-bioinformatics/teams -------------- next part -------------- An HTML attachment was scrubbed... URL: From arne at bioinfo.se Mon Aug 15 16:10:51 2022 From: arne at bioinfo.se (Arne Elofsson) Date: Mon, 15 Aug 2022 16:10:51 +0200 Subject: [SocBiN] Fwd: Open Data Steward positions at NBIS In-Reply-To: References: Message-ID: The National Bioinformatics Infrastructure Sweden (NBIS) is looking to expand our team of *Data Stewards* with 1-2 persons, with a focus on human data. For more information about the open positions please see the ads on the Uppsala University site by using the link below. Application deadline is this *Friday 19 August*. *Please note that the work title is officially called bioinformatician, but the content is about Data Management and Data Stewardship, so we welcome applicants with other relevant training and experiences.* https://www.uu.se/en/about-uu/join-us/details/?positionId=524533 Best regards, - Niclas _____________________________________ Niclas Jareborg, PhD Data Manager *NBIS - National **Bioinformatics Infrastructure Sweden** - **nbis.se* *ELIXIR Sweden* *SciLifeLab** - www.scilifelab.se * *DBB, Stockholm University** - www.dbb.su.se * *Postal address: **Visiting address:* *PO Box 1031 **Tomtebodavägen 23 A* *171 21 Solna Solna* *Sweden* *Phone: +46 733 866605* *email: *niclas.jareborg at nbis.se*, niclas.jareborg at scilifelab.se , niclas.jareborg at dbb.su.se * ORCID: 0000-0002-4520-044X my publicly-auditable identity on keybase: nicjar -- 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 xffhello at gmail.com Mon Aug 29 15:33:30 2022 From: xffhello at gmail.com (Feifei Xu) Date: Mon, 29 Aug 2022 15:33:30 +0200 Subject: [SocBiN] Bioinformatician position in Phillipsons lab at Uppsala University Message-ID: <892ADBB7-072F-430D-B3AA-DD5D5DD70129@gmail.com> The ad for the position is out now. You are welcome to apply. https://www.uu.se/en/about-uu/join-us/details/?positionId=537573 Best Feifei -------------- next part -------------- An HTML attachment was scrubbed... URL: From rune.linding at gmail.com Tue Aug 30 14:09:46 2022 From: rune.linding at gmail.com (Rune Linding) Date: Tue, 30 Aug 2022 14:09:46 +0200 Subject: [SocBiN] Only 24hrs left for early registration to major systems biology conference of the year! Message-ID: Dear All Last chance for early bird registration for ICSB in Berlin. We have a stellar line up and this is your chance to get out of the zoom pandemic. Please join us. PS: Abstracts can be submitted through 30th September. *https://www.icsb2022.berlin * Best wishes Conference chairs - Rune Linding, Edda Klipp -------------- next part -------------- An HTML attachment was scrubbed... URL: From leo.lahti at utu.fi Wed Aug 31 10:01:59 2022 From: leo.lahti at utu.fi (Leo Lahti) Date: Wed, 31 Aug 2022 08:01:59 +0000 Subject: [SocBiN] Open PhD/research position in microbiome bioinformatics and data science, Turku, Finland Message-ID: <6eca2fbdfef64ae39ae238cecd723287@utu.fi> Open position for doctoral researcher/project researcher in microbiome bioinformatics and data science. At the Department of Computing, University of Turku, Finland datascience.utu.fi The project aims to discover associations with health outcomes, gut microbiomes, and antibiotic resistance loads in large population cohorts, machine learning applications for microbiome studies, and developing bioinformatic pipelines for high-throughput analysis in high-performance computing (HPC) clusters. The work will be supervised by Associate Prof. Leo Lahti & Dr. Katariina Pärnänen. Application DL: Monday, Sep 19, 2022 For more information on the project, living in Finland, and application submissions, see: https://tinyurl.com/2r2a6s9w