- BBClist - maillist.psb.ugent.be

Student positions - Computational Cancer Research
by Vosberg, Sebastian 10 Aug '22

10 Aug '22

Dear list members, for my research group (Computational Cancer Research) at Medical University of Graz, I am seeking for a PhD candidate with a high interest in implementing bioinformatics approaches to cancer research questions. Candidates may have any background such as bioinformatics/biology/genetics/biotechnology/medicine/etc. Here a quick overview of our work: We are aiming at developing novel computational approaches for cancer research with a major focus on characterizing the molecular background of tumors across different omics levels and its evolution under therapy. We want to learn about mechanisms of treatment resistance and/or cancer recurrence and to stratify personalized treatment options. Our projects are motivated by actual clinical research questions and we work in a highly interactive environment with very close contact to clinicians and wet-lab researchers. In particular, I am currently seeking for a PhD student for a computational cancer research project focusing on epigenetic signatures in lung and breast cancer, starting as soon as possible. More details can be found at https://www.medunigraz.at/doktoratsstudien/phd-program/phd, interested candidates may apply via the online form until September 20. Thank you very much and best wishes, Sebastian Vosberg

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Postdoc position in integrated omics at Karolinska Institute in Sweden
by Sebastian Lewandowski 09 Aug '22

09 Aug '22

We are recruiting a highly motivated and independent Postdoc candidate with experience in next-generation sequencing data analysis, computational genomics, medical statistics, imaging analysis, and/or computational biology. The project combines single-cell, multi-omic data with large-scale human genetics to investigate the cellular origin of amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD) and Alzheimer’s disease (AD). Our recent work (Månberg et al. Nature Medicine 2021) showed that vascular and glial cells contribute to the dynamics of neurodegeneration and this project will aim to refine our understanding of cellular mechanisms, biomarkers and genetic risk of ALS, FTD and Alzheimer’s disease. The postdoc candidate will work closely with researchers in the team as well as with our collaborators and be responsible for data analysis, visualization, and development of new computational methods for processing and analysis of large-scale omics data. We welcome applications from candidates with pure computational backgrounds and those combining experimental and theoretical approaches. Advertisement link at the Karolinska Institute jobs portal: https://ki.varbi.com/en/what:job/jobID:521783/ DM me for specific questions. With kind regards Sebastian Lewandowski Sebastian Lewandowski PhD --------------------- Karolinska Institutet, CMM, L8:04 Karolinska vägen 8A SE-171 64 Solna Twitter @LewandowskiSA https://staff.ki.se/people/seblew När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://ki.se/medarbetare/integritetsskyddspolicy>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI’s processing of personal data here<https://ki.se/en/staff/data-protection-policy>.

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CMSB 2022: call for participation
by Ion Petre 09 Aug '22

09 Aug '22

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(a)utu.fi) and Andrei Paun (apaun(a)fmi.unibuc.ro) Prof. Dr. Ion Petre Department of Mathematics and Statistics University of Turku, Finland

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Assistant Professor in Quantitative Biology and Data Integration (Tenure track 0.8 – 1.0 FTE) Utrecht University
by Berend Snel 09 Aug '22

09 Aug '22

Dear Subscribers to the BBC mailing list, The Institute of Biodynamics and Biocomplexity at Utrecht University is looking for an ambitious and enthusiastic scientist to strengthen its research and teaching activities in the fields of quantitative biology, bioinformatics, and epigenomic data integration. You will have the opportunity to establish your own independent research group and contribute to training the next generation of scientists at the Bachelor’s and Master’s level. The position will be embedded in three divisions: Developmental Biology, Theoretical Biology & Bioinformatics, and Genome Biology & Epigenetics. Furthermore, your group will be part of the Utrecht Bioinformatics Center (UBC), which coordinates bioinformatic activities across the Utrecht Science Park and unites more than 40 research groups with strong bioinformatics research. We would particularly like to hear from candidates with a special interest in integrating large-scale datasets to reveal the hidden patterns and biological mechanisms underlying gene regulation, epigenetics, and/or developmental processes. Ideally, you will be helping to answer fundamental biological questions by utilizing novel bioinformatic and AI approaches to analyze single cell, multi-omics, Hi-C and other novel data sets. You will start as an Assistant Professor with a tenure track, with a career development plan that outlines the goals in research, teaching, and personal development. If your evaluation is positive, you will be offered a permanent position. For more information see: https://www.uu.nl/organisatie/werken-bij-de-universiteit-utrecht/vacatures/… sincerely yours, Berend Snel

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Vacancies for java developers at Genetwister (Wageningen)
by Lidija Berke 08 Aug '22

08 Aug '22

Dear all, At Genetwister, a biotech company in Wageningen, we are looking for two java developers (back-end and full stack) to join our software development team: https://www.genetwister.nl/jobs/. I would appreciate if you can share the vacancies in your network. Kind regards, Lidija [cid:image003.png@01D8AB06.6FAFDF20] Lidija Berke Team Lead Bioinformatics & Software Development Genetwister Technologies B.V. Nieuwe Kanaal 7b | 6709 PA Wageningen | The Netherlands +31 317 466 420 | l.berke(a)genetwister.nl<mailto:l.berke@genetwister.nl> | www.genetwister.nl<https://www.genetwister.nl> Disclaimer This e-mail and any files transmitted with it are intended solely for the addressee[s] and may contain personal or confidential information. Use of such information by persons other than the addressee[s] and use by persons not authorized to receive such information is prohibited. If you have received this e-mail in error please notify the sender immediately, delete this e-mail from your system and do not disseminate, distribute or copy this e-mail. This e-mail does not constitute a binding agreement unless expressly confirmed in writing by Genetwister. The addressee[s] should check this e-mail and any attachments for the presence of viruses. Genetwister accepts no liability for any damage caused by any virus transmitted by this e-mail or damage caused by the use of the information contained in this e-mail. Genetwister Technologies B.V. is a limited liability company registered in Wageningen, The Netherlands under number 11043533. For more information, please visit: www.genetwister.nl<http://www.genetwister.nl/>.

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Job opportunity: Bioinformatician @ the Max Planck Institute for Multidisciplinary Sciences, Goettingen, Germany
by Sonja Lorenz 06 Aug '22

06 Aug '22

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 <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(a)mpinat.mpg.de <mailto:ausschreibung40-22@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 <http://www.mpinat.mpg.de/de/rink>

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Postdoctoral position bioinformatics in Brussels
by ROOMAN Marianne 05 Aug '22

05 Aug '22

The Computational Biology and Bioinformatics group of the Brussels University (ULB) (https://3bio.polytech.ulb.be/en/bioinfo) is seeking candidates for a postdoctoral position. Research context: Unraveling the biophysical mechanisms that drive single nucleobase substitutions in different regions of the human genome is one of the key questions of the post-genomic era. These mutations, whether inherited or somatic, are potentially responsible for a huge range of rare and complex diseases. The rationalization of these mechanisms is highly intricate and often requires a diverse set of approaches, since base substitutions depend on the nucleotide sequence context and can be triggered by a wide range of physical, chemical or biological factors. Objective: The AtOme project aims to bridge the gap between the atomic-level characterization of mutagenesis processes and the resulting phenotypic traits, by using innovative multiscale computational approaches combining genomic and proteomic data with machine learning techniques. The end-goal of the project is the deployment of a novel predictor of genome mutability and of the impact of mutations on regulatory mechanisms, protein fitness and pathogenicity. The project will be carried out within a highly multi-disciplinary and enthusiastic bioinformatics team, in collaboration with molecular biologists and clinicians who are experts in complex diseases (cancer, autism). Offer: We are offering you a full-time postdoctoral position for 2 years, to come and work on the AtOme project in a laboratory with strong expertise in the field of bioinformatics and an attentive care to our work culture. The starting date is flexible (between now and January 2023) and there is a possibility of extension through an FNRS postdoctoral research grant or a Marie Curie EC grant. Required: - PhD degree in Sciences (Bioinformatics, Bioengineer, Physics, Chemistry, Informatics). - Excellent programming skills. - Excellent publication record. - Maximum 6 years research experience after PhD. - International mobility (maximum 24 months of residence in Belgium in the last 3 years). Desirable: Experience in machine learning and/or bioinformatics. Contact: Please submit: (1) a cover letter detailing your background and interest in the position, (2) a full CV and (3) two references (with email address and phone number), to Pr. M. Rooman (marianne.rooman(a)ulb.be) Application deadline: October 1, 2022.

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VIB/ELIXIT training - Don't miss the opportunity to join!
by Bruna Piereck Moura 04 Aug '22

04 Aug '22

[cid:image001.png@01D8A7E8.AD3C6FA0] [signature_2008044598] Stay tuned! Donnot miss the opportunity to improve your skills and talk science! Dear, As soon as September you have the chance to join us once again at the Git&GitHub<https://training.vib.be/all-trainings/introduction-git-github-4> training! To happen on the 13th of September in Ghent. Click in the link to have more information and join us for this great Face-to-face session. Introduction to Git & GitHub 13 June 2022 - Ghent This workshop will take you through the basic use of Git and GitHub. Git is a free and open source distributed version-control system designed to maintain code, track changes, recover old versions and collaborate with other developers. Subscription and info: https://training.vib.be/all-trainings/introduction-git-github-4 VIB Bioinformatics Core ELIXIR Belgium Training Coordinator Technologiepark-Zwijnaarde 75 9052 Zwijnaarde, Belgium For questions: Bruna Piereck tel +32 0497 2988 73

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Vacancy for scientific research coordinator
by Kemmeren-2, P.P.C.W. (Patrick) 04 Aug '22

04 Aug '22

Dear all, Within the Princess Maxima Center for Pediatric Oncology we are looking for a scientific research coordinator who can help us in our journey in building an ML and AI ready data infrastructure and make the most out of the vast amounts of data generated. A background in machine learning, AI or bioinformatics is very much welcomed! Interested? Then apply through: https://werkenbijprinsesmaximacentrum.nl/en/vacancy/scientific-research-coo… Regards, Patrick -- Patrick Kemmeren, PhD Principal Investigator & head Big Data Core Princess Máxima Center Associate Professor UMC Utrecht T +31 (0)88 972 90 00 | M +31 (0)6 53 11 25 53 [signature_3129348511] [signature_1704258484] Princess Máxima Center for Pediatric Oncology Heidelberglaan 25 | 3584 CS Utrecht | T +31 (0)88 972 90 00 | > Website<https://research.prinsesmaximacentrum.nl/en/research-groups/kemmeren-group>

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Callout for workshop "Simulating cellular behaviours: advancing HPC-enabled Computational Biology"
by Arnau Montagud 03 Aug '22

03 Aug '22

Dear all, >From PerMedCoE <https://permedcoe.eu/> , BSC and EMBL-EBI are organising a workshop in the ECCB 2022 conference <https://eccb2022.org/> titled “Simulating cellular behaviours: advancing HPC-enabled Computational Biology” that will take place virtually on the 13 of September 2022, from 13h30 to 16h30 (Paris, Madrid, Berlin, Barcelona time). The aim is to bring together researchers that develop or employ methodologies and tools for data analytics, modelling and/or machine learning focusing on simulating cellular behaviours. The focus will be on identifying ways to combine HPC-based methods to scale up computation with mechanistic and statistical modelling to build predictive dynamical models. The keynote speaker will be Dr Elena J Fertig <https://fertiglab.com/> , Director of the Research Program in Quantitative Sciences, Co-Director of the Convergence Institute and Associate Director of Quantitative Sciences at the Johns Hopkins Kimmel Cancer Center. Additionally, we will have 6 selected talks from a call from abstracts for which we would like to gather interesting (and interested) people. Thus, *we kindly ask you to send contributions to this call for abstracts and to spread the word to interested parties*. Note that PerMedCoE can cover registration costs of several participants to the workshop. Specifically, PerMedCoE encourages the participation of young female researchers/technicians. Contact us if interested. Link to the workshop details: https://permedcoe.eu/call-for-abstracts-simulating-cellular-behaviours-adva… and https://eccb2022.org/ntb-w03/ Link to the call for abstracts: https://easychair.org/conferences/?conf=eccb202 (select “NTB-W03 | Simulating cellular behaviours: advancing HPC-enabled Computational Biology” track) – Deadline extended to 21st August Link to the tweet announcing the call for abstracts: https://twitter.com/PerMedCoE/status/1552896796795469824 Best regards, Arnau Montagud Computational Biology Group Life Sciences Department Barcelona Supercomputing Center (BSC)

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