- BBClist - maillist.psb.ugent.be

Research Assistant/Postdoc position in scRNAseq analysis
by Giorgia Tosoni 15 Aug '22

15 Aug '22

The Neurogenesis & Neurodegeneration lab at the Netherlands Institute for Neuroscience (Amsterdam, NL) has a position open for Post-doc / Research Assistant in Computational Biology. The Neurogenesis & Neurodegeneration laboratory led by Dr. Evgenia Salta employs transcriptomics and other molecular and imaging approaches to map the cellular and molecular complexity of the adult hippocampal neurogenic niche and dissect the biological pathways that are deregulated in Alzheimer’s disease. Check out the vacancies: -Research Assistant: https://nin.nl/about-us/vacancies/research-assistant-in-computational-biolo… -Post-doc: https://nin.nl/about-us/vacancies/postdoc-in-computational-biology/

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BioSB course Integrated Modeling and Optimization (preliminary announcement)
by Bosnacki, Dragan 15 Aug '22

15 Aug '22

Dear colleagues, Also in the new academic year the BioSB research school, Wageningen University & Reserach and Eindhoven University of Technology will organize the course: *Integrated Modeling and Optimization* 12-16 December 2022, Wageningen University Computational modelling is an absolute requisite to gain understanding of the biological mechanisms underlying patterns observed in experimental data. However, one could say that modelling is a craftsmanship, that can only be learned via intense exercising and ‘learning by doing’. In this course we offer the participants the possibility to learn and exercise the modeling process and the optimization techniques needed to fit models to data. In the course the students will learn: - to understand the common ground and the differences for applications of dynamic modeling in metabolic, regulatory, signaling, and multi-scale biological processes - how to set-up a dynamic model to represent biological networks using different interaction mechanisms - to implement, simulate and analyze dynamic network models - to understand the wide variety of problems in modelling that can be solved with optimization · - to apply different types of numerical optimization methods: global and local search methods: steepest descent, Levenberg-Marquardt, genetic algorithms, linear programming. - the combination of dynamic modeling and optimization to integrate experimental data in modelling, estimate model parameters and design experiments. - to understand how numerical optimization (linear programming) works in flux balance analysis to simulate metabolic network models. Lecturers: · Prof. Natal van Riel, Eindhoven University of Technology (course coordinator) · Dr. Aalt-Jan van Dijk, Wageningen University & Research · Prof. Jaap Molenaar, Wageningen University & Research · Dr. Hans Stigter, Wageningen University & Research · Dr. Robert Smith, Wageningen University & Research · Dr. Dragan Bosnacki, Eindhoven University of Technology Target audience: The course is aimed at PhD students with a background in bioinformatics, systems biology, computer science or a related field, and life sciences. Participants from the private sector are also welcome. A working knowledge of mathematics, especially differential equations, is recommendable, but we will distribute preparation material to be studied by students missing the required background. Furthermore, at the start we offer a math refresher to help those participants who are not (yet) involved in modelling on a daily basis. More about the last year's edition: https://www.dtls.nl/courses/integrated-modeling-and-optimization/<https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.dtls.…>  <image001.jpg><https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.dtls.…> Integrated modeling and optimization - Dutch Techcentre for Life Sciences<https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.dtls.…> Course date 13-17 December 2021, Wageningen Location: The course will be held at: Forum Building (building nr 102), with number B0409. A Biocafe (on Thursday) will be held in “The Spot” in Building Orion (gebouw nummer 103) in the Wageningen… www.dtls.nl<https://eur02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.dtls.n…>  More details about the programme and the registration will follow soon. Please feel free to contact Dragan Bosnacki (D.Bosnacki(a)tue.nl) for more information. --------------------- *About BioSB* The Netherlands Bioinformatics and Systems Biology research school (BioSB) is the national platform in which the Dutch community of researchers in bioinformatics and systems biology is organized. BioSB also organizes: 1. fundamental and advanced post-graduate courses <https://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.biosb…<https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.biosb…>> 2. the yearly BioSB conference <https://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.biosb…<https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.biosb…>> 3. hot topics meetings <https://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.biosb…<https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.biosb…>> The aim of the BioSB research school is to offer PhD students, postdocs and senior researchers a vibrant environment for their scientific development as well as education in bioinformatics and systems biology. In addition, BioSB acts as a parent organization for YoungCB <https://eur04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.youngc…<https://eur02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.youngc…>>, the official Regional Student Group (RSG) of the International Society of Computational Biology (ISCB).

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Colloquium on Bioinformatics Learning, Education and Training (CoBLET) and GOBLET AGM, 11-14 October 2022, Istanbul, Turkey (Hybrid event)
by Celia van Gelder 14 Aug '22

14 Aug '22

Dear all, We are delighted to invite you to the 1st Colloquium on Bioinformatics Learning, Education and Training (CoBLET), which will be held hybridly from 11-14th October 2022. CoBLET2022 will be in conjunction with the 11th annual general meeting (AGM) of the Global Organisation for Bioinformatics Learning, Education and Training (GOBLET). CoBLET2022 will be a hybrid event and will be held for the first time in Turkey, hosted by Bezmialem Vakıf University, Istanbul. We have a great organizing team in place from Bezmialem Vakif University, and under the lead of Asif Khan, GOBLET Executive Board Member, an award was obtained from Code for Science & Society, made possible by a grant from The Chan Zuckerberg Initiative. COBLET2022 will focus on thematic discussions targeting education and training in bioinformatics. A mix of keynotes, short talks, poster sessions and an Eduthon shall foster an interactive environment for integrated bioinformatics education and training. We invite you to look at the programme and submit your abstracts for oral presentations and/or workshops at https://coblet2022.bezmialem.edu.tr/ ! The deadline for the abstract submission is 30 August 2022. Registration is free of charge and you can register at https://coblet2022.bezmialem.edu.tr/registration . We are looking forward to seeing you at CoBLET2022, whether it will be in person or virtually! Best regards Celia van Gelder, Chair of GOBLET Ayesha Fatima, Chair of the COBLET 2022 Organizing Committee -- Dr. Celia W.G. van Gelder Training Programme Manager DTL/ELIXIR-NL/Health-RI tel. +31613375327 e-mail: celia.van.gelder(a)dtls.nl websites: https://www.dtls.nl/, https://www.health-ri.nl/, https://www.elixir-europe.org/platforms/training twitter: celia_vgelder Office: DTL | Jaarbeurs Innovation Mile (JIM) | 6th floor Beatrixgebouw | Jaarbeursplein 6 | 3521 AL Utrecht While I may be sending this email outside my normal office hours, I have no expectation to receive a reply outside yours. -- Dr. Celia W.G. van Gelder Training Programme Manager DTL/ELIXIR-NL/Health-RI tel. +31613375327 e-mail: celia.van.gelder(a)dtls.nl websites: https://www.dtls.nl/, https://www.health-ri.nl/, https://www.elixir-europe.org/platforms/training twitter: celia_vgelder Office: DTL | Jaarbeurs Innovation Mile (JIM) | 6th floor Beatrixgebouw | Jaarbeursplein 6 | 3521 AL Utrecht While I may be sending this email outside my normal office hours, I have no expectation to receive a reply outside yours.

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Job opening for a clinical bioinformatician
by Kemmeren-2, P.P.C.W. (Patrick) 11 Aug '22

11 Aug '22

Dear all, Within the Princess Maxima Center for Pediatric Oncology we currently have an opening for a clinical bioinformatician to develop and operate our whole-exome and RNA-sequencing based diagnostic pipelines. Interested in working in a stimulating, cross-disciplinary research hospital dedicated to curing children with cancer, then please apply using the link below! https://werkenbijprinsesmaximacentrum.nl/en/vacancy/clinical-bioinformatici… Also on behalf of Dr. Jayne Hehir-Kwa. 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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Permanent position of Scientist in Modelling and Systems biology at Gencovery
by Karoline Faust 10 Aug '22

10 Aug '22

Permanent position of Scientist in Modelling and Systems biology * Company: Gencovery SAS * Website: https://gencovery.com * Starting date: Sept 2022 * Contact: D. A. Ouattara, douattara(a)gencovery.com<mailto:douattara@gencovery.com> Description of the company GENCOVERY is a software company based in Lyon (France) which develops a collaborative AI software to accelerate bioengineering and bioproduction processes of biotechnology and pharmaceutical companies. The developments of the company are focused on two axes: * - a collection of algorithms for the construction and simulation of cell metabolic models, and * - a collaborative software suite, ConstellabTM, designed to handle complex omics data and analytical pipelines. Generated in silico models, called digital twins of cell metabolism, can be used to simulate experiments, and assess biological hypothesis, thereby significantly shortening time and cost of in vivo and in vitro experiments. The company is looking today for a talented scientist in systems biology and cell metabolism modelling to develop and manage its modeling pipelines. Required qualifications * You have a PhD in systems biology and/or bioinformatics * You have a strong expertise in the modelling of cell metabolism, modelling of the metabolism of microbial communities (e.g. whole-genome metabolic modelling, metabolic network reconstruction, flux balance/variability analysis, cell metabolic interactions, keystone species analysis, etc.). Gencovery, SAS – 47 Boulevard du 11 Novembre 1918, 69100 Villeurbanne, https://gencovery.com Connecting people through innovation [page2image38214352] * You have a good experience in the analysis of omics data (e.g. genomics, transcriptomics, proteomics, metabolomics data). * You have a good experience on standard bioinformatics tools and databases: o Python, R, Jupyter lab, o Biopython, Scikit-learn, Pandas, o Reference Fluxomics / FBA toolboxes (e.g. OpenCobra) o NCBI databases, EMBL-EBI databases, Kegg, BioCyc, etc. o BioModels, BiGG, Agora databases, etc. Missions * You will be in charge of developing the in-house bioinformatics and modeling pipelines that will feed our portfolio of analytics methods. * You will be accountable of the execution and delivery of the bioinformatics analyses to our clients (data integration and curation, modelling and simulation, reporting). * Your will be in charge of the supervision of bioinformaticians and students. Working place Gencovery technologies are designed for collaborative remote work. This is important for next-generation research and development with the COVID-19 pandemic. Gencovery has therefore decided to encourage and develop remote work for its own employees. The recruited candidate must be autonomous and committed to quality reporting. She/He will have the opportunity to be based outside Lyon during the first 3 months but is expected to move to Lyon after. Closing application date: 31 Aug. 2022 Position type: Permanent position Salary: Attractive with career evolution opportunities To apply for this position, please send a resume and cover letter to: douattara(a)gencovery.com<mailto:douattara@gencovery.com>

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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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