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Fully funded PhD project (3.5 years) at University of Southampton and University of Jena
by Franklin Luzia De Nobrega 27 Nov '21

27 Nov '21

LS, Please see below for the project outline of a fully funded PhD project (3.5 years) in collaboration with Professor Bas Dutilh at the University of Jena. Start on February 2022. Please forward this to any students who may be interested and ask them to contact us. Investigating prokaryotic defence and bacteriophage anti-defence systems Project outline: Microbes and their viruses, known as bacteriophages, have co-evolved for billions of years. As a result of their co-evolution, microbes developed multiple lines of defence to withstand the predatory attacks of phages, and phages responded with multiple forms to overcome these barriers. Microbial defence systems such as restriction-modification (RM), abortive infection (Abi), and CRISPR-Cas have been known for years and used extensively to develop molecular biology and biotechnological tools. Recently, the field has bloomed with the discovery of tens of completely novel defence systems that microbes encode to protect from phage predation [Kronheim, Swarts, Goldfarb, Ofir, Cohen, Doron, Gao, Millman, Rousset]. With the realization that the arsenal of microbial defences is much more diverse than previously perceived, came exciting new questions, such as Do defence systems actively cooperate for better protection? Are there preferred combinations of defence systems? Furthermore, the discovery of new defence systems in microbes suggests that phages also carry anti-defence systems to help them overcome these prokaryotic barriers. This may help reconcile the number of proteins of unknown function in phage genomes that have been found to be dispensable for infection of permissible hosts [Miller, Pires]. This raises important additional questions, such as Which mechanisms do phages employ to escape the new systems? How do phages protect against such large diversity of defence mechanisms while maintaining a compact genome? References: - Kronheim, S. et al. A chemical defence against phage infection. Nature 564, 283-286, doi:10.1038/s41586-018-0767-x (2018). - Swarts, D. C. et al. DNA-guided DNA interference by a prokaryotic Argonaute. Nature 507, 258-261, doi:10.1038/nature12971 (2014). - Goldfarb, T. et al. BREX is a novel phage resistance system widespread in microbial genomes. The EMBO journal 34, 169-183, doi:10.15252/embj.201489455 (2015). - Ofir, G. et al. DISARM is a widespread bacterial defence system with broad anti-phage activities. Nature Microbiology 3, 90-98, doi:10.1038/s41564-017-0051-0 (2018). - Cohen, D. et al. Cyclic GMP–AMP signalling protects bacteria against viral infection. Nature 574, 691-695, doi:10.1038/s41586-019-1605-5 (2019). - Doron, S. et al. Systematic discovery of antiphage defense systems in the microbial pangenome. Science 359, eaar4120, doi:10.1126/science.aar4120 (2018). - Gao, L. et al. Diverse enzymatic activities mediate antiviral immunity in prokaryotes. Science 369, 1077-1084, doi:10.1126/science.aba0372 (2020). - Millman, A. et al. Bacterial Retrons Function In Anti-Phage Defense. Cell 183, 1551-1561.e1512, doi:10.1016/j.cell.2020.09.065 (2020). - Rousset, F., Dowding, J., Bernheim, A., Rocha, E. P. C. & Bikard, D. Prophage-encoded hotspots of bacterial immune systems. bioRxiv, 2021.2001.2021.427644, doi:10.1101/2021.01.21.427644 (2021). - Miller, E. S. et al. Bacteriophage T4 genome. Microbiol Mol Biol Rev 67, 86-156, doi:10.1128/mmbr.67.1.86-156.2003 (2003). - Pires, D. P. et al. Designing P. aeruginosa synthetic phages with reduced genomes. Scientific Reports 11, 2164, doi:10.1038/s41598-021-81580-2 (2021). Franklin Nóbrega, PhD Lecturer in Microbiology Microbial Interactions Lab University of Southampton Life Sciences Building 85 Highfield Campus Southampton SO17 1BJ UK fnobregalab.org<http://fnobregalab.org> Prof. Dr. Bas E. Dutilh<https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Ftbb.bio.uu…> Viral Ecology and Omics Group | Metagenomics Group Microverse Cluster<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmicrovers…> | Theoretical Biology and Bioinformatics<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Ftbb.bio.u…> European Virus Bioinformatics Centre<https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fevbc.uni-j…> | Utrecht Bioinformatics Center<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fubc.uu.nl…> Friedrich Schiller University Jena<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.uni-j…> | Utrecht University<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.uu.nl…>

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Postdoc position on Capsicum pan-genomics
by Ridder, Dick de 24 Nov '21

24 Nov '21

Dear all, We are looking for an enthusiastic bionformatics postdoc candidate on a two year project on Capsicum (pepper plants) pan-genomics. The goal is to chart the genetic variation in Capsicum species, to address research questions in breeding. The candidate will develop and apply pan-genomics methods in our PanTools platform to analyze data from 108 different Capsicum accessions, to characterize the core and dispensable genome, inventory (structural) variations, and identify candidate genes underlying traits like disease resistance, stress tolerance, seed weight, or fruit development. Candidates should hold a PhD degree in bioinformatics, plant biotechnology/genomics or related field. We are specifically seeking a candidate with a strong programming skills (Java and/or Python), communciation skills, experience in genomics tools and affinity with practical applications in crop research and plant breeding. Additional information about the position can be found at https://www.wur.nl/en/vacancy/Postdoctoral-Researcher-Capsicum-pan-genomics…. Interested candidates can apply up to January 2, 2022 through this website. Best regards, Dick de Ridder Bioinformatics Group, Wageningen University, The Netherlands

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Research position at INRIA Bonus France
by El-ghazali Talbi 22 Nov '21

22 Nov '21

Open Research Position at Inria Lille – Nord Europe Research group: BONUS Last annual activity report:https://www.inria.fr/en/inria-ecosystem Attached the PDF version Description ----------- The INRIA research institute (https://www.inria.fr/en/inria-ecosystem) invites applications for multiple permanent researcher positions to start in the 2022-2023 academic year. High performance computing (HPC) and/or Machine Learningassisted big optimization is among its top priorities for the recruitment. This hot topic is a major focus of the BONUS research group, which is part of the INRIA Lille – Nord Europe research center located at Lille (North of France). Qualified applicants in Computer Science are invited to apply with the objective to join the BONUS research group as a permanent researcher. Qualifications -------------- The BONUS team addresses big optimization problems (high-dimensional in decision variables and/or objectives, and/or with computationally expensive black-box functions) using mainly Machine Learning-assisted optimization and High-performance (parallel) optimization. Candidates should hold a Ph.D. or equivalent degree in Computer Science or a related discipline. BONUS is interested in applicants having a strong background in at least one of its research lines: Machine Learning-assisted optimization or parallel optimization. Candidates with only HPC-related profile, highly motivated to adapt their activities to the context of big optimization using HPC in keeping with the BONUS research program, are also invited to apply. Some benefits in addition to the salary --------------------------------------- − Subsidized meals, − Partial reimbursement of public transport costs, − Leave: 7 weeks of annual leave + 10 extra days off due to RTT (statutory reduction in working hours) + possibility of exceptional leave (sick children, moving home, etc.), − Possibility of teleworking (after 6 months of employment) and flexible organization of working hours, − Professional equipment available (videoconferencing, loan of computer equipment, etc.) − Social, cultural and sports events and activities, − Access to vocational training, − Social security coverage. Application Instructions / Contact ----------------------------------- Applicants are asked to contact the leader of the BONUS team, Prof. Nouredine Melab atNouredine.Melab(a)inria.fr. After this contact, if a candidate is encouraged to apply he/she will do it officially through the INRIA online application process that will be soon indicated here:https://www.inria.fr/en/talents ------------------------------ -- ********************************************************************** OLA'2022 International Conference on Optimization and Learning (SCOPUS, Springer) 18-20 July 2022, Syracuse, Sicilia, Italy http://ola2022.sciencesconf.org *********************************************************************** Prof. El-ghazali TALBI Polytech'Lille, University Lille - INRIA CRISTAL - CNRS

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CFP: Special issue Movement Analysis for Health and Biometrics (Applied science)
by Nicole Dalia CILIA 22 Nov '21

22 Nov '21

*CALL FOR PAPERS* *Movement Analysis for Health and Biometrics* https://www.mdpi.com/journal/applsci/special_issues/Movement_Analysis_Healt… Applied Sciences, MDPI - (IF: 2.679; CiteScore: 3.0, JCR - Q2 (Engineering, Multidisciplinary) / CiteScore - Q2 (General Engineering)) // DEADLINE FOR MANUSCRIPT SUBMISSION \\ \\ 31 MARCH 2022 // Movement is being investigated in biomechanics, neuroscience, psychology, and artificial intelligence. The progress that has been made in modeling and analyzing movement is contributing to both the understanding of human movement and the development of new applications. In particular, the availability of low cost and pervasive devices for recording movements (wearable devices, smartphones, tablets, cameras, etc.), together with machine learning methods for the quantitative and automatic analysis of movement, has put forward the development of systems for user authentication, medical diagnosis, and rehabilitation monitoring. A leading example is the use of artificial intelligence methods for the analysis of complex movements such as handwriting and gait, which is improving our knowledge of the mechanisms underlying human movement and, at the same time, enriching the fields of e-health and e-security with new applications. Another successful example is the design of control systems for prosthetic devices that exploit knowledge about movement execution and artificial intelligence methods. This Special Issue aims to highlight how movement analysis and new technologies are innovating the fields of health and biometrics and contributing to human movement understanding. *TOPICS* Topics include but are not limited to the following: - gait analysis - handwriting analysis - pose estimation - speech analysis - eye-tracking analysis - neurodegenerative disorder diagnosis and prognosis - assessment of movement disorders - assessment of neurodevelopmental disorders - characterization of fine motor problems - user authentication - signature verification - writer verification - movement-based biometric systems - wearable devices - biomechanical models - assistive robots for rehabilitation - prosthetic devices - brain–computer interfaces *DATES * - Deadline for manuscript submission: 31 March 2022 *Why you should submit a paper to this special issue* If this issue publishes 10 papers, we will print it into an E-book and real book, making your works highly circulated. See http://www.mdpi.com/books/pdfview/book/250 (with ISBN number). Some other researchers in this area have confirmed to contribute, we will be very honored if you are able to participate as well. Benefits of publishing with Applied Sciences: 1. Open access (unlimited and free access for readers). 2. Indexed by the Science Citation Index Expanded (Web of Science) [search for "Applied Sciences-Basel", 2.679], Scopus[CiteScore: 3.0, (Q2 in "Engineering, Multidisciplinary" and "Physics, Applied”)], Inspec (IET) and other databases. 3. Rapid Publication: manuscripts are peer-reviewed and a first decision provided to authors approximately 13.8 days after submission (median values for papers published in this journal in the first half of 2021). *SUBMISSIONS * Manuscripts should be submitted online at www.mdpi.com by registering <https://www.mdpi.com/user/register/> and logging in to this website <https://www.mdpi.com/user/login/>. Once you are registered, click here to go to the submission form <https://susy.mdpi.com/user/manuscripts/upload/?journal=applsci>. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website. Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors <https://www.mdpi.com/journal/applsci/instructions> page. *Applied Sciences* <https://www.mdpi.com/journal/applsci/> is an international peer-reviewed open access semimonthly journal published by MDPI. Please visit the Instructions for Authors <https://www.mdpi.com/journal/applsci/instructions> page before submitting a manuscript. The Article Processing Charge (APC) <https://www.mdpi.com/about/apc/> for publication in this open access <https://www.mdpi.com/about/openaccess/> journal is 2000 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service <https://www.mdpi.com/authors/english> prior to publication or during author revisions. *GUEST EDITORS* *Antonio Parziale*, Department of Electrical and Information Engineering and Applied Mathematics (DIEM), Università di Salerno, Salerno, Italy. Rosa Senatore, Department of Electrical and Information Engineering and Applied Mathematics (DIEM), University of Salerno, Salerno, Italy. Nicole Dalia Cilia, Department of Electrical and Information Engineering, University of Cassino and Southern Lazio, Cassino, Italy Contact Information: Nicole Dalia Cilia, nicoledalia.cilia(a)unicas.it -- Nicole Dalia Cilia, Ph.D Postdoctoral Researcher at Department of Electrical and Information Engineering University of Cassino and Southern Lazio Ph.D Department of Philosophy Sapienza, Rome University

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open PhD position in Bioinformatics
by Beltran, Eduardo Dr.rer.nat. 18 Nov '21

18 Nov '21

Dear BBClist admins, we have an open PhD position in bioinformatics with a focus on the development of bioinformatic methods for integrative analysis of scRNA-seq and snRNA-seq datasets from multiple sclerosis human samples and related models. https://twitter.com/edubeltran_lab/status/1446401194885275652?t=jx_GeYs2EsZ… https://www.neuroimmunology-munich.de/open-positions/4eebea3ce75dec99 The Beltrán and Kerschensteiner Labs at the Biomedical Center of the Ludwig-Maximilians University Munich are looking for a PhD student in Bioinformatics. The candidate will develop bioinformatic methods for integrative analysis of scRNA-seq and snRNA-seq datasets from multiple sclerosis (MS) human samples and related MS models. Such integrative analysis of MS related data sets will allow us to identify and remove from the equation the species-specific or model-specific mechanisms and thereby improve the translational predictability of preclinical models and facilitate the functional interpretation of MS-related changes in the immune and nervous systems. We are looking for highly motivated, enthusiastic and hard-working applicants with bioinformatics background, who are fluent in English. The starting date for this position is flexible, but we aim for beginning of 2020. Funding for this project is secured for 3 years. If you are interested in the position please send a letter of motivation, your CV and the names and contact details of 2 to 3 references to: Eduardo.Beltran(a)med.uni-muenchen.de<mailto:%20eduardo.beltran@med.uni-muenchen.de> Dr. Eduardo Beltrán, Group Leader, Single-cell Genomics Lab, Institute of Clinical Neuroimmunology Prof. Dr. med. Martin Kerschensteiner, Chair, Institute of Clinical Neuroimmunology ____________________________________________________________________________ Selected recent publications from our groups: • Hiltensperger et al., Nature Immunology 22, 880–892 (2021) • Jafari et al., Nature Neuroscience 24(3):355-367 (2021) • Beltrán et al., Journal of Clinical Investigations 129(11):4758-4768 (2019) • Locatelli et al., Nature Neuroscience 21:1196-1208 (2018) ____________________________________________________________________________ Please share it in the BBClist! Thank you very much. Best, Edu Dr. Eduardo Beltrán [cid:image001.png@01D7DCA7.29402DC0] <https://orcid.org/0000-0002-7266-4098> Group Leader – scGenomics Lab Institut für klinische Neuroimmunologie　　 BioMedizinisches Zentrum – LMU Großhaderner Str. 9 N.B. 3.OG, Raum 024 82152 Planegg-Martinsried Germany Tel: +49 89 2180 71664 [cid:image002.png@01D7DCA7.29402DC0]<https://www.neuroimmunology-munich.de/neuroimmunology-munich> [Kontakt - Biomedizinisches Centrum München - LMU München]<https://www.bmc.med.uni-muenchen.de/index.html>

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Postdoc position in Paris
by Juan Rodriguez Rivas 18 Nov '21

18 Nov '21

Dear Colleagues, Please find attached a PDF for a postdoc position to work on epistatic landscapes of phenotypic effects, protein-protein interactions and structural bioinformatics in the Analytical Genomics lab at the Sorbonne University in Paris. Best wishes, Juan

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Job opening for Researcher in Machine Learning for Huntington’s Disease
by Eleni Mina 18 Nov '21

18 Nov '21

Hi there BBC list. The Biosemantics group in Leiden has an exciting job opening. In short, this position is about applying machine learning in the Enroll-HD database, a large worldwide longitudinal observational study for Huntington’s disease. This is a multidisciplinary project, in which you will work closely with the Biosemantics and the NeuroD group of the Department of Human Genetics and the Department of Neurology of the Leiden University Medical Center. More information: https://www.lumc.nl/over-het-lumc/werken-bij/overzicht/Onderzoeker-Machine-… If you have any questions, please do not hesitate to contact me and feel free to share this opening with your peers! Best, Eleni

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Data Solutions Specialist - Ontoforce
by Bérénice Wulbrecht 17 Nov '21

17 Nov '21

Dear all, Ontoforce is currently hiring several Data Solutions Specialists to strengthen its Solution Delivery team in Ghent, Belgium. If you are interested, please go to https://www.ontoforce.com/about/careers/ . Best regards Berenice -- [image: ONTOFORCE - Links for lives] <https://www.ontoforce.com/> Bérénice Wulbrecht Solution Delivery Director [image: Online] www.ontoforce.com or visit the contact page <https://www.ontoforce.com/contact/> [image: Mobile] +33 6 21 87 87 88 <+33+6+21+87+87+88> [image: Phone] BE +32 9 292 80 37 <003292928037> / US +1 617 315 9650 <0016173159650> [image: LinkedIn] <https://www.linkedin.com/company/ontoforce/> [image: Twitter] <https://twitter.com/ONTOFORCE> Would you like to receive our Newsletter to stay updated? Subscribe here <http://eepurl.com/dwoymH> DISCLAIMER This message (including any attachments) may contain information which is confidential and/or protected by intellectual property rights and is intended for the sole use of the recipient(s) named above. Any use of the information herein (including, but not limited to, total or partial reproduction, communication or distribution in any form) by persons other than the designated recipient(s) is prohibited. If you have received it by mistake, please notify the sender by return email and delete this message from your system. Please note that emails are susceptible to change. ONTOFORCE shall not be liable for the improper or incomplete transmission of the information contained in this communication nor for any delay in its receipt or damage to your system. ONTOFORCE does not guarantee that the integrity of this communication is free of viruses interceptions or interference.

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Open positions @ Amsterdam UMC
by Sie, D.L.S. (Daud) 16 Nov '21

16 Nov '21

Dear BBC list, We have two open positions in Amsterdam. Manager position and bioinformatics position in the Human Genetics department of the Amsterdam UMC. https://werkenbij.amsterdamumc.org/nl/vacatures/zorg/manager-bioinformatica… https://werkenbij.amsterdamumc.org/nl/vacatures/ondersteunende-diensten/bio… Be sure to apply in time and drop me a mail if you have any questions! Kind regards, Daoud [cid:image002.png@01D40E30.3E299A80] Dr. Daoud Sie | Head Bioinformatics | Consultant Core Facility Genomics Department of Human Genetics Location VUmc | MF-G423 | Van der Boechosrtstraat 7, 1081 BT Amsterdam Location AMC | K2-211 | Meibergdreef 9, 1105 AZ Amsterdam T: (+31)20-4442428 | E: d.sie(a)amsterdamumc.nl www.amsterdamumc.nl<http://www.amsterdamumc.nl/> | www.vumc.nl<http://www.vumc.nl/> / www.amc.nl<http://www.amc.nl/> ______________________________________________________ VUmc disclaimer: www.vumc.nl/disclaimer<http://www.vumc.nl/disclaimer> ______________________________________________________ VUmc disclaimer : www.vumc.nl/disclaimer AMC disclaimer : www.amc.nl/disclaimer

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Survey for Research Software Engineers - people who write software used in research - a warm request to fill it in
by Alexander Botzki 16 Nov '21

16 Nov '21

Dear all, I'd like to send you the link for a survey which a number of international supporters for Research Software Engineering have put together recently. Our effort has been lead by Simon Hettrick from the Software Sustainability Institute. A blog about the results from 2018 is here: https://www.software.ac.uk/blog/2019-02-15-rse-survey-2018-results We would be delighted to have as many as possible answers from persons who write software used in research. So, please have a look at this link for more information and the questions: https://softwaresaved.limequery.com/386272?lang=en The survey will stay open for 2 months. Thanks a lot for your consideration. Best regards, Alex Alexander Botzki - Head of VIB Bioinformatics Core, ELIXIR Belgium Training Coordinator VIB Bioinformatics Core Technologiepark-Zwijnaarde 75 9052 Zwijnaarde Belgium tel +32 9 224 9870 https://vib.be/labs/vib-bioinformatics-core/research | https://www.bits.vib.be | @vibbioinfocore [cid:image002.jpg@01D7DADD.0B4185B0]

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