- BBClist - maillist.psb.ugent.be

Bioinformatician - Netherlands Cancer Institute
by p.dimitriadis＠nki.nl 14 Apr '21

14 Apr '21

Dear community members, Are you a highly motivated and talented computational biologist looking for a position to apply bioinformatics and machine learning in unique Melanona datasets ? Do you wish to join a multidisciplinary team working with advanced melanoma patient and contribute in improving personalized medicine and discover new therapies ? If yes, the Lab of Dr Christian Blank at the Netherlands Cancer institute is seeking for a bioinformatician to join the team. For more details visit the following link https://www.nki.nl/careers-study/vacancies/computational-biologist-personal… Please feel free to share this opening with anyone who may be interested. Best regards, Petros Dimitriadis Bionformatician Blank Lab Netherlands Cancer Institute

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PhD position: machine learning on pangenomes
by Ridder, Dick de 13 Apr '21

13 Apr '21

We are looking for an enthusiastic bioinformatics PhD candidate for a project on new detection strategies and analyses of plant quarantine organisms (q-organisms) based on a pan-genome approach. Research includes the development of machine-learning methodology on pan-genome graphs, to identify important features associated to pathogenicity or host specificity for instance, and visualizations to support genome analyses and outbreak management. This project is a collaboration between Wageningen Research Biointeractions and Plant Health and the Wageningen University Bioinformatics Group. The PhD student will also work with experts from the National Plant Protection organization (NPPO-NL) and industrial partners. Candidates should hold an MSc degree in bioinformatics, computer science (with a demonstrable affinity for biology) or related area. We are specifically seeking a candidate with a strong background in algorithm development and machine learning, and demonstrable skills in mathematics and statistics. Good organisational skills, enthusiasm for working in an interdisciplinary team and an interest in bringing bioinformatics to real-world application are important characteristics as well. Additional information about the position can be found at https://www.wur.nl/en/vacancy/PhD-student-Pangenome-mining-for-quarantine-o…. Interested candidates can apply up to May 9, 2021 through this website. Best regards, Dick de Ridder Bioinformatics Group, Wageningen University, The Netherlands

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Phd and Postdoc positions (France)
by El-ghazali Talbi 12 Apr '21

12 Apr '21

The BONUS (Big Optimization and Ultra-scale Optimization -https://sites.google.com/view/bonus-research-group/) research group has three PhD and one post-doctoral proposals. The detailed decsriptions can be found following the Web links given below. - PhD Position F/M [Industrial collaboration] Multi-objective automated design of deep neural networks Details in pdf file enclosed - PhD Position F/M [Campagne doctorant 2021 - CRI Lille] Quantum-assisted optimization https://jobs.inria.fr/public/classic/fr/offres/2021-03448 - PhD Position F/M [Université de Lille - Université du Luxembourg] Productivity-aware parallel cooperative combinatorial optimization for ultra-scale supercomputers https://www.cristal.univ-lille.fr/sujets-these/details.html?id=50e6963dbe06… - Post-Doctoral Research Visit F/M [Campagne Post-doctorant 2021 - CRI Lille] Parallel surrogate-assisted optimization for automatic hyper-parameter and neural architecture search in Deep Learning (M/F) https://jobs.inria.fr/public/classic/fr/offres/2021-03418 Best regards, -- ********************************************************************** META'2021 International Conference on Metaheuristics and Nature Inspired Computing 27-30 Oct 2021, Marrakech, Morocco http://meta2021.sciencesconf.org *********************************************************************** Prof. El-ghazali TALBI Polytech'Lille, University Lille - INRIA CRISTAL - CNRS guide2research.com -- L'absence de virus dans ce courrier électronique a été vérifiée par le logiciel antivirus Avast. https://www.avast.com/antivirus

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Tenure track position for a group leader translational tumor bioinformatics
by Christian.Gilissen＠radboudumc.nl 10 Apr '21

10 Apr '21

Dear all, We currently have a tenure track position for a group leader translational tumor bioinformatics in Nijmegen (RadboudUMC, The Netherlands). Find all of the details attached. Kind regards, Christian Gilissen, Ph.D. Associate professor Genome Bioinformatics Head of Bioinformatics Christian.Gilissen(a)radboudumc.nl<mailto:Christian.Gilissen@radboudumc.nl> T +31 (0)24 366 89 40 F +31 (0)24 361 66 58 https://www.radboudumc.nl/en/people/christian-gilissen http://orcid.org/0000-0003-1693-9699 Radboud university medical center Department of Human Genetics (848) P.O. box 9101, 6500 HB Nijmegen www.radboudumc.nl<http://www.radboudumc.nl/> De informatie in dit bericht is uitsluitend bestemd voor de geadresseerde. Aan dit bericht en de bijlagen kunnen geen rechten worden ontleend. Heeft u deze e-mail onbedoeld ontvangen? Dan verzoeken wij u het te vernietigen en de afzender te informeren. Openbaar maken, kopiëren en verspreiden van deze e-mail of informatie uit deze e-mail is alleen toegestaan met voorafgaande schriftelijke toestemming van de afzender. Het Radboudumc staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 80262783. The content of this message is intended solely for the addressee. No rights can be derived from this message or its attachments. If you are not the intended recipient, we kindly request you to delete the message and inform the sender. It is strictly prohibited to disclose, copy or distribute this email or the information inside it, without a written consent from the sender. Radboud university medical center is registered with the Dutch Chamber of Commerce trade register with number 80262783.

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Plant bioinformatics vacancy at Genetwister (Wageningen, NL)
by Lidija Berke 09 Apr '21

09 Apr '21

Dear all, At Genetwister, located in Wageningen, we are looking for a new colleague to join our bioinformatics team. The vacancy description is attached. Kind regards, Lidija [cid:image001.png@01D72D2A.C0519F50] Disclaimer This e-mail and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom/which they are addressed. 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 shall not constitute a binding agreement unless expressly confirmed in writing by one of the Directors of Genetwister. Please note that any views or opinions presented in this e-mail are solely those of the author and do not necessarily represent those of Genetwister. Finally, the recipient 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. / Chamber of Commerce Arnhem, The Netherlands no.: 11043533

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postdoc at UWisconsin_Madison.EvolutionaryComparativeGenomics
by Stephane Rombauts 09 Apr '21

09 Apr '21

> Begin forwarded message: > > From: Carol Eunmi LEE <0000061f866e8d38-dmarc-request(a)LISTSERV.KSU.EDU> > Subject: [Newsletter] [ARTHROPODNEWS] UWisconsin_Madison.EvolutionaryComparativeGenomics > Date: 9 April 2021 at 08:17:44 CEST > To: ARTHROPODNEWS(a)LISTSERV.KSU.EDU > Reply-To: Carol Eunmi LEE <carollee(a)WISC.EDU> > > Dear Colleagues, > > I am currently looking for a postdoc to join my lab. We have a lot of data, a vibrant lab, and a great study system. > > Feel free to forward this ad to those that might be interested. > > > > > Postdoctoral Position in Evolutionary Population and Comparative Genomics > > A postdoctoral position is available to work on an NSF-funded project in > the laboratory of Professor Carol Lee, in the Department of Integrative > Biology at the University of Wisconsin, Madison. > > This project focuses on Rapid Evolutionary Responses to Global > Change using the copepod Eurytemora affinis species complex as a model > system. With changes in global climate, coastal high latitude waters are > experiencing rapid declines in salinity, due to increases in ice melt > and precipitation. We have found evolutionary shifts in ion transport > function, genome-wide gene expression, and population genomic signatures > of selection associated with changes in salinity (see pubs in the links > below). This postdoc project will entail conducting comparative genomic > and population genomic analyses associated with temperature and salinity > change in wild and laboratory populations. > > The E. affinis complex presents an exemplary model, with its short > generation time (20d), ease of culturing large numbers (thousands > per population), and ability to generate inbred lines. The Lee Lab > is generating multiple full reference genomes (PacBio and Oxford > Nanopore) from the E. affinis species complex to the chromosome level. > Additionally, the multiple independent environmental clines have enabled > us to observe exceptional cases of parallel polygenetic adaptation > (to the level of SNPs). > > The ideal candidate should hold a Ph.D. and have publications in > peer-reviewed journals. A background in evolutionary genetics is > required, especially in population genetics/genomics or comparative > genomics. Relevant areas of expertise include molecular evolutionary > genetics, computational and programming skills, and statistics. > > Review of applications will begin immediately and will continue > until the position is filled. The appointment could persist for up > to three years. Interested candidates should email their application > to Prof. Carol Lee (carollee(a)wisc.edu <mailto:carollee@wisc.edu>), including: (1) a CV, (2) a > cover letter describing qualifications and relevant experience, (3) > a list of references (recommenders), and (4) samples of first authored > publications. Enquiries regarding this position are most welcome. > > The University of Wisconsin-Madison offers a large and intellectually > vibrant community of evolutionary/population biologists, providing > ample opportunities for interaction with excellent scientists (see > https://evolution.wisc.edu/people/faculty/ <https://evolution.wisc.edu/people/faculty/>) and first rate departments of > Statistics and Biostatistics, computational facilities, and a Biotech > Center. Madison is a culturally-rich community, in relative close > proximity to Chicago. > > Representative publications: > https://carollee.labs.wisc.edu/pdfs/Stern&Lee_NatureE&E_2020suppfiles.pdf <https://carollee.labs.wisc.edu/pdfs/Stern&Lee_NatureE&E_2020suppfiles.pdf> > https://carollee.labs.wisc.edu/pdfs/PosaviEtal_2020.pdf <https://carollee.labs.wisc.edu/pdfs/PosaviEtal_2020.pdf> > https://carollee.labs.wisc.edu/pdfs/Eyun_etal2017.pdf <https://carollee.labs.wisc.edu/pdfs/Eyun_etal2017.pdf> > https://carollee.labs.wisc.edu/pdfs/Posavi_etal2014.pdf <https://carollee.labs.wisc.edu/pdfs/Posavi_etal2014.pdf> > > The University of Wisconsin is an Equal Opportunity/Affirmative Action > Employer. > > Carol Eunmi LEE > Professor > Department of Integrative Biology > University of Wisconsin, Madison > Madison, WI 53706 > carollee(a)wisc.edu <mailto:carollee@wisc.edu> > > > Carol Eunmi LEE <carollee(a)wisc.edu <mailto:carollee@wisc.edu>> > > > > ================= You can manage your subscription for this list at: > http://listserv.ksu.edu/web?SUBED1=ARTHROPODNEWS&A=1 <http://listserv.ksu.edu/web?SUBED1=ARTHROPODNEWS&A=1>

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UBC-NIOZ online mini-conference on Monday April 12 (16:00 - 17:30)
by Melquiond, A.S.J. (Adrien) 08 Apr '21

08 Apr '21

The Utrecht Bioinformatics Center<https://ubc.uu.nl/> is organising an online mini-conference on Monday April 12 (16:00 - 17:30) with three speakers from NIOZ<https://www.nioz.nl/en> (Royal Netherlands Institute for Sea Research): Dr. Nina Dombrowski<https://www.nioz.nl/en/about/organisation/staff/nina-dombrowski>, MSc. Jeroen Hoekendijk<https://www.nioz.nl/en/about/organisation/staff/jeroen-hoekendijk> and Dr. Julia Engelmann<https://www.nioz.nl/en/about/organisation/staff/julia-engelmann>. A short introduction of the speakers and the title of their talks is provided below. If you are interested in joining (free attendance), check the event link: https://ubc.uu.nl/first-nioz-ubc-webinar-on-monday-april-12/ --------------------------- Nina Dombrowski: "Undinarchaeota illuminate DPANN phylogeny and the impact of gene transfer on evolution" Nina Dombrowski is a marine microbiologist and works on increasing our understanding of uncultivable microbes. She is particularly interested in the DPANN archaea, a lineage of ultra-small and genome reduced archaea. Due to their reduced genomes, most DPANN archaea rely on a host to grow and proliferate, however, it is unknown how this specific interaction evolved - thus this question forms a key research interest of our research team at NIOZ. Jeroen Hoekendijk: "Automated detection of seals, using convolutional neural networks" Jeroen Hoekendijk is a marine biologist and PhD candidate at the NIOZ. He applies deep learning to detect marine mammals from aerial and satellite imagery. By using remote sensing techniques in combination with computer vision, valuable time and resources can be saved, while providing new opportunities to survey remote and inaccessible regions. Julia Engelmann: "Elucidating bacterial and eukaryotic microbial community interactions on plastic with causal network modelling" Julia Engelmann is a marine computational biologist at the NIOZ. She uses causal network modelling on marine microbial community composition data to generate hypothesis about which organisms are interacting with each other and their environment. Besides furthering the understanding of metabolic dependencies and the nutrient cycles in the ocean, she is particularly interested in how microbial communities are affected by anthropogenic environmental changes. --------------------------- Kind regards, Adrien Melquiond ------------------------------------------------------------------------ Adrien Melquiond<https://www.uu.nl/staff/ASJMelquiond>, PhD * Coordinator of the Utrecht Bioinformatics Center (UBC) | Hans Freudenthal 0.07 | Budapestlaan 6, 3584CD Utrecht | https://ubc.uu.nl<https://ubc.uu.nl/> | +31.(0)30.2536617 | ubc_AT_uu.nl<mailto:ubc@uu.nl> * Asst. Prof. in Bioinformatics at the Center for Molecular Medicine (CMM), UMC Utrecht | Stratenum 1.304 | Universiteitsweg 100, 3584CG Utrecht | +31.(0)88.75.68790 | a.s.j.melquiond_AT_umcutrecht.nl<mailto:a.s.j.melquiond@umcutrecht.nl> Contact hours: UBC: Tue-Thu | CMM: Mon-Wed-Fri ------------------------------------------------------------------------ Who are we and what do we do? Watch our movie<https://goo.gl/mx1mPN>

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WABI 2021 -- 2nd Call for Papers
by El-Kebir, Mohammed 06 Apr '21

06 Apr '21

WABI 2021 Call for Papers 21th Workshop on Algorithms in Bioinformatics Chicago, USA (virtual), August 2-4 2021 https://acm-bcb.org/WABI/2021/ SCOPE WABI is an international conference covering research in algorithmic work in bioinformatics, computational biology and systems biology. The emphasis is mainly on discrete algorithms and machine-learning methods that address important problems in molecular biology, that are founded on sound models, that are computationally efficient, and that provide evidence of their potential usefulness in practice, preferably by testing on appropriately chosen simulated or real datasets. The goal is to present recent research results, including significant work-in-progress, and to identify and explore directions of future research. PAPER SUBMISSION Submissions must be formatted in LaTeX using the LIPIcs style <https://submission.dagstuhl.de/styles/download-tag/lipics/v2021.1/authors/z…> and must not exceed 15 pages excluding references. For details please see the information for authors <https://submission.dagstuhl.de/documentation/authors>. Each paper must contain a succinct statement of the issues and of their motivation, a summary of the main results, and a brief explanation of their significance, all accessible to non-specialist readers. All submissions must be made online, through the EasyChair submission system, at: https://easychair.org/conferences/?conf=wabi2021 For scientific information, please contact one of the WABI program committee co-chairs, Alessandra Carbone (Alessandra.Carbone(a)lip6.fr<mailto:Alessandra.Carbone@lip6.fr>) or Mohammed El-Kebir (melkebir(a)illinois.edu<mailto:melkebir@illinois.edu>). For organizational information, please refer to the ACM-BCB 2021 <https://acm-bcb.org/> website. You will need to register on the EasyChair web site before submitting. A standard .pdf file must be received by April 16, 2021 (time zone of your choice) in order for your submission to be considered. Re-submission of already submitted papers will be possible until April 18, 2021 (time zone of your choice). Simultaneous submission to another conference with published proceedings is not permitted, but simultaneous submission to a journal is allowed, provided that the authors notify the program chairs; if published in a journal, such a contribution will be published as a short abstract in the WABI proceedings. Depositing in arxiv.org<http://arxiv.org> <http://arxiv.org/> or biorxiv.org<http://biorxiv.org> <http://biorxiv.org/> is allowed. By submitting a paper the authors acknowledge that in case of acceptance at least one of the authors must register at ACM-BCB 2021 or WABI 2021, attend the conference, and present the paper. PROCEEDINGS Accepted papers will be published in WABI proceedings in the LIPIcs Leibniz International Proceedings in Informatics <https://www.dagstuhl.de/publikationen/lipics/>. Selected papers will be invited for an extended publication in a thematic series in Algorithms for Molecular Biology (AMB) <http://almob.biomedcentral.com/>. Previous proceedings of WABI appeared in LNCS/LNBI volumes until 2015. As of 2016, they appeared in LIPICS volumes. IMPORTANT DATES Paper submission deadline: April 16, 2021 Submitted papers can be updated or withdrawn until April 18, 2021 Notification of paper acceptance: May 21, 2021 Final version of accepted paper due: May 31, 2021 Conference: August 2 - 4, 2021, virtual PROGRAM COMMITTEE Tatsuya Akutsu, Kyoto University, Japan Marco Antoniotti, Universita di Milano-Bicocca, Italy Anne Bergeron, Universite du Quebec a Montreal, Canada Paola Bonizzoni, Universita di Milano-Bicocca, Italy Christina Boucher, University of Florida, USA Alessandra Carbone, Sorbonne Universite, France (co-chair) Leonid Chindelevitch, Imperial College London, UK Lenore Cowen, Tufts University, USA Daniel Doerr, University of Duesseldorf, Germany Mohammed El-Kebir, University of Illinois at Urbana-Champaign, USA (co-chair) Nadia El-Mabrouk, University of Montreal, Canada Anna Gambin, Warsaw University, Poland Bjarni Halldorsson, deCODE genetics and Reykjavik University, Iceland Katharina Huber, University of East Anglia, UK Carl Kingsford, Carnegie Mellon University, USA Gunnar Klau, Heinrich Heine University Dusseldorf, Germany Gregory Kucherov, University of Paris Est, France Manuel Lafond, Universite de Sherbrooke, Canada Elodie Laine, Sorbonne Universite, France Yu Lin, Austrialia National University, Australia Stefano Lonardi, University of California Riverside, USA Veli Makinen, University of Helsinki, Finland Guillaume Marcais, Carnegie Mellon University, USA Tobias Marschall, Heinrich Heine University, Germany Erin Molloy, University of Maryland College Park / UCLA, US Bernard Moret, Ecole Polytechnique Federale de Lausanne, Switzerland Vincent Moulton, University of East Anglia, UK Francesca Nadalin, EMBL-EBI / ITT, Italy, England Mihai Pop, University of Maryland, USA Teresa Przytycka, NCBI, NIH, USA William Stafford Noble, University of Washington, USA Aida Ouangraoua, Universite de Sherbrooke, Canada Ion Petre, Turku University, Finland Nadia Pisanti, University of Pisa, Italy Solon Pissis, CWI Amsterdam, the Netherlands Alberto Policriti, University of Udine, Italy Sven Rahmann, University of Duisburg-Essen, Germany Knut Reinert, FU Berlin, Germany Eric Rivals, LIRMM - Universite de Montpellier, France Sebastien Roch, University of Wisconsin Madison, US Giovanna Rosone, University of Pisa, Italy Marie-France Sagot, INRIA Rhone-Alpes, France Alexander Schoenhuth, Bielefeld University, Germany Mingfu Shao, Penn State, US Jens Stoye, Bielefeld University, Germany Krister Swenson, CNRS & Universite de Montpellier, France Ewa Szczurek, Warsaw University, Poland Sharma Thankachan, University of Central Florida, USA Alexandru Tomescu, University of Helsinki, Finland Helene Touzet, CNRS, France Esko Ukkonen, University of Helsinki, Finland Gianluca Della Vedova, University of Milano-Bicocca, Italy Tomas Vinar, Comenius University, Slovakia Prudence W.H.Wong, University of Liverpool, UK Tandy Warnow, University of Illinois at Urbana-Champaign, USA Simone Zaccaria, UCL Cancer Institute, UK Louxin Zhang, National University of Singapore, Singapore Xiuwei Zhang, Georgia Tech, US Michal Ziv-Ukelson, Ben Gurion University of the Negev, Israel -- Mohammed El-Kebir<http://www.el-kebir.net> Assistant Professor 3216 Siebel Center Computer Science Department University of Illinois Urbana-Champaign 217-300-7369

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Position available Max Planck Tubingen
by Susana Coelho 05 Apr '21

05 Apr '21

Dear all We have a position available in our group for a staff bioinformatician - please see attached advert! Thanks for posting Best wishes Susana --------- Susana Coelho Department of Algal Development and Evolution Max Planck Institute for Developmental Biology Max-Planck-Ring 5 72076 Tübingen Tel.: +49 7071-601-1307 E-mail: susana.coelho(a)tuebingen.mpg.de https://www.eb.tuebingen.mpg.de/department-of-algal-development-and-evoluti…

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Project Lead Artificial Intelligence and Data Science - DUmmen Orange the Netherlands
by Camillo Berenos 02 Apr '21

02 Apr '21

Dear all, For our Research team at Dummen Orange (a leading ornamental breeding company) we are looking for a Project Lead Artificial Intelligence and Data Science to work on transforming images and other types of high dimensional data into (pre)breeding decisions with an impact! https://emea.dummenorange.com/site/nl/vacatures/detail?job=project-lead-art… *Camillo Berenos*

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