February 2021 - BBClist - maillist.psb.ugent.be

PhD position in Integrating of multiple -omics datasets
by Claesen Jürgen 04 Jun '24

04 Jun '24

Dear all, SCK CEN and UHasselt are looking for candidates for a PhD project with the title: "Integromics - Towards integration of big biomolecular data to enable systems biology" Description The last decades, development of high-throughput technologies such as next-generation sequencing, microarrays and mass spectrometry has led to a paradigm shift in biology and life sciences. Where previously one biomolecule (for example, a gene, or a protein) was studied as a single entity, these experimental techniques allow to study a set of biomolecules (for example, the genome or the proteome) in one go and in a limited amount of time. While, at first, experiments were analyzed independently from each other, combining information of several experimental techniques, and correlating them with environmental and/or clinical parameters, is, nowadays, of great interest. As a consequence, novel statistical and computational methodologies for the analysis of multi-omics datasets have to be developed, allowing a multi-dimensional view on complex biological processes. In this PhD project, we aim at the development of computational methods for the analysis of multi-omics datasets, that are commonly generated by the three biology units of SCK*CEN, which will improve the understanding and valorization of the data, and which will keep the biology units up to date with current developments in biology and bioinformatics. Profile and diploma As a doctorate researcher you will join the dynamic bioinformatics team at SCK CEN and CenStat (UHasselt). A successful candidate should have : * A master degree in biostatistics/applied statistics/bioinformatics/statistical bioinformatics. * You are acquainted with statistical methodologies and had exposure to computer programming in SAS/R/Winbugs/Python. * You can work independently and within a team. * You have excellent communication skills. * You are interested to develop new methodology from both theoretical and applied aspects. * You enjoy working in a multidisciplinary and multicultural environment. * You are willing to closely collaborate with biologists/biostatisticians. * You speak and write English fluently. * You have work experience with at least two different "omics" platforms. For more information contact: Dr. Claesen Jürgen (SCK-CEN), jclaesen(a)sckcen.be<https://academy.sckcen.be/en/Mailform?contactid=b22040b5-cf18-496f-a82a-3bc…> Prof. Shkedy Ziv (Hasselt University), ziv.shkedy(a)uhasselt.be<https://academy.sckcen.be/en/Mailform?contactid=51ae7733-8006-4347-b211-9a4…> Link to the project in SCK-CEN: https://academy.sckcen.be/en/Your_thesis_internship/AllTopics/Integromics--… Kind Regards, Jürgen

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NERC Bursaries for Edinburgh Genomics Courses
by TRAIN edgenomics-training 02 Mar '22

02 Mar '22

Dear All We are pleased to announce we have a number of bursaries available to cover up-to the full fees of any of our upcoming bioinformatics courses. These bursaries are available to UK based students or researchers funded by the NERC or working on research that falls under the remit of the NERC (https://nerc.ukri.org/research/portfolio/remit/) Bursaries are available for any of our courses (see below) but are available for a LIMITED TIME ONLY: They are available for any course booked BEFORE 27th MARCH. So please don't wait to sign up! Our upcoming courses: Linux for Genomics, 13th March - An introduction to working on the command line, running commands and handling data relevant to bioinformatics. https://genomics.ed.ac.uk/services/linux-genomics R for Genomics, 14-15th March - An introduction to the statistical environment R, taking you from the very basics to writing basic functions and creating beautiful figures with ggplot2 https://genomics.ed.ac.uk/services/r-genomics Introduction to Python for Biologists, 18-22 March - This introductory course gives an overview of the language with an emphasis on practical problem-solving, using examples and exercises drawn from various aspects of bioinformatics work. https://genomics.ed.ac.uk/services/introduction-python-biologists-0 Data Manipulation and Visualisation with Python, 08 - 12 April - Python has a many high-quality libraries for working with scientific data. In this workshop we will see how to leverage these libraries to efficiently work with and visualise large volumes of data. https://genomics.ed.ac.uk/services/data-manipulation-and-visualisation-pyth… Introduction to RNA-seq Data Analysis, 9-10th May - This two-day course takes you through a tried-and-tested workflow for analysing RNA-seq data, from read mapping and QC to differential expression and result visualisation. https://genomics.ed.ac.uk/services/introduction-rna-seq-data-analysis If you think you are provably eligible for one of these bursaries, sign up to your desired course through the link provided and we will be in contact regarding fees. Kind Regards Nathan Medd Training and Outreach Manager - Edinburgh Genomics G.06, Ashworth Laboratories, Charlotte Auerbach Road, The King's Buildings, The University of Edinburgh, EH9 3FL, Edinburgh, Scotland Edinburgh Genomics' Privacy Notice can be viewed at: http://genomics.ed.ac.uk/about-us/privacy-notice This email and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. If you have received it in error, please destroy all copies and inform the sender. The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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WABI 2021 -- Call for Papers
by El-Kebir, Mohammed 25 Feb '21

25 Feb '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) or Mohammed El-Kebir (melkebir(a)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/> or 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 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 College Park, 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 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 -- 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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CFP META'2021 @Marrakech
by El-ghazali Talbi 25 Feb '21

25 Feb '21

Dear colleagues, please distribute the CFP of META Conf. in your networks. Thanks for your collaboration. Apologies for cross-posting. Appreciate if you can distribute this CFP to your network. ********************************************************************** META'2021 International Conference on Metaheuristics and Nature Inspired Computing 27-30 Oct 2021 Marrakech, Morocco http://meta2021.sciencesconf.org/ ********************************************************************** META is one of the main event focusing on the progress of the area of metaheuristics and their applications. As in previous editions, META’2021 will provide an opportunity to the international research community in metaheuristics to discuss recent research results, to develop new ideas and collaborations, and to meet old friends and make new ones in a friendly and relaxed atmosphere. All selected long papers will be published in the Springer (SCOPUS, ISI, DBLP) conference proceedings. At least, 2 special special issues in ISI and SCOPUS journals are also confirmed. META'2021 welcomes presentations that cover any aspects of metaheuristic research such as new algorithmic developments, high-impact applications, new research challenges, theoretical developments, implementation issues, and in-depth experimental studies. META'2021 strives for a high-quality program that will be completed by a number of invited talks, tutorials, workshops and special sessions. The scope of the META conference includes, but is not limited to: * Local search, tabu search, simulated annealing, VNS, ILS, … * Evolutionary algorithms, swarm intelligence, bio-inspired algorithms, … * Emergent nature inspired algorithms: quantum computing, artificial immune systems, bee colony, DNA computing, … * Quantum computing * Parallel and distributed algorithms * Decomposition methods * Hybrid methods with machine learning, game theory, mathematical programming, constraint programming, co-evolutionary, … * Application to: logistics and transportation, networks, scheduling, data mining, engineering design, energy, cloud, bio-medical, … * Theory of metaheuristics, landscape analysis, convergence, problem difficulty, very large neighbourhoods, … * Multi-objective optimization, bi-level optimization * Dynamic optimization, problems with uncertainty, stochastic optimization, … * Parameter tuning (static, dynamic, adaptive, self-adaptive) * Hyper-heuristics, cross-domain metaheuristics * Software frameworks for metaheuristics and nature inspired computing Submission of papers: ____________________ - Submission of papers via the website S1) Short papers: Extended abstracts of work-in-progress and position papers of a maximum of 3 pages. S2) Long papers: Original research contributions of a maximum of 10 pages. S3) Journal papers: High-quality manuscripts that have recently, within the last year, been submitted or accepted for journal publication. For this special case, the submission should have the same title that the accepted work, the abstract AND the complete reference of the work. - Proceedings of the conference will be provided. Selected papers of type S2 will be published in a Springer book (SCOPUS, ISI, DBLP). - Predefined styles are available on the website http://meta2021.sciencesconf.org/ - Proposals for invited sessions, workshops and tutorials: Deadline April 9, 2021, contact meta2021(a)sciencesconf.org Important dates: _______________ - Submission deadline: April 30, 2021 - Notification of acceptance: June 11, 2021 -- ********************************************************************** 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

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Senior Bioinformatician for Oligonucleotide Therapeutics in AstraZeneca - Gothenburg (Sweden)
by Sergio Martinez Cuesta 25 Feb '21

25 Feb '21

*Are you a quantitatively-minded scientist looking to apply bioinformatics and machine learning to design oligonucleotides for therapeutic use? Do you wish to join a growing team where you will have the possibility to further exploit our drug discovery platforms? If yes, we have the position for you at AstraZeneca in Gothenburg!* We are currently looking for a Senior Bioinformatician for Oligonucleotide Therapeutics to join us at AstraZeneca in Gothenburg, Sweden. In this position you’ll be a part of the Data Sciences and Quantitative Biology team that works as part of the Discovery Sciences organisation, within BioPharma R&D. https://careers.astrazeneca.com/job/gothenburg/senior-bioinformatician-for-… *Application deadline February 28th!* Thanks, Sergio

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Register now for 2 Helis Academy FAIR data stewardship events
by Celia van Gelder 24 Feb '21

24 Feb '21

DTL Newsletter - View this email in your browser <https://mailchi.mp/dtls/register-now-for-2-helis-academy?e=f6e850c160> *for data-driven life sciences* Register now for 2 Helis Academy FAIR data stewardship events *Are you interested in capacity building in data stewardship in the life sciences? We would like to bring your attention to two events of the Helis Academy.* *Are you a professional advancing digital skills in the life sciences? * Then join the Helis Academy event March 15th. You will learn about the portfolio of courses in Data Analysis & Data Stewardship and the possible next steps to close the gap for digital skills in life sciences and health. For more information and registration please click here <https://dtls.us3.list-manage.com/track/click?u=3cef2d6f6da8f8059e2288298&id…> . *Are you a researcher, (starting) data steward or generally interested in the topic of FAIR Data Stewardship?* Then make sure to join this 6 half day introductory course organised by the Helis Academy which runs in the period March 17-31. Make sure to register soon, as only 30 participants can join. Find more information here. <https://dtls.us3.list-manage.com/track/click?u=3cef2d6f6da8f8059e2288298&id…> [image: Twitter] <https://dtls.us3.list-manage.com/track/click?u=3cef2d6f6da8f8059e2288298&id…> [image: Website] <https://dtls.us3.list-manage.com/track/click?u=3cef2d6f6da8f8059e2288298&id…> *Copyright © *2021 Dutch Techcentre for Life Sciences content is open. Please reuse under CC0, citing us where appropriate. * update your preferences <https://dtls.us3.list-manage.com/profile?u=3cef2d6f6da8f8059e2288298&id=d62…> - unsubscribe from this list <https://dtls.us3.list-manage.com/unsubscribe?u=3cef2d6f6da8f8059e2288298&id…> - DTL privacy statement <https://dtls.us3.list-manage.com/track/click?u=3cef2d6f6da8f8059e2288298&id…> -- Dr. Celia W.G. van Gelder Programme Manager DTL Learning Training Coordinator ELIXIR-NL ELIXIR Training Platform Leader tel. +31613375327 e-mail: celia.van.gelder(a)dtls.nl websites: https://www.dtls.nl/, https://www.elixir-europe.org/platforms/training skype: celia.van.gelder Office: DTL | Jaarbeurs Innovation Mile (JIM) | 6th floor Beatrixgebouw | Jaarbeursplein 6 | 3521 AL Utrecht Postal address: Postbus 8500 | 3503 RM 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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Five (5) AI4B.io PhD positions TU Delft
by Thomas Abeel 22 Feb '21

22 Feb '21

Dear all, In the context of AI4B.io, we have 5 PhD positions available at Delft University of Technology in collaboration with DSM. https://www.academictransfer.com/en/298076/phd-position-machine-learning-fo… https://www.academictransfer.com/en/298075/phd-position-machine-learning-fo… https://www.academictransfer.com/en/298080/phd-position-reinforcement-learn… https://www.academictransfer.com/en/298080/phd-position-reinforcement-learn… https://www.academictransfer.com/en/298077/phd-position-digital-twin-and-sm… kind regards, Thomas

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HIDSS4Health PhD program Heidelberg/Karlsruhe
by Marc Jan Bonder 19 Feb '21

19 Feb '21

Dear all, I hope this email finds you well. The HIDSS4Health research school performs an annual candidate selection process. We are looking for excellent graduates holding master degrees, received by July 2021 at the latest, in computer science, mathematics, engineering, physics or related quantitative sciences (e.g., bioinformatics or medical informatics). Suitable candidates are selected in a three-step process: (1) the written application, (2) a virtual one-day selection event for short-listed applicants, and (3) matching projects and candidates. Please find a description of the 2021 project proposals here ( https://www.hidss4health.de/documents/Proposals_2021.pdf) Evaluation criteria for the candidates are an excellent academic record and a strong motivation for the interdisciplinary nature of the projects. The institutions are committed to increasing the percentage of female scientists and encouraging female applicants to apply. If you are interested please apply by the 1st of march: https://www.hidss4health.de/#apply More information can be found here: https://www.hidss4health.de/ Best regards, Marc Jan Bonder

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Open positions for Bioinformatics Postdoc/IT technician
by Lena Wiese 19 Feb '21

19 Feb '21

Dear colleagues. Please consider the following job announcements and feel free to forward them to appropriate interested candidates. Positions are open to all qualified persons independent of gender, disabilities, religion, etc... Applications will be possible until 25th of February. 1) One Postdoctoral researcher at ITEM Hannover (Germany): We are looking for a highly qualified person with a PhD degree in Computer Science/Bioinformatics/Medical Informatics with expertise in biomedical data management for managing research projects in different areas of biomedical data analysis. Apply via Fraunhofer Recruiting portal in German https://recruiting.fraunhofer.de/Vacancies/56703/Description/1 or English https://recruiting.fraunhofer.de/Vacancies/56703/Description/2 2) One IT technician at ITEM Hannover (Germany): We are looking for a highly qualified person with an MSc degree in Computer Science/Bioinformatics/Medical Informatics for maintaining scientific databases and data analysis pipelines. Apply via Fraunhofer Recruiting portal https://recruiting.fraunhofer.de/Vacancies/56719/Description/1 More information on the group can be found at https://www.item.fraunhofer.de/de/angebot/bioinformatik.html Best regards Lena Wiese -- Prof. Dr. Lena Wiese Database Technologies and Data Analytics Goethe University Frankfurt http://www.dbda.cs.uni-frankfurt.de/ http://wiese.free.fr

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Associate Professor / Full Professor of Modeling of Biological Systems
by Karoline Faust 17 Feb '21

17 Feb '21

Dear All, This is to inform you about an Associate/Full Professorship in Modeling of Biological Systems at the University of Copenhagen: https://jobportal.ku.dk/alle-opslag/?show=153390 Kind regards, Karoline Karoline Faust --------------------------------------------------- Email: karoline.faust(a)kuleuven.be<mailto:karoline.faust@kuleuven.be> Web: http://tinyurl.com/MicrobialSysBio --------------------------------------------------- Room 7.A130, Rega Institute Laboratory of Molecular Bacteriology Department of Microbiology, Immunology and Transplantation KU Leuven, Campus Gasthuisberg Herestraat 49, postbus 1028 3000 Leuven Belgium ---------------------------------------------------

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