- BBClist - maillist.psb.ugent.be

Workshop on biological data visualisation
by Jan Aerts 26 Sep '19

26 Sep '19

Dear all, We are again organising the workshop on biological data visualisation at the EBI in March 2020. Participants of this workshop will get acquainted with the fundamentals of data visualisation, be introduced to visual design, and practise coding these visualisations (depending on their background: in vega or D3). For more information and registration, see here: https://www.ebi.ac.uk/training/events/2020/data-visualisation-biology-pract… Jan Aerts

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Job: Bioconductor infrastructure for the integration of genomics, transcriptomics and proteomics data
by Laurent Gatto 26 Sep '19

26 Sep '19

A position for a PhD student or post-doctoral research is open in the group of Prof Laurent Gatto at the UCLouvain (Brussels, Belgium) in collaboration with Prof Vince Carey at Harvard University (Boston, MA, USA) to develop the necessary infrastructure and statistical software to integrate genomic, mass spectrometry-based quantitative proteomics and transcriptomics expression data. The promise of omics integrative approaches is that the whole will become more than the sum of its parts and will thus reveal new insights into the comprehension of the underlying biology. Natural candidates for such integration are proteomics and transcriptomics. Both approaches aim, among other things, at measuring differences in expression of genes, albeit measuring different biological entities. Different studies have recorded diverging observations about the correlation of the measurements. The goal of this project is to develop and expand the Bioconductor infrastructure into an integrative proteogenomics framework to ensuring explicit and robust integration of quantitative proteomics, transcriptomics and genomics data. The successful candidate will be able to demonstrate experience in the following areas: - You have a master's degree or a PhD in computational biology/bioinformatics, computer science, data science, statistics, computer/electrical engineering, physics, or other related fields. - You have hands-on experience in analysing and interpreting omics data. - You have created/maintained/used software to address research problems in high throughput biology. - You are committed to open research best practices and know how to adapt these to biomedical research contexts. The ideal candidate will be able to demonstrate at least some of the following skills: - Experience with the processing and analysis of omics data (important). - Good knowledge of the R programming language and the Bioconductor infrastructure (important). - Experience in open and reproducible research, open source software and open data (important). - Experience in high performance computing (desirable). - Experience in C/C++ (desirable). - Experience with code versioning and collaborative tools such as, for example, git, and GitHub/GitLab (desirable). - Experience with other languages commonly used in computational biology and bioinformatics like Python or Julia (optional). - Knowledge of French and English is desirable. The contract is full time for a duration of 3 years (for the post-doctoral position) or 4 years (for the PhD position) and is available immediately. Candidates must be in a situation of “international mobility”, i.e. they should not have resided or carried out their main activity (work, studies, etc.) in Belgium for more than 12 months in the 3-year period before submission of their application. We value equality, diversity and an open, collaborative and welcoming work environment. To apply, please send your application by email to Laurent Gatto referencing this position, including a CV with publications and software outputs, a 1-page statement of research interests and names and email addresses of three references. Do not hesitate to contact Laurent Gatto (laurent.gatto(a)uclouvain.be) for additional information.

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2nd ATCR meeting on T-cell receptor sequencing advances
by Pieter Meysman 26 Sep '19

26 Sep '19

Dear all, On the 9th&10th of December 2019 the second Antwerp T-cell Receptor (TCR) Meeting will be organised, following the success of last year’s edition. This two-day international meeting aims to offer a venue for researchers working on TCR sequencing, analysis and applications to present their data and discuss their views on this quickly evolving field. We have assembled a list of leading researchers in the field to provide keynotes for the meeting, including Dr. Victor Greiff (University of Oslo), Dr. Aridaman Pandit (University Medical Center Utrecht), Dr. Sarina Ravens (Hannover Medical School), Dr. Mikhail Shugay (Skoltech Faculty), and Dr. Paul Thomas (St. Jude Children's Research Hospital). Thanks to sponsorship from the University of Antwerp, Research Foundation Flanders and Adaptive Biotechnologies, we are able to provide registration at a reduced rate. For more information on the programme and registration: https://www.uantwerpen.be/en/projects/audacis/antwerp-tcr-meeting/ . Our beautiful venue is limited to 140 visitors, thus we advise you to register on time if you are planning to come. We welcome researchers to present their latest TCR related work via an oral or poster presentation. If you are interested, submit your abstract before the 19th of October: https://easychair.org/conferences/?conf=atcr2019 We hope that you will join us in December! Best wishes, Benson Ogunjimi & Pieter Meysman ATCR2019 chairs https://www.uantwerpen.be/en/projects/audacis/

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VIB Applied Bioinformatics in Life Sciences - February 13-14, 2020 Leuven - registration is open
by Alexander Botzki 26 Sep '19

26 Sep '19

Dear all, We would like to invite you warmly to our VIB Applied Bioinformatics Conference early next year. You could find more details here: https://vibconferences.be/event/applied-bioinformatics-in-life-sciences-3rd… Registration is open. Best regards, Alex Click here https://email.vibconferences.be/t/r-e-jdyhuylk-l-g/ Dear colleague, After two sold out meetings the third edition of Applied Bioinformatics in Life Sciences will host internationally renowned speakers. These including Diafeng Wang, Roser Vento, Klaus Mayer and many more, who will shed light on the future perspectives of their research in the following plenary sessions: Microbial & plant genomics: from simple to complexProteomics Structural and BioinformaticsData integration, machine learning and networksSingle Cell Bioinformatics This conference is organized by VIB, a non-profit life sciences research institute, and will take place on February 13-14, 2020 in the beautiful historic city of Leuven. Find out more [https://vibconferences.be/event/applied-bioinformatics-in-life-sciences-3rd…] Packed program offers new insight in Bioinformatics research We are honored to showcase the following academic world leaders: Roser Vento, Sanger Institute, UKKlaus Mayer, Helmholtz Zentrum München, DEThijs Ettema, Wageningen University, NLRohit Pappu, Washington University, USPatrick Aloy, IRB Barcelona, ESHelen Parkinson, EMBL-EBI, UKNick Loman, University of Birmingham, UKDaifeng Wang, University of Wisconsin-Madison, USSushmita Roy, University of Wisconsin, USOlga Vitek, Northeastern University, USNikolai Slavov, Northeastern University, USEvangelia Petsalaki, EMBL-EBI, UKAedin Culhane, Dana-Farber Cancer Institute & Harvard TH Chan School of Public Health, USAshley Lu, VIB-KU Leuven Center for Brain & Disease Research, BESofia Forslund, Experimental and Clinical Research Centre (ECRC), DELaurent Gatto, De Duve Institute - UC Louvain, BEErik Garrison, UC Santa Cruz, US For more information about the speakers and the program please visit the website: Visit the conference website [https://vibconferences.be/event/applied-bioinformatics-in-life-sciences-3rd…] Submit your abstract before 2 December To support junior researchers, VIB offers PhD students a special rate when registering before the Early Bird deadline. We also encourage young scientists to show their own research to the international research community during the poster sessions at the conference. The best four abstracts will be selected for a short talk in the plenary program. Submit your abstract [https://vibconferences.be/event/applied-bioinformatics-in-life-sciences-3rd…] Apply for a travel Grant VIB offers 5 travel grants to international attendees, which will reimburse travel costs up to 400 Euros. Are you interested in attending ABLS20 and want to have a chance on a travel grant? Submit your motivation by clicking on the 'Apply for a grant' button before 15 November. The organizing committee will notify you of your travel grant acceptance on 22 November 2019. No registration is needed before submitting a travel grant proposal. When you're awarded with a travel grant you will receive a practical email containing the next steps. Note that being awarded a travel grant does not mean being registered for the conference. Find out more [https://vibconferences.be/event/applied-bioinformatics-in-life-sciences-3rd…] We look forward to welcoming you in Leuven on 13 -14 February 2020! With kind regards, Evy Vierstraete Organizing committee: Alex Botzki, VIB Bioinformatics Core, BE Klaas Vandepoele, VIB-UGent Center for Plant Systems Biology, BE Peter Tompa, VIB-VUB Center for Structural Biology, BE Vera van Noort, Centre of Microbial and Plant Genetics, BE Laurent Gatto, de Duve Institute - UC Louvain, BE Evy Vierstraete, VIB Science Events Manager, BE To stop receiveiving our invitations please click below. Tweet https://email.vibconferences.be/t/r-tw-jdyhuylk-l-w/ Share [https://email.vibconferences.be/t/r-li-jdyhuylk-l-c/] Unsubscribe https://email.vibconferences.be/t/r-u-jdyhuylk-l-yd/ Alexander Botzki - Head of VIB Bioinformatics Core | Training Coordinator ELIXIR-BE VIB Bioinformatics Core Rijvisschestraat 126, 9052 GENT, Belgium | +32 9 248 16 00 www.bits.vib.be<http://www.bits.vib.be/> | @vibbioinfocore | https://corefacilities.vib.be<https://corefacilities.vib.be/> [signatureFooter (002)]

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Post-doctoral researcher in Computational Cancer Epigenomics, German Cancer Research Center (DKFZ)
by Pavlo Lutsik 26 Sep '19

26 Sep '19

Dear all, We are looking for a post-doc to strengthen our computational team within the Cancer Epigenomics Division at the DKFZ in Heidelberg. The successful candidate will help expand and bring to maturity our portfolio of best-practice workflows for epigenomic data. To enable this work we are actively employ and create infrastructure for the Common Workflow Language (http://commonwl.org) The primary focus will be set upon workflows for DNA methylation profiling by whole-genome bisulfite sequencing, both bulk and single-cell, for which we are currently running a large-scale benchmarking study supported by external funding (see this talk for details: https://www.youtube.com/watch?v=eGUO_d-xaIE) The candidate will take active part in finalising and publishing results of the initial phase of the study. Furthermore, the candidate will participate in downstream and integrative analyses of these data types, contributing to several exciting projects in cancer epigenomics. Further details and the application portal are available here: https://jobs.dkfz.de/en/jobs/31521/postdoctoral-researcher-in-the-field-of-… We would be happy to see applicants from your community, please spread the word. Best regards, Pavlo

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SDM 2020 Call for Papers
by Alfredo Cuzzocrea 25 Sep '19

25 Sep '19

20th SIAM International Conference on Data Mining May 7 - May 9, 2020, Cincinnati, OH, USA ======================================== SDM 2020 - http://www.siam.org/meetings/sdm20 Call for Papers Scope ===== Data mining is the computational process for discovering valuable knowledge from data - the core of modern Data Science. It has enormous application in numerous fields, including science, engineering, healthcare, business, and medicine. Typical datasets in these fields are large, complex, and often noisy. Extracting knowledge from these datasets requires the use of sophisticated, high-performance, and principled analysis techniques and algorithms, which are based on sound theoretical and statistical foundations. These techniques in turn require implementations on high performance computational infrastructure that are carefully tuned for performance. Powerful visualization technologies along with effective user interfaces are also essential to make data mining tools appealing to researchers, analysts, data scientists and application developers from different disciplines, as well as usable by stakeholders. The SDM conference provides a venue for researchers who are addressing these problems to present their work in a peer-reviewed forum. It also provides an ideal setting for graduate students and others new to the field to learn about cutting-edge research by hearing outstanding invited speakers and attending presentations and tutorials (included with conference registration). A set of focused workshops is also held on the last day of the conference. The proceedings of the conference are published in archival form and are also made available on the SIAM web site. Topics of Interest ================== *Methods and Algorithms -Anomaly & Outlier Detection -Big Data & Large-Scale Systems -Classification & Semi-Supervised Learning -Clustering & Unsupervised Learning -Data Cleaning & Integration -Deep Learning & Representation Learning -Frequent Pattern Mining -Feature Extraction, Selection and Dimensionality Reduction -Mining Data Streams -Mining Graphs & Complex Data -Mining on Emerging Architectures & Data Clouds -Mining Semi Structured Data -Mining Spatial & Temporal Data -Mining Text, Web & Social Media -Online Algorithms -Optimization Methods -Parallel and Distributed Methods -Probabilistic & Statistical Methods -Scalable & High-Performance Mining -Other Novel Methods *Applications -Astronomy & Astrophysics -Automation & Process Control -Climate / Ecological / Environmental Science -Customer Relationship Management -Data Science -Drug Discovery -Finance -Genomics & Bioinformatics -Healthcare Management -High Energy Physics -Intelligence Analysis -Internet of Things -Intrusion & Fraud detection -Logistics Management -Recommendation -Risk Management -Social Network Analysis -Supply Chain Management -Other Emerging Applications *Human Factors and Social Issues -Ethics of Data Mining -Intellectual Ownership -Interestingness & Relevance -Privacy and Fairness Models -Privacy Preserving Data Mining -Risk Analysis and Risk Management -Transparency and Algorithmic Bias -User Interfaces and Visual Analytics -Other Human and Social Issues Submission URL ============== https://cmt3.research.microsoft.com/SDM2020 Workshop and Tutorials ====================== The conference will feature workshops and tutorials on several special topics. Please see the SDM 2020 website for submission requirements. Examples of workshops and tutorials are available through the SDM 2019 website, http://www.siam.org/meetings/sdm19/ Organization ============ GENERAL CO-CHAIRS Nitesh Chawla, University of Notre Dame, USA Carlotta Domeniconi, George Mason Univeristy, USA PROGRAM CO-CHAIRS Yan Liu, University of Southern California, USA Sriraam Natarajan, University of Texas at Dallas, USA WORKSHOPS CO-CHAIRS Yuxiao Dong, Microsoft Research, USA Gregor Stiglic, University of Maribor, Slovenia TUTORIALS CHAIR Danai Koutra, University of Michigan, USA DOCTORAL FORUM CHAIRS Matteo Riondato, Amherst College, USA Brandeis Marshall, Spelman College, USA PANELS CHAIR Zhenhui Jessie Li, Penn State University, USA PUBLICITY CHAIRS Xiang Ren, University of Southern California, USA Alfredo Cuzzocrea, University of Calabria, Italy Sourangshu Bhattacharya, IIT, Kharagpur, India AWARDS CHAIR TBA STEERING COMMITTEE CHAIR Zoran Obradovic, Temple University, USA LOCAL CHAIR Ping Zhang, Ohio State University, USA Important Dates (tentative) =========================== Abstract Submission: October 4, 2019 11:59pm (US Eastern Time) Paper Submission: October 11, 2019 11:59pm (US Eastern Time) Workshop Proposals: October 4, 2019 11:59pm (US Eastern Time) Tutorial Proposals: October 4, 2019 11:59pm (US Eastern Time)

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ELIXIR-NL Innovation and SME Forum, 10-11 October 2019, Utrecht
by Celia van Gelder 25 Sep '19

25 Sep '19

ELIXIR Innovation & SME Forum: "distributed data analysis - the (health) data train" 10-11 October 2019, Utrecht - Register now! Are you a researcher or professional in the healthcare sector or in agrifood, biotech or nature preservation collaborating with colleagues outside your organisation? Are you facing challenges in working with data generated outside your own lab? Are you involved in making data management and data sharing more effective in your organisation? Or are you just interested to learn more about data-driven innovations in the life-science sector? Then please join us in the ELIXIR Innovation and SME Forum in Utrecht on 10-11 October with a focus on “distributed data analysis – the (health) data train” The <https://dtls.us3.list-manage.com/track/click?u=3cef2d6f6da8f8059e2288298&id…> Personal Health Train approach propagates not to physically share data but to make use of each others data through distributed data analysis. The Dutch government has endorsed this approach in December 2018 and is now preparing to implement this novel strategy in the Dutch health care information system. The ‘FAIR data train’ concept can be more broadly implemented also outside the health sector. A mixture of high-level keynote speakers and interactive sessions (such as Flash Talks for SMEs, Start-Ups and bioinformatics service providers) will give participants from academia, companies, policy makers and collaborators from the <https://dtls.us3.list-manage.com/track/click?u=3cef2d6f6da8f8059e2288298&id…> ELIXIR network a chance to learn more about distributed data analysis in the life sciences sectors. This event is a collaborative effort, organized by ELIXIR, ELIXIR Netherlands and DTL. We particularly invite start-ups, SMEs and research teams providing bioinformatics and data management services to sign up for a flash talk during the 1st day of the event! Check out the <https://dtls.us3.list-manage.com/track/click?u=3cef2d6f6da8f8059e2288298&id…> programme and <https://dtls.us3.list-manage.com/track/click?u=3cef2d6f6da8f8059e2288298&id…> register here. <https://dtls.us3.list-manage.com/track/click?u=3cef2d6f6da8f8059e2288298&id…> For further information please contact <mailto:femke.francissen@dtls.nl> Femke Francissen. If your organisation is a <https://dtls.us3.list-manage.com/track/click?u=3cef2d6f6da8f8059e2288298&id…> DTL Partner, you can announce your <https://dtls.us3.list-manage.com/track/click?u=3cef2d6f6da8f8059e2288298&id…> news, <https://dtls.us3.list-manage.com/track/click?u=3cef2d6f6da8f8059e2288298&id…> events, <https://dtls.us3.list-manage.com/track/click?u=3cef2d6f6da8f8059e2288298&id…> courses, and <https://dtls.us3.list-manage.com/track/click?u=3cef2d6f6da8f8059e2288298&id…> job vacancies on the DTL website. Please send these items to <mailto:communication@dtls.nl> communication(a)dtls.nl Copyright © *2017 Dutch Techcentre for Life Sciences, All rights reserved. <https://dtls.us3.list-manage.com/profile?u=3cef2d6f6da8f8059e2288298&id=d62…> update your preferences or <https://dtls.us3.list-manage.com/unsubscribe?u=3cef2d6f6da8f8059e2288298&id…> unsubscribe from this list. <https://dtls.us3.list-manage.com/track/open.php?u=3cef2d6f6da8f8059e2288298…>

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vacancies bio-informatics/systems biology at Flanders Marine Institute
by Michiel Vandegehuchte 24 Sep '19

24 Sep '19

Dear all Flanders Marine Institute (VLIZ) is recruiting two researchers in the area of bioinformatics and marine systems biology, one post-doc and one junior position: http://www.vliz.be/en/vacancy/2019-09-02-vliz-recruits-researcher-bioinform… http://www.vliz.be/en/vacancy/2019-09-02-vliz-recruits-researcher-molecular… Application deadline is Monday 30 September. Kind regards Michiel Vandegehuchte Research Director Vlaams Instituut voor de Zee vzw Flanders Marine Institute InnovOcean site, Wandelaarkaai 7 8400 Oostende, Belgium T +32-(0)59-34 14 96 M +32 (0)471-61 22 49 michiel.vandegehuchte(a)vliz.be www.vliz.be Save a tree ... please don't print this e-mail unless you really need to.

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Current vacancy for a food and nutrition data scientist/bioinformatician
by maria traka (QIB) 24 Sep '19

24 Sep '19

Dear BBC members, Please see below a current vacancy in our group that I would really appreciate if you could circulate within your mailing list. I would encourage any interested persons to contact me to find out a bit more about the role. Kind regards, Maria Traka We are looking for a highly motivated individual to drive food data analytics within the Food Databanks National Capability<https://fdnc.quadram.ac.uk/> at the Quadram Institute (QI), with an interest in embracing cutting edge computational tools in the study of food composition, food intake and wider nutritional research. https://quadram.ac.uk/vacancies/research-scientist-food-and-nutrition-data-… MARIA TRAKA, PhD, MSc Deputy Head of Food Databanks National Capability (FDNC) Group Leader in Food and Health https://fdnc.quadram.ac.uk/ Quadram Institute Bioscience, Norwich Research Park, NR4 7UQ T: +44 (0)1603 255000 D: +44 (0)1603 255194 maria.traka(a)quadram.ac.uk<mailto:maria.traka@quadram.ac.uk> WE ARE CURRENTLY RECRUITING FOR A FOOD DATA SCIENTIST: https://quadram.ac.uk/vacancies/research-scientist-food-and-nutrition-data-… www.quadram.ac.uk<http://www.quadram.ac.uk/>[/var/folders/zx/8kr8qmqd4z56xtlcxplkkvz5zn2b12/T/com.microsoft.Outlook/WebArchiveCopyPasteTempFiles/cidimage001.png(a)01D55CFE.FA0C0D00]

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Job advert for a bioinformatician at GSK Vaccines Rixensart
by Benoit Dessailly 24 Sep '19

24 Sep '19

We are hiring a bioinformatician at GSK Vaccines, Rixensart. Please share, or even better, apply! 😊 Advert below https://jobs.gsk.com/fr-be/jobs/POSTING-3-17913?lang=en-us&previousLocale=f… https://www.linkedin.com/jobs/view/1510577482/ Regards Benoit GSK monitors email communications sent to and from GSK in order to protect GSK, our employees, customers, suppliers and business partners, from cyber threats and loss of GSK Information. GSK monitoring is conducted with appropriate confidentiality controls and in accordance with local laws and after appropriate consultation.

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