September 2019 - BBClist - maillist.psb.ugent.be

SDM 2020 Call for Papers
by Alfredo Cuzzocrea 18 Sep '19

18 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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Re: [BBC] [Training-coordinators] ELIXIR Survey: Identifying gaps in current training
by Alexander Botzki 18 Sep '19

18 Sep '19

Dear All, I would like to forward you this question of the ELIXIR Training platform and ask if you could fill in the survey about training sessions for the future. Thank you very much for your time to provide your ideas on the bioinformatics training programme of the future. Best regards, Alex From: Training-coordinators <training-coordinators-bounces(a)elixir-europe.org> On Behalf Of Fotis E. Psomopoulos Sent: 18 September 2019 12:23 To: training-coordinators(a)elixir-europe.org Subject: [Training-coordinators] ELIXIR Survey: Identifying gaps in current training [apologies for multiple postings] Dear all, The ELIXIR Training Platform surveyed the training needs of its scientific communities in 2013 and 2016, and consequently took measures to fill the gaps identified with appropriate training. In order to identify potential gaps in current training in Life Sciences across Europe, we would like your input as well. The survey [https://forms.gle/rtMoWFtnmC5D4jPF6] should take no more than 5-10 minutes of your time to complete; questions with an asterisk require a response and it would be immensely helpful if you could spare the time to respond fully to all questions. Participants who share their contact details with us will gain early access to the results and will play a vital role in helping us to optimize the training programme. We value your contribution and look forward to sharing the outcomes with you. Please, feel free to forward this email to whomever you think is relevant. Kind regards, Fotis E. Psomopoulos (ELIXIR-GR), Brane L. Leskosek (ELIXIR-SI), Jessica Lindvall (ELIXIR-SE), Patricia Palagi (ELXIR-CH), Celia van Gelder (ELIXIR-NL) and Pascal Kahlem (TrP) on behalf of the ELIXIR Training Platform -- Fotis E. Psomopoulos Assistant Research Professor INAB - Institute of Applied Biosciences CERTH - Center for Research and Technology Hellas Thermi 57001, Greece Phone: +30 2310 498 478 Fax : +30 2310 498 270 Email: fpsom(a)certh.gr<mailto:fpsom@certh.gr> Site : https://fpsom.github.io<https://fpsom.github.io/> ORCID: 0000-0002-0222-4273 While I may be sending this email outside my normal office hours, I have no expectation to receive a reply outside yours. Η επικοινωνία αυτή είναι εμπιστευτική και ενδεχομένως να προστατεύεται από νομικά πλαίσια. Εάν λάβατε αυτό το e-mail, ενώ δεν προορίζεται για εσάς, σας ενημερώνουμε ότι απαγορεύεται οποιαδήποτε διανομή, αντιγραφή ή χρήση της επικοινωνίας ή/ και των πληροφοριών που περιέχονται σε αυτό. Σας παρακαλούμε να ενημερώσετε κατάλληλα τον αποστολέα και να σβήσετε ή να καταστρέψετε τυχόν αντίγραφά της. Οι επικοινωνίες μέσω του Διαδικτύου δεν είναι ασφαλείς και για τον λόγο αυτό το ΙΝ.Ε.Β./ΕΚΕΤΑ δεν αποδέχεται νομική ευθύνη για τα περιεχόμενα του παρόντος μηνύματος και για οποιαδήποτε ζημιά προκληθεί από ιούς που είναι δυνατόν να εισαγάγει. This communication is confidential and It may also be protected by legal rules. If you are not an intended recipient please note that any form of distribution, copying or use of this communication or the information in it, is prohibited. Please inform the sender appropriately and delete or destroy any copies of it from your system. Internet communications are not secure and therefore INAB/CERTH does not accept legal responsibility for the contents of this message and for any damage whatsoever that is caused by viruses being passed.

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Post-doc position 'Machine Learning for network-based analysis' (UGent)
by Kathleen Marchal 13 Sep '19

13 Sep '19

*Postdoc position Machine Learning for network-based analysis* *Job description*: The DBN group headed by K. Marchal has a vacancy for a postdoctoral researcher interested in a combination of research and teaching (3 year Dr Assistant position). The research will focus on the development and application of systems genetics approaches to identify driver pathways underlying adaptive clonal phenotypes. Innovative methods based on state-of-the-art datamining techniques need to be developed in order to integrate genomic information derived from cohorts of samples with phenotypic information. Methods will be applied to study the evolvability of network rewiring and interclonal interactions during adaptive responses in cancer and/or microbial systems. Next to research also an active involvement in teaching and student supervision is required. *Context*: The DBN group headed by K. Marchal is located at the engineering faculty of Ghent University (IDLab/IMEC). The group’ s research focus is on bioinformatics method development. The group is specialized in combining advanced datamining techniques with biological principles (http://bioinformatics.psb.ugent.be/DBN/) and has major expertise in network inference and network-based data-integration. *Key words:*data sciences, machine learning, cancer genomics, clonal systems *Expertise* •You hold a PhD degree in Sciences; in Bioinformatics, in Applied Biological Sciences (Bioengineering); in Engineering •Strong interest in research and teachingbioinfomatics related courses •Strong interest in method development and data mining •Strong interest in interdisciplinary research •Knowledge in molecular biology or genomics is a plus •Proficiency in programming languages such as Java, Perl or Python, as well as Linux systems. •Fluency in spoken and written English is a strong requirement *For further information:* contact kathleen.marchal(a)ugent.be <mailto:kathleen.marchal@ugent.be> Application deadline: November 26 Application through the UGent site is mandatory: https://www.ugent.be/en/work/vacancies/assisting/applyonline-aap.htm -- Prof. Kathleen Marchal Dept. of Plant Biotechnology and Bioinformatics, Ghent University Dept. of Information Technology, IDLab, imec, Dept. of Genetics, University of Pretoria, South Africa http://bioinformatics.psb.ugent.be/DBN iGent Toren, Technologiepark 126, 9052 Gent, Belgium

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Workshop on Programming For Evolutionary Biology, Berlin (02-18 March 2020)
by Katja Nowick 10 Sep '19

10 Sep '19

Course on Programming for Evolutionary Biology When: March 2nd - March 18th 2020 Location: Berlin, Germany Application deadline: October 25th 2019 Detailed information about the course content and how to apply: http://evop.bioinf.uni-leipzig.de/ In this intensive 17 days course, students will learn how to survive in a Linux environment, get hands-on experience in two widely used programming languages (Python and R), and statistical data analysis. The classes will be given by experts in the field and consist of lectures and exercises with the computer. The aim of the course is to provide the students with the necessary background and skills to perform computational analyses with a focus on solving research questions related to genomics and evolution. The philosophy of the course will be “learning by doing”, which means that the computational skills will be taught using examples and real data from evolutionary biology for the exercises. During the course, students will also propose projects of their own interest and perform them as final projects in small groups under the supervision of a teaching assistant. This summer school is open for students from all countries and targeted toward PhD students and postdocs of evolutionary biology or related research fields with no or little programming experience who want to become proficient in computational evolutionary biology in a couple of weeks. The course takes place at the Free University of Berlin. -- Dr. Katja Nowick Professorin für Humanbiologie Freie Universität Berlin Institut für Zoologie Königin-Luise-Straße 1-3 14195 Berlin Phone: +49 30 83863761

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RNA-seq workshop for beginners: from sequences to visualization using Galaxy and R
by Mateusz Kuzak 10 Sep '19

10 Sep '19

Dear all, the Gallantries team (Freiburg Galaxy Team, DTL, the Netherlands eScience Center, and Erasmus MC in the Netherlands, and INAB CERTH in Greece) offers a Galaxy workshop on RNA-seq data analysis on October 7-9th. The workshop will cover: • Galaxy introduction • Introduction to High-Throughput Sequencing and Quality Control • Reference-based RNA-seq data analysis • Basics of R programming • Post-processing of RNA-seq data using R and Rstudio It will be delivered simultaneously at 3 locations across Europe (Rotterdam, NL; Thessaloniki, GR and Tartu, EE). More information & registration: https://galaxy-carpentries.github.io/gallantries/event/2019-08-27-second-ga… Please, feel free to forward this email to whomever you think is relevant. kind regards, Mateusz

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RECOMB'CG 2019 - CfParticipations - program online - early registration ending soon
by Mathias Weller 06 Sep '19

06 Sep '19

Dear colleagues, The 17th RECOMB Satellite Conference on Comparative Genomics, RECOMB-CG 2019 will be held in Montpellier, France - October 1-4, 2019. **PROGRAM** Preliminary program is available online: <https://recombcg2019.bitbucket.io/program.html> **PARTICIPATION** Registration is open, please check <https://recombcg2019.bitbucket.io> for details. The early registration deadline is SEPTEMBER 9, 2019. **KEYNOTE SPEAKERS** Alessandra Carbone <http://www.ihes.fr/~carbone/> (CNRS - Sorbonne Université) Rute A. R. da Fonseca <https://rutefonseca.wixsite.com/bioinformatics> (University of Copenhagen) Purificación López García <http://www.singek.eu/network/supervisors/purificacion-lopez-garcia/> (CNRS - University Paris-Sud/Paris-Saclay) Romain Koszul <https://research.pasteur.fr/en/member/romain-koszul/> (Insitut Pasteur) Benoît Nabholz <https://sites.google.com/site/benoitnabholz/> (Université de Montpellier) **SCOPE** The RECOMB-CG satellite conference brings together leading researchers in the mathematical, computational and life sciences to discuss cutting edge research in comparative genomics, with an emphasis on computational approaches and novel experimental results. The program includes both invited speakers, contributed talks and poster sessions. Contributions on any theoretical and/or empirical approach to genome-wide comparison are welcome. Topics of interest include genome evolution, population genomics, genome rearrangements, genomic variation, diversity and dynamics, phylogenomics, comparative tools for genome assembly, comparison of functional networks, gene identification or annotation, cancer evolutionary genomics, comparative epigenomics, paleogenomics, epidemiology and related areas. **COMMITTEES** Steering Committee * *Marília Braga * (Bielefeld University) * *Dannie Durand * (Carnegie Mellon University) * *Jens Lagergren * (Stockholm University) * *Aoife McLysaght * (Trinity College Dublin) * *Luay Nakhleh * (Rice University) * *David Sankoff * (University of Ottawa) Organizing Committee * *Severine Berard* (ISEM, University of Montpellier) * *Annie Chateau* (LIRMM, University of Montpellier) * *Krister Swenson* (CNRS, LIRMM, University of Montpellier) * *Mathias Weller* (CNRS, LIGM, University of Eastern Paris - Marne-la-Vallée) * *Virginie Feche* (LIRMM) * *Megane Miquel* (LIRMM) Program Committee Chaired by *Krister Swenson* (CNRS, LIRMM, University of Montpellier), *Annie Chateau* (LIRMM, University of Montpellier), *Severine Berard* (ISEM, University of Montpellier), and *Mathias Weller* (CNRS, LIGM, University of Eastern Paris - Marne-la-Vallée) * *Max Alekseyev * (George Washington University) * *Nikita Alexeev * (ITMO University) * *Lars Arvestad * (Stockholm University) * *Anne Bergeron * (Universite du Quebec a Montreal) * *Marilia Braga * (Bielefeld University) * *Alessandra Carbone * (Sorbonne Université) * *Cedric Chauve * (Simon Fraser University) * *Rayan Chikhi * (Institut Pasteur) * *Daniel Doerr * (Bielefeld University) * *Ingo Ebersberger * (Goethe University Frankfurt) * *Nadia El-Mabrouk * (University of Montreal) * *Oliver Eulenstein * (Iowa State University) * *Guillaume Fertin * (LS2N, Université de Nantes) * *Pawel Gorecki * (University of Warsaw) * *Michael Hallett * (Concordia University) * *Fábio Henrique Viduani Martinez * (Universidade Federal de Mato Grosso do Sul) * *Katharina Jahn * (ETH Zurich) * *Asif Javed * (Genome Institute of Singapore) * *Manuel Lafond * (Université de Sherbrooke) * *Yu Lin * (Australian National University) * *Simone Linz * (The University of Auckland) * *Kevin Liu * (Michigan State University) * *István Miklós * (Rényi Institute, Hungarian Academy of Sciences) * *Bernard Moret * (Ecole Polytechnique Fédérale de Lausanne) * *Luay Nakhleh * (Rice University) * *Aïda Ouangraou * (University of Sherbrooke) * *Fabio Pardi * (CNRS, LIRMM, Université Montpellier) * *Teresa Przytycka * (NCBI) * *Vaibhav Rajan * (National University of Singapore) * *Marie-France Sagot * (INRIA, LBBE, Lyon) * *Michael Sammeth * (Federal University of Rio de Janeiro) * *Celine Scornavacca * (CNRS, ISE-M, Université Montpellier) * *Mingfu Shao * (The Pennsylvania State University) * *Jens Stoye * (Bielefeld University) * *Jijun Tang * (University of South Carolina) * *Eric Tannier * (INRIA, LBBE, Lyon) * *Glenn Tesler * (University of California San Diego) * *Olivier Tremblay-Savard * (University of Manitoba) * *Tamir Tuller * (Tel Aviv University) * *Jean-Stéphane Varré * (CRIStAL, Université Lille 1) * *Tandy Warnow * (University of Illinois at Urbana-Champaign) * *Sophia Yancopoulos * (The Feinstein Institutes for Medical Research, New York) * *Louxin Zhang * (National University of Singapore) * *Xiuwei Zhang * (University of California, Berkeley) * *Jie Zheng * (ShanghaiTech University) We are looking forward to seeing you in Montpellier! The recomb'cg 2019 organizing committee

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ELIXIR Belgium All Hands meeting 2019 - last days to register
by Frederik Coppens 03 Sep '19

03 Sep '19

ELIXIR Belgium All Hands meeting 2019 - last days to register Dear You can still join us at the first ELIXIR Belgium All Hands meeting which takes place on 16 September 2019 in Brussels (KVAB - Royal Flemish Academy of Belgium for Science and the Arts). This event brings together all stakeholders of ELIXIR Belgium, showcases our achievements and plans for the future, as well as provides networking opportunities to meet the people involved. Registration ends in a few days! [ https://elixir-belgium.us14.list-manage.com/track/click?u=d1bc1ab5d122d661a… | Registration ] [ https://elixir-belgium.us14.list-manage.com/track/click?u=d1bc1ab5d122d661a… ] [ https://elixir-belgium.us14.list-manage.com/track/click?u=d1bc1ab5d122d661a… | ELIXIRnodeBE ] [ https://elixir-belgium.us14.list-manage.com/track/click?u=d1bc1ab5d122d661a… ] [ https://elixir-belgium.us14.list-manage.com/track/click?u=d1bc1ab5d122d661a… | www.elixir-belgium.org ] Copyright © 2019 ELIXIR Belgium, All rights reserved. Our mailing address is: ELIXIR Belgium Technologiepark 71 Ghent 9052 Belgium

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