- BBClist - maillist.psb.ugent.be

PhD position in population genetics in Coffea at ILVO (Belgium)
by Tom Ruttink 15 Jul '19

15 Jul '19

Dear, We currently have a PhD position in population genetics in Coffea open and are looking for suitable candidates. Could you please spread the announcement in your network? more information can be found on our website: https://www.ilvo.vlaanderen.be/language/en-US/EN/Work-at-ILVO/PhD-coffee.as… thank you in advance, kind regards, Tom Ruttink Senior Scientist Genomics ILVO Instituut voor Landbouw-, Visserij- en Voedingsonderzoek Flanders research Institute for Agriculture, Fisheries and Food Eenheid Plant | Plant Sciences Unit Caritasstraat 39 9090 Melle (Belgium) T +32 9 272 28 78 tom.ruttink(a)ilvo.vlaanderen.be<mailto:tom.ruttink@ilvo.vlaanderen.be> www.ilvo.vlaanderen.be<http://www.ilvo.vlaanderen.be/> www.ilvogenomics.be<http://www.ilvogenomics.be/> [http://intranet.ilvo/Portals/0/images/Communicatie/Huisstijl/Twitter.jpg]<https://twitter.com/ILVOvlaanderen> [http://intranet.ilvo/Portals/0/images/Communicatie/Huisstijl/FB.jpg?ver=201…] <http://www.facebook.com/instituutvoorlandbouwenvisserijonderzoek> [http://intranet.ilvo/Portals/0/images/Communicatie/Huisstijl/LinkedIn.jpg] <https://www.linkedin.com/company/ilvo> /////////////////////////////////////////////// [http://intranet.ilvo/Portals/0/images/Communicatie/Huisstijl/Leeuw.jpg]

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Okinawa workshop on Qualitative Computational Modeling for Biological Networks
by Yves Moreau 12 Jul '19

12 Jul '19

Dear colleagues, It's our pleasure to invite you to Okinawa for a workshop on Qualitative computational modeling for biological networks. The workshop will be held on October 31st, as a satellite to the 2019 ICSB conference: https://www2.aeplan.co.jp/icsb2019/tutorials_satellite.html <https://www2.aeplan.co.jp/icsb2019/tutorials_satellite.html> The program will cover: • Boolean and logical modeling • Petri nets • molecular interaction maps • community standards development and interoperability • model composition and modularity • analytical methods • network inference • model curation and annotation And we can already announce invited talks by: • Marcelle Kaufman (Free University of Brussels, Belgium) • Edda Klipp (Humboldt University, Berlin, Germany) • Takeyuki Tamura (Institute for Chemical Research, Kyoto University, Kyoto, Japan) Applications are now open for oral presentation based on abstract submission. Call for oral presentations: https://www.easychair.org/cfp/QualMod2019 <https://www.easychair.org/cfp/QualMod2019> Submission link: https://easychair.org/my/conference?conf=qualmod2019 <https://easychair.org/my/conference?conf=qualmod2019> Submissions will be selected after review by the workshop's scientific commitee. Scientific committee: • Tatsuya Akutsu (Institute for Chemical Research, Kyoto University, Kyoto, Japan) • Réka Albert (Pennsylvania State University, Pennsylvania) • Claudine Chaouiya (Aix-Marseille University, France / Gulbenkian Institute, Portugal) • Thomas Helikar (Department of Biochemistry, University of Nebraska, USA) • Ina Koch (Institute of Computer Science, Goethe University, Frankfurt, Germany) • Reinhard Laubenbacher (Jackson Laboratory / UConn School of Medicine, Connecticut) • Hiroshi Matsuno (Yamaguchi University, Japan) • Atsushi Mochizuki (Kyoto University, Japan) • Heike Siebert (Berlin Free University, Germany) Key dates: • Submission deadline: July 13th • Notification of Acceptance: July. 31st Workshop registration: As a satellite to ICSB we don't have a separate registration process. All participants must be registered to the main event. • Early bird registration until June 28th. • Late registration till September 20th https://www2.aeplan.co.jp/icsb2019/registration.html <https://www2.aeplan.co.jp/icsb2019/registration.html> Looking forward to meeting you in Okinawa, Adrien Fauré & Denis Thieffry. -------------------------------------------------- Prof. Denis THIEFFRY Ecole Normale Supérieure - Département de Biologie IBENS - UMR ENS - CNRS 8197 - INSERM 1024 46 rue d'Ulm, 75230 Paris Cedex 05, FRANCE

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Barcelona Supercomputing Center: PhD student in Computer Science and Bioinformatics (R1)
by BSC RRHH 11 Jul '19

11 Jul '19

PhD student in Computer Science and Bioinformatics (R1) Reference: 194_19_LS_ICB_R1 *Context And Mission* Professor Nataša Pržulj is looking for several PhD students to work in machine learning and network science. They will be developing new algorithms for computationally hard problems and applying them to analyzing large-scale molecular and patient data to aid drug discovery and personalizing treatment. The successful candidates will work on the prestigious ERC Consolidator grant of Prof. Pržulj. The successful candidates will complete a PhD in Computer Science, which will address developing and applying sophisticated machine learning and network science models and algorithms. The algorithms will be carefully tuned to extract relevant biological and medical knowledge from systems-level real-world molecular and medical data. The aim is to utilize them to understand the structure of the data that would enable mining the data for new biological and medical insight that would further lead to improving diagnostics, discovering new biomarkers, improving patient stratification and treatment, personalizing treatment and facilitate rational drug development. The successful candidates will join a dynamic research group of Prof. Przulj within BSC. The students will work in a highly sophisticated HPC environment, will have access to systems and computational infrastructures, and will establish collaborations with experts in different areas. *Key Duties* * Complete a PhD in computational biology * Collaborate with various research groups across Europe and elsewhere MORE INFO & APPLY HERE: https://www.bsc.es/join-us/fellowships/19419lsicbr1 http://bsc.es/disclaimer

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VIB: Intermediate Python course 2-3 September 2019 - register at https://bit.ly/2LGkQEd !
by Alexander Botzki 09 Jul '19

09 Jul '19

Dear all, Registration is open at https://bit.ly/2LGkQEd for the intermediate #python course on 2 and 3 September 2019 - learn to use @matplotlib @biopython and pandas using @ProjectJupyter notebooks Best regards, Alex 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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3 vacancies at UMCG
by Patrick Deelen 09 Jul '19

09 Jul '19

4y postdoc semantic web and federated 'big' data science in biomedicine https://www.umcg.nl/EN/corporate/careers/Careers/Medicalscientific_staff/Pa… Javascript Frontend Web App Developer voor Research Data & Analysis Tools https://www.umcg.nl/NL/UMCG/Werken_in_het_UMCG/Vacatures/Externe_vacatures/… Technisch datamanager research data voor genomics & health https://www.umcg.nl/NL/UMCG/Werken_in_het_UMCG/Vacatures/Externe_vacatures/…

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ELIXIR Belgium All Hands meeting - updated program - registration open
by Kim DE RUYCK 09 Jul '19

09 Jul '19

ELIXIR Belgium All Hands meeting - updated program - register now Dear, We are pleased to invite you to the first ELIXIR Belgium All Hands meeting which takes place on 16 September 2019 in Brussels . In this event, we bring together all stakeholders of ELIXIR Belgium, showcase our achievements and plans for the future, as well as provide networking opportunities to meet the people involved. We will touch upon how data management can support your research and drive innovation in data analysis. The session on Human Data will cover collaborative platforms in Belgium and access to human data across Europe . We will also showcase increased collaboration between research infrastructures in Flanders. The day will be closed with a keynote on Human Cell Atlas . Check the [ https://elixir-belgium.us14.list-manage.com/track/click?u=d1bc1ab5d122d661a… | updated program ] and join us in Brussels! This event is open to all scientists from academia, research institutes and industry in life-sciences. We specifically also welcome members from other research infrastructures and policy makers. This is a free event but registration is mandatory. [ https://elixir-belgium.us14.list-manage.com/track/click?u=d1bc1ab5d122d661a… | Program & 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 This email was sent to [ mailto:kim.deruyck@psb.vib-ugent.be | kim.deruyck(a)psb.vib-ugent.be ] [ https://elixir-belgium.us14.list-manage.com/about?u=d1bc1ab5d122d661a68f529… | why did I get this? ] [ https://elixir-belgium.us14.list-manage.com/unsubscribe?u=d1bc1ab5d122d661a… | unsubscribe from this list ] [ https://elixir-belgium.us14.list-manage.com/profile?u=d1bc1ab5d122d661a68f5… | update subscription preferences ] ELIXIR Belgium · Technologiepark 927 · Ghent 9052 · Belgium [ http://www.mailchimp.com/monkey-rewards/?utm_source=freemium_newsletter&utm… ]

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Conference - Genome Science 2019 - 3rd to 5th September EDINBURGH
by WATSON Mick 09 Jul '19

09 Jul '19

Dear All Genome Science is a conference which is held annually in the UK, covers all aspects of genomics and sequencing technologies, and will be held this year in Edinburgh 3rd to 5th September http://genomescience.co.uk/ We have four incredible keynote speakers: * Dr Sarah Teichmann, Wellcome Trust Sanger Institute - Immunogenomics one cell at a time * Professor Wendy Bickmore, Director of the MRC Human Genetics Unit - Understanding function in the non-coding genome * Professor Jane Carlton, NYU Center for Genomics and Systems Biology - Using genomics to understand the biology and evolution of parasites * Dr Kirsten Bos, Max-Planck-Institut für Menschheitsgeschichte - Genomic reconstructions of ancient pathogens Check out our exciting programme here: http://genomescience.co.uk/programme/ Our flagship "Evolving technologies" session will include talks on all of the major sequencing technologies: Illumina, BGI, Oxford Nanopore and PacBio; as well as a number of exciting talks about innovative genomics technologies. New sessions this year include "Single cell genomics" and "Genome Engineering" Register here: http://genomescience.co.uk/register/ Abstract deadline is 15th July! - http://genomescience.co.uk/abstracts/ Please also sign up for the conference dinner, where Oxford Nanopore will give a live demo of their MinION mobile sequencing device; http://genomescience.co.uk/venue/ Many thanks and I look forward to seeing you there! Mick Watson (on behalf of the organising committee) The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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PhD/Postdoc vacancy: Development of deep learning algorithms for the identification of pathogenic species from single-cell MALDI-TOF MS spectra
by Willem Waegeman 05 Jul '19

05 Jul '19

PhD/Postdoc vacancy: Development of deep learning algorithms for the identification of pathogenic species from single-cell MALDI-TOF MS spectra --- Duration of studentship: initially one year, extendable in case of a positive evaluation Start date: flexible between October 2019 and January 2020 Application closing date: August 15th (will be extended if no suitable candidate is found). Apply as soon as possible to avoid disappointment! --- Project description: Matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF-MS) is a well-known technology, widely used in species identification. Specifically, MALDI-TOF-MS is applied on samples that usually include bacterial cells, generating representative spectra for the various bacteria. In traditional MALDI-TOF MS systems, amplification of the bacterial load is performed by a culturing phase. In this project we will apply MALDI-TOF MS to individual bacterial cells, circumventing the need for culturing and isolation, accelerating the whole process. To this end, a large dataset with more than 50,000 spectra is collected by the company BioSparQ. In the next step we intend to develop novel machine learning algorithms to analyze this data and perform single-cell identification. Due to the large size of the training dataset and the complexity of detecting patterns in MALDI-TOF MS data, we believe that deep learning techniques will be particularly useful in this context. Background information: The vacancy is available as a joint initiative between the research unit KERMIT of Ghent University (Belgium),under supervision of Prof. Willem Waegeman, and the company BioSparQ (The Netherlands), under supervision of dr. René Parchen. Both teams have already a collaboration. KERMIT (acronym for Knowledge Extraction and Representation Management by means of Intelligent techniques) is a young interdisciplinary team of mathematicians, engineers and computer scientists, and itdraws upon intelligent techniques resulting from the cross-fertilization between the fields ofcomputational intelligenceandoperations research. The main focus is on mathematical and computational aspects of relational structures as knowledge instruments, with emphasis on the fields of fuzzy set theory and machine learning.KERMITserves as an attraction pole for applications in theapplied biological sciences, and serves colleagues in hydrology, ecology, bacterial taxonomy, genome analysis, integrated water management, geographical information systems, forest management, metabolic engineering, soil science, bioinformatics, systems biology, etc. BiosparQ B.V. is a privately-held in vitro diagnostics company dedicated to provide healthcare professionals with a unique solution for rapid diagnostics of infectious diseases that improves patient outcomes, lowers healthcare costs and helps turn back. BiosparQ has focused its efforts on research into and the development of the Cirrus D20 medical diagnostic platform, based on proprietary DigiTOF^technology. This technology enables direct analysis of patient samples using a Single-cell MALDI-TOF approach. The ideal candidate for the position has the following profile: ·An MSc or PhD degree in (Bio-)Engineering, Bio-informatics, Computer Science, Mathematics,Statistics,Physics, or equivalent – candidates from outside Belgium are welcome to apply. ·An interest for fundamental machine learning research, as well as practical applications in microbiology. ·In-depth experience with at least one programming language (Matlab, R, Python, Java, etc.) ·Good knowledge of deep learning methods is an asset. ·Fluent in English (speaking and writing, as demonstrated by personal texts). ·Knowledge of Dutch is an asset, but not a must. ·Team player with good communication skills. ·This position is available on a PhD and postdoc level, depending on the applications we receive. ·The person hired on this project is expected to travel between Ghent (Belgium) and Leiden (The Netherlands) on a regular basis. How to apply Send your c.v., a motivation letter, a copy of your MSc.- or PhD-thesis and/or any relevant publications to Ruth Van Den Driessche (ruth.vandendriessche(a)ugent.be <mailto:ruth.vandendriessche@ugent.be>). -- Prof. dr. Willem Waegeman Research Unit Knowledge-Based Systems (KERMIT) Department of Data Analysis and Mathematical Modelling Coupure links 653 9000 Ghent, Belgium Phone: + 32 9 264 92 00 Skype: willem.waegeman www.kermit.ugent.be users.ugent.be/~wwaegemn

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PhD Position in Precision Health
by Gokhan Ertaylan 03 Jul '19

03 Jul '19

Dear All, We are looking for a promising Ph.D. candidate at our lab in VITO Health, Mol / Belgium. The aim of this project is to develop new approaches for time series data integration and visualization of high-dimensional cross -omics datasets generated within a unique healthy cohort. More information about the position and application procedure can be found on the following link <https://vito.be/en/jobs/phd-position-xomics-data-analyses-and-integration-p…>. Deadline for applications: 23/08/2019 Best Wishes, Gökhan Ertaylan

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PhD position @ BIOBIX, Ghent University
by Tim De Meyer 03 Jul '19

03 Jul '19

Dear all, We have a vacancy for a doctoral student at our lab (BIOBIX, Dept. Data Analysis and Mathematical Modelling, Faculty of Bioscience Engineering, Ghent University). We are looking for candidates with a strong research interest in omics data analysis and statistical modelling. The aim of the project is to innovate the study of allele-specific expression, which is of major relevance in both health and disease (see attach for more details). Note that students that will obtain their master degree before the start of the project (October 1st) can also apply. Deadline for applications: 15/08/2019. Best regards, Tim De Meyer

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