- BBClist - maillist.psb.ugent.be

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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Barcelona Supercomputing Center: Post-doc Researchers in Computer Science and Bioinformatics (R2)
by BSC RRHH 28 Jun '19

28 Jun '19

Post-doc Researchers in Computer Science and Bioinformatics (R2) *Reference:*180_19_LS_ICB_R2 *Job title:*Post-doc Researchers in Computer Science and Bioinformatics (R2) *About BSC* The Barcelona Supercomputing Center - Centro Nacional de Supercomputación (BSC-CNS) is the leading supercomputing center in Spain. It houses MareNostrum, one of the most powerful supercomputers in Europe, and is a hosting member of the PRACE European distributed supercomputing infrastructure. The mission of BSC is to research, develop and manage information technologies in order to facilitate scientific progress. BSC combines HPC service provision and R&D into both computer and computational science (life, earth and engineering sciences) under one roof, and currently has over 600 staff from 49 countries. Look at the BSC experience: BSC-CNS YouTube Channel <https://www.youtube.com/channel/UC-jQw5yIjnUTRAg4DwOY4aA> Let's stay connected with BSC Folks! <https://www.youtube.com/watch?v=VRkEii7OzRE> *Context And Mission* Professor Nataša Pržulj is looking for several post-docs 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 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* * Conduct high-quality research * Publish in high impact journals and conferences * Present research at national and international conferences and meetings * Collaborate with various research groups across Europe and elsewhere * Help supervise PhD and MSc students * Participate in grant writing and organizational activities * Participate in educational and outreach activities MORE INFO & APPLY HERE: https://www.bsc.es/join-us/job-opportunities/18019lsicbr2 http://bsc.es/disclaimer

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Assistant/associate professor position at Wageningen University
by Ridder, Dick de 28 Jun '19

28 Jun '19

Position: assistant/associate professor in bioinformatics or computational biology The Wageningen Bioinformatics Group has a vacancy for an assistant / associate professor in bioinformatics or computational biology. As a candidate, you have a good scientific track record and a drive to develop your own research line. You can attract funding to build and support a group and you are able to set up a strong academic and industrial network. Your research should connect method development to application, be relevant for plant, animal or microbial biotechnology, and complement the current expertise in the group. Relevant areas include (but are not limited to) metagenomics, metabolomics, proteomics and phenomics. You strive to become an enthusiastic and knowledgeable teacher and supervisor in bioinformatics. Finally, you are a collaborative team member, contributing to the organization of the group, the university and the scientific community at large. Wageningen University & Research focuses on food, health and the living environment and is one of the leading organisations in this domain worldwide. The Bioinformatics Group provides a collaborative working environment with young, dedicated staff with expertise in a number of areas, particularly in genomics. Our group is strongly embedded in the Plant Sciences Group and collaborates intensively with Wageningen Research. We maintain extensive computational resources and have the opportunity to teach (advanced) MSc courses and supervise thesis projects in the Master’s Programme in Bioinformatics. We offer a meaningful job with a competitive salary (depending on your experience) and good benefits. The Wageningen tenure-track system provides an excellent opportunity and support for academic development. For more information and an online application form (deadline September 8, 2019), please see https://tinyurl.com/y3ucfwys or contact Dick de Ridder (dick.deridder(a)wur.nl)

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Barcelona Supercomputing Center: Technician at Text Mining Unit (RE2)
by BSC RRHH 28 Jun '19

28 Jun '19

Technician at Text Mining Unit (RE2) Reference: 179_19_LS_TM_RE2 *Context And Mission* The Text Mining Unit of the BSC-CNS (TeMU-BSC) is funded through the Plan de Impulso de las Tecnologías del Lenguaje de la Agenda Digital, by the Secretary of State of Telecommunications and the Information. It is the first publicly funded text mining unit in Spain and has the aim to promote the development of natural language processing and machine translation resources for Spanish and other co-official languages in the area of biomedicine. We search for a technician who will be responsible of the integration of data, applications and search tools, and the maintenance of the servers and other infrastructure of the unit. *Key Duties* * Administration task on servers, operating systems and applications. * Installation of new releases of software/server patches. * Integration of NLP components using IUMA, GATE, OpenNLP, etc. * Development of mechanisms for the integration of resources and a data warehouse. MORE INFO & APPLY VIA: https://www.bsc.es/join-us/job-opportunities/17919lstmre2 http://bsc.es/disclaimer

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Tenure Track Assistant Professor Artificial Intelligence for Systems Medicine @TUEindhoven
by Riel, N.A.W. van 27 Jun '19

27 Jun '19

We are hiring: Tenure Track Assistant Professor Artificial Intelligence for Systems Medicine @TUEindhoven: https://jobs.tue.nl/en/vacancy/assistant-professor-artificial-intelligence-… . We seek to appoint a scientist/engineer who is passionate about research as well as teaching. We are looking for a creative and pro-active team player to establish a complementary research line. We work on biomedical systems biology, which ranges from fundamental science to clinical applications. Existing research lines focus on oncology and metabolic disease. We search for candidates with a PhD degree in computational biology, biomedical signal processing, or other relevant discipline to develop a research line on 'Artificial Intelligence for Systems Medicine'. In this Tenure Track position model-based data analysis and signal processing will be developed, combining computer simulation models of the human physiological system, stochastic models of uncertainties and variation in the process, and (biosensor) data, for application in systems medicine. Artificial Intelligence (AI) technology is applied for real-time learning and adaptation of the models, to accurately estimate the current state of the system and to predict its future trajectory. In addition to execution of research and education the candidate is expected to actively setup collaborations and secure research funding. The candidate will play an active role in the new TU/e Artificial Intelligence institute. Kind regards, Prof. dr. ir. Natal van Riel

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job opening Genomics Bioinformatician at BRIGHTcore (the VUB-ULB genomics platform) in Brussels
by Catharina Olsen 27 Jun '19

27 Jun '19

Dear all, We are looking for a Genomics Bioinformatician at BRIGHTcore. Details about the position: https://www.uzbrusselwerkt.be/en/vacatures/viewjob/174860 Best regards, Catharina

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JOB: PhD position in the Thomas More University of Applied Sciences and Hasselt University
by Ziv SHKEDY 27 Jun '19

27 Jun '19

Dear All, As a part of a H2020 European project “NanoInformaTIX” ( http://www.nanoinformatix.eu/) we open a PhD position in Biostatistics/Data science in the Thomas More University of Applied Sciences - Radius group (http://radius.thomasmore.be) and the center of statistics (CenStat), Hasselt University (https://www.uhasselt.be/censtat) The 4 years research project will be focused on nanoparticle toxicity modelling. The PhD candidate will be located in the Thomas More Radius group (3-4 days per week) and UHasselt (1-2 days per week). Strating date of the PhD project: *01/10/2019*. Specific research lines of the PhD project include: · Dose-response modelling of nanoparticle toxicity. · Extrapolation of the (in vitro based) dose-response models to an in vivo setting. · Integrated data analysis of several nanoparticle toxicity databases. Your Profile: · Master in biostatistics/statistics/bioinformatics. · Knowledge of R and SAS (knowledge of Winbugs/JAGS would be an asset). · Good written and excellent communication skills. · Ability to work independently and as a part of multidisciplinary team. · Problem solving skills and team player This PhD position offers a unique opportunity to conduct research as a part of multidisciplinary team in collaboration with several European institutes. If you are interested in the position, please contact by email Geert Verheyen (geert.verheyen(a)thomasmore.be) or Ziv Shkedy ( ziv.shkedy(a)uhasselt.be) Closing date to send an email is 07*/07/2019*

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