November 2017 - BBClist - maillist.psb.ugent.be

Bioinformatics position available at the Erasmus MC Cancer Computational Biology Center
by Harmen van de Werken 04 Oct '19

04 Oct '19

A bioinformatics position is currently available at the Erasmus MC Cancer Computational Biology Center. http://www.erasmusmc.nl/vacature/?num=21578 Please apply, if you are enthusiastic and eager to improve our knowledge on cancer biology. Harmen van de Werken

2 1

Postdoc: position Computational Network Biology in Plants - VIB-UGent Center for Plant Systems Biology
by Klaas Vandepoele 28 Nov '17

28 Nov '17

The Comparative Network Biology lab (Klaas Vandepoele) of the VIB Center for Plant Systems Biology is looking for a Postdoc Computational Network Biology in Plants. Our mission Our objective is to extract and validate biological knowledge from large-scale experimental data sets using data integration, comparative sequence and expression analysis, and network analysis. In our lab, we combine computational methods with experimental data to generate new insights about gene function, gene regulation and comparative genome biology. In this project, our objective is to * *delineate high-quality biological networks*in different plant species * *develop new methods to accurately translate biological networks*between different species (model species & crops) with different levels of genome complexity Job description * Fully funded Postdoc position for 2 years (start date March 2018 or later). * You get the freedom to design and execute a personal research project addressing some of the objectives listed above. * Through (inter)national collaborations with wetlab scientists, computational results can be experimentally validated! * Perform co-supervision of research projects of PhD students in the lab. * Access to a diverse set of training programs at VIB (both scientific & soft skills) * Reporting of results through publications in peer-reviewed international journals. * Attending and presenting your results at international scientific events. Your profile * You have PhD degree in Bioinformatics, Computational Biology or related. * You are enthusiastic about scientific research and have a strong interest in studying plant biology using genomics and systems biology approaches. * Through international peer-reviewed publications, you have a track record in plant genomics or systems biology research (people_only_having publications describing experimental/wetlab work will not be retained). * You are fluent with Linux/Unix and have good knowledge of Python or another programming/scripting language. * You have good communication and writing skills. * You are proficient in English. How to apply? Motivated candidates are asked to apply online (https://vibvzw.jobsoid.com/j/10785/postdoc-computational-network-biology-in…) Please make sure your application includes a letter of motivation, a detailed CV and the contact information of 2 references (including e-mail addresses and phone numbers). Applications will be accepted until 31 January 2018. -- best regards, Klaas Vandepoele - Professor Comparative Integrative Genomics VIB-UGent Center for Plant Systems Biology Ghent University Technologiepark 927 - 9052 Ghent - Belgium Tel. +32(0)9 331 38 22 --------------------------------------------------------- Lab website: http://bioinformatics.psb.ugent.be/cig/ Twitter: http://twitter.com/plaza_genomics ---------------------------------------------------------

1 0

BioSB/ELIXIR-NL course on Managing and Integrating Life Science Information, 22-26 January 2018, Amsterdam
by Femke Francissen 28 Nov '17

28 Nov '17

BioSB/ELIXIR-NL course on Managing and Integrating Life Science Information:Approaches using Linked Data and Semantics (5th edition) Course coordinators: Marco Roos (LUMC), Katy Wolstencroft (LIACS, Leiden University) Date: 22-26 January 2018 Location: Amsterdam Science Park, The Netherlands Website link <http://biosb.nl/education/course-portfolio/course-managing-and-integrating-…> Registration link <http://biosb.nl/education/course-portfolio/course-managing-and-integrating-…> Target audience This course is for bioinformaticians who would like to learn about leading-edge data and knowledge integration solutions. You will learn (1) powerful and flexible approaches to data and information management for your bioinformatics application (Semantic Web and Linked Data), (2) how to work with data across remote locations, for instance by applying Web Services and workflows, (3) how to publish your own data to make it available and reusable for the rest of the community. We assume a basic understanding of bioinformatics programming for the hands on sessions. It would suit previous user participants of BYOD meetings <http://www.dtls.nl/fair-data/byod/> who would like more hands-on experience of data integration. It would also suit data providers who would like to explore new ways of serving their data or integrating it with other resources. Description The amount of Life Science data available in the public domain is a vast and growing resource for bioinformatics research. There are over 20 million papers in PubMed and over 1600 biological databases. In many cases finding and applying the information from these resources is far from trivial. Following this course will show you techniques for working with these distributed resources, which includes using the web of Linked data and scientific workflows. It will also focus on methods for using or linking your own data into this large distributed Semantic Web of resources, in order to ensure that your data is FAIR <http://www.dtls.nl/fair-data/> (Findable, Accessible, Interoperable and Reusable). This course introduces modern techniques for the management of life science data and knowledge for bioinformatics applications. After following this course students should be able to start creating their first applications based on these technologies or make more informed design decisions for their current application. In this course you will learn about: Linked Data and the Semantic Web technologies that underpin it How you can use Linked Data for data and knowledge integration in the Life Sciences Available Linked Data resources in the public domain and large-scale projects that use these resources How you can integrate your own data with Linked Data resources How you can combine data integration and analysis over distributed resources, using Web Services and workflows Confirmed lecturers: Frank van Harmelen (Vrije Universiteit Amsterdam), Andre Dekker (Maastricht University) Tentative programme: The program will include the following topics: Introduction to Semantic Interoperability and the Semantic Web; The Semantic Web in Use; The Semantic web in use – systems and guidelines; Data stewardship and making Data Understandable and Searchable (the FAIR principles); Using, Integrating and Analysing Data This course is part of the Education Programme of BioSB <http://biosb.nl/education/course-portfolio-2/>, the Netherlands Bioinformatics and Systems Biology Research School, which offers training and education for in bioinformatics and systems biology. More information about BioSB can be found at www.biosb.nl <http://www.biosb.nl/>. Femke Francissen Community manager BioSB Research School Visiting address (as of 1 July 2017): Jaarbeurs Innovation Mile (JIM) | 6th floor Beatrixgebouw | Jaarbeursplein 6 | 3521 AL Utrecht Postal address (as of 1 July 2017): Postbus 8500 | 3503 RM Utrecht E-mail: femke.francissen(a)biosb.nl <mailto:femke.francissen@biosb.nl> Mobile: +31 6 17 90 4888 Skype: femke.francissen Website: www.biosb.nl <http://www.biosb.nl/> LinkedIn link <http://nl.linkedin.com/in/femkefrancissen>

1 0

Permanent position IT/biologist ULB-Neuroscience Institute
by Matthieu Defrance 28 Nov '17

28 Nov '17

The laboratory of Neurophysiology at the Université libre de Bruxelles (ULB, Brussels), member of the ULB-Neuroscience Institute (https://uni.ulb.ac.be) is recruiting a full time IT manager for a permanent position (http://www.ulb.ac.be/drh/emploi/index.html Référence 2017/41) The functions include: - Computer support for the various activities of the laboratory of Neurophysiology (http://neurophy.ulb.ac.be & http://celegans.ulb.ac.be/wordpress/) which includes both the processing of in vivo and in vitro electrophysiology data, imaging and behavioural analysis; as well as the Microscopy Facilitator Facility (LiMiF http://limif.ulb.ac.be) - Management of the local network and massive data flows (Tbs/year, continuous increase), in vitro and in vivo electrophysiology and imaging, server configuration and maintenance, data security, backup, archiving, etc . ; - IT support and support for the analysis of electrophysiological signals and image analysis to researchers; - Support for the implementation and maintenance of data acquisition systems for electrophysiology (patch clamp and imaging) in vitro and in vivo (Neuralinx) (optogenetics, behaviour, electrophysiology in vivo and calcium imaging by micro-endoscopy (Inscopix ) Development of software and script for coupling electrophysiological recordings or in vivo imaging and behavior (Matlab); - Support for simple analysis of imaging data (generic analyses for most users eg segmentation, counts) by open source software (eg ImageJ / Fiji) or commercial eg (LiMiF) ZEN, Huygens, Imaris, including support for local development of these softwares (macro / plugins). Some specific projects that require further development in image analysis will have to rely on dedicated resources (e.g. Master students in engineering / computer science, post- doc project, etc.); - Management of existing online booking software and their development according to the implementation of new equipments. Profile: Master in Computer Science or Civil Engineer in Computer science or other degrees of Civil Engineer. Experience in a similar function is an obvious but not mandatory asset. A motivated young graduate with a solid background may be suitable for the position. Knowledge and skills required: - Knowledge of computer science (PC, Mac and servers), programming (Matlab, Python, ImageJ, etc.), experience in signal analysis (electrophysiology) and / or in image processing (microscopy and / or video tracking); - Proficiency in written and spoken English is mandatory Desired Qualities: - Ability to work as a team player - while having a capacity for initiative and proactive action; - Sense of service and listening ability to capture the needs of biologists to efficiently translate them into hardware and / or software solutions; - Communication skills in English and, optionally, in French; - Stress resilience; - Adaptability to the various needs of users, often "in the emergency" (deadlines, etc.). To postulate: http://www.ulb.ac.be/drh/emploi/index.html Référence 2017/41 and fulfill the online document

1 0

FW: available position at the NARILIS institute, search for candidates with bioinformatic knowledge
by Vanneste, Kevin 27 Nov '17

27 Nov '17

Dear all, A position requiring strong bioinformatics affinity is available at the lab of Nicolas Gillet in the university of Namur, focusing on the involvement of viral infections in oncogenesis. Please see attachment for more details. Best regards, Kevin [Description: logo ISP-WIV] Kevin Vanneste Bioinformatician Platform Biotechnology and Molecular Biology Expertise, Service Provision and Customer Relations Rue Juliette Wytsmanstraat 14 | 1050 Brussels | Belgium T +32 (0)2 642 50 65 | F +32 (0)2 642 52 92 Email: kevin.vanneste(a)wiv-isp.be<mailto:kevin.vanneste@wiv-isp.be> | Skype: wiv-isp.kevin.vanneste Scientific Institute of Public Health | www.wiv-isp.be<http://www.wiv-isp.be/> ########################################################### Checked as being free of known viruses. Scientific Institute of Public Health, Brussels, Belgium Wetenschappelijk Instituut Volksgezondheid, Brussel, Belgi� Institut scientifique de Sant� publique, Bruxelles, Belgique Visit our website: http://www.wiv-isp.be ############################################################# DISCLAIMER: Please see https://www.wiv-isp.be/EmailDisclaimer #############################################################

1 0

PhD position: meiotic control of recombination in crops
by Ridder, Dick de 27 Nov '17

27 Nov '17

Dear all, We are looking for an enthusiastic bionformatics PhD candidate on a Marie Curie ITN project titled "Meiotic control of recombination in crops". The goal is to analyse crossover formation in crop genomes using novel combinations of high-throughput sequencing (Illumina, PacBio, Oxford Nanopore, 10X Genomics) and optical mapping (BioNano Genomics) data, to learn about crossover frequency in haplotypes, genome structure and structural variation in parental lines and offspring of crops such as tomato, potato, melon, and lettuce. Sequence and genome structural data will be mined using machine learning techniques to find features influencing recombination. Candidates should hold an MSc degree in bioinformatics, computer science (with a demonstrable affinity for biology) or related area. We are specifically seeking a candidate with a strong background in algorithm development, preferably related to machine learning, and demonstrable skills in mathematics and statistics. You will be based in Wageningen, and collaborate with other PhD candidates in this EU-wide project and with researchers at Wageningen University and in industry. Note that under the Marie Curie ITN rules, applicants cannot have resided in The Netherlands for more than 12 months over the past three years. Additional information about the position can be found at https://www.wur.nl/nl/vacature/PhD-position-Meiotic-control-of-recombinatio…. Interested candidates can apply up to January 15, 2018 through this website. Best regards, prof. Dick de Ridder Bioinformatics Group, Wageningen University, The Netherlands

1 0

Bioinformatician: GENMAB - NKI collaboration
by Lodewyk Wessels 26 Nov '17

26 Nov '17

Bioinformatician position: ‘Biomarker discovery for HexaBody-DR5/DR5 therapy’ Partners: Genmab BV, Utrecht, The Netherlands The Netherlands Cancer Institute (NKI), Amsterdam. Project description. How can we find better treatment strategies for solid cancers? How can we select the patient population or individual patients that will show exquisite response to these treatments? Genmab, an international biotechnology company. is currently developing HexaBody®-DR5/DR5, a therapeutic antibody product targeting the DR5 death receptor protein in solid cancers. This agonistic antibody product mimics ligand-induced apoptosis by clustering of DR5. The general aim of this research collaboration is two-fold. First to find molecular biomarkers to identify HexaBody®-DR5/DR5-responsive patients. Second, to understand the mechanism of action of HexaBody®-DR5/DR5. Our strategy is to employ large panels of tumor cell lines and patient-derived xenograft (PDX) tumor models that have been molecularly profiled and screened for response to HexaBody®-DR5/DR5. Specifically, we have whole exome and RNA sequencing data as well as HexaBody®-DR5/DR5 response measurements across tumor cell lines spanning 14 tumor indications and PDX models covering 2 tumor types. To provide more mechanistic insight we also have access to data from functional genetic screens aimed at identifying modulators of HexaBody®-DR5/DR5 response. Public-private collaboration. Genmab is an international biotechnology company specializing in the generation and development of differentiated antibody therapeutics for the treatment of cancer. DARZALEX® and Arzerra® are two approved drugs that were developed by Genmab. Genmab has a strong commitment to research and innovation with numerous external research collaborations akin to this one. The Computational Cancer Biology (CCB) group led by Lodewyk Wessels, has a strong track record in developing predictors of drug response from cell line panels, especially in collaboration with the Wellcome Trust Sanger Institute culminating in the second release of the Genomics of Drug Sensitivity on Cancer (GDSC1000) cell line panel (Iorio et al, Cell, 2016). Together with Genmab, the successful candidate will develop machine learning approaches to integrate the molecular data from the cell lines and PDX models in order to find effective HexaBody®-DR5/DR5 biomarkers and shed light on the mechanisms of response and resistance. The successful candidate will be employed at the NKI but regular visits to and meetings with Genmab will ensure sufficient cohesion and momentum. Candidate profile. We are seeking a highly motivated bioinformatician with: - A degree in bioinformatics, computer science or a related discipline - Experience with high-throughput data analysis, especially sequencing data - Proficiency in bioinformatics programming languages (e.g. R, Python) - Good cross-disciplinary collaborative and communication skills - Experience in statistics, machine learning and/or pattern recognition is a plus - Experience in cancer biology and clinical applications is a plus Interested? Please send CV and motivation letter to Lodewyk Wessels (l.wessels(a)nki.nl) and Jan-Hermen Dannenberg (jhd(a)genmab.com) Please include the names and contact information of at least two references. Deadline: 15 December 2017

1 0

PhD position Plant.ID training Network on hardwood identification in string instruments
by Fons Verbeek 24 Nov '17

24 Nov '17

In a collaborative project between Naturalis Biodiversity Centre and Leiden University (Leiden Institute of Advanced Computer Science) we are looking for a computer scientist with an interest in biology or a bioinformatician with knowledge in pattern recognition and image analysis. Experience with state-of-the-art techniques such as CNN’s are considered valuable. If you are interested you are very much invited to apply for the position. Read about the project in the short project description: Acoustic string instruments are made of several hardwood species including ebony (Diospyros). Many species of ebony are nowadays over-exploited in the wild. The Convention on International Trade in Endangered Species (CITES) placed all species of ebony from Madagascar on Appendix II in 2014 but other species are not legally protected. Computational microscopic phenotyping based on wood anatomical sections, chemical profiling and DNA barcoding are increasingly used to recognize wood traded under Forest Stewardschip Council (FSC) labels. Therefore, anatomy data, DNA barcodes and DART-TOF MS will be collected from reference specimens. Metabarcodes will be generated from ebony wood used in (parts of) instruments supplied by violon and bow builders and compared with microscopy, DART-TOF MS and bomb peak calibrated C14-dates to distinguish antique wood from wood harvested after 2013. Objective:Species-level identification of ebony wood for control of trade in legally protected species. Supervisors: Barbara Gravendeel and Frederic Lens from Naturalis Biodiversity Center, and promotor Fons Verbeek, Leiden University, Leiden Institute of Advanced Computer Science (LIACS). Planned secondments to Leiden University and Copenhagen University and short visits to the Dutch association of violin and bow makers and World Justice Commission. ——— Further information and instructions for application can be found on: https://science.naturalis.nl/en/about-us/jobs-and-fellowships/plantid-phd-f… <https://science.naturalis.nl/en/about-us/jobs-and-fellowships/plantid-phd-f…> http://www.plantid.uio.no/jobs/ <http://www.plantid.uio.no/jobs/> Prof Dr Ir Fons J. Verbeek, Imaging & BioInformatics LIACS, Leiden University The Netherlands f.j.verbeek(a)liacs.leidenuniv.nl

1 0

Edinburgh Genomics Python workshops 2018
by Bert Overduin 22 Nov '17

22 Nov '17

Dear all, Edinburgh Genomics is happy to again offer a range of Python workshops in the first half of 2018. All workshops are taught by Dr. Martin Jones, founder of Python for Biologists (https://pythonforbiologists.com) writer of several books on Python (https://pythonforbiologists.com/python-books/) and most likely the best Python instructor you will ever come across. Details of the workshops can be found below. With kind regards, Bert ************************* *5-day Introduction to Python for Biologists* Date: Mon 19 - Fri 23 February 2018 Registration deadline: Mon 5 February 2018 Places: 20 (first come, first served) Fee: £525 Instructor: Dr. Martin Jones (Python for Biologists) More info and registration: http://genomics.ed.ac.uk/services/introduction- python-biologists *5-day Data Manipulation and Visualisation with Python* Date: Mon 9 - Fri 13 April 2018 Registration deadline: Mon 26 March 2018 Places: 15 (first come, first served) Fee: £525 Instructor: Dr. Martin Jones (Python for Biologists) More info and registration: http://genomics.ed.ac.uk /services/data-manipulation-and-visualisation-python *5-day Advanced Python for Biologists* Date: Mon 9 - Fri 13 July 2018 Registration deadline: Mon 25 June 2018 Places: 15 (first come, first served) Fee: £525 Instructor: Dr. Martin Jones (Python for Biologists) More info and registration: http://genomics.ed.ac.uk/services/advanced- python-biologists <https://genomics.ed.ac.uk/services/advanced-python-biologists> ************************* -- Bert Overduin, PhD TRAINING AND OUTREACH BIOINFORMATICIAN Bert.Overduin(a)ed.ac.uk orcid.org/0000-0002-5281-8838 EDINBURGH GENOMICS The University of Edinburgh Ashworth Laboratories The King's Buildings Charlotte Auerbach Road Edinburgh EH9 3FL Scotland, United Kingdom tel. +44(0)1316507403 http://genomics.ed.ac.uk The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

1 0

Vacancy Scientist Bioinformatics (MEC335) - Galapagos - Mechelen, BE
by Mate Ongenaert 22 Nov '17

22 Nov '17

Galapagos is a clinical-stage biotechnology company, specialized in the discovery and development of small molecule medicines with novel modes of action. Our ambition is to become a leading global biotechnology company, focused on the development and commercialization of novel medicines that will improve people's lives. For our site in Mechelen, we are looking for a Scientist Bioinformatics (MEC335) All info and applications: http://careers.glpg.com/o/scientist-bioinformatics-mechelen Job description Ref: MEC335 As a member of the bioinformatics team you will participate in bioinformatics efforts supporting the drug discovery projects at Galapagos. By carrying out functional analyses, data integration, and implementing and executing data analysis methodologies, you work with the multidisciplinary disease biology and drug discovery teams in acquiring scientific insights to direct the research strategy. You will play a key role in implementing bioinformatics tools and methods supporting a wide range of activities, from research projects to proof-of-concept studies. In collaboration with the Information Systems (IS) team, these tools will be incorporated into Galapagos' informatics infrastructure. This position offers an exciting opportunity to develop and deploy bioinformatics-driven solutions to the scientific community at Galapagos. Requirements * Scientific Master Degree with at least 3 years of relevant work experience or PhD with a demonstrated track record in bioinformatics, preferably in a pharma/biotech setting; * Knowledge of expression data analysis, micro-arrays and/or sequencing-based, and experience in developing analysis strategies and workflows in transcriptomics; * Experience in data-science techniques (regression, machine learning); experience with data structures and data-interchange formats (e.g. JSON) and experience with document databases (such as MongoDB or Cassandra) and/or relational databases; * Working knowledge of Linux and programming expertise (e.g., C#, Java, Perl or Python) * Strong problem-solving ability, and the aptitude and zeal to acquire new skills necessary for the job * Rigorous and well organized; good verbal and written English communication skills; * Team player able to work and communicate effectively in a multidisciplinary environment with people with different professional backgrounds (biology, chemistry, molecular modelling, IS, IT); Desirable skills * Good knowledge of R (and the BioConductor libraries) and experience with reporting in R (sweave/knitr) and interactive web-interfaces (R/shiny); * Demonstrated experience in working out proof of concept workflows, analysis tools or visualizations; * Broadly applicable general bioinformatics skills (pathway analysis, data and text mining, querying databases and repositories in the public domain); * Knowledge of disease-related pathways and systems biology approaches in relation to drug target discovery; [cid:image001.jpg@01D16D66.BD487830]<http://www.glpg.com/> Maté Ongenaert, PhD Senior Scientist Bioinformatics T: +32 15 342 927 Galapagos NV Generaal De Wittelaan L11 A3 2800 Mechelen * Belgium -- This e-mail and its attachment(s) (if any) may contain confidential and/or proprietary information and is intended for its addressee(s) only. Any unauthorized use of the information contained herein (including, but not limited to, alteration, reproduction, communication, distribution or any other form of dissemination) is strictly prohibited. If you are not the intended addressee, please notify the originator promptly and delete this e-mail and its attachment(s) (if any) subsequently. Neither Galapagos nor any of its affiliates shall be liable for direct, special, indirect or consequential damages arising from alteration of the contents of this message (by a third party) or as a result of a virus being passed on.

1 0