August 2018 - 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

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COMPUTATIONAL BIOLOGIST - TUMOR IMMUNOLOGY
by Lodewyk Wessels 25 Jul '19

25 Jul '19

VACANCY COMPUTATIONAL BIOLOGIST - TUMOR IMMUNOLOGY YOUR ROLE WITHIN THE INSTITUTE The research groups of Dr Karin de Visser, dr Marleen Kok and Prof dr Lodewyk Wessels, are looking for a motivated and talented Computational Biologist to join their teams at the Netherlands Cancer Institute (NKI). The Inflammation and Cancer group of dr. Karin de Visser is studying the impact of the immune system on metastatic breast cancer utilizing sophisticated mouse tumor models and state-of-the art ex vivo and in vitro immunological and molecular assays. The lab of de Visser closely collaborates with the translational research group of medical oncologist dr Marleen Kok. The mission of this team is to discover novel mechanisms underlying the crosstalk between breast cancer and the immune system, to optimize immunotherapy for breast cancer patients using novel combination treatments in clinical trials and the discovery of predictive biomarkers. The Computational cancer biology group of Prof dr Lodewyk Wessels is focused on quantifying and understanding treatment response in model systems and patients. To this end we develop bespoke and novel computational methods focusing on data integration and tailored to new technologies. We actively collaborate with many research groups in the NKI and strongly believe in the power of 'team science'. PROJECTS You will be involved in the following projects: 1. MOUSE MODELS FOR METASTATIC ESCAPE FROM IMMUNE CONTROL. To study the causal relationship between immune cells and metastatic breast cancer, we utilize state-of-the art genetically engineered mouse tumor models. We have extensive RNA-sequencing datasets of isolated immune cell populations, as well as RNA-sequencing and exome sequencing data of primary breast tumors and organ-specific metastases from these mouse models. You will be responsible for the computational analyses of the data, and to extract candidate pathways/genes from these datasets that can subsequently be tested in follow up experiments in the lab. Moreover, you will link these pre-clinical data to human datasets. 2. SYSTEMIC AND INTRA-TUMORAL IMMUNOMONITORING FOR PRECISION IMMUNE-MODULATION. We are performing extensive immunomonitoring studies in human breast cancer patients treated with immune checkpoint blockade, with the ultimate aim to validate hypotheses derived from our preclinical research in human cancer patients, and to stratify breast cancer patients for immunomodulatory therapies. We are setting-up multiplex immunohistochemistry with antibody panels that audit intratumoral lymphoid and myeloid cell populations and their functional state. In parallel, we have established an extensive multiplex flow cytometry pipeline to monitor the systemic immune landscape of breast cancer patients and healthy controls. These analyses generate a substantial amount of data which require thorough computational analyses. 3. MAPPING IMMUNO-GENOMIC INTERACTIONS. We are interested in dissecting the impact of the genetic make-up of breast tumors on the intra-tumoral and systemic immune landscape. You will be responsible for the identification and validation of genotype-immunophenotype associations by connecting DNA exome sequencing data, RNA sequencing data and immune profiles derived from our mouse tumor models and cancer patients. You will use both publicly available datasets and newly generated datasets. You will be embedded in the collaborative and enthusiastic international research groups of dr. Karin de Visser, dr Marleen Kok and Prof. dr. Lodewyk Wessels, providing a unique environment that combines computational cancer biology with pre-clinical and translational research into immune-oncology. YOUR PROFILE We seek to recruit an ambitious postdoc, capable of independent thinking, with a strong commitment to translational research. Candidates should hold a degree in bioinformatics, computer science or a related discipline, have experience in statistics and/or machine learning and be proficient in bioinformatics programming languages (e.g. R, Python). We expect candidates to be highly self-motivated, creative, and a team-player with strong communication skills. General background knowledge in biology and immunology is essential, and experience with projects involving the use of genomics and immune profiling data to identifying candidate targets and biomarkers is a plus. WANT MORE INFORMATION? Please visit our home pages https://www.nki.nl/divisions/tumor-biology-immunology/de-visser-k-group/ https://ccb.nki.nl or contact Karin de Visser: k.d.visser(a)nki.nl Marleen Kok: m.kok(a)nki.nl Lodewyk Wessels: l.wessels(a)nki.nl

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POSTDOC: ANT ADAPTATION TO HOT AND ARID AREAS – TRANSCRIPTOMICS DATA ANALYSIS, BRUSSELS
by Matthieu Defrance 30 Aug '18

30 Aug '18

POSTDOC: ANT ADAPTATION TO HOT AND ARID AREAS – TRANSCRIPTOMICS DATA ANALYSIS, BRUSSELS The Evolutionary Biology & Ecology lab (ULB Belgium) and the Interuniversity Institute of Bioinformatics in Brussels (ULB and VUB Belgium) are recruiting a 2-year postdoc researcher to study how desert ants have evolved their extreme degree of thermophily. The project is based on a comparative approach to examine how similar desert conditions have led either to the evolution of convergent traits in different lineages or to the adoption of alternative strategies. The postdoc will use a variety of molecular methods (including but not limited to RNA-seq) to explore the heat-shock responses (HSRs) in ants and will focus on the computational analysis of sequencing data (e.g. RNA-seq de novo assembly, differential expression analysis, clustering). Candidates should have a strong experience with RNA-seq (including library preparation and computational analysis of sequencing data) and must have effective written and oral communication skills, with a demonstrated ability to publish peer-reviewed papers. He/She must have a PhD pending or obtained within the last 3 years in computer science, biology or bioinformatics. The applicant may not have resided or pursued his/her main activity (studies, employment, etc.) in Belgium for more than 24 months during the last 3 years immediately preceding the first period of postdoctoral residence. The post-doc will be based in the the Interuniversity Institute of Bioinformatics in Brussels under direct supervision of Matthieu Defrance (Associate Professor) and Serge Aron (Research Director of the Belgian NSF/ FNRS). He/She will work closely with a PhD student, who will focus on empirical data collection. The position is funded for 2 years. Start date is early 2019. The candidate's salary for the first year will be ~2 450 euros, net of tax; it will increase the second year in accordance with the legal rules in force in Belgium. To apply, please send a cover letter, CV, and names and contact information for three references to Serge Aron (saron(a)ulb.ac.be) and Matthieu Defrance (matthieu.dc.defrance(a)ulb.ac.be) The application deadline is December 1st, 2018. ULB is an Equal Opportunity Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, age, disability, protected veteran status, or any other characteristic protected by law. For more information, please visit the Evolutionary Biology & Ecology lab website (http://ebe.ulb.ac.be) and the Interuniversity Institute of Bioinformatics in Brussels website (ibsquare.be) or contact Serge Aron (saron(a)ulb.ac.be) or Matthieu Defrance (matthieu.dc.defrance(a)ulb.ac.be)

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Fwd: [rsg-belgium] [ELIXIR Belgium workshop] Shell-Git-Python
by Daniele Parisi 24 Aug '18

24 Aug '18

Dear all, We would hereby like to announce an upcoming training in GENT on OCTOBER 24TH AND 25TH, organised by ELIXIR BELGIUM. This two day workshop will aim to teach basic programming skills to PhD researchers in life sciences, who need them to do their research more effectively. The workshop will cover multiple tools, such as SHELL, GIT, and PYTHON. The workshop is FREE OF CHARGE, and sponsored by the ELIXIR-EXCELERATE program. More information is available at the following link: https://orchid00.github.io/2018-10-24-ugent/ Please forward this information to anyone who you think might be interested. With best regards, Daniele Parisi on behalf of Paula Martinez, ELIXIR Belgium trainer -- DANIELE PARISI PhD student at ESAT - STADIUS, Yves Moreau's group President of RSG Belgium Chair of ESCS 2018 Kasteelpark Arenberg 10 - box 01.34 3001 Leuven, Belgium Tel: +32488794394

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Bioinformatician application
by Harmen van de Werken 16 Aug '18

16 Aug '18

The Erasmus MC Cancer Computational Biology Center(CCBC <https://ccbc.erasmusmc.nl/>) is seeking a highly motivated bioinformatician to join our team. If you are eager to combine cancer biology with computational biology please apply. https://www.academictransfer.com/en/49444/bioinformatician/#.W3VWAoiRB_s.li… Kind regards, Harmen van de Werken

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Transcriptomics data analysis expert vacancy
by Jo Vandesompele 13 Aug '18

13 Aug '18

'Transcriptomics data analysis expert' vacancy at UGent spin-off Biogazelle. More information via flanders.bio at https://www.flanders.bio/en/jobs/?jbtClsJobId=1303488 -- prof. dr. ir. Jo Vandesompele Ghent University Center for Medical Genetics Ghent (CMGG) Cancer Research Institute Ghent (CRIG) Bioinformatics Institute Ghent N2N (BIG N2N)

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Bioinfomatician/biostatistician position at LBMCC
by Anthoula Gaigneaux 10 Aug '18

10 Aug '18

Dear all, LBMCC is a research lab located in Luxembourg, dedicated to basic and applied research in the field of cancer and inflammation. We have one job opening for a post-doc scientist with experience in biostatistics and -omics data analysis. Detailed description and contact information can be found in the attached document. Kind regards, Anthoula Gaigneaux, PhD Laboratoire de Biologie Moléculaire et Cellulaire du Cancer (LBMCC) Hôpital Kirchberg 9, rue Edward Steichen L-2540 Luxembourg tel: +352 2468 4046 anthoula.gaigneaux(a)lbmcc.lu <mailto:anthoula.gaigneaux@lbmcc.lu>

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Fwd: postdoc position in my lab
by Lieven Sterck 03 Aug '18

03 Aug '18

> From: "Olivier De Clerck" <Olivier.DeClerck(a)UGent.be> > Dear all, > Assaf Vardi is looking for a bioinformatics postdoc to work Ehux host pathogen > interactions. > See attached. > Please distribute to potential candidates. > Olivier > From: Assaf Vardi [mailto:assaf.vardi@weizmann.ac.il] > Sent: vrijdag 3 augustus 2018 14:07 > To: Olivier De Clerck <Olivier.DeClerck(a)UGent.be> > Subject: postdoc position in my lab > Hi again > If you happen to know a potential candidate for bioinformatics position in my > lab, im looking for a good one please see the attached ad. > Many thanks and enjoy your vacation. > Cheers > Assaf

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FINAL CALL FOR ABSTRACTS: Summer School on Machine Learning in Drug Design, August 20-22, 2018, Leuven, Belgium - ABSTRACT DEADLINE: JULY 22, 2018
by Yves Moreau 01 Aug '18

01 Aug '18

Dear colleague, The Summer School on Machine Learning in Drug Design will take place on August 20-22, 2018 in Leuven, Belgium. This Summer School will bring together the machine learning, chemoinformatics, and bioinformatics communities from academia and industry to tackle the challenges of complex data integration in drug design and discovery. The format of the event will combine multiple keynote presentations, oral contributions selected from submitted abstracts, and extensive poster sessions with ample time for discussion. As this is an emerging area, the event will aim at giving good exposure to promising junior researchers. We invite you to submit your short abstract for oral presentation or poster by July 22, 2018 (extended deadline) at http://mldd.esat.kuleuven.be <http://mldd.esat.kuleuven.be/>. Please forward this announcement to members of your team and to interested colleagues. More information is available below and at http://mldd.esat.kuleuven.be <http://mldd.esat.kuleuven.be/>, or by email at mldd(a)esat.kuleuven.be <mailto:mldd@esat.kuleuven.be>. Apologies for multiple postings. Best regards, Prof. Yves Moreau, University of Leuven Prof. Sepp Hochreiter, Johannes Kepler University of Linz Prof. Samuel Kaski, Aalto University SCOPE The data sets amenable to mining for drug design are rapidly expanding. This holds not only for the volume of conventional annotation of chemicals (i.e., representations of their chemical structure and their activities in a growing set of validated assays). It also goes for less conventional data sources, such as cellular microscopy or gene expression profiles of chemicals acquired at high throughput. Powerful novel machine learning methods unleashed on these massive volumes of heterogeneous and rich, but noisy and biased data, hold the promise of better and safer drugs to address unmet medical needs. To deliver on that promise, the Summer School calls on the machine learning, big data analytics, cheminformatics and bioinformatics communities to join forces and strengthen collaborative work at the interface of their disciplines. The Summer School will bring together contributors from both academia and industry to foster interdisciplinary exchange in this area where the need for expertise is growing rapidly. Contributions will cover recent advances in chemogenomics, strategies for data fusion, and machine learning. PRELIMINARY INVITED SPEAKER PROGRAM * Djork-Arné Clevert (Bayer): Deep learning for proteochemometric modeling * Gerard van Westen (Leiden University): Combining cheminformatics and bioinformatics through deep learning * Gilles Marcou (University of Strasbourg): Chemical space modeling and visualization with Generative Topographic Maps * Günter Klambauer (JKU Linz): Boosting drug discovery with deep learning * Florian Nigsch (Novartis): From heterogeneous data to highly predictive models and their applications in early drug discovery * Daniel Reker (MIT): Machine learning for natural product target prediction and chemogenomic data compression * Tim Becker (Harvard University): Machine learning and deep learning to predict drug-target activity from high-content imaging * Thomas Blaschke (AstraZeneca): The rise of deep learning in drug discovery * Val Gillet (University of Sheffield): TBA INTENDED AUDIENCE AND FORMAT The summer school is intended for academic and industry researchers in machine learning, chemoinformatics, or bioinformatics who are either currently working at the interface between these fields or want to expand their skills to link these three areas. The summer school is also intended as a bridge between academia and industry. The format of the event will combine comprehensive invited presentations, oral contributions selected from submitted abstracts, and extensive poster sessions with ample time for discussion. ABSTRACT SUBMISSION Participants are invited to submit abstracts for oral contributions and posters by July 22, 2018 (extended deadline). Abstracts can submitted for consideration for oral presentation (up to 1,000 words) or for consideration as poster only (up to 250 words). Abstracts selected for oral presentation will be notified by July 25, 2018. Abstracts will be available as a book of abstracts and online, but there will be no full proceedings. REGISTRATION AND FEE Early registration fee (before July 20, 2018): €180 (including VAT) Late registration fee (before August 13, 2018): €300 (including VAT) The fee covers participation to the meeting and includes coffee breaks and lunch (sandwich lunch). VENUE The Summer School will be held at the Irish College, a beautifully restored historical building in the center of Leuven, Belgium.

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