May 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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CORRECTION Announcing CPW2018 during ECCB - Second Bioinformatics and computational pathology summit
by Yves Sucaet 24 Jun '18

24 Jun '18

CALL FOR ABSTRACTS: CPW2018 - Bioinformatics and computational pathology summit (second edition) When? Sunday, September 9, 2018. Where? Athens, Greece (during ECCB2018) Website? http://cpw1018.org Digital pathology is increasingly used to study biological processes and diseases as novel molecular probing and imaging techniques allow the measurement of single molecules in whole tissue sections. Resulting multi-gigapixel images can be viewed on a computer screen via dedicated software. However, automated analysis of such large-scale datasets is challenging and their combination with omics data is not trivial. This workshop wants to facilitate bridging opportunities between the bioinformatics and tissue image analysis communities. This second edition is organised as a full-day workshop during ECCB 2018 (http://www.eccb18.org) KEYNOTE SPEAKERS: The following keynote speakers have already agreed to speak at the conference: Thomas Fuchs, Memorial Sloan Kettering Cancer Center Chakra Chennubhotla, University of Pittsburgh Derek Magee, University of Leeds SUBMISSIONS: The conference solicits oral talks, posters, and proceeding papers contributions of original work or work that was recently accepted or published in a peer-reviewed journal or at a high level international conference. In the latter case, the publication reference should be clearly mentioned, and the abstracts should be checked mainly for relevance, rather than receive a full review. Conference proceedings will be published by the Journal of Pathology Informatics. The program committee will decide which contributions are selected for an oral presentation, and which ones are presented during a poster session. For submission instructions, please refer to https://www.fourwav.es/cpw2018 SCOPE: Computational pathology exists at the interphase between bioinformatics, machine learning, and digital pathology (microscopy). Submissions from all topics of interest are welcome (non-exhaustive list): Machine learning and image analysis for quantification in digital pathology (in 2D & 3D), Novel approaches (e.g. spatial or graph-based methods) to extract high-level features (e.g. molecular networks or spatial expression patterns) from tissue images for systems pathology, Software development methodologies and tools to ease the exploitation of large tissue images and integration with omics data, Novel molecular imaging techniques on tissues (molecular pathology, next generation pathology) and their analysis challenges, e.g. in situ hybridization, mass spectrometry imaging of formalin-fixed paraffin-embedded tissues, mass cytometry, and other spectroscopy techniques (Raman,...)... Research applications on non-human model organisms KEY DATES: Submission deadline: June 15, 2018. Notification of acceptance: June 30, 2018. Conference: Sunday September 9, 2018. Organizing committee: Yves Sucaet, Vrije Universiteit Brussel, Belgium Jeroen Van der Laak, UMC Radboud, Netherlands Zev Leifer, New York College of Podiatric Medicine, USA Yukako Yagi, Memorial Sloan Kettering Cancer Center, USA Raphaël Marée, Universit? de Li?ge, Belgium David Ameisen, IRIF, CNRS and Universit? Paris Diderot, France Paul Van Diest, UMC Utrecht, Netherlands Jeffrey Fine, Magee-Womens Hospital of UPMC

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Register now for BioSB course: Algorithms for Biological Networks - June 25-29, Wageningen
by Femke Francissen 31 May '18

31 May '18

BioSB Course: Algorithms for Biological Networks (5th edition)Course coordinators: dr. Maria Suarez Diez (WUR), prof. dr. Dick de Ridder (WUR), dr. Jeroen de Ridder (UMCU) *Date:* June 25-29, 2018 *Location:* Wageningen University & Research *Website:* link to course page <https://www.biosb.nl/education/course-portfolio/course-algorithms-for-biolo…> *Registration:* link to registration form <https://www.biosb.nl/education/course-portfolio/course-algorithms-for-biolo…> Course description Molecular biology is concerned with the study of the presence of and interactions between molecules, at the cellular and sub-cellular level. In bioinformatics and systems biology, algorithms and tools are developed to model these interactions, with various goals: predicting yet unobserved interactions, assigning functions to yet unknown molecules through their relations with known molecules; predicting certain phenotypes such as diseases; or just to build up biological knowledge in a structured way. Such interaction models are often best modelled as networks or graphs, which opens up the possibility of using a large number of readily available algorithms for inferring networks, performing simulations of biology, optimising paths or flows through networks, graph-based data integration and graph mining. Many of these algorithms can be applied (sometimes with slight alterations) to solve a particular biological problem, such as modeling transcriptional regulation or predicting protein interaction/complex formation, but also to derive systems behaviour by breaking down networks into modules or motifs with certain characteristics. In this course, we will first give a brief overview of molecular biology, the advent of high-throughput measurement techniques and large databases containing biological knowledge, and the importance of networks to model all this. We will highlight a number of peculiar features of biological networks. Next, a number of basic network models (linear, Boolean, Bayesian) will be discussed, as well as methods of inferring these from observed measurement data. A number of alternative network models more suited for high-level simulation of cellular behaviour will also be introduced. Building on the network inference methods, a number of ways of integrating various data sources and databases to refine biological networks will be discussed, with specific attention to the use of sequence information to refine interaction and transcription regulation networks. Finally, we will give some examples of algorithms exploiting the networks found to learn about biology, specifically for inspecting protein interaction networks. Course programme The tentative course programme and course materials can be found here <http://www.bioinformatics.nl/courses/BioSB-AfBN/>. Target audience The course is aimed at PhD students with a background in bioinformatics, computer science or a related field; a working knowledge of basic statistics and linear algebra is assumed. The BioSB course “Pattern recognition” <https://www.biosb.nl/education/course-portfolio/pattern-recognition/> and the ASCI course “Advanced pattern recognition” (a1) discuss many of the tools used in this course, but it is not required to have followed these. Prior knowledge of molecular biology is a bonus, but also not strictly required. BioSB research school 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.

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Fwd: Tenure track in Amsterdam on Multiscale Scientific Computing
by Sanne Abeln 30 May '18

30 May '18

See the link below for a tenure track position in Amsterdam, the closing date is 30 June. http://www.uva.nl/en/content/vacancies/2018/05/18-294-assistant-professor-m… -- Computational Science <http://uva.computationalscience.nl> Lab <http://uva.computationalscience.nl> Master Programme Computational Science <http://www.uva.nl/en/shared-content/subsites/graduate-school-of-sciences/en…> -- -- Sanne Abeln Assistant Professor Bioinformatics - VU University Amsterdam s.abeln(a)vu.nl +31 20 59 87816 www.few.vu.nl/~abeln <http://www.few.vu.nl/%7Eabeln> -- -- Sanne Abeln Assistant Professor Bioinformatics - VU University Amsterdam s.abeln(a)vu.nl +31 20 59 87816 www.few.vu.nl/~abeln <http://www.few.vu.nl/%7Eabeln>

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Upcoming training workshops at Edinburgh Genomics: Linux for Genomics and Intro to RNAseq Analysis
by DUNBAR Donald 29 May '18

29 May '18

Hello all, we have some new dates for our popular Edinburgh Genomics training workshops<https://genomics.ed.ac.uk/services/training>. We now offer registration, on a first come first served basis, to our Linux for Genomics and Introduction to RNAseq Data Analysis workshops developed and taught by our Edinburgh Genomics Bioinformaticians. 1. Introduction to RNAseq Data Analysis, Tuesday 19th to Wednesday 20th June 2018 REGISTER NOW<https://www.surveymonkey.co.uk/r/6QQVF7D> 2. Introduction to RNAseq Data Analysis, Thursday 21st to Friday 22nd June 2018 REGISTER NOW<https://www.surveymonkey.co.uk/r/ZKG5F8N> 3. Linux for Genomics, Monday 25th June 2018 REGISTER NOW<https://www.surveymonkey.co.uk/r/Z8RYF8T> 4. Linux for Genomics, Tuesday 26th June 2018 REGISTER NOW<https://www.surveymonkey.co.uk/r/Z86GFSH> Please use the links provided above to register for a place. These workshops are very popular and have limited places, so please do register as early as you can. We also have a few remaining places on our Advanced Python for Biologists workshop, taught by Dr Martin Jones, founder of Python for Biologists<https://pythonforbiologists.com/>. 1. Advanced Python for Biologists, Monday 9th to Friday 13th July 2018 REGISTER NOW<https://www.surveymonkey.co.uk/r/NDSGYHL> * https://genomics.ed.ac.uk/services/training * https://genomics.ed.ac.uk/services/introduction-rna-seq-data-analysis * https://genomics.ed.ac.uk/services/linux-genomics * https://genomics.ed.ac.uk/services/advanced-python-biologists Please let me know if you have any questions or comments. Feel free to share with colleagues and contacts. With best wishes and we look forward to welcoming you to Edinburgh Genomics. Donald --- Dr Donald Dunbar Bioinformatics Operations Manager Edinburgh Genomics, Genome Science Ashworth Labs, The King's Buildings The University of Edinburgh donald.dunbar(a)ed.ac.uk The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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Job vacancy Cluster Leader Applied Bioinformatics
by Warris, Sven 24 May '18

24 May '18

Dear reader, Our cluster Applied Bioinformatics of Wageningen University and Research is looking for a new cluster leader. For more information about the job vacancy and on how to apply, please visit: https://www.wur.nl/en/Jobs/Vacancies/Show/Cluster-leader-Applied-Bioinforma… Kind regards, Sven Warris

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+++ TRAVEL FELLOWSHIPS - ESCS2018 +++
by Daniele Parisi 24 May '18

24 May '18

Dear colleagues in bioinformatics and computational biology, In order to provide as many people as possible with the opportunity to attend the ESCS 2018 (European student council symposium of bioinformatics and computational biology), we are happy to announce there will be 3 travel fellowship available. The value of the travel fellowship will depend on the distance the recipient has to travel; please note the travel fellowship may not cover all your travel and/or hotel expenses. ELIGIBILITY In order to be eligible for the travel fellowship your abstract should be accepted for presentation at the symposium. Should you be awarded a travel fellowship by ECCB 2018, the ESCS travel fellowship will be withdrawn. HOW TO APPLY Please provide a PDF document containing * The abstract you have submitted * A copy of your curriculum vitae (CV) * A brief motivation describing why you would like to attend the ESCS and why you require a travel fellowship to do so Please send your application to escs(a)iscbsc.org before JULY 7TH, 2018 Your application will be judged based on the scientific quality of your work and your motivation. In addition, your country of origin will be take into consideration; in the case of applications of equal quality preference will be given to applicants from lower income countries. Do not hesitate to spread this mail through your colleagues, Best regards The ESCS2018 executive team -- 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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[Gtpb] DMOS18 - Course announcement / Reminder
by GTPB Administration 23 May '18

23 May '18

Course Announcement / Reminder DMOS18 Data Management and Open Science with Rutger A. Vos, Pedro L. Fernandes and Elves H. Duarte Key terms: Data Management, Fair Data, Open Science, Open Access, Open Data IMPORTANT DATES for this Course Deadline for applications: June 7th 2018 Course date: June 12th - June 15th 2018 The GTPB is proud to announce that the above referenced hands-on training course is open for applications Admission: Candidates with adequate profile will be accepted in the next 72 hours after the application until we reach 20 participants. Course description: In an age of increasingly complex and data-intensive, collaborative scientific practices, scandals of irreproducibility, and a growing societal ethos of transparency and accountability, a new paradigm has arisen: Open Science. In this three day course, we will introduce to you the three organizing principles and practices that undergird this paradigm: Open Access scholarly publishing Open Source software development Open Data integration and sharing For this, we will be introducing a set of technologies and ways of using them. The reasonable expectation is that the participants will feel empowered and start using them for the above purposes in a highly productive way. The use-cases that we will be working on are going to be based on bioinformatics, but the principles are very broadly applicable to other fields. You do not need to have any particular programming or otherwise computational experience beyond what is normally required from a scientist in graduate school and beyond, i.e., you should not be afraid of interacting with a computer and editing simple text files. We will then steer the participants into good practices in data management and work on practical examples taken from published papers and data, showing how these practices influence replicability and reproducibility. At the end we will discuss publication bias and its consequences in current research quality. More information at the GTPB website, http://gtpb.igc.gulbenkian.pt/bicourses/2018/DMOS18/ Hoping that this course meets your interests, Pedro Fernandes -- The Gulbenkian Training Programme in Bioinformatics General Office Rua da Quinta Grande, 6 2780-156 OEIRAS Portugal _______________________________________________ GTPB mailing list GTPB(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb

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Aalto-Janssen postdoctoral position in machine learning
by Herman, Dorota [RNDBE] 23 May '18

23 May '18

Dear All, Aalto University is looking for a postdoctoral researcher with expertise in machine learning to work on an exciting collaboration project between Prof. S. Kaski's team in Finnish Center for Artificial Intelligence FCAI at Aalto University and Janssen Pharmaceutica. The exciting research problem is to learn to infer toxicity of chemicals based on the chemical structure, and the great opportunity is that we have unique data for the learning. This is an outstanding opportunity to both develop new probabilistic machine learning methods and to gain necessary skills to place yourself for success both in the pharmaceutical industry as well as in academia. Janssen Pharmaceutica and FCAI support and expect publication of the outcome of this work in top peer-reviewed journals and scientific conferences. The successful candidate will be employed by Aalto University and work in Otaniemi campus (Helsinki, Finland) for the 1st year of 2-year contract. During the 2nd year, the will be performed at Janssen Pharmaceutica premises in Beerse, Belgium. Full details: http://www.aalto.fi/en/about/careers/jobs/view/1854/. Best regards, Dorota Herman, PhD Scientist - Computational Sciences - Discovery Sciences Janssen Pharmaceutica NV Pharmaceutical Companies of Johnson & Johnson Turnhoutseweg 30 B-2340 Beerse Turnhout Phone +32 1460 5636 dherma20(a)its.jnj.com<mailto:dherma20@its.jnj.com>

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