- BBClist - maillist.psb.ugent.be

Open PhD position (bioinformatics) at UMC Utrecht Netherlands
by Ridder-4, J. de 03 Jun '16

03 Jun '16

You will join the recently established group of dr. de Ridder as a PhD student. The de Ridder lab is focussed on creating and applying advanced computational techniques to high-throughput molecular datasets and develops novel data integration strategies to further disease biology. You will participate in a research project funded by the Gieskes-Strijbis fund. The project is part of a collaboration between the research groups of Dr. W. Kloosterman (Genetics), Prof. H. Clevers, PhD, MD (Hubrecht Institute) and Prof. dr. E. Witteveen (Medical Oncology). Dr. Kloosterman has a strong background in (cancer) genomics and extensive expertise in the analysis of genome and transcriptome sequencing data. Prof. H. Clevers is director of the Princess Maxima Center for pediatric oncology and key scientist behind the organoid culture system. Prof. dr. E. Witteveen is an expert on ovarian cancer biology and focuses on testing of novel cancer drugs in clinical trials. The primary focus of the PhD project is the identification and computational characterization of novel mechanisms of drug sensitivity and resistance in ovarian cancer. This will be achieved by establishing and characterizing a “living” organoid biobank for ovarian cancer using organoid technology, thus capturing to a certain extent the genetic variability of this tumour type. A major part of this project will concern the analysis and interpretation of large-scale genome and transcriptome data and the selection and molecular characterization of novel genetic variations that are associated with response to chemotherapy or targeted drugs. The latter part involves experimental models, such as mouse, cell lines and organoids, followed by functional assays. If you are (or know someone who is) educated as a bioinformatician or computational biologist with a data analysis mindset, please get in touch! The ideal candidate should have affinity with machine learning, statistics and computational science in general and demonstrable knowledge of molecular biology and/or cancer biology. For more information: http://www.werkenbijumcutrecht.nl/vacatures/Paginas/phd-student-group-de-ri… Best Jeroen de Ridder ------------------------------------------------------------------------------ De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197. Denk s.v.p aan het milieu voor u deze e-mail afdrukt. ------------------------------------------------------------------------------ This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. University Medical Center Utrecht is a legal person by public law and is registered at the Chamber of Commerce for Midden-Nederland under no. 30244197. Please consider the environment before printing this e-mail.

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PhD position in Statistics for Biotech Data at GUGC
by Katrijn Vannerum 02 Jun '16

02 Jun '16

Recently a PhD position at GUGC in Korea is opened for research on (bio)statistics. Please see https://edit.ugent.be/en/work/vacancies/assisting/full-time-junior-assistan… or the attached document. Kind regards, Prof. Dr. Arnout Van Messem Centre for Biotech Data Science Ghent University Global Campus #315, 119 Songdomunhwa-Ro Yeonsu-Gu, Incheon, 406-840 South Korea E. Arnout.VanMessem(a)ghent.ac.kr<mailto:Arnout.VanMessem@ghent.ac.kr> T. +82 32 626 4210 F. +82 32 626 4109

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Extended deadline for Bioinformatics meet Digital Pathology workshop at ECCB 2016
by Yves Sucaet 01 Jun '16

01 Jun '16

SECOND CALL FOR ABSTRACTS: CPW2016 - Bioinformatics and computational pathology summit Due to several requests we have decided to extend the MLSB 2016 submission deadline until Friday June 10. The workshop webpage (http://cpw.pathomation.com) has been updated to reflect the changes. When? Saturday, September 3, 2016. Where? Den Hague, Netherlands (during ECCB2016) Website? http://cpw.pathomation.com 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 first edition is organized as a full-day workshop during ECCB 2016 (http://www.eccb2016.org) KEYNOTE SPEAKERS: The following keynote speakers have already agreed to speak at the conference: Jeroen Van der Laak, UMC Radboud Jeffrey Fine, Magee-Womens Hospital of UPMC 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 (http://www.jpathinformatics.org) 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/view/265/info/. 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: Friday June 10, 2016. Notification of acceptance: June 30, 2016. Conference: September 3, 2016. Organizing committee: Yves Sucaet, Vrije Universiteit Brussel, Belgium Jeroen Van der Laak, UMC Radboud, Netherlands Marius Nap, HistoGeneX, Belgium and Rigshospitalet Copenhagen, Denmark Zev Leifer, New York College of Podiatric Medicine, USA Yukako Yagi, Harvard Medical School & Massachusetts General Hospital, USA Raphaël Marée, Université de Liège, Belgium David Ameisen, IRIF, CNRS and Université Paris Diderot, France Paul Van Diest, UMC Utrecht, Netherlands

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Bioinformatics Post-doctoral position @ INRA, France
by emmanuelle morin 31 May '16

31 May '16

*Postdoctoral Position in Comparative Genomics and Symbiosis Evolution * *Institution*: INRA, Lab of Excellence ARBRE *Location*: Nancy, France *Job Description: * A postdoctoral researcher position is available immediately in the lab of Francis Martin at the Tree-Microbe Interactions Department at INRA in Nancy, France. Martin’s lab uses computational approaches to study how saprotrophic and symbiotic (mycorrhizal) fungi evolve and adapt to their environments. Ongoing projects fall into the following broad areas: 1) Studying the emergence of the symbiotic mutualism in fungal and tree species by phylogenomics; 2) Characterization of symbiosis-related genes by using comparative transcriptomics; and 3) Deciphering genomic signatures of fungal adaptations to carbon decay and sequestration in forest habitats by metatranscriptomics. More information about Martin’s lab is available at http://mycor.nancy.inra.fr/blogGenomes/?page_id=149. Qualified applicant must have a Ph.D. in bioinformatics, computational biology, computer science, evolutionary biology or a related field with background and strong interest in molecular evolution of Fungi. The ideal candidate will already have some experience working with large genomic data sets from sequenced fungi or plants. This position requires a high level of proficiency in programming skills, and experience applying computational methods to genomic data is highly desirable. Applicants must possess good communication skills and be fluent in both spoken and written English (or French). Strong skills in the use of unix-based computer software, critical thinking, problem-solving abilities, and the ability to work semi-independently are also required. The responsibilities will include pipeline development for analyses of next-generation data sets and utilization of high-performance computing facilities. The successful candidate should anticipate contributing to a variety of ongoing collaborative research projects with the Joint Genome Institute, including the 1000 Fungal Genomes project and the Mycorrhizal Genomics Initiative, with teams across France, Europe and the United States. In addition to becoming a part of a vibrant research and educational environment, the incumbent can take advantage of professional development programs offered by Laboratory of Excellence ARBRE (http://mycor.nancy.inra.fr/ARBRE/?page_id=2&lang=en) The initial appointment is for one year with the possibility of renewal for up to two additional years contingent upon performance and funding. Review of applications will begin immediately and continue until the position is filled. Start date is July 1st, 2016 at the latest. *Interested applicants should send a single PDF file containing CV, one-page statement of research interests and contact information of three referees to Francis Martin at fmartin[at]nancy.inra.fr.* -- Emmanuelle MORIN UMR 1136 INRA/Université de Lorraine F-54280 Champenoux Tel : + 33 3 83 39 41 33 http://mycor.nancy.inra.fr

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Benelearn 2016: last call for abstracts (with deadline extension)
by Yvan Saeys 31 May '16

31 May '16

LAST CALL FOR ABSTRACTS: BENELEARN 2016 September 12-13, 2016. Kortrijk, Belgium http://www.kuleuven-kulak.be/benelearn/ Benelearn is the annual machine learning conference of Belgium and The Netherlands. It serves as a forum for researchers to exchange ideas, present recent work, and foster collaboration in the broad field of Machine Learning and its applications. The 25th edition will be co-organised by KU Leuven, UGent and the Flemish Supercomputer Centre, in cooperation with the Dutch Research School for Information and Knowledge Systems (SIKS), at the Katholieke Universiteit Leuven, Campus Kortrijk (KULAK). In contrast to previous editions, the anniversary edition of Benelearn will be organised on two days, where the first day will feature a workshop on Big Data, including keynote speakers, a tutorial session, corporate presentations, and ample opportunity for networking. KEYNOTE SPEAKERS: The following keynote speakers have agreed to speak at the conference: Jeff Ullman (Stanford University) Christian Blum (University of the Basque Country) Greg Tsoumakas (Aristotle University of Thessaloniki) Kristian Kersting (TU Dortmund) Emilia Barakova (Technische Universiteit Eindhoven) Hugo Ceulemans (Janssen R&D) Luc De Raedt (KU Leuven) Isaac Triguero (UGent / University of Nottingham) SUBMISSIONS: The conference solicits abstract contributions (2 pages max.) of original work or work that was recently accepted or published in a peer-reviewed machine-learning journal or at a high level international conference. In the latter case, the publication reference should be clearly mentioned, and the abstracts will be checked mainly for relevance, rather than receive a full review. The program committee will decide which contributions are selected for an oral presentation, and which ones are presented during a poster session (with spotlight presentations). Submissions related to Big Data analysis will preferably be presented on the thematic day. All accepted contributions will be published on the Benelearn website, but no copyright will be claimed. For submission instructions, please refer to http://www.kuleuven-kulak.be/benelearn/. SCOPE: Although we particularly encourage submissions related to learning from Big Data, submissions from all topics of interest within machine learning are welcome (non-exhaustive list): Kernel Methods Bayesian Learning Case-based Learning Causal Learning Ensemble Methods Computational Learning Theory Data Mining Evolutionary Computation Inductive Logic Programming Knowledge Discovery in Databases Online Learning Learning in Multi-Agent Systems Neural Networks Deep Learning Reinforcement Learning Robot Learning Feature Selection and Dimensionality Reduction Scientific Discovery Transfer Learning Statistical Learning Ranking / Preference Learning / Information Retrieval Computational models of Human Learning Structured Output Learning Learning for Language and Speech Media Mining and Text Analytics Learning and Ubiquitous Computing Applications of Machine Learning Learning from Big Data KEY DATES: Submission deadline (extended): June 7, 2016. Notification of acceptance: July 1, 2016. Conference: September 12-13, 2016. Organizing committee: Celine Vens (KU Leuven) Patrick De Causmaecker (KU Leuven) Yvan Saeys (UGent) Ewald Pauwels (VSC)

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Bioinformatics Internship at Schneider Lab, University of Luxembourg
by ISCBSC announcement 31 May '16

31 May '16

*Bioinformatics Internship at Schneider Lab, University of Luxembourg* *Title:* Developing web resource for enzymes of unknown function *Deadline:* June 18, 2016 The ISCB Student Council is pleased to announce a 6-month internship position with the Schneider Lab at Bioinformatics Core, Luxembourg Centre For Systems Biomedicine (LCSB), University of Luxembourg. The internship is expected to start in August 2016, and it is available to Undergraduate and Masters students in computational biology or related areas from developing nations. To know more about the position, please click on the link below. We strongly encourage all interested applicants to read the entire description as well as the requirements laid out on the page below before attempting to apply. Incomplete applications will not be processed by our submission system. http://career.iscbsc.org For further questions, contact us at internships(a)iscbsc.org. We wish you all the best with your application and we look forward to receiving it. Please forward this message to all who might be interested! Education and Internships Committee ISCB Student Council <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> Virus-free. www.avast.com <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> <#DDB4FAA8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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MLSB2016 submission deadline extended to June 10, 2016
by Dijk, Aalt-Jan van 30 May '16

30 May '16

Due to several requests we have decided to extend the MLSB 2016 submission deadline until June 10, 2016, and the notification deadline until July 8, 2016. The workshop webpage (http://www.eccb2016.org/programme/workshops/w1/) has been updated to reflect the changes. As a reminder we have two tracks: Manuscript track with papers published in BMC Bioinformatics and Highlights tracks for abstracts describing computational aspects of work that has been recently published in a journal (or is “in press”) as well as unpublished/on-going work. Best regards, MLSB 2016 organizers Juho Rousu Dick de Ridder Harri Lähdesmäki Aalt-Jan van Dijk

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Computational Cancer Biology Position in Amsterdam
by m.michaut＠nki.nl 24 May '16

24 May '16

Hi all, Still 1 week to apply for the positon in the Computational Cancer Biology group at NKI in Amsterdam. Have a nice day, Magali Integrative modelling to identify therapy resistance mechanisms Project description The purpose of this project is to identify the underlying resistance mechanisms in invasive lobular carcinoma (ILC). ILCs are known as ‘slow killers’ as they grow relatively slowly, but respond poorly to therapy, eventually killing the patient. To unravel the resistance mechanisms, we have generated comprehensive molecular profiles (gene expression, mutational, copy number and (phospho-)proteomics profiles) from matched pairs of sensitive and resistant mouse models of ILCs. We will employ integrative computational (Bayesian) modeling to integrate prior knowledge and the molecular datasets to identify candidate resistance factors. These will be validated in genetic and pharmacological perturbation studies in cultured ILC cell lines and mouse models. Knowledge of these mechanisms will enable us to design combination therapies able to block the development of resistance, leading to improved therapy response. The successful candidate will be responsible for carrying out all the computational analyses, including the complete analysis workflow starting at the basic analyses of the DNA and RNA sequencing and mass spectrometry data up to the more complicated integrative analyses and the Bayesian pathway modelling. He/She will also be expected to coordinate the project and to liaise with the molecular biologists, the animal facility, the genomics core facility and the proteomics facility. The project will be carries out in close collaboration with the groups of Jos Jonkers (mouse models of breast cancer) and Maarten Altelaar (proteomics). Candidate profile We are seeking highly motivated Postdoc or PhD candidates with a degree in bioinformatics, computer science or a related discipline. Applicants should be experienced in cancer biology and clinical applications and should be skilled in analysing high-throughput molecular data. Experience in analyses of (phospho)-proteomics data is a plus. The candidate needs to be proficient in common bioinformatics scripting and programming languages (e.g. R, Python). Interested? Please send CV and motivation letter to Magali Michaut (m.michaut(a)nki.nl<mailto:m.michaut@nki.nl>) & Lodewyk Wessels (l.wessels(a)nki.nl<mailto:l.wessels@nki.nl>). Please include a list of publications and the names and contact information of at least two references. See ccb.nki.nl<http://ccb.nki.nl> for further information. Deadline 1 June 2016

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[Gtpb] Course announcement BPBR16 Bioinformatics using Python for Biomedical Researchers
by Pedro Fernandes 23 May '16

23 May '16

ANNOUNCEMENT Applications for BPBR16 - Bioinformatics using Python for Biomedical Researchers with Allegra Via and Vincenza Colonna are open IMPORTANT DATES for this Course Deadline for applications: July 4th 2016 Latest notification of acceptance: July 6th 2016 Course date: July 11th - July 15th 2016 Candidates with adequate profile will be accepted in the next 72 hours after the application until we reach 20 participants. Course Description Python is an object-oriented programming language that is ideal for biological data analysis. The course will start from zero knowledge, and will introduce the participants to all the basic concepts of Python such as calculating, organizing data, reading and writing files, program logic and writing larger programs. All the examples and practical sessions will focus on solving biological problems. In particular the sessions will cover: working with DNA and protein sequences data retrieval from files and their manipulation running applications, such as BLAST, locally and from a script finding motifs in sequence parsing common file formats (Uniprot, GenBank, PDB, BLAST) with Biopython ways to find and correct program errors The course will be highly interactive and the students will continuously put theory into practice while learning. By the end of the course, the participants will have a good understanding of Python basics and will have acquired the skills to manage any type of bioinformatics database record and to run applications from scripts. Basic Unix/Linux skills will be provided at the beginning of the course. Target Audience End-users of bioinformatics databases and tools that aim at developing hands-on capabilities for biological data analysis, ie writing their own or adapting somebody else's Python scripts in an autonomous way. Course Pre-requisites Basic familiarity with bioinformatics data resources such as Uniprot/Swiss-Prot, Blast, ENSEMBL, PDB, etc. The course is directed to biologists with little or no programming experience and aims at making them capable to use Python to autonomously manage and analyse biological data. More details at the GTPB website http://gtpb.igc.gulbenkian.pt/bicourses/BPBR16/ Best wishes Pedro Fernandes -- Pedro Fernandes GTPB Coordinator Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL Tel +351 21 4407912 http://gtpb.igc.gulbenkian.pt _______________________________________________ GTPB mailing list GTPB(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb

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Edinburgh Genomics bioinformatics workshops - Register interest for workshops
by Bert Overduin 20 May '16

20 May '16

Hi all, It is now possible to register your interest for workshops that we are planning to offer in the future, but for which we haven't set a date yet. This helps us to determine whether there is enough interest for a workshop to start organising it. We also will use this information to mail you as soon as registration opens for a workshop you have expressed interest in. At the moment you can register your interest for 5 workshops: Introduction to ChIP-Seq Data Analysis (2 days) Introduction to RAD-Seq Data Analysis (2 days) Introduction to RNA-Seq Data Analysis (2 days) Introduction to Variant Analysis of NGS Data (2 days) Oxford Nanopore MinION Sequencing - Data Handling, Analysis and Applications (1 day) To register your interest for one or more of these workshops, please go to: https://www.surveymonkey.co.uk/r/3LRCW7D With kind regards, Bert -- 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.

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