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three vacancies at BaseClear, Leiden
by Iris Kolder 20 Sep '17

20 Sep '17

Dear All, BaseClear is a contract laboratory specialised in DNA analysis. For all areas in which DNA plays a key role, BaseClear has been offering services in the form of convenient and high-quality solutions for the last 25 years. BaseClear distinguishes itself by having a highly customer orientated approach, working in close collaboration with customers to develop solutions specifically matched to their needs. BaseClear offers a number of service packages based on the innovative Next Generation sequencing technologies. Over the last two decades we have gained considerable experience and expertise in microbial genome and transcriptome analysis and currently offer a comprehensive package of services to customers in these fields. Management of "big data" and the development of reliable lab-supporting software play a crucial role to keep up with the growing interest in these services. We are currently looking for three candidates for the position of: 1. Junior-Bioinformatician 2. Bioinformatics-software-engineer 3. Bioinformatics-software-specialist Please find more information on these positions on our website https://www.baseclear.com/career-jobs Kind regards, Met vriendelijke groet, Iris Kolder, Senior Bioinformatician

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three vacancies at BaseClear, Leiden
by Iris Kolder 20 Sep '17

20 Sep '17

Dear All, BaseClear is a contract laboratory specialised in DNA analysis. For all areas in which DNA plays a key role, BaseClear has been offering services in the form of convenient and high-quality solutions for the last 25 years. BaseClear distinguishes itself by having a highly customer orientated approach, working in close collaboration with customers to develop solutions specifically matched to their needs. BaseClear offers a number of service packages based on the innovative Next Generation sequencing technologies. Over the last two decades we have gained considerable experience and expertise in microbial genome and transcriptome analysis and currently offer a comprehensive package of services to customers in these fields. Management of "big data" and the development of reliable lab-supporting software play a crucial role to keep up with the growing interest in these services. We are currently looking for three candidates for the position of: Junior-Bioinformatician https://www.baseclear.com/career-jobs/Junior-Bioinformatician-(m/f)_30_31.h… Bioinformatics-software-engineer https://www.baseclear.com/career-jobs/Bioinformatics-software-engineer-(m/f… Bioinformatics-software-specialist https://www.baseclear.com/career-jobs/Bioinformatics-software-specialist-(m… Kind regards, Met vriendelijke groet, Iris Kolder, Senior Bioinformatician

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Two postdoc positions in single-cell bioinformatics and machine learning
by Stein Aerts 19 Sep '17

19 Sep '17

Dear colleagues, I have two vacancies in my lab for computational postdocs to work on single-cell regulatory genomics, both in Drosophila and human systems. Kind regards, Stein Aerts

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[Gtpb] GTPB course announcement PM17 Precision Medicine
by Pedro L. Fernandes 19 Sep '17

19 Sep '17

PM17 Precision Medicine with Fátima alShahrour, Javier Perales and Elena Piñeiro IMPORTANT DATES for this Course Deadline for applications: Oct 18th 2017 Course dates: Nov 14th - Nov 17th 2017 Candidates with adequate profile will be accepted in the next 72 hours after the application, until we reach 20 participants. Course description: The implementation of cancer genomics into the clinic is becoming a reality. Personalized medicine or Precision medicine as other authors refers, uses molecular data of a specific patient to guide clinical decisions such as prevention, diagnosis and treatment. This will revolutionize healthcare and will play a dominant role in the future of cancer therapy. Bioinformatics analyses are essential to identify patients who will benefit from treatment based on their molecular profile, and to tailor chemotherapeutic regimens accordingly. The aim of the course is to present a complete computational pipeline for the analysis and interpretation of Next-Generation Sequencing (NGS) data such as exome sequencing or targeted panels that are commonly used in the clinic. We will address the implementation of large-scale genomic sequencing in clinical practice and the recently developed computational strategies for the analysis of NGS data with a particular emphasis on the interpretation of the results, selection of biomarkers of drug response and afford opportunities to match therapies with the characteristics of the individual patient's tumour. Exercises and case studies focused on cancer will be used to illustrate the principles of how genetics influence led to refining diagnoses and personalized treatment of cancer disease. Additional details here: http://gtpb.igc.gulbenkian.pt/bicourses/PM17/ We hope that this training course will meet your interests, Pedro Fernandes -- Pedro L. Fernandes Bioinformatics Training Coordinator Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL 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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(no subject)
by Nicolaes G (BIOCH) 19 Sep '17

19 Sep '17

Dear BBClist subscriber, The NSBM cordially invites all who interested to visit its Fall Meeting, November 29th 2017. Application procedure * Participants should send an email to register (required but free registration) to: g.nicolaes(a)maastrichtuniversity.nl<mailto:science.secr.nmr@uu.nl> * Submission of an abstract is required if you want to present a poster. * Indicate in your email if you want be selected for a short oral presentation. Deadlines: * Registration deadline to be considered for a short talk: November 17th * Registration deadline (including lunch): November 22th Note: The maximum number of participants is limited to 75! So please register on time. Costs Attendance is free of charge but registration is required. Lunch and coffee will be provided thanks to the support of the Nijmegen Centre for Molecular and Biomolecular Informatics Lead contact * Dr. Gerry Nicolaes<http://www.uu.nl/staff/amjjbonvin> - g.nicolaes(a)maastrichtuniversity.nl<mailto::g.nicolaes@maastrichtuniversity.nl> Confirmed Keynote speakers * Prof. Jürgen<http://lbm.epfl.ch/> Pleiss, Universität Stuttgart, Germany. * Prof. Chris<http://www.uu.nl/staff/FGForster> Ulens, KU Leuven, Belgium. * Dr. Tom van den Bergh, Bio-Prodict, Netherlands The full programme will soon be made available via: http://www.3dstructure-function.nl/nsbm-fall-meeting/<http://www.3dstructure-function.nl/?page_id=912&preview=true> A flyer is enclosed. With kind regards, on behalf of the NSBM, Gerry Nicolaes

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EuBIC 2018 developer’s meeting - Extended project submission deadline
by EuBIC developer's meeting 16 Sep '17

16 Sep '17

*— EuBIC 2018 developer’s meeting —* *Project proposal submission deadline extended!* Project submission proposal is now open until *September 24, 2017*. EuBIC members will be present at the HUPO conference in Dublin this week. Find us there at the bioinformatics hub to get more information about the developer’s meeting and discuss your project proposal. To submit a project proposal please follow the instructions provided here: http://uahost.uantwerpen.be/eubic18/submission.html *EuBIC 2018 developer’s meeting* Date: January 9-12, 2018 Venue: Hotel Monasterium PoortAckere, Oude Houtlei 56, 9000 Gent, Belgium For more details on the program, please check the website: http://uahost.uantwerpen.be/eubic18/ *Key dates* *September 24, 2017: Extended project proposal submission deadline* October 2, 2017: Announcement of selected projects October 2, 2017: Conference registration opens January 9-12, 2018: EuBIC 2018 developer's meeting in Ghent *Topics* Hackathon projects can cover all topics in proteomics bioinformatics, including, but not limited to: - Tools - Extension of existing bioinformatics tools under the guidance of their original authors - Development of novel bioinformatics tools to solve open problems - Benchmarking - Compilation of gold-truth datasets - Collection of reference algorithmic implementations - Specification of benchmarking criteria - Workflows - Definition of formal protocols - Development of tutorials for bioinformatics software usage - Data analysis - (Re)analysis of publicly available proteomics datasets *More information* - website: http://uahost.uantwerpen.be/eubic18/ - social media hashtag: #EuBIC18 - conference email: eubic18(a)gmail.com *Sponsorship *inquiries are welcome at eubic18(a)gmail.com We look forward to welcoming you in Ghent! On behalf of the organizing committee, Wout Bittremieux

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Registration open for: BioSB RNA-seq data analysis course (7th edition) on 6-8 November 2017
by Femke Francissen 13 Sep '17

13 Sep '17

BioSB RNA-seq data analysis course (7th edition) Date: 6-8 November 2017 Location: Leiden University Medical Center, the Netherlands Course coordinators: Peter-Bram ‘t Hoen (LUMC), Leon Mei (LUMC), Jan Oosting (LUMC), Szymon Kielbasa (LUMC) Course website: http://biosb.nl/education/course-portfolio/rna-seq/ . Registration: http://biosb.nl/education/course-portfolio/rna-seq/ enrollment-rna-seq-2017/ Course description The BioSB research school and partner LUMC are organizing a 3-day course on RNA-seq data analysis. This is an advanced course for people with experience in NGS. The course will consist of lectures, Galaxy and R practicals and will cover the analysis pipelines for differential transcript expression and variant calling. Examples will be taken from human and mouse studies. The course does not cover prokaryotic RNA profiling nor plant- and metagenomics aspects. Course topics - RNA-seq experimental approaches and study design - Quality control and alignment - Statistics for differential gene expression - eQTL analysis and allele specific expression - Single cell RNA sequencing - Fusion transcript detection - Small RNA profiling - Software for RNA-seq data analysis Target audience Participants for the RNA-seq course should preferably have participated in the general NGS course or otherwise have demonstrated hands-on experience with NGS data analysis. The course is aimed at PhD students and post-docs, but scientific programmers and data analysts with a background in biology and bioinformatics may also attend. NB: The practicals are mostly in R. We require that participants have at least basic knowledge of R and experience in running R scripts. Participants must bring own laptops capable of running RStudio. Please download and install RStudio before the course. For Galaxy tutorial, please install firefox or google chrome web browser. Registrations will be handled on a first-come-first-served basis but experience and motivation will be reviewed.Registrations will be handled on a first-come-first-served basis but experience and motivation will be reviewed. Seats have been reserved for participants in the FP7-funded projects RD-Connect <http://rd-connect.eu/> and BBMRI-NL <https://www.bbmri.nl/>. 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. ** ** *Femke Francissen* Community manager BioSB Research School *NEW V*isiting address (as of 1 July 2017): Jaarbeurs Innovation Mile (JIM) | 6th floor Beatrixgebouw | Jaarbeursplein 6 | 3521 AL Utrecht *NEW **Postal address *(as of 1 July 2017): Postbus 8500 | 3503 RM Utrecht E-mail: femke.francissen(a)biosb.nl Mobile: +31 6 17 90 4888 Skype: femke.francissen Website: www.biosb.nl LinkedIn link <http://nl.linkedin.com/in/femkefrancissen>

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Registration open for BioSB course: Protein Structures (4th edition) - 31 Oct-3 Nov 2017
by Femke Francissen 13 Sep '17

13 Sep '17

BioSB course Protein Structures: production, prowess, power, promises, and problems (4th edition) Date: 31 October - 3 November 2017 Location: CMBI, Radboudumc, Nijmegen, the Netherlands Course coordinator: Gert Vriend (CMBI, Radboudumc) Lecturers: Daniel Hoffmann (University Duisburg/Essen (TBC)), Hanka Venselaar (CMBI), Wouter Touw (CMBI) *Website*: course website <http://biosb.nl/education/course-portfolio/protein-structures-production-pr…> *Registration:* registration form <http://biosb.nl/education/course-portfolio/protein-structures-production-pr…> Target audience The course is suitable for both PhD students working in structural bioinformatics as well as for PhD students in the life sciences who want to learn more about using structural informatioin in their research. The course schedule accommodates both groups, parallel sessions for both groups will be scheduled when necessary. Course Description In the right hands, protein structures are a ‘power’ful tool to answer bio-molecular questions. Knowledge of the structure is a pre-requisite for rational drug design, for biotechnology, for chemical biology, and for answering a whole series of biomedical questions. In this course we will discuss the ‘production’ of protein structures by NMR, X-ray, and homology modelling. These methods all have their pro’s and cons so a certain ‘prowess’ is needed to follow all ‘promises’ and start attacking bio-medical ‘problems’ using protein structures. The course will be split in three parts: - Part 1) Looking and seeing things in protein structures, learning to operate the software, understanding some of the algorithms. - Part 2) Protein structure determination (prediction) with NMR, X-ray, and homology modelling, and the possibilities and problems that come with each of these three techniques. - Part 3) Applying all that was learned in real-life example studies. Course topics Day 1: Homology modelling seminar Day 2: Protein structure comparison seminars Day 3: Electrostatics and molecular dynamics seminars Day 4: Protein structure determination and validation seminars Day 5: Own project executed with help from CMBI staff Examples of questions you will be able to answer after follwing the course: - Why is a person with this mutation sick? Or in other words, how does the molecular phenotype cause a disease state? - This enzyme converts mannose. Can I make is specificity broader? - This enzyme doesn’t function in my in vitro assay. Should I add some ions? - I want to add a tag to my enzyme, should I put it on the N-terminus, the C-terminus, or is something different needed? - This receptor binds a ligand, but if I look at the structure, that ligand doesn’t fit at all. Can I predict motions that take place upon ligand binding? 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. ** ** *Femke Francissen* Community manager BioSB Research School *NEW V*isiting address (as of 1 July 2017): Jaarbeurs Innovation Mile (JIM) | 6th floor Beatrixgebouw | Jaarbeursplein 6 | 3521 AL Utrecht *NEW **Postal address *(as of 1 July 2017): Postbus 8500 | 3503 RM Utrecht E-mail: femke.francissen(a)biosb.nl Mobile: +31 6 17 90 4888 Skype: femke.francissen Website: www.biosb.nl LinkedIn link <http://nl.linkedin.com/in/femkefrancissen>

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post-doc offer
by Eric Bonnet 11 Sep '17

11 Sep '17

Post-doctorate in omics data integration and network science “Proteogenomic analysis of patient-specific network perturbations caused by genetic alterations in cancer” Context The diagnostic of cancer in a patient begins with a clinical examination followed by a blood test, medical imaging and often ends with the histopathological analysis of a tumor biopsy in order to establish the cancer type and the therapeutic strategy. One of the objectives of the France Genomic Medicine 2025 plan is to improve diagnostic and treatment selection by also taking into account genomic profiling obtained from NGS sequencing. However, recent research from the NCI Clinical Proteomic Tumor Analysis Consortium (CPTAC) demonstrated that the integration of proteomic profiles with genomic information, now referred to as "proteogenomics," reveals subtypes of cancers that are inaccessible by NGS. Our project is a transverse initiative (https://proteogenomics.wordpress.com/) between three CEA french research centers CNRGH-LBI (National Human Genome Research Center – Bioinformatics lab), BIG-EDyP (Biosciences and Biotechnology Institute of Grenoble – Proteomics lab), LIST-LADIS (Laboratory of Embedded Systems and Technology – Big data analysis lab) and BIFI-COSNET lab (Institute for Biocomputation and Physics of Complex Systems – Complex systems and networks lab) from the University of Zaragoza to contribute to the emergence of proteogenomics in precision medicine. Our final goal is to implement a "patient-centered" software solution capable of structuring, integrating and interrogating genomic and proteomic profiles from the same tumor in order to improve diagnostic and therapy. We will develop methods that capture and model the deregulations of molecular networks at stake in cancer, to identify patient-specific network perturbations and exploit them to provide better diagnostic. We already achieved significant progress on two in silico developments (not yet published) which can be considered as building blocks to our project: - We designed and implemented a graph-based database to structure and interrogate multi-omic tumoral data. This database was constructed using the triple-store technology to allow writing complex queries and to facilitate aggregation of public biological data repositories. - We developed a proteogenomic workflow to analyse proteomic data using a priori information extracted from transcriptome profiling. This approach, evaluated on a cancer cell line, allowed us to identify genetic alterations translated at the proteome level. Objectives The post-doctorate will develop a methodology to explore patient-specific perturbations on molecular networks and particularly on signaling pathways caused by genetic alterations (single nucleotide variants, aberrant transcript splicing) identified from proteogenomic profiling of tumor biopsies. He will leverage complexity of these multi-omic data to assess the impact of genetic variants on multiple regulatory dimensions, from transcriptional to post-translational levels. To reach this goal, the applicant will first analyse onco-proteogenomic data to infer patient-specific genetic alterations affecting its genome, transcriptome, proteome or phosphoproteome. Then, he/she will work on (i) the structuring of data obtained from each patient to define relationships between multi-omic measurements and (ii) the development of complex queries to reveal multidimensional perturbations. These investigations will be carried out using the multilayer network formalism and algorithms. This rapidly expanding research field was already successfully applied to multi-omic data to extract biological subnetworks, to identify genes with maximum influence on the process of perturbation spreading and to classify patients into cancer subtypes. Resources This methodology will be developed using large-scale omics data made publicly available by several international research consortia (GTEX, CPTAC, NIH Epigenomics Roadmap) and tested on proteogenomic profiles in-house produced from cancer cell lines. Moreover, data storage and computational needs required by this large-scale project will be available at the CEA HPC infrastructure. Host laboratories The recruited young researcher will be hosted by the BIG-EDyP laboratory in Grenoble and will evolve within a multidisciplinary research team. He/she will also spend research periods in collaborating laboratories to optimize progression of the research project. Expected competences The applicant should have a PhD in computational biology or related domains. He/she should be experienced in omics fields with at least one of these fields of expertise: bioinformatics, data integration or network science, and strong interest for all of them. Moreover, programming experience is required. Research contract Funding for a one-year post-doctoral contract is already available with gross annual salary range from about €41,000 to €58,000 depending on experience. We are looking for a candidate motivated to apply for additional funding at the CEA Enhanced Eurotalents Programme (http://eurotalents.cea.fr/) Contact If you are interested by this opportunity please send your CV, a motivation letter and names of referees to christophe.battail(a)cea.fr.

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BBC2017, Leuven 13th-14th December - Registration open
by Daniele Parisi 09 Sep '17

09 Sep '17

Dear Mr/Mrs, we are happy to announce that the registration for the 13th edition of the BENELUX BIOINFORMATICS CONFERENCE is officially opened. The BBC is the key annual event that brings together researchers working at the intersection of a broad range of disciplines including computer science, biology, and medicine in Belgium, the Netherlands and Luxembourg. Don't miss the chance to use the power of our network, join the conference by filling in the REGISTRATION FORM available on this link https://goo.gl/forms/psc1ADA9Ag4o53Z23 The event will take place on WEDNESDAY 13TH AND THURDAY 14TH OF DECEMBER IN LEUVEN. The draft of the program, the list of keynotes and other useful information will be soon uploaded on the WEBSITE https://bbc2017blog.wordpress.com/ We are looking forward to meet you and discover your research at the conference. Kind regards The organization committee -- DANIELE PARISI PhD student at ESAT - STADIUS, Yves Moreau's group President of RSG Belgium Board member of PhD Leuven society Kasteelpark Arenberg 10 - box 2446 3001 Leuven, Belgium Tel: +32488794394

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