May 2011 - BBClist - maillist.psb.ugent.be

Bioinformatics Postdoc
by Lodewyk Wessels 02 Dec '12

02 Dec '12

POST DOCTORAL BIOINFORMATICIAN IDENTIFICATION AND VALIDATION OF NEW TARGETS FOR COLORECTAL CANCER OVERALL OBJECTIVES The aim of this project is to redefine colorectal cancer (CRC) at the molecular level, by identifying and validating new activated pathways and specific drug targets for defined CRC patient populations. The project will employ the complementary expertise and tools at Astra Zeneca, two academic laboratories (those of Lodewyk Wessels and Rene Bernards at the Netherlands Cancer Institute, Amsterdam) and a leading diagnostics company with an established presence in oncology (Agendia BV, Amsterdam). PROJECT OUTLINE AND STRATEGY We will first use computational approaches to perform a ‘pathway’ or ‘module’ level integration of molecular profiling (gene expression and next generation sequencing data) and extensive clinical annotation data from a collection of 400 CRC tumours to identify and prioritise pathways that are deregulated in each CRC sub-disease. Next, we will define for each pathway, targets that are amenable to drug discovery efforts, and that can be validated in cell culture models. To enable target validation, we will develop approaches to identify, based on molecular profiling data, CRC cell lines in the AZ collection that represent each molecular sub-disease. Once these are in place, target validation experiments will be conducted, using established RNAi methodology. Targets whose functions are shown to be essential for cell viability in the appropriate cell line models will then be recommended for new drug discovery projects. These results will be fed back to refine the target section procedure based on the tumor data. EMPLOYER INFORMATION The Netherlands Cancer Institute is a dedicated cancer center conducting research in all major areas of cancer, with a strong emphasis on translational research. The Bioinformatics and Statistics group (Wessels lab.) provides leadership on the collection and analysis of data for the research programs of the institute, by developing novel compuational approaches and performing state of the art analyses of a wide array of data types, including laboratory and animal experiments, clinical trials, and epidemiologic studies. REQUIREMENTS The ideal candidate is a highly motivated postdoc with a strong background in bioinformatics or computational biology. The vacancy is a research position within the field of bioinformatics/computational biology and the research will be carried out in close collaboration with the involved partners: Bernards lab, Astra Zeneca and Agendia. The ideal candidate has a background in the analysis of high throughput molecular data, computational diagnostics, bioinformatics, computer science, statistics or physics with strong analytical and algorithmic skills. EMPLOYMENT CONDITIONS The temporary employment will be for a period of three years. The gross monthly salary for a Postdoc will range from €3140,- to €3.495,- and depends on previous experience. We can help you find housing. The NKI-AVL has been listed in the top 25 of ‘Best Employers’ in 2009 offering a specialized cancer research institute and hospital with good working conditions and an excellent atmosphere. INTERESTED? Please contact Dr. Lodewyk Wessels, tel. +31 20 512 7987 or e-mail: l.wessels(a)nki.nl or Dr George Orphanides, Director of Discovery Medicine, tel. +44 1625 232312 or e-mail George.Orphanides(a)astrazeneca.com. When applying please ensure you include a CV, list of publications and the names and addresses of at least two persons that can be approached to obtain further information. http://bioinformatics.nki.nl CLOSING DATE 1 May 2011

1 2

Integrative Bioinformatics 2011: 2nd call for abstracts
by Jack Leunissen 16 Jul '12

16 Jul '12

Dear colleague, The 2011 International Symposium on Integrative Bioinformatics (IB2011) will take place on March 21-23, 2011 in Wageningen (the Netherlands). This seventh meeting on Integrative Bioinformatics will be of interest to bioinformaticians, computer scientists and all working in, or interested in the developing area of integrative bioinformatics. There will be opportunities to present and discuss methods, theoretical approaches, and their practical applications. We invite you to register for the conference, and to send in an abstract for a presentation at the conference. Accepted abstracts will be invited for a presentation at the conference, and will also be invited to send in a full manuscript, to be published (after peer reviewing) in the IB2011 Special Issue of the Journal of Integrative Bioinformatics. The deadline for sending in an extended abstract is January 15th; submissions should not exceed 4 pages. Authors will be informed of acceptance before February 1st. There are also opportunities for presenting posters and software demonstrations at the Symposium. The deadline for sending in abstracts for posters or a software demo is February 15th, 2011. The best poster will receive an award sponsored by IMBio e.v. The conference website is open for registration and abstract submission, and can be found at www.bioinformatics.nl/ib2011/ and www.imbio.de/ib2011/. We hope to meet you in March in Wageningen. On behalf of the organizing committee, Jack Leunissen Wageningen UR IB2011 is organized by Wageningen University, the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, and IMBio e.V. == Disclaimer: We have tried our best to remove duplicate e-mail addresses from our mailing list to reduce the amount of clutter in your mailbox. It may nevertheless still happen that you receive this mail via different channels. We apologize if you receive this mail more than once.

3 3

INTERNSHIPS at DSM - Bioinformatics / Protein Engineering / Biostatistics
by Roubos, Hans 26 May '11

26 May '11

INTERNSHIPS: BIO-INFORMATICS / PROTEIN ENGINEERING / BIO-STATISTICS On a regular basis we have opportunities for internships in the Delft-based bioinformaticsgroup for M.Sc. students in Bioinformatics, Metabolic engineering, Protein engineering,Genomics, Synthetic Biology or Biostatistics. We apply these technologies to microbial andfungal strain engineering, bio-process and bio-product development in the areas of food,feed, pharma, biofuels and bio-based products. If you are interested in a 5-8 month periodat DSM, please send your CV and a motivation letter to: marco.groot-de(a)dsm.com<mailto:marco.groot-de@dsm.com> DSM - Life Sciences & Materials Sciences Company DSM creates innovative products and services in Life Sciences and Materials Sciences thatcontribute to the quality of life. DSM's products and services are used globally in a widerange of markets and applications, supporting a healthier, more sustainable and moreenjoyable way of life. End markets include human and animal nutrition and health, personalcare, pharmaceuticals, automotive, coatings and paint, electrics and electronics, lifeprotection and housing. DSM has annual sales of almost EUR 8.8 billion and employs some 23,000 people worldwide.Please visit our website at www.dsm.com<http://www.dsm.com/> Hans Roubos Senior Scientist Bioinformatics DSM Biotechnology Center | Alexander Fleminglaan 1 | 2613 AX Delft | The Netherlands | T +31 15 2792147 | F +31 15 2793771 | hans.roubos(a)dsm.com | www.dsm.com | Trade Registration number 27235314 [cid:692192906@26052011-0E3C] ________________________________ DISCLAIMER : This e-mail is for the intended recipient only If you have received it by mistake please let us know by reply and then delete it from your system; access, disclosure, copying, distribution or reliance on any of it by anyone else is prohibited. If you as intended recipient have received this e-mail incorrectly, please notify the sender (via e-mail) immediately.

1 0

Ph.D. studentship in bioinformatics
by Dirk VALKENBORG 19 May '11

19 May '11

Dear Colleagues, May I draw your attention to the following joint vacancy at UHasselt and VITO: Development of novel algorithms for the analysis of post-translational modifications in mass spectrometry data For more information and to apply, please visit: http://www2.uhasselt.be/actueel/vacatures/vac32147e.asp Kind regards, Dirk Valkenborg

1 0

INSERM training workshops: genome-scale approaches to genetic and epigenetic regulation
by Jacques van Helden 16 May '11

16 May '11

The Institut National de la Santé et de la Recherche Médicale (INSERM) organizes two coupled training workshops on genome-scale approaches to genetic and epigenetic regulation. Participants can register to either workshop independently, or to both workshops. Target audience: researchers, physicians, post-docs, technicians, engineers and students in the domains of life science or bioinformatics. All conferences will be given in English. Registration deadline: June 1st, 2011. Detailed programs and registration forms: http://www.rh.inserm.fr/INSERM/IntraRh/RHPublication.nsf/mDisplayMotsClefsW… Email: ateliers(a)inserm.fr Training workshop 211: High-throughput approaches in epigenomics Organizers: Emmanuel Barillot (Institut Curie/INSERM/Mines ParisTech, Paris), Christophe Lavelle (CNRS, Muséum National d'Histoire Naturelle, Paris). Phase I (theory): October 10-12, 2011, Bordeaux (France). Phase II (practical): 2011, Paris, Montpellier, Nice/Marseille (France), and Darmstadt (Germany). Aims. Through its polymorphism, as evidenced by the heterogeneity of its physicochemical properties, chromatin is the support of an information — so-called "epigenetic" — which is superimposed to the genetic information — carried by DNA — to determine cell fate. While genetic sequencing, more and more efficient, provides data at a dizzying pace, the "epigenetic sequencing" is in turn becoming a priority in an attempt to gather all information necessary for the deciphering of cellular function. The challenge of this new quest is obvious when we know that, contrary to genetic information, epigenetic information varies from one cell to another (within the same organism) and in regard with the cell cycle, making the epigenome particularly difficult to establish. However, the first high-resolution epigenetical maps begin to emerge, including information as diverse (and complementary) as the position of nucleosomes, the presence of histone variants and their modifications, the distribution of transcription factors and remodeling factors, and location of DNA methylation. While these profiles accumulate, the need is urgent to develop analytical tools that allow efficient analysis of these data, in hopes of eventually cracking the epigenetic code. The objective of this workshop is to present the most recent techniques (mainly ChIP-seq) in this area, focusing on possible problems commonly encountered in their implementation. Beyond the "wet" technical aspects, a presentation of the most common bioinformatics tools for analysis (peak finding, differential analysis, integrative analysis of profiles, databases, ...) will also be provided. Training workshop 212: Bioinformatics approaches to decipher genome regulation from high-throughput data Organizers: Jacques van Helden (ULB, Belgium), Philipp Bucher (SIB/ISREC, Switzerland). Phase I (theory): October 12-14, 2011, Bordeaux (France). Phase II (practical): December 12-16, 2011, Marseille (France). Aims. Genome regulation plays a crucial role in embryonic development, adaptation of cells, tissues and organisms to their environment, and evolution. This regulation occurs at multiple levels: transcription, RNA maturation (splicing, degradation), micro-RNA, nucleosome occupancy, chromosome conformation. New high-throughput methods offer unprecedented ways to characterize regulatory elements at a genome scale: expression microarrays, ChIP-on-chip, ChIP-seq, RNA-seq, protein binding arrays, etc. Sequencing platforms become available in many institutes, but researchers generally feel some perplexity when they are first confronted to the terabases of novel data. New software tools re being developed to answer those new needs, but their utilization requires to understand the underlying principles, master the parameters, and interpret the significance of the result. The goal of this workshop is to provide researchers with a theoretical and practical training enabling them to apprehend the whole flow of data analysis, from data acquisition to biological interpretation of the results. Jacques van Helden Jacques.van.Helden(a)ulb.ac.be http://www.bigre.ulb.ac.be/Users/jvanheld/ Laboratoire de Bioinformatique des Génomes et des Réseaux (BiGRe) Université Libre de Bruxelles, CP263 Boulevard du Triomphe, Accès 2, Campus Plaine. B-1050 Bruxelles, Belgium

1 0

Support Letter for BEDTools!!
by Stéphane Plaisance 11 May '11

11 May '11

Dear all, If you use BEDTools in your daily work, please consider supporting Aaron by following his instructions below. I am a great fan of BEDTools and find that Aaron greatly deserves this for all the time he saved me with BEDTools in the last years. Stephane Begin forwarded message: > From: bedtools-discuss+noreply(a)googlegroups.com > Date: 10 May 2011 23:53:00 GMT+02:00 > To: Digest Recipients <bedtools-discuss+digest(a)googlegroups.com> > Subject: [bedtools-discuss] Digest for bedtools-discuss(a)googlegroups.com - 2 Messages in 2 Topics > Reply-To: bedtools-discuss(a)googlegroups.com > > Today's Topic Summary > Group: http://groups.google.com/group/bedtools-discuss/topics > > BEDTools Needs Your Support! [1 Update] > Topic: BEDTools Needs Your Support! > Aaron Quinlan <aaronquinlan(a)gmail.com> May 09 10:26PM -0400 ^ > > Dear BEDTools User, > > Thus far, BEDTools has had no formal funding and has been supported by myself and a handful of talented and dedicated contributors. A primary goal of my new laboratory is to continue to improve, support and maintain these tools. More ambitiously, I intend to develop a suite of scalable and efficient algorithms for genome arithmetic (e.g., intersect, count, complement, subtract, merge) in order to accommodate the size and complexity of current and future genomic datasets. These new algorithms will be capable of interrogating multiple datasets at once (i.e., moving beyond pairwise comparisons), use less memory, exploit parallel computing architectures, and will have improved support for many more file formats. In turn, "BEDTools 2" will provide entirely new classes of tools for large-scale genomic analyses. > > In order to fulfill these goals, I am seeking NIH funding and I would like to ask for your help. If you find BEDTools to be at all useful in your research, I would like to ask you to write a brief letter of support. Your letter will be included as a supplement to the grant application and it will greatly improve the strength of the grant. > > If you would be willing to document your support of BEDTools, I ask that you: > > - Send an email directly to me (aaronquinlan(a)gmail.com) Please include your name and affiliation. > - Write a few sentences documenting: > . your support for the project > . how you use the tools > . what, if anything, you like about them. > . how they have benefited, improved, or expedited your research. > > Thanks so much in advance for your assistance - a couple of minutes writing an email of support will certainly help me immensely. > > If you know of other users that are not on the BEDTools list but might be interested in helping out, please pass this on. > > Sincerely, > Aaron > > Aaron Quinlan, Ph.D. > Assistant Professor > Department of Public Health Sciences > Center for Public Health Genomics > University of Virginia

1 0

Bioinformatics PhD job opening at Radboud University Nijmegen Medical Centre
by Sacha van Hijum 08 May '11

08 May '11

Dear all, there is a job-opening for a bioinformatics PhD student at the Radboud University Nijmegen Medical Centre. For those interested, please see below for details. Best regards, Sacha van Hijum Job profile The PhD student will work in a multidisciplinary team with other scientists and medical doctors to discuss, plan and perform bioinformatics research in a highly stimulating environment. Work-place will be the Laboratory of Pediatric Infectious Diseases (Prof. dr. P. Hermans) and the Bacterial Genomics group (Dr. S. van Hijum). • Independently generate and analyze data • Present results at (inter)national scientific meetings and in international peer-reviewed journals Requirements • Msc degree in (molecular) life sciences, specializing in bioinformatics • Background in statistics and understanding of bioinformatics algorithms. Knowledge of Perl/Python and R is a plus • Preferably experience in microbiology, molecular biology and biochemistry • Fluent in English (speaking, reading and writing) • An independent and well-structured working style • Teamplayer and a strong motivation to succeed in scientific and translational research Organization unit Laboratory of Pediatric Infectious Diseases The Laboratory of Pediatric Infectious Diseases at Radboud University Nijmegen Medical Centre is an academic research lab in which scientists and medical doctors work closely together to conduct translational research on the pathogenesis, immunology, and epidemiology of pediatric respiratory tract infections. Our studies aim to increase the molecular and clinical understanding of the interactions occurring between host and pathogen during infection. This knowledge is used to design improved and novel diagnostic, therapeutic, and preventive strategies. The Laboratory of Pediatric Infectious Diseases participates in the Nijmegen Institute for Infection, Inflammation, and Immunity (N4i) and the Nijmegen Center for Molecular Life Science (NCMLS), with focus on basic science and its translation into pioneering treatments for disease. The innovations are advanced through technology platforms such as genomics, proteomics, and molecular imaging. The Laboratory of Pediatric Infectious Diseases works in close collaboration with the… Bacterial Genomics group Focus of the Bacterial Genomics group (Radboud University Nijmegen Medical Centre) is on the bioinformatics analysis of ~omics data of (consortia of) bacteria in the context of industrial fermentations, health and safety. The research involves (meta)genome sequencing and assembly, annotation, comparative genomics, RNA-seq, transcriptomics and multivariate analysis of ~omics datasets, all in relation to exploration and exploitation of the enormous microbial diversity that is found in Nature. The Bacterial Genomics group is part of the CMBI (Centre for Molecular and Biomolecular Informatics). The CMBI pursues a rigorous research program with topics ranging from computational small-molecule chemistry to bioinformatics. The CMBI is among the largest bioinformatics departments in the Netherlands producing dozens of high impact peer-reviewed publications each year. It consists of 4 research groups (Prof. Vriend, Prof. Huynen, Prof. de Vlieg and Dr. van Hijum) with strong connections with the NBiC, centre of excellence and the largest bioinformatics cluster in the Netherlands. Information Prof. dr. P.W.M. Hermans, head of the laboratory, (024) 3666406, P.Hermans(a)cukz.umcn.nl Dr. A.L. Zomer, bioinformatician, (024) 3651545, A.Zomer(a)cukz.umcn.nl Dr. S.A.F.T. van Hijum, group leader Bacterial Genomics (024) 3619389, svhijum(a)cmbi.ru.nl More information and online application via this link: http://www.umcn.nl/OVERUMCSTRADBOUD/WERKENBIJ/Pages/Vacature.aspx?VacatureN… -- Dr. Sacha van Hijum Group leader CMBI Bacterial Genomics Group leader Bioinformatics NIZO food research B.V. Bioinformatics coordinator Top Institute Food and Nutrition T: +31(0)318 659 570 F: +31(0)318 650 400 M: +31(0)624782895 E: sacha.vanhijum(a)nizo.nl or svhijum(a)cmbi.ru.nl P.O. Box 20, 6710 BA EDE, The Netherlands Kernhemseweg 2, 6718 ZB EDE, The Netherlands

1 0

Ph.D. /Postdoc positions -ICT & computational research for health care -at IBBT -K.U.Leuven Future Health Department at ESAT
by mimi deprez 02 May '11

02 May '11

Dear members: The IBBT-K.U.Leuven Future Health Department has several job openings for Ph.D. and or postdocs in ICT and computational research for health care located at ESAT. All details can be found on www.kuleuven.be/ibbt/jobopenings <http://www.kuleuven.be/ibbt/jobopenings> or see below the detailed research topics. Positions focusing on genomics and next gen sequencing for translational medicine * Reporting of genome sequencing results in a clinical setting <https://phd.kuleuven.be/set/voorstel.php?id=2204&none=display> * Identification and visualization of structural variation in the human genome <https://phd.kuleuven.be/set/voorstel.php?id=2205&none=display> * High-performance data analytics for nextgeneration sequencing data analysis <https://phd.kuleuven.be/set/voorstel.php?id=2212&none=display> * Network analysis of analysis of disease phenotypes and drug responses <https://phd.kuleuven.be/set/voorstel.php?id=2213&none=display> * Federated and collaborative knowledge bases for genomic medicine <https://phd.kuleuven.be/set/voorstel.php?id=2195&none=display> Positions focusing on biomedical signal processing and hearing aids * Advanced algorithms for integrated EEG-fMRI data processing <https://phd.kuleuven.be/set/voorstel.php?id=2210&none=display> * Compressive Sensing for Biomedical Signals <https://phd.kuleuven.be/set/voorstel.php?id=2207&none=display> * Distributed Noise Reduction in Hearing Aids <https://phd.kuleuven.be/set/voorstel.php?id=2206&none=display> Positions focusing on data mining and biostatistics for pattern recognition, data analysis and data fusion * Policy Decision Support Systems to objectively evaluate care <https://phd.kuleuven.be/set/voorstel.php?id=2203&none=display> * Mass Spectrometry Imaging and Bioinformatics <https://phd.kuleuven.be/set/voorstel.php?id=2202&none=display> * Decision Support Systems for Cardiovascular Diseases <https://phd.kuleuven.be/set/voorstel.php?id=2208&none=display> * Analysis of multicentre data on the preoperative diagnosis of ovarian tumours based on standard and advanced prediction models <https://phd.kuleuven.be/set/voorstel.php?id=2209&none=display> * Biomedical text mining and network analysis for disease gene discovery <https://phd.kuleuven.be/set/voorstel.php?id=2211&none=display> For more information on these positions and requirements please contact inge.thijs(a)esat.kuleuven.be <mailto:inge.thijs@esat.kuleuven.be> or steven.vandeput(a)esat.kuleuven.be <mailto:steven.vandeput@esat.kuleuven.be> ** /The IBBT-K.U.Leuven Future Health Department is part of IBBT, the Institute for Broad Band Technology. IBBT aims to create a lasting and positive impact on society through ICT innovation. IBBT Future Health directs this innovation towards a healthy society, by developing information technologies for health care. To this end, IBBT Future Health combines pioneering research with market-driven R&D, creates synergies with stakeholders and engages in societal outreach. We indeed believe that the key to accessible and efficient health care lies in the cross-fertilization between research, technology and health care itself. IBBT Future Health joins the forces of 80 researchers in four K.U.Leuven research groups, and enables an interdisciplinary approach of innovative ICT for health care thanks to its multifaceted expertise, including data mining, bioinformatics, biomedical data processing, advanced image computing, the creation of e-learning environment, and user experience research. //More info at /www.kuleuven.be/ibbt <http://www.kuleuven.be/ibbt>. -- Mimi Deprez Project coordinator K.U.Leuven, ESAT/SCD (SISTA) Kasteelpark Arenberg 10 -- bus 2446 B-3001 Leuven, Belgium Tel. +32/16/32.85.55 Fax. +32/16/32.19.70 mimi.deprez(a)esat.kuleuven.be

1 0