September 2010 - BBClist - maillist.psb.ugent.be

Call for registration and posters, MLSB 2010
by Simon Rogers 28 Sep '10

28 Sep '10

Apologies for multiple posting. Dear all, Just a reminder that registration is open for Machine Learning in Systems Biology (MLSB 2010), Edinburgh 15th, 16th October 2010 (http://mlsb10.ijs.si/) Register online at: http://mlsb10.ijs.si/registration.html Poster submissions are still welcome (deadline is this Friday, October 1st). Please submit at: https://www.easychair.org/account/signin.cgi?timeout=1;conf=mlsb10 -- Dr Simon Rogers Lecturer in Inference School of Computing Science University of Glasgow simon.rogers(a)glasgow.ac.uk<mailto:simon.rogers@glasgow.ac.uk> skype: sdrogersskype ________________________________ The University of Glasgow, charity number SC004401

1 0

Postdoc Position Systems Biology of African trypanosomes
by fred opperdoes 20 Sep '10

20 Sep '10

Postdoc Position Systems Biology of African trypanosomes (SilicoTryp) Working environment The University Medical Centre Groningen (UMCG) offers an excellent environment for research and training of scientific skills. Together with the Faculty of Mathematics and Natural Sciences of the University of Groningen, the UMCG has recently established a new Systems Biology Centre for Energy Metabolism and Ageing (SBS-EMA). The Systems Biology group headed by Dr. B.M. Bakker is part of the Centre for Liver, Digestive and Metabolic Diseases. Project description The SysMO-funded SilicoTryp project aims at developing a computational model of Trypanosoma brucei, the causative agent of African sleeping sickness, by combining cutting edge post-genomic technologies and advanced statistical, mathematical and bioinformatics approaches. The work is carried out in a close collaboration of several European research universities. The consortium consists of modellers, statisticians, biochemists and molecular cell biologists. Trypanosomes, blood-borne parasites transmitted by tsetse flies, are the causal agent of African sleeping sickness, a deadly disease for humans and cattle. A systems biology study of trypanosomes is particularly timely and has the potential to provide critical insights to the fundamental mechanisms controlling this parasite. Indeed, due to some of the trypanosome’s unique biological characteristics and the wealth of information obtained in biomedical studies, this organism is particularly suited to a systems biological approach. Computational models of glucose metabolism as well as of the unusual gene-expression cascade of the organism have provided insight into the regulation of its physiology. The next step, which the SilicoTryp consortium will take, is to link glucose metabolism to the redox - trypanothione pathway and oxidative stress, as well as to signalling and gene expression. Job description Based on the information generated by the experimental partners, the postdoc will build a computational model that will integrate redox and energy metabolism with signal transduction and gene expression. The postdoc will collaborate with other theoreticians as well as with experimental partners. Research visits to partner labs will be part of the project. Furthermore, the postdoc will collaborate with colleagues in SBC-EMA, sharing Systems Biology expertise to understand the regulation of metabolism in various organisms. What do we need We are searching for an excellent, highly motivated postdoc, with expertise in computational modelling of biochemical and/or gene-expression networks. The postdoc is expected to communicate efficiently with experimentalists, mostly located abroad (Edinburgh, Glasgow, Heidelberg). The UMCG has a preventive Hepatitis B policy. This means that you must have built up sufficient protection against Hepatitis B before you can be appointed. What do we offer • The University Medical Centre Groningen offers a salary of €.2,435 up to €.3,860 gross per month (salary scale 10), depending on experience. • The position will be for three years. • The conditions of employment comply with the Collective Labour Agreement for Medical Centres (CAO-UMC). Additional information For more information, please contact Dr. Barbara Bakker (http://www.labpediatricsrug.nl/, 050 361 1542). See also: Parasitology (2010) 137, 1333-41. Applying for a job The UMCG would prefer to receive your job application in digital form. You can use the digital application form at the foot of this page. Alternatively you may apply for this vacancy in writing, not later than 21-09-2010, by sending your application to: University Medical Center Groningen Wervingssecretariaat LB 13 P.O. Box 30.001 9700 RB Groningen The Netherlands If you are applying for this job in writing, always give the vacancy number 10311 in your letter and please mention the name of the publication or place where you saw the vacancy for the first time (newspaper, specialist journal, internet site).

1 0

Topical Day on Bioinformatics - 19 November 2010 - Mol, Belgium
by Janssen Paul 16 Sep '10

16 Sep '10

Apologies if this message is redundant (the same message may have been sent to you separately) Regards, Paul Janssen http://www.sckcen.be/mcb/ ============================== (Message in English and French below) ============================== Geachte vrienden en collega's, Met plezier nodig ik u uit op onze Topical Day on Bioinformatics: "From Base to Byte and back" welke plaats heeft in het SCK-CEN te Mol op Vrijdag 19 november 2010. Topical Days hebben als doel nieuwe concepten en hedendaagse ontwikkelingen voor een breed publiek te brengen en om nieuwe samenwerkingsverbanden mogelijk te maken. "Hoe kunnen we de enorme hoeveelheid aan diverse biologische data integreren zodat deze bereikbaar en begrijpelijk blijven?", "Welke hulpmiddelen zijn daarbij nodig en wat kunnen we ervan leren?", "Op welke wijze kan men biologische systemen tot in het kleinste detail ontleden?", en " Zijn we in staat levende systemen in andere banen te leiden of zelfs 'de novo' leven te creëren?". Deze en andere vragen worden benaderd door 9 internationaal erkende sprekers die werkzaam zijn op de voorgrond van Bioinformatica, Systeem Biologie, en Synthetische Biologie. Registreer voor 16 oktober 2010 en geniet van een vermindering in deelnamekosten. Meer informatie op http://www.sckcen.be/nl/Evenementen/TD_BIOINFO/ <http://www.sckcen.be/nl/Evenementen/TD_BIOINFO/> Ik verheug me erop u in Mol te kunnen verwelkomen, In naam van de MCB groep (http://www.sckcen.be/mcb/) Paul Janssen -------------------------------------------------------------------------------------- Chers amis et collègues, J'ai le plaisir de vous inviter à notre Topical Day sur le thème de la bioinformatique : « From Base to Byte and back » qui aura lieu au SCK*CEN de Mol le vendredi 19 novembre 2010. Le but des Topical Days est de mettre en avant de nouveaux concepts et tendances pour un large publique, et d'encourager de nouvelles collaborations. « Comment pouvons-nous dompter l'énorme quantité de données biologiques afin de les rendre accessible et interprétable ? », « De quels outils avons-nous besoin et que pouvons-nous apprendre ? », « Comment visualiser et disséquer les systèmes biologiques ? », et « Pouvons-nous rediriger ou peut-être même créer la Vie ? ». Ces questions et beaucoup d'autres seront abordées par 9 orateurs de classe internationale travaillant et enseignant dans les domaines de la Bioinformatique, la Biologie Intégrative (System Biology) et la Biologie Synthétique. Enregistrez-vous avant le 16 octobre 2010 et vous profiterez d'une réduction sur les frais d'inscription ! Vous trouverez plus d'information à l'adresse suivante : http://www.sckcen.be/nl/Evenementen/TD_BIOINFO/ <http://www.sckcen.be/nl/Evenementen/TD_BIOINFO/> Dans l'attente d'avoir le plaisir de vous accueillir à Mol, Au nom du groupe MCB (http://www.sckcen.be/mcb/ <http://www.sckcen.be/mcb/> ), Paul Janssen ------------------------------------------------------------------------- Dear Friends and Colleagues, It is my pleasure to invite you to our Topical Day on Bioinformatics: "From Base to Byte and back" taking place at SCK-CEN in Mol on Friday 19 November 2010. Topical Days aim to bring new concepts and trends to the broad public and to foster new collaborations. "How can we mold the vast amount of diverse biological data in an accessible, interpretable way", "Which tools do we need and what can we learn", "How to visualize and dissect biological systems", and "Can we redirect or even create Life". These and other questions will be addressed by 9 internationally renowned speakers working and teaching at the foreground of Bioinformatics, Systems Biology, and Synthetic Biology. Register before 16 Oktober 2010 and enjoy a reduced registration fee! Further information on http://www.sckcen.be/nl/Evenementen/TD_BIOINFO/ I am looking forward to welcoming you to Mol, On behalve of the MCB group (http://www.sckcen.be/mcb/ <http://www.sckcen.be/mcb/> ), Paul Janssen --------------------------------------------------------------------------- Dr. Ir. Paul J.D. Janssen Molecular and Cellular Biology - Unit of Microbiology Institute for Environment, Health and Safety (EHS) Belgian Nuclear Research Centre SCK/CEN Boeretang 200, B-2400-MOL, Belgium Tel: +32-(0)14-332129 Mobile: +32-(0)486-571043 http://www.sckcen.be/mcb/ SCK·CEN Disclaimer: www.sckcen.be/en/Legal-aspects/E-mail-disclaimer

1 0

Postdoc in Metabolomic Systems Biology of Cancer
by R.Breitling 15 Sep '10

15 Sep '10

A 3-year postdoctoral position in Metabolomic Systems Biology is available immediately for a joint project on the metabolomics of cancer cells at the University of Glasgow (Rainer Breitling) and the Beatson Institute for Cancer Research (Eyal Gottlieb). The project will focus on the development of creative bioinformatics approaches for the analysis and interpretation of high-accuracy mass spectrometry datasets, including kinetic data based on stable-isotope labeling, and their integration with transcript information and metabolic modeling. The aim of the project is to understand the metabolic rewiring observed to be a critical factor in the pathology of many human cancers. Candidates should have a strong background in bioinformatics, molecular systems biology, biochemistry, biostatistics and/or bioengineering. Solid programming skills are essential and experience with cancer biology would be a plus. A proven ability of performing creative interdisciplinary research is required. We also expect a pro-active attitude and the ability to initiate and execute research lines independently. Excellent communication and reporting skills are necessary. Qualified applicants are invited to send their applications, including a motivation letter, complete CV, a pdf copy of their 3 best papers and the contact details of academic referees directly to Rainer Breitling (rainer.breitling(a)glasgow.ac.uk; http://www.tinyurl.com/rbreitling) Key literature: Tennant DA, Durán RV, Gottlieb E. (2010) Targeting metabolic transformation for cancer therapy. Nature Reviews Cancer. 10(4):267-77. Rogers S, Scheltema RA, Girolami M, Breitling R (2009) Probabilistic assignment of formulas to mass peaks in metabolomics experiments. Bioinformatics. 25(4):512-8. Scheltema RA, Decuypere S, Dujardin JC, Watson D, Jansen RC, Breitling R (2009): A simple data reduction method for high resolution LC/MS data in metabolomics. Bioanalysis 1:1569–1578. Breitling R, Vitkup D, Barrett MP (2008) New surveyor tools for charting microbial metabolic maps. Nature Reviews Microbiol. 6(2):156-61. Prof. Dr. Rainer Breitling SULSA Professor of Systems Biology, University of Glasgow Honorary Professor of Computational Systems Biology, University of Groningen Mailing address: Institute of Molecular, Cell and Systems Biology College of Medical, Veterinary and Life Sciences Joseph Black Building, B3.10 University of Glasgow Glasgow G12 8QQ Scotland, United Kingdom tel: (+44) (0)141-330-7374 e-mail: rainer.breitling(a)glasgow.ac.uk http://tinyurl.com/rbreitling http://gbic.biol.rug.nl/~rbreitling

1 0

Bioinformatics PhD position Whole genome sequence analysis in tomato: Mechanisms of introgression breeding
by Roeland van Ham 14 Sep '10

14 Sep '10

Please find below and attached a vacancy for a PhD position in plant genome bioinformatics. roeland van ham dr Roeland CHJ van Ham Cluster Leader Applied Bioinformatics Plant Research International Droevendaalsesteeg 1 6708 PB Wageningen The Netherlands Tel: + 31 317 481053 PhD position ‘Whole genome sequence analysis in tomato: Mechanisms of introgression breeding’ Applied Bioinformatics, Plant Sciences Group, Wageningen University & Research Centre (WUR) Wageningen, The Netherlands 38 hours per week Reference number: PSG-BIOS-0001 Background: Wageningen University and Research Centre (WUR) is worldwide renowned for its research and education in the fields of life sciences, plant improvement and sustainability. Through these activities it aims to make essential contributions to the quality of life. A focus of pioneering research towards increased yields and improved quality is the genome biology of economically valuable crops such as tomato and potato. The Plant Sciences Group of WUR has an important position in international efforts to elucidate and use the genome sequence of these crops. The Applied Bioinformatics group of the PSG participates in these efforts through next generation sequencing, genome assembly, annotation and extracting biologically relevant knowledge from such genome sequences. WUR is also a partner in the Centre for BioSystems Genomics (CBSG2012). The CBSG and the National Institute for Plant Genome Research in Delhi, India, have received a grant from the Netherlands Organisation for Scientific Research (NWO) to start a joint research project on development and application of next generation sequencing technologies to one of CBSG’s crop targets, tomato, which is also an important crop in India. Job description: the job concerns a PhD position in the Applied Bioinformatics group of the Plant Sciences Group of WUR. In this project, we will analyze the genomes of three tomato genotypes: two parents of the well-studied introgression line population, S. lycopersicum cv. Allround and S. pennellii LA716, and the genome of one F5 offspring line. Sequencing of these genomes will be performed in an associated project and will involve a combination of next generation sequencing technologies. Comparative bioinformatic analyses of the parent and offspring genomes will be geared towards obtaining novel insights into the molecular mechanisms underlying genetic introgression in plants. The PhD student will assemble, annotate and compare the three genome sequences with the aim to study the pattern of genome reorganization from chromosome- down to nucleotide-level detail. We will test and employ a variety of bioinformatics tools for genome assembly, annotation and whole-genome comparison, and perform SNP mining for breeding purposes. The collaboration within this project with the National Institute for Plant Genome Research in New Delhi, India, will imply that the PhD student will spend a maximum of 2 years of the 4-year PhD study at the sister institute in India. In addition, the PhD student will actively cooperate with an Indian counterpart (PhD student) based in Delhi and working on the breeding aspects of the project. This PhD student in return will spend a maximum of 2 years in Wageningen. Location: Wageningen, The Netherlands What do we look for? We are looking for an enthusiast team player with: * an excellent academic record (MSc) in bioinformatics * interest in genome informatics and bioinformatics for breeding * demonstrable skills in programming (perl or python, java, R) and databases (MySQL) * good oral and written communication skills in English * willingness to spend several periods amounting to 2 years of the PhD period in New Delhi, India * people skills in connection with biologists, breeders and bioinformaticians What do we offer? You will be part of a young, dynamic and focused applied bioinformatics group of ~15 people consisting of computational biologists and biology-oriented informaticians that focus on bioinformatics challenges in genomics. We offer a state-of-the art computational infrastructure and have close collaboration with plant biologists and breeding companies with considerable expert knowledge of the biological issues and wishes concerning the data. The position is available for 4 years, full time (38 hrs/wk), 2 years of which will be housed in New Delhi, India. The student will be part of the graduate school of Experimental Plant Sciences (EPS). The research should result in the successful defence of a PhD after 4 years. In line with the quality protocol of EPS, after 12 months and assuming progress and performance of the PhD student meets requirements the position will be continued for the full period. Preferred starting date: as soon as possible. Estimated maximum salary: € 2042/month in the first year, rising to € 2612/month in the fourth year (Dutch university PhD) Need to know more? Additional information about this project can be obtained from dr. Roeland van Ham, +31-317-481053, roeland.vanham(a)wur.nl <mailto:roeland.vanham@wur.nl> How to apply? You can apply for this job before October 1st, 2010 at http://www.wur.nl/UK/work

1 0

MLSB 2010, call for papers & registration open
by Simon Rogers 11 Sep '10

11 Sep '10

Apologies for multiple postings: ************************** Call for Posters ***************************** MLSB 2010 The Fourth International Workshop on Machine Learning in Systems Biology 15-16 October 2010, Edinburgh, Scotland *********************************************************************** http://mlsb10.ijs.si/ **REGISTRATION IS NOW OPEN** MOTIVATION Molecular biology and all the biomedical sciences are undergoing a true revolution as a result of the emergence and growing impact of a series of new disciplines/tools sharing the "-omics" suffix in their name. These include in particular genomics, transcriptomics, proteomics and metabolomics, devoted respectively to the examination of the entire systems of genes, transcripts, proteins and metabolites present in a given cell or tissue type. The availability of these new, highly effective tools for biological exploration is dramatically changing the way one performs research in at least two respects. First, the amount of available experimental data is not a limiting factor any more; on the contrary, there is a plethora of it. Given the research question, the challenge has shifted towards identifying the relevant pieces of information and making sense out of it (a "data mining" issue). Second, rather than focus on components in isolation, we can now try to understand how biological systems behave as a result of the integration and interaction between the individual components that one can now monitor simultaneously (so called "systems biology"). Taking advantage of this wealth of "genomic" information has become a conditio sine qua non for whoever ambitions to remain competitive in molecular biology and in the biomedical sciences in general. Machine learning naturally appears as one of the main drivers of progress in this context, where most of the targets of interest deal with complex structured objects: sequences, 2D and 3D structures or interaction networks. At the same time bioinformatics and systems biology have already induced significant new developments of general interest in machine learning, for example in the context of learning with structured data, graph inference, semi-supervised learning, system identification, and novel combinations of optimization and learning algorithms. The Workshop is organized as "core - event" of Pattern Analysis, Statistical Modelling and Computational Learning - Network of Excellence 2 (PASCAL 2, http://www.pascal-network.org/) OBJECTIVE The aim of this workshop is to contribute to the cross-fertilization between the research in machine learning methods and their applications to systems biology (i.e., complex biological and medical questions) by bringing together method developers and experimentalists. We encourage submissions bringing forward methods for discovering complex structures (e.g. interaction networks, molecule structures) and methods supporting genome-wide data analysis. LOCATION AND CO-LOCATION The workshop will take place 15-16 October 2010 at the Edinburgh International Conference Centre and the Informatics Forum of the University of Edinburgh. It will be part of the wokshop program of ICSB 2010, The 11th International Conference on Systems Biology (11-14 OCT 2010, http://www.icsb2010.org.uk/) POSTER SUBMISSION INSTRUCTIONS We invite you to submit an extended abstract of at least 1 page describing new or recently published (2010) results, formatted according to the Springer Lecture Notes in Computer Science style. Each extended abstract must be submitted online via the Easychair submission system: http://www.easychair.org/conferences/?conf=mlsb10 KEY DATES Poster submission deadline: September 30th 2010 TOPICS A non-exhaustive list of topics suitable for this workshop is given below: Methods Machine learning algorithms Bayesian methods Data integration/fusion Feature/subspace selection Clustering Biclustering/association rules Kernel methods Probabilistic inference Structured output prediction Systems identification Graph inference, completion, smoothing Semi-supervised learning Applications Sequence annotation Gene expression and post-transcriptional regulation Inference of gene regulation networks Gene prediction and whole genome association studies Metabolic pathway modeling Signaling networks Systems biology approaches to biomarker identification Rational drug design methods Metabolic reconstruction Protein function and structure prediction Protein-protein interaction networks Synthetic biology INVITED SPEAKERS (confirmed) Florence d'Alche Buc, Universite d'Evry-Val d'Essonne, Evry, France Nir Friedman, The Hebrew University of Jerusalem, Jerusalem, Israel Ursula Kummer, BIOQUANT, University of Heidelberg, Germany Hans Lehrach, Max Planck Institute for Molecular Genetics, Berlin, Germany Vebjorn Ljosa, The Broad Institute of MIT and Harvard, USA MLSB10 PROGRAM CHAIRS Saöo Dûeroski, Jozef Stefan Institute, Ljubljana, Slovenia Simon Rogers, University of Glasgow, UK Guido Sanguinetti, University of Sheffield/University of Edinburgh, UK -- Dr Simon Rogers Lecturer in Inference School of Computing Science University of Glasgow simon.rogers(a)glasgow.ac.uk skype: sdrogersskype The University of Glasgow, charity number SC004401

1 0

ESCS1 Call for participation
by Thomas Abeel 06 Sep '10

06 Sep '10

Dear Colleagues, The first European Student Council Symposium (ESCS1) will be held on September 26, 2010 in Ghent, Belgium, as a satellite meeting of the European Conference on Computational Biology (ECCB). The European Student Council Symposium is a forum for students and young researchers in the fields of Computational Biology and Bioinformatics. Participants will have the opportunity to present their work to an international audience, build a network within the computational biology community and develop important soft skills in an environment that fosters exchange of ideas and knowledge. You can register to the student symposium even if you do not attend ECCB and it only costs 100 euros. http://escs.iscbsc.org/registration The program is available on our website and includes: - a keynote presentation by Yves Van de Peer about Generating hypotheses for molecular biology through (top-down) systems biology - a soft skill workshop on the use of theatre skills for presenting - student presentations from abstract submissions - a poster session See http://escs.iscbsc.org/program for more information Looking forward to seeing you in Belgium! Magali Michaut ESCS1 chair Thomas Abeel ESCS1 co-chair

1 0

Job announcement: Bioinformatician – Sugar Beet Biotechnology (m/f)
by Thomas Van Parys 03 Sep '10

03 Sep '10

Job description in attachment. -- ================================================================== Thomas Van Parys Tel:+32 (0)9 331 36 95 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM thomas.vanparys(a)psb.vib-ugent.be http://bioinformatics.psb.ugent.be ==================================================================

1 0