- BBClist - maillist.psb.ugent.be

BeneLearn and PMLS 2012: Deadline Extension
by Willem Waegeman 01 Mar '12

01 Mar '12

EXTENSION OF THE SUBMISSION DEADLINE *** The extended and final deadline for the submission of abstracts and full papers is Monday March 12th, 2012 *** BENELEARN 2012 -- PMLS 2012 The 21st annual Machine Learning Conference of Belgium and The Netherlands Workshop Predictive Modeling for the Life Sciences www.benelearn2012.ugent.be May 24th and 25th, 2012 Ghent University, Belgium Last Call for Abstracts and Full Papers 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 21st edition of the annual Belgian-Dutch Conference on Machine Learning (BeneLearn) will be organized in Ghent, in conjunction with a workshop on Predictive Modeling in Life Sciences (PMLS). This year we have chosen for a two-day program to showcase the use of predictive modeling in the life sciences. This is in part motivated by the increasing focus on applicability of scientific research. The joint event takes place on the 24th and 25th of May 2012 at the Faculty of Bioscience Engineering of Ghent University. It is organized by the research unit Knowledge-based Systems (KERMIT). Keynote speakers Ricardo Silva (Gatsby Unit, UCL) : Structured Copula Models in Supervised and Unsupervised Learning Peter Challenor (National Oceanography Centre UK): Climate, Models and Uncertainty Tijl De Bie (Univeristy of Bristol): Structured Output Prediction, from Biology to Music Scope We invite the submission of abstracts or full papers on all aspects of machine learning and related disciplines, including, but not limited to Kernel Methods Bayesian Learning Case-based Learning Ensemble Methods Computational Learning Theory Data Mining Evolutionary Computation Hybrid Learning Systems Graphical Models Inductive Logic Programming Knowledge Discovery in Databases Online Learning Web/Link Mining Learning in Multi-Agent Systems Learning in Dynamic Domains / Data Streams Multi-Strategy Learning Neural Networks Reinforcement Learning Robot Learning Feature Selection and Dimensionality Reduction Scientific Discovery Multi-task and Transfer Learning Statistical Learning Ranking / Preference Learning / Information Retrieval Computational models of Human Learning Structured Output Prediction / Learning from Multi-Label Data Learning for Language and Speech Image, Video, Audio and Text Analysis Applications of Machine Learning Learning and Ubiquitous Computing In addition to theoretical and applied work in machine learning in general, we warmly welcome applications for the PMLS workshop, in areas such as: Bioinformatics Medicine / Biomedical Engineering Systems Biology / Microbiology Chemometrics / Computational Drug Discovery Ecology / Environmental Sciences Agriculture and Soil Management Food Sciences Geographical Information Systems Weather and Climate Forecasting Submission One can submit full papers up to 6 pages or one-page abstracts. Full papers need to report original, unpublished work and they are meant for researchers that prefer to obtain an official publication via BeneLearn, including feedback from the program committee. Abstracts can also concern work in progress and past published work, if the precise references to the original publication are mentioned. This way we aim to provide the same broad overview as in previous years, and make it attractive and easy to attend by both senior as well as junior researchers, from both academia and industry. To attract as many people as possible, registration fees will be low and three international speakers are invited for a keynote talk. We consider a single submission procedure for the main conference and its satellite workshop. The program committee will make a selection for oral presentations among abstracts and full papers to ensure a program that has academic quality but is also interesting and inspiring for the attendees. The remainder of the submissions will be presented during a poster session and poster spotlight presentations. Abstracts and papers should be submitted electronically, no later than Friday March 12th, 2012. Notification of acceptance is on Friday April 6th. Please follow the guidelines that are mentioned on our website: http://www.benelearn2012.ugent.be/submission.php During submission authors will be able to indicate their preference for an oral or a poster presentation. Submissions that concern an application in the life sciences will be considered for PMLS, all other submissions will be considered for the main conference day. Organizing Committee Bernard De Baets, Michaël Rademaker, Willem Waegeman (UGent) Bernard Manderick (VUB)

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Postdoc in algorithmics for NextGen Sequencing data, Inria Rennes, France
by Leonor Palmeira 29 Feb '12

29 Feb '12

Inria project team SYMBIOSE is seeking highly qualified and motivated candidates for a 12 months postdoctoral position. Research Program : Next Generation Sequencing technologies generate data of a new type in huge volumes and crucial computational developments are needed to take full advantage of these data. The successful candidate will develop new algorithms to identify complex genomic variants, such as structural variants, in such data from multiple samples without the use of a reference genome. Our approach relies on a formal model based on the De-Bruijn graph data structure to handle huge amounts of data and extract biologically relevant information. For further details visit our website http://www.irisa.fr/symbiose/ and the project description http://www.irisa.fr/symbiose/index.php?option=com_docman&task=doc_download&… Profile : - PhD in computational biology or algorithmics with a strong interest for biology - good programming skills (C, C++, python, java, ...) - background in sequence and graph algorithmics - a prior experience with high throughput sequencing data will be appreciated Working environment : The position is located in France, in the city of Rennes at the INRIA Rennes - Bretagne Atlantique center. SYMBIOSE is a dynamic and multi-disciplinary research team working in computational biology and bioinformatics, and with a strong expertise in short reads assembly. The contract is for 12 months, starting as soon as January 2012. Salary is 2620 euros monthly before taxes deduction. Application : Please send a cover letter, a CV with publications and two references contacts to claire.lemaitre(a)inria.fr.

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PhD Student Positions in Machine Learning at Radboud University Nijmegen
by E.Marchiori＠cs.ru.nl 28 Feb '12

28 Feb '12

The Machine Learning group at Radboud University Nijmegen is looking for two PhD students. Both PhD students will be working on the development and application of machine learning algorithms for improved analysis of data related to neurological disorders. First, a PhD position is available within the NWO project MacBrain. The goal of MacBrain is to mine data from the Netherlands Brain Bank (NBB) describing clinical and pathological information collected from thousands of donors who are either healthy or affected by neuro-degenerative diseases (including Alzheimer's). Your task will be to develop machine learning methods for discovering computational disease profiles characterized by few features, which may be used by domain experts to perform targeted studies aimed at improving the prognosis, diagnosis and treatment of neuro-degenerative diseases. Second, a PhD position is available within the EU FP7 project TACTICS. The goal of TACTICS is to better understand the neural, genetic and molecular bases of compulsivity disorders such as autism spectrum disorder (ASD) and obsessive compulsive disorder (OCD). Your task will be to design machine learning methods that can integrate the different sources of data gathered by the various partners within the consortium. Requirements As a PhD student you should meet the following requirements: - a Master's degree (or equivalent) in Computer Science, Mathematics or a related field, with a strong interest in machine learning; - commitment and a cooperative attitude; - excellent proficiency in written and spoken English. You will be appointed for an initial period of 18 months, after which your performance will be evaluated. If the evaluation is positive, the contract will be extended by 2.5 years. The gross starting salary amounts to 2,042 per month based on full-time employment, and will increase to 2,612 per month in the fourth year. About Radboud University Nijmegen Radboud University Nijmegen is one of the leading academic communities in the Netherlands and is renowned for its leafy campus, modern buildings and state-of-the-art equipment. It has seven faculties and enrols over 17,500 students in approximately 90 study programmes. The university is situated in Nijmegen, the oldest city in the Netherlands, which has a rich history and one of the liveliest city centres in the Netherlands. The Intelligent Systems section of the Institute for Computing and Information Sciences (iCIS) at Radboud University Nijmegen conducts research on machine learning for applications in, for example, neuroscience and bioinformatics. iCIS in general and the Intelligent Systems section in particular received excellent scores in a recent national research assessment. Additional information Dr. Elena Marchiori (main contact for MacBrain) +31 24 3652467 elenam(a)cs.ru.nl Prof.dr. Tom Heskes (main contact for TACTICS) +31 24 3652696 tomh(a)cs.ru.nl How to apply http://www.ru.nl/vacatures/details/details_vacature_0?recid=507799

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workshop metabolomics data analysis
by R.Breitling 24 Feb '12

24 Feb '12

Dear colleague, On March 29/30, 2012 we will be holding the Fourth Workshop on Metabolomics Data Analysis at Glasgow University. Attendance is limited to 25 participants, but there are still a few places available. The workshop is divided into two sections, an introduction to metabolomics data analysis on Day 1, and an advanced session focusing on mzMatch analyses on Day 2. Both days can be booked together or individually. Details on the program and how to register are available at: http://mzmatch.sourceforge.net/workshop.php Best regards, Rainer Breitling 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

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7th Netherlands Bioinformatics Conference (NBIC2012), April 24 & 25, Lunteren, the Netherlands
by Femke Francissen 14 Feb '12

14 Feb '12

We are proud to announce the 7th edition of the annual Netherlands Bioinformatics Conference (NBIC2012) organized by the Netherlands Bioinformatics Centre (http://www.nbic.nl) - Conference website: http://conference.nbic.nl - Abstract submission deadline: March 12th, 2012 - Registration is open! ** Conference programme ** - 3 confirmed keynote speakers: o Gerard Kleywegt - Protein Data Bank in Europe (PDBe), EMBL-EBI o Dorus Gadella - the Centre for Advanced Microscopy (CAM), University of Amsterdam o Harmen Bussemakers - Columbia University, Biological Sciences - Parallel sessions with contributed lectures (by abstract selection) - Poster presentations and an application showcase, parallel workshops - Social activities: conference diner and drinks on the evening of April 24th - Awards for: best poster, best lecture, best application showcase The day before the conference (Monday, April 23rd) a PhD retreat is organized by the RSG Netherlands: http://www.nbic.nl/about-nbic/nbic-conferences/nbic-conference-2012/program… For more information about abstract submission, registration and programme, visit the conference website: http://conference.nbic.nl Contact person at the NBIC Office: Femke Francissen, femke.francissen(a)nbic.nl<mailto:femke.francissen@nbic.nl>

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CALL FOR ABSTRACTS - 8th ISCB Student Council Symposium 2012
by Francescatto, M. 13 Feb '12

13 Feb '12

8th ISCB Student Council Symposium 2012 Submit your abstract now for the 8th Symposium of the International Society for Computational Biology Student Council, to be held on the 13th of July, 2012 in Long Beach, California, as a satellite meeting of the International Conference on Intelligent Systems for Molecular Biology (ISMB)! The ISCB Student Council Symposium 2012 will bring together young computational biologists from several research areas and regions of the world. As the central part of our symposium, 10 students will be selected for an oral presentation from the submitted abstracts. This is your chance to present your work to an international audience of young scientists. We welcome abstracts covering both scientific studies as well as novel tools and applications in the field of computational biology and bioinformatics. All abstracts accepted for oral presentation will be published in a special issue of BMC Bioinformatics journal. As in previous editions, awards will be given to outstanding posters and presentations. Travel Fellowships will also be available: all candidates with accepted abstracts are encouraged to apply! Travel Fellowship submission will be open for one entire week after acceptance notification. Submission information: http://symposium.iscbsc.org/content/submissions Travel Fellowship information: http://symposium.iscbsc.org/content/travel-fellowships General information: http://symposium.iscbsc.org/ Important dates January 30, 2012: Abstract and Travel Fellowship submission open April 2, 2012: Abstract submission closes April 16, 2012: Abstract acceptance notifications April 23, 2012: Travel Fellowships submission closes April 30, 2012: Travel Fellowships acceptance notification We look forward to receiving your abstract, Alexander Goncearenco Chair, 8th ISCB Student Council Symposium 2012 Olga Botvinnik Co-Chair, 8th ISCB Student Council Symposium 2012

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Fwd: Trans.: opening for project leader in computational genomics
by Marc Lensink 13 Feb '12

13 Feb '12

-- Marc F. Lensink, CR1, PhD Interdisciplinary Research Institute (IRI) - USR3078 CNRS Computational Biology marc.lensink(a)iri.univ-lille1.fr Parc de la Haute Borne, 50 Avenue de Halley, BP 70478 F-59658 Villeneuve d'Ascq, France tel: +33 3 62 53 17 28 fax: +33 3 62 53 17 01

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(no subject)
by Nicolaes G (BIOCH) 10 Feb '12

10 Feb '12

Dear , I would like to post of job opening on the BCC list, the text is as follows: Structural Bioinformatician (M/F) - POSTDOC student position - 3 years Within the 3D structure-function group, part of the department of Biochemistry at the Cardiovascular Research Institute Maastricht (CARIM, Maastricht University), Main research Area I (Thrombosis and Haemostasis) there is a position for a Postdoc (m/f). The research group focuses on the implementation of structural bioinformatics techniques within the research infrastructure of the cardiovascular research that is currently being performed. Main topics of the group include protein modeling, molecular dynamics simulations, protein-protein docking, docking of small molecules (virtual ligand screening) and peptides onto relevant targets. The current project concerns the in silico drug design, using both small molecules and peptides and is performed under the supervision of Dr. Gerry Nicolaes in collaboration with other principal investigators. The group of Dr. Nicolaes has a main focus on the structure-function study of proteins, involved in thrombosis, bleeding, inflammation or atherosclerosis and provides an active input in other research areas within CARIM. Within our group we have a vacancy for an enthusiastic Postdoc (m/f). Suitable candidates should have a background in the biological, biochemical, pharmaceutical or medical sciences with a strong track record in structural bioinformatics and will be experienced in the use of molecular modeling packages, docking approaches and virtual ligand screening. The postdoc will be stationed at the Biochemistry department, which is composed of ~60 people, staff and students. Ability to speak, write and understand English fluently is a prerequisite and ability to speak Dutch will be considered an advantage. You will be responsible for the generation, processing, analysis and storage of data generated and drive the development of new approaches to the common research objectives. You are a team player, with good social skills working in collaboration with Dr. Nicolaes as well as with 3 PhD students. Our group has a close collaboration with the group of Dr. B. Villoutreix (INSERM U648, Paris, France) in the field of structural bioinformatics as well as with that of Prof. Vriend (CMBI, Nijmegen, the Netherlands). Salary will be according to standard Netherlands University Grades (depending on skills and experience); a moving allowance will be provided up to a maximum. An evaluation will be made after 1 year and upon positive outcome of the evaluation, the position may be extended for another 2 years. Maastricht is the most Bourgundic city in the Netherlands, being situated in a so-called Euregio with distances to Liège (French speaking part of Belgium) of 25 km and Aachen (Germany) of 35 km and good connections to the Thalys train. You may send a CV, with the names and addresses of two referees and a covering letter to Dr. G. Nicolaes, Department of Biochemistry, Cardiovascular Research Institute Maastricht, Universiteitssingel 50, 6229 ER, Maastricht, the Netherlands. Tel: +31-43-3881688 For further information on the research topic contact Dr. G.A.F. Nicolaes G.Nicolaes(a)maastrichtuniversity.nl<mailto:G.Nicolaes@maastrichtuniversity.nl> http://www.carimmaastricht.nl/ www.unimaas.nl/3dstructure-function<http://www.unimaas.nl/3dstructure-function> For your convenience, I also included the text as a MS Word file, should you be needing that, Thanks for posting it! Regards, Gerry Nicolaes [cid:image001.jpg@01CCE7DB.D9C740F0] Gerry Nicolaes, PhD Senior Researcher Cardiovascular Research Institute Maastricht Biochemistry Department g.nicolaes(a)maastrichtuniversity.nl<mailto:g.nicolaes@maastrichtuniversity.nl> www.maastrichtuniversity.nl <http://www.maastrichtuniversity.nl/> Universiteitssingel 50, 6229 ER Maastricht P.O. Box 616, 6200 MD Maastricht, The Netherlands T +31 43 3881688 F +31 43 3884159 http://www.unimaas.nl/3dstructure-function [cid:image002.jpg@01CCE7DB.D9C740F0]Please consider your environmental responsibility before printing this e-mail.

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Job opening (postdoc): Epigenomic analyses within nation-wide functional genomics initiative (Leiden, The Netherlands)
by B.T.Heijmans＠lumc.nl 07 Feb '12

07 Feb '12

Epigenomic analyses within nation-wide functional genomics initiative Bioinformatician (postdoc), Leiden University Medical Center, The Netherlands Apply before February 27, 2012 at www.academictransfer.com/11762<http://www.academictransfer.com/11762> Job description As bioinformatician/postdoc you will analyze genome-wide DNA methylation profiles of 4000 individuals and link them to genetic, transcriptomic and phenotypic variation within a nation-wide functional genomics infrastructure to gain mechanistic insights into complex disease phenotypes. The project Recently, a high-profile €2M project was initiated to establish a nation-wide functional genomics infrastructure. The overall aim of the project is two-fold: (1) to gain insight in the mechanisms through which genetic variants identified in GWASs contribute to complex disease phenotypes and (2) to improve the classification of high-risk individuals by developing integrated genomic risk factors incorporating genetic, epigenomic and transcriptomic data. To this end, transcriptome (RNA-seq) and DNA methylome (Illumina 450k Chips and whole genome bisulfite sequencing) data will be generated in 4000 samples selected from in-depth characterized Dutch biobanks with GWAS and whole genome sequencing data. Hence, you will have the opportunity to work on a unique data set obtained with state-of-the-art technology and of unprecedented scale providing a platform for comprehensive and powerful analyses. As a bioinformatician/postdoc you will be responsible for the analyses in the epigenomics work package. This entails implementing a pipeline for the processing and analysis of 450k methylation data and creating genome-wide catalogs of genetic variation influencing DNA methylation (mQTLs) and DNA methylation influencing transcription. Moreover, your work will involve the execution of epigenome-wide association studies (EWASs) and the integration of 450k data with whole genome bisulfite sequencing data. The project is a collaborative effort and you will work with experts on functional genomics and biobank research in The Netherlands, including three other bioinformaticians/postdocs working on the other work packages. The project offers an excellent opportunity to develop an extended network and your successful role in project can be expected to result in good prospects for continuation of your career at a high level. Your research will be embedded within The Netherlands hub of the Biobanking and Biomolecular Research Infrastructure (BBMRI-NL). For a background on the project, read the article in BBMRI-NL newsletter (see http://tinyurl.com/fungenomics, page 2). Requirements You hold a PhD (preferred) or Masters degree in bioinformatics or biostatistics with a focus on solving biological research questions. You have a strong background in the analysis and interpretation of high-dimensional data as evidenced by publications in peer-reviewed journals, you are an efficient programmer in various languages for the analysis of such data and you have shown to effectively collaborate with researchers from other disciplines. Experience with the analysis of Illumina 27k/450k methylation data, micro-array/RNA-seq data and/or high-throughput bisulfite sequencing data is recommended. Conditions of employment You will be employed on the basis of a 36-hour week for a period of two years. Your salary will, depending on experience, be maximum € 3,899 gross per month based on a full time position (scale 10 of the Collective Labour Agreement for University Hospitals). Contract type: Temporary, Appointment for two years. Additional information You can find the extended vacancy text on http://www.lumc.nl/home/0004/23583/80611011354221/1110280250005720?internal…. If you have any questions, or if you want more information about this position, please contact Dr. Bas Heijmans, principal investigator, telephone +31 (0)71 526 9785. Or by e-mail: bas.heijmans(a)lumc.nl.

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MLG Seminar : Structure, Unstructure and Alternative Splicing
by Tom Lenaerts 06 Feb '12

06 Feb '12

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% ULB Machine Learning Group (MLG) S E M I N A R %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Apologies for cross-postings. Please send it to interested colleagues and students. Thanks! Title: "Structure, Unstructure and Alternative Splicing" by: Dr. Philip Kim, The Donnelly Centre for Cellular and Biomolecular Research Banting and Best Department of Medical Research Departments of Molecular Genetics and Computer Science University of Toronto http://www.kimlab.org http://www.thedonnellycentre.utoronto.ca When: 22 February 2012 at 16:00 (until 17:30) Where: Building NO, Sale Solvay (5th floor in the rotule) Université Libre de Bruxelles Boulevard du Triomphe 1050 Bruxelles Campus access : http://mlg.ulb.ac.be/access Abstract: Many protein interactions, in particular those in signaling networks, are mediated by peptide recognition domains. These recognize short, linear amino acid stretches on the surface of their cognate partners with high specificity. Residues in these stretches are usually assumed to contribute independently to binding, which has led to a simplified understanding of protein interactions. Conversely, in large binding peptide data sets different residue positions display highly significant correlations for many domains in three distinct families (PDZ, SH3 and WW). These correlation patterns reveal a widespread occurrence of multiple binding specificities and give novel structural insights into protein interactions. For example, a new binding mode of PDZ domains can be predicted and structurally rationalized for DLG1 PDZ1. While protein structure is very important for peptide binding domains, the regions they bind are usually unstructured (intrinsically disordered). These regions are widespread, especially in proteomes of higher eukaryotes, and have been associated with a plethora of different cellular functions. Aside from general importance for signaling networks, they are also important for such diverse processes as protein folding or DNA binding. Leveraging knowledge from systems biology can help to structure the phenomenon. Strikingly, disorder can be partitioned into three biologically distinct phenomena: regions where disorder is conserved but with quickly evolving amino acid sequences (flexible disorder), regions of conserved disorder with also highly conserved amino acid sequence (constrained disorder) and, lastly, non-conserved disorder. I will also introduce new efforts to map protein interactions affected by alternative splicing. Speaker:Dr. Philip Kim is Associate professor at University of Toronto (The Donnelly Centre for Cellular and Biomolecular Research) where he has set up a research group investigating protein interaction and genetic variation His group has pioneered some integrative approaches combining structural and systems knowledge (see Kim et al. Science 2006), as well as methodologies from genetics and network biology (see Kim et al. PNAS 2007), in an active attempt to bring genetic and protein biophysical research closer together. He has also played an import role in the understanding of specificities of the modular domains typically found in proteins. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% MLG http://mlg.ulb.ac.be/ %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

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