- BBClist - maillist.psb.ugent.be

PhD and Postdoc positions KU Leuven Belgium
by Vera van Noort 13 Jun '13

13 Jun '13

van Noort Group is looking for PhD and Postdoctoral fellows We currently access an unprecedented knowledge on the basic components making up living systems. An ever growing number of new technologies are being developed with the capacity to systematically measure the behaviour of multiple cellular components, such as biochemical activities, biophysical properties, subcellular localization and interaction. These technologies produce large amounts of raw data that can be transformed into information by software and tools developed both in academia and industry. However, this biological information does not equal biological knowledge. As biology becomes large-scale, new methods have to be developed to integrate, visualize and query the large amounts of information available. This is usually beyond the expertise of experimental labs. The goal of this young computational systems biology group is to generate biological sense from the growing amount of biological data becoming available and turn biological information into biological knowledge. http://www.biw.kuleuven.be/m2s/cmpg/research/CSB Position 1: Mycobacterium tuberculosis (MTB) is the causative agent of tuberculosis. It is estimated that a third of the world’s population has been infected by this pathogen, with approximately one new infection per second resulting in around 9 million new cases of active disease and 1.6 million deaths annually. The goal of the European project Systems Biology of MTb (SysteMTb) is to understand this organism better at the molecular level in conditions that are relevant for infection. Within this project large amounts of RNA-seq, CHIP-seq, metabolomics and proteomics data are being generated. The task of the postdoctoral fellow working to be appointed is to analyse and integrate these data to form hypotheses that can be tested in the laboratories of our collaborators. For more information about the project visit http://systemtb.eu or contact prof. Vera van Noort (vera.vannoort(a)gmail.com) In your application please include a CV with research experience and interests as well as a minimum of two letters of recommendation. Starting date: from 1st of October 2013 Position 2: A specific focus of the newly founded computational biology group will be Post Translational Modifications (PTMs). Inside the cell, proteins are the main entities responsible for carrying out molecular functions. These proteins can be modified by the addition of small moieties such as phosphate or acetyl groups. The modifications are called post-translational modifications (PTMs). These moieties change the properties of proteins and can thereby cause changes in what substrates they can bind to or what reactions they catalyse. In response to changes inside or outside an organism, a cell can quickly adapt by means of these PTMs in signalling networks. The PhD student will work on the analysis and integration of data to better understand the functions and mechanisms of PTMs. Requirements include being able to write scripts in perl/python, working with databases and basic molecular biology knowledge. Additional expertise such as working with LINUX, queuing systems and phylogenetic inference methods is certainly an advantage. For more information contact prof. Vera van Noort ( vera.vannoort(a)gmail.com) In your application please include a CV describing coursework, grades and previous research experience as well as a minimum of two letters of recommendation. Starting date: from 1st of October 2013 Position 3: We seek a PhD student who will work as a computational biologist in the interdisciplinary project NATAR. Understanding the relationship between an organism’s genotype and phenotype remains one of biology’s fundamental challenges. In the project two model organisms, budding yeast and *E. coli,*will be exploited to better understand two complex genetic traits: ethanol and high temperature tolerance*. *For both organisms both natural variation and the outcomes of experimental evolution will be correlated with phenotypes. The first challenge in the project will be to identify which of the many variants in these genomes have functional effects. Then we will try to facilitate unravelling complex interactions between alleles, for example through functional gene networks that are based on a combination of published data. An important part of the generated data that underlies this project consists of high-throughput sequencing of DNA and mRNA of populations and isolates. For answering specific questions data integration with other data sources will be needed as well as the application of specific machine learning techniques. Basic molecular biology knowledge and basic programming skills are a prerequisite for this position. Experience with high throughput sequencing analysis methods, machine learning, protein interaction databases, perl/python scripting or BioconductoR are preferred. For more information contact prof. Rob Jelier (r.jelier(a)gmail.com) or prof. Vera van Noort (vera.vannoort(a)gmail.com) In your application please include a CV describing coursework, grades and previous research experience as well as a minimum of two letters of recommendation. Starting date: from 1st of October 2013 -- Vera van Noort, PhD EMBL - Structural and Computational Biology Meyerhofstrasse 1 69117 Heidelberg Germany from October 2013: Centre of Molecular and Plant Genetics Department of Microbial and Molecular Systems (M2S) KU Leuven Kasteelpark Arenberg 20 3001 Leuven Belgium

1 0

Fwd: SYMPOSIUM : New genomics toward personalized medicine LILLE - October 2013 10th
by Olivier Sand 13 Jun '13

13 Jun '13

1 0

Course Small molecules, gene products and their interaction, 1-5 July 2013, Maastricht, the Netherlands
by Celia van Gelder 12 Jun '13

12 Jun '13

Small molecules, gene products and their interaction EBI Roadshow, Pathway-Network course and DiXa Training Course General information Date:July 1- 5, 2013 Location:Maastricht, the Netherlands Website:http://www.nbic.nl/education/course-overview/pages3/1/coursedetails/small-molecules-gene-products-and-their-interaction/ Organisers:Chris Evelo (Maastricht University), Egon Willighagen (Maastricht University), Tom Hancocks (EMBL-EBI), Vera Matser (EMBL-EBI & DiXa), Celia van Gelder (NBIC) Registration:http://www.nbic.nl/education/nbic-phd-school/enrolment/ Contact:Celia van Gelder (NBIC), education(a)nbic.nl <mailto:education@nbic.nl> Course description This five day course introduces various databases and data analysis tools to get grips on the big data in the life sciences. The course consists of two parts: Part 1 (day 1-3) introduces the advanced uses of the gene and genomes databases, small molecule resources, the protein sequence databases, and interaction and pathway databases at EBI (a.o. UniPROT, ENSEMBL, CHEMBL, IntAct and Reactome). This first part is an EBIRoadshow hosted by UM & NBIC. The second part (day 4-5) focuses on real data analysis using pathway and network approaches with links to the databases covered in first part. Tools that will be used include WikiPathways, PathVisio and Cytoscape. Covered aspects include pathway creation, data preparation for analysis, pathway analysis. network analysis and network extension using target information. This second part is provided by the department of Bioinformatics-BiGCaT at Maastricht University in collaboration with the DiXa FP7 project (www.dixa-fp7.eu) on systems biology approaches in toxicogenomics. The DiXa project will provide examples about (re)use and (re)analysis of large genomics datasets. *Teachers* Denise Carvalho-Silva, Louisa Bellis, Sandra Orchard, Chris Evelo, Martina Kutmon, Christoper Hardt, Stathis Kanterakis, Anwesha Dutta, Egon Willighagen. *Target audience *This course is intended for researchers in Life Sciences, Bioinformatics and Systems Biology, Pharmacology, Toxicology. *Course Programme* See http://www.nbic.nl/uploads/media/Programme_Maastricht.pdf -- Dr. Celia W.G. van Gelder Coordinator Education CMBI Projectleader Education NBIC tel. +31-(0)24-3666120 e-mail:C.vanGelder@cmbi.ru.nl websites:www.cmbi.ru.nl,www.nbic.nl Postal address: CMBI 260 Radboud University Nijmegen-Medical Centre /NCMLS PO Box 9101, 6500 HB Nijmegen The Netherlands

1 1

BeNeLux Bioinformatics Conference 2013 - Call for abstracts
by BBC2013 12 Jun '13

12 Jun '13

BBC2013 – BeNeLux Bioinformatics Conference 2013 Date: December 9 & 10, 2013 Venue: Salle Dupréel (Université Libre de Bruxelles), Brussels, Belgium Website: http://bbc2013.ibsquare.be Abstract submission deadline: October 1, 2013 Early registration deadline: November 1, 2013 Dear Colleagues, We are happy to announce the 8th edition of the BeNeLux Bioinformatics Conference, which will take place in Brussels on the 9th and 10th of December 2013. The theme of this year's conference is: "Bioinformatics at all scales of life". Since 2005, the BeNeLux Bioinformatics Conference gives bioinformaticians, from the BeNeLux and beyond, the opportunity to discuss their results and build new collaborations, in a relaxed and friendly atmosphere. This year's edition will be enhanced by the presence of three distinguished keynote speakers: Alfonso Valencia (Spanish National Cancer Research Center, http://bit.ly/14SAITQ) Anna Tramontano (University of Rome "La Sapienza", http://www.biocomputing.it) and Jim Haseloff (Plant Synthetic Biology, University of Cambridge, http://www.haseloff-lab.org) Call for abstracts We invite you to submit an abstract for an oral presentation (20 available slots: 6 long, 14 short) and/or a poster presentation. Contributions from all fields of bioinformatics are welcome and encouraged. We have provided a template to use for submission. Details on the submission procedure can be found at http://bbc2013.ibsquare.be/content/call-abstracts . We hope to see you all in Brussels! -- The BBC 2013 organising committee BeNeLux Bioinformatics Conference 2013 December 9-10, 2013 (Brussels)

1 0

Postdoc position: Bioinformatics of gene regulation
by Stein Aerts 12 Jun '13

12 Jun '13

Postdoc position: Bioinformatics of gene regulation The Stein Aerts lab<http://med.kuleuven.be/lcb/> at the University of Leuven has a postdoc position for a highly motivated scientist to study cis-regulatory control and cis-regulatory variation. You will use and develop computational biology approaches to map gene regulatory networks and to decipher enhancer logic underlying cellular differentiation. To this end, you will combine multiple layers of regulatory information, including spatiotemporal gene expression patterns (RNA-seq, Tag-seq), genome-wide TF localization data (ChIP-seq, damID-seq), and open chromatin profiling data (FAIRE-seq). Although this is mainly a computational position, depending on your interest you can also perform wet-lab experiments, fly genetics, and next-generation sequencing yourself, together with colleagues in the lab. Finally, you can apply your systems biology approaches to study gene regulation in cancer, using a Drosophila cancer model in the eye, studying how mutations in transcription factors, but also mutations in the non-coding genome can contribute to oncogenesis. Qualifications: * PhD degree in Life sciences or related field * Strong publication record * Experience with Drosophila is a plus, but is not required. * Funding is available, but the candidate will apply for a postdoctoral fellowship<http://www.kuleuven.be/research/postdoc/> at the national level (e.g., IWT, FWO, VLK), or at the international level (e.g., EMBO, HFSP) during or after the first year. Links: * The Laboratory of Computational Biology<http://med.kuleuven.be/bioinformatics/> * Center for Human Genetics<http://med.kuleuven.be/cme/> * University of Leuven<http://www.kuleuven.be/english/> Interested? Send your CV to stein.aerts(a)med.kuleuven.be<mailto:stein.aerts@med.kuleuven.be>.

1 0

Senior Bioinformatics position with AgResearch Ltd
by Mark Fiers 10 Jun '13

10 Jun '13

FYI: ------------------------------------- SENIOR BIOINFORMATICIAN Palmerston North, New Zealand AgResearch is a Crown Research Institute with the purpose of enhancing the value, productivity and profitability of New Zealand’s agricultural sector. The Bioinformatics team supports the Biological research in a range of areas working for the improvement of pastoral agricultural sector. We are seeking a highly motivated individual with excellent training in Bioinformatics to join our team. This is a permanent position. You will be responsible for providing Bioinformatics consultancy to a range of Science projects involved in the scientific discovery in plants, animals, fungi and microbes and will be responsible for analysing high throughput/high-dimensional ‘Omics data from non-model organisms. This includes the design, development, implementation and testing of bioinformatics pipelines and tools, assembly of NGS and RNA-Seq data, network and pathway analyses. You will also have some experience or interest in integrating multi-faceted Omics data to understand underlying systems and biological networks. Successful applicant will have a PhD or high level postgraduate qualification in Bioinformatics or related field with five years of related work experience. A thorough knowledge of Unix, scripting language (Perl/Python or similar) and an understanding of Biological databases along with various Bioinformatics tools is required. This is a highly collaborative role, where the incumbent will be working with Scientists on a regular basis thus requiring a good knowledge of Genetics and Molecular Biology. Strong communication skills, with the ability to effectively articulate complex, technical information to the clients is highly desirable. You will also have good organisational abilities along with excellent interpersonal and relationship building skills. The position will be based at AgResearch Grasslands campus in Palmerston North and will be part of wider Bioinformatics and Statistics team. Palmerston North, a university city, is 30 km from the coast, 2 hours from ski fields, and 2 hours from Wellington. The AgResearch Grasslands campus is situated in pleasant rural surroundings with easy access to the central city. The surrounding area offers many outdoor recreational opportunities. To find out more about this position and to apply online please visit: https://secure.agresearch.co.nz/careers/vacancies.aspx Applications not submitted online will not be accepted. Contact Philippa.Maternaghan(a)agresearch.co.nz if you have any questions about this vacancy. Applications close Sunday 07 July 2013. -------------------------------------

1 0

SLSP 2013: call for participation
by GRLMC 09 Jun '13

09 Jun '13

*To be removed from our mailing list, please respond to this message with UNSUBSCRIBE in the subject line* ************************************************************************************************ 1st INTERNATIONAL CONFERENCE ON STATISTICAL LANGUAGE AND SPEECH PROCESSING SLSP 2013 Tarragona, Spain July 29-31, 2013 http://grammars.grlmc.com/SLSP2013/ ************************************************************************************************ PROGRAMME Monday, July 29: 8:00 - 8:50 Registration 8:50 - 9:00 Opening 9:00 - 9:50 Yoshua Bengio: Deep Learning of Representations: Looking Forward (I) - Invited Tutorial 9:50 - 10:20 Coffee Break 10:20 - 11:35 Horacio Saggion, Stefan Bott, and Luz Rello: Comparing Resources for Spanish Lexical Simplification Borbála Siklósi, Attila Novák, and Gábor Prószéky: Context-aware Correction of Spelling Errors in Hungarian Medical Documents Attia Nehar, Djelloul Ziadi, and Hadda Cherroun: Rational Kernels for Arabic Text Classification 11:35 - 11:45 Break 11:45 - 13:00 Horia Cucu, Andi Buzo, Laurent Besacier, and Corneliu Burileanu: Statistical Error Correction Methods for Domain-Specific ASR Systems Myung-Jae Kim, Il-Ho Yang, and Ha-Jin Yu: Histogram Equalization Using Centroids of Fuzzy C-Means of Background Speakers' Utterances for Speaker Identification Layla El Asri, Romain Laroche, and Olivier Pietquin: Reward Shaping for Statistical Optimisation of Dialogue Management 13:00 - 14:30 Lunch 14:30 - 15:20 Samuel W. K. Chan and Mickey M. C. Chong: Predicting Part-of-Speech Tags and Morpho-Syntactic Relations using Similarity-based Technique Nobal Niraula, Rajendra Banjade, Dan Ștefănescu, and Vasile Rus: Experiments with Semantic Similarity Measures based on LDA and LSA 15:20 - 15:30 Break 15:30 - 16:20 Yoshua Bengio: Deep Learning of Representations: Looking Forward (II) - Invited Tutorial Tuesday, July 30: 9:00 - 9:50 Christof Monz: Challenges and Opportunities of Multilingual Information Access - Invited Lecture 9:50 - 10:20 Coffee Break 10:20 - 11:35 Akira Hayashi, Kazunori Iwata, and Nobuo Suematsu: Finding the Most Likely Upper Level State Sequence for Hierarchical HMMs Jordan Rodu, Dean P. Foster, Weichen Wu, and Lyle H. Ungar: Using Regression for Spectral Estimation of HMMs Amit Kirschenbaum: Unsupervised Segmentation for Different Types of Morphological Processes Using Multiple Sequence Alignment 11:35 - 11:45 Break 11:45 - 13:00 Abdessalam Bouchekif, Géraldine Damnati, and Delphine Charlet: Complementarity of Lexical Cohesion and Speaker Role Information for Story Segmentation of French TV Broadcast News Markus Saers, Karteek Addanki, and Dekai Wu: Iterative Rule Segmentation under Minimum Description Length for Unsupervised Transduction Grammar Induction Ngoc Thang Vu, Heike Adel, and Tanja Schultz: An Investigation of Code-Switching Attitude Dependent Language Modeling 13:00 - 14:30 Lunch 14:30 - 15:20 Hans Moen and Erwin Marsi: Cross-Lingual Random Indexing for Information Retrieval Javad Nouri, Lidia Pivovarova, and Roman Yangarber: MDL-based Models for Transliteration Generation 15:20 - 15:30 Break 15:30 - 16:20 Sanja Štajner and Richard Evans: Can Statistical Tests Be Used for Feature Selection in Diachronic Text Classification? Luis Trindade, Hui Wang, William Blackburn, and Niall Rooney: Factored Semantic Sequence Kernel for Sentiment Polarity Classification 17:30 Visit to the City Wednesday, July 31: 9:00 - 9:50 Tanja Schultz: Multilingual Speech Processing with a special emphasis on Rapid Language Adaptation - Invited Lecture 9:50 - 10:20 Coffee Break 10:20 - 11:35 Fethi Bougares, Mickael Rouvier, Nathalie Camelin, Paul Deléglise, and Yannick Estève: An Investigation of Single-pass ASR System Combination for Spoken Language Understanding Marwa Graja, Maher Jaoua, and Lamia Hadrich Belguith: Discriminative Framework for Spoken Tunisian Dialect Understanding Bassam Jabaian, Fabrice Lefèvre, and Laurent Besacier: Generalization of Discriminative Approaches for Speech Language Understanding in a Multilingual Context 11:35 - 11:45 Break 11:45 - 13:00 Felix Stahlberg, Tim Schlippe, Stephan Vogel, and Tanja Schultz: Pronunciation Extraction from Phoneme Sequences Through Cross-Lingual Word-to-Phoneme Alignment Stanisław Kacprzak and Mariusz Ziółko: Speech/Music Discrimination via Energy Density Analysis Karteek Addanki and Dekai Wu: Unsupervised Rhyme Scheme Identification in Hip Hop Lyrics using Hidden Markov Models 13:00 Closing

1 0

[Gtpb] GTPB Course Announcement: ABBTU13 Advanced Biostatistics for Bioinformatics Tool Users
by Pedro Fernandes 07 Jun '13

07 Jun '13

Course announcement ABBTU13 Advanced Biostatistics for Bioinformatics Tool Users with Lisete Sousa and Carina Silva-Fortes IMPORTANT DATES for this Course Deadline for applications: June 28th 2013 Course date: July 8st - July 12th 2013 Candidates with adequate profile will be accepted in the next 72 hours after the application, until we reach 20 participants. NOTE: Some participants in this course may ish to acquire the pre-reqested skills via the introductory course IBBTU13 that is scheduled for just before. In that case separate applications are required. Course description This is one of our "Foundations" type courses, providing a systematic and detailed review of fundamental concepts and techniques used in Bioinformatics. This course is a standalone advanced Biostatistics course that can be taken as a continuation of the Introductory Biostatistics for Bioinformatics (IBB) course that precedes it in GTPB. It is targeted for Biostatistical techniques often employed in analytical tools for high throughput data and multivariate data. Participants can expect to attend a thorough set of lectures that will reveal the conceptual frameworks that are needed to understand the methods. Extensive hands-on practice will be the main vehicle for providing the skills and user independence. To keep things in context, the course is exclusively based on biological examples. Methodology The course will introduce a relatively high number of concepts and methods. To keep it highly practical, we will spend most of the time in hands-on sessions. - We will focus on each method using examples taken from real world Bioinformatics practice. - We will then dissect the method, identifying the concepts and exploring their interrelationships. - The applicability and limitations of each method will be emphasized. - The use of the method will be illustrated using appropriate Bioinformatics tools and biological data resources. Target Audience Everybody using Bioinformatics methods is implicitly using statistical methods. Moreover, proper judgment of the results often calls for a deeper level of understanding than what is required to solve scholarly exercises. We will look into particular areas such Simulation, Bayesian Inference, Hidden Markov Chains and Multivariate methods with the attitude, eyes and brains of a statistician that wants to understand how the methods work. and systematic way. Course Pre-requisites Intermediate knowledge in Statistics is necessary. Elementary skills in computer usage are also needed. We will assume that all the participants have checked their knowledge in: - probability - conditional probability - distributions - statistical tests - hypothesis testing - inference More information, including "how to apply", detailed schedule, etc. is available at: http://gtpb.igc.gulbenkian.pt/bicourses/ABBTU13 -- Pedro Fernandes GTPB Coordinator Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL Tel +351 21 4407912 http://gtpb.igc.gulbenkian.pt _______________________________________________ Gtpb mailing list Gtpb(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb

1 0

[Gtpb] GTPB Course Announcement: IBBTU13 Introductory Biostatistics for Bioinformatics Tool Users
by Pedro Fernandes 07 Jun '13

07 Jun '13

Course announcement IBBTU13 Introductory Biostatistics for Bioinformatics Tool Users with Ana Luisa Papoila and Fernanda Diamantino IMPORTANT DATES for this Course Deadline for applications: June 21st 2013 Course date: July 1st - July 5th 2013 Candidates with the adequate profile will be accepted in the next 72 hours after the application, until we reach 20 participants. NOTE: Some participants in this course may be interested in the advanced course ABBTU13 that is scheduled for right after. In that case separate applications are required. Course description This is one of our "Foundations" type courses, providing a systematic and detailed review of fundamental concepts and techniques used in Bioinformatics. Many analytical and inferential methods, regardless of their novelty, have their niches of application all over the place in Bioinformatics. We will be looking at statistical methods, digging into their inner workings, wearing the skins of professional statisticians. Participants can expect a thorough set of lectures that will reveal the conceptual frameworks that are needed to understand the methods, and extensive hands-on practice, exclusively based on biological examples. Methodology The course will introduce a relatively high number of concepts and methods. To keep it highly practical, we will spend most of the time in hands-on sessions. - We will focus on each method using examples taken from real world Bioinformatics practice. - We will then dissect the method, identifying the concepts and exploring their interrelationships. - The applicability and limitations of each method will be emphasized. - The use of the method will be illustrated using appropriate Bioinformatics tools and biological data resources. Target Audience Everybody using Bioinformatics methods is implicitly using statistical methods. Most people have had one or more semester courses in Statistics in their graduate education. For many, Statistics happened in their lives a long time ago, and that makes it difficult to go back and manipulate the concepts with full confidence. Attending this course is a chance of revisiting subjects like experimental design, hypothesis testing, inference and prediction in an intensive and systematic way. More information, including "how to apply", detailed schedule, etc. is available at: http://gtpb.igc.gulbenkian.pt/bicourses/IBBTU13 -- Pedro Fernandes GTPB Coordinator Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL Tel +351 21 4407912 http://gtpb.igc.gulbenkian.pt _______________________________________________ Gtpb mailing list Gtpb(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb

1 0

PhD / Postdoc position on Evolutionary Cell Biology of the Mitotic Checkpoint
by berend snel 06 Jun '13

06 Jun '13

*PhD / Postdoc position on Evolutionary Cell Biology of the Mitotic Checkpoint.* We are looking for a motivated PhD student or postdoc with experience in evolutionary bioinformatics, and with affinity for understanding the role of protein networks in biological processes. The project seeks to derive functional insights into chromosome segregation from the study of protein co-evolution at the residue, motif, domain and protein level within the mitotic checkpoint signaling pathway. Novel and improved co-evolution studies are now possible thanks to an avalanche of new complete genomes. The project will encompass development of new tools and continuous refinement of a pipeline to describe and detect co-evolution between proteins. Importantly this bioinformatic pipeline will be used for generating detailed predictions on function and evolution of mitotic checkpoint proteins. As such, the candidate is expected to develop extensive expertise on chromosome segregation in general, and the mitotic checkpoint in particular, to push the limits on these predictions. *Department information* The lab of Geert Kops is part of the department of Medical Oncology and the department of Molecular Cancer Research at the UMC Utrecht. These departments are renowned for their fundamental and translational cancer research. The lab is located in the Stratenum building, that additionally houses various state-of-the-art facilities, including microscopy, proteomics, cell-screening, biochemistry and next-generation sequencing. The Kops lab consist of 6 PhD student, 3 postdocs and 4 technicians. The lab of Berend Snel is part of the Institute for Biodynamics and Biocomplexity of the Faculty of Science. This institute aims to achieve a systems-level understanding of complex dynamic processes and their evolution through close interaction between experimentation and computational biology. The Snel group currently consists of 4 PhD students and 1 postdoc working on the evolution and function of different biological systems. *How to apply* Please send your CV, along with a cover letter outlining your specific qualifications for the preferred positions including contact information for at least two references to Dr. Berend Snel, B.Snel(a)uu.nl.

1 1