- BBClist - maillist.psb.ugent.be

international shortcourse on next generation sequencing
by Marja Peters 20 Feb '14

20 Feb '14

Dear reader, We, Avans University of Applied Sciences, Research Group Analysis Techniques in Life Science, organize an international shortcourse on next generation sequencing in Breda from 1 until 4 April 2014. Aim of the course: DNA sequencing technologies are currently developing at an incredible speed and new applications are presented monthly, incl. DNA/RNA profiling, ChIP-seq, re-sequencing, de novo genome sequencing and metagenomics. The aim of this course is to introduce next generation sequencing technologies, highlight different applications of these new technologies, and show ways to analyse data. Please visit the course website for detailed information: http://www.alsavans.nl/avans-training-2542.htm Looking forward to meeting you in Breda Best regards, Marja peters Avans university of applied science p.o. box 90116 Disclaimer ( http://www.avans.nl/over-avans/e-mail-disclaimer )

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Deadline Abstract submission February 23: NSBM Spring meeting 2014 April 8th - NBIC Conference
by Barbara.vanKampen＠radboudumc.nl 20 Feb '14

20 Feb '14

Abstract submission deadline for oral presentations: February 23, 2014 [logo.png]NSBM Spring meeting April 8th 2014 In conjunction with the Netherlands Bioinformatics Conference 2014 Venue: Congrescentrum De Werelt, Lunteren The Netherlands Society on Biomolecular Modelling (NSBM) cordially invites you to visit its spring meeting, a topical track of the Netherlands Bioinformatics Conference 2014 (NBIC2014) on April 8th 2014. During several parallel sessions, the floor will be given to PhD students and postdocs who study protein structure and/or structural bioinformatics or related topics (see a list below). Speakers and attendees will have the opportunity to join the NBIC2014 activities and visit keynote lectures. Programme April 8th Invited speaker: Christian Ottmann<https://www.aanmelder.nl/nbic2014/wiki/christian%20ottmann>, Eindhoven University of Technology, the Netherlands Abstract submission All abstracts should be submitted via the NBIC2014 abstract submission system<https://www.aanmelder.nl/nbic2014/wiki/abstract%20submission>. Please indicate in the form that you are submitting for the NSBM Spring meeting. Starting PhD students are particularly encouraged to present their research! For questions regarding the abstract or meeting please contact Gert Vriend, gerrit.vriend(a)radboudumc.nl<mailto:gerrit.vriend@radboudumc.nl> Topics for presentations may include, but are not limited to: * Computational Biology and Bioinformatics * Computer-aided drug design * Drug design and drug discovery * Grid computing * Homology modelling * Molecular and supramolecular dynamics * Molecular modeling and simulation * Mutational analysis * Protein crystallography * Protein NMR * Protein structure analysis * Protein structure prediction * Protein-protein interactions * Protein-small molecules interaction * Protein software design * Proteomics * Structural bioinformatics * Structure-function analysis * Text mining & information extraction * Virtual screening Registration Registration should be done via the NBIC2014 registration form<https://www.aanmelder.nl/nbic2014/wiki/registration>. Registration for the conference (for one day/April 8th) includes: participation to conference and evening poster session on April 8th, lunch, coffee/tea during breaks, internet access and conference dinner. Should a lack of funding be a hurdle for visiting the NSBM Spring meeting, please contact prof. Gert Vriend at gerrit.vriend(a)radboudumc.nl<mailto:gerrit.vriend@radboudumc.nl> so that an arrangement can be made. Key dates * Abstract submission deadline for oral presentations: February 23, 2014 * Notification date selection oral presentations: March 4, 2014 * Abstact submission deadline for posters & demos: April 4, 2014 Sponsored by: [DSM]<http://www.dsm.com/> [Genalice] <http://www.genalice.com/> [Keygene NV]<http://www.keygene.com/> [Bio-prodict] <http://www.bio-prodict.nl/> NSBM Mailing list --- NEW EMAIL: barbara.vankampen(a)radboudumc.nl<mailto:barbara.vankampen@radboudumc.nl> Barbara van Kampen [Radboudumckleine.png] CMBI 260 Radboud University Medical Centre / RIMLS CMBI Office / Room 0.02 PO Box 9101 Geert-Grooteplein 26-28 6500 HB Nijmegen 6525 GA Nijmegen Phone: +31(0)24 36 19390 Fax: +31 (0)24 36 19395 www.cmbi.ru.nl<http://www.cmbi.ru.nl/> Het Radboudumc staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629. The Radboud university medical center is listed in the Commercial Register of the Chamber of Commerce under file number 41055629.

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Call for Systems Biology Abstracts, NBIC2014
by l.wessels＠nki.nl 20 Feb '14

20 Feb '14

You are invited to submit an abstract for oral presentation at a SPECIAL SESSION ON SYSTEMS BIOLOGY at the NETHERLANDS BIOINFORMATICS CONFERENCE 2014 (NBIC2014) APRIL 8 & 9, 2014 CONFERENCE CENTER DE WERELT, LUNTEREN, THE NETHERLANDS Conference website: https://www.aanmelder.nl/nbic2014/ The special parallel Systems Biology session will take place on the first day of the conference, 8 April 2014, the same day on which a keynote lecture will be delivered by Dr Ilya Shmulevich from the Institute of Systems Biology, Seattle, Washington. ABSTRACT SUBMISSION DEADLINE: 23 February 2014 (this Sunday). NOTIFICATION DATE: 4 March 2014 Registration: https://www.aanmelder.nl/nbic2014/wiki/registration NBIC2014 Keynote speakers * Marcus Claesson * Ilya Shmulevich * Jelle Goeman * Christian Ottmann * Yves van de Peer

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LATA 2014: call for participation
by GRLMC 15 Feb '14

15 Feb '14

*To be removed from our mailing list, please respond to this message with UNSUBSCRIBE in the subject line* ************************************************************************* 8th INTERNATIONAL CONFERENCE ON LANGUAGE AND AUTOMATA THEORY AND APPLICATIONS LATA 2014 Madrid, Spain March 10-14, 2014 http://grammars.grlmc.com/lata2014/ ********************************************************************* PROGRAM Monday, March 10: 9:30 - 10:30 Registration 10:30 - 10:40 Opening 10:40 - 11:30 Helmut Seidl: Interprocedural Information Flow Analysis of XML Processors - Invited Lecture 11:30 - 11:45 Break 11:45 - 13:00 Alberto Dennunzio, Enrico Formenti, Luca Manzoni: Extremal Combinatorics of Reaction Systems Fernando Arroyo, Sandra Gómez Canaval, Victor Mitrana, Ștefan Popescu: Networks of Polarized Evolutionary Processors are Computationally Complete Liang Ding, Abdul Samad, Xingran Xue, Xiuzhen Huang, Russell L. Malmberg, Liming Cai: Stochastic k-Tree Grammar and its Application in Biomolecular Structure Modeling 13:00 - 14:30 Lunch 14:30 - 15:45 Béatrice Bérard, Olivier Carton: Channel Synthesis Revisited Daniel Průša: Weight-reducing Hennie Machines and Their Descriptional Complexity Manfred Droste, Stefan Dück: Weighted Automata and Logics for Infinite Nested Words 15:45 - 16:00 Break 16:00 - 17:15 Friedrich Otto, František Mráz: Extended Two-Way Ordered Restarting Automata for Picture Languages Sang-Ki Ko, Yo-Sub Han, Kai Salomaa: Top-Down Tree Edit-Distance of Regular Tree Languages Bertram Felgenhauer, René Thiemann: Reachability Analysis with State-Compatible Automata 17:15 - 17:45 Coffee Break 17:45 - 18:35 Leslie A. Goldberg: The Complexity of Approximate Counting - Invited Lecture Tuesday, March 11: 9:00 - 9:50 Sanjeev Khanna: Matchings, Random Walks, and Sampling - Invited Lecture 9:50 - 10:00 Break 10:00 - 11:15 Niko Beerenwinkel, Stefano Beretta, Paola Bonizzoni, Riccardo Dondi, Yuri Pirola: Covering Pairs in Directed Acyclic Graphs Eike Best, Raymond Devillers: Characterisation of the State Spaces of Live and Bounded Marked Graph Petri Nets María Martos-Salgado, Fernando Rosa-Velardo: Expressiveness of Dynamic Networks of Timed Petri Nets 11:15 - 11:45 Coffee Break 11:45 - 13:00 Bireswar Das, Patrick Scharpfenecker, Jacobo Torán: Succinct Encodings of Graph Isomorphism Matthias Gallé, Matías Tealdi: On Context-Diverse Repeats and their Incremental Computation Marcella Anselmo, Dora Giammarresi, Maria Madonia: Picture Codes with Finite Deciphering Delay 13:00 - 14:30 Lunch 14:30 - 15:45 Paul Tarau: Computing with Catalan Families Joan Boyar, Shahin Kamali, Kim S. Larsen, Alejandro López-Ortiz: On the List Update Problem with Advice Rob Gysel: Minimal Triangulation Algorithms for Perfect Phylogeny Problems 15:45 - 16:00 Break 16:00 - 17:15 Grégoire Laurence, Aurélien Lemay, Joachim Niehren, Sławek Staworko, Marc Tommasi: Learning Sequential Tree-to-word Transducers Dariusz Kalociński: On Computability and Learnability of the Pumping Lemma Function Slimane Bellaouar, Hadda Cherroun, Djelloul Ziadi: Efficient List-based Computation of the String Subsequence Kernel Wednesday, March 12: 9:00 - 9:50 Oscar H. Ibarra: On the Parikh Membership Problem for FAs, PDAs, and CMs - Invited Lecture 9:50 - 10:00 Break 10:00 - 11:15 Marius Konitzer, Hans Ulrich Simon: DFA with a Bounded Activity Level Shenggen Zheng, Jozef Gruska, Daowen Qiu: On the State Complexity of Semi-Quantum Finite Automata Vojtěch Vorel: Complexity of a Problem Concerning Reset Words for Eulerian Binary Automata 11:15 - 11:45 Coffee Break 11:45 - 13:00 Pascal Caron, Marianne Flouret, Ludovic Mignot: (k,l)-Unambiguity and Quasi-Deterministic Structures: an Alternative for the Determinization Zuzana Bednárová, Viliam Geffert: Two Double-Exponential Gaps for Automata with a Limited Pushdown Parosh Aziz Abdulla, Mohamed Faouzi Atig, Jari Stenman: Computing Optimal Reachability Costs in Priced Dense-Timed Pushdown Automata 13:00 - 14:30 Lunch 15:45 - 17:45 Sightseeing in Madrid by Bus Thursday, March 13: 9:00 - 9:50 Javier Esparza: A Brief History of Strahler Numbers (I) - Invited Tutorial 9:50 - 10:00 Break 10:00 - 11:15 Zeinab Mazadi, Ziyuan Gao, Sandra Zilles: Distinguishing Pattern Languages with Membership Examples Francine Blanchet-Sadri, Andrew Lohr, Sean Simmons, Brent Woodhouse: Computing Depths of Patterns Alexandre Blondin Massé, Sébastien Gaboury, Sylvain Hallé, Michaël Larouche: Solving Equations on Words with Morphisms and Antimorphisms 11:15 - 11:45 Coffee Break 11:45 - 13:00 Anton Cerný: Solutions to the Multi-Dimensional Equal Powers Problem Constructed by Composition of Rectangular Morphisms Enrico Formenti, Markus Holzer, Martin Kutrib, Julien Provillard: ω-rational Languages: High Complexity Classes vs. Borel Hierarchy Thomas Weidner: Probabilistic ω-Regular Expressions 13:00 - 14:30 Lunch 14:30 - 15:45 Haizhou Li, François Pinet, Farouk Toumani: Probabilistic Simulation for Probabilistic Data-aware Business Processes Daniel Bundala, Jakub Závodný: Optimal Sorting Networks Etienne Dubourg, David Janin: Algebraic Tools for the Overlapping Tile Product 15:45 - 16:00 Break 16:00 - 17:15 Luca Breveglieri, Stefano Crespi Reghizzi, Angelo Morzenti: Shift-Reduce Parsers for Transition Networks Gadi Aleksandrowicz, Andrei Asinowski, Gill Barequet, Ronnie Barequet: Formulae for Polyominoes on Twisted Cylinders Alexandre Blondin Massé, Amadou Makhtar Tall, Hugo Tremblay: On the Arithmetics of Discrete Figures Friday, March 14: 9:00 - 9:50 Javier Esparza: A Brief History of Strahler Numbers (II) - Invited Tutorial 9:50 - 10:00 Break 10:00 - 11:15 Hanna Klaudel, Maciej Koutny, Zhenhua Duan: Interval Temporal Logic Semantics of Box Algebra Pierre Ganty, Ahmed Rezine: Ordered Counter-Abstraction: Refinable Subword Relations for Parameterized Verification Matthew Gwynne, Oliver Kullmann: On SAT Representations of XOR Constraints 11:15 - 11:45 Coffee Break 11:45 - 13:00 Bernd Finkbeiner, Hazem Torfah: Counting Models of Linear-time Temporal Logic Claudia Carapelle, Shiguang Feng, Oliver Fernández Gil, Karin Quaas: Satisfiability for MTL and TPTL over Non-Monotonic Data Words Joachim Klein, David Müller, Christel Baier, Sascha Klüppelholz: Are Good-for-games Automata Good for Probabilistic Model Checking? 13:00 Closing

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Advertentie Bioinformatician Diadic Wageningen The Netherlands
by m.zhou 11 Feb '14

11 Feb '14

Dear fellow colleagues: Please see below a bioinformatician position from Diadic (The Netherlands, Wageningen). ###################################################################### Position for a Bioinformatician (MSc, PhD, m/f) Dyadic Netherlands (www.dyadic.nl) represents the R&D centre of Dyadic International. Its facilities are located in Wageningen, The Netherlands. Amongst others the company develops strains of the C1-fungus for the production of enzymes and specialty proteins applied in the biofuels, textile, pulp & paper, animal feed and pharmaceutical industry. Dyadic Netherlands offers a challenging position as we are looking for an experienced bioinformatician who will set up a new in-house bioinformatics facility, which will support R&D in close contact with our molecular biologists. Candidates should: be experienced in next generation sequencing (NGS) data handling be knowledgeable with software to analyze, compare and visualize NGS data, able to design new algorithms and be knowledgeable with IT in general be experienced in the assembly and annotation of eukaryotic (preferably fungal) genomes; comparative genomics be experienced in designing and / or maintaining genome databases be experienced in RNAseq data analyses i.e. transcriptomics, (comparative) quantification of gene expression levels, qualitative mRNA analyses be a team player able to efficiently communicate with molecular biologists with respect to experimental design and data analyses show initiatives and be able to work independently be creative and eager to solve relevant biological questions possess good communicative skills to interact both internally and with external partners or data providers and possess a good working knowledge of English More information about the position can be obtained from Dr. Hans Visser. Interested candidates are invited to send their application with resume to Dr. Wim van der Wilden (General Manager). Dr. Ir. Wim van der Wilden Dr. Hans Visser Tel. +31 (0)6-20368609 Tel. +31 (0)317-465457 E-mail: wwilden(a)dyadic.nl E-Mail: hvisser(a)dyadic.nl ###################################################################### -- Dr. ir. M.Zhou Bioinformatician Fungal Physiology CBS-KNAW FUNGAL BIODIVERSITY CENTRE Institute of the Royal Netherlands Academy of Arts and Sciences(KNAW) visiting address: Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands Postal address: P.O. Box 85167, 3508 AD, Utrecht, The Netherlands tel: + 31 (0)30 2122600, fax:+ 31 (0)30 2512097 m.zhou(a)cbs.knaw.nl, www.cbs.knaw.nl, www.knaw.nl

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SSTiC 2014: February 15, 3rd registration deadline
by GRLMC 08 Feb '14

08 Feb '14

*To be removed from our mailing list, please respond to this message with UNSUBSCRIBE in the subject line* ********************************************************************* 2014 TARRAGONA INTERNATIONAL SUMMER SCHOOL ON TRENDS IN COMPUTING SSTiC 2014 Tarragona, Spain July 7-11, 2014 Organized by Rovira i Virgili University http://grammars.grlmc.com/sstic2014/ ********************************************************************* --- February 15, 3rd registration deadline --- ********************************************************************* AIM: SSTiC 2014 is the second edition in a series started in 2013. For the previous event, see http://grammars.grlmc.com/SSTiC2013/ SSTiC 2014 will be a research training event mainly addressed to PhD students and PhD holders in the first steps of their academic career. It intends to update them about the most recent developments in the diverse branches of computer science and its neighbouring areas. To that purpose, renowned scholars will lecture and will be available for interaction with the audience. SSTiC 2014 will cover the whole spectrum of computer science through 6 keynote lectures and 24 six-hour courses dealing with some of the most lively topics in the field. The organizers share the idea that outstanding speakers will really attract the brightest students. ADDRESSED TO: Graduate students from around the world. There are no formal pre-requisites in terms of the academic degree the attendee must hold. However, since there will be several levels among the courses, reference may be made to specific knowledge background in the description of some of them. SSTiC 2014 is also appropriate for more senior people who want to keep themselves updated on developments in their own field or in other branches of computer science. They will surely find it fruitful to listen and discuss with scholars who are main references in computing nowadays. REGIME: In addition to keynotes, 3 parallel sessions will be held during the whole event. Participants will be able to freely choose the courses they will be willing to attend as well as to move from one to another. VENUE: SSTiC 2014 will take place in Tarragona, located 90 kms. to the south of Barcelona. The venue will be: Campus Catalunya Universitat Rovira i Virgili Av. Catalunya, 35 43002 Tarragona KEYNOTE SPEAKERS: Larry S. Davis (U Maryland, College Park), A Historical Perspective of Computer Vision Models for Object Recognition and Scene Analysis David S. Johnson (Columbia U, New York), Open and Closed Problems in NP-Completeness George Karypis (U Minnesota, Twin Cities), Recommender Systems Past, Present, & Future Steffen Staab (U Koblenz), Explicit and Implicit Semantics: Two Sides of One Coin Philip Wadler (U Edinburgh), You and Your Research and The Elements of Style Ronald R. Yager (Iona C, New Rochelle), Social Modeling COURSES AND PROFESSORS: Divyakant Agrawal (U California, Santa Barbara), [intermediate] Scalable Data Management in Enterprise and Cloud Computing Infrastructures Pierre Baldi (U California, Irvine), [intermediate] Big Data Informatics Challenges and Opportunities in the Life Sciences Rajkumar Buyya (U Melbourne), [intermediate] Cloud Computing John M. Carroll (Pennsylvania State U, University Park), [introductory] Usability Engineering and Scenario-based Design Kwang-Ting (Tim) Cheng (U California, Santa Barbara), [introductory/intermediate] Smartphones: Hardware Platform, Software Development, and Emerging Apps Amr El Abbadi (U California, Santa Barbara), [introductory] The Distributed Foundations of Data Management in the Cloud Richard M. Fujimoto (Georgia Tech, Atlanta), [introductory] Parallel and Distributed Simulation Mark Guzdial (Georgia Tech, Atlanta), [introductory] Computing Education Research: What We Know about Learning and Teaching Computer Science David S. Johnson (Columbia U, New York), [introductory] The Traveling Salesman Problem in Theory and Practice George Karypis (U Minnesota, Twin Cities), [intermediate] Programming Models/Frameworks for Parallel & Distributed Computing Aggelos K. Katsaggelos (Northwestern U, Evanston), [intermediate] Optimization Techniques for Sparse/Low-rank Recovery Problems in Image Processing and Machine Learning Arie E. Kaufman (U Stony Brook), [advanced] Visualization Carl Lagoze (U Michigan, Ann Arbor), [introductory] Curation of Big Data Dinesh Manocha (U North Carolina, Chapel Hill), [introductory/intermediate] Robot Motion Planning Bijan Parsia (U Manchester), [introductory] The Empirical Mindset in Computer Science Charles E. Perkins (FutureWei Technologies, Santa Clara), [intermediate] Beyond LTE: the Evolution of 4G Networks and the Need for Higher Performance Handover System Designs Sudhakar M. Reddy (U Iowa, Iowa City), [introductory] Test and Design for Test of Digital Logic Circuits Robert Sargent (Syracuse U), [introductory] Validation of Models Mubarak Shah (U Central Florida, Orlando), [intermediate] Visual Crowd Analysis Steffen Staab (U Koblenz), [intermediate] Programming the Semantic Web Mike Thelwall (U Wolverhampton), [introductory] Sentiment Strength Detection for Twitter and the Social Web Jeffrey D. Ullman (Stanford U), [introductory] MapReduce Algorithms Nitin Vaidya (U Illinois, Urbana-Champaign), [introductory/intermediate] Distributed Consensus: Theory and Applications Philip Wadler (U Edinburgh), [intermediate] Topics in Lambda Calculus and Life ORGANIZING COMMITTEE: Adrian Horia Dediu (Tarragona) Carlos Martín-Vide (Tarragona, chair) Florentina Lilica Voicu (Tarragona) REGISTRATION: It has to be done at http://grammars.grlmc.com/sstic2014/registration.php The selection of up to 8 courses requested in the registration template is only tentative and non-binding. For the sake of organization, it will be helpful to have an approximation of the respective demand for each course. Since the capacity of the venue is limited, registration requests will be processed on a first come first served basis. The registration period will be closed when the capacity of the venue will be complete. It is very convenient to register prior to the event. FEES: As far as possible, participants are expected to attend for the whole (or most of the) week (full-time). Fees are a flat rate allowing one to participate to all courses. They vary depending on the registration deadline. ACCOMMODATION: Information about accommodation will be available on the website of the School in due time. CERTIFICATE: Participants will be delivered a certificate of attendance. QUESTIONS AND FURTHER INFORMATION: florentinalilica.voicu(a)urv.cat POSTAL ADDRESS: SSTiC 2014 Lilica Voicu Rovira i Virgili University Av. Catalunya, 35 43002 Tarragona, Spain Phone: +34 977 559 543 Fax: +34 977 558 386 ACKNOWLEDGEMENTS: Departament dEconomia i Coneixement, Generalitat de Catalunya Universitat Rovira i Virgili

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Fwd: Bioinformatics position in Munich
by Arjan van der Velde 06 Feb '14

06 Feb '14

FYI Begin forwarded message: > > On 2/6/14 11:57 AM, "Barenboim, Maxim" > <Maxim.Barenboim(a)lrz.tu-muenchen.de> wrote: > >> Hi Leo, >> Here in our group in Munich we advertise new bioinformatics position >> (Master level but could be with Ph.D.) preferably with computer science >> background and with ability to do to some extent linux sysadmin work. >> >> Do you know somebody who might be interested? Thanks a lot. >> >> Here you can find this ad: >> http://www.dkfz.de/en/stellenangebote/index.php?id=016/2014 >> >> Best, >> >> Max >> >> -- >> ************************************************************ >> Maxim Barenboim, Ph.D. >> Technische Universität München >> Klinikum rechts der Isar >> II. Medizinische Klinik >> Bau 514/ 2.OG, R 02.1 >> Trogerstr. 9 >> 81675 München >> Tel.: +49 (0)89 4140-6033 >> E-mail: maxim.barenboim(a)lrz.tum.de >> ************************************************************ >

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AlCoB 2014: extended submission deadline 11 February
by GRLMC 01 Feb '14

01 Feb '14

*To be removed from our mailing list, please respond to this message with UNSUBSCRIBE in the subject line* ---------------------------------------------------------------------------- ***** SUBMISSION DEADLINE EXTENDED: February 11 ***** ---------------------------------------------------------------------------- ********************************************************************* 1st INTERNATIONAL CONFERENCE ON ALGORITHMS FOR COMPUTATIONAL BIOLOGY AlCoB 2014 Tarragona, Spain July 1-3, 2014 Organized by: Research Group on Mathematical Linguistics (GRLMC) Rovira i Virgili University http://grammars.grlmc.com/alcob2014/ ********************************************************************* AIMS: AlCoB aims at promoting and displaying excellent research using string and graph algorithms and combinatorial optimization to deal with problems in biological sequence analysis, genome rearrangement, evolutionary trees, and structure prediction. The conference will address several of the current challenges in computational biology by investigating algorithms aimed at: 1) assembling sequence reads into a complete genome, 2) identifying gene structures in the genome, 3) recognizing regulatory motifs, 4) aligning nucleotides and comparing genomes, 5) reconstructing regulatory networks of genes, and 6) inferring the evolutionary phylogeny of species. Particular focus will be put on methodology and significant room will be reserved to young scholars at the beginning of their career. VENUE: AlCoB 2014 will take place in Tarragona, located 90 kms. to the south of Barcelona. The venue will be the Catalunya Campus. SCOPE: Topics of either theoretical or applied interest include, but are not limited to: Exact sequence analysis Approximate sequence analysis Pairwise sequence alignment Multiple sequence alignment Sequence assembly Genome rearrangement Regulatory motif finding Phylogeny reconstruction Phylogeny comparison Structure prediction Compressive genomics Proteomics: molecular pathways, interaction networks ... Transcriptomics: splicing variants, isoform inference and quantification, differential analysis Next-generation sequencing: population genomics, metagenomics, metatranscriptomics ... Microbiome analysis Systems biology STRUCTURE: AlCoB 2014 will consist of: invited talks invited tutorials peer-reviewed contributions INVITED SPEAKERS: Michael Galperin (National Center for Biotechnology Information, Bethesda), Comparative Genomics Approaches to Identifying Functionally Related Genes Uwe Ohler (Max-Delbrück Centre for Molecular Medicine, Berlin), Decoding Non-coding Regulatory Regions in DNA and RNA (tutorial) Jason Papin (University of Virginia, Charlottesville), Network Analysis of Microbial Pathogens PROGRAMME COMMITTEE: Tatsuya Akutsu (Kyoto, JP) Amihood Amir (Ramat-Gan, IL) Alberto Apostolico (Atlanta, US) Joel Bader (Baltimore, US) Pierre Baldi (Irvine, US) Serafim Batzoglou (Stanford, US) Bonnie Berger (Cambridge, US) Francis Y.L. Chin (Hong Kong, HK) Benny Chor (Tel Aviv, IL) Keith A. Crandall (Washington, US) Bhaskar DasGupta (Chicago, US) Joaquín Dopazo (Valencia, ES) Liliana Florea (Baltimore, US) Olivier Gascuel (Montpellier, FR) David Gilbert (Uxbridge, UK) Gaston H. Gonnet (Zurich, CH) Roderic Guigó (Barcelona, ES) Dan Gusfield (Davis, US) Vasant Honavar (University College, US) Sorin Istrail (Providence, US) Tao Jiang (Riverside, US) Inge Jonassen (Bergen, NO) Anders Krogh (Copenhagen, DK) Giovanni Manzini (Alessandria, IT) Carlos Martín-Vide (Tarragona, ES, chair) Satoru Miyano (Tokyo, JP) Burkhard Morgenstern (Göttingen, DE) Shinichi Morishita (Tokyo, JP) Cédric Notredame (Barcelona, ES) Graziano Pesole (Bari, IT) Mark Ragan (Brisbane, AU) Timothy Ravasi (Thuwal, SA) Allen G. Rodrigo (Durham, US) Steven Salzberg (Baltimore, US) David Sankoff (Ottawa, CA) Thomas Schiex (Toulouse, FR) João C. Setubal (São Paulo, BR) Steven Skiena (Stony Brook, US) Peter F. Stadler (Leipzig, DE) Wing-Kin Sung (Singapore, SG) Alfonso Valencia (Madrid, ES) Jacques van Helden (Marseille, FR) Arndt von Haeseler (Vienna, AT) Lusheng Wang (Hong Kong, HK) Limsoon Wong (Singapore, SG) Xiaohui Xie (Irvine, US) Dong Xu (Columbia, US) Zohar Yakhini (Santa Clara, US) Alex Zelikovsky (Atlanta, US) Michael Q. Zhang (Dallas, US) ORGANIZING COMMITTEE: Adrian Horia Dediu (Tarragona) Carlos Martín-Vide (Tarragona, chair) Bianca Truthe (Magdeburg) Florentina Lilica Voicu (Tarragona) SUBMISSIONS: Authors are invited to submit non-anonymized papers in English presenting original and unpublished research. Papers should not exceed 12 single-spaced pages (including eventual appendices) and should be formatted according to the standard format for Springer Verlag's LNCS series (see http://www.springer.com/computer/lncs?SGWID=0-164-6-793341-0) Submissions have to be uploaded to: https://www.easychair.org/conferences/?conf=alcob2014 PUBLICATIONS: A volume of proceedings published by Springer in the LNCS/LNBI series will be available by the time of the conference. A special issue of IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB, 2012 impact factor: 1.616) will be later published containing peer-reviewed extended versions of some of the papers contributed to the conference. Submissions to it will be by invitation. REGISTRATION: The period for registration is open from September 21, 2013 to July 1, 2014. The registration form can be found at: http://grammars.grlmc.com/alcob2014/Registration.php DEADLINES: Paper submission: February 11, 2014 (23:59 CET) EXTENDED Notification of paper acceptance or rejection: March 15, 2014 Final version of the paper for the LNCS/LNBI proceedings: March 22, 2014 Early registration: March 29, 2014 Late registration: June 17, 2014 Starting of the conference: July 1, 2014 End of the conference: July 3, 2014 Submission to the post-conference TCBB special issue: October 3, 2014 QUESTIONS AND FURTHER INFORMATION: florentinalilica.voicu(a)urv.cat POSTAL ADDRESS: AlCoB 2014 Research Group on Mathematical Linguistics (GRLMC) Rovira i Virgili University Av. Catalunya, 35 43002 Tarragona, Spain Phone: +34 977 559543 Fax: +34 977 558386 ACKNOWLEDGEMENTS: Departament dEconomia i Coneixement, Generalitat de Catalunya Universitat Rovira i Virgili

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Open industrial position: Computational scientist immunology at Janssen, Beerse
by Ceulemans, Hugo [JRDBE] 31 Jan '14

31 Jan '14

Computational Scientist position Date: 30-Jan-2014, for updates on position availability and application, kindly visit http://bit.ly/1eiF2Ee Company: Janssen, Johnson & Johnson Location Beerse, BE Description Janssen Discovery Sciences is supporting transformational research harnessing state-of-the-art multi-parametric platforms and systems analysis of the immune response in preclinical models and clinical studies to identify and evaluate innovative interventions in oncology, pathogenic infections and auto-immune diseases and guide prophylactic and therapeutic vaccine development. This commitment aims to bridge the gap between the single molecule/single regimen pharmacology and the orchestration of host response in animal models and in the clinic, taking into consideration the cooperative and cross-talking, non-linear processes of immune cells transitioning in a continuum of states and leading to emergent deleterious or disease resolving behaviors. Internal investments in mass cytometry, high-content imaging, single cell sequencing and access to new emerging platforms that allow the systematic evaluation of single cell behaviors with a buildup of a network of key strategic academic partners in the evolving scientific field are key components of our systems immunology strategy. SCOPE A major scope is the integration of high dimensional data from preclinical and clinical compound profiling studies and disease models, often from different biological levels single cell, tissue and patient level. Contribution to the design and the selection of new experiments and studies is an integral part of the role. The transition to tractable molecular determinants and experimental model systems will demand close coordination with the experimental scientists to identify relevant and testable hypotheses as well as assayable readout combinations. Collaborations with game-changing scientific teams in the field should provide a choice of optimal analysis and modeling approaches, also driven by incentives to publish the non-proprietary new science. Qualifications - PhD in Computational Biology or a related multidisciplinary field with at least three years of post-doctoral experience in an academic or industrial setting in the field of host response or related fields, focusing on the analysis and modeling of control mechanisms of heterogeneous multicellular processes. - Demonstrated experience with high-dimensional data integration and biological interpretation that led to hypothesis driven simulation and experimental testing. - Demonstrated experience in handling high-dimensional single cell data, e.g. mass cytometry, high-content imaging derived features, single cell transcriptomics, and their integration at the population level. Strong programming and scripting skills that enable the development of functional prototypes. Experience in the analysis of genomics, proteomics, image analysis and/or flow cytometry data using R/Bioconductor or similar software. Experience with graph based probabilistic modeling, ODE/PDE based modeling or related predictive approaches would be an asset - Excellent communication, reporting and team working skills, yet able to work independently Primary Location:Europe/Middle East/Africa-Belgium-Antwerp-Beerse Organization: Janssen Pharmaceutica N.V. Job Function: R&D

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NSBM Spring meeting 2014 April 8th - NBIC Conference
by Barbara.vanKampen＠radboudumc.nl 31 Jan '14

31 Jan '14

[logo.png]NSBM Spring meeting April 8th 2014 In conjunction with the Netherlands Bioinformatics Conference 2014 Venue: Congrescentrum De Werelt, Lunteren The Netherlands Society on Biomolecular Modelling (NSBM) cordially invites you to visit its spring meeting, a topical track of the Netherlands Bioinformatics Conference 2014 (NBIC2014) on April 8th 2014. During several parallel sessions, the floor will be given to PhD students and postdocs who study protein structure and/or structural bioinformatics or related topics (see a list below). Speakers and attendees will have the opportunity to join the NBIC2014 activities and visit keynote lectures of a.o. Yves van de Peer (VIB UGent, Belgium). Programme April 8th Invited speaker: Christian Ottmann<https://www.aanmelder.nl/nbic2014/wiki/christian%20ottmann>, Eindhoven University of Technology, the Netherlands Abstract submission All abstracts should be submitted via the NBIC2014 abstract submission system<https://www.aanmelder.nl/nbic2014/wiki/abstract%20submission>. Please indicate in the form that you are submitting for the NSBM Spring meeting. Starting PhD students are particularly encouraged to present their research! For questions regarding the abstract or meeting please contact Gert Vriend, gerrit.vriend(a)radboudumc.nl<mailto:gerrit.vriend@radboudumc.nl> Topics for presentations may include, but are not limited to: * Computational Biology and Bioinformatics * Computer-aided drug design * Drug design and drug discovery * Grid computing * Homology modelling * Molecular and supramolecular dynamics * Molecular modeling and simulation * Mutational analysis * Protein crystallography * Protein NMR * Protein structure analysis * Protein structure prediction * Protein-protein interactions * Protein-small molecules interaction * Protein software design * Proteomics * Structural bioinformatics * Structure-function analysis * Text mining & information extraction * Virtual screening Registration Registration should be done via the NBIC2014 registration form<https://www.aanmelder.nl/nbic2014/wiki/registration>. Registration for the conference (for one day/April 8th) includes: participation to conference and evening poster session on April 8th, lunch, coffee/tea during breaks, internet access and conference dinner. Should a lack of funding be a hurdle for visiting the NSBM Spring meeting, please contact prof. Gert Vriend at gerrit.vriend(a)radboudumc.nl<mailto:gerrit.vriend@radboudumc.nl> so that an arrangement can be made. Key dates * Abstract submission deadline for oral presentations: February 23, 2014 * Notification date selection oral presentations: March 4, 2014 * Abstact submission deadline for posters & demos: April 4, 2014 Sponsored by: [DSM]<http://www.dsm.com/> [Genalice] <http://www.genalice.com/> [Keygene NV]<http://www.keygene.com/> [Bio-prodict] <http://www.bio-prodict.nl/> NSBM Mailing list --- NEW EMAIL: barbara.vankampen(a)radboudumc.nl Barbara van Kampen [Radboudumckleine.png] CMBI 260 Radboud University Medical Centre / RIMLS CMBI Office / Room 0.02 PO Box 9101 Geert-Grooteplein 26-28 6500 HB Nijmegen 6525 GA Nijmegen Phone: +31(0)24 36 19390 Fax: +31 (0)24 36 19395 www.cmbi.ru.nl<http://www.cmbi.ru.nl/> Het Radboudumc staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629. The Radboud university medical center is listed in the Commercial Register of the Chamber of Commerce under file number 41055629.

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