September 2014 - BBClist - maillist.psb.ugent.be

PhD position: Haplotyping in polyploid crops
by Ridder, Dick de 28 Oct '14

28 Oct '14

We have an exciting opportunity for an enthusiastic PhD student to develop new methodology for haplotyping genomes of polyploid crops, using novel genotyping-by-sequencing approaches. We are looking for an ambitious PhD student with an MSc degree in bioinformatics, computer sciences, statistics, biotechnology, biology or plant sciences. The PhD project 'Haplotyping in polyploid crops using genetics, genomics and bioinformatics' aims at solving important questions in crops like potato, leek, rose, chrysanthemum, that have four or six copies of a genome: what is the composition (haplotype) of each of the underlying genomes, both locally (gene level) and over larger distances (chromosome level)? Can we distinguish different dosages of haplotypes? Can we characterize plants in terms of haplotype composition? Can we relate observed haplotypes to variation in phenotypic traits? In this project, the goal is to develop statistical, genetics and bioinformatics tools for novel genotyping-by-sequencing (GBS) approaches for polyploid crops. The project will deliver effective strategies for haplotyping in polyploid crops, faster discovery of candidate genes and of their allelic variants for traits of interest to plant breeders. It is a collaborative initiative of the Bioinformatics and Plant Breeding chair groups at Wageningen University. You will work in close cooperation with other PhD students and researchers involved in related projects on the development of a genetic analysis pipeline for polyploid crops and novel sequencing strategies for polyploid genomes. More information about the position, the research groups involved, and a possibility to apply for this position can be found at: http://www.wageningenur.nl/en/Education-Programmes/PhD-Programme/PhD-Vacanc… Interested candidates can apply up to September 15, 2014 through the above-mentioned website. Dr. Chris Maliepaard (Quantitative aspects of Plant Breeding) Prof. Dick de Ridder (Bioinformatics) Wageningen University The Netherlands

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Text Mining PhD scholarship at ULisboa
by Francisco Couto 30 Sep '14

30 Sep '14

PhD scholarship for the Development of a Text Mining Approach to Disease Network Discovery at the University of Lisbon (BioSyS PhD programme): The deadline for applications is *October 31th 2014*. http://biofig.fc.ul.pt/sites/default/files/BioSys_FranciscoCouto&LukaClarke… http://biofig.fc.ul.pt/training-phd-programme -- fcoutowww.di.fc.ul.pt/~fjmc

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[Gtpb] HP
by Pedro Fernandes 29 Sep '14

29 Sep '14

ANNOUNCEMENT The Gulbenkian Training Programme in Bioinformatics is pleased to announce that the applications for the hands-on Bioinformatics training course HPND14 Hunting for Promoters with NGS data are now OPEN. Please have a look at our website here: http://gtpb.igc.gulbenkian.pt/bicourses/HPND14/ We will have Edgar Wingender and Philip Stegmaier as instructors. Course description: This course is set-up to review the basic principles of gene regulation and the corresponding bioinformatic problems. It will start with the computational prediction of promoters and distant enhancers and will deal with the analysis of the structure of such regions by identifying binding sites for transcription factors. The most intriguing parts of genomes, still not completely understood, are the gene regulatory regions â mostly promoters and enhancers. A complete annotation of a newly sequenced genome has to address the identification of these regions in addition to the classical task of finding genes in terms of coding regions. Regulatory regions define when, where and under what conditions genes become active and, thus, are part of the fundamental function of a gene. In this course, we will overview some of the experimental methods such as next generation sequencing (NGS) techniques for genome-wide epigenetic analysis such as ChIP-seq, which have revolutionized our ways for studying the gene regulatory mechanisms. The attendees will learn about several techniques of finding promoters and enhancers and the principles on which these methods are based on. In the "hands on" exercises, several analytical tools will be introduced and the results critically evaluated to assess their reliability. Objectives: The course will consist of lectures that lay out the conceptual framework as needed and and "hands on" exercises, which will provide the practical insight on the use of the methods, gradually, in order to produce skills that can be used with a relatively high degree of independence. Participants will learn how to set-up some of the programs, and use publicly available servers for more complex analytical jobs, in an informed fashion, so that they fully understand the output generated and how its quality can be assessed. Participants will also learn the novel principles of organization of gene regulatory regions, which will help them to interpret their results of genomic and transcriptomic studies. Thank you for your continued interest P.Fernandes GTPB Coordinator -- Pedro Fernandes Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL Tel +351 21 4407912 http://gtpb.igc.gulbenkian.pt -- Pedro Fernandes 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

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9th Benelux Bioinformatics Conference (BBC 2014) - second call for abstracts
by Joanna SMULA-OSTASZEWSKA 25 Sep '14

25 Sep '14

Dear Colleagues, Luxembourg Centre for System Biomedicine of University of Luxembourg (LCSB) and Centre de Recherché Public de la Santé (CRP-Santé) organize the 9th edition of the Benelux Bioinformatics Conference (BBC 2014). The conference is affiliated by International Society for Computational Biology (ISCB)<http://www.iscb.org/>. The event entitled "Bioinformatics: Integrating data, teams and disciplines" will take place in Novotel-Kirchberg in Luxembourg, on December 8th-9th. Conference coordinators invite you to submit your abstracts through the registration/submission system<http://lcsb.ldorganisation.lu/v2/produits.php?langue=english&cle_menus=1240…>. Conference topics cover all fields of bioinformatics, including: * Biotechnologies * Computational biology * Research on biological networks * Structural bioinformatics * The analysis of the high-throughput sequencing data * Micro-array expression data, etc. Detailed information may be found on the conference website http://www.bbc2014.lu/ We anticipate that the BBC 2014 will once again greatly foster the collaboration and research activities between scientists in the Benelux area. Please feel free to distribute this announcement to your interested colleagues and do not hesitate to contact us in case of further questions. Regards, Joanna Smula-Ostaszewska [cid:image002.jpg@01CFD8BD.719C7010] Dr.Eng. Joanna Smula-Ostaszewska Scientific assistant Université du Luxembourg Luxembourg Centre for Systems Biomedicine (LCSB) Campus Belval; 7, Avenue des Hauts-Fourneaux; L-4362 Esch-Belval; Luxembourg T: +352 46 66 44 6373 http://lcsb.uni.lu<http://lcsb.uni.lu/> --- This message is confidential and may contain privileged information. It is intended for the named recipient only. If you receive it in error please notify me and permanently delete the original message and any copies.

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Registration - Multiscale Modeling of Biomolecular Systems - 28 November 2014
by Sanne Abeln 24 Sep '14

24 Sep '14

You are cordially invited to the Multiscale Modeling of Biomolecular Systems (MMBS) symposium on Friday 28 November 2014. This meeting is jointly organized by the Amsterdam Center for Multiscale Modeling (ACMM) and the Netherlands Society for Biomolecular Modeling (NSBM). The meeting aims to bridge multiple levels of modeling, from structural bioinformatics to biomolecular simulation at various scales. You are now able to register at: https://www.aanmelder.nl/79914/subscribe?survey_id=59573 The deadline for registration is 31 October 2014. Scope: The meeting will focus on multiscale and multilevel modeling of biomolecular systems including proteins, DNA or RNA. Topics will cover (but are not limited to): bioinformatics sequence analysis, structure analysis, structure prediction methods (including docking), coarse grained simulations, full atomistic classical force field simulations, combined QM/MM, ab initio and/or DFT calculations, and enhanced sampling methods. Keynote Speakers: Prof. David Jones (UCL, UK) Prof. Ursula Roethlisberger (EPFL, Switzerland) Date: 28 November 2014 - 11:00 - 18:00 Location: VU University, De Boelelaan 1081, Amsterdam, the Netherlands Registration & posters: https://www.aanmelder.nl/79914/subscribe?survey_id=59573 Program Committee: Jocelyne Vreede (UvA), Paola Gori-Giorgi (VU) Daan Geerke (VU), Sanne Abeln (VU) Advisory board (NSBM+ACMM): Gerry Nicolaes (UM), Gert Vriend (UMCN) Peter Bolhuis (UvA), Evert Jan Meijer (UvA) Matthias Bickelhaupt (VU), Luuk Visscher (VU) Best regards, Jocelyne Vreede, Paola Gori-Giorgi, Daan Geerke, Sanne Abeln -- Sanne Abeln Assistant Professor Bioinformatics - VU University Amsterdam s.abeln(a)vu.nl +31 20 59 87816 www.few.vu.nl/~abeln

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PhD Position at Maastricht University: Identification of gene-environment interactions in the development of psychosis
by Viechtbauer Wolfgang (STAT) 23 Sep '14

23 Sep '14

Subject: PhD Position at Maastricht University Project: Identification of gene-environment interactions in the development of psychosis [Project] A psychotic disorder is a psychiatric condition characterized by delusions, hallucinations, and social and emotional problems. Various environmental factors, such as the use of cannabis and experiencing traumatic events, increase the risk of a psychosis, but the risk-increasing effects of these factors are much higher in people with a pre-existing genetic vulnerability. This phenomenon is also called gene-environment interaction. New technical possibilities in modern genetics, such as genome-wide genotyping, now make it possible to systematically investigate the genes that make people more susceptible to such environmental factors and the biological pathways to which these genes belong. In 2010, a major European study on the importance of gene-environment interactions in the etiology of psychotic disorders was launched. Now that the data collection phase is close to completion, there is an open position for a doctoral student to examine the genome-wide data from this study for gene-environment interactions in a systematic way. [Tasks] Your task is to identify genes and biological systems that interact in a plausible manner with relevant environmental factors. For this purpose, you derive sets of genes linked together in a biologically plausible way and analyze whether they can explain sensitivity to environmental factors. You work on large data sets that have already been collected. The development of new and/or the application of advanced statistical methods to analyze such data, in consultation with a statistician, is an important ambition of the project. [Requirements] Graduated in bioinformatics or a related discipline. Good communication skills, fluent in English, and some affinity for research on psychiatric disorders. Demonstrated interest in clinical research. Some research experience is recommended. [Conditions of employment] The terms of employment of Maastricht University are set out in the Collective Labour Agreement of Dutch Universities (CAO). Furthermore, local UM provisions also apply (see http://www.maastrichtuniversity.nl/web/Main/Employees/AZ.htm) This is a temporary employment for 4 years. Your salary would be € 2.083,-- gross per month in the first year up to € 2.664,-- gross per month in the fourth year according to the PhD-student salary scale. Each year an evaluation will take place. [Organization] Maastricht University (http://www.maastrichtuniversity.nl/) is renowned for its unique, innovative, problem-based learning system, which is characterized by a small-scale and student-oriented approach. Research at UM is characterized by a multidisciplinary and thematic approach, and is concentrated in research institutes and schools. Maastricht University has around 15,000 students and 4,000 employees. Reflecting the university's strong international profile, a fair amount of both students and staff are from abroad. The university hosts 6 faculties: Faculty of Health, Medicine and Life Sciences, Faculty of Law, School of Business and Economics, Faculty of Humanities and Sciences, Faculty of Arts and Social Sciences, Faculty of Psychology and Neuroscience. The School for Mental Health and Neuroscience (http://mhens.unimaas.nl/) is one of the internationally leading institutes on neuroscience research, and aims at advancing our understanding of brain-behavior relationships by adopting an integrated approach between the various disciplines in neuro- and behavioral science, medicine, and the life sciences. The project is embedded in Division 2, Cognitive Neuropsychiatry & Clinical Neuroscience. The mission of Division 2 is to generate new insights into the neurocognitive and neurobehavioral mechanisms in order to improve treatment and care for people with cognitive disorders and other neurological disorders. [Contact] For more information about this position and/or to submit your application materials (CV, letter of motivation, and contact information for two references), please contact Dr. Ruud van Winkel at: ruud.vanwinkel(a)maastrichtuniversity.nl Dr. Ruud van Winkel Dr. Wolfgang Viechtbauer Department of Psychiatry and Psychology School for Mental Health and Neuroscience Faculty of Health, Medicine, and Life Sciences Maastricht University, P.O. Box 616 (VIJV1) 6200 MD Maastricht, The Netherlands

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FW: vacature nexsplorer.iph
by Katrijn Vannerum 23 Sep '14

23 Sep '14

Dear, The WIV/ISP has a vacant PhD position for the project 'Development of next generation sequencing data analysis tools in support of a fast response for public health and food chain safety'. Best regards, Katrijn Vannerum Project manager N2N (From Nucleotides to Networks) Multidisciplinary Research Partnership Bioinformatics and Systems Biology Ghent University http://www.nucleotides2networks.be/ twitter: @N2N_UGent Katrijn.Vannerum(a)UGent.be<mailto:Katrijn.Vannerum@UGent.be> Technologiepark 927 9052 Gent, Belgium +32 (0)9 331 36 85 [cid:image001.png@01CFD737.B4E567A0]

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[Gtpb] REMINDER: TA-AFADM14 - Bioinformatics Training Course
by Pedro Fernandes 23 Sep '14

23 Sep '14

Dear GTPB mailing list member Please allow me to remind you that this hands-on training course joins together of two connected subjects - RNAseq using open source tools - Automatic Functional Annotation using Blast2GO In the feedblack collected in previous editions, this course is considered highly efficient in skills transfer If you have not yet done so, please consider applying or indicating the course to a colleague or collaborator. The published deadline is Sept 26th. Thank ,Pedro Fernaandes GTPB Coodinator REMINDER IMPORTANT DATES for TA-AFADM14 Deadline for applications: September 26th 2014 <================= Notification of acceptance dates: EARLY: Sept 19th 2014 (on special request, see Application) NORMAL: September 26th 2014 Course date: October 6th - October 9th 2014 The Gulbenkian Training Programme in Bioinformatics is pleased to announce that the applications for the hands-on Bioinformatics training course TA-AFADM14 Transcriptome Assembly, Automatic Annotation and Data Mining are now OPEN. Please have a look at our website here: http://gtpb.igc.gulbenkian.pt/bicourses/TA-AFADM14/ Course duration: 4 days Course fee: Euro 320.00 We will have Stefan Goetz and Riccardo Alese Cigliano as instructors. This course has already been run here several times with a great deal of success, as revealed by very positive feedback reports and subsequent recruitment by word of mouth by satisfied attendees. Course description: This is a combined course in RNA-seq and functional annotation aimed at scientists working in next generation sequencing transcriptomics who want to extract the best possible information from their data. The course covers all aspects of RNA-seq analysis, from quality control, to mapping, reconstruction of transcripts and differential expression. Participants will learn how to deal with RNA-seq data both in the presence and absence of a reference genome. The second part of the course is a practical workshop on Blast2GO, the most popular framework for functional annotation of sequence data. Participants will learn how to generate de novo functional labels, such as GO terms and KEGG pathways, for their sequence data and how to extract relevant information from these annotations, i.e. visualisation and enrichment analysis using the Gene Ontology. This part will be based on the use of the Blast2GO application and will mainly comprise exercises and practical cases. Participants may bring their own data. Who should attend? Experimentalists and bioinformaticians working on EST, NextGeneration Sequencing and microarray design projects, specially (but not exclusively) of non-model species. No programming knowledge is required. Thank you for your continued interest P.Fernandes GTPB Coordinator -- Pedro Fernandes 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

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PhD opportunity at Wageningen Univeristy
by Besten, Heidy den 19 Sep '14

19 Sep '14

Dear sir/madam, Please find below the links to a PhD vacancy in the Food Science Domain of Wageningen University. We are looking for a MSc student with a genuine interest in bioinformatics and (food)microbiology. I would be grateful if you can please pass this information on to relevant contacts/people that may be interested in applying. http://www.wageningenur.nl/en/Jobs/Vacancies/Show/PhD-Food-Safety-System-Dy… https://www.academictransfer.com/employer/WUR/vacancy/23158/lang/en/ Thanks in advance, Heidy den Besten dr. ir. H. M. W. den Besten (Heidy) Assistant Professor in Food Microbiology Wageningen University Laboratory of Food Microbiology Postal address: PO Box 17, 6700 AA Wageningen, The Netherlands Visiting address: Building 118 (Axis-X office 3.10B), Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands T: +31-317-483213 E-mail: heidy.denbesten(a)wur.nl<mailto:heidy.denbesten@wur.nl> I: www.fhm.wur.nl<http://www.fhm.wur.nl/>

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[Gtpb] REMINDER: TA-AFADM14 - Bioinformatics Training Course
by Pedro Fernandes 19 Sep '14

19 Sep '14

REMINDER IMPORTANT DATES for TA-AFADM14 Deadline for applications: September 26th 2014 <================= Notification of acceptance dates: EARLY: Sept 19th 2014 (on special request, see Application) NORMAL: September 26th 2014 Course date: October 6th - October 9th 2014 The Gulbenkian Training Programme in Bioinformatics is pleased to announce that the applications for the hands-on Bioinformatics training course TA-AFADM14 Transcriptome Assembly, Automatic Annotation and Data Mining are now OPEN. Please have a look at our website here: http://gtpb.igc.gulbenkian.pt/bicourses/TA-AFADM14/ Course duration: 4 days Course fee: Euro 320.00 We will have Stefan Goetz and Riccardo Alese Cigliano as instructors. This course has already been run here several times with a great deal of success, as revealed by very positive feedback reports and subsequent recruitment by word of mouth by satisfied attendees. Course description: This is a combined course in RNA-seq and functional annotation aimed at scientists working in next generation sequencing transcriptomics who want to extract the best possible information from their data. The course covers all aspects of RNA-seq analysis, from quality control, to mapping, reconstruction of transcripts and differential expression. Participants will learn how to deal with RNA-seq data both in the presence and absence of a reference genome. The second part of the course is a practical workshop on Blast2GO, the most popular framework for functional annotation of sequence data. Participants will learn how to generate de novo functional labels, such as GO terms and KEGG pathways, for their sequence data and how to extract relevant information from these annotations, i.e. visualisation and enrichment analysis using the Gene Ontology. This part will be based on the use of the Blast2GO application and will mainly comprise exercises and practical cases. Participants may bring their own data. Who should attend? Experimentalists and bioinformaticians working on EST, NextGeneration Sequencing and microarray design projects, specially (but not exclusively) of non-model species. No programming knowledge is required. Thank you for your continued interest P.Fernandes GTPB Coordinator -- Pedro Fernandes Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL Tel +351 21 4407912 http://gtpb.igc.gulbenkian.pt ----- End forwarded message ----- _______________________________________________ Gtpb mailing list Gtpb(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb

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