NGS workshop and conference MouseGene 2014:
27. – 31. 10. 2014, Nové Hrady
Speaking language: English
3 days of intensive theoretical and practical workshop focused on NGS methods and handling of NGS data
2 days of conference focused on application of NGS in conservation and evolutionary genetics and molecular ecology
The Institute of Vertebrate Biology Academy of Sciences of the Czech Republic (IVB AS CR) is organising a next generation sequencing (NGS) workshop from October 27 to 29 in Nové Hrady, CZ.
The main aim of this workshop: to present current NGS methods and their application in conservation and evolutionary genetics and molecular ecology. Workshop will be focused also on practical trainings (see program below) which aim to facilitate to use of new sequencing technologies. Lectures will be given by experts from different fields and countries so official language will be English.
Students interested in participation will be invited to shortly (5-10min) present their research or their experience with NGS during conference MouseGene 2014 which will follow NGS workshop. Each day of the workshop will be finished by informal discussion where speakers will be ready to answer all questions.
Stuart Baird, IVB AS CR, Studenec, Czech Republic
Mark Blaxter, University of Edinburgh, Scotland
Emanuel Heitlinger, Humbold University of Berlin, Germany
Jakub Kreisinger, Edmund Mach Foundation, Italy
Jean Francois Martin,CBGP, Montpellier, France
Libor Morkovsky, Charles University in Prague, Czech Republic
Wasimuddin,IVB AS CR, Studenec, Czech Republic
Anja Westram, University of Sheffield, United Kingdom
Oleksiy Yanchukov, IVB AS CR, Studenec, Czech Republic
Who is eligible to apply?
The workshop is designed for Czech master students, PhD-students and post-docs currently or prospectively working on NGS analysis. A basic knowledge of UNIX would be beneficial. Unfortunately students from Prague are not allowed to apply.
Application deadline: September 14, 2014
Admission notification: September 30, 2014
CV (maximum 2 pages)
Letter of motivation including your experience with NGS data analysis and a statement of the relevance for your research project (maximum 1 page)
Title of conference contribution with short specification of talk topic (5-10 min, presenting of own research regarding NGS or own experience with NGS, etc..)
The workshop is free of charge (including also travel expenses, accommodation and meal).
PROGRAMME (preliminary version, will be continuously actualize)
Sunday, 26. 10. 2014, arrival to Nové Hrady at 18:00, diner and welcome party (19:00-23:00)
Monday, 27. 10. 2014
9:00 - 10:30, Jean Francois Martin: Overview of current NGS methods (theoretical lecture)
10:30 - 12:00, Jean Francois Martin: Overview of current NGS methods (theoretical lecture)
13:00 - 14:30, Libor Morkovsky: Genomes and Unix (theoretical lecture)
15:00 - 17:00, Libor Morkovsky: Handling important NGS data formats in UNIX (practical training course)
17:30 - 19:00, Informal discussion
9:00 - 10:30, Emanuel Heitlinger: Bioninformatic design of DNA capture baits for population genomics (theoretical lecture)
10:30 - 12:00, Emanuel Heitlinger: Bait design - extracting and screening regions from blast searches (practical training course)
13:00 - 14:30, Jean Francois Martin: Amplicon NGS data analysis (theoretical training course)
15:00 - 16:30, Jean Francois Martin: Amplicon NGS data analysis (practical training course)
17:00 - 18:30, Wasimuddin and Jakub Kreisinger: QIIME (quantitative insights into microbial ecology) – presenting of a software package for comparison and analysis of microbial communities, primarily based on high-throughput amplicon sequencing data (mainly 16S rRNA barcoding) (theoretical training course)
18:30 - 19:00, Informal discussion
Wednesday, 29. 10. 2014
9:00 - 10:00, Stuart Baird: How to use STRUCTURE (or other population-genetic model based inference software) to treat NGS data - in particular long sequences or (equivalently) SNPs which are dense on the map, i.e. cases where loci cannot be treated as independent (theoretical course)
10:30 - 12:00, Stuart Baird: Haplotype reconstruction from NGS data (practical training course)
13:00 - 14:00, Oleksiy Yanchukov: Digital PCR to genotype the gene copy number
14:30 – 16:00, Anja Westram: Highlighting advantages/pitfalls of RADseq or RNA seq
16:30 - 18:30, Mark Blaxter: NextGen applications to non-model organisms
18:30 - 19:00, Informal discussion
Workshop will be followed by the conference „THE CENTRAL EUROPEAN MEETING ON GENES, GENE EXPRESSION, AND BEHAVIOUR”. Conference will be held in Nové Hrady from October 30 to November 1, 2014 as well. The conference is organised by the Department of Zoology, Faculty of Science, Charles University in Prague and IVB AS CR.
V úterý 1. 7. 2014 se v nové zasedací místnosti na pracovišti ÚBO ve Studenci od 13:00 bude konat seminář na téma - Horizon 2020 - jak na to - rady, tipy, návody - jak vyhledat správnou výzvu, jak se tvoří konsorcium, na co si dát při přípravě projektu pozor, co je to impact v H2020, problematiku Open Acess v H2020.
1st International Conference on Algorithms for Computational Biology
AlCoB 2014 Tarragona, Spain July 1-3, 2014
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:
ü assembling sequence reads into a complete genome,
ü identifying gene structures in the genome,
ü recognizing regulatory motifs,
ü aligning nucleotides and comparing genomes,
ü reconstructing regulatory networks of genes, and
ü 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.
February 4, 2014 paper submission (closing at 23:59h, CET)
March 29, 2014 early registration
June 17, 2014 late registration
Přednáška Genomics of Introgression across a Species Barrier: Half a Million SNPs across the European House Mouse Hybrid Zone
21.6.2013 se na Ústavu biologie obratlovců, detašovaném pracovišti ve Studenci konala přednáška na téma Genomics of Introgression across a Species Barrier: Half a Million SNPs across the European House Mouse Hybrid Zone. Přednášel Stuart J.E.Baird.
Autoři: Stuart J.E. Baird, Miloš Macholán, Pavel Munclinger, Jaroslav Piálek
Abstract: Understanding speciation as a birth-death process requires study not only of the maintenance of species barriers, but also of those forces acting to break them down. We use the European House Mouse hybrid zone as a natural experiment to examine such forces. When SNP marker data is dense on the recombination map it cannot be treated as a series of independent loci but can, instead and more naturally, be analysed in terms of Fisher’s representation of the outcome of admixture and recombination: the ancestral source of blocks of DNA along the genome and the position of junctions (arising from recombination) where that source state changes. Cascades in the size of blocks allow ancestral polymorphism to be distinguished from introgression polymorphism. Frequency spectra of introgressed block sizes allow inference of the time since secondary contact. Geographic outlier analysis of blocks allow regions of the genome associated with the introgression of a Y chromosome across the species barrier to be identified. These insights increase our understanding not only of the mouse species barrier, but also how it can decay in its natural setting.