Vol 17

Supplement B

COST Action BM1006 Scientific Meeting 2011

Table of Contents

Entire issue

EMBnet.journal 17 Suppl. B
 
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Editorial
 
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p. 2
COST description
 
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p. 3
COST Action BM 1006 (SeqAhead): MC BUSINESS MEETING AND SCIENTIFIC MEETING
 
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pp. 4-7
Programme
 
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pp. 8-9

Oral Presentations

A combinatorial and integrated method to analyse RNA-seq reads
Nicolas Philippe, Mikael Salson, Therese Commes, Eric Rivals
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p. 11
Bioinformatics developments for NGS data analysis at PRABI
Franck Picard, Guy Perrière
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p. 12
Exploration of environmental metagenomes and metatranscriptomes: current possibilities and limitations in data analysis
Petr Baldrian
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p. 13
HTS Science and Technology Watch Tour
Jean Imbert
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p. 14
NGS data analysis: the user POV
Jose R. Valverde, Jose M. Rodríguez, Alexandro Rodriguez-Rojas, Alejandro Couce, Jesus Blazquez
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p. 15
NGS research and service at the CBU
Kjell Petersen, Inge Jonassen
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p. 16
Innovation and Trends with In-Memory Technology
Matthias Steinbrecher
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p. 17
NOIseq: a RNA-seq differential expression method robust for sequencing depth biases
Sonia Tarazona, Fernando García, Alberto Ferrer, Joaquín Dopazo, Ana Conesa
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pp. 18-19
RSAT peak-motifs: fast extraction of transcription factor binding motifs from full-size ChIP-seq datasets
Morgane Thomas-Chollier, Matthieu Defrance, Olivier Sand, Carl Herrmann, Denis Thieffry, Jacques van Helden
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p. 20
smallRNA data analysis
Angelica Tulipano, Andreas Gisel
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p. 21
The Norwegian Sequencing Centre (NSC)
Robert Lyle, Tim Hughes, Dag Undlien, Kjetill Jakobsen
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p. 22
The Seal suite of distributed software for high-throughput sequencing
Luca Pireddu, Simone Leo, Gianluigi Zanetti
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p. 23
The Vital-IT HPC and the Swiss-Prot group
Laurent Falquet
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p. 24

Demos

Linking research data with scholarly publications
Teresa K Attwood, Philip McDermott, James Marsh, Steve R Pettifer, David Thorne
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p. 26

Posters

Algorithm for error detection in metagonomics NGS data
Dimitar Vassilev, Milko Krachunov, Ivan Popov, Elena Todorovska, Valeria Simeonova, Pawel Szczesny, Pawel Siedlecki, Urszula Zelenkiewicz
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pp. 28
An Integrated RNA-seq Atlas of the Murine T-Helper Cell Transcriptome
Andrew Deonarine
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p. 29
bcbio-nextgen: Automated, distributed next-gen sequencing pipeline
Roman Valls Guimera
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p. 30
BioinformaticsTools@bioacademy.gr
Athanasia Pavlopoulou, Sophia Kossida
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p. 31
Digital gene expression data, cross-species conservation and noncoding RNA
Nicolas Philippe, Florence Ruffle, Elias Bou-Samra, Anthony Boureux, Thérèse Commes, Eric Rivals
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p. 32
Epigenomic and transcriptional effects of Dnmt3b mutations in human ICF syndrome-derived B cell lines.
Sole Gatto, Claudia Angelini, Sylwia Leppert, Valentina Proserpio, Sarah Teichmann, Maurizio D’Esposito, Maria R. Matarazzo
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p. 33
EU COST Action TD0801: Statistical Challenges On The 1000 Euro Genome Sequences In Plants
Marco C.A.M. Bink, Thomas Schiex
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p. 34
From cutadapt to sequencetools (sqt): a versatile toolset for sequencing projects
Marcel Martin, Sven Rahmann
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p. 35
Improved analysis of fungal communities using the next-generation-sequencing analysis of rpb2 genes
Tomas Vetrovsky, Jana Voriskova, Lucia Zifcakova, Michaela Urbanova, Petr Baldrian
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p. 36
In the Shadow of the Genome: A Challenging Journey to Diversity in Leishmania donovani
Hideo Imamura, An Mannaert, Tim Downing, Matthew Berriman, Jean-Claude Dujardin
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p. 37
IT Future of Medicine: Next Generation Sequencing is the Key to Future Personalized Medicine
Hans Lehrach, Babette Regierer
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p. 38
Massive-scale RNA-Seq experiments in human genetic diseases
Valerio Costa, Marianna Aprile, Roberta Esposito, Maria Rosaria Ambrosio, Margherita Scarpato, Carmela Ziviello, Italia De Feis, Claudia Angelini, Alfredo Ciccodicola
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p. 39
Oncogenomics of the Hormone-responsive Breast Cancer Phenotype by NGS
Alessandro Weisz
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p. 40
Power and limits of capture‐based, targeted DNA resequencing for mutation detection
Fabrice Lopez, Hélène Holota, François-Xavier Théodule, Jean Imbert
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p. 41
Statistical approaches for the analysis of RNA-Seq and ChIP-seq data and their integration
Claudia Angelini, Italia De Feis
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p. 42
TAPYR: An efficient high-throughput sequence aligner for re-sequencing applications
Francisco Fernandes, Paulo G.S. da Fonseca, Luis M.S. Russo, Arlindo L. Oliveira, Ana T. Freitas
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p. 43
UPPNEX - A solution for Next Generation Sequencing data management and analysis
Samuel Lampa, Jonas Hagberg, Ola Spjuth
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p. 44
Read indexing
Nicolas Philippe, Mikael Salson, Thierry Lecroq, Martine Leonard, Therese Commes, Eric Rivals
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p. 45