Vol. 17: Supplement B

Entire issue

• EMBnet.journal 17 Suppl. B

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• Editorial

  p. 2

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• COST description

  p. 3

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• COST Action BM 1006 (SeqAhead): MC BUSINESS MEETING AND SCIENTIFIC MEETING

  pp. 4-7

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• Programme

  pp. 8-9

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Oral Presentations

• A combinatorial and integrated method to analyse RNA-seq reads

  Nicolas Philippe, Mikael Salson, Therese Commes, Eric Rivals

  p. 11

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• Bioinformatics developments for NGS data analysis at PRABI

  Franck Picard, Guy Perrière

  p. 12

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• Exploration of environmental metagenomes and metatranscriptomes: current possibilities and limitations in data analysis

  Petr Baldrian

  p. 13

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• HTS Science and Technology Watch Tour

  Jean Imbert

  p. 14

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• NGS data analysis: the user POV

  Jose R. Valverde, Jose M. Rodríguez, Alexandro Rodriguez-Rojas, Alejandro Couce, Jesus Blazquez

  p. 15

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• NGS research and service at the CBU

  Kjell Petersen, Inge Jonassen

  p. 16

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• Innovation and Trends with In-Memory Technology

  Matthias Steinbrecher

  p. 17

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• NOIseq: a RNA-seq differential expression method robust for sequencing depth biases

  Sonia Tarazona, Fernando García, Alberto Ferrer, Joaquín Dopazo, Ana Conesa

  pp. 18-19

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• 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

  p. 20

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• smallRNA data analysis

  Angelica Tulipano, Andreas Gisel

  p. 21

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• The Norwegian Sequencing Centre (NSC)

  Robert Lyle, Tim Hughes, Dag Undlien, Kjetill Jakobsen

  p. 22

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• The Seal suite of distributed software for high-throughput sequencing

  Luca Pireddu, Simone Leo, Gianluigi Zanetti

  p. 23

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• The Vital-IT HPC and the Swiss-Prot group

  Laurent Falquet

  p. 24

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Demos

• Linking research data with scholarly publications

  Teresa K Attwood, Philip McDermott, James Marsh, Steve R Pettifer, David Thorne

  p. 26

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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

  pp. 28

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• An Integrated RNA-seq Atlas of the Murine T-Helper Cell Transcriptome

  Andrew Deonarine

  p. 29

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• bcbio-nextgen: Automated, distributed next-gen sequencing pipeline

  Roman Valls Guimera

  p. 30

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• BioinformaticsTools@bioacademy.gr

  Athanasia Pavlopoulou, Sophia Kossida

  p. 31

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• Digital gene expression data, cross-species conservation and noncoding RNA

  Nicolas Philippe, Florence Ruffle, Elias Bou-Samra, Anthony Boureux, Thérèse Commes, Eric Rivals

  p. 32

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• 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

  p. 33

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• EU COST Action TD0801: Statistical Challenges On The 1000 Euro Genome Sequences In Plants

  Marco C.A.M. Bink, Thomas Schiex

  p. 34

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• From cutadapt to sequencetools (sqt): a versatile toolset for sequencing projects

  Marcel Martin, Sven Rahmann

  p. 35

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• Improved analysis of fungal communities using the next-generation-sequencing analysis of rpb2 genes

  Tomas Vetrovsky, Jana Voriskova, Lucia Zifcakova, Michaela Urbanova, Petr Baldrian

  p. 36

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• 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

  p. 37

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• IT Future of Medicine: Next Generation Sequencing is the Key to Future Personalized Medicine

  Hans Lehrach, Babette Regierer

  p. 38

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• 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

  p. 39

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• Oncogenomics of the Hormone-responsive Breast Cancer Phenotype by NGS

  Alessandro Weisz

  p. 40

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• Power and limits of capture‐based, targeted DNA resequencing for mutation detection

  Fabrice Lopez, Hélène Holota, François-Xavier Théodule, Jean Imbert

  p. 41

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• Statistical approaches for the analysis of RNA-Seq and ChIP-seq data and their integration

  Claudia Angelini, Italia De Feis

  p. 42

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• 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

  p. 43

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• UPPNEX - A solution for Next Generation Sequencing data management and analysis

  Samuel Lampa, Jonas Hagberg, Ola Spjuth

  p. 44

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• Read indexing

  Nicolas Philippe, Mikael Salson, Thierry Lecroq, Martine Leonard, Therese Commes, Eric Rivals

  p. 45

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