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Home > Archives > Vol 19

Table of Contents

Entire issue

EMBnet.journal 19 Suppl. A

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ARTICLES

Editorial

PDF p. 2

The Next NGS Challenge Conference: Data Processing and Integration Erik Bongcam-Rudloff, Teresa K Attwood, Ana Conesa, Andreas Gisel, Burkhard Rost

PDF p. 3

Scientific Programme

PDF pp. 5-6

Keynote Lectures

How domestic animal genomics can teach human medicine and evolutionary biology Leif Andersson

PDF p. 8

High-throughput DNA analysis Ivo Gut

PDF p. 9

Sequencing ancient genomes Janet Kelso

PDF p. 10

Structural variation and the plant pan genomes Michele Morgante

PDF p. 11

The role of gene architecture in gene expression Karla Neugebauer

PDF p. 12

Oral Presentations

Supporting NGS pipelines in the cloud Ignacio Blanquer Blanquer, Goetz Brasche, Jacek Cala, Fabrizio Gagliardi, Dennis Gannon, Hugo Hiden, Hakan Soncu, Kenji Takeda, Andrés Tomás, Simon Woodman

PDF pp. 14-16

Toward highly accurate and fast variant and de novo mutation identification from high-throughput sequencing data by joint Bayesian family calling Francisco M. De La Vega, Mehul Rathod, Richard Littin, Len Trigg, John G. Cleary

PDF pp. 17-18

Automated transcription start site prediction for comparative Transcriptomics using the SuperGenome Alexander Herbig, Cynthia Sharma, Kay Nieselt

PDF pp. 19-20

Viral Metagenomics – New applications for the broad-range detection of viromes in veterinary and public health settings Oskar Erik Karlsson, Martin Norling, Fredrik Granberg, Sándor Belák, Erik Bongcam-Rudloff

PDF pp. 21-22

Automated and traceable processing for large-scale high-throughput sequencing facilities Luca Pireddu, Gianmauro Cuccuru, Luca Lianas, Matteo Vocale, Giorgio Fotia, Gianluigi Zanetti

PDF pp. 23-24

Challenges in whole exome sequencing to identify disease-causing variants in human rare diseases Javier Santoyo Lopez

PDF p. 25

Developing a software suite to analyze the interplay between nucleosome arrangement, DNA methylation and transcription factor binding Vladimir B. Teif, Daria A. Beshnova, Yevhen Vainshtein, Thomas Höfer, Karsten Rippe

PDF pp. 26-27

RSAT peak-motifs: Efficient prediction of transcription factor motifs and binding sites from genome-wide sequencing peak sets Morgane Thomas-Chollier, Matthieu Defrance, Olivier Sand, Carl Herrman, Denis Thieffry, van Helden Jacques

PDF pp. 28-29

Translational systems biology understanding the limits of animal models as predictors of human biology Carine Poussin, Leonidas Alexopoulos, Vincenzo Belcastro, Erhan Bilal, Carole Mathis, Pablo Meyer, Raquel Norel, Jeremy J Rice, Gustavo Stolovitzky, Julia Hoeng, Manuel Peitsch

PDF p. 30

Automated finished microbial genomes and epigenomes to understand infectious diseases Ralph Vogelsang

PDF p. 31

Interplay between DNA sequence motifs and the human epigenome John William Whitaker, Zhao Chen, Wei Wang

PDF pp. 32-33

Posters

Application of whole genome resequencing in the dissection of QTLs affecting boar taint Rahul Agarwal, Maren Van Son, Matthew Peter Kent, Sigbjørn Lien, Eli Grindflek

PDF pp. 35-36

Deep sequencing exposes small RNA transcriptome differences between low- and high-temperature stress responses in Arabidopsis Vesselin Baev, Ivan Milev, Mladen Naydenov, Tihomir Vachev, Elena Apostolova, Nikolay Mehterov, Mariana Gozmanova, Ivan Minkov, Galina Yahubyan

PDF p. 37

A reliable pipeline for a transcriptome reference in Non-Model Species Hicham Benzekri, Rocío Bautista, Darío Guerrero-Fernández, Noé Fernández-Pozo, M. Gonzalo Claros

PDF pp. 38-39

RNA-Seq expression profiling of genes related to neurodegenerative disorders affecting the human retina Laura Campello, José Martín-Nieto

PDF pp 40-41

Next-masigpro: Dealing with RNA-seq time series Ana Conesa, María José Nueda

PDF pp. 42-43

Lessons learned from implementing a national infrastructure in Sweden for storage and analysis of next-generation sequencing data Martin Dahlö

PDF p. 44

Improving automated de-novo transcriptome definition in non-model organisms by integrating manually defined gene information Ester Feldmesser, Shilo Rosenwasser, Assaf Vardi, Shifra Ben-Dor

PDF pp. 45-46

Understanding biology of potato- virus PVY interaction Kristina Gruden

PDF p. 47

Retroviral diversity of laboratory and wild mice M. musculus domesticus Stefanie Hartmann, Jens Mayer, Camila Mazzoni, Alex D Greenwood

PDF p. 48

A better sequence-read generator program for metagenomics Stephen Eric Johnson, Brett Trost, Jeffrey R Long, Anthony Kusalik

PDF pp. 49-50

De novo assembly and annotation of the grey reindeer lichen (Cladonia rangiferina) transcriptome Sini Junttila, Stephen Rudd

PDF pp. 51-52

Biologist-friendly analysis software for NGS data Aleksi Kallio, Taavi Hupponen, Massimiliano Gentile, Jarno Tuimala, Kimmo Mattila, Ari-Matti Saren, Petri Klemelä, Ilari Scheinin, Eija Korpelainen

PDF pp. 53-54

Metagenomics sample preparation and sequencing. Oskar Erik Karlsson, Martin Norling, Erik Bongcam-Rudloff

PDF pp. 55-56

DGW: an exploratory data analysis tool for clustering and visualisation of epigenomic marks Saulius Lukauskas, Gabriele Schweikert, Guido Sanguinetti

PDF pp. 57-59

Ion Torrent sequencing and pipeline assembly of the first genome sequence of a mesophilic syntrophic acetate oxidizing bacterium (SAOB) Shahid Manzoor, Erik Bongcam-Rudloff, Anna Schnürer, Bettina Müller

PDF pp. 60-61

Comparison of variant calling methods in exome sequencing of matched tumor-normal sample pairs Sara Monzon, Javier Alonso, Gonzalo Gómez, David Gonzalez-Pisano, Isabel Cuesta

PDF pp. 62-63

Pipeliner: A tool to evaluate NGS pipelines and optimize experimental designs for resequencing studies. Bruno Nevado, Miguel Perez-Enciso

PDF pp. 64-65

Genome sequence of plant associated rhizobacterium Bacillus amyloliquefaciens strain UCMB5033 Adnan Niazi, Shahid Manzoor, Sarosh Bejai, Johan Meijer, Erik Bongcam-Rudloff

PDF pp. 66-67

The bioinformatics of viral metagenomics Martin Norling, Oskar Karlsson, Erik Bongcam-Rudloff

PDF pp. 68-69

Modulation of the host cell RNA splicing program by the gastric pathogen Helicobacter pylori Frithjof Glowinski, Fernando Garcia-Alcalde, Konstantin Okonechnikov, Thomas F Meyer

PDF pp. 70-71

Reditools: Efficient RNA editing detection by RNA-seq data Ernesto Picardi, Graziano Pesole

PDF pp. 72-73

Semi- supervised ensemble learning to boost miRNA target predictions. Gianvito Pio, Domenica D'Elia, Donato Malerba, Michelangelo Ceci

PDF pp. 74-75

A comprehensive comparison between reference-based and ‘de novo’ isoform assembly approaches Oscar Rodriguez, Juan Carlos Triviño, Rebeca Miñambres, Sheila Zuñiga, Sonia Santillán, Mayte Gil, Reyes Claramunt, Celia Buades

PDF p. 76

Generation of expression calls for RNA-seq data Marta Rosikiewicz, Marc Robinson-Rechavi

PDF pp. 77-78

Analysis pipeline for the detection of mutations causative of rare diseases on whole exome sequencing data Antonio Rueda, Francisco Javier López, Javier Pérez, Pablo Arce, Luis Miguel Cruz, José Carbonell, Jorge Jiménez-Almazán, Enrique Vidal, Guillermo Antiñolo, Joaquín Dopazo, Javier Santoyo

PDF pp. 79-80

Error profiles for Next Generation sequencing technologies Melanie Schirmer, Linda D'Amore, Neil Hall, Christopher Quince

PDF pp. 81-83

Scripting for large-scale sequencing based on Hadoop André Schumacher, Luca Pireddu, Aleksi Kallio, Matti Niemenmaa, Eija Korpelainen, Gianluigi Zanetti, Keijo Heljanko

PDF pp. 84-85

Shape matters: differential peak detection for Chip-seq data sets Gabriele Schweikert, Guido Sanguinetti

PDF pp. 86-87

Comparison of oligonucleotide microarray and RNA-seq technologies in the context of gene expression analysis Nicolas Sierro, Florian Martin, Carine Poussin, Julia Hoeng, Nikolai V. Ivanov

PDF p. 88

Rapid whole genome sequencing investigation of a familial outbreak of E. coli O121:H19 with a sheep farm as the suspected source Robert Söderlund, Cecilia Jernberg, Christine Källman, Ingela Hedenström, Erik Eriksson, Erik Bongcam-Rudloff, Anna Aspán

PDF pp. 89-90

SOFTvenom: an omics drug discovery approach from animal venoms Juan Carlos Triviño, Miñambres Rebeca, Raquel Rodríguez-dePablos, Mayte Gil, Pierre Escoubas, Marion Verdenaud, Sheila Zuñiga, Sheila Zuñiga

PDF p. 91

Integrated analysis of diverse genomic data Georgia Tsiliki, Konstantinos Tsaramirsis, Sophia Kossida

PDF pp. 92-93

Computational cleaning of noisy 5' end tag sequencing data sets from rare in vivo cells Johannes Eichler Waage, Ilka Hoof, Jette Bornholdt, Esben Pedersen, Mette Jørgesen, Kim Theilgaard, Cord Brakebusch, Bo Porse, Albin Sandelin

PDF pp. 94-95