Vol. 19: Supplement A

Entire issue

• EMBnet.journal 19 Suppl. A

  • PDF

ARTICLES

• Editorial

  p. 2

  • PDF

• The Next NGS Challenge Conference: Data Processing and Integration

  p. 3

  • PDF

• Scientific Programme

  pp. 5-6

  • PDF

Keynote Lectures

• How domestic animal genomics can teach human medicine and evolutionary biology

  Leif Andersson

  p. 8

  • PDF

• High-throughput DNA analysis

  Ivo Gut

  p. 9

  • PDF

• Sequencing ancient genomes

  Janet Kelso

  p. 10

  • PDF

• Structural variation and the plant pan genomes

  Michele Morgante

  p. 11

  • PDF

• The role of gene architecture in gene expression

  Karla Neugebauer

  p. 12

  • PDF

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

  pp. 14-16

  • PDF

• 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

  pp. 17-18

  • PDF

• Automated transcription start site prediction for comparative Transcriptomics using the SuperGenome

  Alexander Herbig, Cynthia Sharma, Kay Nieselt

  pp. 19-20

  • PDF

• 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

  pp. 21-22

  • PDF

• Automated and traceable processing for large-scale high-throughput sequencing facilities

  Luca Pireddu, Gianmauro Cuccuru, Luca Lianas, Matteo Vocale, Giorgio Fotia, Gianluigi Zanetti

  pp. 23-24

  • PDF

• Challenges in whole exome sequencing to identify disease-causing variants in human rare diseases

  Javier Santoyo Lopez

  p. 25

  • PDF

• 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

  pp. 26-27

  • PDF

• 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

  pp. 28-29

  • PDF

• 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

  p. 30

  • PDF

• Automated finished microbial genomes and epigenomes to understand infectious diseases

  Ralph Vogelsang

  p. 31

  • PDF

• Interplay between DNA sequence motifs and the human epigenome

  John William Whitaker, Zhao Chen, Wei Wang

  pp. 32-33

  • PDF

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

  pp. 35-36

  • PDF

• 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

  p. 37

  • PDF

• A reliable pipeline for a transcriptome reference in Non-Model Species

  Hicham Benzekri, Rocío Bautista, Darío Guerrero-Fernández, Noé Fernández-Pozo, M. Gonzalo Claros

  pp. 38-39

  • PDF

• RNA-Seq expression profiling of genes related to neurodegenerative disorders affecting the human retina

  Laura Campello, José Martín-Nieto

  pp 40-41

  • PDF

• Next-masigpro: Dealing with RNA-seq time series

  Ana Conesa, María José Nueda

  pp. 42-43

  • PDF

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

  Martin Dahlö

  p. 44

  • PDF

• 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

  pp. 45-46

  • PDF

• Understanding biology of potato- virus PVY interaction

  Kristina Gruden

  p. 47

  • PDF

• Retroviral diversity of laboratory and wild mice M. musculus domesticus

  Stefanie Hartmann, Jens Mayer, Camila Mazzoni, Alex D Greenwood

  p. 48

  • PDF

• A better sequence-read generator program for metagenomics

  Stephen Eric Johnson, Brett Trost, Jeffrey R Long, Anthony Kusalik

  pp. 49-50

  • PDF

• De novo assembly and annotation of the grey reindeer lichen (Cladonia rangiferina) transcriptome

  Sini Junttila, Stephen Rudd

  pp. 51-52

  • PDF

• 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

  pp. 53-54

  • PDF

• Metagenomics sample preparation and sequencing.

  Oskar Erik Karlsson, Martin Norling, Erik Bongcam-Rudloff

  pp. 55-56

  • PDF

• DGW: an exploratory data analysis tool for clustering and visualisation of epigenomic marks

  Saulius Lukauskas, Gabriele Schweikert, Guido Sanguinetti

  pp. 57-59

  • PDF

• 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

  pp. 60-61

  • PDF

• 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

  pp. 62-63

  • PDF

• Pipeliner: A tool to evaluate NGS pipelines and optimize experimental designs for resequencing studies.

  Bruno Nevado, Miguel Perez-Enciso

  pp. 64-65

  • PDF

• Genome sequence of plant associated rhizobacterium Bacillus amyloliquefaciens strain UCMB5033

  Adnan Niazi, Shahid Manzoor, Sarosh Bejai, Johan Meijer, Erik Bongcam-Rudloff

  pp. 66-67

  • PDF

• The bioinformatics of viral metagenomics

  Martin Norling, Oskar Karlsson, Erik Bongcam-Rudloff

  pp. 68-69

  • PDF

• Modulation of the host cell RNA splicing program by the gastric pathogen Helicobacter pylori

  Frithjof Glowinski, Fernando Garcia-Alcalde, Konstantin Okonechnikov, Thomas F Meyer

  pp. 70-71

  • PDF

• Reditools: Efficient RNA editing detection by RNA-seq data

  Ernesto Picardi, Graziano Pesole

  pp. 72-73

  • PDF

• Semi- supervised ensemble learning to boost miRNA target predictions.

  Gianvito Pio, Domenica D'Elia, Donato Malerba, Michelangelo Ceci

  pp. 74-75

  • PDF

• 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

  p. 76

  • PDF

• Generation of expression calls for RNA-seq data

  Marta Rosikiewicz, Marc Robinson-Rechavi

  pp. 77-78

  • PDF

• 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

  pp. 79-80

  • PDF

• Error profiles for Next Generation sequencing technologies

  Melanie Schirmer, Linda D'Amore, Neil Hall, Christopher Quince

  pp. 81-83

  • PDF

• Scripting for large-scale sequencing based on Hadoop

  André Schumacher, Luca Pireddu, Aleksi Kallio, Matti Niemenmaa, Eija Korpelainen, Gianluigi Zanetti, Keijo Heljanko

  pp. 84-85

  • PDF

• Shape matters: differential peak detection for Chip-seq data sets

  Gabriele Schweikert, Guido Sanguinetti

  pp. 86-87

  • PDF

• 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

  p. 88

  • PDF

• 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

  pp. 89-90

  • PDF

• 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

  p. 91

  • PDF

• Integrated analysis of diverse genomic data

  Georgia Tsiliki, Konstantinos Tsaramirsis, Sophia Kossida

  pp. 92-93

  • PDF

• 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

  pp. 94-95

  • PDF