Vol 19

Supplement A

Next NGS Challenge

Table of Contents

Entire issue

EMBnet.journal 19 Suppl. A PDF


Editorial PDF
  p. 2
The Next NGS Challenge Conference: Data Processing and Integration PDF
Erik Bongcam-Rudloff, Teresa K Attwood, Ana Conesa, Andreas Gisel, Burkhard Rost p. 3
Scientific Programme PDF
  pp. 5-6

Keynote Lectures

How domestic animal genomics can teach human medicine and evolutionary biology PDF
Leif Andersson p. 8
High-throughput DNA analysis PDF
Ivo Gut p. 9
Sequencing ancient genomes PDF
Janet Kelso p. 10
Structural variation and the plant pan genomes PDF
Michele Morgante p. 11
The role of gene architecture in gene expression PDF
Karla Neugebauer p. 12

Oral Presentations

Supporting NGS pipelines in the cloud PDF
Ignacio Blanquer Blanquer, Goetz Brasche, Jacek Cala, Fabrizio Gagliardi, Dennis Gannon, Hugo Hiden, Hakan Soncu, Kenji Takeda, Andrés Tomás, Simon Woodman pp. 14-16
Toward highly accurate and fast variant and de novo mutation identification from high-throughput sequencing data by joint Bayesian family calling PDF
Francisco M. De La Vega, Mehul Rathod, Richard Littin, Len Trigg, John G. Cleary pp. 17-18
Automated transcription start site prediction for comparative Transcriptomics using the SuperGenome PDF
Alexander Herbig, Cynthia Sharma, Kay Nieselt pp. 19-20
Viral Metagenomics – New applications for the broad-range detection of viromes in veterinary and public health settings PDF
Oskar Erik Karlsson, Martin Norling, Fredrik Granberg, Sándor Belák, Erik Bongcam-Rudloff pp. 21-22
Automated and traceable processing for large-scale high-throughput sequencing facilities PDF
Luca Pireddu, Gianmauro Cuccuru, Luca Lianas, Matteo Vocale, Giorgio Fotia, Gianluigi Zanetti pp. 23-24
Challenges in whole exome sequencing to identify disease-causing variants in human rare diseases PDF
Javier Santoyo Lopez p. 25
Developing a software suite to analyze the interplay between nucleosome arrangement, DNA methylation and transcription factor binding PDF
Vladimir B. Teif, Daria A. Beshnova, Yevhen Vainshtein, Thomas Höfer, Karsten Rippe pp. 26-27
RSAT peak-motifs: Efficient prediction of transcription factor motifs and binding sites from genome-wide sequencing peak sets PDF
Morgane Thomas-Chollier, Matthieu Defrance, Olivier Sand, Carl Herrman, Denis Thieffry, van Helden Jacques pp. 28-29
Translational systems biology understanding the limits of animal models as predictors of human biology PDF
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
Automated finished microbial genomes and epigenomes to understand infectious diseases PDF
Ralph Vogelsang p. 31
Interplay between DNA sequence motifs and the human epigenome PDF
John William Whitaker, Zhao Chen, Wei Wang pp. 32-33


Application of whole genome resequencing in the dissection of QTLs affecting boar taint PDF
Rahul Agarwal, Maren Van Son, Matthew Peter Kent, Sigbjørn Lien, Eli Grindflek pp. 35-36
Deep sequencing exposes small RNA transcriptome differences between low- and high-temperature stress responses in Arabidopsis PDF
Vesselin Baev, Ivan Milev, Mladen Naydenov, Tihomir Vachev, Elena Apostolova, Nikolay Mehterov, Mariana Gozmanova, Ivan Minkov, Galina Yahubyan p. 37
A reliable pipeline for a transcriptome reference in Non-Model Species PDF
Hicham Benzekri, Rocío Bautista, Darío Guerrero-Fernández, Noé Fernández-Pozo, M. Gonzalo Claros pp. 38-39
RNA-Seq expression profiling of genes related to neurodegenerative disorders affecting the human retina PDF
Laura Campello, José Martín-Nieto pp 40-41
Next-masigpro: Dealing with RNA-seq time series PDF
Ana Conesa, María José Nueda pp. 42-43
Lessons learned from implementing a national infrastructure in Sweden for storage and analysis of next-generation sequencing data PDF
Martin Dahlö p. 44
Improving automated de-novo transcriptome definition in non-model organisms by integrating manually defined gene information PDF
Ester Feldmesser, Shilo Rosenwasser, Assaf Vardi, Shifra Ben-Dor pp. 45-46
Understanding biology of potato- virus PVY interaction PDF
Kristina Gruden p. 47
Retroviral diversity of laboratory and wild mice M. musculus domesticus PDF
Stefanie Hartmann, Jens Mayer, Camila Mazzoni, Alex D Greenwood p. 48
A better sequence-read generator program for metagenomics PDF
Stephen Eric Johnson, Brett Trost, Jeffrey R Long, Anthony Kusalik pp. 49-50
De novo assembly and annotation of the grey reindeer lichen (Cladonia rangiferina) transcriptome PDF
Sini Junttila, Stephen Rudd pp. 51-52
Biologist-friendly analysis software for NGS data PDF
Aleksi Kallio, Taavi Hupponen, Massimiliano Gentile, Jarno Tuimala, Kimmo Mattila, Ari-Matti Saren, Petri Klemelä, Ilari Scheinin, Eija Korpelainen pp. 53-54
Metagenomics sample preparation and sequencing. PDF
Oskar Erik Karlsson, Martin Norling, Erik Bongcam-Rudloff pp. 55-56
DGW: an exploratory data analysis tool for clustering and visualisation of epigenomic marks PDF
Saulius Lukauskas, Gabriele Schweikert, Guido Sanguinetti pp. 57-59
Ion Torrent sequencing and pipeline assembly of the first genome sequence of a mesophilic syntrophic acetate oxidizing bacterium (SAOB) PDF
Shahid Manzoor, Erik Bongcam-Rudloff, Anna Schnürer, Bettina Müller pp. 60-61
Comparison of variant calling methods in exome sequencing of matched tumor-normal sample pairs PDF
Sara Monzon, Javier Alonso, Gonzalo Gómez, David Gonzalez-Pisano, Isabel Cuesta pp. 62-63
Pipeliner: A tool to evaluate NGS pipelines and optimize experimental designs for resequencing studies. PDF
Bruno Nevado, Miguel Perez-Enciso pp. 64-65
Genome sequence of plant associated rhizobacterium Bacillus amyloliquefaciens strain UCMB5033 PDF
Adnan Niazi, Shahid Manzoor, Sarosh Bejai, Johan Meijer, Erik Bongcam-Rudloff pp. 66-67
The bioinformatics of viral metagenomics PDF
Martin Norling, Oskar Karlsson, Erik Bongcam-Rudloff pp. 68-69
Modulation of the host cell RNA splicing program by the gastric pathogen Helicobacter pylori PDF
Frithjof Glowinski, Fernando Garcia-Alcalde, Konstantin Okonechnikov, Thomas F Meyer pp. 70-71
Reditools: Efficient RNA editing detection by RNA-seq data PDF
Ernesto Picardi, Graziano Pesole pp. 72-73
Semi- supervised ensemble learning to boost miRNA target predictions. PDF
Gianvito Pio, Domenica D'Elia, Donato Malerba, Michelangelo Ceci pp. 74-75
A comprehensive comparison between reference-based and ‘de novo’ isoform assembly approaches PDF
Oscar Rodriguez, Juan Carlos Triviño, Rebeca Miñambres, Sheila Zuñiga, Sonia Santillán, Mayte Gil, Reyes Claramunt, Celia Buades p. 76
Generation of expression calls for RNA-seq data PDF
Marta Rosikiewicz, Marc Robinson-Rechavi pp. 77-78
Analysis pipeline for the detection of mutations causative of rare diseases on whole exome sequencing data PDF
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
Error profiles for Next Generation sequencing technologies PDF
Melanie Schirmer, Linda D'Amore, Neil Hall, Christopher Quince pp. 81-83
Scripting for large-scale sequencing based on Hadoop PDF
André Schumacher, Luca Pireddu, Aleksi Kallio, Matti Niemenmaa, Eija Korpelainen, Gianluigi Zanetti, Keijo Heljanko pp. 84-85
Shape matters: differential peak detection for Chip-seq data sets PDF
Gabriele Schweikert, Guido Sanguinetti pp. 86-87
Comparison of oligonucleotide microarray and RNA-seq technologies in the context of gene expression analysis PDF
Nicolas Sierro, Florian Martin, Carine Poussin, Julia Hoeng, Nikolai V. Ivanov p. 88
Rapid whole genome sequencing investigation of a familial outbreak of E. coli O121:H19 with a sheep farm as the suspected source PDF
Robert Söderlund, Cecilia Jernberg, Christine Källman, Ingela Hedenström, Erik Eriksson, Erik Bongcam-Rudloff, Anna Aspán pp. 89-90
SOFTvenom: an omics drug discovery approach from animal venoms PDF
Juan Carlos Triviño, Miñambres Rebeca, Raquel Rodríguez-dePablos, Mayte Gil, Pierre Escoubas, Marion Verdenaud, Sheila Zuñiga, Sheila Zuñiga p. 91
Integrated analysis of diverse genomic data PDF
Georgia Tsiliki, Konstantinos Tsaramirsis, Sophia Kossida pp. 92-93
Computational cleaning of noisy 5' end tag sequencing data sets from rare in vivo cells PDF
Johannes Eichler Waage, Ilka Hoof, Jette Bornholdt, Esben Pedersen, Mette Jørgesen, Kim Theilgaard, Cord Brakebusch, Bo Porse, Albin Sandelin pp. 94-95

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ISSN: 2226-6089