Volume 14 Supplement 5

Proceedings of the Third Annual RECOMB Satellite Workshop on Massively Parallel Sequencing (RECOMB-seq 2013)

Proceedings

Edited by Haixu Tang, Tao Jiang and Xuegong Zhang

The supplement has not received any external sponsorship, full details can be found in the Declarations of each individual article.

RECOMB-seq: Third Annual Recomb Satellite Workshop on Massively Parallel Sequencing. Go to conference site.

Beijing, China

11-12 April 2013

  1. Proceedings

    Discovering motifs that induce sequencing errors

    Elevated sequencing error rates are the most predominant obstacle in single-nucleotide polymorphism (SNP) detection, which is a major goal in the bulk of current studies using next-generation sequencing (NGS)....

    Manuel Allhoff, Alexander Schönhuth, Marcel Martin, Ivan G Costa, Sven Rahmann and Tobias Marschall

    BMC Bioinformatics 2013 14(Suppl 5):S1

    Published on: 10 April 2013

  2. Proceedings

    Joint genotype inference with germline and somatic mutations

    The joint sequencing of related genomes has become an important means to discover rare variants. Normal-tumor genome pairs are routinely sequenced together to find somatic mutations and their associations with...

    Eric Bareke, Virginie Saillour, Jean-François Spinella, Ramon Vidal, Jasmine Healy, Daniel Sinnett and Miklós Csűrös

    BMC Bioinformatics 2013 14(Suppl 5):S3

    Published on: 10 April 2013

  3. Proceedings

    Discovering and mapping chromatin states using a tree hidden Markov model

    New biological techniques and technological advances in high-throughput sequencing are paving the way for systematic, comprehensive annotation of many genomes, allowing differences between cell types or betwee...

    Jacob Biesinger, Yuanfeng Wang and Xiaohui Xie

    BMC Bioinformatics 2013 14(Suppl 5):S4

    Published on: 10 April 2013

  4. Proceedings

    De Bruijn Superwalk with Multiplicities Problem is NP-hard

    De Bruijn Superwalk with Multiplicities Problem is the problem of finding a walk in the de Bruijn graph containing several walks as subwalks and passing through each edge the exactly predefined number of times...

    Evgeny Kapun and Fedor Tsarev

    BMC Bioinformatics 2013 14(Suppl 5):S7

    Published on: 10 April 2013

  5. Proceedings

    A random-permutations-based approach to fast read alignment

    Read alignment is a computational bottleneck in some sequencing projects. Most of the existing software packages for read alignment are based on two algorithmic approaches: prefix-trees and hash-tables. We pro...

    Roy Lederman

    BMC Bioinformatics 2013 14(Suppl 5):S8

    Published on: 10 April 2013

  6. Proceedings

    An optimized algorithm for detecting and annotating regional differential methylation

    DNA methylation profiling reveals important differentially methylated regions (DMRs) of the genome that are altered during development or that are perturbed by disease. To date, few programs exist for regional...

    Sheng Li, Francine E Garrett-Bakelman, Altuna Akalin, Paul Zumbo, Ross Levine, Bik L To, Ian D Lewis, Anna L Brown, Richard J D'Andrea, Ari Melnick and Christopher E Mason

    BMC Bioinformatics 2013 14(Suppl 5):S10

    Published on: 10 April 2013

  7. Proceedings

    Gene prediction in metagenomic fragments based on the SVM algorithm

    Metagenomic sequencing is becoming a powerful technology for exploring micro-ogranisms from various environments, such as human body, without isolation and cultivation. Accurately identifying genes from metage...

    Yongchu Liu, Jiangtao Guo, Gangqing Hu and Huaiqiu Zhu

    BMC Bioinformatics 2013 14(Suppl 5):S12

    Published on: 10 April 2013

  8. Proceedings

    CLASS: constrained transcript assembly of RNA-seq reads

    RNA-seq has revolutionized our ability to survey the cellular transcriptome in great detail. However, while several approaches have been developed, the problem of assembling the short reads into full-length tr...

    Li Song and Liliana Florea

    BMC Bioinformatics 2013 14(Suppl 5):S14

    Published on: 10 April 2013

  9. Proceedings

    A novel min-cost flow method for estimating transcript expression with RNA-Seq

    Through transcription and alternative splicing, a gene can be transcribed into different RNA sequences (isoforms), depending on the individual, on the tissue the cell is in, or in response to some stimuli. Rec...

    Alexandru I Tomescu, Anna Kuosmanen, Romeo Rizzi and Veli Mäkinen

    BMC Bioinformatics 2013 14(Suppl 5):S15

    Published on: 10 April 2013

  10. Proceedings

    Optimal assembly for high throughput shotgun sequencing

    We present a framework for the design of optimal assembly algorithms for shotgun sequencing under the criterion of complete reconstruction. We derive a lower bound on the read length and the coverage depth req...

    Guy Bresler, Ma'ayan Bresler and David Tse

    BMC Bioinformatics 2013 14(Suppl 5):S18

    Published on: 9 July 2013