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Volume 15 Supplement 9

Proceedings of the Fourth Annual RECOMB Satellite Workshop on Massively Parallel Sequencing (RECOMB-Seq 2014)


Edited by Mihai Pop and Ali Bashir

Publication of this supplement has been partly funded by the RECOMB-Seq Workshop. Articles are based on presentations made at the conference. Information about the source of funding for the remaining publication charges can be found in the individual articles. The peer review process was overseen by the Supplement Editors in accordance with BioMed Central’s peer review guidelines for supplements. Supplement Editor declarations: Ali Bashir declares that he has previously been employed at Pacific Biosciences (2009-2011); Mihai Pop has no competing interests to declare.

RECOMB-Seq: Fourth Annual RECOMB Satellite Workshop on Massively Parallel Sequencing. Go to conference site.

Pittsburgh, PA, USA31 March - 1 April 2014

  1. There is a widening gap between the throughput of massive parallel sequencing machines and the ability to analyze these sequencing data. Traditional assembly methods requiring long execution time and large amo...

    Authors: Jintao Meng, Bingqiang Wang, Yanjie Wei, Shengzhong Feng and Pavan Balaji
    Citation: BMC Bioinformatics 2014 15(Suppl 9):S2
  2. Recent work identified the fundamental limits on the information requirements in terms of read length and coverage depth required for successful de novo genome reconstruction from shotgun sequencing data, based o...

    Authors: Ka-Kit Lam, Asif Khalak and David Tse
    Citation: BMC Bioinformatics 2014 15(Suppl 9):S4
  3. Recent advances in RNA sequencing (RNA-Seq) technology have offered unprecedented scope and resolution for transcriptome analysis. However, precise quantification of mRNA abundance and identification of differ...

    Authors: Jinghua Gu, Xiao Wang, Leena Halakivi-Clarke, Robert Clarke and Jianhua Xuan
    Citation: BMC Bioinformatics 2014 15(Suppl 9):S6
  4. Data from large Next Generation Sequencing (NGS) experiments present challenges both in terms of costs associated with storage and in time required for file transfer. It is sometimes possible to store only a s...

    Authors: Roye Rozov, Ron Shamir and Eran Halperin
    Citation: BMC Bioinformatics 2014 15(Suppl 9):S7
  5. Metatranscriptomic sequencing is a highly sensitive bioassay of functional activity in a microbial community, providing complementary information to the metagenomic sequencing of the community. The acquisition...

    Authors: Wazim Mohammed Ismail, Yuzhen Ye and Haixu Tang
    Citation: BMC Bioinformatics 2014 15(Suppl 9):S8
  6. Interest in de novo genome assembly has been renewed in the past decade due to rapid advances in high-throughput sequencing (HTS) technologies which generate relatively short reads resulting in highly fragmented ...

    Authors: James Lindsay, Hamed Salooti, Ion Măndoiu and Alex Zelikovsky
    Citation: BMC Bioinformatics 2014 15(Suppl 9):S9
  7. We introduce a novel method, called PuFFIN, that takes advantage of paired-end short reads to build genome-wide nucleosome maps with larger numbers of detected nucleosomes and higher accuracy than existing too...

    Authors: Anton Polishko, Evelien M Bunnik, Karine G Le Roch and Stefano Lonardi
    Citation: BMC Bioinformatics 2014 15(Suppl 9):S11
  8. Although there are many different algorithms and software tools for aligning sequencing reads, fast gapped sequence search is far from solved. Strong interest in fast alignment is best reflected in the $106 prize...

    Authors: Milad Gholami, Aryan Arbabi, Ali Sharifi-Zarchi, Hamidreza Chitsaz and Mehdi Sadeghi
    Citation: BMC Bioinformatics 2014 15(Suppl 9):S12
  9. There are many programs available for generating simulated whole-genome shotgun sequence reads. The data generated by many of these programs follow predefined models, which limits their use to the authors' ori...

    Authors: Stephen Johnson, Brett Trost, Jeffrey R Long, Vanessa Pittet and Anthony Kusalik
    Citation: BMC Bioinformatics 2014 15(Suppl 9):S14
  10. Recent advances in RNA structure probing technologies, including the ones based on high-throughput sequencing, have improved the accuracy of thermodynamic folding with quantitative nucleotide-resolution struct...

    Authors: Ping Ge, Cuncong Zhong and Shaojie Zhang
    Citation: BMC Bioinformatics 2014 15(Suppl 9):S15
  11. It has recently become possible to rapidly and accurately detect epigenetic signatures in bacterial genomes using third generation sequencing data. Monitoring the speed at which a single polymerase inserts a b...

    Authors: Noam D Beckmann, Sashank Karri, Gang Fang and Ali Bashir
    Citation: BMC Bioinformatics 2014 15(Suppl 9):S16

Annual Journal Metrics

  • 2022 Citation Impact
    3.0 - 2-year Impact Factor
    4.3 - 5-year Impact Factor
    0.938 - SNIP (Source Normalized Impact per Paper)
    1.100 - SJR (SCImago Journal Rank)

    2023 Speed
    19 days submission to first editorial decision for all manuscripts (Median)
    146 days submission to accept (Median)

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