Volume 15 Supplement 9
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
With the advent of Next-Generation Sequencing technologies (NGS), a large amount of short read data has been generated. If a reference genome is not available, the assembly of a template sequence is usually ch...
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...
The advancement of RNA sequencing (RNA-seq) has provided an unprecedented opportunity to assess both the diversity and quantity of transcript isoforms in an mRNA transcriptome. In this paper, we revisit the co...
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...
Multi-assembly problems have gathered much attention in the last years, as Next-Generation Sequencing technologies have started being applied to mixed settings, such as reads from the transcriptome (RNA-Seq), ...
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...
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...
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...
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 ...
Merging the forward and reverse reads from paired-end sequencing is a critical task that can significantly improve the performance of downstream tasks, such as genome assembly and mapping, by providing them wi...
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...
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...
Acquiring genomes at single-cell resolution has many applications such as in the study of microbiota. However, deep sequencing and assembly of all of millions of cells in a sample is prohibitively costly. A pr...
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...
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...
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...
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