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September and October's Bioinformatics Papers of Note


Chen T, Jiang R, Zeng F. et al.
PyroHMMvar: a sensitive and accurate method to call short indels and SNPs for Ion Torrent and 454 data.
Bioinformatics 2013 Sep 26. [Epub ahead of print]

Gordon D, Green P.
Consed: a graphical editor for next-generation sequencing.
Bioinformatics 2013 Sep 26. [Epub ahead of print]

Cong Q, Grishin NV et al.
M2SG: Mapping Human Disease-Related Genetic Variants to ProteinSequences and Genomic Loci.
Bioinformatics 2013 Sep 3. [Epub ahead of print]

Kojima K, Nagasaki M et al.
A statistical variant calling approach from pedigree information and local haplotyping with phase informative reads.
Bioinformatics 2013 Sep 26. [Epub ahead of print]

Akiyama Y, Ishida T et al.
MEGADOCK 3.0: a high-performance protein-protein interaction prediction software using hybrid parallel computing for petascale supercomputing environments.
Source Code Biol Med. 2013 Sep 3;8(1):18. [Epub ahead of print]

Fargo D, Huang W, et al.
PAVIS: a tool for Peak Annotation and Visualization.
Bioinformatics 2013 Sep 24. [Epub ahead of print]

Calin GA, Coombes KR, et al.
targetHub: a programmable interface for miRNA-gene interactions.
Bioinformatics 2013 Sep 11. [Epub ahead of print]

Browne K, Granger D, et al.
Explicet: graphical user interface software for metadata-driven management, analysis and visualization of microbiome data.
Bioinformatics 2013 Sep 29. [Epub ahead of print]

Bhatia K, Nordberg H, et al.
BioPig: A Hadoop-based Analytic Toolkit for Large-Scale Sequence Data.
Bioinformatics 2013 Sep 10. [Epub ahead of print]

Camiolo S, Porceddu A.
gff2Sequence, a new user friendly tool for the generation of genomic sequences.
BioData Min. 2013 Sep 11. [Epub ahead of print]

De S, Pedersen BS, Yang IV
CruzDB:software for annotation of genomic intervals with UCSC genome-browser database.
Bioinformatics 2013 Sep 12. [Epub ahead of print]

Haig SM, Knaus BJ, et al.
SSR_pipeline: A Bioinformatic Infrastructure for Identifying Microsatellites From Paired-End Illumina High-Throughput DNA Sequencing Data.
J Hered. 2013 Sep 21. [Epub ahead of print]

Escalettes F, Fotheringhamet al.
Meta4: a web application for sharing and annotating metagenomic gene predictions using web services.
Front Genet. 2013 Sep 5;4:168. doi: 10.3389/fgene.2013.00168.

Becker G, Chaivorapol C, et al.
ReportingTools: an automated result processing and presentation toolkit for high throughput genomic analyses.
Bioinformatics 2013 Sep 29. [Epub ahead of print]

Hancock RE, Lyle NH, et al.
INVEX - a web-based tool for integrative visualization of expression data.
Bioinformatics 2013 Sep 26. [Epub ahead of print]

Ecker J, Jia H, et al.
STAR: An Integrated Solution to Management and Visualization of Sequencing Data.
Bioinformatics 2013 Sep 27. [Epub ahead of print]

Cohen H, Bar-Joseph Z, et al.
ExpressionBlast: mining large, unstructured expression databases.
Nat. Methods. 2013 Sep 27;10(10):925-6. doi: 10.1038/nmeth.2630.

Han S, Gelernter J, et al.
Variant callers for next-generation sequencing data: a comparison study.
PLoS One. 2013 Sep 27;8(9):e75619. doi: 10.1371/journal.pone.0075619.

Bajic VB, Kalnis P, Kleftogiannis D
Comparing memory-efficient genome assemblers on stand-alone and cloud infrastructures.
PLoS One. 2013 Sep 27;8(9):e75505. doi: 10.1371/journal.pone.0075505.

Blaxter M, Jones M.
afterParty: turning raw transcriptomes into permanent resources.
BMC Bioinformatics 2013 Oct 7;14(1):301. [Epub ahead of print]

Dooner HK, Du C, et al.
InsertionMapper: a pipeline tool for the identification of targeted sequences from multidimensional high throughput sequencing data.
BMC Genomics 2013 Oct 4;14(1):679. [Epub ahead of print]

Cano L, Kamoun S, et al.
Coval: improving alignment quality and variant calling accuracy for next-generation sequencing data.
PLoS One. 2013 Oct 8;8(10):e75402. doi: 10.1371/journal.pone.0075402.

Konstantinidis KT, Rodriguez-R LM
Nonpareil: A redundancy-based approach to assess the level of coverage in metagenomic datasets.
Bioinformatics 2013 Oct 11. [Epub ahead of print]

Cai K, Hu Z, et al.
NeSSM: A Next-Generation Sequencing Simulator for Metagenomics.
PLoS One 2013 Oct 4;8(10):e75448. doi: 10.1371/journal.pone.0075448.

H Ahrens C, Müller S, et al.
Protter: interactive protein feature visualization and integration with experimental proteomic data.
Bioinformatics 2013 Oct 24. [Epub ahead of print]

Bauer S, Gilissen C, et al.
Improved exome prioritization of disease genes through cross species phenotype comparison.
Genome Res. 2013 Oct 25. [Epub ahead of print]

Childress M, Dragomir I, et al.
HAMR: high-throughput annoation of modified ribonucleotides.
RNA 2013 Oct 22. [Epub ahead of print]

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