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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]

Filed under

The Scan

Positive Framing of Genetic Studies Can Spark Mistrust Among Underrepresented Groups

Researchers in Human Genetics and Genomics Advances report that how researchers describe genomic studies may alienate potential participants.

Small Study of Gene Editing to Treat Sickle Cell Disease

In a Novartis-sponsored study in the New England Journal of Medicine, researchers found that a CRISPR-Cas9-based treatment targeting promoters of genes encoding fetal hemoglobin could reduce disease symptoms.

Gut Microbiome Changes Appear in Infants Before They Develop Eczema, Study Finds

Researchers report in mSystems that infants experienced an enrichment in Clostridium sensu stricto 1 and Finegoldia and a depletion of Bacteroides before developing eczema.

Acute Myeloid Leukemia Treatment Specificity Enhanced With Stem Cell Editing

A study in Nature suggests epitope editing in donor stem cells prior to bone marrow transplants can stave off toxicity when targeting acute myeloid leukemia with immunotherapy.