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February's Bioinformatics Papers of Note


Karlsson FH, Nielsen J, et al.
FANTOM: Functional and taxonomic analysis of metagenomes.
BMC Bioinformatics. 2013 Feb 1;14(1):38.

Boehm C, Hamosh A, et al.
PhenoDB: A New Web-Based Tool for the Collection, Storage and Analysis of Phenotypic Features.
Hum Mutat. 2013 Feb 1. [Epub ahead of print]

Brauer H, Grossmann J, et al.
An automated pipeline for high-throughput label-free quantitative proteomics.
J Proteome Res. 2013 Feb 8. [Epub ahead of print]

Creevey CJ, Doran AG.
SNPdat: Easy and rapid annotation of results from de novo SNP discovery projects for model and non-model organisms.
BMC Bioinformatics. 2013 Feb 8;14(1):45.

Henzler AM, Rarey M, et al.
Fast Protein Binding Site Comparison via an Index-Based Screening Technology.
J Chem Inf Model. 2013 Feb 7. [Epub ahead of print]

Bailey-Kellogg C, He L, et al.
Ballast: A Ball-based Algorithm for Structural Motifs.
J Comput Biol. 2013 Feb;20(2):137-51.

Kondratowicz B, Li W, et al.
The annotation-enriched non-redundant patent sequence databases.
Database (Oxford). 2013 Feb 9.

Bureeva S, Peregrim D, et al.
Discovery of novel biomarkers and phenotypes by semantic technologies.
BMC Bioinformatics. 2013 Feb 13;14(1):51.

Berry MW, Gao T, et al.
PolyLens: software for map-based visualisation and analysis of genome-scale polymorphism data.
Int J Comput Biol Drug Des. Epub 2013 Feb 21.

Chi AK, Davis RW, et al.
Rare variant detection using family-based sequencing analysis.
Proc Natl Acad Sci U S A. 2013 Feb 20. [Epub ahead of print]

Cao Q, Li C, et al.
canEvolve: A Web Portal for Integrative Oncogenomics.
PLOS One. Epub 2013 Feb 13.

Anderson I, Chen IM, et al.
Improving microbial genome annotations in an integrated database context.
PLOS One. Epub 2013 Feb 12.

Hartley SW, Sebastiani P.
PleioGRiP: genetic risk prediction with pleiotropy.
Bioinformatics. 2013 Feb 17. [Epub ahead of print]

Chin L, Gehlenborg N, et al.
Nozzle: a report generation toolkit for data analysis pipelines.
Bioinformatics. 2013 Feb 17. [Epub ahead of print]

Bruce JE, Chavez JD, et al.
XLink-DB: database and software tools for storing and visualizing protein interaction topology data.
J Proteome Res. 2013 Feb 17. [Epub ahead of print]

Decorte R, Larmuseau MH, et al.
AMY-tree: an algorithm to use whole genome SNP calling for Y chromosomal phylogenetic applications.
BMC Genomics. 2013 Feb 13;14(1):101.

He M, Gao G, et al.
SOAPfuse: an algorithm for identifying fusion transcripts from paired-end RNA-Seq data.
Genome Biol. 2013 Feb 14;14(2):R12.

Yang Y, Yooseph S.
SPA: a short peptide assembler for metagenomic data.
Nucleic Acids Res. 2013 Feb 23. [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.