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In Print: April's Bioinformatics Papers of Note


Amarasinghe KC, Doyle MA, et al
CONTRA: copy number analysis for targeted resequencing.
Bioinformatics 2012 Apr 2. [Epub ahead of print]

Li Z, Liu X, et al
An examination of the OMIM database for associating mutation to a consensus reference sequence.
Protein Cell. 2012 Apr 4. [Epub ahead of print]

Adkins JN, Cannon WR, et al
VESPA: software to facilitate genomic annotation of prokaryotic organisms through integration of proteomic and transcriptomic data.
BMC Genomics. 2012 Apr 5;13(1):131.

Högberg J, Korhonen A, et al
Text mining for literature review and knowledge discovery in cancer risk assessment and research.
PLoS One. 2012;7(4):e33427.

Bhardwaj G, Dave F, et al
PHYRN: A Robust Method for Phylogenetic Analysis of Highly Divergent Sequences.
PLoS One. 2012;7(4):e34261.

Chin FY, Leung HC, et al
IDBA-UD: A De Novo Assembler for Single-Cell and Metagenomic Sequencing Data with Highly Uneven Depth.
Bioinformatics. 2012 Apr 11. [Epub ahead of print]

Ding R, Duan L, et al
A de novo metagenomic assembly program for shotgun DNA reads.
Bioinformatics. 2012 Apr 11. [Epub ahead of print]

Gritsenko AA, Nijkamp JF, et al
GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies.
Bioinformatics. 2012 Apr 6. [Epub ahead of print]

Childress DM, Gregory BD, et al
SAVoR: a server for sequencing annotation and visualization ofRNA structures.
Nucleic Acids Res. 2012 Apr 6. [Epub ahead of print]

Bernard M, Dillies MA, et al
Eoulsan: A Cloud Computing-Based Framework Facilitating High Throughput Sequencing Analyses.
Bioinformatics. 2012 Apr 5. [Epub ahead of print]

Huang J, Huang Q, et al
EnzyBase: a novel database for enzybiotic studies.
BMC Microbiol. 2012 Apr 11;12(1):54.

Oshlack A, Pope B, et al
Bpipe: A Tool for Running and Managing Bioinformatics Pipelines.
Bioinformatics. 2012 Apr 12. [Epub ahead of print]

Anderson CA, Barrett JC, et al
optiCall: A robust genotype-calling algorithm for rare, low frequency and common variants.
Bioinformatics. 2012 Apr 12. [Epub ahead of print]

Bai F, Chen Y, et al
pIRS: Profile based Illumina pair-end Reads Simulator.
Bioinformatics. 2012 Apr 15. [Epub ahead of print]

Alekseyev MA, Antipov D, et al
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing.
J Comput Biol. 2012 Apr 16. [Epub ahead of print]

Boutros PC, Chu K, et al
NanoStringNorm: An Extensible R Package for the Pre-Processing of NanoString mRNA and miRNA Data.
Bioinformatics. 2012 Apr 17. [Epub ahead of print]

Lee PH, O'Dushlaine C, et al
INRICH: Interval-based Enrichment Analysis for Genome Wide Association Studies.
Bioinformatics. 2012 Apr 17. [Epub ahead of print]

Erlich Y, Golan D, et al
lobSTR: A short tandem repeat profiler for personal genomes.
Genome Res. 2012 Apr 20. [Epub ahead of print]

Bogliolo A, Freschi V.
A lossy compression technique enabling duplication-aware sequence alignment.
Evol Bioinform Online. 2012;8:171-80.

Jia P, Pao W, et al
NGS catalog: A database of next generation sequencing studies in humans.
Hum Mutat. 2012 Apr 19. [Epub ahead of print]

Cheng J, Deng X, et al
The MULTICOM Toolbox for Protein Structure Prediction.
BMC Bioinformatics. 2012 Apr 30;13(1):65.

Filed under

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Researchers in the Journal of Molecular Diagnostics describe and assess a Clear Labs Dx automated workflow, sequencing, and bioinformatic analysis method for quickly identifying SARS-CoV-2 lineages.

UK Team Presents Genetic, Epigenetic Sequencing Method

Using enzymatic DNA preparation steps, researchers in Nature Biotechnology develop a strategy for sequencing DNA, along with 5-methylcytosine and 5-hydroxymethylcytosine, on existing sequencers.