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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

The Scan

More Boosters for US

Following US Food and Drug Administration authorization, the Centers for Disease Control and Prevention has endorsed booster doses of the Moderna and Johnson & Johnson SARS-CoV-2 vaccines, the Washington Post writes.

From a Pig

A genetically modified pig kidney was transplanted into a human without triggering an immune response, Reuters reports.

For Privacy's Sake

Wired reports that more US states are passing genetic privacy laws.

Science Paper on How Poaching Drove Evolution in African Elephants

In Science this week: poaching has led to the rapid evolution of tuskless African elephants.