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In Print: January's Bioinformatics Papers of note


Delcher AL, Salzberg SL, et al.
GAGE: A critical evaluation of genome assemblies and assembly algorithms.
Genome Res. 2012 Jan 12. [Epub ahead of print]

Emery JS, Halperin RF, et al.
GuiTope: an application for mapping random-sequence peptides topProtein sequences.
BMC Bioinformatics 2012 Jan 3;13(1):1.

Gao G, Gu X, et al.
ABrowse — a customizable next-generation genome browser framework.
BMC Bioinformatics 2012 Jan 5;13:2.

Lameijer EW, Ning Z, et al.
PASSion: A pattern growth algorithm based pipeline for splice junction detection in paired-end RNA-seq data.
Bioinformatics 2012 Jan 4. [Epub ahead of print]

Bray TS, Kron SJ, Sylvester JE
Annotator: Post-processing software for generating function-based signatures from quantitative mass spectrometry.
J Proteome Res. 2012 Jan 9. [Epub ahead of print]

Challis D, Coarfa C, et al.
An integrative variant analysis suite for whole exome next-generation sequencing data.
BMC Bioinformatics. 2012 Jan 12;13(1):8.

Du J, Gerstein M, et al.
IQSeq: integrated isoform quantification analysis based on next-generation sequencing.
PLoS One. 2012;7(1):e29175.

Boc A, Diallo AB, et al.
Armadillo 1.1: an original workflow platform for designing and conducting phylogenetic analysis and simulations.
PLoS One. 2012;7(1):e29903.

Chittenden TW, Quackenbush J, et al.
nEASE: a method for Gene Ontology sub-classification of high throughput gene expression data.
Bioinformatics. 2012 Jan 13. [Epub ahead of print]

Cheung MS, Klus P, et al.
BarraCUDA — a fast short read sequence aligner using graphics processing units.
BMC Res Notes. 2012 Jan 13;5(1):27.

Buxbaum JD, Cai G, et al.
AnnTools: A comprehensive and versatile annotation toolkit for genomic variants.
Bioinformatics. 2012 Jan 18. [Epub ahead of print]

Emberly E, Kobor MS, et al.
CHROMATRA: a Galaxy tool for visualizing genome-wide chromatin signatures.
Bioinformatics. 2012 Jan 11. [Epub ahead of print]

McDonald JF, Mittal VK, et al.
R-SAP: a multi-threading computational pipeline for the characterization of high-throughput RNA-sequencing data.
Nucleic Acids Res. 2012 Jan 28. [Epub ahead of print].

Chu X, Lam TW, et al.
SOAP3: Ultra-fast GPU-based parallel alignment tool for short reads.
Bioinformatics. 2012 Jan 28. [Epub ahead of print].

Liu N, Wu J, et al.
Genotype calling from next generation sequencing data using haplotype information of reads.
Bioinformatics. 2012 Jan 27. [Epub ahead of print].

Crisan A, Ding J, et al.
JointSNVMix: A probabilistic model for accurate detection of somatic mutations in normal/tumour paired next generation sequencing data.
Bioinformatics. 2012 Jan 27. [Epub ahead of print].

Adams D, Boerkoel CF, et al.
VAR-MD: A tool to analyze whole exome/genome variants in small human pedigrees with Mendelian inheritance.
Hum Mutat. 2012 Jan 30. [Epub ahead of print]

Filed under

The Scan

Steps for Quick Review

The US Food and Drug Administration is preparing for the quick review of drugs and vaccines for the Omicron variant, according to the Wall Street Journal.

Moving Away From Using Term 'Race'

A new analysis finds that geneticists are using the term "race" in their papers less than in years past, as Science reports.

Point of the Program

The Guardian writes that some scientists have called the design of a UK newborn sequencing program into question.

Science Papers Present Multi-Omic Analysis of Lung Cells, Regulation of Cardiomyocyte Proliferation

In Science this week: a multi-omic analysis of lung cells focuses on RIT1-regulated pathways, and more.