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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]

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Study Examines Insights Gained by Adjunct Trio RNA Sequencing in Complex Pediatric Disease Cases

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