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October’s Bioinformatics Papers of Note


Abecasis GR, Busonero F, et al.
A likelihood-based framework for variant calling and de novo mutation detection in families.
PLoS Genet. 2012 Oct;8(10):e1002944.

Cong Q, Grishin NV.
MESSA: Meta-Server for protein Sequence Analysis.
BMC Biol. 2012 Oct 2;10(1):82.

Girgis HZ, Sheetlin SL.
MsDetector: toward a standard computational tool for DNAmicrosatellites detection.
Nucleic Acids Res. 2012 Oct 2. [Epub ahead of print]

Hansen KD, Irizarry RA, Langmead B.
BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions.
Genome Biol. 2012 Oct 3;13(10):R83.

Albrecht F, Bast H, et al.
EpiExplorer: live exploration and global analysis of large epigenomic datasets.
Genome Biol. 2012 Oct 3;13(10):R96.

Barker GL, Cooper DN, et al.
Predicting the functional, molecular, and phenotypic consequences of amino acid substitutions using hidden Markov models.
Hum Mutat. 2012 Oct 3. [Epub ahead of print]

Daran JM, Geertman JM, et al.
De novo detection of copy number variation by co-assembly.
Bioinformatics. 2012 Oct 9. [Epub ahead of print]

Chen J, Li W, et al.
MGAviewer: A desktop visualization tool for analysis of metagenomics alignment data.
Bioinformatics. 2012 Oct 8. [Epub ahead of print]

Chen H, Ma C, et al.
KGBassembler: A karyotype-based genome assembler for Brassicaceae species.
Bioinformatics. 2012 Oct 7. [Epub ahead of print]

Amaral PP, Cattenoz PB, et al.
Pinstripe: a suite of programs for integrating transcriptomic and proteomic datasets identifies novel proteins and improves differentiation of protein-coding and non-coding genes.
Bioinformatics. 2012 Oct 7. [Epub ahead of print]

Sun J, Zhao M, Zhao Z.
TSGene: a web resource for tumor suppressor genes.
Nucleic Acids Res. 2012 Oct 12. [Epub ahead of print]

Chitsaz M, Mayo SL.
GRID: A high-resolution protein structure refinement algorithm.
J Comput Chem. 2012 Oct 15. [Epub ahead of print]

Barrett JC, Morris JA.
Olorin: Combining gene flow with exome sequencing in large family studies of complex disease.
Bioinformatics. 2012 Oct 10. [Epub ahead of print]

Blankenberg D, Hobert O, et al.
CloudMap: A Cloud-based Pipeline for Analysis of Mutant Genome Sequences.
Genetics. 2012 Oct 11. [Epub ahead of print]

Bostick RM, Long Q, et al.
Modeling clinical outcome using multiple correlated functional biomarkers: A Bayesian approach.
Stat Methods Med Res. 2012 Oct 14. [Epub ahead of print]

Diaz A, Nellore A, Song JS.
CHANCE: comprehensive software for quality control and validation of ChIP-seq data.
Genome Biol. 2012 Oct 15;13(10):R98.

Arumugam M, Chen H, et al.
MOCAT: A Metagenomics Assembly and Gene Prediction Toolkit.
PLoS One. 2012;7(10):e47656. Epub 2012 Oct 17.

Agus DB, Amodei D, et al.
A cross-platform toolkit for mass spectrometry and proteomics.
Nat Biotechnol. 2012 Oct 10;30(10):918-20.

Aw PP, Bertrand D, et al.
LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets.
Nucleic Acids Res. 2012 Oct 12. [Epub ahead of print]

Bink MC, van de Weg WE, Voorrips RE.
Pedimap: Software for the Visualization of Genetic and Phenotypic Data in Pedigrees.
J Hered. 2012 Oct 19. [Epub ahead of print]

Filed under

The Scan

Octopus Brain Complexity Linked to MicroRNA Expansions

Investigators saw microRNA gene expansions coinciding with complex brains when they analyzed certain cephalopod transcriptomes, as they report in Science Advances.

Study Tracks Outcomes in Children Born to Zika Virus-Infected Mothers

By following pregnancy outcomes for women with RT-PCR-confirmed Zika virus infections, researchers saw in Lancet Regional Health congenital abnormalities in roughly one-third of live-born children.

Team Presents Benchmark Study of RNA Classification Tools

With more than 135 transcriptomic datasets, researchers tested two dozen coding and non-coding RNA classification tools, establishing a set of potentially misclassified transcripts, as they report in Nucleic Acids Research.

Breast Cancer Risk Related to Pathogenic BRCA1 Mutation May Be Modified by Repeats

Several variable number tandem repeats appear to impact breast cancer risk and age at diagnosis in almost 350 individuals carrying a risky Ashkenazi Jewish BRCA1 founder mutation.