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October's Bioinformatics Papers of Note

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Ameur A, Bunikis I, et al.
CanvasDB: a local database infrastructure for analysis of targeted- and whole genome re-sequencing projects.
Database (Oxford). 2014 Oct 3;2014. pii: bau098. doi: 10.1093/database/bau098.


Czeschik JC, Doelken SC, et al.
Clinical interpretation of CNVs with cross-species phenotype data.
J Med Genet. 2014 Nov;51(11):766-72. Epub 2014 Oct 3.


Berger B, Chindelevitch L, et al.
An exact arithmetic toolbox for a consistent and reproducible structural analysis of metabolic network models.
Nat Commun. 2014 Oct 7;5:4893. doi: 10.1038/ncomms5893.


Lindgreen S, Krogh A, Pedersen JS
SNPest: a probabilistic graphical model for estimating genotypes.
BMC Res Notes. 2014 Oct 7;7:698. doi: 10.1186/1756-0500-7-698.


Beerenwinkel N, Gerstung M, et al.
Cancer evolution: mathematical models and computational inference.
Syst Biol. 2014 Oct 7. pii: syu081. [Epub ahead of print]


Beccuti M, Calogero RA, et al.
Chimera: a Bioconductor package for secondary analysis of fusion products.
Bioinformatics. 2014 Oct 6. pii: btu662. [Epub ahead of print]


Peng G, Fan Y, Wang W.
FamSeq: A Variant Calling Program for Family-Based Sequencing Data Using Graphics Processing Units.
PLoS Comput Biol. 2014 Oct 30;10(10):e1003880. doi: 10.1371/journal.pcbi.1003880.


Cao Q, Ho ED, et al.
VAS: a convenient web portal for efficient integration of genomic features with millions of genetic variants.
BMC Genomics. 2014 Oct 11;15:886. doi: 10.1186/1471-2164-15-886.


Andrews T, Steinberg J, et al.
GeneNet Toolbox for MATLAB: a flexible platform for the analysis of gene connectivity in biological networks.
Bioinformatics. 2014 Oct 14. pii: btu669. [Epub ahead of print]


Pers TH, Timshel P, Hirschhorn JN.
SNPsnap: a Web-based tool for identification and annotation of matched SNPs.
Bioinformatics. 2014 Oct 13. pii: btu655. [Epub ahead of print]


Melsted P, Halldórsson BV
KmerStream: Streaming algorithms for k-mer abundance estimation.
Bioinformatics. 2014 Oct 28. pii: btu713. [Epub ahead of print]


Chen JY, Huang H, et al.
SLDR: a computational technique to identify novel genetic regulatory relationships.
BMC Bioinformatics 2014 Oct 21;15 Suppl 11:S1. doi: 10.1186/1471-2105-15-S11-S1.


Grace SC, Embry S, Luo H.
Haystack, a web-based tool for metabolomics research.
BMC Bioinformatics 2014 Oct 21;15 Suppl 11:S12.


Barker ND, Gong P, et al.
SeqAssist: a novel toolkit for preliminary analysis of next-generation sequencing data.
BMC Bioinformatics Epub 2014 Oct 21.


Casper J, Clawson H, Haussler D,et al.
Navigating protected genomics data with UCSC Genome Browser in a Box.
Bioinformatics 2014 Oct 27. pii: btu712. [Epub ahead of print]


Han BW, Wang W,et al.
piPipes: a set of pipelines for piRNA and transposon analysis via smallRNA-seq, RNA-seq, degradome- and CAGE-seq, ChIP-seq and genomicDNA sequencing.
Bioinformatics 2014 Oct 17. pii: btu647. [Epub ahead of print]


Artyomenko A, Campo DS,et al.
Computational Framework for Next-Generation Sequencing of Heterogeneous Viral Populations using Combinatorial Pooling.
Bioinformatics 2014 Oct 29. pii: btu726. [Epub ahead of print]


Ochoa I, Hernaez M, Weissman T
iDoComp: A Compression Scheme for Assembled Genomes.
Bioinformatics 2014 Oct 24. pii: btu698. [Epub ahead of print]


Dang CC, Gascuel O, et al.
FastMG: a simple, fast, and accurate maximum likelihood procedure to estimate amino acid replacement rate matrices from large data sets.
BMC Bioinformatics 2014 Oct 24;15(1):341.[Epub ahead of print]


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.