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October's Bioinformatics Papers of Note


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

Positive Framing of Genetic Studies Can Spark Mistrust Among Underrepresented Groups

Researchers in Human Genetics and Genomics Advances report that how researchers describe genomic studies may alienate potential participants.

Small Study of Gene Editing to Treat Sickle Cell Disease

In a Novartis-sponsored study in the New England Journal of Medicine, researchers found that a CRISPR-Cas9-based treatment targeting promoters of genes encoding fetal hemoglobin could reduce disease symptoms.

Gut Microbiome Changes Appear in Infants Before They Develop Eczema, Study Finds

Researchers report in mSystems that infants experienced an enrichment in Clostridium sensu stricto 1 and Finegoldia and a depletion of Bacteroides before developing eczema.

Acute Myeloid Leukemia Treatment Specificity Enhanced With Stem Cell Editing

A study in Nature suggests epitope editing in donor stem cells prior to bone marrow transplants can stave off toxicity when targeting acute myeloid leukemia with immunotherapy.