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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]


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The Scan

Study Points to Tuberculosis Protection by Gaucher Disease Mutation

A mutation linked to Gaucher disease in the Ashkenazi Jewish population appears to boost Mycobacterium tuberculosis resistance in a zebrafish model of the lysosomal storage condition, a new PNAS study finds.

SpliceVault Portal Provides Look at RNA Splicing Changes Linked to Genetic Variants

The portal, described in Nature Genetics, houses variant-related messenger RNA splicing insights drawn from RNA sequencing data in nearly 335,700 samples — a set known as the 300K-RNA resource.

Automated Sequencing Pipeline Appears to Allow Rapid SARS-CoV-2 Lineage Detection in Nevada Study

Researchers in the Journal of Molecular Diagnostics describe and assess a Clear Labs Dx automated workflow, sequencing, and bioinformatic analysis method for quickly identifying SARS-CoV-2 lineages.

UK Team Presents Genetic, Epigenetic Sequencing Method

Using enzymatic DNA preparation steps, researchers in Nature Biotechnology develop a strategy for sequencing DNA, along with 5-methylcytosine and 5-hydroxymethylcytosine, on existing sequencers.