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In Print: February's Bioinformatics Papers of Note


Asp P, Dynlacht BD, et al.
Picking ChIP-seq peak detectors for analyzing chromatin modification experiments.
Nucleic Acids Res. 2012 Feb 15. [Epub ahead of print]

Mishra B, Narzisi G, Vezzi F.
Feature-by-Feature — Evaluating De Novo Sequence Assembly.
PLoS One. 2012;7(2):e31002.

Elasri MO, George G,et al.
CAPRG: Sequence Assembling Pipeline for Next Generation Sequencing of Non-Model Organisms.
PLoS One. 2012;7(2):e30370.

Bischoff R, Breitling R,et al.
msCompare: a framework for quantitative analysis of label-free LC-MS data for comparative biomarker studies.
Mol Cell Proteomics. 2012 Feb 7. [Epub ahead of print].

Côté RG, Csordas A,et al.
PRIDE Inspector: a tool to visualize and validate MS proteomics data.
Nat Biotechnol. 2012 Feb 8;30(2):135-7.

Fairbrother W, Lim KH
Spliceman — A computational web server that predicts sequence variations in pre-mRNA splicing.
Bioinformatics. 2012 Feb 10. [Epub ahead of print].

Hatzimanikatis V, Overney J, Racle J
A computational framework for the design of optimal protein synthesis.
Biotechnol Bioeng. 2012 Feb 14. [Epub ahead of print].

Arnold P, Erb I,et al.
MotEvo: integrated Bayesian probabilistic methods for inferring regulatory sites and motifs on multiple alignments of DNA sequences.
Bioinformatics. 2012 Feb 15;28(4):487-94.

Chen CK, Doelken SC,et al.
MouseFinder: candidate disease genes from mouse phenotype data.
Hum Mutat. 2012 Feb 13. [Epub ahead of print].

Abreu VA, Azevedo V,et al.
PIPS: Pathogenicity Island Prediction Software.
PLoS One. 2012;7(2):e30848.

Alcaraz N, Baumbach J,et al.
Efficient key pathway mining: combining networks and OMICS data.
Integr Biol (Camb). 2012 Feb 21. [Epub ahead of print].

Childs LH, Lisec J, Walther D.
Matapax: An online high-throughput genome-wide association study pipeline.
Plant Physiol. 2012 Feb 21. [Epub ahead of print].

The Scan

Enzyme Involved in Lipid Metabolism Linked to Mutational Signatures

In Nature Genetics, a Wellcome Sanger Institute-led team found that APOBEC1 may contribute to the development of the SBS2 and SBS13 mutational signatures in the small intestine.

Family Genetic Risk Score Linked to Diagnostic Trajectory in Psychiatric Disorders

Researchers in JAMA Psychiatry find ties between high or low family genetic risk scores and diagnostic stability or change in four major psychiatric disorders over time.

Study Questions Existence of Fetal Microbiome

A study appearing in Nature this week suggests that the reported fetal microbiome might be the result of sample contamination.

Fruit Fly Study Explores Gut Microbiome Effects on Circadian Rhythm

With gut microbiome and gene expression experiments, researchers in PNAS see signs that the microbiome contributes to circadian rhythm synchronicity and stability in fruit flies.