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In Print: Last Week's Sequencing-Related Papers of Note: Jul 31, 2012


Novel microRNAs differentially expressed during aging in the mouse brain.
Inukai S, de Lencastre A, Turner M, Slack F.
PLoS One. 2012;7(7):e40028.

Genome-wide localization of protein-DNA binding and histone modification by a Bayesian change-point method with ChIP-seq data.
Xing H, Mo Y, Liao W, Zhang MQ.
PLoS Comput Biol. 2012 Jul;8(7):e1002613.

High-throughput amplicon sequencing reveals distinct communities within a corroding concrete sewer system.
Cayford BI, Dennis PG, Keller J, Tyson GW, Bond PL.
Appl Environ Microbiol. 2012 Jul 27. [Epub ahead of print]

Mili and Miwi target RNA repertoire reveals piRNA biogenesis and function of Miwi in spermiogenesis.
Vourekas A, Zheng Q, Alexiou P, Maragkakis M, et al.
Nat Struct Mol Biol. 2012 Jul 29. [Epub ahead of print]

Evolutionary history and adaptation from high-coverage whole-genome sequences of diverse African hunter-gatherers.
Lachance J, Vernot B, Elbers CC, Ferwerda B, et al.
Cell. 2012 Jul 25. [Epub ahead of print]

First exon length controls active chromatin signatures and transcription.
Bieberstein NI, Oesterreich FC, Straube K, Neugebauer KM.
Cell Rep. 2012 Jul 26;2(1):62-8.

Phylogenomic analyses support the position of turtles as the sister group of birds and crocodiles (Archosauria).
Chiari Y, Cahais V, Galtier N, Delsuc F.
BMC Biol. 2012 Jul 27;10(1):65.

Short-read reading-frame predictors are not created equal: sequence error causes loss of signal.
Trimble WL, Keegan KP, D'Souza M, Wilke A, et al..
BMC Bioinformatics. 2012 Jul 28;13(1):183.

Fast isogenic mapping-by-sequencing of EMS-induced mutant bulks.
Hartwig B, Velikkakam James G, Konrad K, Schneeberger K, Turck F.
Plant Physiol. 2012 Jul 26. [Epub ahead of print]

A complete workflow for the analysis of full-size ChIP-seq (and similar) data sets using peak-motifs.
Thomas-Chollier M, Darbo E, Herrmann C, Defrance M, et al.
Nat Protoc. 2012 Jul 26;7(8):1551-68.

The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments.
Ingolia NT, Brar GA, Rouskin S, McGeachy AM, Weissman JS.
Nat Protoc. 2012 Jul 26;7(8):1534-50.

Bioinformatic analysis of barcoded cDNA libraries for small RNA profiling by next-generation sequencing.
Farazi TA, Brown M, Morozov P, Ten Hoeve JJ, et al.
Methods. 2012 Jul 23. [Epub ahead of print]

Novel roles for KLF1 in erythropoiesis revealed by mRNA-seq.
Tallack MR, Magor GW, Dartigues B, Sun L, et al.
Genome Res. 2012 Jul 26. [Epub ahead of print]

Sequencing of the smallest Apicomplexan genome from the human pathogen Babesia microti.
Cornillot E, Hadj-Kaddour K, Dassouli A, Noel B, et al.
Nucleic Acids Res. 2012 Jul 24. [Epub ahead of print]

DELIMINATE - A fast and efficient method for loss-less compression of genomic sequences.
Mohammed MH, Dutta A, Bose T, Chadaram S, Mande SS.
Bioinformatics. 2012 Jul 25. [Epub ahead of print]

Independent studies using deep sequencing resolve the same set of core bacterial species dominating gut communities of honey bees.
Sabree ZL, Hansen AK, Moran NA.
PLoS One. 2012;7(7):e41250.

Comparison of next-generation sequencing systems.
Liu L, Li Y, Li S, Hu N, et al.
J Biomed Biotechnol. 2012;2012:251364.

Bacterial genome mapper: A comparative bacterial genome mapping tool.
Lee KS, Kim RN, Yoon BH, Kim DS, et al.
Bioinformation. 2012;8(11):532-4.

Nebula — a web-server for advanced ChIP-seq data analysis.
Boeva V, Lermine A, Barette C, Guillouf C, Barillot E.
Bioinformatics. 2012 Jul 24. [Epub ahead of print]

Automatic knowledge extraction in sequencing analysis with multiagent system and grid computing.
González R, Zato C, Benito R, Bajo J, et al.
J Integr Bioinform. 2012 Jul 24;9(3):206.

A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers.
Quail M, Smith ME, Coupland P, Otto TD, et al.
BMC Genomics. 2012 Jul 24;13(1):341.
(See our coverage of this paper here.)

The Triform algorithm: improved sensitivity and specificity in ChIP-seq peak finding.
Kornacker K, Rye MB, Håndstad T, Drabløs F.
BMC Bioinformatics. 2012 Jul 24;13(1):176.

A fine scale phenotype-genotype virulence map of a bacterial pathogen.
van Opijnen T, Camilli A.
Genome Res. 2012 Jul 23. [Epub ahead of print]

Recombinatorial biases and convergent recombination determine interindividual TCRβ sharing in murine thymocytes.
Li H, Ye C, Ji G, Wu X, et al.
J Immunol. 2012 Jul 23. [Epub ahead of print]

Sequence-based association and selection scans identify drug resistance loci in the Plasmodium falciparum malaria parasite.
Park DJ, Lukens AK, Neafsey DE, Schaffner SF, et al.
Proc Natl Acad Sci U S A. 2012 Jul 23. [Epub ahead of print]

The Scan

Genetic Risk Factors for Hypertension Can Help Identify Those at Risk for Cardiovascular Disease

Genetically predicted high blood pressure risk is also associated with increased cardiovascular disease risk, a new JAMA Cardiology study says.

Circulating Tumor DNA Linked to Post-Treatment Relapse in Breast Cancer

Post-treatment detection of circulating tumor DNA may identify breast cancer patients who are more likely to relapse, a new JCO Precision Oncology study finds.

Genetics Influence Level of Depression Tied to Trauma Exposure, Study Finds

Researchers examine the interplay of trauma, genetics, and major depressive disorder in JAMA Psychiatry.

UCLA Team Reports Cost-Effective Liquid Biopsy Approach for Cancer Detection

The researchers report in Nature Communications that their liquid biopsy approach has high specificity in detecting all- and early-stage cancers.