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In Print: Last Week's Sequencing-Related Papers of Note: Jun 25, 2013


Employing 454 amplicon pyrosequencing to reveal intragenomic divergence in the internal transcribed spacer rDNA region in fungi.
Lindner DL, Carlsen T, Henrik Nilsson R, Davey M, et al.
Ecol Evol. 2013 Jun;3(6):1751-64.

SHAPE-Seq: High-throughput RNA structure analysis.
Mortimer SA, Trapnell C, Aviran S, Pachter L, Lucks JB.
Curr Protoc Chem Biol. 2012 Dec 1;4(4):275-97.

PING 2.0: An R/Bioconductor package for nucleosome positioning using next-generation sequencing data.
Woo S, Zhang X, Sauteraud R, Robert F, Gottardo R.
Bioinformatics. 2013 Jun 20. [Epub ahead of print]

Harnessing virtual machines to simplify next generation DNA sequencing analysis.
Nocq J, Celton M, Gendron P, Lemieux S, Wilhelm BT.
Bioinformatics. 2013 Jun 20. [Epub ahead of print]

Insights into fungal communities in composts revealed by 454-pyrosequencing: implications for human health and safety.
De Gannes V, Eudoxie G, Hickey WJ.
Front Microbiol. 2013 Jun 13;4:164.

Exact algorithms for haplotype assembly from whole-genome sequence data.
Chen ZZ, Deng F, Wang L.
Bioinformatics. 2013 Jun 18. [Epub ahead of print]

Nonenzymatic labeling of 5-hydroxymethylcytosine in nanopore sequencing.
Lu X, He C.
Chembiochem. 2013 Jun 18. [Epub ahead of print]

mirTools 2.0 for non-coding RNA discovery, profiling and functional annotation based on high-throughput sequencing.
Wu J, Liu Q, Wang X, Zheng J, et al.
RNA Biol. 2013 May 29;10(7).

Coverage bias and sensitivity of variant calling for four whole-genome sequencing technologies.
Rieber N, Zapatka M, Lasitschka B, Jones D, et al.
PLoS One. 2013 Jun 11;8(6):e66621.

Life on human surfaces: skin metagenomics.
Mathieu A, Delmont TO, Vogel TM, Robe P, et al.
PLoS One. 2013 Jun 12;8(6):e65288.

miRspring: a compact standalone research tool for analyzing miRNA-seq data.
Humphreys DT, Suter CM.
Nucleic Acids Res. 2013 Jun 17. [Epub ahead of print]

Boron nitride nanopores: highly sensitive DNA single-molecule detectors.
Liu S, Lu B, Zhao Q, Li J, et al.
Adv Mater. 2013 Jun 17. [Epub ahead of print]

User guide for mapping-by-sequencing in Arabidopsis.
Velikkakam James G, Patel V, Nordstrom KJ, Klasen JR, et al.
Genome Biol. 2013 Jun 17;14(6):R61.

Transcriptome sequencing and de novo annotation of the critically endangered Adriatic sturgeon.
Vidotto M, Grapputo A, Boscari E, Barbisan F, et al.
BMC Genomics. 2013 Jun 18;14(1):407.

Combined methylation mapping of 5mC and 5hmC during early embryonic stages in bovine.
de Montera B, Fournier E, Shojaei Saadi HA, Gagné D, et al.
BMC Genomics. 2013 Jun 18;14(1):406.

High-throughput sequencing of methylated cytosine enriched by modification-dependent restriction endonuclease MspJI.
Huang X, Lu H, Wang JW, Xu L, et al.
BMC Genet. 2013 Jun 18;14(1):56.

Quantifying single nucleotide variant detection sensitivity in exome sequencing.
Meynert AM, Bicknell LS, Hurles ME, Jackson AP, Taylor MS .
BMC Bioinformatics. 2013 Jun 18;14(1):195.

kmer-SVM: a web server for identifying predictive regulatory sequence features in genomic data sets.
Fletez-Brant C, Lee D, McCallion AS, Beer MA.
Nucleic Acids Res. 2013 Jun 14. [Epub ahead of print]

A probabilistic approach to learn chromatin architecture and accurate inference of the NF-κB/RelA regulatory network using ChIP-seq.
Yang J, Mitra A, Dojer N, Fu S, et al.
Nucleic Acids Res. 2013 Jun 14. [Epub ahead of print]

Uniform, optimal signal processing of mapped deep-sequencing data.
Kumar V, Muratani M, Rayan NA, Kraus P, et al.
Nat Biotechnol. 2013 Jun 16. [Epub ahead of print]

General framework for meta-analysis of rare variants in sequencing association studies.
Lee S, Teslovich TM, Boehnke M, Lin X.
Am J Hum Genet. 2013 Jun 12. [Epub ahead of print]

STRait Razor: A length-based forensic STR allele-calling tool for use with second generation sequencing data.
Warshauer DH, Lin D, Hari K, Jain R, et al.
Forensic Sci Int Genet. 2013 Jul;7(4):409-17.

FusionQ: a novel approach for gene fusion detection and quantification from paired-end RNA-seq.
Liu C, Ma J, Chang CJ, Zhou X.
BMC Bioinformatics. 2013 Jun 15;14(1):193.

The Scan

White-Tailed Deer Harbor SARS-CoV-2 Variants No Longer Infecting Humans, Study Finds

A new study in PNAS has found that white-tailed deer could act as a reservoir of SARS-CoV-2 variants no longer found among humans.

Study Points to Benefits of Local Consolidative Therapy, Targeted Treatments in Cancer Care

In JCO Precision Oncology, researchers report that local consolidative therapy combined with molecularly targeted treatments could improve survival for some lung cancer patients.

Genetic Variants That Lower LDL Cholesterol Linked to Reduced Heart Disease Risk

Rare variants in two genes that lower LDL cholesterol are also associated with a decreased risk of coronary heart disease, according to a new JAMA Cardiology study.

Study Links Evolution of Longevity, Social Organization in Mammals

With the help of comparative phylogenetics and transcriptomics, researchers in Nature Communications see ties between lifespan and social organization in mammals.