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In Print: Last Week's Sequencing-Related Papers of Note: Oct 23, 2012


Mechanisms of formation of structural variation in a fully sequenced human genome.
Pang AW, Migita O, Macdonald JR, Feuk L, Scherer SW.
Hum Mutat. 2012 Oct 19. [Epub ahead of print]

Characterization of H3K9me3- and H4K20me3-associated circulating nucleosomal DNA by high-throughput sequencing in colorectal cancer.
Gezer U, Ustek D, Yörüker EE, Cakiris A, et al.
Tumour Biol. 2012 Oct 20. [Epub ahead of print]

CLIP-seq of eIF4AIII reveals transcriptome-wide mapping of the human exon junction complex.
Saulière J, Murigneux V, Wang Z, Marquenet E, et al.
Nat Struct Mol Biol. 2012 Oct 21. [Epub ahead of print]

Microdissection of spatially identified single nuclei in a solid tumor for single cell whole genome sequencing.
Guo Y, Yang Y, Zhou J, Czajkowsky DM, et al.
Biotechniques. 2012 May 17;2012.

Short-read, high-throughput sequencing technology for STR genotyping.
Bornman DM, Hester ME, Schuetter JM, Kasoji MD, et al.
Biotechniques. 2012 May 10;2012.

dsPIG: a tool to predict imprinted genes from the deep sequencing of whole transcriptomes.
Li H, Su X, Gallegos J, Lu Y, et al.
BMC Bioinformatics. 2012 Oct 19;13(1):271

MOCAT: a metagenomics assembly and gene prediction toolkit.
Kultima JR, Sunagawa S, Li J, Chen W, et al.
PLoS One. 2012;7(10):e47656.

Hybrid sequencing approach applied to human fecal metagenomic clone libraries revealed clones with potential biotechnological applications.
Džunková M, D'Auria G, Pérez-Villarroya D, Moya A.
PLoS One. 2012;7(10):e47654.

Metagenomic exploration of viruses throughout the Indian Ocean.
Williamson SJ, Allen LZ, Lorenzi HA, Fadrosh DW, et al.
PLoS One. 2012;7(10):e42047.

Host remodeling of the gut microbiome and metabolic changes during pregnancy.
Koren O, Goodrich JK, Cullender TC, Spor A, et al.
Cell. 2012 Aug 3;150(3):470-80.

A global genome segmentation method for exploration of epigenetic patterns.
Steiner L, Hopp L, Wirth H, Galle J, et al.
PLoS One. 2012;7(10):e46811.

DNA extraction from museum specimens of parasitic hymenoptera.
Andersen JC, Mills NJ.
PLoS One. 2012;7(10):e45549.

Universal heteroplasmy of human mitochondrial DNA.
Payne BA, Wilson IJ, Yu-Wai-Man P, Coxhead J, et al.
Hum Mol Genet. 2012 Oct 16. [Epub ahead of print]

A physical, genetic and functional sequence assembly of the barley genome.
The International Barley Genome Sequencing Consortium; Mayer KF, Waugh R, Langridge P, et al.
Nature. 2012 Oct 17. [Epub ahead of print]

Reference-independent comparative metagenomics using cross-assembly: crAss.
Dutilh BE, Schmieder R, Nulton J, Felts B, et al.
Bioinformatics. 2012 Oct 16. [Epub ahead of print]

Gene fusion markup language: a prototype for exchanging gene fusion data.
Kalyana-Sundaram S, Shanmugam A, Chinnaiyan AM.
BMC Bioinformatics. 2012 Oct 16;13(1):269.

Temporal dynamics of the human vaginal microbiota.
Gajer P, Brotman RM, Bai G, Sakamoto J, et al.
Sci Transl Med. 2012 May 2;4(132):132ra52.

Detecting identity by descent and homozygosity mapping in whole-exome sequencing data.
Zhuang Z, Gusev A, Cho J, Pe'er I.
PLoS One. 2012;7(10):e47618.

Species-level analysis of DNA sequence data from the NIH Human Microbiome Project.
Conlan S, Kong HH, Segre JA.
PLoS One. 2012;7(10):e47075.

Characterization of the fecal microbiota using high-throughput sequencing reveals a stable microbial community during storage.
Carroll IM, Ringel-Kulka T, Siddle JP, Klaenhammer TR, Ringel Y.
PLoS One. 2012;7(10):e46953.

lociNGS: a lightweight alternative for assessing suitability of next-generation loci for evolutionary analysis.
Hird SM.
PLoS One. 2012;7(10):e46847.

The Paramecium germline genome provides a niche for intragenic parasitic DNA: evolutionary dynamics of internal eliminated sequences.
Arnaiz O, Mathy N, Baudry C, Malinsky S, et al.
PLoS Genet. 2012 Oct;8(10):e1002984.

SortMeRNA: Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data.
Kopylova E, Noé L, Touzet H.
Bioinformatics. 2012 Oct 15. [Epub ahead of print]

Selective capture of 5-hydroxymethylcytosine from genomic DNA.
Li Y, Song CX, He C, Jin P.
J Vis Exp. 2012 Oct 5;(68).

Nucleotide-resolution profiling of RNA recombination in the encapsidated genome of a eukaryotic RNA virus by next-generation sequencing.
Routh A, Ordoukhanian P, Johnson JE.
J Mol Biol. 2012 Oct 12. [Epub ahead of print]

BIGrat: a repeat resolver for pyrosequencing-based re-sequencing with Newbler.
Zhang T, Luo Y, Chen Y, Li X, Yu J.
BMC Res Notes. 2012 Oct 15;5(1): 2101791285670512.

CHANCE: comprehensive software for quality control and validation of ChIP-seq data.
Diaz A, Nellore A, Song JS.
Genome Biol. 2012 Oct 15;13(10):R98.

Fine mapping of complex traits in non-model species: using next generation sequencing and advanced intercross lines in Japanese quail.
Fresard L, Leroux S, Dehais P, Servin B, et al.
BMC Genomics. 2012 Oct 15;13(1):551.

The Scan

NFTs for Genome Sharing

Nature News writes that non-fungible tokens could be a way for people to profit from sharing genomic data.

Wastewater Warning System

Time magazine writes that cities and college campuses are monitoring sewage for SARS-CoV-2, an approach officials hope lasts beyond COVID-19.

Networks to Boost Surveillance

Scientific American writes that new organizations and networks aim to improve the ability of developing countries to conduct SARS-CoV-2 genomic surveillance.

Genome Biology Papers on Gastric Cancer Epimutations, BUTTERFLY, GUNC Tool

In Genome Biology this week: recurrent epigenetic mutations in gastric cancer, correction tool for unique molecular identifier-based assays, and more.