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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

Pig Organ Transplants Considered

The Wall Street Journal reports that the US Food and Drug Administration may soon allow clinical trials that involve transplanting pig organs into humans.

'Poo-Bank' Proposal

Harvard Medical School researchers suggest people should bank stool samples when they are young to transplant when they later develop age-related diseases.

Spurred to Develop Again

New Scientist reports that researchers may have uncovered why about 60 percent of in vitro fertilization embryos stop developing.

Science Papers Examine Breast Milk Cell Populations, Cerebral Cortex Cellular Diversity, Micronesia Population History

In Science this week: unique cell populations found within breast milk, 100 transcriptionally distinct cell populations uncovered in the cerebral cortex, and more.