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Last Week's Sequencing-Related Papers of Note: Aug 23, 2011


A bioinformatics approach for determining sample identity from different lanes of high-throughput sequencing data.
Goldfeder RL, Parker SC, Ajay SS, Ozel Abaan H, Margulies EH.
PLoS One. 2011;6(8):e23683.

LOCAS - A low coverage assembly tool for resequencing projects.
Klein JD, Ossowski S, Schneeberger K, Weigel D, Huson DH.
PLoS One. 2011;6(8):e23455.

High diversity of the saliva microbiome in batwa pygmies.
Nasidze I, Li J, Schroeder R, Creasey JL, et al.
PLoS One. 2011;6(8):e23352.

Eu-Detect: An algorithm for detecting eukaryotic sequences in metagenomic data sets.
Mohammed MH, Chadaram S, Komanduri D, Ghosh TS, Mande SS.
J Biosci. 2011 Sep;36(4):709-17.

Comparative analysis of algorithms for next-generation sequencing read alignment.
Ruffalo M , Laframboise T, Koyutürk M.
Bioinformatics. 2011 Aug 19. [Epub ahead of print]

Chromosomal haplotypes by genetic phasing of human families.
Roach JC, Glusman G, Hubley R, Montsaroff SZ, et al.
Am J Hum Genet. 2011 Aug 17. [Epub ahead of print]

The human mitochondrial transcriptome.
Mercer TR, Neph S, Dinger ME, Crawford J, et al.
Cell. 2011 Aug 19;146(4):645-58.

Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development.
Renfree MB, Papenfuss AT, Deakin JE, Lindsay J, et al.
Genome Biol. 2011 Aug 19;12(8):R81. [Epub ahead of print]

Highly sensitive pyrosequencing system with polymer-supported enzymes for high-throughput DNA analysis.
Shiari M, Goto M, Suzuki S, Kono K, et al.
Anal Chem. 2011 Aug 21. [Epub ahead of print]

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Comparative analysis of salivary bacterial microbiome diversity in edentulous infants and their mothers or primary care givers using pyrosequencing.
Cephas KD, Kim J, Mathai RA, Barry KA, et al.
PLoS One. 2011;6(8):e23503.

Analysis of DNA methylation in a three-generation family reveals widespread genetic influence on epigenetic regulation.
Gertz J, Varley KE, Reddy TE, Bowling KM, et al.
PLoS Genet. 2011 Aug;7(8):e1002228.

SAMQA: error classification and validation of high-throughput sequenced read data.
Robinson T, Killcoyne S, Bressler R, Boyle J.
BMC Genomics. 2011 Aug 18;12(1):419.

Nephele: Genotyping via complete composition vectors and MapReduce.
Colosimo ME, Peterson MW, Mardis S, Hirschman L.
Source Code Biol Med. 2011 Aug 18;6(1):13.

PARalyzer: Definition of RNA binding sites from PAR-CLIP short-read sequence data.
Corcoran DL, Georgiev S, Mukherjee N, Gottwein E, et al.
Genome Biol. 2011 Aug 18;12(8):R79.

Comparative deep transcriptional profiling of four developing oilseeds.
Troncoso-Ponce MA, Kilaru A, Cao X, Durrett TP, et al.
Plant J. 2011 Aug 18. doi: 10.1111/j.1365-313X.2011.04751.x. [Epub ahead of print]

Deep sequencing of microRNA precursors reveals extensive 3' end modification.
Newman MA, Mani V, Hammond SM.
RNA. 2011 Aug 17. [Epub ahead of print]

The head-regeneration transcriptome of the planarian Schmidtea mediterranea.
Sandmann T, Vogg MC, Owlarn S, Boutros M, Bartscherer K.
Genome Biol. 2011 Aug 16;12(8):R76.

The Scan

Study Reveals Details of SARS-CoV-2 Spread Across Brazil

A genomic analysis in Nature Microbiology explores how SARS-CoV-2 spread into, across, and from Brazil.

New Study Highlights Utility of Mutation Testing in Anaplastic Thyroid Cancer

Genetic mutations in BRAF and RAS are associated with patient outcomes in anaplastic thyroid carcinoma, a new JCO Precision Oncology study reports.

Study Points to Increased Risk of Dangerous Blood Clots in COVID-19 Patients

An analysis in JAMA Internal Medicine finds that even mild COVID-19 increases risk of venous thromboembolism.

Y Chromosome Study Reveals Details on Timing of Human Settlement in Americas

A Y chromosome-based analysis suggests South America may have first been settled more than 18,000 years ago, according to a new PLOS One study.