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Last Week's Sequencing-Related Papers of Note: Aug 16, 2011


ChimeraScan: A tool for identifying chimeric transcription in sequencing data.
Iyer MK, Chinnaiyan AM, Maher CA.
Bioinformatics. 2011 Aug 11. [Epub ahead of print]

Inference of population mutation rate and detection of segregating sites from next-generation sequence data.
Kang CJ, Marjoram P.
Genetics. 2011 Aug 11. [Epub ahead of print]

A statistical framework for eQTL mapping using RNA-seq data.
Sun W.
Biometrics. 2011 Aug 12. doi: 10.1111/j.1541-0420.2011.01654.x. [Epub ahead of print]

High-resolution description of antibody heavy-chain repertoires in humans.
Arnaout R, Lee W, Cahill P, Honan T, et al.
PLoS One. 2011;6(8):e22365.

Differential gene expression in the siphonophore Nanomia bijuga (cnidaria) assessed with multiple next-generation sequencing workflows.
Siebert S, Robinson MD, Tintori SC, Goetz F, et al.
PLoS One. 2011;6(7):e22953.

Oral microbiome profiles: 16S rRNA pyrosequencing and microarray assay comparison.
Ahn J, Yang L, Paster BJ, Ganly I, et al.
PLoS One. 2011;6(7):e22788.

Comparative analysis of Korean human gut microbiota by barcoded pyrosequencing.
Nam YD, Jung MJ, Roh SW, Kim MS, Bae JW.
PLoS One. 2011;6(7):e22109.

Genome evolution and meiotic maps by massively parallel DNA sequencing: spotted gar, an outgroup for the teleost genome duplication.
Amores A, Catchen J, Ferrara A, Fontenot Q, Postlethwait JH.
Genetics. 2011 Aug;188(4):799-808.

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Transcriptome profiling and sequencing of differentiated human hematopoietic stem cells reveal lineage specific expression and alternative splicing of genes.
Liu P, Barb J, Woodhouse K, Taylor JG, et al.
Physiol Genomics. 2011 Aug 9. [Epub ahead of print]

Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV.
Sathirapongsasuti JF, Lee H, Horst BA, Brunner G, et al.
Bioinformatics. 2011 Aug 9. [Epub ahead of print]

TopHat-Fusion: an algorithm for discovery of novel fusion transcripts.
Kim D, Salzberg SL.
Genome Biol. 2011 Aug 11;12(8):R72.

Quantification of histone modification ChIP-seq enrichment for data mining and machine learning applications.
Hoang SA, Xu X, Bekiranov S.
BMC Res Notes. 2011 Aug 11;4(1):288.

Comparing next-generation sequencing and microarray technologies in a toxicological study of the effects of aristolochic acid on rat kidneys.
Su Z, Li Z, Chen T, Li QZ, et al.
Chem Res Toxicol. 2011 Aug 11. [Epub ahead of print]

Evaluation of next-generation sequencing software in mapping and assembly.
Bao S, Jiang R, Kwan W, Wang B, et al.
J Hum Genet. 2011 Aug 11. doi: 10.1038/jhg.2011.91. [Epub ahead of print]

The genome sequence of Atlantic cod reveals a unique immune system.
Star B , Nederbragt AJ, Jentoft S, Grimholt U, et al.
Nature. 2011 Aug 10. doi: 10.1038/nature10342. [Epub ahead of print]

Efficient counting of k-mers in DNA sequences using a Bloom filter.
Melsted P, Pritchard JK.
BMC Bioinformatics. 2011 Aug 10;12(1):333.

FDM: A graph-based statistical method to detect differential transcription using RNA-seq data.
Singh D, Orellana CF, Hu Y, Jones CD, et al.
Bioinformatics. 2011 Aug 8. [Epub ahead of print]

The Scan

WHO OKs Emergency Use of Sinopharm Vaccine

The World Health Organization has granted emergency approval for Sinopharm's SARS-CoV-2 vaccine, the Guardian reports.

Scientific Integrity Panel to Meet

According to the Associated Press, a new US scientific integrity panel is to meet later this week.

Trying in the Eye

NPR reports that a study of Editas Medicine's CRISPR therapy for Leber congenital amaurosis has begun.

PLOS Papers on Cerebellum Epigenetics, Copy Number Signature Tool, Acute Lung Injury Networks

In PLOS this week: epigenetics analysis of brain tissue, bioinformatics tool to find copy number signatures in cancer, and more.