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Papers of Note: Feb 1, 2011


Massive parallel DNA pyrosequencing analysis of the tumor suppressor BRG1/SMARCA4 in lung primary tumors.
Rodriguez-Nieto S, Cañada A, Pros E, Pinto AI, et al.
Hum Mutat. 2011 Feb;32(2):E1999-2017.

Forces affecting double-stranded DNA translocation through synthetic nanopores.
Chen L, Conlisk AT.
Biomed Microdevices. 2011 Jan 29. [Epub ahead of print]

Bambino: a variant detector and alignment viewer for next-generation sequencing data in the SAM/BAM format.
Edmonson MN, Zhang J, Yan C, Finney RP, et al.
Bioinformatics. 2011 Jan 28. [Epub ahead of print]

Identity-by-descent filtering of exome sequence data for disease-gene
identification in autosomal recessive disorders.
Rödelsperger C, Krawitz P, Bauer S, Hecht J, et al.
Bioinformatics. 2011 Jan 28. [Epub ahead of print]

Quality control and preprocessing of metagenomic datasets.
Schmieder R, Edwards R.
Bioinformatics. 2011 Jan 28. [Epub ahead of print]

CHILD: a new tool for detecting low-abundance insertions and deletions in standard sequence traces.
Zhidkov I, Cohen R, Geifman N, Mishmar D, Rubin E.
Nucleic Acids Res. 2011 Jan 28. [Epub ahead of print]

Quantitative determination of allele frequency in pooled DNA by using sequencing
Cao P, Wang QJ, Zhu XT, Zhou H, et al.
J Chromatogr B Analyt Technol Biomed Life Sci. 2011 Jan 15. [Epub ahead of print]

Removing noise from pyrosequenced amplicons.
Quince C, Lanzen A, Davenport RJ, Turnbaugh PJ.
BMC Bioinformatics. 2011 Jan 28;12(1):38.

Fluorinated amphiphiles control the insertion of α hemolysin pores into lipid bilayers.
Raychaudhuri P, Li Q, Mason A, Mikhailova E, et al.
Biochemistry. 2011 Jan 28. [Epub ahead of print]

A deep-sequencing study of chronic myeloid leukemia patients in blast crisis(BC-CML) detects mutations in 76.9% of cases.
Grossmann V, Kohlmann A, Zenger M, Schindela S, et al.
Leukemia. 2011 Jan 28. [Epub ahead of print]

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Metagenomic discovery of biomass-degrading genes and genomes from cow rumen.
Hess M, Sczyrba A, Egan R, Kim TW, et al.
Science. 2011 Jan 28;331(6016):463-467.

Rapid pneumococcal evolution in response to clinical interventions.
Croucher NJ, Harris SR, Fraser C, Quail MA, et al.
Science. 2011 Jan 28;331(6016):430-434.

Model SNP development for complex genomes based on hexaploid oat using high-throughput 454 sequencing technology.
Oliver RE, Lazo GR, Lutz JD, Rubenfield MJ, et al.
BMC Genomics. 2011 Jan 27;12(1):77.

Comparative and demographic analysis of orang-utan genomes.
Locke DP, Hillier LW, Warren WC, Worley KC, et al.
Nature. 2011 Jan 27;469(7331):529-533.

Next generation massively parallel sequencing of targeted exomes to identify genetic mutations in primary ciliary dyskinesia: Implications for application to clinical testing.
Berg JS, Evans JP, Leigh MW, Omran H, et al.
Genet Med. 2011 Jan 25. [Epub ahead of print]

Genomic sequencing and analysis of a Chinese Hamster ovary cell line using Illumina sequencing technology.
Hammond S, Swanberg JC, Kaplarevic M, Lee KH.
BMC Genomics. 2011 Jan 26;12(1):67.

A novel compression tool for efficient storage of genome resequencing data.
Wang C, Zhang D.
Nucleic Acids Res. 2011 Jan 25. [Epub ahead of print]

Rapid identification of mutations in GJC2 in primary lymphoedema using whole exome sequencing combined with linkage analysis with delineation of the phenotype.
Ostergaard P, Simpson MA, Brice G, Mansour S, et al.
J Med Genet. 2011 Jan 25. [Epub ahead of print]

Annotation-based genome-wide SNP discovery in the large and complex Aegilops tauschii genome using next-generation sequencing without a reference genome sequence.
You FM, Huo N, Deal KR, Gu YQ, et al.
BMC Genomics. 2011 Jan 25;12(1):59.

PoolHap: Inferring haplotype frequencies from pooled samples by next generation sequencing.
Long Q, Jeffares DC, Zhang Q, Ye K, et al.
PLoS One. 2011 Jan 5;6(1):e15292.

Mutation of HIV-1 genomes in a clinical population treated with the mutagenic nucleoside KP1461.
Mullins JI, Heath L, Hughes JP, Kicha J, et al.
PLoS One. 2011 Jan 14;6(1):e15135.

Deep RNA sequencing analysis of readthrough gene fusions in human prostate adenocarcinoma and reference samples.
Nacu S, Yuan W, Kan Z, Bhatt D, et al.
BMC Med Genomics. 2011 Jan 24;4(1):11.

PileLine: a toolbox to handle genome position information in next-generation sequencing studies.
Glez-Pena D, Gomez-Lopez G, Reboiro-Jato M, Fdez-Riverola F, Pisano DG.
BMC Bioinformatics. 2011 Jan 24;12(1):31.

The Scan

Could Mix It Up

The US Food and Drug Administration is considering a plan that would allow for the mixing-and-matching of SARS-CoV-2 vaccines and boosters, the New York Times says.

Closest to the Dog

New Scientist reports that extinct Japanese wolf appears to be the closest known wild relative of dogs.

Offer to Come Back

The Knoxville News Sentinel reports that the University of Tennessee is offering Anming Hu, a professor who was acquitted of charges that he hid ties to China, his position back.

PNAS Papers on Myeloid Differentiation MicroRNAs, Urinary Exosomes, Maize Domestication

In PNAS this week: role of microRNAs in myeloid differentiation, exosomes in urine, and more.