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Papers of Note: Jan 11, 2011


Comparison of constitutional and replication stress-induced genome structural variation by SNP array and mate-pair sequencing.
Arlt MF, Ozdemir AC, Birkeland SR, Lyons RH, et al.
Genetics. 2011 Jan 6. [Epub ahead of print]

Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons.
Haas BJ, Gevers D, Earl A, Feldgarden M, et al.
Genome Res. 2011 Jan 6. [Epub ahead of print]

Exome sequencing reveals a novel mutation for autosomal recessive nonsyndromic mental retardation in the TECR gene on chromosome 19p13.
Caliskan M, Chong JX, Uricchio L, Anderson R, et al.
Hum Mol Genet. 2011 Jan 6. [Epub ahead of print]

Flexible taxonomic assignment of ambiguous sequencing reads.
Clemente JC, Jansson J, Valiente G.
BMC Bioinformatics. 2011 Jan 7;12(1):8.

The SOX2 response program in glioblastoma multiforme: an integrated ChIP-seq, expression microarray, and microRNA analysis.
Fang X, Yoon JG, Li L, Yu W, et al.
BMC Genomics. 2011 Jan 6;12(1):11.

A widespread distribution of genomic CeMyoD binding sites revealed and cross validated by ChIP-chip and ChIP-seq techniques.
Lei H, Fukushige T, Niu W, Sarov M, et al.
PLoS One. 2010 Dec 29;5(12):e15898.

Mutation detection with next-generation resequencing through a mediator genome.
Wurtzel O, Dori-Bachash M, Pietrokovski S, Jurkevitch E, Sorek R.
PLoS One. 2010 Dec 31;5(12):e15628.

Combinatorial analysis and algorithms for quasispecies reconstruction using next-generation sequencing.
Prosperi MC, Prosperi L, Bruselles A, Abbate I, et al.
BMC Bioinformatics. 2011 Jan 5;12(1):5.

Observation and prediction of recurrent human translocations mediated by NAHR between nonhomologous chromosomes.
Ou Z, Stankiewicz P, Xia Z, Breman AM, et al.
Genome Res. 2011 Jan;21(1):33-46.

Gene inactivation and its implications for annotation in the era of personal genomics.
Balasubramanian S, Habegger L, Frankish A, Macarthur DG, et al.
Genes Dev. 2011 Jan 1;25(1):1-10.

NanoCAGE: A high-resolution technique to discover and interrogate cell transcriptomes.
Salimullah M, Mizuho S, Plessy C, Carninci P.
Cold Spring Harb Protoc. 2011 Jan 1;2011:pdb.prot5559.

A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries.
Fisher S, Barry A, Abreu J, Minie B, et al.
Genome Biol. 2011 Jan 4;12(1):R1.

Microbial diversity in saliva of oral squamous cell carcinoma.
Pushalkar S, Mane SP, Ji X, Li Y, et al.
FEMS Immunol Med Microbiol. 2010 Dec 28.

Bar-coded, multiplexed sequencing of targeted DNA regions using the Illumina Genome Analyzer.
Szelinger S, Kurdoglu A, Craig DW.
Methods Mol Biol. 2011;700:89-104.

Somatic mutation profiles of MSI and MSS colorectal cancer identified by whole exome next generation sequencing and bioinformatics analysis.
Timmermann B, Kerick M, Roehr C, Fischer A, et al.
PLoS One. 2010 Dec 22;5(12):e15661.

The utility of next-generation sequencing in the evaluation of the posterior polymorphous corneal dystrophy 1 locus.
Lai IN, Yellore VS, Rayner SA, D'Silva NC, et al.
Mol Vis. 2010 Dec 18;16:2829-38.

Identification of new microRNAs in paired normal and tumor breast tissue suggests a dual role for the ERBB2/Her2 gene.
Persson H, Kvist A, Rego N, Staaf J, et al.
Cancer Res. 2011 Jan 1;71(1):78-86.

An Alport syndrome mutation in mouse Col4a4 identified by whole genome sequencing and bulk segregation rates.
Arnold CN, Xia Y, Lin P, Ross C, et al.
Genetics. 2010 Dec 31. [Epub ahead of print]

Targeted high-throughput sequencing identifies mutations in atlastin-1 as a cause of hereditary sensory neuropathy type I.
Guelly C, Zhu PP, Leonardis L, Papić L, et al.
Am J Hum Genet. 2010 Dec 29. [Epub ahead of print]

An unbiased metagenomic search for infectious agents using monozygotic twins discordant for chronic fatigue.
Sullivan PF, Allander T, Lysholm F, Goh S, et al.
BMC Microbiol. 2011 Jan 2;11(1):2. [Epub ahead of print]

Genome-wide SNP identification by high-throughput sequencing and selective mapping allows sequence assembly positioning using a framework genetic linkage map.
Celton JM, Christoffels A, Sargent DJ, Xu X, Rees DJ.
BMC Biol. 2010 Dec 30;8(1):155.

Detection and reconstruction of tandemly organized de novo copy number variations.
He D, Furlotte N, Eskin E.
BMC Bioinformatics. 2010 Dec 14;11 Suppl 11:S12.

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