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Papers of Note: Mar 22, 2011


Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling.
Gu H, Smith ZD, Bock C, Boyle P, et al.
Nat Protoc. 2011 Apr;6(4):468-81.

AnyExpress: Integrated toolkit for analysis of cross-platform gene expression data using a fast interval matching algorithm.
Kim J, Patel K, Jung H, Kuo WP, Ohno-Machado L.
BMC Bioinformatics. 2011 Mar 17;12(1):75.

Improving RNA-seq expression estimates by correcting for fragment bias.
Roberts A, Trapnell C, Donaghey J, Rinn JL, Pachter L.
Genome Biol.2011 Mar 16;12(3):R22.

Sequencing illustrates the transcriptional response of Legionella pneumophila during infection and identifies seventy novel small non-coding RNAs.
Weissenmayer BA, Prendergast JG, Lohan AJ, Loftus BJ.
PLoS One.2011 Mar 3;6(3):e17570.

AGeS: A software system for microbial genome sequence annotation.
Kumar K, Desai V, Cheng L, Khitrov M, et al.
PLoS One.2011 Mar 7;6(3):e17469.

Testing for an unusual distribution of rare variants.
Neale BM, Rivas MA, Voight BF, Altshuler D, et al.
PLoS Genet.2011 Mar;7(3):e1001322.

Fast identification and removal of sequence contamination from genomic and metagenomic datasets.
Schmieder R, Edwards R.
PLoS One.2011 Mar 9;6(3):e17288.

Decoding a substantial set of samples in parallel by massive sequencing.
Neiman M, Lundin S, Savolainen P, Ahmadian A.
PLoS One.2011 Mar 9;6(3):e17785.

Sequence dependence of the binding energy in chaperone-driven polymer translocation through a nanopore.
Abdolvahab RH, Ejtehadi MR, Metzler R.
Phys Rev E Stat Nonlin Soft Matter Phys.2011 Jan;83(1-1):011902

Measuring single-molecule DNA hybridization by active control of DNA in a nanopore.
Gyarfas B, Abu-Shumays R, Wang H, Dunbar WB.
Biophys J.2011 Mar 16;100(6):1509-16.

Transcriptome sequencing and annotation of the microalgae Dunaliella tertiolecta: Pathway description and gene discovery for production of next-generation biofuels.
Rismani-Yazdi H, Haznedaroglu BZ, Bibby K, Peccia J.
BMC Genomics.2011 Mar 14;12(1):148.

The Scan

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.

Team Presents Cattle Genotype-Tissue Expression Atlas

Using RNA sequences representing thousands of cattle samples, researchers looked at relationships between cattle genotype and tissue expression in Nature Genetics.

Researchers Map Recombination in Khoe-San Population

With whole-genome sequences for dozens of individuals from the Nama population, researchers saw in Genome Biology fine-scale recombination patterns that clustered outside of other populations.

Myotonic Dystrophy Repeat Detected in Family Genome Sequencing Analysis

While sequencing individuals from a multi-generation family, researchers identified a myotonic dystrophy type 2-related short tandem repeat in the European Journal of Human Genetics.