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Papers of Note: May 24, 2011


Determinants of nucleosome organization in primary human cells.
Valouev A, Johnson SM, Boyd SD, Smith CL, et al.
Nature. 2011 May 22. [Epub ahead of print]

Identification of factors required for meristem function in Arabidopsis using a novel next generation sequencing fast forward genetics approach.
Mokry M, Nijman IJ, van Dijken A, Benjamins R, et al.
BMC Genomics. 2011 May 20;12(1):256.

CLOTU: An online pipeline for processing and clustering of 454 amplicon reads into OTUs followed by taxonomic annotation.
Kumar S, Carlsen T, Mevik BH, Enger P, et al.
BMC Bioinformatics. 2011 May 20;12(1):182.

Isolation and analysis of high quality nuclear DNA with reduced organellar DNA for plant genome sequencing and resequencing.
Lutz KA, Wang W, Zdepski A, Michael TP.
BMC Biotechnol. 2011 May 20;11(1):54.

The sensitivity of massively parallel sequencing for detecting candidate infectious agents associated with human tissue.
Moore RA, Warren RL, Freeman JD, Gustavsen JA, et al.
PLoS One. 2011;6(5):e19838. Epub 2011 May 13.

Theoretical and experimental study of nanopore drilling by a focused electron beam in transmission electron microscopy.
Kim HM, Lee MH, Kim KB.
Nanotechnology. 2011 May 20;22(27):275303.

Electrochemical protection of thin film electrodes in solid state nanopores.
Harrer S, Waggoner PS, Luan B, Afzali-Ardakani A, Goldfarb DL, et al.
Nanotechnology. 2011 May 20;22(27):275304.

Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans.
Muegge BD, Kuczynski J, Knights D, Clemente JC, et al.
Science. 2011 May 20;332(6032):970-4.

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Inference of site frequency spectra from high-throughput sequence data: quantification of selection on nonsynonymous and synonymous sites in humans.
Keightley PD, Halligan DL.
Genetics. 2011 May 19. [Epub ahead of print]

Unamplified cap analysis of gene expression on a single-molecule sequencer.
Kanamori-Katayama M, Itoh M, Kawaji H, Lassmann T, et al.
Genome Res. 2011 May 19. [Epub ahead of print]

GenPlay, a multi-purpose genome analyzer and browser.
Lajugie J, Bouhassira E.
Bioinformatics. 2011 May 19. [Epub ahead of print]

Analysis of genomic variation in non-coding elements using population-scale sequencing data from the 1000 Genomes Project.
Mu XJ, Lu ZJ, Kong Y, Lam HY, Gerstein MB.
Nucleic Acids Res. 2011 May 19. [Epub ahead of print]

EMIRGE: Reconstruction of full length ribosomal genes from microbial community short read sequencing data.
Miller CS, Baker BJ, Thomas BC, Singer SW, Banfield JF.
Genome Biol. 2011 May 19;12(5):R44.

FusionMap: detecting fusion genes from next-generation sequencing data at base-pair resolution.
Ge H, Liu K, Juan T, Fang F, et al.
Bioinformatics. 2011 May 18. [Epub ahead of print]

454 sequencing of pooled BAC clones on chromosome 3H of barley.
Sato K, Motoi Y, Yamaji N, Yoshida H.
BMC Genomics. 2011 May 19;12(1):246.

Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing.
Gilles A, Meglecz E, Pech N, Ferreira S, et al.
BMC Genomics. 2011 May 19;12(1):245.

Genome of Herbaspirillum seropedicae strain SmR1, a specialized diazotrophic endophyte of tropical grasses.
Pedrosa FO, Monteiro RA, Wassem R, Cruz LM, et al.
PLoS Genet. 2011 May;7(5):e1002064. Epub 2011 May 12.

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Large scale library generation for high throughput sequencing.
Borgström E, Lundin S, Lundeberg J.
PLoS One. 2011 Apr 27;6(4):e19119.

Detection and quantification of rare mutations with massively parallel sequencing.
Kinde I, Wu J, Papadopoulos N, Kinzler KW, Vogelstein B.
Proc Natl Acad Sci U S A. 2011 May 17. [Epub ahead of print]

Taxonomic classification of metagenomic shotgun sequences with CARMA3.
Gerlach W, Stoye J.
Nucleic Acids Res. 2011 May 17. [Epub ahead of print]

Sensitive and fast mapping of di-base encoded reads.
Hormozdiari F, Hach F, Sahinalp SC, Eichler EE, Alkan C.
Bioinformatics. 2011 May 17. [Epub ahead of print]

Sequence-specific error profile of Illumina sequencers.
Nakamura K, Oshima T, Morimoto T, Ikeda S, et al.
Nucleic Acids Res. 2011 May 16. [Epub ahead of print]

HapEdit: an accuracy assessment viewer for haplotype assembly using massively parallel DNA-sequencing technologies.
Kim JH, Kim WC, Li LM, Park S.
Nucleic Acids Res. 2011 May 16. [Epub ahead of print]

High-quality genome sequence of Pichia pastoris CBS7435.
Küberl A, Schneider J, Thallinger GG, Anderl I, et al.
Biotechnol. 2011 May 6. [Epub ahead of print]

Observations on novel splice junctions from RNA sequencing data.
Wang L, Wang X, Wang X, Liang Y, Zhang X.
Biochem Biophys Res Commun. 2011 May 7. [Epub ahead of print]

NSMAP: A method for spliced isoforms identification and quantification from RNA-seq.
Xia Z, Wen J, Chang CC, Zhou X.
BMC Bioinformatics. 2011 May 16;12(1):162.

RAPSearch: a fast protein similarity search tool for short reads.
Ye Y, Choi JH, Tang H.
BMC Bioinformatics. 2011 May 15;12(1):159.

Translocation of single-wall carbon nanotubes through solid-state nanopores.
Hall AR, Keegstra JM, Duch MC, Hersam MC, Dekker C.
Nano Lett. 2011 May 16. [Epub ahead of print]

The Scan

Genome Sequences Reveal Range Mutations in Induced Pluripotent Stem Cells

Researchers in Nature Genetics detect somatic mutation variation across iPSCs generated from blood or skin fibroblast cell sources, along with selection for BCOR gene mutations.

Researchers Reprogram Plant Roots With Synthetic Genetic Circuit Strategy

Root gene expression was altered with the help of genetic circuits built around a series of synthetic transcriptional regulators in the Nicotiana benthamiana plant in a Science paper.

Infectious Disease Tracking Study Compares Genome Sequencing Approaches

Researchers in BMC Genomics see advantages for capture-based Illumina sequencing and amplicon-based sequencing on the Nanopore instrument, depending on the situation or samples available.

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.