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Papers of Note: Jul 12, 2011


Genome sequence and analysis of the tuber crop potato.
The Potato Genome Sequencing Consortium; The Potato Genome Consortium
Nature 2011 Jul 10. [Epub ahead of print]

Egg forensics: An appraisal of DNA sequencing to assist in species identification of illegally smuggled eggs.
Coghlan ML, White NE, Parkinson L, Haile J, et al.
Forensic Sci Int Genet 2011 Jul 6. [Epub ahead of print]

To clone or not to clone: method analysis for retrieving consensus sequences in ancient DNA samples.
Winters M, Barta JL, Monroe C, Kemp BM.
PLoS One 2011;6(6):e21247.

A flexible approach for highly multiplexed candidate gene targeted resequencing.
Natsoulis G, Bell JM, Xu H, Buenrostro JD, et al.
PLoS One 2011;6(6):e21088.

Target region selection is a critical determinant of community fingerprints generated by 16S pyrosequencing.
Kumar PS, Brooker MR, Dowd SE, Camerlengo T.
PLoS One 2011;6(6):e20956.

Maps of open chromatin guide the functional follow-up of genome-wide association signals: application to hematological traits.
Paul DS, Nisbet JP, Yang TP, Meacham S, et al.
PLoS Genet 2011 Jun;7(6):e1002139.

Variant identification in multi-sample pools by Illumina Genome Analyzer sequencing.
Margraf RL, Durtschi JD, Dames S, Pattison DC, et al.
J Biomol Tech 2011 Jul;22(2):74-84.

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Analysis of the DNA sequencing quality and efficiency of the Apollo100 robotic microcycler in a core facility setting.
Logsdon ME, Trounstine MC, Zianni MR.
J Biomol Tech 2011 Jul;22(2):53-9.

Genome-wide analysis reveals conserved and divergent features of Notch1/RBPJ binding in human and murine T-lymphoblastic leukemia cells.
Wang H, Zou J, Zhao B, Johannsen E, et al.
Proc Natl Acad Sci U S A 2011 Jul 7. [Epub ahead of print]

Whole-transcriptome RNAseq analysis from minute amount of total RNA.
Tariq MA, Kim HJ, Jejelowo O, Pourmand N.
Nucleic Acids Res 2011 Jul 6. [Epub ahead of print]

Bisulfite genomic sequencing of DNA from dried blood spot microvolume samples.
Xu H, Zhao Y, Liu Z, Zhu W, et al.
Forensic Sci Int Genet 2011 Jul 5. [Epub ahead of print]

ReadDB provides efficient storage for mapped short reads.
Rolfe PA, Gifford DK.
BMC Bioinformatics 2011 Jul 7;12(1):278.

An integrated ChIP-seq analysis platform with customizable workflows.
Giannopoulou EG, Elemento O.
BMC Bioinformatics 2011 Jul 7;12(1):277.

Genome sequence and global sequence variation map with 5.5 million SNPs in Chinese rhesus macaque.
Fang X, Zhang Y, Zhang R, Yang L, et al.
Genome Biol 2011 Jul 6;12(7):R63.

A comparative analysis of DNA methylation across human embryonic stem cell lines.
Chen PY, Feng S, Joo JW, Jacobsen SE, Pellegrini M.
Genome Biol 2011 Jul 6;12(7):R62.

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Transcription factor AP1 potentiates chromatin accessibility and glucocorticoid receptor binding.
Biddie SC, John S, Sabo PJ, Thurman RE, et al.
Cell 2011 Jul 8;43(1):145-55.

Genome assembly has a major impact on gene content: A comparison of annotation in two Bos Taurus assemblies.
Florea L, Souvorov A, Kalbfleisch TS, Salzberg SL.
PLoS One 2011;6(6):e21400.

Deterministic and stochastic allele specific gene expression in single mouse blastomeres.
Tang F, Barbacioru C, Nordman E, Bao S, et al.
PLoS One 2011;6(6):e21208.

Modeling the conductance and DNA blockade of solid-state nanopores.
Kowalczyk SW, Grosberg AY, Rabin Y, Dekker C.
Nanotechnology 2011 Jul 6;22(31):315101.

Demographic history and rare allele sharing among human populations.
Gravel S, Henn BM, Gutenkunst RN, Indap AR, The 1000 Genomes Project, et al.
Proc Natl Acad Sci U S A 2011 Jul 5. [Epub ahead of print]

Exome-wide DNA capture and next generation sequencing in domestic and wild species.
Cosart T, Beja-Pereira A, Chen S, Ng SB, et al.
BMC Genomics 2011 Jul 5;12(1):347.

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.