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In Print: Last Week's Sequencing-Related Papers of Note: Feb 7, 2012


DNase I sensitivity QTLs are a major determinant of human expression variation.
Degner JF, Pai AA, Pique-Regi R, Veyrieras JB, et al.
Nature. 2012 Feb 5. [Epub ahead of print]

Picking ChIP-seq peak detectors for analyzing chromatin modification experiments.
Micsinai M, Parisi F, Strino F, Asp P, et al.
Nucleic Acids Res. 2012 Feb 3. [Epub ahead of print]

Library-free methylation sequencing with bisulfite padlock probes.
Diep D, Plongthongkum N, Gore A, Fung HL, et al.
Nat Methods. 2012 Feb 5. [Epub ahead of print]

Breakpointer: using local mapping artifacts to support sequence breakpoint discovery from single-end reads.
Sun R, Love MI, Zemojtel T, Emde AK, et al.
Bioinformatics. 2012 Feb 1. [Epub ahead of print]

ArchTEx: accurate extraction and visualization of next-generation sequence data.
Lai WK, Bard JE, Buck MJ.
Bioinformatics. 2012 Feb 2. [Epub ahead of print]

Hadoop-BAM: Directly manipulating next generation sequencing data in the cloud.
Niemenmaa M, Kallio A, Schumacher A, Klemelä P, et al.
Bioinformatics. 2012 Feb 2. [Epub ahead of print]

cn.MOPS: mixture of Poissons for discovering copy number variations in next-generation sequencing data with a low false discovery rate.
Klambauer G, Schwarzbauer K, Mayr A, Clevert DA, et al.
Nucleic Acids Res. 2012 Feb 1. [Epub ahead of print]

A comparative transcriptomic study of an allotetraploid and its diploid progenitors illustrates the unique advantages and challenges of RNA-seq in plant species.
Ilut DC, Coate JE, Luciano AK, Owens TG, et al.
Am J Bot. 2012 Feb 1. [Epub ahead of print]

Coverage-based consensus calling (CbCC) of short sequence reads and comparison of CbCC results to identify SNPs in chickpea (Cicer arietinum; Fabaceae), a crop species without a reference genome.
Azam S, Thakur V, Ruperao P, Shah T, et al.
Am J Bot. 2012 Feb 1. [Epub ahead of print]

Untangling genomes from metagenomes: revealing an uncultured class of marine Euryarchaeota.
Iverson V, Morris RM, Frazar CD, Berthiaume CT, et al.
Science. 2012 Feb 3;335(6068):587-90.

Copy number variation of individual cattle genomes using next-generation sequencing.
Bickhart DM, Hou Y, Schroeder SG, Alkan C, et al.
Genome Res. 2012 Feb 2. [Epub ahead of print]

MetaCluster 4.0: A novel binning algorithm for NGS reads and huge number of species.
Wang Y, Leung HC, Yiu SM, Chin FY.
J Comput Biol. 2012 Feb;19(2):241-9.

Automated workflow for preparation of cDNA for cap analysis of gene expression on a single molecule sequencer.
Itoh M, Kojima M, Nagao-Sato S, Saijo E, et al.
PLoS One. 2012;7(1):e30809.

An on-bead tailing/ligation approach for sequencing resin-bound RNA libraries.
Wiesmayr A, Fournier P, Jäschke A.
Nucleic Acids Res. 2012 Jan 31. [Epub ahead of print]

Enhanced discrimination of DNA molecules in nanofluidic channels through multiple measurements.
Sen YH, Jain T, Aguilar CA, Karnik R.
Lab Chip. 2012 Feb 2. [Epub ahead of print]

SpliceGrapher: Detecting patterns of alternative splicing from RNA-seq data in the context of gene models and EST data.
Rogers MF, Thomas J, Reddy AS, Ben-Hur A.
Genome Biol. 2012 Jan 31;13(1):R4.

Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes.
St John JA, Braun EL, Isberg SR, Miles LG, et al.
Genome Biol. 2012 Jan 31;13(1):415.

Fast and controllable fabrication of suspended graphene nanopore devices.
Liu S, Zhao Q, Xu J, Yan K, et al.
Nanotechnology. 2012 Mar 2;23(8):085301.

A powerful method for transcriptional profiling of specific cell types in eukaryotes: laser-assisted microdissection and RNA sequencing.
Schmid MW, Schmidt A, Klostermeier UC, Barann M, et al.
PLoS One. 2012;7(1):e29685.

Sequencing of pooled DNA samples (Pool-seq) uncovers complex dynamics of transposable element insertions in Drosophila melanogaster.
Kofler R, Betancourt AJ, Schlötterer C.
PLoS Genet. 2012 Jan;8(1):e1002487.

Quality and quantity of data recovered from massively parallel sequencing: examples in Asparagales and Poaceae.
Steele PR, Hertweck KL, Mayfield D, McKain MR, et al.
Am J Bot. 2012 Jan 30. [Epub ahead of print]

Assessing the enrichment performance in targeted resequencing experiments.
Frommolt P, Abdallah AT, Altmüller J, Motameny S, et al.
Hum Mutat. 2012 Jan 30. [Epub ahead of print]

miRDeepFinder: a miRNA analysis tool for deep sequencing of plant small RNAs.
Xie F, Xiao P, Chen D, Xu L, Zhang B.
Plant Mol Biol. 2012 Jan 31. [Epub ahead of print]

DNA methylome analysis using short bisulfite sequencing data.
Krueger F, Kreck B, Franke A, Andrews SR.
Nat Methods. 2012 Jan 30;9(2):145-51.

A cost-effective and universal strategy for complete prokaryotic genomic sequencing proposed by computer simulation.
Jiang J, Li J, Kwan HS, Au CH, et al.
BMC Res Notes. 2012 Jan 31;5(1):80.

BIGpre: A quality assessment package for next-generation sequencing data.
Zhang T, Luo Y, Liu K, Pan L, et al.
Genomics Proteomics Bioinformatics. 2011 Dec;9(6):238-44.

Whole genome profiling provides a robust framework for physical mapping and sequencing in the highly complex and repetitive wheat genome.
Philippe R, Choulet F, Paux E, van Oeveren J, et al.
BMC Genomics. 2012 Jan 30;13(1):47.

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.