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In Print: Last Week's Sequencing-Related Papers of Note: May 1, 2012


Assessing the accuracy and power of population genetic inference from low-pass next-generation sequencing data.
Crawford JE, Lazzaro BP.
Front Genet. 2012;3:66. Epub 2012 Apr 24.

Comparison of large-insert, small-insert and pyrosequencing libraries for metagenomic analysis.
Danhorn T, Young CR, Delong EF.
ISME J. 2012 Apr 26. [Epub ahead of print]

A generalized linear model for peak calling in ChIP-seq data.
Xu J, Zhang Y.
J Comput Biol. 2012 Apr 25. [Epub ahead of print]

RNA-SeQC: RNA-seq metrics for quality control and process optimization.
Deluca DS, Levin JZ, Sivachenko A, Fennell T, et al.
Bioinformatics. 2012 Apr 25. [Epub ahead of print]

Quantitative sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution.
Booth MJ, Branco MR, Ficz G, Oxley D, et al.
Science. 2012 Apr 26. [Epub ahead of print]

Enabling proteomic studies with RNA-seq: The proteome of tomato pollen as a test case.
Lopez-Casado G, Covey PA, Bedinger PA, Mueller LA, et al.
Proteomics. 2012 Mar;12(6):761-74.

Cell type-specific chromatin immunoprecipitation from multicellular complex samples using BiTS-ChIP.
Bonn S, Zinzen RP, Perez-Gonzalez A, Riddell A, et al.
Nat Protoc. 2012 Apr 26;7(5):978-94.

TBC: A clustering algorithm based on prokaryotic taxonomy.
Lee JH, Yi H, Jeon YS, Won S, Chun J.
J Microbiol. 2012 Apr;50(2):181-5.

Towards accurate detection and genotyping of expressed variants from whole transcriptome sequencing data.
Duitama J, Srivastava PK, Măndoiu II.
BMC Genomics. 2012 Apr 12;13 Suppl 2:S6.

Haplotype and minimum-chimerism consensus determination using short sequence data.
O'Neil ST, Emrich SJ.
BMC Genomics. 2012 Apr 12;13 Suppl 2:S4.

Fast, accurate error-correction of amplicon pyrosequences using Acacia.
Bragg L, Stone G, Imelfort M, Hugenholtz P, Tyson GW.
Nat Methods. 2012 Apr 27;9(5):425-6.

Background mutations in parental cells account for most of the genetic heterogeneity of induced pluripotent stem cells.
Young MA, Larson DE, Sun CW, George DR, et al.
Cell Stem Cell. 2012 Apr 26. [Epub ahead of print]

Concentration polarization in translocation of DNA through nanopores and nanochannels.
Das S, Dubsky P, van den Berg A, Eijkel JC.
Phys Rev Lett. 2012 Mar 30;108(13):138101.

Reference-free transcriptome assembly in non-model animals from next-generation sequencing data.
Cahais V, Gayral P, Tsagkogeorga G, Melo-Ferreira J, et al.
Mol Ecol Resour. 2012 Apr 30. [Epub ahead of print]

Evaluation of normalization methods in mammalian microRNA-seq data.
Garmire LX, Subramaniam S.
RNA. 2012 Apr 24. [Epub ahead of print]

Genome-wide identification and characterization of replication origins by deep sequencing.
Xu J, Yanagisawa Y, Tsankov AM, Hart C, et al.
Genome Biol. 2012 Apr 24;13(4):R27.

Limited genetic diversity preceded extinction of the Tasmanian tiger.
Menzies BR, Renfree MB, Heider T, Mayer F, et al.
PLoS One. 2012;7(4):e35433.

Altered subcellular localization of transcription factor TEAD4 regulates first mammalian cell lineage commitment.
Home P, Saha B, Ray S, Dutta D, et al.
Proc Natl Acad Sci U S A. 2012 Apr 23. [Epub ahead of print]

Whole-genome resequencing of two elite sires for the detection of haplotypes under selection in dairy cattle.
Larkin DM, Daetwyler HD, Hernandez AG, Wright CL, et al.
Proc Natl Acad Sci U S A. 2012 Apr 23. [Epub ahead of print]

Analysis of the methylome of human embryonic stem cells employing methylated DNA immunoprecipitation coupled to next-generation sequencing.
Grimm C, Adjaye J.
Methods Mol Biol. 2012;873:281-95.

Passive and electrically actuated solid-state nanopores for sensing and manipulating DNA.
Jiang Z, Mihovilovic M, Teich E, Stein D.
Methods Mol Biol. 2012;870:241-64.

Measuring single-wall carbon nanotubes with solid-state nanopores.
Hall AR, Keegstra JM, Duch MC, Hersam MC, Dekker C.
Methods Mol Biol. 2012;870:227-39.

Graphene nanopore devices for DNA sensing.
Merchant CA, Drndić M.
Methods Mol Biol. 2012;870:211-26.

Polymer translocation through an electrically tunable nanopore in a multilayered semiconductor membrane.
Melnikov DV, Nikolaev A, Leburton JP, Gracheva ME.
Methods Mol Biol. 2012;870:187-207.

Optimization of the molecular dynamics method for simulations of DNA and ion transport through biological nanopores.
Wells DB, Bhattacharya S, Carr R, Maffeo C, et al.
Methods Mol Biol. 2012;870:165-86.

DNA characterization by transverse electrical current in a nanochannel.
Di Ventra M, Krems M, Wilson J, Pershin YV.
Methods Mol Biol. 2012;870:149-63.

Analyzing single DNA molecules by nanopore translocation.
Steinbock LJ, Keyser UF.
Methods Mol Biol. 2012;870:135-45.

Optical tweezers for mechanical control over DNA in a nanopore.
Keyser UF.
Methods Mol Biol. 2012;870:115-34.

DNA sequencing by nanopore-induced photon emission.
Singer A, McNally B, Torre RD, Meller A.
Methods Mol Biol. 2012;870:99-114.

DNA characterization with ion beam-sculpted silicon nitride nanopores.
Rollings RC, McNabb DS, Li J.
Methods Mol Biol. 2012;870:79-97.

DNA unzipping and protein unfolding using nanopores.
Merstorf C, Cressiot B, Pastoriza-Gallego M, Oukhaled AG, et al.
Methods Mol Biol. 2012;870:55-75.

Measurements of DNA immobilized in the alpha-hemolysin nanopore.
Purnell R, Schmidt J.
Methods Mol Biol. 2012;870:39-53.

The Scan

Researchers Compare WGS, Exome Sequencing-Based Mendelian Disease Diagnosis

Investigators find a diagnostic edge for whole-genome sequencing, while highlighting the cost advantages and improving diagnostic rate of exome sequencing in EJHG.

Researchers Retrace Key Mutations in Reassorted H1N1 Swine Flu Virus With Avian-Like Features

Mutations in the acidic polymerase-coding gene boost the pathogenicity and transmissibility of Eurasian avian-like H1N1 swine influenza viruses, a PNAS paper finds.

Genome Sequences Reveal Evolutionary History of South America's Canids

An analysis in PNAS of South American canid species' genomes offers a look at their evolutionary history, as well as their relationships and adaptations.

Lung Cancer Response to Checkpoint Inhibitors Reflected in Circulating Tumor DNA

In non-small cell lung cancer patients, researchers find in JCO Precision Oncology that survival benefits after immune checkpoint blockade coincide with a dip in ctDNA levels.