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In Print: Last Week's Sequencing-Related Papers of Note: Oct 8, 2013


Metagenomic screening for aromatic compound-responsive transcriptional regulators.
Uchiyama T, Miyazaki K.
PLOS One. 2013 Sep 30;8(9):e75795.

Application of genotyping-by-sequencing on semiconductor sequencing platforms: a comparison of genetic and reference-based marker ordering in barley.
Mascher M, Wu S, Amand PS, Stein N, Poland J.
PLOS One. 2013 Oct 3;8(10):e76925.

Subcellular RNA sequencing reveals broad presence of cytoplasmic intron-sequence retaining transcripts in mouse and rat neurons.
Khaladkar M, Buckley PT, Lee MT, Francis C, et al.
PLOS One. 2013 Oct 3;8(10):e76194.

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position.
Buenrostro JD, Giresi PG, Zaba LC, Chang HY, Greenleaf WJ.
Nat Methods. 2013 Oct 6. [Epub ahead of print]

Haplotype estimation using sequencing reads.
Delaneau O, Howie B, Cox AJ, Zagury JF, Marchini J.
Am J Hum Genet. 2013 Oct 3;93(4):687-696.

AfterParty: turning raw transcriptomes into permanent resources.
Jones M, Blaxter M.
BMC Bioinformatics. 2013 Oct 7;14(1):301.

Assembling single-cell genomes and mini-metagenomes from chimeric MDA products.
Nurk S, Bankevich A, Antipov D, Gurevich AA, et al.
J Comput Biol. 2013 Oct;20(10):714-737.

Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals.
Battle A, Mostafavi S, Zhu X, Potash JB, et al.
Genome Res. 2013 Oct 3. [Epub ahead of print]

DNA sequencing using electrical conductance measurements of a DNA polymerase.
Chen YS, Lee CH, Hung MY, Pan HA, et al.
Nat Nanotechnol. 2013 Oct 4;8(10):781.

InsertionMapper: a pipeline tool for the identification of targeted sequences from multidimensional high throughput sequencing data.
Xiong W, He L, Li Y, Dooner HK, Du C.
BMC Genomics. 2013 Oct 4;14(1):679.

Efficient and accurate whole genome assembly and methylome profiling of E. coli..
Powers JG, Weigman VJ, Shu J, Pufky JM, et al.
BMC Genomics. 2013 Oct 3;14(1):675.

Empirical validation of viral quasispecies assembly algorithms: state-of-the-art and challenges.
Prosperi MC, Yin L, Nolan DJ, Lowe AD, et al.
Sci Rep. 2013 Oct 3;3:2837.

The dynamics of genome replication using deep sequencing.
Müller CA, Hawkins M, Retkute R, Malla S, et al.
Nucleic Acids Res. 2013 Oct 1. [Epub ahead of print]

A comparison of next-generation sequencing and clone-based sequencing in analysis of HBV RT quasispecies heterogeneity.
Gong L, Han Y, Chen L, Liu F, et al.
J Clin Microbiol. 2013 Oct 2. [Epub ahead of print]

Sample size calculation for differential expression analysis of RNA-seq data under Poisson distribution.
Li CI, Su PF, Guo Y, Shyr Y.
Int J Comput Biol Drug Des. 2013;6(4):358-375.

An evaluation of allele frequency estimation accuracy using pooled sequencing data.
Guo Y, Cai Q, Li C, Li J, et al.
Int J Comput Biol Drug Des. 2013;6(4):279-293.

Calculation of Tajima's D and other neutrality test statistics from low depth next-generation sequencing data.
Korneliussen TS, Moltke I, Albrechtsen A, Nielsen R.
BMC Bioinformatics. 2013 Oct 2;14(1):289.

Novel CIC point mutations and an exon-spanning, homozygous deletion identified in oligodendroglial tumors by a comprehensive genomic approach including transcriptome sequencing.
Eisenreich S, Abou-El-Ardat K, Szafranski K, Campos Valenzuela JA, et al.
PLOS One. 2013 Sep 27;8(9):e76623.

The origin of biased sequence depth in sequence-independent nucleic acid amplification and optimization for efficient massive parallel sequencing.
Rosseel T, Van Borm S, Vandenbussche F, Hoffmann B, et al.
PLOS One. 2013 Sep 26;8(9):e76144.

Variant callers for next-generation sequencing data: a comparison study.
Liu X, Han S, Wang Z, Gelernter J, Yang BZ.
PLOS One. 2013 Sep 27;8(9):e75619.

Comparing memory-efficient genome assemblers on stand-alone and cloud infrastructures.
Kleftogiannis D, Kalnis P, Bajic VB.
PLOS One. 2013 Sep 27;8(9):e75505.

Whole-exome sequencing reveals a rapid change in the frequency of rare functional variants in a founding population of humans.
Casals F, Hodgkinson A, Hussin J, Idaghdour Y, et al.
PLOS Genet. 2013 Sep;9(9):e1003815.

Ultra-sensitive sequencing reveals an age-related increase in somatic mitochondrial mutations that are inconsistent with oxidative damage.
Kennedy SR, Salk JJ, Schmitt MW, Loeb LA.
PLOS Genet. 2013 Sep;9(9):e1003794.

Next-generation survey sequencing and the molecular organization of wheat chromosome 6B.
Tanaka T, Kobayashi F, Joshi GP, Onuki R, et al.
DNA Res. 2013 Oct 1. [Epub ahead of print]

Slow DNA transport through nanopores in hafnium oxide membranes.
Larkin J, Henley R, Bell DC, Cohen-Karni T, et al.
ACS Nano. 2013 Oct 1. [Epub ahead of print]

An evaluation of the PacBio RS platform for sequencing and de novo assembly of a chloroplast genome.
Ferrarini M, Moretto M, Ward JA, Urbanovski N, et al.
BMC Genomics. 2013 Oct 1;14(1):670.

Graphene quantum point contact transistor for DNA sensing.
Girdhar A, Sathe C, Schulten K, Leburton JP.
Proc Natl Acad Sci U S A. 2013 Sep 30. [Epub ahead of print]

Comparison of RNA- or LNA-hybrid oligonucleotides in template-switching reactions for high-speed sequencing library preparation.
Harbers M, Kato S, de Hoon M, Hayashizaki Y, et al.
BMC Genomics. 2013 Sep 30;14(1):665.