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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.

The Scan

Positive Framing of Genetic Studies Can Spark Mistrust Among Underrepresented Groups

Researchers in Human Genetics and Genomics Advances report that how researchers describe genomic studies may alienate potential participants.

Small Study of Gene Editing to Treat Sickle Cell Disease

In a Novartis-sponsored study in the New England Journal of Medicine, researchers found that a CRISPR-Cas9-based treatment targeting promoters of genes encoding fetal hemoglobin could reduce disease symptoms.

Gut Microbiome Changes Appear in Infants Before They Develop Eczema, Study Finds

Researchers report in mSystems that infants experienced an enrichment in Clostridium sensu stricto 1 and Finegoldia and a depletion of Bacteroides before developing eczema.

Acute Myeloid Leukemia Treatment Specificity Enhanced With Stem Cell Editing

A study in Nature suggests epitope editing in donor stem cells prior to bone marrow transplants can stave off toxicity when targeting acute myeloid leukemia with immunotherapy.