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In Print: Last Week's Sequencing-Related Papers of Note: Jul 10, 2012

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On the synthesis of DNA error correcting codes.
Ashlock D, Houghten SK, Brown JA, Orth J.
Biosystems. 2012 Jul 5. [Epub ahead of print]


Technical and biological variance structure in mRNA-seq data: life in the real world.
Oberg AL, Bot BM, Grill DE, Poland GA, Therneau TM.
BMC Genomics. 2012 Jul 7;13(1):304.


Transcriptome analysis of the Octopus vulgaris central nervous system.
Zhang X, Mao Y, Huang Z, Qu M, et al.
PLoS One. 2012;7(6):e40320.


Use of mutagenesis, genetic mapping and next generation transcriptomics to investigate insecticide resistance mechanisms.
Kalajdzic P, Oehler S, Reczko M, Pavlidi N, et al.
PLoS One.2012;7(6):e40296.


An improvement of shotgun proteomics analysis by adding next-generation sequencing transcriptome data in orange.
Song J, Sun R, Li D, Tan F, et al.
PLoS One.2012;7(6):e39494.


A map of the cis-regulatory sequences in the mouse genome.
Shen Y, Yue F, McCleary DF, Ye Z, et al.
Nature.2012 Jul 1. [Epub ahead of print]


Control of DNA capture by nanofluidic transistors.
Paik KH, Liu Y, Tabard-Cossa V, Waugh MJ, et al.
ACS Nano.2012 Jul 4. [Epub ahead of print]


FusionFinder: A software tool to identify expressed gene fusion candidates from RNA-seq data.
Francis RW, Thompson-Wicking K, Carter KW, Anderson D, et al.
PLoS One.2012;7(6):e39987.


Reconstruction of ribosomal RNA genes from metagenomic data.
Fan L, McElroy K, Thomas T.
PLoS One.2012;7(6):e39948.


Biases during DNA extraction of activated sludge samples revealed by high throughput sequencing.
Guo F, Zhang T.
Appl Microbiol Biotechnol.2012 Jul 4. [Epub ahead of print]


Detection of rare genomic variants from pooled sequencing using SPLINTER.
Vallania F, Ramos E, Cresci S, Mitra RD, Druley TE.
J Vis Exp.2012 Jun 23;(64). pii: 3943.


A tool kit for quantifying eukaryotic rRNA gene sequences from human microbiome samples.
Dollive S, Peterfreund GL, Sherrill-Mix S, Bittinger K, et al.
Genome Biol.2012 Jul 3;13(7):R60.


The genome of flax (Linum usitatissimum) assembled de novo from short shotgun sequence reads.
Wang Z, Hobson N, Galindo L, Zhu S, et al.
Plant J.2012 Jul 3. [Epub ahead of print]


The genome of melon (Cucumis melo L.) .
Garcia-Mas J, Benjak A, Sanseverino W, Bourgeois M, et al.
Proc Natl Acad Sci U S A.2012 Jul 2. [Epub ahead of print]


An in-depth map of polyadenylation sites in cancer.
Lin Y, Li Z, Ozsolak F, Kim SW, et al.
Nucleic Acids Res.2012 Jun 29. [Epub ahead of print]


forestSV: structural variant discovery through statistical learning.
Michaelson JJ, Sebat J.
Nat Methods.2012 Jul 1. [Epub ahead of print]


Unraveling cell type-specific and reprogrammable human replication origin signatures associated with G-quadruplex consensus motifs.
Besnard E, Babled A, Lapasset L, Milhavet O, et al.
Nat Struct Mol Biol.2012 Jul 1. [Epub ahead of print]


Hybrid error correction and de novo assembly of single-molecule sequencing reads.
Koren S, Schatz MC, Walenz BP, Martin J, et al.
Nat Biotechnol.2012 Jul 1. [Epub ahead of print]
(see our coverage of this work, IS 1/24/2012.)


A hybrid approach for the automated finishing of bacterial genomes.
Bashir A, Klammer AA, Robins WP, Chin CS, et al.
Nat Biotechnol.2012 Jul 1. [Epub ahead of print]


GenomeGems: evaluation of genetic variability from deep sequencing data.
Ben-Zvi S, Givati A, Shomron N.
BMC Res Notes.2012 Jul 2;5(1):338.


AdapterRemoval: easy cleaning of next generation sequencing reads.
Lindgreen S.
BMC Res Notes.2012 Jul 2;5(1):337.


Single nucleotide polymorphism discovery from wheat next-generation sequence data.
Lai K, Duran C, Berkman PJ, Lorenc MT, et al.
Plant Biotechnol J.2012 Jul 3. [Epub ahead of print]


TAPDANCE: an automated tool to identify and annotate transposon insertion CISs and associations between CISs from next generation sequence data.
Sarver AL, Erdman J, Starr T, Largaespada DA, Silverstein KA.
BMC Bioinformatics.2012 Jun 29;13(1):154.


A systematic comparison and evaluation of high density exon arrays and RNA-seq technology used to unravel the peripheral blood transcriptome of sickle cell disease.
Raghavachari N, Barb J, Yang Y, Liu P, et al.
BMC Med Genomics.2012 Jun 29;5(1):28.
(See our coverage of this paper here.)


Whole-genome sequencing and analysis of the Malaysian cynomolgus macaque (Macaca fascicularis) genome.
Higashino A, Sakate R, Kameoka Y, Takahashi I, et al.
Genome Biol. 2012 Jul 2;13(7):R58.


Molecular dynamics study of MspA arginine-mutants predicts slow DNA translocations and ion current blockades indicative of DNA sequence.
Bhattacharya S, Derrington IM, Pavlenok M, Niederweis M, et al.
ACS Nano. 2012 Jul 2. [Epub ahead of print]

The Scan

Study Links Evolution of Longevity, Social Organization in Mammals

With the help of comparative phylogenetics and transcriptomics, researchers in Nature Communications see ties between lifespan and social organization in mammals.

Tumor Microenvironment Immune Score Provides Immunotherapy Response, Prognostic Insights

Using multiple in situ analyses and RNA sequence data, researchers in eBioMedicine have developed a score associated with immunotherapy response or survival.

CRISPR-Based Method for Finding Cancer-Associated Exosomal MicroRNAs in Blood

A team from China presents in ACS Sensors a liposome-mediated membrane fusion strategy for detecting miRNAs carried in exosomes in the blood with a CRISPR-mediated reporter system.

Drug Response Variants May Be Distinct in Somatic, Germline Samples

Based on variants from across 21 drug response genes, researchers in The Pharmacogenomics Journal suspect that tumor-only DNA sequences may miss drug response clues found in the germline.