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In Print: Last Week's Sequencing-Related Papers of Note: Mar 19, 2013


Analysis of metagenomic data containing high biodiversity levels.
Valverde JR, Mellado RP
PLoS One. 2013;8(3):e58118.

Genome structure and metabolic features in the red seaweed Chondrus crispus shed light on evolution of the Archaeplastida.
Collén J, Porcel B, Carré W, Ball SG, et al.
Proc Natl Acad Sci U S A. 2013 Mar 15. [Epub ahead of print]

Next-generation museomics disentangles one of the largest primate radiations.
Guschanski K, Krause J, Sawyer S, Valente LM, et al.
Syst Biol. 2013 Mar 16. [Epub ahead of print]

Nucleotide-resolution DNA double-strand break mapping by next-generation sequencing.
Crosetto N, Mitra A, Silva MJ, Bienko M, et al.
Nat Methods. 2013 Mar 17. [Epub ahead of print]

Integrated detection of both 5-mC and 5-hmC by high-throughput tag sequencing technology highlights methylation reprogramming of bivalent genes during cellular differentiation.
Xia Y, Wang J, Luo H, Gao Z, et al.
Epigenetics. 2013 Mar 15;8(4).

A combined strategy involving Sanger and 454 pyrosequencing increases genomic resources to aid in the management of reproduction, disease control and genetic selection in the turbot (Scophthalmus maximus) .
Ribas L, Pardo BG, Fernández C, Alvarez-Diós JA, et al.
BMC Genomics. 2013 Mar 15;14(1):180.

A comparison of methods for differential expression analysis of RNA-seq data.
Soneson C, Delorenzi M.
BMC Bioinformatics. 2013 Mar 9;14(1):91.

Deep sequencing for de novo construction of a marine fish (Sparus aurata) transcriptome database with a large coverage of protein-coding transcripts.
Calduch-Giner JA, Bermejo-Nogales A, Benedito-Palos L, Estensoro I, et al.
BMC Genomics. 2013 Mar 15;14(1):178.

Population-genomic variation within RNA viruses of the Western honey bee, Apis mellifera, inferred from deep sequencing.
Cornman RS, Boncristiani H, Dainat B, Chen Y, et al.
BMC Genomics. 2013 Mar 7;14:154.

Determination of dosage compensation of the mammalian X chromosome by RNA-seq is dependent on analytical approach.
Jue NK, Murphy MB, Kasowitz SD, Qureshi SM, et al.
BMC Genomics. 2013 Mar 6;14(1):150.

De novo assembly and characterization of Camelina sativa transcriptome by paired-end sequencing.
Liang C, Liu X, Yiu SM, Lim BL.
BMC Genomics. 2013 Mar 5;14(1):146.

Comparative genomics of parasitic silkworm microsporidia reveal an association between genome expansion and host adaptation.
Pan G, Xu J, Li T, Xia Q, et al.
BMC Genomics. 2013 Mar 16;14(1):186.

A comparison across non-model animals suggests an optimal sequencing depth for de novo transcriptome assembly.
Francis WR, Christianson LM, Kiko R, Powers ML, et al.
BMC Genomics. 2013 Mar 12;14(1):167.

Nearly finished genomes produced using gel microdroplet culturing reveal substantial intraspecies genomic diversity within the human microbiome.
Fitzsimons MS, Novotny M, Lo CC, Dichosa AE, et al.
Genome Res. 2013 Mar 14. [Epub ahead of print]

BRANCH: boosting RNA-seq assemblies with partial or related genomic sequences.
Bao E, Jiang T, Girke T.
Bioinformatics. 2013 Mar 14. [Epub ahead of print]

Single-stranded DNA library preparation for the sequencing of ancient or damaged DNA.
Gansauge MT, Meyer M.
Nat Protoc. 2013 Mar 14;8(4):737-748.

Expression of mRNA transcripts encoding membrane transporters detected with whole transcriptome sequencing of human brain and liver.
Webb A, Papp AC, Sanford JC, Huang K, et al.
Pharmacogenet Genomics. 2013 Mar 12. [Epub ahead of print]

A draft genome sequence of the pulse crop chickpea (Cicer arietinum L.).
Jain M, Misra G, Patel RK, Priya P, et al.
Plant J. 2013 Mar 12. [Epub ahead of print]

Degradome sequencing reveals an endogenous microRNA target in C. elegans.
Park JH, Ahn S, Kim S, Lee J, et al.
FEBS Lett. 2013 Feb 25. [Epub ahead of print]

DNA manipulation and separation in sub-lithographic scale nanowire array.
Yasui T, Rahong S, Motoyama K, Yanagida T, et al.
ACS Nano. 2013 Mar 13. [Epub ahead of print]

Dandruff is associated with disequilibrium in the proportion of the major bacterial and fungal populations colonizing the scalp.
Clavaud C, Jourdain R, Bar-Hen A, Tichit M, et al.
PLoS One. 2013;8(3):e58203.

Targeted genome enrichment for efficient purification of endosymbiont DNA from host DNA.
Geniez S, Foster JM, Kumar S, Moumen B, et al.
Symbiosis. 2012 Dec;58(1-3):201-207.

Fragment Merger: an online tool to merge overlapping long sequence fragments.
Bell TG, Kramvis A.
Viruses. 2013 Mar 12;5(3):824-833.

When is a microbial culture "pure"? Persistent cryptic contaminant escapes detection even with deep genome sequencing.
Shrestha PM, Nevin KP, Shrestha M, Lovley DR.
MBio. 2013 Mar 12;4(2).

Whole-genome sequencing of Oryza brachyantha reveals mechanisms underlying Oryza genome evolution.
Chen J, Huang Q, Gao D, Wang J, et al.
Nat Commun. 2013 Mar 12;4:1595.

Using Illumina next-generation sequencing technologies to sequence multigene families in de novo species.
Hughes GM, Gang L, Murphy WJ, Higgins DG, Teeling EC.
Mol Ecol Resour. 2013 Mar 9. [Epub ahead of print]

Integrated view of genome structure and sequence of a single DNA molecule in a nanofluidic device.
Marie R, Pedersen JN, Bauer DL, Rasmussen KH, et al.
Proc Natl Acad Sci U S A. 2013 Mar 11. [Epub ahead of print]

Galaxy LIMS for next generation sequencing.
Scholtalbers J, Rößler J, Sorn P, de Graaf J, et al.
Bioinformatics. 2013 Mar 11. [Epub ahead of print]

The origin, evolution and functional impact of short insertion-deletion variants identified in 179 human genomes.
Montgomery SB, Goode D, Kvikstad E, Albers CA, et al.
Genome Res. 2013 Mar 11. [Epub ahead of print]