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Recent Sequencing-Related Papers of Note: Jul 29, 2014


JAGuaR: Junction Alignments to Genome for RNA-Seq Reads.

Butterfield YS, Kreitzman M, Thiessen N, Corbett RD, Li Y, et al.
PLoS One. 2014 Jul 25;9(7):e102398.

Appearances Can Be Deceptive: Revealing a Hidden Viral Infection with Deep Sequencing in a Plant Quarantine Context.

Candresse T, Filloux D, Muhire B, Julian C, Galzi S, Fort G, et al.
PLoS One. 2014 Jul 25;9(7):e102945.

Transcriptome sequencing of different narrow-leafed lupin tissue types provides a comprehensive uni-gene assembly and extensive gene-based molecular markers.

Kamphuis LG, Hane JK, Nelson MN, Gao L, Atkins CA, Singh KB.
Plant Biotechnol J. 2014 Jul 24.

Annotation of the zebrafish genome through an integrated transcriptomic and proteomic analysis.

Kelkar DS, Provost E, Chaerkady R, Muthusamy B, Manda SS, et al.
Mol Cell Proteomics. 2014 Jul 24. pii: mcp.M114.038299.

A New Dataset of Spermatogenic vs. Oogenic Transcriptomes in the Nematode Caenorhabditis elegans.

Ortiz MA, Noble D, Sorokin EP, Kimble J.
G3 (Bethesda). 2014 Jul 24.

Detection of runs of homozygosity from whole exome sequencing data: state of the art and perspectives for clinical, population and epidemiological studies.

Pippucci T, Magi A, Gialluisi A, Romeo G.
Hum Hered. 2014;77(1-4):63-72.

TITAN: Inference of copy number architectures in clonal cell populations from tumor whole genome sequence data.

Ha G, Roth A, Khattra J, Ho J, Yap D, Prentice LM, Melnyk N, et al.
Genome Res. 2014 Jul 24.

Draft Genome Sequence of the Multidrug-Resistant Clinical Isolate Dermabacter hominis 1368.

Albersmeier A, Bomholt C, Glaub A, Rückert C, Soriano F, et al.
Genome Announc. 2014 Jul 24;2(4).

Genome Sequence of a Newly Isolated Nicotine-Degrading Bacterium, Ochrobactrum sp. SJY1.

Yu H, Li Y, Tang H, Xu P.
Genome Announc. 2014 Jul 24;2(4)

Genome Sequences of Cupriavidus metallidurans Strains NA1, NA4, and NE12, Isolated from Space Equipment.

Monsieurs P, Mijnendonckx K, Provoost A, Venkateswaran K, et al.
Genome Announc. 2014 Jul 24;2(4).

Characterization of the Whole-Genome Sequence of a Beak and Feather Disease Virus Isolate from a Mallee Ringneck Parrot (Barnardius zonarius barnardi).

Das S, Sarker S, Forwood JK, Ghorashi SA, Raidal SR.
Genome Announc. 2014 Jul 24;2(4).

RNA-seq of the aging brain in the short-lived fish N. furzeri - conserved pathways and novel genes associated with neurogenesis.

Baumgart M, Groth M, Priebe S, Savino A, Testa G, Dix A, et al.
Aging Cell. 2014 Jul 25.

The Expanded Diversity of Methylophilaceae from Lake Washington through Cultivation and Genomic Sequencing of Novel Ecotypes.

Beck DA, McTaggart TL, Setboonsarng U, Vorobev A, et al.
PLoS One. 2014 Jul 24;9(7):e102458.

A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes.

Dutilh BE, Cassman N, McNair K, Sanchez SE, Silva GG, Boling L, et al.
Nat Commun. 2014 Jul 24;5:4498.

Identification and Characterization of MicroRNAs in Small Brown Planthopper (Laodephax striatellus) by Next-Generation Sequencing.

Zhou G, Wang T, Lou Y, Cheng J, Zhang H, Xu JH.
PLoS One. 2014 Jul 24;9(7):e103041.

Deep sequencing of norovirus genomes defines evolutionary patterns in an urban tropical setting.

Cotten M, Petrova V, Phan MV, Rabaa MA, Watson SJ, Ong SH, Kellam P, Baker S.
J Virol. 2014 Jul 23. [Epub ahead of print]

An efficient and sensitive method for preparing cDNA libraries from scarce biological samples.

Sterling CH, Veksler-Lublinksy I, Ambros V.
Nucleic Acids Res. 2014 Jul 23. [Epub ahead of print]

VNTRseek-a computational tool to detect tandem repeat variants in high-throughput sequencing data.

Gelfand Y, Hernandez Y, Loving J, Benson G.
Nucleic Acids Res. 2014 Jul 23. [Epub ahead of print]

Genome sequence and virulence variation-related transcriptome profiles of Curvularia lunata, an important maize pathogenic fungus.

Gao S, Li Y, Gao J, Suo Y, Fu K, Li Y, Chen J.
BMC Genomics. 2014 Jul 24;15(1):627.

Fecal Source Tracking in Water by Next-Generation Sequencing Technologies Using Host-Specific Escherichia coli Genetic Markers.

Gomi R, Matsuda T, Matsui Y, Yoneda M.
Environ Sci Technol. 2014 Jul 23. [Epub ahead of print]

Transcriptome Analysis of the Mud Crab (Scylla paramamosain) by 454 Deep Sequencing: Assembly, Annotation, and Marker Discovery.

Ma H, Ma C, Li S, Jiang W, Li X, Liu Y, Ma L.
PLoS One. 2014 Jul 23;9(7):e102668.