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In Print: Last Week's Sequencing-Related Papers of Note: Jul 30, 2013


Metagenome-wide analysis of antibiotic resistance genes in a large cohort of human gut microbiota.
Hu Y, Yang X, Qin J, Lu N, Cheng G, Wu N, Pan Y, Li J, Zhu L, Wang X, Meng Z, et al.
Nat Commun. 2013 Jul 23;4:2151.

GLiMMPS: Robust statistical model for regulatory variation of alternative splicing using RNA-Seq data.
Zhao K, Lu ZX, Park JW, Zhou Q, Xing Y.
Genome Biol. 2013 Jul 22;14(7):R74.

Stretching and Controlled Motion of Single-Stranded DNA in Locally Heated Solid-State Nanopores.
Belkin M, Maffeo C, Wells DB, Aksimentiev A.
ACS Nano. 2013 Jul 22. [Epub ahead of print]

Cloud-based uniform ChIP-Seq processing tools for modENCODE and ENCODE.
Trinh QM, Jen FY, Zhou Z, Chu KM, Perry MD, Kephart E, Contrino S, Ruzanov P, Stein LD.
BMC Genomics. 2013 Jul 22;14(1):494.

Long-term temporal analysis of the human fecal microbiota revealed a stable core of dominant bacterial species.
Martínez I, Muller CE, Walter J.
PLoS One. 2013 Jul 16;8(7):e69621.

TCW: Transcriptome Computational Workbench.
Soderlund C, Nelson W, Willer M, Gang DR.
PLoS One. 2013 Jul 17;8(7):e69401.

A DNA 'barcode blitz': rapid digitization and sequencing of a natural history collection.
Hebert PD, Dewaard JR, Zakharov EV, Prosser SW, Sones JE, McKeown JT, Mantle B, La Salle J.
PLoS One. 2013 Jul 10;8(7):e68535.

MutMap+: Genetic Mapping and Mutant Identification without Crossing in Rice.
Fekih R, Takagi H, Tamiru M, Abe A, Natsume S, Yaegashi H, Sharma S, Sharma S, et al.
PLoS One. 2013 Jul 10;8(7):e68529.

Normalizing RNA-Sequencing Data by Modeling Hidden Covariates with Prior Knowledge.
Mostafavi S, Battle A, Zhu X, Urban AE, Levinson D, Montgomery SB, Koller D.
PLoS One. 2013 Jul 18;8(7):e68141.

Genotyping by genome reducing and sequencing for outbred animals.
Chen Q, Ma Y, Yang Y, Chen Z, Liao R, Xie X, Wang Z, He P, Tu Y, Zhang X, Yang C, et al.
PLoS One. 2013 Jul 18;8(7):e67500.

GEMINI: Integrative Exploration of Genetic Variation and Genome Annotations.
Paila U, Chapman BA, Kirchner R, Quinlan AR.
PLoS Comput Biol. 2013 Jul;9(7):e1003153.

Genomic landscapes of Chinese hamster ovary cell lines as revealed by the Cricetulus griseus draft genome.
Lewis NE, Liu X, Li Y, Nagarajan H, Yerganian G, O'Brien E, Bordbar A, Roth AM, et al.
Nat Biotechnol. 2013 Jul 21. [Epub ahead of print]

BRIC-seq: a genome-wide approach for determining RNA stability in mammalian cells.
Imamachi N, Tani H, Mizutani R, Imamura K, Irie T, Suzuki Y, Akimitsu N.
Methods. 2013 Jul 16. pii: S1046-2023(13)00263-6. [Epub ahead of print]

A systematic evaluation of hybridization-based mouse exome capture system.
Gao Q, Sun W, You X, Froehler S, Chen W.
BMC Genomics. 2013 Jul 21;14(1):492.

Deep Ion Torrent sequencing identifies soil fungal community shifts after frequent prescribed fires in a southeastern US forest ecosystem.
Brown SP, Callaham MA, Oliver AK, Jumpponen A.
FEMS Microbiol Ecol. 2013 Jul 19. [Epub ahead of print]

Assessing the Fecal Microbiota: An Optimized Ion Torrent 16S rRNA Gene-Based Analysis Protocol.
Milani C, Hevia A, Foroni E, Duranti S, Turroni F, Lugli GA, Sanchez B, Martín R, et al.
PLoS One. 2013 Jul 15;8(7):e68739.

E-probe Diagnostic Nucleic acid Analysis (EDNA): A theoretical approach for handling of next generation sequencing data for diagnostics.
Stobbe AH, Daniels J, Espindola AS, Verma R, Melcher U, Ochoa-Corona F, Garzon C, et al.
J Microbiol Methods. 2013 Jul 15. pii: S0167-7012(13)00216-9. [Epub ahead of print]

Integrated OMICS guided engineering of biofuel butanol-tolerance in photosynthetic Synechocystis sp. PCC 6803.
Zhu H, Ren X, Wang J, Song Z, Shi M, Qiao J, Tian X, Liu J, Chen L, Zhang W.
Biotechnol Biofuels. 2013 Jul 25;6(1):106. [Epub ahead of print]

Transposon fingerprinting using low coverage whole genome shotgun sequencing in Cacao (Theobroma cacao L.) and related species.
Sveinsson S, Gill N, Kane NC, Cronk Q.
BMC Genomics. 2013 Jul 24;14(1):502. [Epub ahead of print]

The Scan

Researchers Compare WGS, Exome Sequencing-Based Mendelian Disease Diagnosis

Investigators find a diagnostic edge for whole-genome sequencing, while highlighting the cost advantages and improving diagnostic rate of exome sequencing in EJHG.

Researchers Retrace Key Mutations in Reassorted H1N1 Swine Flu Virus With Avian-Like Features

Mutations in the acidic polymerase-coding gene boost the pathogenicity and transmissibility of Eurasian avian-like H1N1 swine influenza viruses, a PNAS paper finds.

Genome Sequences Reveal Evolutionary History of South America's Canids

An analysis in PNAS of South American canid species' genomes offers a look at their evolutionary history, as well as their relationships and adaptations.

Lung Cancer Response to Checkpoint Inhibitors Reflected in Circulating Tumor DNA

In non-small cell lung cancer patients, researchers find in JCO Precision Oncology that survival benefits after immune checkpoint blockade coincide with a dip in ctDNA levels.