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In Print: Last Week's Sequencing-Related Papers of Note: Sep 4, 2012


SeqTrace: a graphical tool for rapidly processing DNA sequencing chromatograms.
Stucky BJ.
J Biomol Tech. 2012 Sep;23(3):90-3.

Rainbow: an integrated tool for efficient clustering and assembling RAD-seq reads..
Chong Z, Ruan J, Wu CI.
Bioinformatics. 2012 Sep 1. [Epub ahead of print]

Statistical challenges associated with detecting copy number variations with next-generation sequencing.
Teo SM, Pawitan Y, Ku CS, Chia KS, Salim A.
Bioinformatics. 2012 Aug 31. [Epub ahead of print]

A robust model for read count data in exome sequencing experiments and implications for copy number variant calling.
Plagnol V, Curtis J, Epstein M, Mok K, et al.
Bioinformatics. 2012 Aug 31. [Epub ahead of print]

The Einstein Genome Gateway using WASP − a high throughput multi-layered life sciences portal for XSEDE.
Golden A, McLellan AS, Dubin RA, Jing Q, et al.
Stud Health Technol Inform. 2012;175:182-91.

Exploring functional variant discovery in non-coding regions with SInBaD.
Lehmann KV, Chen T.
Nucleic Acids Res. 2012 Aug 31. [Epub ahead of print]

Exome RNA sequencing reveals rare and novel alternative transcripts.
Halvardson J, Zaghlool A, Feuk L.
Nucleic Acids Res. 2012 Aug 31. [Epub ahead of print]

Composition-based classification of short metagenomic sequences elucidates the landscapes of taxonomic and functional enrichment of microorganisms.
Liu J, Wang H, Yang H, Zhang Y, et al.
Nucleic Acids Res. 2012 Aug 31. [Epub ahead of print]

CpG_MPs: identification of CpG methylation patterns of genomic regions from high-throughput bisulfite sequencing data.
Su J, Yan H, Wei Y, Liu H, et al.
Nucleic Acids Res. 2012 Aug 31. [Epub ahead of print]

Iterative correction of Hi-C data reveals hallmarks of chromosome organization.
Imakaev M, Fudenberg G, McCord RP, Naumova N, et al.
Nat Methods. 2012 Sep 2. [Epub ahead of print]

CEL-Seq: single-cell RNA-seq by multiplexed linear amplification.
Hashimshony T, Wagner F, Sher N, Yanai I.
Cell Rep. 2012 Aug 29. [Epub ahead of print]

Strand-specific RNA-seq reveals ordered patterns of sense and antisense transcription in Bacillus anthracis.
Passalacqua KD, Varadarajan A, Weist C, Ondov BD, et al.
PLoS One. 2012;7(8):e43350.

The shared antibiotic resistome of soil bacteria and human pathogens.
Forsberg KJ, Reyes A, Wang B, Selleck EM et al.
Science. 2012 Aug 31;337(6098):1107-11.

Development of chromosome-arm-specific microsatellite markers in Triticum aestivum (Poaceae) using NGS technology.
Nie X, Li B, Wang L, Liu P, et al.
Am J Bot. 2012 Aug 30. [Epub ahead of print]

Intraspecific sequence comparisons reveal similar rates of non-collinear gene insertion in the B and D genomes of bread wheat.
Bartos J, Vlcek C, Choulet F, Dzunková M, et al.
BMC Plant Biol. 2012 Aug 30;12(1):155.

Normalization of a chromosomal contact map.
Cournac A, Marie-Nelly H, Marbouty M, Koszul R, Mozziconacci J.
BMC Genomics. 2012 Aug 30;13(1):436.

Single-neuron RNA-seq: technical feasibility and reproducibility.
Qiu S, Luo S, Evgrafov O, Li R, et al.
Front Genet. 2012;3:124.
(see our coverage of this paper here)

Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies..
Klindworth A, Pruesse E, Schweer T, Peplies J, et al.
Nucleic Acids Res. 2012 Aug 28. [Epub ahead of print]

High variety of known and new RNA and DNA viruses of diverse origins in untreated sewage.
Ng TF, Marine R, Wang C, Simmonds P, et al.
J Virol. 2012 Aug 29. [Epub ahead of print]

Expression patterns reveal niche diversification in a marine microbial assemblage.
Gifford SM, Sharma S, Booth M, Moran MA.
ISME J. 2012 Aug 30. [Epub ahead of print]

Measuring cation dependent DNA polymerase fidelity landscapes by deep sequencing.
Zamft BM, Marblestone AH, Kording K, Schmidt D, et al.
PLoS One. 2012;7(8):e43876.

Genometa − a fast and accurate classifier for short metagenomic shotgun reads.
Davenport CF, Neugebauer J, Beckmann N, Friedrich B, et al.
PLoS One. 2012;7(8):e41224.

Global mapping of translation initiation sites in mammalian cells at single-nucleotide resolution.
Lee S, Liu B, Lee S, Huang SX, et al.
Proc Natl Acad Sci U S A. 2012 Aug 27. [Epub ahead of print]

Anomalies of the anaerobic tricarboxylic acid cycle in Shewanella oneidensis revealed by Tn-seq..
Brutinel ED, Gralnick JA.
Mol Microbiol. 2012 Aug 27. [Epub ahead of print]

Optimization of dengue virus genome assembling using GS FLX 454 pyrosequencing data: evaluation of assembling strategies.
Casseb SM, Cardoso JF, Ramos R, Carneiro A, et al.
Genet Mol Res. 2012 Aug 17;11(AOP).

The Scan

Study Reveals New Details About Genetics of Major Cause of Female Infertility

Researchers in Nature Medicine conducted a whole-exome sequencing study of mote than a thousand patients with premature ovarian insufficiency.

Circulating Tumor DNA Shows Potential as Biomarker in Rare Childhood Cancer

A study in the Journal of Clinical Oncology has found that circulating tumor DNA levels in rhabdomyosarcoma may serve as a biomarker for prognosis.

Study Recommends Cancer Screening for Dogs Beginning Age Seven, Depending on Breed

PetDx researchers report in PLOS One that annual cancer screening for dogs should begin by age seven.

White-Tailed Deer Harbor SARS-CoV-2 Variants No Longer Infecting Humans, Study Finds

A new study in PNAS has found that white-tailed deer could act as a reservoir of SARS-CoV-2 variants no longer found among humans.