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


iReckon: Simultaneous isoform discovery and abundance estimation from RNA-seq data.
Mezlini AM, Smith EJ, Fiume M, Buske O, et al.
Genome Res. 2012 Nov 29. [Epub ahead of print]

Musket: a multistage k-mer spectrum based error corrector for Illumina sequence data.
Liu Y, Schröder J, Schmidt B.
Bioinformatics. 2012 Nov 29. [Epub ahead of print]

Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing.
Bokulich NA, Subramanian S, Faith JJ, Gevers D, et al.
Nat Methods. 2012 Dec 2. [Epub ahead of print]

Improved transcriptome quantification and reconstruction from RNA-seq reads using partial annotations.
Mangul S, Caciula A, Glebova O, Mandoiu I, Zelikovsky A.
In Silico Biol. 2012 Jan 1;11(5):251-61.

Reconstructing viral quasispecies from NGS amplicon reads.
Mancuso N, Tork B, Skums P, Ganova-Raeva L, et al.
In Silico Biol. 2012 Jan 1;11(5):237-49.

QColors: An algorithm for conservative viral quasispecies reconstruction from short and non-contiguous next generation sequencing reads.
Huang A, Kantor R, Delong A, Schreier L, Istrail S.
In Silico Biol. 2012 Jan 1;11(5):193-201.

Evaluation of viral heterogeneity using next-generation sequencing, end-point limiting-dilution and mass spectrometry.
Dimitrova Z, Campo DS, Ramachandran S, Vaughan G, et al.
In Silico Biol. 2012 Jan 1;11(5):183-92.

Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants.
Fu W, O'Connor TD, Jun G, Kang HM, et al.
Nature. 2012 Nov 28. [Epub ahead of print]

Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs.
Curtis BA, Tanifuji G, Burki F, Gruber A, et al.
Nature. 2012 Nov 28. [Epub ahead of print]

Correlating microbial community structure and composition with aeration intensity in submerged membrane bioreactors by 454 high-throughput pyrosequencing.
Ma J, Wang Z, Yang Y, Mei X, Wu Z.
Water Res. 2012 Nov 17. [Epub ahead of print]

Thermophoretic manipulation of DNA translocation through nanopores.
He Y, Tsutsui M, Scheicher RH, Bai F, et al.
ACS Nano. 2012 Dec 2. [Epub ahead of print]

Tips and tricks for the assembly of a Corynebacterium pseudotuberculosis genome using a semiconductor sequencer.
Ramos RT, Carneiro AR, Soares SD, Santos AR, et al.
Microb Biotechnol. 2012 Dec 2. [Epub ahead of print]

Tet-assisted bisulfite sequencing of 5-hydroxymethylcytosine.
Yu M, Hon GC, Szulwach KE, Song CX, et al.
Nat Protoc. 2012 Nov 29;7(12):2159-70.

Coaggregation occurs amongst bacteria within and between biofilms in domestic showerheads.
Vornhagen J, Stevens M, McCormick DW, Dowd SE, et al.
Biofouling. 2013 Jan;29(1):53-68.

iASeq: integrative analysis of allele-specificity of protein-DNA interactions in multiple ChIP-seq datasets.
Wei Y, Li X, Wang QF, Ji H.
BMC Genomics. 2012 Nov 29;13(1):681.

Technical considerations for reduced representation bisulfite sequencing with multiplexed libraries.
Chatterjee A, Rodger EJ, Stockwell PA, Weeks RJ, Morison IM.
J Biomed Biotechnol. 2012;2012:741542.

DANPOS: Dynamic Analysis of Nucleosome Position and Occupancy by Sequencing.
Chen K, Xi Y, Pan X, Li Z, et al.
Genome Res. 2012 Nov 28. [Epub ahead of print]

OTU Analysis using metagenomic shotgun sequencing data.
Hao X, Chen T.
PLoS One. 2012;7(11):e49785.

Molecular characterization of transgene integration by next-generation sequencing in transgenic cattle.
Zhang R, Yin Y, Zhang Y, Li K, et al.
PLoS One. 2012;7(11):e50348.

Evaluating methods for isolating total RNA and predicting the success of sequencing phylogenetically diverse plant transcriptomes.
Johnson MT, Carpenter EJ, Tian Z, Bruskiewich R, et al.
PLoS One. 2012;7(11):e50226.

Two different high throughput sequencing approaches identify thousands of de novo genomic markers for the genetically depleted bornean elephant.
Sharma R, Goossens B, Kun-Rodrigues C, Teixeira T, et al.
PLoS One. 2012;7(11):e49533.

BG7: A new approach for bacterial genome annotation designed for next generation sequencing data.
Pareja-Tobes P, Manrique M, Pareja-Tobes E, Pareja E, Tobes R.
PLoS One. 2012;7(11):e49239.

Exploring Pandora's box: potential and pitfalls of low coverage genome surveys for evolutionary biology.
Leese F, Brand P, Rozenberg A, Mayer C, et al.
PLoS One. 2012;7(11):e49202.

Mind the Gap: Upgrading genomes with Pacific Biosciences RS long-read sequencing technology.
English AC, Richards S, Han Y, Wang M, et al.
PLoS One. 2012;7(11):e47768.

MirPlex: A tool for identifying miRNAs in high-throughput sRNA datasets without a genome.
Mapleson D, Moxon S, Dalmay T, Moulton V.
J Exp Zool B Mol Dev Evol. 2012 Nov 26:1-10.

Decoding human cytomegalovirus.
Stern-Ginossar N, Weisburd B, Michalski A, Le VT, et al.
Science. 2012 Nov 23;338(6110):1088-93.

Suppression of artifacts and barcode bias in high-throughput transcriptome analyses utilizing template switching.
Tang DT, Plessy C, Salimullah M, Suzuki AM, et al.
Nucleic Acids Res. 2012 Nov 24. [Epub ahead of print]

The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions.
Guo S, Zhang J, Sun H, Salse J, et al.
Nat Genet. 2012 Nov 25. [Epub ahead of print]

The draft genome of sweet orange (Citrus sinensis).
Xu Q, Chen LL, Ruan X, Chen D, et al.
Nat Genet. 2012 Nov 25. [Epub ahead of print]

Next generation sequencing and de novo transcriptome analysis of Costus pictus. D. Don, a non-model plant with potent anti-diabetic properties.
Annadurai RS, Jayakumar V, Mugasimangalam RC, Katta MA, et al.
BMC Genomics. 2012 Nov 23;13(1):663.

The effect of strand bias in Illumina short-read sequencing data.
Guo Y, Li J, Li CI, Long J, et al.
BMC Genomics. 2012 Nov 24;13(1):666.

The Scan

Genome Sequences Reveal Range Mutations in Induced Pluripotent Stem Cells

Researchers in Nature Genetics detect somatic mutation variation across iPSCs generated from blood or skin fibroblast cell sources, along with selection for BCOR gene mutations.

Researchers Reprogram Plant Roots With Synthetic Genetic Circuit Strategy

Root gene expression was altered with the help of genetic circuits built around a series of synthetic transcriptional regulators in the Nicotiana benthamiana plant in a Science paper.

Infectious Disease Tracking Study Compares Genome Sequencing Approaches

Researchers in BMC Genomics see advantages for capture-based Illumina sequencing and amplicon-based sequencing on the Nanopore instrument, depending on the situation or samples available.

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.