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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

Shape of Them All

According to BBC News, researchers have developed a protein structure database that includes much of the human proteome.

For Flu and More

The Wall Street Journal reports that several vaccine developers are working on mRNA-based vaccines for influenza.

To Boost Women

China's Ministry of Science and Technology aims to boost the number of female researchers through a new policy, reports the South China Morning Post.

Science Papers Describe Approach to Predict Chemotherapeutic Response, Role of Transcriptional Noise

In Science this week: neural network to predict chemotherapeutic response in cancer patients, and more.