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In Print: Last Week's Sequencing-Related Papers of Note: Feb 19, 2013


Sequencing ancient calcified dental plaque shows changes in oral microbiota with dietary shifts of the Neolithic and Industrial revolutions.
Adler CJ, Dobney K, Weyrich LS, Kaidonis J, et al.
Nat Genet. 2013 Feb 17. [Epub ahead of print]
(See coverage of this paper in our sister publication GenomeWeb Daily News here.)

mRNA expression, splicing and editing in the embryonic and adult mouse cerebral cortex.
Dillman AA, Hauser DN, Gibbs JR, Nalls MA, et al.
Nat Neurosci. 2013 Feb 17. [Epub ahead of print]

Efficient comparison of sets of intervals with NC-lists.
Zytnicki M, Luo Y, Quesneville H.
Bioinformatics. 2013 Feb 14. [Epub ahead of print]

Wessim: A whole exome sequencing simulator based on in silico exome capture.
Kim S, Jeong K, Bafna V.
Bioinformatics. 2013 Feb 14. [Epub ahead of print]

An approximate Bayesian approach to mapping paired-end DNA reads to a reference genome.
Shrestha AM, Frith MC.
Bioinformatics. 2013 Feb 14. [Epub ahead of print]

High-resolution nucleosome mapping of targeted regions using BAC-based enrichment.
Yigit E, Zhang Q, Xi L, Grilley D, et al.
Nucleic Acids Res. 2013 Feb 14. [Epub ahead of print]

Multiplexed chromosome conformation capture sequencing for rapid genome-scale high-resolution detection of long-range chromatin interactions.
Stadhouders R, Kolovos P, Brouwer R, Zuin J, et al.
Nat Protoc. 2013 Feb 14;8(3):509-24.

High-resolution DNA methylome analysis of primordial germ cells identifies gender-specific reprogramming in mice.
Kobayashi H, Sakurai T, Miura F, Imai M, et al.
Genome Res. 2013 Feb 14. [Epub ahead of print]

Marker density and read-depth for genotyping populations using genotyping-by-sequencing.
Beissinger TM, Hirsch CN, Sekhon RS, Foerster JM, et al.
Genetics. 2013 Feb 14. [Epub ahead of print]

SOAPfuse: an algorithm for identifying fusion transcripts from paired-end RNA-seq data.
Jia W, Qiu K, He M, Song P, et al.
Genome Biol. 2013 Feb 14;14(2):R12.

Simultaneous amplicon sequencing to explore co-occurrence patterns of bacterial, archaeal and eukaryotic microorganisms in rumen microbial communities.
Kittelmann S, Seedorf H, Walters WA, Clemente JC, et al.
PLoS One. 2013;8(2):e47879.

Genome-wide comparison of DNA hydroxymethylation in mouse embryonic stem cells and neural progenitor cells by a new comparative hMeDIP-seq method.
Tan L, Xiong L, Xu W, Wu F, et al.
Nucleic Acids Res. 2013 Feb 13. [Epub ahead of print]

Efficient identification of rare variants in large populations: deep re-sequencing the CRP locus in the CARDIA study.
Chen CT, McDavid AN, Kahsai OJ, Zebari AS, Carlson CS.
Nucleic Acids Res. 2013 Feb 13. [Epub ahead of print]

TriageTools: tools for partitioning and prioritizing analysis of high-throughput sequencing data.
Fimereli D, Detours V, Konopka T.
Nucleic Acids Res. 2013 Feb 13. [Epub ahead of print]

VIROME: a standard operating procedure for analysis of viral metagenome sequences.
Wommack KE, Bhavsar J, Polson SW, Chen J, et al.
Stand Genomic Sci. 2012 Jul 30;6(3):427-39.

A dynamic Bayesian Markov model for phasing and characterizing haplotypes in next generation sequencing.
Zhang Y.
Bioinformatics. 2013 Feb 13. [Epub ahead of print]

Short-read assembly of full-length 16S amplicons reveals bacterial diversity in subsurface sediments.
Miller CS, Handley KM, Wrighton KC, Frischkorn KR, et al.
PLoS One. 2013;8(2):e56018.

Rapid genome mapping in nanochannel arrays for highly complete and accurate de novo sequence assembly of the complex Aegilops tauschii genome.
Hastie AR, Dong L, Smith A, Finklestein J, et al.
PLoS One. 2013;8(2):e55864.

Transcriptome profiling of the goose (Anser cygnoides) ovaries identify laying and broodiness phenotypes.
Xu Q, Zhao W, Chen Y, Tong Y, et al.
PLoS One. 2013;8(2):e55496.

Expression profile of ectopic olfactory receptors determined by deep sequencing.
Flegel C, Manteniotis S, Osthold S, Hatt H, Gisselmann G.
PLoS One. 2013;8(2):e55368.

Comparison of sequencing platforms for single nucleotide variant calls in a human sample.
Ratan A, Miller W, Guillory J, Stinson J, et al.
PLoS One. 2013;8(2):e55089.
(See our coverage of this paper in last week's issue here.)

Ultra-deep mutant spectrum profiling: improving sequencing accuracy using overlapping read pairs.
Chen-Harris H, Borucki MK, Torres C, Slezak TR, Allen JE.
BMC Genomics. 2013 Feb 12;14(1):96.

Coupling mutagenesis and parallel deep sequencing to probe essential residues in a genome or gene.
Robins WP, Faruque SM, Mekalanos JJ.
Proc Natl Acad Sci U S A. 2013 Feb 11. [Epub ahead of print]

Gut microbiota of healthy Canadian infants: profiles by mode of delivery and infant diet at 4 months.
Azad MB, Konya T, Maughan H, Guttman DS, et al.
CMAJ. 2013 Feb 11. [Epub ahead of print]

Genetics professionals' perspectives on reporting incidental findings from clinical genome-wide sequencing.
Lohn Z, Adam S, Birch P, Townsend A, Friedman J.
Am J Med Genet A. 2013 Feb 7. [Epub ahead of print]

Estimation of CpG coverage in whole methylome next-generation sequencing studies.
van den Oord EJ, Bukszar J, Rudolf G, Nerella S, et al.
BMC Bioinformatics. 2013 Feb 12;14(1):50.

Accelerating read mapping with FastHASH.
Xin H, Lee D, Hormozdiari F, Yedkar S, et al.
BMC Genomics. 2013 Jan 21;14 Suppl 1:S13.

Unraveling overlapping deletions by agglomerative clustering.
Wittler R.
BMC Genomics. 2013 Jan 21;14 Suppl 1:S12.

A unified approach for allele frequency estimation, SNP detection and association studies based on pooled sequencing data using EM algorithms.
Chen Q, Sun F.
BMC Genomics. 2013 Jan 21;14 Suppl 1:S1.

CoNVEX: copy number variation estimation in exome sequencing data using HMM.
Amarasinghe KC, Li J, Halgamuge SK.
BMC Bioinformatics. 2013;14 Suppl 2:S2.

Improved moderation for gene-wise variance estimation in RNA-seq via the exploitation of external information.
Patrick E, Buckley M, Lin DM, Yang YH.
BMC Genomics. 2013 Jan 21;14 Suppl 1:S9.

Genome reassembly with high-throughput sequencing data.
Parrish N, Sudakov B, Eskin E.
BMC Genomics. 2013 Jan 21;14 Suppl 1:S8.

BayesHammer: Bayesian clustering for error correction in single-cell sequencing.
Nikolenko SI, Korobeynikov AI, Alekseyev MA.
BMC Genomics. 2013 Jan 21;14 Suppl 1:S7.

A computational approach for identifying microRNA-target interactions using high-throughput CLIP and PAR-CLIP sequencing.
Chou CH, Lin FM, Chou MT, Hsu SD, et al.
BMC Genomics. 2013 Jan 21;14 Suppl 1:S2.