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In Print: Last Week's Sequencing-Related Papers of Note: Jul 16, 2013


Progress toward an aberration-corrected low energy electron microscope for DNA sequencing and surface analysis.
Mankos M, Shadman K, N'diaye AT, Schmid AK, et al.
J Vac Sci Technol B Nanotechnol Microelectron. 2012 Nov;30(6):6F402.

Principal component analysis reveals the 1000 Genomes Project does not sufficiently cover the human genetic diversity in Asia.
Lu D, Xu S.
Front Genet. 2013 Jul 4;4:127.

Quantitative trait analysis in sequencing studies under trait-dependent sampling.
Lin DY, Zeng D, Tang ZZ.
Proc Natl Acad Sci U S A. 2013 Jul 11. [Epub ahead of print]

Inference of alternative splicing from RNA-seq data with probabilistic splice graphs.
Legault LH, Dewey CN.
Bioinformatics. 2013 Jul 11. [Epub ahead of print]

Chromatin tandem affinity purification sequencing.
Soleimani VD, Palidwor GA, Ramachandran P, Perkins TJ, Rudnicki MA.
Nat Protoc. 2013 Aug;8(8):1525-1534.

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis.
Haas BJ, Papanicolaou A, Yassour M, Grabherr M, et al.
Nat Protoc. 2013 Aug;8(8):1494-1512.

jMOSAiCS: joint analysis of multiple ChIP-seq datasets.
Zeng X, Sanalkumar R, Bresnick EH, Li H, et al.
Genome Biol. 2013 Apr 29;14(4):R38.

Molecule-hugging graphene nanopores.
Garaj S, Liu S, Golovchenko JA, Branton D.
Proc Natl Acad Sci U S A. 2013 Jul 8. [Epub ahead of print]

Rapid evolution of the human gut virome.
Minot S, Bryson A, Chehoud C, Wu GD, et al.
Proc Natl Acad Sci U S A. 2013 Jul 8. [Epub ahead of print]

Identification of grouped rare and common variants via penalized logistic regression.
Ayers KL, Cordell HJ.
Genet Epidemiol. 2013 Jul 8. [Epub ahead of print]

Transient exposure to low levels of insecticide affects metabolic networks of honeybee larvae.
Derecka K, Blythe MJ, Malla S, Genereux DP, et al.
PLoS One. 2013 Jul 2;8(7):e68191.

Comparison of DNA extraction methods in analysis of salivary bacterial communities.
Lazarevic V, Gaïa N, Girard M, François P, Schrenzel J.
PLoS One. 2013 Jul 3;8(7):e67699.

ANOVA-like differential expression (ALDEx) analysis for mixed population RNA-seq.
Fernandes AD, Macklaim JM, Linn TG, Reid G, Gloor GB.
PLoS One. 2013 Jul 2;8(7):e67019.

dbNSFP v2.0: A database of human non-synonymous SNVs and their functional predictions and annotations.
Liu X, Jian X, Boerwinkle E.
Hum Mutat. 2013 Jul 10. [Epub ahead of print]

Pathoscope: Species identification and strain attribution with unassembled sequencing data.
Francis OE, Bendall M, Manimaran S, Hong C, et al.
Genome Res. 2013 Jul 10. [Epub ahead of print]

Tissue-specific mitochondrial heteroplasmy at position 16,093 within the same individual.
Krjutškov K, Koltšina M, Grand K, Võsa U, et al.
Curr Genet. 2013 Jul 11. [Epub ahead of print]

MIG: Multi-Image Genome viewer.
McGowan SJ, Hughes JR, Han ZP, Taylor S.
Bioinformatics. 2013 Jul 10. [Epub ahead of print]

Inferring demography from runs of homozygosity in whole genome sequence, with correction for sequence errors.
Macleod IM, Larkin DM, Lewin HA, Hayes BJ, Goddard ME.
Mol Biol Evol. 2013 Jul 10. [Epub ahead of print]

DBATE: database of alternative transcripts expression.
Bianchi V, Colantoni A, Calderone A, Ausiello G, et al.
Database (Oxford). 2013 Jul 9;2013(0):bat050.

Complete genome sequencing and variant analysis of a Pakistani individual.
Azim MK, Yang C, Yan Z, Choudhary MI, et al.
J Hum Genet. 2013 Jul 11. [Epub ahead of print]

The genome sequence of the colonial chordate, Botryllus schlosseri.
Voskoboynik A, Neff NF, Sahoo D, Newman AM, et al.
Elife. 2013 Jul 2;2:e00569.

Choosing a benchtop sequencing machine to characterise Helicobacter pylori genomes.
Perkins TT, Tay CY, Thirriot F, Marshall B.
PLoS One. 2013 Jun 28;8(6):e67539.

Transcriptome profiling of radish (Raphanus sativus L.) root and identification of genes involved in response to lead (Pb) stress with next generation sequencing.
Wang Y, Xu L, Chen Y, Shen H, et al.
PLoS One. 2013 Jun 20;8(6):e66539.

Read and assembly metrics inconsequential for clinical utility of whole-genome sequencing in mapping outbreaks.
Harris SR, Török ME, Cartwright EJ, Quail MA, et al.
Nat Biotechnol. 2013 Jul 9;31(7):592-4.

Variant discovery in targeted resequencing using whole genome amplified DNA.
Indap AR, Cole R, Crunge McW Edu CL, Marth GT, Olivier M.
BMC Genomics. 2013 Jul 10;14(1):468.

Multiplexed Illumina sequencing libraries from picogram quantities of DNA.
Bowman SK, Simon MD, Deaton AM, Tolstorukov M, et al.
BMC Genomics. 2013 Jul 9;14(1):466.

Assessing de novo transcriptome assembly metrics for consistency and utility.
O'Neil ST, Emrich SJ.
BMC Genomics. 2013 Jul 9;14(1):465.

NURD: an implementation of a new method to estimate isoform expression from non-uniform RNA-seq data.
Ma X, Zhang X.
BMC Bioinformatics. 2013 Jul 10;14(1):220.

TCC: an R package for comparing tag count data with robust normalization strategies.
Sun J, Nishiyama T, Shimizu K, Kadota K.
BMC Bioinformatics. 2013 Jul 9;14(1):219.

Rapid evolution of the human gut virome.
Minot S, Bryson A, Chehoud C, Wu GD, et al.
Proc Natl Acad Sci U S A. 2013 Jul 8. [Epub ahead of print]

The value of statistical or bioinformatics annotation for rare variant association with quantitative trait.
Byrnes AE, Wu MC, Wright FA, Li M, Li Y.
Genet Epidemiol. 2013 Jul 8. [Epub ahead of print]