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In Print: Last Week's Sequencing-Related Papers of Note: May 21, 2013

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Transcriptome sequencing of neonatal thymic epithelial cells.
St-Pierre C, Brochu S, Vanegas JR, Dumont-Lagacé M, et al.
Sci Rep. 2013 May 17;3:1860.


ACCUSA2: Multi-purpose SNV calling enhanced by probabilistic integration of quality scores.
Piechotta M, Dieterich C.
Bioinformatics. 2013 May 16. [Epub ahead of print]


Electrophoresis of a DNA coil near a nanopore.
Rowghanian P, Grosberg AY.
Phys Rev E Stat Nonlin Soft Matter Phys. 2013 Apr;87(4-1):042723.


Electrophoretic capture of a DNA chain into a nanopore.
Rowghanian P, Grosberg AY.
Phys Rev E Stat Nonlin Soft Matter Phys. 2013 Apr;87(4-1):042722.


Translocation of a polymer through a nanopore across a viscosity gradient.
de Haan HW, Slater GW.
Phys Rev E Stat Nonlin Soft Matter Phys. 2013 Apr;87(4-1):042604.


454-pyrosequencing analyses of bacterial and archaeal richness in 21 full-scale biogas digesters.
Sundberg C, Al-Soud WA, Larsson M, Alm E, et al.
FEMS Microbiol Ecol. 2013 May 16. [Epub ahead of print]


Translocating kilobase RNA through the staphylococcal α-hemolysin nanopore.
Cracknell JA, Japrung D, Bayley H.
Nano Lett. 2013 May 16. [Epub ahead of print]


Comparative analysis of RNA sequencing methods for degraded or low-input samples.
Adiconis X, Borges-Rivera D, Satija R, Deluca DS, et al.
Nat Methods. 2013 May 19. [Epub ahead of print]


Specificity control for read alignments using an artificial reference genome guided false discovery rate.
Giese SH, Zickmann F, Renard BY.
Bioinformatics. 2013 May 17. [Epub ahead of print]


Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells.
Shalek AK, Satija R, Adiconis X, Gertner RS, et al.
Nature. 2013 May 19. [Epub ahead of print]


Optimizing preservation protocols to extract high-quality RNA from different tissues of echinoderms for next-generation sequencing.
Pérez-Portela R, Riesgo A.
Mol Ecol Resour. 2013 May 20. [Epub ahead of print]


ReviSTER: An automated pipeline to revise misaligned reads to simple tandem repeats.
Tae H, McMahon KW, Settlage RE, Bavarva JH, Garner HR.
Bioinformatics. 2013 May 15. [Epub ahead of print]


Updating RNA-seq analyses after re-annotation.
Roberts A, Schaeffer L, Pachter L.
Bioinformatics. 2013 May 14. [Epub ahead of print]


Genomic architecture of adaptive color pattern divergence and convergence in Heliconius butterflies.
Supple MA, Hines HM, Dasmahapatra KK, Lewis JJ, et al.
Genome Res. 2013 May 14. [Epub ahead of print]


The genomics of selection in dogs and the parallel evolution between dogs and humans.
Wang GD, Zhai W, Yang HC, Fan RX, et al.
Nat Commun. 2013 May 14;4:1860.


Single-cell and metagenomic analyses indicate a fermentative and saccharolytic lifestyle for members of the OP9 lineage.
Dodsworth JA, Blainey PC, Murugapiran SK, Swingley WD, et al.
Nat Commun. 2013 May 14;4:1854.


Optimizing de novo assembly of short-read RNA-seq data for phylogenomics.
Yang Y, Smith SA.
BMC Genomics. 2013 May 14;14(1):328.


DROMPA: easy-to-handle peak calling and visualization software for the computational analysis and validation of ChIP-seq data.
Nakato R, Itoh T, Shirahige K.
Genes Cells. 2013 May 15. [Epub ahead of print]


r3Cseq: an R/Bioconductor package for the discovery of long-range genomic interactions from chromosome conformation capture and next-generation sequencing data.
Thongjuea S, Stadhouders R, Grosveld FG, Soler E, Lenhard B.
Nucleic Acids Res. 2013 May 13. [Epub ahead of print]


Fine de novo sequencing of a fungal genome using only SOLiD short read data: verification on Aspergillus oryzae RIB40.
Umemura M, Koyama Y, Takeda I, Hagiwara H, et al.
PLoS One. 2013 May 7;8(5):e63673.


A multi-platform draft de novo genome assembly and comparative analysis for the scarlet Macaw (Ara macao).
Seabury CM, Dowd SE, Seabury PM, Raudsepp T, et al.
PLoS One. 2013 May 8;8(5):e62415.


A next-generation sequencing method for genotyping-by-sequencing of highly heterozygous autotetraploid potato.
Uitdewilligen JG, Wolters AM, D'hoop BB, Borm TJ, et al.
PLoS One. 2013 May 8;8(5):e62355.


High-throughput tetrad analysis.
Ludlow CL, Scott AC, Cromie GA, Jeffery EW, et al.
Nat Methods. 2013 May 12. [Epub ahead of print]


Sequence comparative analysis using networks (SCAN): software for evaluating de novo transcript assembly from next generation sequencing.
Misner I, Bicep C, Lopez P, Halary S, et al.
Mol Biol Evol. 2013 May 10. [Epub ahead of print]


Identification of a Tibetan-specific mutation in the hypoxic gene EGLN1 and its contribution to high-altitude adaptation.
Xiang K, Ouzhuluobu, Peng Y, Yang Z, et al.
Mol Biol Evol. 2013 May 10. [Epub ahead of print]


Sequence-based mapping of the polyploid wheat genome.
Saintenac C, Zhang D, Wang S, Akhunov E.
G3 (Bethesda). 2013 May 11. [Epub ahead of print]


A statistical framework for power calculations in ChIP-seq experiments.
Zuo C, Keles S.
Bioinformatics. 2013 May 10. [Epub ahead of print]


GAGE-B: An evaluation of genome assemblers for bacterial organisms.
Magoc T, Pabinger S, Canzar S, Liu X, et al.
Bioinformatics. 2013 May 10. [Epub ahead of print]


A bi-Poisson model for clustering gene expression profiles by RNA-seq.
Wang N, Wang Y, Hao H, Wang L, et al.
Brief Bioinform. 2013 May 10. [Epub ahead of print]


Efficient isolation of polymorphic microsatellites from high-throughput sequence data based on number of repeats.
Cardoso SD, Gonçalves D, Robalo JI, Almada VC, et al.
Mar Genomics. 2013 May 7. [Epub ahead of print]


Strand-seq: a unifying tool for studies of chromosome segregation.
Falconer E, Lansdorp PM.
Semin Cell Dev Biol. 2013 May 7. [Epub ahead of print]


Transcriptional and epigenetic dynamics during specification of human embryonic stem cells.
Gifford CA, Ziller MJ, Gu H, Trapnell C, et al.
Cell. 2013 May 7. [Epub ahead of print]


Sequencing platform and library preparation choices impact viral metagenomes.
Solonenko SA, Ignacio-Espinoza JC, Alberti A, Cruaud C, et al.
BMC Genomics. 2013 May 10;14(1):320.


Characterization of human plasma-derived exosomal RNAs by deep sequencing.
Huang X, Yuan T, Tschannen M, Sun Z, et al.
BMC Genomics. 2013 May 10;14(1):319.


Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.).
Ming R, Vanburen R, Liu Y, Yang M, et al.
Genome Biol. 2013 May 10;14(5):R41.


Lane-by-lane sequencing using Illumina's Genome Analyzer II.
Gravina MT, Lin JH, Levine SS.
Biotechniques. 2013 May;54(5):265-9.

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