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Papers of Note: May 17, 2011


A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species.
Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, Mitchell SE.
PLoS One. 2011 May 4;6(5):e19379.

Protocol dependence of sequencing-based gene expression measurements.
Raz T, Kapranov P, Lipson D, Letovsky S, Milos PM, Thompson JF.
PLoS One. 2011 May 6;6(5):e19287.

Complete genome sequence of Mycoplasma suis and insights into its biology and adaption to an erythrocyte niche.
Guimaraes AM, Santos AP, Sanmiguel P, Walter T, Timenetsky J, Messick JB.
PLoS One. 2011 May 10;6(5):e19574.

Full-length transcriptome assembly from RNA-seq data without a reference genome.
Grabherr MG, Haas BJ, Yassour M, et al.
Nat Biotechnol. 2011 May 15. [Epub ahead of print]

Genome-wide detection of chromosomal rearrangements, indels, and mutations in circular chromosomes by short read sequencing.
Skovgaard O, Bak M, Løbner-Olesen A, Tommerup N.
Genome Res. 2011 May 9. [Epub ahead of print]

Zebrafish mRNA sequencing decipher novelties in transcriptome dynamics during maternal to zygotic transition.
Aanes H, Winata CL, Lin CH, et al.
Genome Res. 2011 May 9. [Epub ahead of print]

Enhancing genome assemblies by integrating non-sequence based data.
Heider TN, Lindsay J, Wang C, O'Neill RJ, Pask AJ.
BMC Proc. 2011 May 28;5 Suppl 2:S7.

PeakRanger: A cloud-enabled peak caller for ChIP-seq data.
Feng X, Grossman R, Stein L.
BMC Bioinformatics. 2011 May 9;12(1):139. [Epub ahead of print]

ChIP-seq analysis in R (CSAR): An R package for the statistical detection of protein-bound genomic regions.
Muino JM, Kaufmann K, van Ham RC, Angenent GC, Krajewski P.
Plant Methods. 2011 May 9;7(1):11. [Epub ahead of print]

Large scale detection of rare variants via pooled multiplexed next generation sequencing: towards next generation Ecotilling.
Marroni F, Pinosio S, Di Centa E, et al.
Plant J. 2011 May 7. [Epub ahead of print]

Comparison of three targeted enrichment strategies on the SOLiD sequencing platform.
Hedges DJ, Guettouche T, Yang S, et al.
PLoS One. 2011 Apr 29;6(4):e18595.

Genome sequencing and analysis of Yersina pestis KIM D27, an avirulent strain exempt from select agent regulation.
Losada L, Varga JJ, Hostetler J, et al.
PLoS One. 2011 Apr 29;6(4):e19054.

Comparing de novo genome assembly: the long and short of it.
Narzisi G, Mishra B.
PLoS One. 2011 Apr 29;6(4):e19175.

Genome annotation test with validation on transcription start site and ChIP-seq for Pol-II binding data.
Bedo J, Kowalczyk A.
Bioinformatics. 2011 May 9. [Epub ahead of print]

Towards standardization of the description and publication of next-generation sequencing datasets of fungal communities.
Henrik Nilsson R, Tedersoo L, Lindahl BD, et al.
New Phytol. 2011 May 9. [Epub ahead of print]

Counting individual DNA molecules by the stochastic attachment of diverse labels.
Fu GK, Hu J, Wang PH, Fodor SP.
Proc Natl Acad Sci U S A. 2011 May 11. [Epub ahead of print]

Protocol matters: which methylome are you actually studying?
Robinson MD, Statham AL, Speed TP, Clark SJ.
Epigenomics. 2010 Aug 1;2(4):587-598.

BiQ Analyzer HT: locus-specific analysis of DNA methylation by high-throughput bisulfite sequencing.
Lutsik P, Feuerbach L, Arand J, Lengauer T, Walter J, Bock C.
Nucleic Acids Res. 2011 May 11. [Epub ahead of print]

Current next generation sequencing technology may not meet forensic standards.
Bandelt HJ, Salas A.
Forensic Sci Int Genet. 2011 May 10. [Epub ahead of print]

A rapid column-based ancient DNA extraction method for increased sample throughput.
Rohland N, Siedel H, Hofreiter M.
Mol Ecol Resour. 2010 Jul;10(4):677-83. Epub 2009 Dec 29.

Reproducibility of read numbers in high-throughput sequencing analysis of nematode community composition and structure.
Porazinska DL, Sung W, Giblin-Davis RM, Thomas WK.
Mol Ecol Resour. 2010 Jul;10(4):666-76. Epub 2009 Dec 15.

Allele-specific PCR can improve the efficiency of experimental resolution of heterozygotes in resequencing studies.
Chen H, Morrell PL, Toleno DM, Lundy KE, Clegg MT.
Mol Ecol Resour. 2010 Jul;10(4):647-58. Epub 2009 Dec 21.

ComB: SNP calling and mapping analysis for color and nucleotide space platforms.
Souaiaia T, Frazier Z, Chen T.
J Comput Biol. 2011 May 12. [Epub ahead of print]

The Scan

Octopus Brain Complexity Linked to MicroRNA Expansions

Investigators saw microRNA gene expansions coinciding with complex brains when they analyzed certain cephalopod transcriptomes, as they report in Science Advances.

Study Tracks Outcomes in Children Born to Zika Virus-Infected Mothers

By following pregnancy outcomes for women with RT-PCR-confirmed Zika virus infections, researchers saw in Lancet Regional Health congenital abnormalities in roughly one-third of live-born children.

Team Presents Benchmark Study of RNA Classification Tools

With more than 135 transcriptomic datasets, researchers tested two dozen coding and non-coding RNA classification tools, establishing a set of potentially misclassified transcripts, as they report in Nucleic Acids Research.

Breast Cancer Risk Related to Pathogenic BRCA1 Mutation May Be Modified by Repeats

Several variable number tandem repeats appear to impact breast cancer risk and age at diagnosis in almost 350 individuals carrying a risky Ashkenazi Jewish BRCA1 founder mutation.