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Last Week's Sequencing-Related Papers of Note: Aug 30, 2011

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Multiple reference genomes and transcriptomes for Arabidopsis thaliana.
Gan X, Stegle O, Behr J, Steffen JG, et al.
Nature. 2011 Aug 28. [Epub ahead of print]


Whole-genome sequencing of multiple Arabidopsis thaliana populations.
Cao J, Schneeberger K, Ossowski S, Günther T, et al.
Nat Genet. 2011 Aug 28. [Epub ahead of print]


The genome of the mesopolyploid crop species Brassica rapa.
The Brassica rapa Genome Sequencing Project Consortium, Wang X, Wang H, Wang J, et al.
Nat Genet. 2011 Aug 28. [Epub ahead of print]


Extending KNIME for next generation sequencing data analysis.
Jagla B, Wiswedel B, Coppée JY.
Bioinformatics. 2011 Aug 27. [Epub ahead of print]


A powerful and flexible statistical framework for testing hypotheses of allele-specific gene expression from RNA-seq data.
Skelly DA, Johansson M, Madeoy J, Wakefield J, Akey JM.
Genome Res. 2011 Aug 26. [Epub ahead of print]


Enzyme digestion of entrapped single-DNA molecules in nanopores.
Lee S, Kang SH, Yeung ES.
Talanta. 2011 Sep 30;85(4):2135-41.


Whole genome sequencing of environmental Vibrio cholerae O1 from 10 nanograms of DNA using short reads.
Pérez Chaparro PJ, McCulloch JA, Cerdeira LT, Al-Dilaimi A, et al.
Microbiol Methods. 2011 Aug 17. [Epub ahead of print]


Rapid whole genome optical mapping of Plasmodium falciparum.
Riley MC, Kirkup BC Jr, Johnson JD, Lesho EP, Ockenhouse CF.
Malar J. 2011 Aug 26;10(1):252.


A new strategy for next generation sequencing: merging the Sanger's method and the sequencing by synthesis through replacing extension.
Xiao L, Zhang J, Sirois P, He N, Li K.
J Biomed Nanotechnol. 2011 Aug;7(4):568-71.


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The real cost of sequencing: higher than you think!
Sboner A, Mu XJ, Greenbaum D, Auerbach RK, Gerstein MB.
Genome Biol. 2011 Aug 25;12(8):125.


Parallelized short read assembly of large genomes using de Bruijn graphs.
Liu Y, Schmidt B, Maskell DL.
BMC Bioinformatics. 2011 Aug 25;12(1):354.


Recognizing nucleotides by cross-tunneling currents for DNA sequencing.
Bagci VM, Kaun CC.
Phys Rev E Stat Nonlin Soft Matter Phys. 2011 Jul;84(1-1):011917.


Competitive genomic screens of barcoded yeast libraries.
Smith AM, Durbic T, Oh J, Urbanus M, et al.
J Vis Exp. 2011 Aug 11;(54). pii: 2864.


On differential gene expression using RNA-seq data.
Lee J, Ji Y, Liang S, Cai G, Müller P.
Cancer Inform. 2011;10:205-15.


Discovery of lost diversity of paternal horse lineages using ancient DNA.
Lippold S, Knapp M, Kuznetsova T, Leonard JA, et al.
Nat Commun. 2011 Aug 23;2:450.


Relating CNVs to transcriptome data at fine-resolution: Assessment of the effect of variant size, type, and overlap with functional regions.
Schlattl A, Anders S, Waszak SM, Huber W, Korbel JO.
Genome Res. 2011 Aug 23. [Epub ahead of print]


An integer programming approach to DNA sequence assembly.
Chang Y, Sahinidis NV.
Comput Biol Chem. 2011 Aug 10;35(4):251-258.


Deep sequencing reveals as-yet-undiscovered small RNAs in Escherichia coli.
Shinhara A, Matsui M, Hiraoka K, Nomura W, et al.
BMC Genomics. 2011 Aug 24;12(1):428.


"DNA-Dressed Nanopore" for complementary sequence detection.
Mussi V, Fanzio P, Repetto L, Firpo G, et al.
Biosens Bioelectron. 2011 Aug 9. [Epub ahead of print]

The Scan

CDC Calls Delta "Variant of Concern"

CNN reports the US Centers for Disease Control and Prevention now considers the Delta variant of SARS-CoV-2 to be a "variant of concern."

From FDA to Venture Capital

Former FDA Commissioner Stephen Hahn is taking a position at a venture capital firm, leading some ethicists to raise eyebrows, according to the Washington Post.

Consent Questions

Nature News writes that there are questions whether informed consent was obtained for some submissions to a database of Y-chromosome profiles.

Cell Studies on Multimodal Single-Cell Analysis, Coronaviruses in Bats, Urban Microbiomes

In Cell this week: approach to analyze multimodal single-cell genomic data, analysis of bat coronaviruses, and more.