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


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

Boosters Chasing Variants

The New York Times reports that an FDA advisory panel is to weigh updated booster vaccines for COVID-19.

Not Yet

The World Health Organization says monkeypox is not yet a global emergency, the Washington Post reports.

More Proposed for Federal Research

Science reports that US House of Representatives panels are seeking to increase federal research funding.

PLOS Papers on Breast Cancer Metastasis, Left-Sided Cardiac Defects, SARS-CoV-2 Monitoring

In PLOS this week: link between breast cancer metastasis and CLIC4, sequencing analysis of left-sided cardiac defects, and more.