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Papers of Note: Nov 10, 2009


Sequencing-Related Papers of Note, Oct. 2009

Major histocompatibility complex genotyping with massively parallel pyrosequencing.
Wiseman RW, Karl JA, Bimber BN, O'Leary CE, Lank SM, Tuscher JJ, Detmer AM, et al.
Nat Med. 2009 Nov;15(11):1322-6. Epub 2009 Oct 11.

inGAP: an integrated next-generation genome analysis pipeline.
Qi J, Zhao F, Buboltz A, Schuster SC.
Bioinformatics. 2009 Oct 30. [Epub ahead of print]

MicroRazerS: Rapid alignment of small RNA reads.
Emde AK, Grunert M, Weese D, Reinert K, Sperling SR.
Bioinformatics. 2009 Oct 29. [Epub ahead of print]

BARCRAWL and BARTAB: Software tools for the design and implementation of barcoded primers for highly multiplexed DNA sequencing.
Frank DN.
BMC Bioinformatics. 2009 Oct 29;10(1):362. [Epub ahead of print]

Single-nucleotide differences (SNDs) in the dbSNP database may lead to errors in genotyping and haplotyping studies.
Musumeci L, Arthur JW, Cheung FS, Hoque A, Lippman S, Reichardt JK.
Hum Mutat. 2009 Oct 29. [Epub ahead of print]

The GNUMAP algorithm: unbiased probabilistic mapping of oligonucleotides from next-generation sequencing.
Clement NL, Snell Q, Clement MJ, Hollenhorst PC, Purwar J, Graves BJ, et al.
Bioinformatics. 2009 Oct 27. [Epub ahead of print]

Genetic diagnosis by whole exome capture and massively parallel DNA sequencing.
Choi M, Scholl UI, Ji W, Liu T, Tikhonova IR, Zumbo P, Nayir A, Bakkaloglu A, et al.
Proc Natl Acad Sci U S A. 2009 Oct 27. [Epub ahead of print]

NGSView: an extensible open source editor for next-generation sequencing data.
Arner E, Hayashizaki Y, Daub CO.
Bioinformatics. 2009 Oct 24. [Epub ahead of print]

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DEGseq: an R package for identifying differentially expressed genes from RNA-seq data.
Wang L, Feng Z, Wang X, Wang X, Zhang X.
Bioinformatics. 2009 Oct 24. [Epub ahead of print]

Next-generation sequence analysis for mitochondrial disorders.
Vasta V, Ng SB, Turner EH, Shendure J, Hahn SH.
Genome Med. 2009 Oct 23;1(10):100. [Epub ahead of print]

DDBJ launches a new archive database with analytical tools for next-generation sequence data.
Kaminuma E, Mashima J, Kodama Y, Gojobori T, Ogasawara O, Okubo K, Takagi T, Nakamura Y.
Nucleic Acids Res. 2009 Oct 22. [Epub ahead of print]

The theory of discovering rare variants via DNA sequencing.
Wendl MC, Wilson RK.
BMC Genomics. 2009 Oct 20;10(1):485. [Epub ahead of print]

Bind-n-Seq: high-throughput analysis of in vitro protein-DNA interactions using massively parallel sequencing.
Zykovich A, Korf I, Segal DJ.
Nucleic Acids Res. 2009 Oct 20. [Epub ahead of print]

Large-scale single nucleotide polymorphism discovery in unsequenced genomes using second-generation high-throughput sequencing technology: applied to turkey.
Kerstens HH, Crooijmans RP, Veenendaal A, Dibbits BW, Chin-A-Woeng TF, et al.
BMC Genomics. 2009 Oct 16;10:479.

Enrichment of sequencing targets from the human genome by solution hybridization.
Tewhey R, Nakano M, Wang X, Pabon-Pena C, Novak B, Giuffre A, Lin E, et al.
Genome Biol. 2009 Oct 16;10(10):R116. [Epub ahead of print]

Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts.
Levin JZ, Berger MF, Adiconis X, Rogov P, Melnikov A, Fennell T, Nusbaum C, et al.
Genome Biol. 2009 Oct 16;10(10):R115. [Epub ahead of print]

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Characterization of meiotic crossovers and gene conversion by whole-genome sequencing in Saccharomyces cerevisiae.
Qi J, Wijeratne AJ, Tomsho LP, Hu Y, Schuster SC, Ma H.
BMC Genomics. 2009 Oct 15;10:475.

Investigating repetitively matching short sequencing reads: The enigmatic nature of H3K9me3.
Rosenfeld JA, Xuan Z, Desalle R.
Epigenetics. 2009 Oct 14;4(7). [Epub ahead of print]

Deep short-read sequencing of chromosome 17 from the mouse strains A/J and CAST/Ei identifies significant germline variation and candidate genes that regulate liver triglyceride levels.
Sudbery I, Stalker J, Simpson JT, Keane T, Rust AG, Hurles ME, Walter K, et al.
Genome Biol. 2009 Oct 13;10(10):R112. [Epub ahead of print]

Genome-wide analysis of allelic expression imbalance in human primary cells by high-throughput transcriptome resequencing.
Heap GA, Yang JH, Downes K, Healy BC, Hunt KA, Bockett N, Franke L, et al.
Hum Mol Genet. 2009 Oct 13. [Epub ahead of print]

miRExpress: analyzing high-throughput sequencing data for profiling microRNA expression.
Wang WC, Lin FM, Chang WC, Lin KY, Huang HD, Lin NS.
BMC Bioinformatics. 2009 Oct 12;10:328.

Comprehensive mapping of long-range interactions reveals folding principles of the human genome.
Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, et al.
Science. 2009 Oct 9;326(5950):289-93.

Characterization of unknown genetic modifications using high-throughput sequencing and computational subtraction.
Tengs T, Zhang H, Holst-Jensen A, Bohlin J, Butenko MA, Kristoffersen AB, et al.
BMC Biotechnol. 2009 Oct 8;9:87.

Staphylococcus aureus strain typing by single-molecule DNA mapping in fluidic microchips with fluorescent tags.
White EJ, Fridrikh SV, Chennagiri N, Cameron DB, Gauvin GP, Gilmanshin R.
Clin Chem. 2009 Oct 8. [Epub ahead of print]

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Slowing DNA translocation through nanopores using a solution containing organic salts.
de Zoysa RS, Jayawardhana DA, Zhao Q, Wang D, Armstrong DW, Guan X.
J Phys Chem B. 2009 Oct 8;113(40):13332-6.

Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution.
Shah SP, Morin RD, Khattra J, Prentice L, Pugh T, Burleigh A, Delaney A, Gelmon K, et al.
Nature. 2009 Oct 8;461(7265):809-13.

A simple method for directional transcriptome sequencing using Illumina technology.
Croucher NJ, Fookes MC, Perkins TT, Turner DJ, Marguerat SB, Keane T, Quail MA, et al.
Nucleic Acids Res. 2009 Oct 8. [Epub ahead of print]

Effect of noise on DNA sequencing via transverse electronic transport.
Krems M, Zwolak M, Pershin YV, Di Ventra M.
Biophys J. 2009 Oct 7;97(7):1990-6.

Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data.
Degner JF, Marioni JC, Pai AA, Pickrell JK, Nkadori E, Gilad Y, Pritchard JK.
Bioinformatics. 2009 Oct 6. [Epub ahead of print]

DNA profiling using solid-state nanopores: detection of DNA-binding molecules.
Wanunu M, Sutin J, Meller A.
Nano Lett. 2009 Oct;9(10):3498-502.

A pharmacogene database enhanced by the 1000 Genomes Project.
Gamazon ER, Zhang W, Huang RS, Dolan ME, Cox NJ.
Pharmacogenet Genomics. 2009 Oct;19(10):829-32.

The Scan

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