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Papers of Note: Jan 5, 2010


Sequencing-Related Papers of Note, Dec. 2009

Improving the efficiency of genomic loci capture using oligonucleotide arrays for high throughput resequencing.
Lee H, O'Connor BD, Merriman B, Funari VA, Homer N, Chen Z, Cohn DH, Nelson SF.
BMC Genomics. 2009 Dec 31;10(1):646. [Epub ahead of print]

Differentially expressed alternatively spliced genes in malignant pleural mesothelioma identified using massively parallel transcriptome sequencing.
Dong L, Jensen RV, De Rienzo A, Gordon GJ, Xu Y, Sugarbaker DJ, Bueno R.
BMC Med Genet. 2009 Dec 31;10(1):149. [Epub ahead of print]

High-throughput sequencing of retrotransposon integration provides a saturated profile of target activity in Schizosaccharomyces pombe.
Guo Y, Levin HL.
Genome Res. 2009 Dec 29. [Epub ahead of print]

High throughput sequencing and proteomics to identify immunogenic proteins of a new pathogen: the dirty genome approach.
Greub G, Kebbi-Beghdadi C, Bertelli C, Collyn F, Riederer BM, Yersin C, Croxatto A, Raoult D.
PLoS One. 2009 Dec 23;4(12):e8423.

Mutations in TRPV4 cause Charcot-Marie-Tooth disease type 2C.
Landouré G, Zdebik AA, Martinez TL, Burnett BG, Stanescu HC, Inada H, Shi Y, Taye AA, Kong L, et al.
Nat Genet. 2009 Dec 27. [Epub ahead of print]

Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library.
Lam HY, Mu XJ, Stütz AM, Tanzer A, Cayting PD, Snyder M, Kim PM, Korbel JO, Gerstein MB.
Nat Biotechnol. 2009 Dec 27. [Epub ahead of print]

Next generation transcriptomes for next generation genomes using est2assembly.
Papanicolaou A, Stierli R, Ffrench-Constant RH, Heckel DG.
BMC Bioinformatics. 2009 Dec 24;10(1):447. [Epub ahead of print]

Complex landscapes of somatic rearrangement in human breast cancer genomes.
Stephens PJ, McBride DJ, Lin ML, Varela I, Pleasance ED, Simpson JT, Stebbings LA, Leroy C, et al.
Nature. 2009 Dec 24;462(7276):1005-10.

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A blind deconvolution approach to high-resolution mapping of transcription factor binding sites from ChIP-seq data.
Lun DS, Sherrid A, Weiner B, Sherman DR, Galagan JE.
Genome Biol. 2009 Dec 22;10(12):R142. [Epub ahead of print]

Pebble and rock band: heuristic resolution of repeats and scaffolding in the velvet short-read de novo assembler.
Zerbino DR, McEwen GK, Margulies EH, Birney E.
PLoS One. 2009 Dec 22;4(12):e8407.

Maternal plasma DNA analysis with massively parallel sequencing by ligation for noninvasive prenatal diagnosis of trisomy 21.
Chiu RW, Sun H, Akolekar R, Clouser C, Lee C, McKernan K, Zhou D, Nicolaides KH, Lo YM.
Clin Chem. 2009 Dec 21. [Epub ahead of print]

Electrostatic focusing of unlabelled DNA into nanoscale pores using a salt gradient.
Wanunu M, Morrison W, Rabin Y, Grosberg AY, Meller A.
Nat Nanotechnol. 2009 Dec 20. [Epub ahead of print]

RNA-seq gene expression estimation with read mapping uncertainty.
Li B, Ruotti V, Stewart RM, Thomson JA, Dewey CN.
Bioinformatics. 2009 Dec 18. [Epub ahead of print]

Copy number variant detection in inbred strains from short read sequence data.
Simpson JT, McIntyre RE, Adams DJ, Durbin R.
Bioinformatics. 2009 Dec 18. [Epub ahead of print]

WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads.
Gerlach W, Junemann S, Tille F, Goesmann A, Stoye J.
BMC Bioinformatics. 2009 Dec 18;10(1):430. [Epub ahead of print]

De novo assembly of human genomes with massively parallel short read sequencing.
Li R, Zhu H, Ruan J, Qian W, Fang X, Shi Z, Li Y, Li S, Shan G, Kristiansen K, Li S, Yang H, Wang J, Wang J.
Genome Res. 2009 Dec 17. [Epub ahead of print]

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A SNP discovery method to assess variant allele probability from next-generation resequencing data.
Shen Y, Wan Z, Coarfa C, Drabek R, Chen L, Ostrowski EA, Liu Y, Weinstock GM, Wheeler DA, Gibbs RA, Yu F.
Genome Res. 2009 Dec 17. [Epub ahead of print]

Identification of MIR390a precursor processing-defective mutants in Arabidopsis by direct genome sequencing.
Cuperus JT, Montgomery TA, Fahlgren N, Burke RT, Townsend T, Sullivan CM, Carrington JC.
Proc Natl Acad Sci U S A. 2009 Dec 14. [Epub ahead of print]

A practical comparison of methods for detecting transcription factor binding sites in ChIP-seq experiments.
Laajala TD, Raghav S, Tuomela S, Lahesmaa R, Aittokallio T, Elo LL.
BMC Genomics. 2009 Dec 18;10(1):618. [Epub ahead of print]

A small-cell lung cancer genome with complex signatures of tobacco exposure.
Pleasance ED, Stephens PJ, O'Meara S, McBride DJ, Meynert A, Jones D, Lin ML, Beare D, et al.
Nature. 2009 Dec 16. [Epub ahead of print]

A comprehensive catalogue of somatic mutations from a human cancer genome.
Pleasance ED, Cheetham RK, Stephens PJ, McBride DJ, Humphray SJ, Greenman CD, Varela I, et al.
Nature. 2009 Dec 16. [Epub ahead of print]

The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants.
Cock PJ, Fields CJ, Goto N, Heuer ML, Rice PM.
Nucleic Acids Res. 2009 Dec 16. [Epub ahead of print]

Impact of genome assembly status on ChIP-Seq and ChIP-PET data mapping.
Buisine N, Sachs L.
BMC Res Notes. 2009 Dec 16;2(1):257. [Epub ahead of print]

Discovery of candidate disease genes in ENU-induced mouse mutants by large-scale sequencing, including a splice-site mutation in nucleoredoxin.
Boles MK, Wilkinson BM, Wilming LG, Liu B, Probst FJ, Harrow J, Grafham D, Hentges KE, et al.
PLoS Genet. 2009 Dec;5(12):e1000759. Epub .

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The sequence and de novo assembly of the giant panda genome.
Li R, Fan W, Tian G, Zhu H, He L, Cai J, Huang Q, Cai Q, Li B, Bai Y, Zhang Z, Zhang Y, Wang W, et al.
Nature. [Epub ahead of print]

Estimating DNA coverage and abundance in metagenomes using a gamma approximation.
Hooper SD, Dalevi D, Pati A, Mavromatis K, Ivanova NN, Kyrpides NC.
Bioinformatics. [Epub ahead of print]

SeqBuster, a bioinformatic tool for the processing and analysis of small RNAs datasets, reveals ubiquitous miRNA modifications in human embryonic cells.
Pantano L, Estivill X, Martí E.
Nucleic Acids Res. [Epub ahead of print]

QDD: a user-friendly program to select microsatellite markers and design primers from large sequencing projects.
Meglécz E, Costedoat C, Dubut V, Gilles A, Malausa T, Pech N, Martin JF.
Bioinformatics. [Epub ahead of print]

Targeted next-generation sequencing appoints C16orf57 as clericuzio-type poikiloderma with neutropenia gene.
Volpi L, Roversi G, Colombo EA, Leijsten N, Concolino D, Calabria A, Mencarelli MA, Fimiani M, Macciardi F, Pfundt R, Schoenmakers EF, Larizza L.
Am J Hum Genet. [Epub ahead of print] No abstract available.

Defining the healthy "core microbiome" of oral microbial communities.
Zaura E, Keijser BJ, Huse SM, Crielaard W.
BMC Microbiol. 9(1):259. [Epub ahead of print]

Multichannel simultaneous measurements of single-molecule translocation in alpha-hemolysin nanopore array.
Osaki T, Suzuki H, Le Pioufle B, Takeuchi S.
Anal Chem. 2009 Dec 15;81(24):9866-70.

Building the sequence map of the human pan-genome.
Li R, Li Y, Zheng H, Luo R, Zhu H, Li Q, Qian W, Ren Y, Tian G, Li J, Zhou G, Zhu X, Wu H, Qin J, et al.
Nat Biotechnol. 2009 Dec 7. [Epub ahead of print]

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ChIP-seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells.
Ouyang Z, Zhou Q, Wong WH.
Proc Natl Acad Sci U S A. 2009 Dec 7. [Epub ahead of print]

deepBase: a database for deeply annotating and mining deep sequencing data.
Yang JH, Shao P, Zhou H, Chen YQ, Qu LH.
Nucleic Acids Res. 2010 Jan;38(Database issue):D123-30. Epub 2009 Dec 4.

Archiving next generation sequencing data.
Shumway M, Cochrane G, Sugawara H.
Nucleic Acids Res. 2010 Jan;38(Database issue):D870-1. Epub 2009 Dec 3.

Enzyme-modulated DNA translocation through a nanopore.
Panwar AS, Muthukumar M.
J Am Chem Soc. 2009 Dec 30;131(51):18563-70.

Breakpoint analysis of balanced chromosome rearrangements by next-generation paired-end sequencing.
Chen W, Ullmann R, Langnick C, Menzel C, Wotschofsky Z, Hu H, Döring A, Hu Y, Kang H, et al.
Eur J Hum Genet. 2009 Dec 2. [Epub ahead of print]

mRNA-sequencing whole transcriptome analysis of a single cell on the SOLiD system.
Lao KQ, Tang F, Barbacioru C, Wang Y, Nordman E, Lee C, Xu N, Wang X, Tuch B, Bodeau J, et al.
J Biomol Tech. 2009 Dec;20(5):266-71.

High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis.
Patwardhan RP, Lee C, Litvin O, Young DL, Pe'er D, Shendure J.
Nat Biotechnol. 2009 Dec;27(12):1173-5. Epub.

Data analysis of translocation events in nanopore experiments.
Anal Chem. 2009 Dec 1;81(23):9689-94.
Pedone D, Firnkes M, Rant U.

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 Dec;37(22):e151. Epub

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Deep sequencing to reveal new variants in pooled DNA samples.
Out AA, van Minderhout IJ, Goeman JJ, Ariyurek Y, Ossowski S, Schneeberger K, Weigel D, et al.
Hum Mutat. 2009 Dec;30(12):1703-12.

A simple method for directional transcriptome sequencing using Illumina technology.
Croucher NJ, Fookes MC, Perkins TT, Turner DJ, Marguerat SB, Keane T, Quail MA, He M, et al.
Nucleic Acids Res. 2009 Dec;37(22):e148. Epub.

Electrophoretic force on a protein-coated DNA molecule in a solid-state nanopore.
Hall AR, van Dorp S, Lemay SG, Dekker C.
Nano Lett. 2009 Dec;9(12):4441-5.

The Scan

Germline-Targeting HIV Vaccine Shows Promise in Phase I Trial

A National Institutes of Health-led team reports in Science that a broadly neutralizing antibody HIV vaccine induced bnAb precursors in 97 percent of those given the vaccine.

Study Uncovers Genetic Mutation in Childhood Glaucoma

A study in the Journal of Clinical Investigation ties a heterozygous missense variant in thrombospondin 1 to childhood glaucoma.

Gene Co-Expression Database for Humans, Model Organisms Gets Update

GeneFriends has been updated to include gene and transcript co-expression networks based on RNA-seq data from 46,475 human and 34,322 mouse samples, a new paper in Nucleic Acids Research says.

New Study Investigates Genomics of Fanconi Anemia Repair Pathway in Cancer

A Rockefeller University team reports in Nature that FA repair deficiency leads to structural variants that can contribute to genomic instability.