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Papers of Note: Jun 29, 2010

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Sequencing-Related Papers of Note, May 2010

Dual primer emulsion PCR for next-generation DNA sequencing.
Xu MY, Aragon AD, Mascarenas MR, Torrez-Martinez N, Edwards JS.
Biotechniques. 2010 May;48(5):409-12.


High-throughput sequencing for the identification of binding molecules from DNA-encoded chemical libraries.
Buller F, Steiner M, Scheuermann J, Mannocci L, et al.
Bioorg Med Chem Lett. 2010 May 20. [Epub ahead of print]


Effect of genome-wide association studies, direct-to-consumer genetic testing, and high-speed sequencing technologies on predictive genetic counselling for cancer risk.
Speicher MR, Geigl JB, Tomlinson IP.
Lancet Oncol. 2010 May 25. [Epub ahead of print]


SNP discovery performance of two second-generation sequencing platforms in the NOD2 gene region.
Melum E, May S, Schilhabel MB, Thomsen I, et al.
Hum Mutat. 2010 May 18;31(7):875-885. [Epub ahead of print]


Deep sequencing of human nuclear and cytoplasmic small RNAs reveals an unexpectedly complex subcellular distribution of miRNAs and tRNA 3' trailers.
Liao JY, Ma LM, Guo YH, Zhang YC, et al.
PLoS One. 2010 May 14;5(5):e10563.


A paired-end sequencing strategy to map the complex landscape of transcription initiation.
Ni T, Corcoran DL, Rach EA, Song S, et al.
Nat Methods. 2010 May 23. [Epub ahead of print]

Analyzing 454 amplicon resequencing experiments using the modular and database oriented Variant Identification Pipeline.
De Schrijver JM, De Leeneer K, Lefever S, Sabbe N, et al.
BMC Bioinformatics. 2010 May 20;11:269.


Second-generation sequencing of the mesothelioma tumor genome.
Bueno R, De Rienzo A, Dong L, Gordon GJ, et al.
PLoS One. 2010 May 13;5(5):e10612.


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Multiplexed resequencing analysis to identify rare variants in pooled DNA with barcode indexing using next-generation sequencer.
Mitsui J, Fukuda Y, Azuma K, Tozaki H, et al.
J Hum Genet. 2010 May 20. [Epub ahead of print]


DNA translocation and unzipping through a nanopore: some geometrical effects.
Muzard J, Martinho M, Mathé J, Bockelmann U, Viasnoff V.
Biophys J. 2010 May 19;98(10):2170-8.


Cost-effective sequencing of full-length cDNA clones powered by a de novo-reference hybrid assembly.
Kuroshu RM, Watanabe J, Sugano S, Morishita S, Suzuki Y, Kasahara M.
PLoS One. 2010 May 7;5(5):e10517


Rapid identification of heterozygous mutations in Drosophila melanogaster using genomic capture sequencing.
Wang H, Chattopadhyay A, Li Z, Daines B, et al.
Genome Res. 2010 May 14. [Epub ahead of print]


Deep sequencing reveals differential expression of microRNAs in favorable versus unfavorable neuroblastoma.
Schulte JH, Marschall T, Martin M, Rosenstiel P, et al.
Nucleic Acids Res. 2010 May 13. [Epub ahead of print]


Highly-multiplexed barcode sequencing: an efficient method for parallel analysis of pooled samples.
Smith AM, Heisler LE, St Onge RP, Farias-Hesson E, et al.
Nucleic Acids Res. 2010 May 11. [Epub ahead of print]


A 454 multiplex sequencing method for rapid and reliable genotyping of highly polymorphic genes in large-scale studies.
Galan M, Guivier E, Caraux G, Charbonnel N, Cosson JF.
BMC Genomics. 2010 May 11;11:296.


Modeling non-uniformity in short-read rates in RNA-seq data.
Li J, Jiang H, Wong WH.
Genome Biol. 2010 May 11;11(5):R50. [Epub ahead of print]

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Ultra-high throughput sequencing-based small RNA discovery and discrete statistical biomarker analysis in a collection of cervical tumours and matched controls.
Witten D, Tibshirani R, Gu SG, Fire A, Lui WO.
BMC Biol. 2010 May 11;8:58.


Massively parallel sequencing of pooled DNA samples — the next generation of molecular markers.
Futschik A, Schlötterer C.
Genetics. 2010 May 10. [Epub ahead of print]


Sensitivity of noninvasive prenatal detection of fetal aneuploidy from maternal plasma using shotgun sequencing is limited only by counting statistics.
Fan HC, Quake SR.
PLoS One. 2010 May 3;5(5):e10439.


Direct detection of DNA methylation during single-molecule, real-time sequencing.
Flusberg BA, Webster DR, Lee JH, Travers KJ, et al.
Nat Methods. 2010 Jun;7(6):461-5. Epub 2010 May 9.


Tracing the derivation of embryonic stem cells from the inner cell mass by single-cell RNA-seq analysis.
Tang F, Barbacioru C, Bao S, Lee C, et al.
Cell Stem Cell. 2010 May 7;6(5):468-78.


Comparison of standard PCR/cloning to single genome sequencing for analysis of HIV-1 populations.
Jordan MR, Kearney M, Palmer S, Shao W, et al.
J Virol Methods. 2010 May 6. [Epub ahead of print]


Massively parallel sequencing of exons on the X chromosome identifies RBM10 as the gene that causes a syndromic form of cleft palate.
Johnston JJ, Teer JK, Cherukuri PF, Hansen NF, et al.
Am J Hum Genet. 2010 May 14;86(5):743-8. Epub 2010 May 6.


Targeted investigation of the Neandertal genome by array-based sequence capture.
Burbano HA, Hodges E, Green RE, Briggs AW, et al.
Science. 2010 May 7;328(5979):723-5.


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A comparison of massively parallel nucleotide sequencing with oligonucleotide microarrays for global transcription profiling.
Bradford JR, Hey Y, Yates T, Li Y, et al.
BMC Genomics. 2010 May 5;11:282.


Urea facilitates the translocation of single-stranded DNA and RNA through the alpha-hemolysin nanopore.
Japrung D, Henricus M, Li Q, Maglia G, Bayley H.
Biophys J. 2010 May 19;98(9):1856-63.


Direct sequencing of the human microbiome readily reveals community differences.
Kuczynski J, Costello EK, Nemergut DR, Zaneveld J, et al.
Genome Biol. 2010 May 5;11(5):210. [Epub ahead of print]


Characterization of missing human genome sequences and copy-number polymorphic insertions.
Kidd JM, Sampas N, Antonacci F, Graves T, et al.
Nat Methods. 2010 May;7(5):365-71.


Analysis of multiple EMS-mutagenized Caenorhabditis elegans strains by whole genome sequencing.
Sarin S, Bertrand V, Bigelow H, Boyanov A, et al.
Genetics. 2010 May 3. [Epub ahead of print]


Whole-genome profiling of mutagenesis in Caenorhabditis elegans.
Flibotte S, Edgley ML, Chaudhry I, Taylor J, et al.
Genetics. 2010 May 3. [Epub ahead of print]


Using deep sequencing to characterize the biophysical mechanism of a transcriptional regulatory sequence.
Kinney JB, Murugan A, Callan CG Jr, Cox EC.
Proc Natl Acad Sci U S A. 2010 May 18;107(20):9158-63. Epub 2010 May 3.


De novo mutations of SETBP1 cause Schinzel-Giedion syndrome.
Hoischen A, van Bon BW, Gilissen C, Arts P, et al.
Nat Genet. 2010 Jun;42(6):483-5. Epub 2010 May 2.


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Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation.
Trapnell C, Williams BA, Pertea G, Mortazavi A, et al.
Nat Biotechnol. 2010 May;28(5):511-5. Epub 2010 May 2.
PMID: 20436464 [PubMed - in process]


Single base-resolution methylome of the silkworm reveals a sparse epigenomic map.
Xiang H, Zhu J, Chen Q, Dai F, et al.
Nat Biotechnol. 2010 May;28(5):516-20. Epub 2010 May 2.


Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs.
Guttman M, Garber M, Levin JZ, Donaghey J, et al.
Nat Biotechnol. 2010 May;28(5):503-10. Epub 2010 May 2.


Clinical assessment incorporating a personal genome.
Ashley EA, Butte AJ, Wheeler MT, Chen R, et al.
Lancet. 2010 May 1;375(9725):1525-35.


Challenges in the clinical application of whole-genome sequencing.
Ormond KE, Wheeler MT, Hudgins L, Klein TE, et al.
Lancet. 2010 May 15;375(9727):1749-51. Epub 2010 Apr 29.


Intensity normalization improves color calling in SOLiD sequencing.
Wu H, Irizarry RA, Bravo HC.
Nat Methods. 2010 May;7(5):336-7. No abstract available.


Analysis of ancient human genomes: using next generation sequencing, 20-fold coverage of the genome of a 4,000-year-old human from Greenland has been obtained.
Shapiro B, Hofreiter M.
Bioessays. 2010 May;32(5):388-91.


Characterization of the RNA content of chromatin.
Mondal T, Rasmussen M, Pandey GK, Isaksson A, Kanduri C.
Genome Res. 2010 May 13. [Epub ahead of print]


An efficient strategy for sequencing-by-synthesis.
Gao L, Lu H, Xu L, Lu Z.
J Nanosci Nanotechnol. 2010 May;10(5):2988-93.

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