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Papers of Note: Sep 15, 2009

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Sequencing-Related Papers of Note, Aug. 2009

Personalized copy number and segmental duplication maps using next-generation sequencing.
Alkan C, Kidd JM, Marques-Bonet T, Aksay G, Antonacci F, Hormozdiari F, et al.
Nat Genet. 2009 Aug 30. [Epub ahead of print]


Complete resequencing of 40 genomes reveals domestication events and genes in silkworm (Bombyx).
Xia Q, Guo Y, Zhang Z, Li D, Xuan Z, Li Z, Dai F, Li Y, Cheng D, Li R, Cheng T, Jiang T, Becquet C, et al.
Science. 2009 Aug 27. [Epub ahead of print]


Assisted assembly: how to improve a de novo genome assembly by using related species.
Gnerre S, Lander ES, Lindblad-Toh K, Jaffe DB.
Genome Biol. 2009 Aug 27;10(8):R88. [Epub ahead of print]


Benchmarking next-generation transcriptome sequencing for functional and evolutionary genomics.
Gibbons JG, Janson EM, Hittinger CT, Johnston M, Abbot P, Rokas A.
Mol Biol Evol. 2009 Aug 25. [Epub ahead of print]


Mapping accessible chromatin regions using Sono-Seq.
Auerbach RK, Euskirchen G, Rozowsky J, Lamarre-Vincent N, Moqtaderi Z, Lefrançois P, et al.
Proc Natl Acad Sci U S A. 2009 Aug 18. [Epub ahead of print]


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Rapid high-throughput HLA typing by massively-parallel pyrosequencing for high-resolution allele identification.
Gabriel C, Danzer M, Hackl C, Kopal G, Hufnagl P, Hofer K, Polin H, Stabentheiner S, Pröll J.
Hum Immunol. 2009 Aug 22. [Epub ahead of print]


Characterization of circulating DNA by parallel tagged sequencing on the 454 platform.
van der Vaart M, Semenov DV, Kuligina EV, Richter VA, Pretorius PJ.
Clin Chim Acta. 2009 Aug 19. [Epub ahead of print]


Analyzing diet of small herbivores: the efficiency of DNA barcoding coupled with high-throughput pyrosequencing for deciphering the composition of complex plant mixtures.
Soininen EM, Valentini A, Coissac E, Miquel C, Gielly L, Brochmann C, Brysting AK, et al.
Front Zool. 2009 Aug 20;6(1):16. [Epub ahead of print]


Discrimination of single base substitutions in a DNA strand immobilized in a biological nanopore.
Purnell RF, Schmidt JJ.
ACS Nano. 2009 Aug 20. [Epub ahead of print]


High throughput sequencing in mice: a platform comparison identifies a preponderance of cryptic SNPs.
Walter NA, Bottomly D, Laderas T, Mooney MA, Darakjian P, Searles RP, Harrington CA, et al.
BMC Genomics. 2009 Aug 17;10(1):379. [Epub ahead of print]


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Sensitive digital quantification of DNA methylation in clinical samples.
Li M, Chen WD, Papadopoulos N, Goodman SN, Bjerregaard NC, Laurberg S, Levin B, et al.
Nat Biotechnol. 2009 Aug 16. [Epub ahead of print]


Targeted capture and massively parallel sequencing of 12 human exomes.
Ng SB, Turner EH, Robertson PD, Flygare SD, Bigham AW, Lee C, Shaffer T, et al.
Nature. 2009 Aug 16. [Epub ahead of print]


Improved base calling for the Illumina Genome Analyzer using machine learning strategies.
Kircher M, Stenzel U, Kelso J.
Genome Biol. 2009 Aug 14;10(8):R83. [Epub ahead of print]


LookSeq: a browser-based viewer for deep sequencing data.
Manske HM, Kwiatkowski DP.
Genome Res. 2009 Aug 13. [Epub ahead of print]


PerM: efficient mapping of short sequencing reads with periodic full sensitive spaced seeds.
Chen Y, Souaiaia T, Chen T.
Bioinformatics. 2009 Aug 13. [Epub ahead of print]


Application of massive parallel sequencing to whole genome SNP discovery in the porcine genome.
Amaral AJ, Megens HJ, Kerstens HH, Heuven HC, Dibbits B, Crooijmans RP, Dunnen JD, Groenen MA.
BMC Genomics. 2009 Aug 12;10(1):374. [Epub ahead of print]


Analysis of splicing patterns by pyrosequencing.
Méreau A, Anquetil V, Cibois M, Noiret M, Primot A, Vallée A, Paillard L.
Nucleic Acids Res. 2009 Aug 11. [Epub ahead of print]


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Single-molecule sequencing of an individual human genome.
Pushkarev D, Neff NF, Quake SR.
Nat Biotechnol. 2009 Sep;27(9):847-50. Epub 2009 Aug 10.


Digital transcriptome profiling using selective hexamer priming for cDNA synthesis.
Armour CD, Castle JC, Chen R, Babak T, Loerch P, Jackson S, Shah JK, Dey J, et al.
Nat Methods. 2009 Sep;6(9):647-9. Epub 2009 Aug 9.


Accurate determination of microbial diversity from 454 pyrosequencing data.
Quince C, Lanzén A, Curtis TP, Davenport RJ, Hall N, Head IM, Read LF, Sloan WT.
Nat Methods. 2009 Sep;6(9):639-41. Epub 2009 Aug 9.


BreakDancer: an algorithm for high-resolution mapping of genomic structural variation.
Chen K, Wallis JW, McLellan MD, Larson DE, Kalicki JM, Pohl CS, McGrath SD, et al.
Nat Methods. 2009 Sep;6(9):677-81. Epub 2009 Aug 9.


Whole genome sequencing of a single Bos taurus animal for single nucleotide polymorphism discovery.
Eck SH, Benet-Pagès A, Flisikowski K, Meitinger T, Fries R, Strom TM.
Genome Biol. 2009 Aug 6;10(8):R82. [Epub ahead of print]


Recurring mutations found by sequencing an acute myeloid leukemia genome.
Mardis ER, Ding L, Dooling DJ, Larson DE, McLellan MD, Chen K, Koboldt DC, et al.
N Engl J Med. 2009 Sep 10;361(11):1058-66. Epub 2009 Aug 5.


Sensitive and accurate detection of copy number variants using read depth of coverage.
Yoon S, Xuan Z, Makarov V, Ye K, Sebat J.
Genome Res. 2009 Sep;19(9):1586-92. Epub 2009 Aug 5.


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Statistical aspects of discerning indel-type structural variation via DNA sequence alignment.
Wendl MC, Wilson RK.
BMC Genomics. 2009 Aug 5;10(1):359. [Epub ahead of print]


Design of a high density SNP genotyping assay in the pig using SNPs identified and characterized by next generation sequencing technology.
Ramos AM, Crooijmans RP, Affara NA, Amaral AJ, Archibald AL, Beever JE, Bendixen C, et al.
PLoS One. 2009 Aug 5;4(8):e6524.


ShortRead: a Bioconductor package for input, quality assessment, and exploration of high throughput sequence data.
Morgan M, Anders S, Lawrence M, Aboyoun P, Pagès H, Gentleman R.
Bioinformatics. 2009 Aug 3. [Epub ahead of print]


Comparison of next generation sequencing technologies for transcriptome characterization.
Wall PK, Leebens-Mack J, Chanderbali AS, Barakat A, Wolcott E, Liang H, Landherr L, et al.
BMC Genomics. 2009 Aug 1;10:347.


SHOREmap: simultaneous mapping and mutation identification by deep sequencing.
Schneeberger K, Ossowski S, Lanz C, Juul T, Petersen AH, Nielsen KL, Jørgensen JE, Weigel D, Andersen SU.
Nat Methods. 2009 Aug;6(8):550-1. No abstract available.


MAQGene: software to facilitate C. elegans mutant genome sequence analysis.
Bigelow H, Doitsidou M, Sarin S, Hobert O.
Nat Methods. 2009 Aug;6(8):549. No abstract available.


Distinguishing single- and double-stranded nucleic acid molecules using solid-state nanopores.
Skinner GM, van den Hout M, Broekmans O, Dekker C, Dekker NH.
Nano Lett. 2009 Aug;9(8):2953-60.

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