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Papers of Note: Dec 8, 2009


Sequencing-Related Papers of Note, Nov. 2009

Constitutional translocation breakpoint mapping by genome-wide paired-end sequencing identifies HACE1 as a putative Wilms tumor susceptibility gene.
Slade I, Stephens P, Douglas J, Barker K, Stebbings L, Abbaszadeh F, et al.
J Med Genet. 2009 Nov 30. [Epub ahead of print]

Chromatin profiling by directly sequencing small quantities of immunoprecipitated DNA.
Goren A, Ozsolak F, Shoresh N, Ku M, Adli M, Hart C, Gymrek M, Zuk O, Regev A, Milos PM, Bernstein BE.
Nat Methods. 2009 Nov 29. [Epub ahead of print]

JANE: efficient mapping of prokaryotic ESTs and variable length sequence reads on related template genomes.
Liang C, Schmid A, Lopez-Sanchez MJ, Moya A, Gross R, Bernhardt J, Dandekar T.
BMC Bioinformatics. 2009 Nov 29;10(1):391. [Epub ahead of print]
PMID: 19943962 [PubMed - as supplied by publisher]

DNA nanowire translocation phenomena in nanopores.
Chen L, Conlisk AT.
Biomed Microdevices. 2009 Nov 27. [Epub ahead of print]

Single nucleotide polymorphism discovery in rainbow trout by deep sequencing of a reduced representation library.
Castano-Sanchez C, Smith TP, Wiedmann RT, Vallejo RL, Salem M, Yao J, Rexroad CE 3rd.
BMC Genomics. 2009 Nov 25;10(1):559. [Epub ahead of print]

Use of high throughput sequencing to observe genome dynamics at a single cell level.
Parkhomchuk D, Amstislavskiy V, Soldatov A, Ogryzko V.
Proc Natl Acad Sci U S A. 2009 Nov 23. [Epub ahead of print]

Combining next-generation pyrosequencing with microarray for large scale expression analysis in non-model species.
Bellin D, Ferrarini A, Chimento A, Kaiser O, Levenkova N, Bouffard P, Delledonne M.
BMC Genomics. 2009 Nov 24;10(1):555. [Epub ahead of print]

Searching for SNPs with cloud computing.
Langmead B, Schatz MC, Lin J, Pop M, Salzberg SL.
Genome Biol. 2009 Nov 20;10(11):R134. [Epub ahead of print]

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De novo 454 sequencing of barcoded BAC pools for comprehensive gene survey and genome analysis in the complex genome of barley.
Steuernagel B, Taudien S, Gundlach H, Seidel M, Ariyadasa R, Schulte D, et al.
BMC Genomics. 2009 Nov 20;10:547.

BING: Biomedical informatics pipeline for Next Generation Sequencing.
Kriseman J, Busick C, Szelinger S, Dinu V.
J Biomed Inform. 2009 Nov 27. [Epub ahead of print]

3' tag digital gene expression profiling of human brain and universal reference RNA using Illumina Genome Analyzer.
Asmann YW, Klee EW, Thompson EA, Perez EA, Middha S, Oberg AL, et al.
BMC Genomics. 2009 Nov 16;10:531.

Analysis of short tandem repeats by parallel DNA threading.
Zajac P, Oberg C, Ahmadian A.
PLoS One. 2009 Nov 13;4(11):e7823.

Exome sequencing identifies the cause of a Mendelian disorder.
Ng SB, Buckingham KJ, Lee C, Bigham AW, Tabor HK, Dent KM, Huff CD, et al.
Nat Genet. 2009 Nov 13. [Epub ahead of print]

Model-based quality assessment and base-calling for second-generation sequencing data.
Bravo HC, Irizarry RA.
Biometrics. 2009 Nov 13. [Epub ahead of print]

DNA sequence capture and enrichment by microarray followed by next-generation sequencing for targeted resequencing: neurofibromatosis type 1 gene as a model.
Chou LS, Liu CS, Boese B, Zhang X, Mao R.
Clin Chem. 2009 Nov 12. [Epub ahead of print]

The effect of sequencing errors on metagenomic gene prediction.
Hoff KJ.
BMC Genomics. 2009 Nov 12;10:520.

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BFAST: an alignment tool for large scale genome resequencing.
Homer N, Merriman B, Nelson SF.
PLoS One. 2009 Nov 11;4(11):e7767.

Archived HIV-1 minority variants detected by ultra-deep pyrosequencing in provirus may be fully replication competent.
Rozera G, Abbate I, Bruselles A, Vlassi C, D'Offizi G, Narciso P, Chillemi G, et al.
AIDS. 2009 Nov 27;23(18):2541-3. No abstract available.

Sole-Search: an integrated analysis program for peak detection and functional annotation using ChIP-seq data.
Blahnik KR, Dou L, O'Geen H, McPhillips T, Xu X, Cao AR, Iyengar S, et al.
Nucleic Acids Res. 2009 Nov 11. [Epub ahead of print]

MBD-isolated genome sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome.
Serre D, Lee BH, Ting AH.
Nucleic Acids Res. 2009 Nov 11. [Epub ahead of print]

Detection of local protein structures along DNA using solid-state nanopores.
Kowalczyk SW, Hall AR, Dekker C.
Nano Lett. 2009 Nov 10. [Epub ahead of print]

Systematic subcellular localization of novel proteins identified by large-scale cDNA sequencing.
Simpson JC, Wellenreuther R, Poustka A, Pepperkok R, Wiemann S.
EMBO Rep. 2009 Dec;10(12):1363. Epub 2009 Nov 6. No abstract available.

Translocation of double-stranded DNA through membrane-adapted phi29 motor protein nanopores.
Wendell D, Jing P, Geng J, Subramaniam V, Lee TJ, Montemagno C, Guo P.
Nat Nanotechnol. 2009 Nov;4(11):765-72. Epub 2009 Sep 27.

Genome sequence, comparative analysis, and population genetics of the domestic horse.
Wade CM, Giulotto E, Sigurdsson S, Zoli M, Gnerre S, Imsland F, Lear TL, et al.
Science. 2009 Nov 6;326(5954):865-7.

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Human genome sequencing using unchained base Reads on self-assembling DNA nanoarrays.
Drmanac R, Sparks AB, Callow MJ, Halpern AL, Burns NL, Kermani BG, et al.
Science. 2009 Nov 5. [Epub ahead of print]

An integrated pipeline for next-generation sequencing and annotation of mitochondrial genomes.
Jex AR, Hall RS, Littlewood DT, Gasser RB.
Nucleic Acids Res. 2009 Nov 5. [Epub ahead of print]

Genome 10K: a proposal to obtain whole-genome sequence for 10,000 vertebrate species.
Genome 10K Community of Scientists.
J Hered. 2009 Nov-Dec;100(6):659-74. Epub 2009 Nov 5.

High-throughput sequencing of microdissected chromosomal regions.
Weise A, Timmermann B, Grabherr M, Werber M, Heyn P, Kosyakova N, et al.
Eur J Hum Genet. 2009 Nov 4. [Epub ahead of print]

A single-base resolution map of an archaeal transcriptome.
Wurtzel O, Sapra R, Chen F, Zhu Y, Simmons BA, Sorek R.
Genome Res. 2009 Nov 24. [Epub ahead of print]

The genome of the cucumber, Cucumis sativus L.
Huang S, Li R, Zhang Z, Li L, Gu X, Fan W, Lucas WJ, Wang X, Xie B, Ni P, et al.
Nat Genet. 2009 Dec;41(12):1275-81. Epub 2009 Nov 1.

An integrative approach to reveal driver gene fusions from paired-end sequencing data in cancer.
Wang XS, Prensner JR, Chen G, Cao Q, Han B, Dhanasekaran SM, Ponnala R, et al.
Nat Biotechnol. 2009 Nov;27(11):1005-11. Epub 2009 Nov 1.

Microdroplet-based PCR enrichment for large-scale targeted sequencing.
Tewhey R, Warner JB, Nakano M, Libby B, Medkova M, David PH, et al.
Nat Biotechnol. 2009 Nov;27(11):1025-31. Epub 2009 Nov 1.

High-resolution, high-throughput HLA genotyping by next-generation sequencing.
Bentley G, Higuchi R, Hoglund B, Goodridge D, Sayer D, Trachtenberg EA, Erlich HA.
Tissue Antigens. 2009 Nov;74(5):393-403.

ABySS-Explorer: visualizing genome sequence assemblies.
Nielsen CB, Jackman SD, Birol I, Jones SJ.
IEEE Trans Vis Comput Graph. 2009 Nov-Dec;15(6):881-8.

DNA strands from denatured duplexes are translocated through engineered protein nanopores at alkaline pH.
Maglia G, Henricus M, Wyss R, Li Q, Cheley S, Bayley H.
Nano Lett. 2009 Nov;9(11):3831-6.