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Papers of Note: Mar 30, 2010


Sequencing-Related Papers of Note, February 2010

RNA-Seq analysis to capture the transcriptome landscape of a single cell.
Tang F, Barbacioru C, Nordman E, Li B, Xu N, Bashkirov VI, Lao K, Surani MA.
Nat Protoc. 2010;5(3):516-35. Epub 2010 Feb 25.

Assessing serotonin receptor mRNA editing frequency by a novel ultra high-throughput sequencing method.
Abbas AI, Urban DJ, Jensen NH, Farrell MS, Kroeze WK, Mieczkowski P, Wang Z, Roth BL.
Nucleic Acids Res. 2010 Feb 25. [Epub ahead of print]

Gene-specific FACS sorting method for target selection in high-throughput amplicon sequencing.
Sandberg J, Neiman M, Ahmadian A, Lundeberg J.
BMC Genomics. 2010 Feb 26;11:140.

PANGEA: pipeline for analysis of next generation amplicons.
Giongo A, Crabb DB, Davis-Richardson AG, Chauliac D, Mobberley JM, Gano KA, Mukherjee N, et al. ISME J. 2010 Feb 25. [Epub ahead of print]

Analysis of chemotherapy response programs in ovarian cancers by the next-generation sequencing technologies.
Cheng L, Lu W, Kulkarni B, Pejovic T, Yan X, Chiang JH, Hood L, Odunsi K, Lin B.
Gynecol Oncol. 2010 Feb 22. [Epub ahead of print]

Genome-wide analysis of aberrant methylation in human breast cancer cells using methyl-DNA immunoprecipitation combined with high-throughput sequencing.
Ruike Y, Imanaka Y, Sato F, Shimizu K, Tsujimoto G.
BMC Genomics. 2010 Feb 25;11:137.

ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing.
Li G, Fullwood MJ, Xu H, Mulawadi FH, Velkov S, Vega V, Ariyaratne PN, Mohamed YB, et al. Genome Biol. 2010 Feb 25;11(2):R22. [Epub ahead of print]

Whole methylome analysis by ultra-deep sequencing using two-base encoding.
Bormann Chung CA, Boyd VL, McKernan KJ, Fu Y, Monighetti C, Peckham HE, Barker M.
PLoS One. 2010 Feb 22;5(2):e9320.

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Integrative analysis of the melanoma transcriptome.
Berger MF, Levin JZ, Vijayendran K, Sivachenko A, Adiconis X, Maguire J, Johnson LA, et al.
Genome Res. 2010 Feb 23. [Epub ahead of print]

DraGnET: software for storing, managing and analyzing annotated draft genome sequence data.
Duncan S, Sirkanungo R, Miller L, Phillips GJ.
BMC Bioinformatics. 2010 Feb 22;11(1):100.

HIV drug resistance surveillance using pooled pyrosequencing.
Ji H, Massé N, Tyler S, Liang B, Li Y, Merks H, Graham M, Sandstrom P, Brooks J.
PLoS One. 2010 Feb 17;5(2):e9263.

Tumor transcriptome sequencing reveals allelic expression imbalances associated with copy number alterations.
Tuch BB, Laborde RR, Xu X, Gu J, Chung CB, Monighetti CK, Stanley SJ, Olsen KD, et al.
PLoS One. 2010 Feb 19;5(2):e9317.

Controlling nanopore size, shape and stability.
van den Hout M, Hall AR, Wu MY, Zandbergen HW, Dekker C, Dekker NH.
Nanotechnology. 2010 Mar 19;21(11):115304. Epub 2010 Feb 22.

Targeted capture and next-generation sequencing identifies C9orf75, encoding taperin, as the mutated gene in nonsyndromic deafness DFNB79.
Rehman AU, Morell RJ, Belyantseva IA, Khan SY, Boger ET, Shahzad M, Ahmed ZM, Riazuddin S, et al.
Am J Hum Genet. 2010 Mar 12;86(3):378-88. Epub 2010 Feb 18.

Evaluation of statistical methods for normalization and differential expression in mRNA-seq experiments.
Bullard JH, Purdom E, Hansen KD, Dudoit S.
BMC Bioinformatics. 2010 Feb 18;11:94.

Finding sRNA generative locales from high-throughput sequencing data with NiBLS.
MacLean D, Moulton V, Studholme DJ.
BMC Bioinformatics. 2010 Feb 18;11:93.

Complete Khoisan and Bantu genomes from southern Africa.
Schuster SC, Miller W, Ratan A, Tomsho LP, Giardine B, Kasson LR, Harris RS, Petersen DC, Zhao F, et al.
Nature. 2010 Feb 18;463(7283):943-7.

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Accurate SNP and mutation detection by targeted custom microarray-based genomic enrichment of short-fragment sequencing libraries.
Mokry M, Feitsma H, Nijman IJ, de Bruijn E, van der Zaag PJ, Guryev V, Cuppen E.
Nucleic Acids Res. 2010 Feb 17. [Epub ahead of print]

Monitoring genomic sequences during SELEX using high-throughput sequencing: neutral SELEX.
Zimmermann B, Gesell T, Chen D, Lorenz C, Schroeder R.
PLoS One. 2010 Feb 11;5(2):e9169.

Next-generation sequencing of a 40 Mb linkage interval reveals TSPAN12 mutations in patients with familial exudative vitreoretinopathy.
Nikopoulos K, Gilissen C, Hoischen A, van Nouhuys CE, Boonstra FN, Blokland EA, Arts P, et al.
Am J Hum Genet. 2010 Feb 12;86(2):240-7.

Prediction of alternative isoforms from exon expression levels in RNA-seq experiments.
Richard H, Schulz MH, Sultan M, Nürnberger A, Schrinner S, Balzereit D, Dagand E, Rasche A, et al.
Nucleic Acids Res. 2010 Feb 11. [Epub ahead of print]

Genome sequencing and analysis of the model grass Brachypodium distachyon.
International Brachypodium Initiative.
Nature. 2010 Feb 11;463(7282):763-8.

Ancient human genome sequence of an extinct Palaeo-Eskimo.
Rasmussen M, Li Y, Lindgreen S, Pedersen JS, Albrechtsen A, Moltke I, Metspalu M, Metspalu E, et al.
Nature. 2010 Feb 11;463(7282):757-62.

Fast and SNP-tolerant detection of complex variants and splicing in short reads.
Wu TD, Nacu S.
Bioinformatics. 2010 Apr 1;26(7):873-81. Epub 2010 Feb 10.

Rapid interactome profiling by massive sequencing.
Di Niro R, Sulic AM, Mignone F, D'Angelo S, Bordoni R, Iacono M, Marzari R, Gaiotto T, Lavric M, et al.
Nucleic Acids Res. 2010 Feb 9. [Epub ahead of print]

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Microindel detection in short-read sequence data.
Krawitz P, Rödelsperger C, Jäger M, Jostins L, Bauer S, Robinson PN.
Bioinformatics. 2010 Mar 15;26(6):722-9. Epub 2010 Feb 9.

An effective approach for identification of in vivo protein-DNA binding sites from paired-end ChIP-seq data.
Wang C, Xu J, Zhang D, Wilson ZA, Zhang D.
BMC Bioinformatics. 2010 Feb 9;11:81.

Targeted high throughput sequencing of a cancer-related exome subset by specific sequence capture with a fully automated microarray platform.
Summerer D, Schracke N, Wu H, Cheng Y, Bau S, Stähler CF, Stähler PF, Beier M.
Genomics. 2010 Feb 6. [Epub ahead of print]

A scalable, fully automated process for construction of sequence-ready barcoded libraries for 454.
Lennon NJ, Lintner RE, Anderson S, Alvarez P, Barry A, Brockman W, Daza R, Erlich RL, et al.
Genome Biol. 2010 Feb 5;11(2):R15. [Epub ahead of print]

SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors.
Goya R, Sun MG, Morin RD, Leung G, Ha G, Wiegand KC, Senz J, Crisan A, Marra MA, Hirst M, et al.
Bioinformatics. 2010 Mar 15;26(6):730-6. Epub 2010 Feb 3.

The Roche Cancer Genome database (RCGDB).
Küntzer J, Eggle D, Lenhof HP, Burtscher H, Klostermann S.
Hum Mutat. 2010 Feb 2. [Epub ahead of print]

A new strategy for genome assembly using short sequence reads and reduced representation libraries.
Young AL, Abaan HO, Zerbino D, Mullikin JC, Birney E, Margulies EH.
Genome Res. 2010 Feb;20(2):249-56.

An integrated system for DNA sequencing by synthesis using novel nucleotide analogues.
Guo J, Yu L, Turro NJ, Ju J.
Acc Chem Res. 2010 Feb 3. [Epub ahead of print]

Identification of novel non-coding RNAs using profiles of short sequence reads from next generation sequencing data.
Jung CH, Hansen MA, Makunin IV, Korbie DJ, Mattick JS.
BMC Genomics. 2010 Feb 1;11:77.

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Monitoring the escape of DNA from a nanopore using an alternating current signal.
Lathrop DK, Ervin EN, Barrall GA, Keehan MG, Kawano R, Krupka MA, White HS, Hibbs AH.
J Am Chem Soc. 2010 Feb 17;132(6):1878-85.

Nanopore based sequence specific detection of duplex DNA for genomic profiling.
Singer A, Wanunu M, Morrison W, Kuhn H, Frank-Kamenetskii M, Meller A.
Nano Lett. 2010 Feb 10;10(2):738-42.

Current blockade in nanopores in the presence of double-stranded DNA and the microscopic mechanisms.
Cui S.
J Phys Chem B. 2010 Feb 11;114(5):2015-22.

Direct force measurements on double-stranded RNA in solid-state nanopores.
van den Hout M, Vilfan ID, Hage S, Dekker NH.
Nano Lett. 2010 Feb 10;10(2):701-7.

Rapid sequencing of individual DNA molecules in graphene nanogaps.
Postma HW.
Nano Lett. 2010 Feb 10;10(2):420-5.

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.