Sequencing-Related
Papers of Note, December 2008
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Authors | Title | Citation |
Armougom F, Raoult D. | Use of pyrosequencing and DNA barcodes to monitor variations in Firmicutes and Bacteroidetes communities in the gut microbiota of obese humans. | BMC Genomics. 2008 Dec 1;9(1):576. [Epub ahead of print] |
Aury JM, Cruaud C, Barbe V, Rogier O, et al. | High quality draft sequences for prokaryotic genomes using a mix of new sequencing technologies. | BMC Genomics. 2008 Dec 16;9(1):603. [Epub ahead of print] |
Baba T, Kuwahara-Arai K, Uchiyama I, Takeuchi F, Ito T, Hiramatsu K. | Complete genome sequence determination of a Macrococcus caseolyticus strain JSCS5402 reflecting the ancestral genome of the human pathogenic staphylococci. | J Bacteriol. 2008 Dec 12. [Epub ahead of print] |
Bagwell CE, Bhat S, Hawkins GM, Smith BW, et al. | Survival in nuclear waste, extreme resistance, and potential applications gleaned from the genome sequence of Kineococcus radiotolerans SRS30216. | PLoS ONE. 2008;3(12): e3878. Epub 2008 Dec 5. |
Butler TZ, Pavlenok M, Derrington IM, Niederweis M, Gundlach JH. | Single-molecule DNA detection with an engineered MspA protein nanopore. | Proc Natl Acad Sci U S A. 2008 Dec 30;105(52): 20647-52. Epub 2008 Dec 19. |
Chaisson MJ, Brinza D, Pevzner PA. | De novo fragment assembly with short mate-paired reads: Does the read length matter? | Genome Res. 2008 Dec 3. [Epub ahead of print] |
Chiu RW, Chan KC, Gao Y, Lau VY, et al. | Noninvasive prenatal diagnosis of fetal chromosomal aneuploidy by massively parallel genomic sequencing of DNA in maternal plasma. | Proc Natl Acad Sci U S A. 2008 Dec 23;105(51):20458-63. Epub 2008 Dec 10. |
Core LJ, Waterfall JJ, Lis JT. | Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. | Science. 2008 Dec 19;322(5909):1845-8. Epub 2008 Dec 4. |
Denoeud F, Aury JM, Da Silva C, Noel B, Rogier O, et al. | Annotating genomes with massive-scale RNA-sequencing. | Genome Biol. 2008 Dec 16;9(12):R175. [Epub ahead of print] |
Farrer RA, Kemen E, Jones JD, Studholme DJ. | De novo assembly of the Pseudomonas syringae pv. syringae B728a genome using Illumina/Solexa short sequence reads. | FEMS Microbiol Lett. 2008 Dec 9. [Epub ahead of print] |
Forster RE, Chiesl TN, Fredlake CP, White CV, Barron AE. | Hydrophobically modified polyacrylamide block copolymers for fast, high-resolution DNA sequencing in microfluidic chips. | Electrophoresis. 2008 Dec;29(23):4669-76. |
Fredlake CP, Hert DG, Root BE, Barron AE. | Polymer systems designed specifically for DNA sequencing by microchip electrophoresis: A comparison with commercially available materials. | Electrophoresis. 2008 Dec;29(23):4652-62. |
Goossens D, Moens LN, Nelis E, Lenaerts AS, et al. | Simultaneous mutation and copy number variation (CNV) detection by multiplex PCR-based GS-FLX sequencing. | Hum Mutat. 2008 Dec 4. [Epub ahead of print] |
Hampton OA, Den Hollander P, Miller CA, Delgado DA, et al. | A sequence-level map of chromosomal breakpoints in the MCF-7 breast cancer cell line yields insights into the evolution of a cancer genome. | Genome Res. 2008 Dec 9. [Epub ahead of print] |
Hert DG, Fredlake CP, Barron AE. | DNA sequencing by microchip electrophoresis using mixtures of high- and low-molar mass poly(N,N-dimethylacrylamide) matrices. | Electrophoresis. 2008 Dec;29(23):4663-8. |
Hjerde E, Lorentzen MS, Holden MT, Seeger K, et al. | The genome sequence of the fish pathogen Aliivibrio salmonicida strain LFI1238 shows extensive evidence of gene decay. | BMC Genomics. 2008 Dec 19;9(1):616. [Epub ahead of print] |
Höper D, Hoffmann B, Beer M. | Simple, sensitive, and swift sequencing of complete avian influenza H5N1 genomes. | J Clin Microbiol. 2008 Dec 24. [Epub ahead of print] |
Kalman EB, Sudre O, Vlassiouk I, Siwy ZS. | Control of ionic transport through gated single conical nanopores. | Anal Bioanal Chem. 2008 Dec 17. [Epub ahead of print] |
Kearney M, Maldarelli F, Shao W, Margolick JB, Daar ES, Mellors JW, Rao V, Coffin JM, Palmer S. | HIV-1 population genetics and adaptation in newly infected individuals. | J Virol. 2008 Dec 30. [Epub ahead of print] |
Kececi K, Sexton LT, Buyukserin F, Martin CR. | Resistive-pulse detection of short dsDNAs using a chemically functionalized conical nanopore sensor. | Nanomed. 2008 Dec;3 (6):787-96. |
Kumagai
H, Utsunomiya S, Nakamura S, Yamamoto R, et al. |
Large-scale microfabricated channel plates for high-throughput, fully automated DNA sequencing. | Electrophoresis. 2008 Dec;29(23):4723-32. |
Lee A, Hansen KD, Bullard J, Dudoit S, Sherlock G. | Novel low abundance and transient RNAs in yeast revealed by tiling microarrays and ultra high-throughput sequencing are not conserved across closely related yeast species. | PLoS Genet. 2008 Dec;4(12):e1000299. Epub 2008 Dec 19. |
Li H, Lovci MT, Kwon YS, Rosenfeld MG, Fu XD, Yeo GW. | Determination of tag density required for digital transcriptome analysis: application to an androgen-sensitive prostate cancer model. | Proc Natl Acad Sci U S A. 2008 Dec 23;105(51):20179-84. Epub 2008 Dec 16. |
Ng TF, Manire C, Borrowman K, Langer T, Ehrhart L, Breitbart M. | Discovery of a novel single-stranded DNA virus from a sea turtle fibropapilloma using viral metagenomics. | J Virol. 2008 Dec 30. [Epub ahead of print] |
Nix DA, Courdy SJ, Boucher KM. | Empirical methods for controlling false positives and estimating confidence in chIP-seq peaks. | BMC Bioinformatics. 2008 Dec 5;9(1):523. [Epub ahead of print] |
Nusbaum C, Ohsumi TK, Gomez J, Aquadro J, Victor TC, Warren RM, Hung DT, Birren BW, Lander ES, Jaffe DB. | Sensitive, specific polymorphism discovery in bacteria using massively parallel sequencing. | Nat Methods. 2009 Jan;6(1):67-9. Epub 2008 Dec 14. |
Pierce E, Xie G, Barabote RD, Saunders E, Han CS, Detter JC, et al. | The complete genome sequence of Moorella thermoacetica (f. Clostridium thermoaceticum). | Environ Microbiol. 2008 Jun 17. [Epub ahead of print] |
Quail MA, Kozarewa I, Smith F, Scally A, Stephens PJ, Durbin R, Swerdlow H, Turner DJ. | A large genome center's improvements to the Illumina sequencing system. | Nat Methods. 2008 Dec;5(12):1005-10. |
Ravin
NV, Mardanov AV, Beletsky AV, Kublanov IV, et al. |
Complete genome sequence of the anaerobic, protein-degrading hyperthermophilic crenarchaeon Desulfurococcus kamchatkensis. | J Bacteriol. 2008 Dec 29. [Epub ahead of print] |
Reinhardt JA, Baltrus DA, Nishimura MT, Jeck WR, Jones CD, Dangl JL. | Efficient de novo assembly of bacterial genomes using low coverage short read sequencing. | Genome Res. 2008 Dec 1. [Epub ahead of print] |
Rodriguez JA, Guiteau JJ, Nazareth L, Reid JG, Goss JA, Gibbs RA, Gingras MC. | Sequencing the full-length of the phosphatase and tensin homolog (PTEN) gene in hepatocellular carcinoma (HCC) using the 454 GS20 and Illumina GA DNA sequencing platforms. | World J Surg. 2008 Dec 10. [Epub ahead of print] |
Salzberg SL, Puiu D, Sommer DD, Nene V, Lee NH. | The genome sequence of Wolbachia endosymbiont of Culex quinquefasciatus JHB. | J Bacteriol. 2008 Dec 29. [Epub ahead of print] |
Sanapareddy N, Hamp TJ, Gonzalez LC, Hilger HA, Fodor AA, Clinton SM. | Molecular diversity of a North Carolina wastewater treatment plant as revealed by pyrosequencing. | Appl Environ Microbiol. 2008 Dec 29. [Epub ahead of print] |
Schaefer M, Pollex T, Hanna K, Lyko F. | RNA cytosine methylation analysis by bisulfite sequencing. | Nucleic Acids Res. 2008 Dec 5. [Epub ahead of print] |
Sen YH, Karnik R. | Investigating the translocation of lambda-DNA molecules through PDMS nanopores. | Anal Bioanal Chem. 2008 Dec 3. [Epub ahead of print] |
Shen Y, Sarin S, Liu Y, Hobert O, Pe'er I. | Comparing platforms for C. elegans mutant identification using high-throughput whole-genome sequencing. | PLoS ONE. 2008;3(12): e4012. Epub 2008 Dec 24. |
Smeets
RM, Kowalczyk SW, Hall AR, Dekker NH, Dekker C. |
Translocation of RecA-coated double-stranded DNA through solid-state nanopores. | Nano Lett. 2008 Dec 3. [Epub ahead of print] |
Solmone M, Vincenti D, Prosperi MC, Bruselles A, Ippolito G, Capobianchi MR. | Use of massively parallel ultra-deep pyrosequencing to characterize genetic diversity of HBV in drug-resistant and naïve patients and to detect minor variants in RT and HBsAg. | J Virol. 2008 Dec 10. [Epub ahead of print] |
Szittya G, Moxon S, Santos DM, Jing R, Fevereiro MP, Moulton V, Dalmay T | High-throughput sequencing of Medicago truncatula short RNAs identifies eight new miRNA families. | BMC Genomics. 2008 Dec 9;9(1):593. [Epub ahead of print] |
Tyner
JW, Erickson H, Deininger MW, Willis SG, et al. |
High-throughput sequencing screen reveals novel, transforming RAS mutations in myeloid leukemia patients. | Blood. 2008 Dec 15. [Epub ahead of print] |
Valen E, Pascarella G, Chalk A, Maeda N, Kojima M, et al. | Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE. | Genome Res. 2008 Dec 11. [Epub ahead of print] |
Volkening JD, Spatz SJ. | Purification of DNA from the cell-associated herpesvirus Marek's disease virus for 454 pyrosequencing using micrococcal nuclease digestion and polyethylene glycol precipitation. | J Virol Methods. 2008 Dec 19. [Epub ahead of print] |
Wang X, Sun Q, McGrath SD, Mardis ER, Soloway PD, Clark AG. | Transcriptome-wide identification of novel imprinted genes in neonatal mouse brain. | PLoS ONE. 2008;3(12): e3839. Epub 2008 Dec 4. |
Wiedmann RT, Smith TP, Nonneman DJ. | SNP discovery in swine by reduced representation and high throughput pyrosequencing. | BMC Genet. 2008 Dec 4;9:81. |
Xiong Z, Jiang Y, Qi D, Lu H, et al. | The complete genome sequence of the extremophilic Bacillus cereus strain Q1 with industrial applications. | J Bacteriol. 2008 Dec 5. [Epub ahead of print] |
Xue X, Sun J, Zhang Q, Wang Z, Huang Y, Pan W. | Identification and characterization of novel microRNAs from Schistosoma japonicum. | PLoS ONE. 2008;3(12): e4034. Epub 2008 Dec 24. |
Yashiro Y, Bannai H, Minowa T, Yabiku T, Miyano S, Osawa M, Iwama A, Nakauchi H | Transcriptional profiling of hematopoietic stem cells by high-throughput sequencing. | Int J Hematol. 2008 Dec 3. [Epub ahead of print] |
Yue M, Yang F, Yang J, Bei W, Cai X, Chen L, Dong J, Zhou R, Jin M, Jin Q, Chen H. | Complete genome sequence of Haemophilus parasuis SH0165. | J Bacteriol. 2008 Dec 12. [Epub ahead of print] |
Zhou D, Yang L, Yang R, Song W, Peng S, Wang Y. | Novel quasi-interpenetrating network/functionalized multi-walled carbon nanotubes double-network composite matrices for DNA sequencing by CE. | Electrophoresis. 2008 Dec;29(23):4637-45. |
Zhou X, Sunkar R, Jin H, Zhu JK, Zhang W. | Genome-wide identification and analysis of small RNAs originated from natural antisense transcripts in Oryza sativa. | Genome Res. 2008 Dec 3. [Epub ahead of print] |