Sequencing-Related Papers of Note, December 2008
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]