Sequencing-Related Papers of Note, April 2008
Authors Title Citation
Alcaraz LD, Olmedo G, Bonilla G, Cerritos R, et al.

The genome of Bacillus coahuilensis reveals adaptations essential for survival in the relic of an ancient marine environment.

Proc Natl Acad Sci U S A. 2008 Apr 15;105(15):5803-8. Epub 2008 Apr 11.
Bashir A, Volik S, Collins C, Bafna V, Raphael BJ. Evaluation of paired-end sequencing strategies for detection of genome rearrangements in cancer. PLoS Comput Biol. 2008 Apr 11;4(4):e1000051.
Blow MJ, Zhang T, Woyke T, Spelle CF, et al. Identification of the source of ancient remains through genomic sequencing. Genome Res. 2008 Apr 21. [Epub ahead of print]
Brinkmeyer-Langford C, Raudsepp T, Gustafson-Seabury A, Chowdhary BP. A BAC contig map over the proximal approximately 3.3 Mb region of horse chromosome 21. Cytogenet Genome Res. 2008;120(1-2):164-72. Epub 2008 Apr 30.
Burnside J, Ouyang M, Anderson A, Bernberg E, et al. Deep sequencing of chicken microRNAs. BMC Genomics. 2008 Apr 22;9:185.
Campbell PJ, Stephens PJ, Pleasance ED, O'Meara S, et al. Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nat Genet. 2008 Apr 27. [Epub ahead of print]
Crossman LC, Gould VC, Dow JM, Vernikos GS, et al. The complete genome, comparative and functional analysis of Stenotrophomonas maltophilia reveals an organism heavily shielded by drug resistance determinants. Genome Biol. 2008 Apr 17;9(4):R74. [Epub ahead of print]
Datema E, Mueller LA, Buels R, Giovannoni JJ, et al. Comparative BAC end sequence analysis of tomato and potato reveals overrepresentation of specific gene families in potato. BMC Plant Biol. 2008 Apr 11;8:34.
Eriksson N, Pachter L, Mitsuya Y, Rhee SY, et al. Viral population estimation using pyrosequencing. PLoS Comput Biol. 2008 Apr 25;4(4):e1000074.
Fedorova ND, Khaldi N, Joardar VS, Maiti R, et al. Genomic islands in the pathogenic filamentous fungus Aspergillus fumigatus. PLoS Genet. 2008 Apr 11;4(4):e1000046.
Friedländer MR, Chen W, Adamidi C, Maaskola J, et al. Discovering microRNAs from deep sequencing data using miRDeep. Nat Biotechnol. 2008 Apr;26(4):407-15.
Harris TD, Buzby PR, Babcock H, Beer E, et al. Single-molecule DNA sequencing of a viral genome. Science. 2008 Apr 4;320(5872):106-9.
Hongoh Y, Sharma VK, Prakash T, Noda S, et al. Complete genome of the uncultured Termite Group 1 bacteria in a single host protist cell. Proc Natl Acad Sci U S A. 2008 Apr 8;105(14):5555-60. Epub 2008 Apr 7.
Iacono M, Villa L, Fortini D, Bordoni R, et al. Whole genome pyrosequencing of an epidemic multidrug resistant Acinetobacter baumannii of the European clone II. Antimicrob Agents Chemother. 2008 Apr 14. [Epub ahead of print]
Kumaresan P, Yang CJ, Cronier SA, Blazej RG, Mathies RA. High-throughput single copy DNA amplification and cell analysis in engineered nanoliter droplets. Anal Chem. 2008 May 15;80(10):3522-9. Epub 2008 Apr 15.
La Scola B, Elkarkouri K, Li W, Wahab T, et al. Rapid comparative genomic analysis for clinical microbiology: The Francisella tularensis paradigm. Genome Res. 2008 May;18(5):742-50. Epub 2008 Apr 11.
Li K, Brownley A, Stockwell T, Beeson K, et al. Novel computational methods for increasing PCR primer design effectiveness in directed sequencing. BMC Bioinformatics. 2008 Apr 11;9(1):191. [Epub ahead of print]
Lin SW, Chang GL, Lin CH. Novel wavelength-resolved fluorescence detection for a high-throughput capillary electrophoresis system under a diascopic configuration. J Chromatogr A. 2008 May 23;1192(1):198-201. Epub 2008 Apr 3.
Ming R, Hou S, Feng Y, Yu Q, et al. The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature. 2008 Apr 24;452(7190):991-6.
Montgomery KT, Iartchouck O, Li L, Perera A, et al. Mutation detection using automated fluorescence-based sequencing. Curr Protoc Hum Genet. 2008 Apr;Chapter 7:Unit7.9
Norton JM, Klotz MG, Stein LY, Arp DJ, et al. Complete genome sequence of Nitrosospira multiformis, an ammonia-oxidizing bacterium from the soil environment. Appl Environ Microbiol. 2008 Apr 4. [Epub ahead of print]
Parker NJ, Parker AG. Simple tools for assembling and searching high-density picolitre pyrophosphate sequence data. Source Code Biol Med. 2008 Apr 18;3:5.
Sattley WM, Madigan MT, Swingley WD, Cheung PC, et al. The genome of Heliobacterium modesticaldum, a phototrophic representative of the Firmicutes containing the simplest photosynthetic apparatus. J Bacteriol. 2008 Apr 25. [Epub ahead of print]
Schutzer SE, Schlater LR, Ronning CM, DeShazer D, et al. Characterization of clinically-attenuated Burkholderia mallei by whole genome sequencing: candidate strain for exclusion from Select Agent lists. PLoS ONE. 2008 Apr 30;3(4):e2058.
Stinear TP, Seemann T, Harrison PF, Jenkin GA, et al. Insights from the complete genome sequence of Mycobacterium marinum on the evolution of Mycobacterium tuberculosis. Genome Res. 2008 May;18(5):729-41. Epub 2008 Apr 10.
Takarada H, Sekine M, Kosugi H, Matsuo Y, et al. Complete genome sequence of the soil actinomycete Kocuria rhizophila. J Bacteriol. 2008 Apr 11. [Epub ahead of print]
Tringe SG, Zhang T, Liu X, Yu Y, et al. The airborne metagenome in an indoor urban environment. PLoS ONE. 2008 Apr 2;3(4):e1862.
Turnbaugh PJ, Bäckhed F, Fulton L, Gordon JI. Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome. Cell Host Microbe. 2008 Apr 17;3(4):213-23.
Wang F, Wang J, Jian H, Zhang B, et al. Environmental adaptation: genomic analysis of the piezotolerant and psychrotolerant deep-sea iron reducing bacterium Shewanella piezotolerans WP3. PLoS ONE. 2008 Apr 9;3(4):e1937.
Wang GP, Garrigue A, Ciuffi A, Ronen K, et al. DNA bar coding and pyrosequencing to analyze adverse events in therapeutic gene transfer. Nucleic Acids Res. 2008 Apr 14. [Epub ahead of print]
Wheeler DA, Srinivasan M, Egholm M, Shen Y, et al. The complete genome of an individual by massively parallel DNA sequencing. Nature. 2008 Apr 17;452(7189):872-6.