Sequencing-Related Papers of Note, February 2008
Authors Title Citation
Anderson I, Rodriguez J, Susanti D, Porat I, et al.

Genome sequence of Thermofilum pendens reveals an exceptional loss of biosynthetic pathways without genome reduction.

J Bacteriol. 2008 Feb 8 [Epub ahead of print]
Chen J, Kim YC, Jung YC, Xuan Z, Dworkin G, et al. Scanning the human genome at kilobase resolution. Genome Res. 2008 Feb 21 [Epub ahead of print]
Cokus SJ, Feng S, Zhang X, Chen Z, et al. Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 2008 Feb 17 [Epub ahead of print]
Durfee T, Nelson R, Baldwin S, Plunkett G 3rd, et al. The complete genome sequence of Escherichia coli DH10B: Insights into the biology of a laboratory workhorse. J Bacteriol. 2008 Feb 1 [Epub ahead of print]
Frumkin D, Wasserstrom A, Itzkovitz S, Harmelin A, et al. Amplification of multiple genomic loci from single cells isolated by laser micro-dissection of tissues. BMC Biotechnol. 2008 Feb 20;8(1):17 [Epub ahead of print]
Fullwood MJ, Tan JJ, Ng PW, Chiu KP, et al. The use of multiple displacement amplification to amplify complex DNA libraries. Nucleic Acids Res. 2008 Feb 19 [Epub ahead of print]
Goto T, Yamashita A, Hirakawa H, Matsutani M, et al. Complete genome sequence of Finegoldia magna, an anaerobic opportunistic pathogen. DNA Res. 2008 Feb 29;15(1):39-47. Epub 2008 Feb 7.
Hamady M, Walker JJ, Harris JK, Gold NJ, Knight R. Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex. Nat Methods. 2008 Mar;5(3):235-7. Epub 2008 Feb 10.
Hu X, Fan W, Han B, Liu H, Zheng D, et al. Complete genome sequence of the mosquitocidal bacterium Bacillus sphaericus C3-41 and comparison with closely related Bacillus species. J Bacteriol. 2008 Feb 22 [Epub ahead of print]
Kim JF, Jeong H, Lee JS, Choi SH, et al. The complete genome sequence of Leuconostoc citreum KM20. J Bacteriol. 2008 Feb 15 [Epub ahead of print]
King N, Westbrook MJ, Young SL, Kuo A, et al. The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans. Nature 2008 Feb 14;451(7180):783-8.
Loriaux MM, Levine RL, Tyner JW, Frohling S, et al. High-throughput sequence analysis of the tyrosine kinome in acute myeloid leukemia. Blood 2008 Feb 5 [Epub ahead of print]
Malde K. The effect of sequence quality on sequence alignment. Bioinformatics 2008 Feb 23 [Epub ahead of print]
Mathee K, Narasimhan G, Valdes C, Qiu X, et al. Dynamics of Pseudomonas aeruginosa genome evolution. Proc Natl Acad Sci U S A 2008 Feb 26;105(8):3100-5. Epub 2008 Feb 19.
McKenna P, Hoffmann C, Minkah N, Aye PP, et al. The macaque gut microbiome in health, lentiviral infection, and chronic enterocolitis. PLoS Pathog. 2008 Feb 1;4(2):e20 [Epub ahead of print]
Morin RD, O'Connor MD, Griffith M, Kuchenbauer F, et al. Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells. Genome Res. 2008 Feb 19 [Epub ahead of print]
Pelletier E, Kreimeyer A, Bocs S, Rouy Z, et al. "Candidatus Cloacamonas acidaminovorans": genome sequence reconstruction provides a first glimpse of a new bacterial division. J Bacteriol. 2008 Feb 1 [Epub ahead of print]
Picardeau M, Bulach DM, Bouchier C, Zuerner RL, et al. Genome sequence of the saprophyte Leptospira biflexa provides insights into the evolution of Leptospira and the pathogenesis of leptospirosis. PLoS ONE 2008 Feb 13;3(2):e1607.
Rohde C, Zhang Y, Jurkowski TP, Stamerjohanns H, Reinhardt R, Jeltsch A. Bisulfite sequencing Data Presentation and Compilation (BDPC) web server — a useful tool for DNA methylation analysis. Nucleic Acids Res. 2008 Feb 22 [Epub ahead of print]
Smith AD, Xuan Z, Zhang MQ. Using quality scores and longer reads improves accuracy of Solexa read mapping. BMC Bioinformatics 2008 Feb 28;9(1):128 [Epub ahead of print]
Steinberg KM, Okou DT, Zwick ME. Applying rapid genome sequencing technologies to characterize pathogen genomes. Anal Chem. 2008 Feb 1;80(3):520-8.
Sugarbaker DJ, Richards WG, Gordon GJ, Dong L, et al. Transcriptome sequencing of malignant pleural mesothelioma tumors. Proc Natl Acad Sci U S A 2008 Mar 4;105(9):3521-6. Epub 2008 Feb 26.
Sunkar R, Zhou X, Zheng Y, Zhang W, Zhu JK. Identification of novel and candidate miRNAs in rice by high-throughput sequencing. BMC Plant Biol. 2008 Feb 29;8(1):25 [Epub ahead of print]
Timko MP, Rushton PJ, Laudeman TW, Bokoviec MT, et al. Sequencing and analysis of the gene-rich space of cowpea. BMC Genomics 2008 Feb 27;9(1):103 [Epub ahead of print]
Turcatti G, Romieu A, Fedurco M, Tairi AP. A new class of cleavable fluorescent nucleotides: synthesis and optimization as reversible terminators for DNA sequencing by synthesis. Nucleic Acids Res. 2008 Mar;36(4):e25. Epub 2008 Feb 7.
Vera JC, Wheat CW, Fescemyer HW, Frilander MJ, et al. Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing. Mol Ecol. 2008 Feb 5 [Epub ahead of print]