Sequencing-Related Papers of Note, October 2007
Author(s) Title Citation
Ahsan B, Kobayashi D, Yamada T, Kasahara M, Sasaki S, Saito TL, Nagayasu Y, Doi K, Nakatani Y, Qu W, Jindo T, Shimada A, et al.

UTGB/medaka: genomic resource database for medaka biology.

 Nucleic Acids Res. 2007 Oct 11; [Epub ahead of print]
Albert TJ, Molla MN, Muzny DM, Nazareth L, Wheeler D, Song X, Richmond TA, Middle CM, Rodesch MJ, Packard CJ, Weinstock GM, Gibbs RA. Direct selection of human genomic loci by microarray hybridization. Nat Methods. 2007 Epub Oct 14.
Baba T, Bae T, Schneewind O, Takeuchi F, Hiramatsu K. Genome sequence of Staphylococcus aureus strain Newman and comparative analysis of staphylococcal genomes: polymorphism and evolution of two major pathogenicity islands. J Bacteriol. 2007 Oct 19; [Epub ahead of print]
Brayton KA, Lau AO, Herndon DR, Hannick L, Kappmeyer LS, Berens SJ, Bidwell SL, et al. Genome sequence of Babesia bovis and comparative analysis of apicomplexan hemoprotozoa. PLoS Pathog. 2007 Oct 19;3(10):e148.
Chen YC, Kraft P, Bretsky P, Ketkar S, Hunter DJ, Albanes D, Altshuler D, Andriole G, Berg CD, Boeing H, Burtt N, et al. Sequence variants of estrogen receptor beta and risk of prostate cancer in the National Cancer Institute Breast and Prostate Cancer Cohort Consortium. Cancer Epidemiol Biomarkers Prev. 2007 Oct;16(10):1973-81.
Cunat S, Giansily-Blaizot M, Bismuth M, Blanc F, Dereure O, Larrey D, et al. Global sequencing approach for characterizing the molecular background of hereditary iron disorders. Clin Chem. 2007 Oct 19; [Epub ahead of print]
Dohm JC, Lottaz C, Borodina T, Himmelbauer H. SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing. Genome Res. 2007 Epub 2007 Oct 1.
Feng J, Yan J, Li W, Chen J, Sommer SS. Candidate gene analyses by scanning or brute force fluorescent sequencing: A comparison of DOVAM-S with gel-based and capillary-based sequencing. Genet Test. 2007 Fall;11(3):235-40.
Lasken RS. Single-cell genomic sequencing using multiple displacement amplification. Curr Opin Microbiol. 2007 Oct 6; [Epub ahead of print]
Markowitz VM, Ivanova NN, Szeto E, Palaniappan K, Chu K, Dalevi D, Chen IM, Grechkin Y, Dubchak I, Anderson I, Lykidis A, Mavromatis K, et al. IMG/M: a data management and analysis system for metagenomes. Nucleic Acids Res. 2007 Oct 11; [Epub ahead of print]
Markowitz VM, Szeto E, Palaniappan K, Grechkin Y, Chu K, Chen IM, Dubchak I, Anderson I, Lykidis A, Mavromatis K, Ivanova NN, Kyrpides NC. The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions. Nucleic Acids Res. 2007 Oct 12; [Epub ahead of print]
Merchant SS, Prochnik SE, Vallon O, Harris EH, Karpowicz SJ, Witman GB, Terry A, Salamov A, Fritz-Laylin LK, Maréchal-Drouard L, et al. The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science. 2007 Oct 12;318(5848):245-50.
Okou DT, Steinberg KM, Middle C, Cutler DJ, Albert TJ, Zwick ME. Microarray-based genomic selection for high-throughput resequencing. Nat Methods. 2007 Epub Oct 14.
Papanicolaou A, Gebauer-Jung S, Blaxter ML, Owen McMillan W, Jiggins CD. ButterflyBase: a platform for lepidopteran genomics. Nucleic Acids Res. 2007 Oct 12; [Epub ahead of print]
Parameswaran P, Jalili R, Tao L, Shokralla S, Gharizadeh B, Ronaghi M, Fire AZ. A pyrosequencing-tailored nucleotide barcode design unveils opportunities for large-scale sample multiplexing. Nucleic Acids Res. 2007 Oct 11; [Epub ahead of print]
Piganeau G, Moreau H. Screening the Sargasso Sea metagenome for data to investigate genome evolution in Ostreococcus (Prasinophyceae, Chlorophyta). Gene. 2007 Oct 3; [Epub ahead of print]
Porreca GJ, Zhang K, Li JB, Xie B, Austin D, Vassallo SL, Leproust EM, Peck BJ, Emig CJ, Dahl F, Gao Y, Church GM, Shendure J. Multiplex amplification of large sets of human exons. Nat Methods. 2007 Epub Oct 14.
Qamar S, Williams PM, Lindsay S. Can an atomic force microscope sequence DNA using a nanopore? Biophys J. 2007 Oct 26; [Epub ahead of print]
Schneiker S, Perlova O, Kaiser O, Gerth K, Alici A, Altmeyer MO, Bartels D, Bekel T, Beyer S, Bode E, et al. Complete genome sequence of the myxobacterium Sorangium cellulosum. Nat Biotechnol. 2007 Oct 28; [Epub ahead of print]
Wall JD, Kim SK. Inconsistencies in Neanderthal genomic DNA sequences. PLoS Genet. 2007 Oct 12;3(10):e175.
Wood LD, Parsons DW, Jones S, Lin J, Sjöblom T, Leary RJ, Shen D, Boca SM, Barber T, Ptak J, Silliman N, Szabo S, Dezso Z, et al. The genomic landscapes of human breast and colorectal cancers. Science. 2007 Oct 11; [Epub ahead of print]
Wu J, Zhang S, Meng Q, Cao H, Li Z, Li X, Shi S, Kim DH, Bi L, Turro NJ, Ju J. 3'-O-modified nucleotides as reversible terminators for pyrosequencing.

Proc Natl Acad Sci U S A. 2007 Oct 16;104 (42):16462-7.
Yu L, Li YW, Ryder OA, Zhang YP. Analysis of complete mitochondrial genome sequences increases phylogenetic resolution of bears (Ursidae), a mammalian family that experienced rapid speciation. BMC Evol Biol. 2007 Oct 24;7(1):198 [Epub ahead of print]