Sequencing-Related Papers of Note, August 2007
Author(s) Title Citation
Audic S, Robert C, Campagna B, Parinello H, Claverie JM, Raoult D, Drancourt M.

Genome analysis of Minibacterium massiliensis highlights the convergent evolution of water-living bacteria.

PLoS Genet. 2007 Aug 24;3(8):e138. Epub 2007 Jul 5.
Auerbach RK, Tuanyok A, Probert WS, Kenefic L, Vogler AJ, Bruce DC, Munk C, Brettin TS, Eppinger M, Ravel J, Wagner DM, Keim P. Yersinia pestis evolution on a small timescale: comparison of whole genome sequences from North America. PLoS ONE. 2007 Aug 22;2:e770.
Beres SB, Musser JM. Contribution of exogenous genetic elements to the group A Streptococcus metagenome. PLoS ONE. 2007 Aug 29;2(8):e800.
Bignell GR, Santarius T, Pole JC, Butler AP, Perry J, Pleasance E, Greenman C, Menzies A, Taylor S, Edkins S, Campbell P, Quail M, Plumb B, Matthews L, McLay K, Edwards PA, Rogers J, Wooster R, Futreal PA, Stratton MR. Architectures of somatic genomic rearrangement in human cancer amplicons at sequence-level resolution. Genome Res. 2007 Sep;17(9):1296-303. Epub 2007 Aug 3.
Briggs AW, Stenzel U, Johnson PL, Green RE, Kelso J, Prüfer K, Meyer M, Krause J, Ronan MT, Lachmann M, Pääbo S. Patterns of damage in genomic DNA sequences from a Neandertal. Proc Natl Acad Sci U S A. 2007 Aug 21; [Epub ahead of print]
Burki F, Shalchian-Tabrizi K, Minge M, Skjaeveland A, Nikolaev SI, Jakobsen KS, Pawlowski J. Phylogenomics reshuffles the eukaryotic supergroups. PLoS ONE. 2007 Aug 29;2(8):e790.
Chen XH, Koumoutsi A, Scholz R, Eisenreich A, Schneider K, Heinemeyer I, Morgenstern B, Voss B, Hess WR, Reva O, Junge H, Voigt B, Jungblut PR, Vater J, Süssmuth R, Liesegang H, Strittmatter A, Gottschalk G, Borriss R. Comparative analysis of the complete genome sequence of the plant growth-promoting bacterium Bacillus amyloliquefaciens FZB42. Nat Biotechnol. 2007 Aug 19; [Epub ahead of print]
Diancourt L, Passet V, Chervaux C, Garault P, Smokvina T, Brisse S. Multilocus sequence typing of Lactobacillus casei (L. paracasei) reveals a clonal population structure with low levels of homologous recombination. Appl Environ Microbiol. 2007 Aug 17; [Epub ahead of print]
Hart EA, Caccamo M, Harrow JL, Humphray SJ, Gilbert JG, Trevanion S, Hubbard T, Rogers J, Rothschild MF. Lessons learned from the initial sequencing of the pig genome: comparative analysis of an 8 Mb region of pig chromosome 17. Genome Biol. 2007 Aug 17;8(8):R168 [Epub ahead of print]
Hiller NL, Janto B, Hogg JS, Boissy R, Yu S, Powell E, Keefe R, Ehrlich NE, Shen K, Hayes J, Barbadora K, Klimke W, Dernovoy D, Tatusova T, Parkhill J, Bentley SD, Post JC, Ehrlich GD, Hu FZ. Comparative genomic analyses of seventeen Streptococcus pneumoniae strains: insights into the pneumococcal supragenome.
J Bacteriol. 2007 Aug 3; [Epub ahead of print]
Hotopp JC, Clark ME, Oliveira DC, Foster JM, Fischer P, Torres MC, Giebel JD, Kumar N, Ishmael N, Wang S, Ingram J, Nene RV, Shepard J, Tomkins J, Richards S, Spiro DJ, Ghedin E, Slatko BE, Tettelin H, Werren JH. Widespread lateral gene transfer from intracellular bacteria to multicellular eukaryotes. Science. 2007 Aug 30; [Epub ahead of print]
Karpathy SE, Qin X, Gioia J, Jiang H, Liu Y, Petrosino JF, Yerrapragada S, Fox GE, Haake SK, Weinstock GM, Highlander SK. Genome sequence of Fusobacterium nucleatum subspecies polymorphum — a genetically tractable fusobacterium. PLoS ONE. 2007 Aug 1;2:e659.
Kullberg M, Hallström B, Arnason U, Janke A. Expressed sequence tags as a tool for phylogenetic analysis of placental mammal evolution. PLoS ONE. 2007 Aug 22;2:e775.
Lemos B. The opossum genome reveals further evidence for regulatory evolution in mammalian diversification. Genome Biol. 2007 Aug 9;8(8):223 [Epub ahead of print]
Lin J, Gan CM, Zhang X, Jones S, Sjöblom T, Wood LD, Parsons DW, Papadopoulos N, Kinzler KW, Vogelstein B, Parmigiani G, Velculescu VE. A multidimensional analysis of genes mutated in breast and colorectal cancers. Genome Res. 2007 Sep;17(9):1304-18. Epub 2007 Aug 10.
Meyer M, Stenzel U, Myles S, Prüfer K, Hofreiter M. Targeted high-throughput sequencing of tagged nucleic acid samples. Nucleic Acids Res. 2007;35(15):e97. Epub 2007 Aug 1.
Mußmann M, Hu FZ, Richter M, de Beer D, Preisler A, Jørgensen BB, Huntemann M, Glöckner FO, Amann R, Koopman WJ, Lasken RS, Janto B, Hogg J, Stoodley P, Boissy R, Ehrlich GD. Insights into the genome of large sulfur bacteria revealed by analysis of single filaments. PLoS Biol. 2007 Aug 28;5(9):e230 [Epub ahead of print]
Raymond JA, Fritsen C, Shen K. An ice-binding protein from an Antarctic sea ice bacterium. FEMS Microbiol Ecol. 2007 Aug;61(2):214-21.
Snelling WM, Chiu R, Schein JE, et al. A physical map of the bovine genome. Genome Biol. 2007 Aug 14;8(8):R165 [Epub ahead of print]
Steegen K, Luchters S, Demecheleer E, Dauwe K, Mandaliya K, Jaoko W, Plum J, Temmerman M, Verhofstede C. Feasibility of detecting HIV-1 drug resistance in DNA extracted from whole blood or dry blood spots. J Clin Microbiol. 2007 Aug 1; [Epub ahead of print]
The French-Italian Public Consortium for Grapevine Genome Characterization, Jaillon O, Aury JM, Noel B, et al. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature. 2007 Aug 26; [Epub ahead of print]
Trepagnier EH, Radenovic A, Sivak D, Geissler P, Liphardt J.

Controlling DNA capture and propagation through artificial nanopores.

Nano Lett. 2007 Aug 18; [Epub ahead of print]
Wang GP, Ciuffi A, Leipzig J, Berry CC, Bushman FD. HIV integration site selection: analysis by massively parallel pyrosequencing reveals association with epigenetic modifications. Genome Res. 2007 Aug;17(8):1186-94. Epub 2007 Jun 1.
Wang YZ, Wu GX, Luo LB, Chen M, Ruan LH. Oligonucleotide chip, real-time PCR and sequencing for genotyping of hepatitis B virus. World J Gastroenterol. 2007 Aug 21;13(31):4260-3.
Zhang J, Guy JS, Snijder EJ, Denniston DA, Timoney PJ, Balasuriya UB. Genomic characterization of equine coronavirus. Virology. 2007 Aug 10; [Epub ahead of print]
Zhou S, Bechner MC, Place M, Churas CP, Pape L, Leong SA, Runnheim R, Forrest DK, Goldstein S, Livny M, Schwartz DC. Validation of rice genome sequence by optical mapping. BMC Genomics. 2007 Aug 15;8(1):278 [Epub ahead of print]
Zuber S, Ngom-Bru C, Barretto C, Bruttin A, Bruessow H, Denou E. Genome analysis of phage JS98 defines a fourth major subgroup of T4-like phages in Escherichia coli. J Bacteriol. 2007 Aug 10; [Epub ahead of print]