Sequencing-Related Papers of Note, Sept. 2007
Authors Title Citation
Akhras MS, Unemo M, Thiyagarajan S, Nyrén P, Davis RW, Fire AZ, Pourmand N. Connector inversion probe technology: a powerful one-primer multiplex DNA amplification system for numerous scientific applications. PLoS ONE.
2007 Sep 19;2(9):e915.
Alkan C, Ventura M, Archidiacono N, Rocchi M, Sahinalp SC, Eichler EE. Organization and evolution of primate centromeric DNA from whole-genome shotgun sequence data. PLoS Comput Biol.
2007 Sep 28;3(9):1807-18.
Beckstrom-Sternberg SM, Auerbach RK, et al. Complete genomic characterization of a pathogenic A.II strain of Francisella tularensis subspecies tularensis. PLoS ONE. 2007 Sep 26;2(9):e947.
Bergeron A, Belcaid M, Steward GF, Poisson G. Divide and conquer: enriching environmental sequencing data. PLoS ONE.
2007 Sep 5;2(9):e830.
Bianchetti L, Wu Y, Guerin E, Plewniak F, Poch O. SAGETTARIUS: a program to reduce the number of tags mapped to multiple transcripts and to plan SAGE sequencing stages. Nucleic Acids Res.
2007 Sep 20;
[Epub ahead of print]
Cox-Foster DL, Conlan S, Holmes EC, et al. A metagenomic survey of microbes in honey bee colony collapse disorder. Science.
2007 Sep 6;
[Epub ahead of print]
Cuomo CA, Güldener U, Xu JR, et al. The Fusarium graminearum genome reveals a link between localized polymorphism and pathogen. specialization. Science.
2007 Sep 7;317(5843):1400-2.
Ghedin E, Wang S, Spiro D, et al. Draft genome of the filarial nematode parasite Brugia malayi. Science.
2007 Sep 21;317(5845):1756-60.
Gilbert MT, Tomsho LP, Rendulic S, et al. Whole-genome shotgun sequencing of mitochondria from ancient hair shafts. Science.
2007 Sep 28;317(5846):1927-30.
Gioia J, Yerrapragada S, Qin X, et al. Paradoxical DNA repair and peroxide resistance gene conservation in Bacillus pumilus SAFR-032. PLoS ONE.
2007 Sep 26;2(9):e928.
Greenberg DE, Porcella SF, Zelazny AM, Virtaneva K, Sturdevant DE, Kupko JJ 3rd, Barbian KD, Babar A, Dorward DW, Holland SM. Genome sequence analysis of the emerging human pathogenic acetic acid bacterium Granulibacter bethesdensis. J Bacteriol.
2007 Sep 7;
[Epub ahead of print]
He X, Chang S, Zhang J, Zhao Q, Xiang H, Kusonmano K, Yang L, Sun ZS, Yang H, Wang J. MethyCancer: the database of human DNA methylation and cancer. Nucleic Acids Res.
2007 Sep 21;
[Epub ahead of print]
Hene L, Sreenu VB, Vuong MT, Abidi SH, Sutton JK, Rowland-Jones SL, Davis SJ, Evans EJ. Deep analysis of cellular transcriptomes - LongSAGE versus classic MPSS. BMC Genomics.
2007 Sep 24;8(1):333
[Epub ahead of print]
Jeck WR, Reinhardt JA, Baltrus DA, Hickenbotham MT, Magrini V, Mardis ER, Dangl JL, Jones CD. Extending assembly of short DNA sequences to handle error. Bioinformatics.
2007 Sep 24;
[Epub ahead of print]
Johnson JK, Arduino SM, Stine OC, Johnson JA, Harris AD.
Multilocus sequencing typing (MLST) compared to pulsed-field gel electrophoresis (PFGE) for molecular typing of Pseudomonas aeruginosa.
J Clin Microbiol.
2007 Sep 19;
[Epub ahead of print]
Kang H, Yun HS, Song MY, Lee JK, Kwack K. Identification of novel HLA-G subtype, HLA-G*0109, by sequencing in the Korean population. Tissue Antigens.
2007 Sep 27;
[Epub ahead of print]
Korbel JO, Urban AE, Affourtit JP, et al. Paired-end mapping reveals extensive structural variation in the human genome. Science.
2007 Sep 27;
[Epub ahead of print]
Krause J, Orlando L, Serre D, Viola B, Prüfer K, Richards MP, Hublin J-J, Hänni C, Derevianko AP, Pääbo S. Neanderthals in central Asia and Siberia. Nature.
2007 Sep 30;
[Epub ahead of print]
Latreille P, Norton S, Goldman BS, Henkhaus J, Miller N, Barbazuk B, Bode HB, Darby C, Du Z, Forst S, Gaudriault S, Goodner B, Goodrich-Blair H, Slater S. Optical mapping as a routine tool in bacterial genome sequencing. BMC Genomics.
2007 Sep 14;8(1):321
[Epub ahead of print]
Levy S, Sutton G, Ng PC, et al. The diploid genome sequence of an individual human. PLoS Biol.
2007 Sep 4;5(10):e254
[Epub ahead of print]
Li WF, Hu Z, Rao NY, Song CG, Zhang B, Cao MZ, Su FX, Wang YS, He PQ, Di GH, Shen KW, Wu J, Lu JS, Luo JM, Liu XY, Zhou J, Wang L, Zhao L, Liu YB, Yuan WT, Yang L, Shen ZZ, Huang W, Shao ZM. The prevalence of BRCA1 and BRCA2 germline mutations in high-risk breast cancer patients of Chinese Han nationality: two recurrent mutations were identified. Breast Cancer Res Treat. 2007 Sep 13; [Epub ahead of print]
Liu Z, Lozupone C, Hamady M, Bushman FD, Knight R. Short pyrosequencing reads suffice for accurate microbial community analysis. Nucleic Acids Res.
2007 Sep 18;
[Epub ahead of print]
Lyle R, Prandini P, Osoegawa K, et al. Islands of euchromatin-like sequence and expressed polymorphic sequences within the short arm of human chromosome 21. Genome Res.
2007 Sep 25;
[Epub ahead of print]
Makarova KS, Omelchenko MV, Gaidamakova EK, et al. Deinococcus geothermalis: The pool of extreme radiation resistance genes shrinks. PLoS ONE.
2007 Sep 26;2(9):e955.
Marcy Y, Ishoey T, Lasken RS, Stockwell TB, Walenz BP, Halpern AL, Beeson KY, Goldberg SM, Quake SR. Nanoliter reactors improve multiple displacement amplification of genomes from single cells. PLoS Genet.
2007 Sep 21;3(9):e155
[Epub ahead of print]
Martín-Cuadrado AB, López-García P, Alba JC, Moreira D, Monticelli L, Strittmatter A, Gottschalk G, Rodríguez-Valera F. Metagenomics of the deep mediterranean, a warm bathypelagic habitat. PLoS ONE.
2007 Sep 19;2(9):e914.
Meuzelaar LS, Lancaster O, Pasche JP, Kopal G, Brookes AJ. MegaPlex PCR: a strategy for multiplex amplification. Nat Methods.
2007 Oct;4(10):835-7. Epub 2007 Sep 16.
Morrison HG, McArthur AG, Gillin FD, et al. Genomic minimalism in the early diverging intestinal parasite Giardia lamblia. Science.
2007 Sep 28;317(5846):1921-6.
Mussmann M, Hu FZ, Richter M, de Beer D, Preisler A, Jřrgensen 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 Sep;5(9):e230.
Pearson BM, Gaskin DJ, Segers RP, Wells JM, Nuijten PJ, van Vliet AH. The complete genome sequence of Campylobacter jejuni strain 81116 (NCTC11828). J Bacteriol.
2007 Sep 14; [Epub ahead of print]
Pennathur S, Baldessari F, Santiago JG, Kattah MG, Steinman JB, Utz PJ. Free-solution oligonucleotide separation in nanoscale channels. Anal Chem. 2007 Sep 21; [Epub ahead of print]
Prasad A, Schiex T, McKay S, Murdoch B, Wang Z, Womack JE, Stothard P, Moore SS. High resolution radiation hybrid maps of bovine chromosomes 19 and 29: comparison with the bovine genome sequence assembly. BMC Genomics. 2007 Sep 4;8(1):310 [Epub ahead of print]
Robinson MD, Smyth GK. Moderated statistical tests for assessing differences in tag abundance. Bioinformatics. 2007 Sep 19; [Epub ahead of print]
Schlueter JA, Lin JY, Schlueter SD, Vasylenko-Sanders IF, Deshpande S, Yi J, O'bleness M, Roe BA, Nelson RT, Scheffler BE, Jackson SA, Shoemaker RC. Gene duplication and paleopolyploidy in soybean and the implications for whole genome sequencing. BMC Genomics. 2007 Sep 19;8(1):330 [Epub ahead of print]
Soni GV, Meller A. Progress toward ultrafast DNA sequencing using solid-state nanopores. Clin Chem.
2007 Sep 21; [Epub ahead of print]
Suetsugu Y, Minami H, Shimomura M, Sasanuma SI, Narukawa J, Mita K, Yamamoto K. End-sequencing and characterization of silkworm (Bombyx mori) bacterial artificial chromosome libraries. BMC Genomics.
2007 Sep 7;8(1):314 [Epub ahead of print]
Taylor KH, Kramer RS, Davis JW, Guo J, Duff DJ, Xu D, Caldwell CW, Shi H. Ultradeep bisulfite sequencing analysis of DNA methylation patterns in multiple gene promoters by 454 sequencing. Cancer Res. 2007 Sep 15;67(18):8511-8.
Toth AL, Varala K, Newman TC, Miguez FE, Hutchison SK, Willoughby DA, Simons JF, Egholm M, Hunt JH, Hudson ME, Robinson GE. Wasp gene expression supports an evolutionary link between maternal behavior and eusociality. Science.
2007 Sep 27; [Epub ahead of print]
Wang CY, Wang HW, Yao YG, Kong QP, Zhang YP. Somatic mutations of mitochondrial genome in early stage breast cancer. Int J Cancer.
2007 Sep 15;121(6):1253-6.
Wani AA, Ahanger SH, Bapat SA, Rangrez AY, Hingankar N, Suresh CG, Barnabas S, Patole MS, Shouche YS. Analysis of mitochondrial DNA sequences in childhood encephalomyopathies reveals new disease-associated variants. PLoS ONE.
2007 Sep 26;2(9):e942.
Xu YH, Manoharan HT, Pitot HC. CpG PatternFinder: a Windows-based utility program for easy and rapid identification of the CpG methylation status of DNA. Biotechniques.
2007 Sep;43(3):334, 336-40, 342.