Sequencing-Related Papers of Note, November 2008
Authors Title Citation
Abouelhoda MI, Kurtz S, Ohlebusch E. CoCoNUT: an efficient system for the comparison and analysis of genomes. BMC Bioinformatics. 2008 Nov 12;9(1):476. [Epub ahead of print]
Babak T, Deveale B, Armour C, Raymond C, et al. Global survey of genomic imprinting by transcriptome sequencing. Curr Biol. 2008 Nov 25;18(22):1735-41.
Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP,
et al.
Accurate whole human genome sequencing using reversible terminator chemistry. Nature. 2008 Nov 6;456(7218):53-9.
Cheung F, Win J, Lang JM, Hamilton J, et al. Analysis of the Pythium ultimum transcriptome using Sanger and pyrosequencing approaches. BMC Genomics. 2008 Nov 15;9(1):542. [Epub ahead of print]
Chiang DY, Getz G, Jaffe DB, O'Kelly MJ, Zhao X, et al. High-resolution mapping of copy-number alterations with massively parallel sequencing. Nat Methods. 2008 Nov 30. [Epub ahead of print]
Dethlefsen L, Huse S, Sogin ML, Relman DA. The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol. 2008 Nov 18;6(11):e280. [Epub ahead of print]
Eid J, Fehr A, Gray J, Luong K, et al. Real-time DNA sequencing from single polymerase molecules. Science. 2008 Nov 20. [Epub ahead of print]
Girirajan S, Chen L, Graves T, Marques T, et al. Sequencing human-gibbon breakpoints of synteny reveals mosaic new insertions at rearrangement sites. Genome Res. 2008 Nov 24. [Epub ahead of print]
Grzymski JJ, Murray AE, Campbell BJ, Kaplarevic M,
et al.
Metagenome analysis of an extreme microbial symbiosis reveals eurythermal adaptation and metabolic flexibility. Proc Natl Acad Sci U S A. 2008 Nov 11;105(45):17516-21. Epub 2008 Nov 5.
Hongoh Y, Sharma VK, Prakash T, Noda S, et al. Genome of an endosymbiont coupling N2 fixation to cellulolysis within protist cells in termite gut. Science. 2008 Nov 14;322(5904):1108-9
Ji H, Jiang H, Ma W, Johnson DS, Myers RM, Wong WH. An integrated software system for analyzing ChIP-chip and ChIP-seq data. Nat Biotechnol. 2008 Nov;26(11):1293-300. Epub 2008 Nov 2.
Keijser BJ, Zaura E, Huse SM, van der Vossen JM, et al.. Pyrosequencing analysis of the oral microflora of healthy adults. J Dent Res. 2008 Nov;87(11):1016-20.
Kharchenko PV, Tolstorukov MY, Park PJ. Design and analysis of ChIP-seq experiments for DNA-binding proteins. Nat Biotechnol. 2008 Nov 16. [Epub ahead of print]
Kim JF, Jeong H, Yu DS, Choi SH, et al. Genome sequence of the probiotic bacterium Bifidobacterium animalis subsp. lactis AD011. J Bacteriol. 2008 Nov 14. [Epub ahead of print]
Kotewicz ML, Mammel MK, LeClerc JE, Cebula TA. Optical mapping and 454 sequencing of Escherichia coli O157: H7 isolates linked to the US 2006 spinach-associated outbreak. Microbiology. 2008 Nov;154(Pt 11):3518-28.
Kumagai H, Utsunomiya S, Nakamura S, Yamamoto R,
et al.
Large-scale microfabricated channel plates for high-throughput, fully automated DNA sequencing. Electrophoresis. 2008 Nov 17;29(23):4723-4732. [Epub ahead of print]
Ley TJ, Mardis ER, Ding L, Fulton B, et al. DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome. Nature. 2008 Nov 6;456(7218):66-72.
Licatalosi DD, Mele A, Fak JJ, Ule J, et al. HITS-CLIP yields genome-wide insights into brain alternative RNA processing. Nature. 2008 Nov 27;456(7221):464-9. Epub 2008 Nov 2.
Lim SK, Kim SJ, Cha SH, Oh YK, et al. Complete genome sequence of Rhodobacter sphaeroides KD131. J Bacteriol. 2008 Nov 21. [Epub ahead of print]
Lind PA, Andersson DI. Whole-genome mutational biases in bacteria. Proc Natl Acad Sci U S A. 2008 Nov 18;105(46):17878-83. Epub 2008 Nov 10.
Mannocci L, Zhang Y, Scheuermann J, Leimbacher M, et al. High-throughput sequencing allows the identification of binding molecules isolated from DNA-encoded chemical libraries. Proc Natl Acad Sci U S A. 2008 Nov 18;105(46):17670-5. Epub 2008 Nov 10.
Miller W, Drautz DI, Ratan A, Pusey B, et al. Sequencing the nuclear genome of the extinct woolly mammoth. Nature. 2008 Nov 20;456(7220):387-90.
Mir KU, Qi H, Salata O, Scozzafava G. Sequencing by Cyclic Ligation and Cleavage (CycLiC) directly on a microarray captured template. Nucleic Acids Res. 2008 Nov 16. [Epub ahead of print]
Molina Medina CM, Rotter B, Horres R, Udupa S,et al. SuperSAGE: the drought stress-responsive transcriptome of chickpea roots. BMC Genomics. 2008 Nov 24;9(1):553. [Epub ahead of print]
Mudge J, Miller NA, Khrebtukova I, Lindquist IE,
et al.
Genomic convergence analysis of schizophrenia: mRNA sequencing reveals altered synaptic vesicular transport in post-mortem cerebellum. PLoS ONE. 2008;3(11): e3625. Epub 2008 Nov 5.
Oda Y, Larimer FW, Chain PS, Malfatti S, et al. Multiple genome sequences reveal adaptations of a phototrophic bacterium to sediment microenvironments. Proc Natl Acad Sci U S A. 2008 Nov 25;105(47):18543-8. Epub 2008 Nov 19.
Orsi RH, Borowsky ML, Lauer P, Young SK, et al. Short-term genome evolution of Listeria monocytogenes in a non-controlled environment. BMC Genomics. 2008 Nov 13;9(1):539. [Epub ahead of print]
Pan Q, Shai O, Lee LJ, Frey BJ, Blencowe BJ. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet. 2008 Dec;40(12):1413-5. Epub 2008 Nov 2.
Podar M, Anderson I, Makarova KS, Elkins JG,
et al.
A genomic analysis of the archaeal system Ignicoccus hospitalis-Nanoarchaeum equitans. Genome Biol. 2008 Nov 10;9(11):R158. [Epub ahead of print]
Salzberg SL, Sommer DD, Schatz MC, Phillippy AM,
et al.
Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A. BMC Genomics. 2008 Nov 11;9:534.
Schmidt D, Stark R, Wilson MD, Brown GD, Odom DT. Genome-scale validation of deep-sequencing libraries. PLoS ONE. 2008;3(11): e3713. Epub 2008 Nov 12.
Sela DA, Chapman J, Adeuya A, Kim JH, et al. The genome sequence of Bifidobacterium longum subsp. infantis reveals adaptations for milk utilization within the infant microbiome. Proc Natl Acad Sci U S A. 2008 Dec 2;105(48):18964-9. Epub 2008 Nov 24.
Tito RY, Macmil S, Wiley G, Najar F, et al. Phylotyping and functional analysis of two ancient human microbiomes. PLoS ONE. 2008;3(11): e3703. Epub 2008 Nov 11.
Tokuda G, Lo N, Takase A, Yamada A, Hayashi Y, Watanabe H. Purification and partial genome characterization of the bacterial endosymbiont Blattabacterium cuenoti from the fat bodies of cockroaches. BMC Res Notes. 2008 Nov 25;1(1):118. [Epub ahead of print]
Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL,
et al.
A core gut microbiome in obese and lean twins. Nature. 2008 Nov 30. [Epub ahead of print]
Wang ET, Sandberg R, Luo S, Khrebtukova I, et al. Alternative isoform regulation in human tissue transcriptomes. Nature. 2008 Nov 27;456(7221):470-6.
Wang J, Wang W, Li R, Li Y, et al. The diploid genome sequence of an Asian individual. Nature. 2008 Nov 6;456(7218):60-5.
Zhang Y, Shin H, Song JS, Lei Y, Liu XS. Identifying positioned nucleosomes with epigenetic marks in human from ChIP-Seq. BMC Genomics. 2008 Nov 13;9(1):537.