Sequencing-Related
Papers of Note, November 2008
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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. |