Sequencing-Related Papers of Note, September 2008
Authors Title Citation
Ashcroft BA, Spadola Q, Qamar S, et al.

An AFM/rotaxane molecular reading head for sequence-dependent DNA structures.

 Small. 2008 Sep;4(9):1468-75.
Baillet A, Mandon-Pépin B, Cabau C, Poumerol E, Pailhoux E, Cotinot C. Identification of transcripts involved in meiosis and follicle formation during ovine ovary development. BMC Genomics. 2008 Sep 23;9:436.
Bartos J, Paux E, Kofler R,
et al.		 A first survey of the rye (Secale cereale) genome composition through BAC end sequencing of the short arm of chromosome 1R. BMC Plant Biol. 2008
Sep 19;8:95.
Borneman AR, Forgan AH, Pretorius IS, Chambers PJ. Comparative genome analysis of a Saccharomyces cerevisiae wine strain. FEMS Yeast Res. 2008 Sep 4. [Epub ahead of print]
Boyle AP, Guinney J, Crawford GE, Furey TS. F-Seq: A feature density estimator for high-throughput sequence tags. Bioinformatics. 2008 Sep 10. [Epub ahead of print]
Craig DW, Pearson JV, Szelinger S, Sekar A, et al. Identification of genetic variants using bar-coded multiplexed sequencing. Nat Methods. 2008 Oct;5(10):887-93. Epub 2008 Sep 14.
Dieterich C, Clifton SW, Schuster LN, Chinwalla A,
et al.		 The Pristionchus pacificus genome provides a unique perspective on nematode lifestyle and parasitism. Nat Genet. 2008 Oct;40(10):1193-8.
Epub 2008 Sep 21.
Feng W, Liu Y, Wu J, Nephew KP, Huang TH, Li L. A Poisson mixture model to identify changes in RNA polymerase II binding quantity using high-throughput sequencing technology. BMC Genomics. 2008 Sep 16;9 Suppl 2:S23.
Fyta M, Melchionna S, Succi S, Kaxiras E. Hydrodynamic correlations in the translocation of a biopolymer through a nanopore: Theory and multiscale simulations. Phys Rev E Stat Nonlin Soft Matter Phys. 2008 Sep;78(3 Pt 2):036704. Epub 2008 Sep 17.
Gruntman E, Qi Y, Slotkin RK, Roeder T, Martienssen RA, Sachidanandam R. Kismeth: analyzer of plant methylation states through bisulfite sequencing. BMC Bioinformatics. 2008 Sep 11;9:371.
Hanriot L, Keime C, Gay N, et al. A combination of LongSAGE with Solexa sequencing is well suited to explore the depth and the complexity of transcriptome. BMC Genomics. 2008 Sep 16;9:418.
Jones S, Zhang X, Parsons DW, Lin JC, et al. Core signaling pathways in human pancreatic cancers revealed by global genomic analyses. Science. 2008 Sep 26;321(5897):1801-6.
Epub 2008 Sep 4.
Kalyuzhnaya MG, Lapidus A, Ivanova N, et al. High-resolution metagenomics targets specific functional types in complex microbial communities. Nat Biotechnol. 2008 Sep;26(9):1029-34.
Koshino M, Solin N, Tanaka T, Isobe H, Nakamura E. Imaging the passage of a single hydrocarbon chain through a nanopore. Nat Nanotechnol. 2008 Oct;3(10):595-7. Epub 2008 Sep 14.
Lee HS, Kang SG, Bae SS, Lim JK et al. The complete genome sequence of Thermococcus onnurineus NA1 reveals a mixed heterotrophic and carboxydotrophic metabolism. J Bacteriol. 2008 Sep 12. [Epub ahead of print]
Lescot M, Audic S, Robert C, Nguyen TT, et al. The genome of Borrelia recurrentis, the agent of deadly louse-borne relapsing fever, is a degraded subset of tick-borne Borrelia duttonii. PLoS Genet. 2008 Sep 12;4(9):e1000185.
Li H, Ruan J, Durbin R. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res. 2008 Sep 25. [Epub ahead of print]
McShan WM, Ferretti JJ, Karasawa T, et al. Genome sequence of a nephritogenic and highly transformable M49 strain of Streptococcus pyogenes. J Bacteriol. 2008 Sep 26. [Epub ahead of print]
Meyer F, Paarmann D, D'Souza M, Olson R, et al. The metagenomics RAST server — a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics. 2008 Sep 19;9:386.
Nobuta K, Lu C, Shrivastava R, Pillay M, et al. Distinct size distribution of endogeneous siRNAs in maize: Evidence from deep sequencing in the mop1-1 mutant. Proc Natl Acad Sci
U S A. 2008 Sep 30;105(39):14958-63.
Epub 2008 Sep 24.
Opperman CH, Bird DM, Williamson VM, et al. Sequence and genetic map of Meloidogyne hapla: A compact nematode genome for plant parasitism. Proc Natl Acad Sci
U S A. 2008 Sep 30;105(39):14802-7.
Epub 2008 Sep 22.
Ossowski S, Schneeberger K, Clark RM, Lanz C, Warthmann N, Weigel D. Sequencing of natural strains of Arabidopsis thaliana with short reads. Genome Res. 2008 Sep 25. [Epub ahead of print]
Parsons DW, Jones S,
Zhang X, et al.		 An integrated genomic analysis of human glioblastoma multiforme. Science. 2008 Sep 26;321(5897):1807-12. Epub 2008 Sep 4.
Payne CM, Zhao X, Cummings PT. Electrophoresis of ssDNA through nanoelectrode gaps from molecular dynamics: Impact of gap width and chain length. J Phys Chem B. 2008
Oct 9;112(40):12851-8. Epub 2008 Sep 11.
Reith ME, Singh RK, Curtis B, Boyd JM, et al. The genome of Aeromonas salmonicida subsp. salmonicida A449: insights into the evolution of a fish pathogen. BMC Genomics. 2008 Sep 18;9:427.
Robertson AG, Bilenky M, Tam A, Zhao Y, et al. Genome wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding. Genome Res. 2008 Sep 11. [Epub ahead of print]
Robinson SJ, Parkin IA. Differential SAGE analysis in Arabidopsis uncovers increased transcriptome complexity in response to low temperature. BMC Genomics. 2008 Sep 22;9:434.
Salzberg SL, Sommer DD, Puiu D, Lee VT. Gene-boosted assembly of a novel bacterial genome from very short reads. PLoS Comput Biol. 2008 Sep 26;4(9):e1000186.
Sivaraman K, Venkataraman N, Tsai J, Dewell S, Cole AM. Genome sequencing and analysis reveals possible determinants of Staphylococcus aureus nasal carriage. BMC Genomics. 2008 Sep 22;9:433.
Smith DR, Quinlan AR, Peckham HE, Makowsky K, et al. Rapid whole-genome mutational profiling using next-generation sequencing technologies. Genome Res. 2008 Oct;18(10):1638-42.
Epub 2008 Sep 4.
Tang C, Shi X, Li X, Lu Z. DNA sequencing by synthesis with degenerate primers. J Genet Genomics. 2008 Sep;35(9):545-51.
Terol J, Naranjo MA, Ollitrault P, Talon M. Development of genomic resources for Citrus clementina: characterization of three deep-coverage BAC libraries and analysis of 46,000 BAC end sequences. BMC Genomics. 2008 Sep 18;9:423.
The Cancer Genome Atlas Research Network Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature. 2008 Sep 4.
[Epub ahead of print]
Thomas T, Evans FF, Schleheck D, et al. Analysis of the Pseudoalteromonas tunicata genome reveals properties of a surface-associated life style in the marine environment. PLoS ONE. 2008 Sep 24;3(9):e3252.
van den Berg MA, Albang R, Albermann K, et al. Genome sequencing and analysis of the filamentous fungus Penicillium chrysogenum. Nat Biotechnol. 2008 Oct;26(10):1161-8.
Epub 2008 Sep 28.
Welsh EA, Liberton M, Stöckel J, et al. The genome of Cyanothece 51142, a unicellular diazotrophic cyanobacterium important in the marine nitrogen cycle. Proc Natl Acad Sci
U S A. 2008 Sep 30;105(39):15094-9.
Epub 2008 Sep 23.
Zhang Y, Liu T, Meyer CA, Eeckhoute J, et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008
Sep 17;9(9):R137.
[Epub ahead of print]