Sequencing-Related Papers of Note, October 2008
Authors Title Citation
Alexandrov NN, Brover VV, Freidin S, Troukhan ME, et al. Insights into corn genes derived from large-scale cDNA sequencing. Plant Mol Biol. 2008 Oct 21. [Epub ahead of print]
Antranikian G, Ruepp A, Gordon PM, Ballschmiter M, et al. Rapid access to genes of biotechnologically useful enzymes by partial genome sequencing: the thermoalkaliphile Anaerobranca gottschalkii. J Mol Microbiol Biotechnol. 2009;16(1-2):81-90. Epub 2008 Oct 29.
Babiarz JE, Ruby JG, Wang Y, Bartel DP, Blelloch R. Mouse ES cells express endogenous shRNAs, siRNAs, and other Microprocessor-independent, Dicer-dependent small RNAs. Genes Dev. 2008 Oct 15;22(20):2773-85.
Baltrus DA, Amieva MR, Covacci A, Lowe TM, Merrell DS, Ottemann KM, Stein M, Salama NR, Guillemin K. The complete genome sequence of Helicobacter pylori strain G27. J Bacteriol. 2008 Oct 24. [Epub ahead of print]
Bau S, Schracke N, Kränzle M, Wu H, Stähler PF, Hoheisel JD, Beier M, Summerer D. Targeted next-generation sequencing by specific capture of multiple genomic loci using low-volume microfluidic DNA arrays. Anal Bioanal Chem. 2008 Oct 29. [Epub ahead of print]
Bordoni R, Bonnal R, Rizzi E, Carrera P, et al. Evaluation of human gene variant detection in amplicon pools by the GS-FLX parallel pyrosequencer. BMC Genomics. 2008 Oct 8;9:464.
Bowler C, Allen AE, Badger JH, Grimwood J, et al. The Phaeodactylum genome reveals the evolutionary history of diatom genomes. Nature. 2008 Nov 13;456(7219):239-44. Epub 2008 Oct 15.
Carlton JM, Adams JH, Silva JC, Bidwell SL, et al. Comparative genomics of the neglected human malaria parasite Plasmodium vivax. Nature. 2008 Oct 9;455(7214):757-63.
Chen X, Ba Y, Ma L, Cai X, Yin Y, et al. Characterization of microRNAs in serum: a novel class of biomarkers for diagnosis of cancer and other diseases. Cell Res. 2008 Oct;18(10):997-1006
Chen YJ, Huang X. DNA sequencing by denaturation: Principle and thermodynamic simulations. Anal Biochem. 2008 Oct 7. [Epub ahead of print]
Cochrane G, Akhtar R, Bonfield J, Bower L, et al. Petabyte-scale innovations at the European Nucleotide Archive. Nucleic Acids Res. 2008 Oct 31. [Epub ahead of print]
Ding L, Getz G, Wheeler DA, Mardis ER, et al. Somatic mutations affect key pathways in lung adenocarcinoma. Nature. 2008 Oct 23;455(7216):1069-75.
Fan HC, Blumenfeld YJ, Chitkara U, Hudgins L, Quake SR. Noninvasive diagnosis of fetal aneuploidy by shotgun sequencing DNA from maternal blood. Proc Natl Acad Sci U S A. 2008 Oct 21;105(42):16266-71. Epub 2008 Oct 6.
Frank DN. XplorSeq: a software environment for integrated management and phylogenetic analysis of metagenomic sequence data. BMC Bioinformatics. 2008 Oct 7;9:420.
Iguchi A, Thomson NR,
Ogura Y, Saunders D, et al.		 The complete genome sequence and comparative genome analysis of enteropathogenic E. coli O127:H6 strain E2348/69. J Bacteriol. 2008 Oct 24. [Epub ahead of print]
Ingman M, Gyllensten U. SNP frequency estimation using massively parallel sequencing of pooled DNA. Eur J Hum Genet. 2008 Oct 15. [Epub ahead of print]
Jeong JR, Llandro J, Hong B, Hayward TJ, et al. Rewritable remote encoding and decoding of miniature multi-bit magnetic tags for high-throughput biological analysis. Lab Chip. 2008 Nov;8(11):1883-7. Epub 2008 Oct 7.
Kuchenbauer F, Morin RD, Argiropoulos B, Petriv OI, et al. In-depth characterization of the microRNA transcriptome in a leukemia progression model. Genome Res. 2008 Nov;18(11):1787-97. Epub 2008 Oct 10.
Leary RJ, Lin JC, Cummins J, Boca S, et al. Integrated analysis of homozygous deletions, focal amplifications, and sequence alterations in breast and colorectal cancers. Proc Natl Acad Sci U S A. 2008 Oct 21;105(42):16224-9. Epub 2008 Oct 13.
Matsumura H, Krüger DH,
Kahl G, Terauchi R.		 SuperSAGE: a modern platform for genome-wide quantitative transcript profiling. Curr Pharm Biotechnol. 2008 Oct;9(5):368-74.
Miller JR, Delcher AL, Koren S, Venter E, Walenz BP, Brownley A, Johnson J, Li K, Mobarry C, Sutton G. Aggressive assembly of pyrosequencing reads with mates. Bioinformatics. 2008 Oct 28. [Epub ahead of print]
Ondov B, Varadarajan A, Passalacqua KD, Bergman NH. Efficient mapping of Applied Biosystems SOLiD sequence data to a reference genome for functional genomic applications. Bioinformatics. 2008 Oct 7. [Epub ahead of print]
Oshima K, Toh H, Ogura Y, Sasamoto H, et al. Complete genome sequence and comparative analysis of the wild-type commensal Escherichia coli strain SE11 isolated from a healthy adult. DNA Res. 2008 Oct 17. [Epub ahead of print]
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 Oct 29. [Epub ahead of print]
Pain A, Böhme U, Berry AE, Mungall K, et al. The genome of the simian and human malaria parasite Plasmodium knowlesi. Nature. 2008 Oct 9;455(7214):799-803.
Pan X, Urban AE, Palejev D, Schulz V, Grubert F, Hu Y, Snyder M, Weissman SM. A procedure for highly specific, sensitive, and unbiased whole-genome amplification. Proc Natl Acad Sci U S A. 2008 Oct 7;105(40):15499-504. Epub 2008 Oct 1.
Pomraning KR, Smith KM, Freitag M. Genome-wide high throughput analysis of DNA methylation in eukaryotes. Methods. 2008 Oct 21. [Epub ahead of print]
Poole RL, Barker GL, Werner K, Biggi GF, et al. Analysis of wheat SAGE tags reveals evidence for widespread antisense transcription. BMC Genomics. 2008 Oct 10;9(1):475. [Epub ahead of print]
Puiu D, Salzberg SL. Re-assembly of the genome of Francisella tularensis subsp. holarctica OSU18. PLoS ONE. 2008; 3(10):e3427. Epub 2008 Oct 17.
Ralph SG, Chun HJ, Kolosova N, Cooper D, et al. A conifer genomics resource of 200,000 spruce (Picea spp.) ESTs and 6,464 high-quality, sequence-finished full-length cDNAs for Sitka spruce (Picea sitchensis). BMC Genomics. 2008 Oct 14;9:484.
Ravel J, Jiang L, Stanley ST, Wilson MR, et al. The complete genome sequence of Bacillus anthracis Ames "Ancestor". J Bacteriol. 2008 Oct 24. [Epub ahead of print]
Richter DC, Ott F, Auch AF, Schmid R, Huson DH. MetaSim: a sequencing simulator for genomics and metagenomics. PLoS ONE. 2008 Oct 8;3(10):e3373
Rougemont J, Amzallag A,
Iseli C, Farinelli L, Xenarios I, Naef F.		 Probabilistic base calling of Solexa sequencing data. BMC Bioinformatics. 2008 Oct 13;9:431.
Salvagiotto G, Zhao Y, Vodyanik M, Ruotti V, et al. Molecular profiling reveals similarities and differences between primitive subsets of hematopoietic cells generated in vitro from human embryonic stem cells and in vivo during embryogenesis. Exp Hematol. 2008 Oct;36(10):1377-89.
Santos S, Sá D, Bastos E, Guedes-Pinto H, Gut I, Gärtner F, Chaves R. An efficient protocol for genomic DNA extraction from formalin-fixed paraffin-embedded tissues. Res Vet Sci. 2008 Oct 14. [Epub ahead of print]
Soh J, Gordon PM, Taschuk ML, Dong A, Ah-Seng AC, Turinsky AL, Sensen CW. Bluejay 1.0: genome browsing and comparison with rich customization provision and dynamic resource linking. BMC Bioinformatics. 2008 Oct 22;9(1):450. [Epub ahead of print]
Sorber K, Chiu C, Webster D, Dimon M, Ruby JG, Hekele A, DeRisi JL. The long march: a sample preparation technique that enhances contig length and coverage by high-throughput short-read sequencing. PLoS ONE. 2008; 3(10):e3495. Epub 2008 Oct 22.
Sugawara H, Ikeo K, Fukuchi S, Gojobori T, Tateno Y. DDBJ dealing with mass data produced by the second generation sequencer. Nucleic Acids Res. 2008 Oct 16. [Epub ahead of print]
't Hoen PA, Ariyurek Y, Thygesen HH, Vreugdenhil E, Vossen RH, de Menezes RX, Boer JM, van Ommen GJ, den Dunnen JT. Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms. Nucleic Acids Res. 2008 Oct 31. [Epub ahead of print]
Umezawa T, Sakurai T, Totoki Y, Toyoda A, et al. Sequencing and analysis of approximately 40 000 soybean cDNA clones from a full-length-enriched cDNA library. DNA Res. 2008 Oct 16. [Epub ahead of print]
Varley KE, Mitra RD. Nested Patch PCR enables highly multiplexed mutation discovery in candidate genes. Genome Res. 2008 Nov;18(11):1844-50. Epub 2008 Oct 10.
Viasnoff V, Chiaruttini N, Bockelmann U. Probing DNA base pairing energy profiles using a nanopore. Eur Biophys J. 2008 Oct 3. [Epub ahead of print]
Wicker T, Narechania A, Sabot F, Stein J, Vu GT, Graner A, Ware D, Stein N. Low-pass shotgun sequencing of the barley genome facilitates rapid identification of genes, conserved non-coding sequences and novel repeats. BMC Genomics. 2008 Oct 31;9(1):518. [Epub ahead of print]
Zhou X, Sunkar R, Jin H, Zhu JK, Zhang W. Genome-wide identification and analysis of small RNAs originated from natural antisense transcripts in Oryza sativa. Genome Res. 2008 Oct 29. [Epub ahead of print]