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Papers of Note: Oct 13, 2009

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Sequencing-Related Papers of Note, Sept. 2009

Genomic diversity and evolution of Mycobacterium ulcerans revealed by next-generation sequencing.
Qi W, Käser M, Röltgen K, Yeboah-Manu D, Pluschke G.
PLoS Pathog. 2009 Sep;5(9):e1000580. Epub 2009 Sep 11.


Quantized ionic conductance in nanopores.
Zwolak M, Lagerqvist J, Di Ventra M.
Phys Rev Lett. 2009 Sep 18;103(12):128102. Epub 2009 Sep 17.


A report on the 2009 SIG on short read sequencing and algorithms (Short-SIG).
Brudno M, Medvedev P, Stoye J, De La Vega F.
Bioinformatics. 2009 Sep 24. [Epub ahead of print]


Electrophoretic force on a protein-coated DNA molecule in a solid-state nanopore.
Hall AR, van Dorp S, Lemay SG, Dekker C.
Nano Lett. 2009 Sep 25. [Epub ahead of print]


The fabrication of high-aspect-ratio, size-tunable nanopore arrays by modified nanosphere lithography.
Chen X, Wei X, Jiang K.
Nanotechnology. 2009 Oct 21;20(42):425605. Epub 2009 Sep 25.


Identification of novel MHC class I sequences in pig-tailed macaques by amplicon pyrosequencing and full-length cDNA cloning and sequencing.
O'Leary CE, Wiseman RW, Karl JA, Bimber BN, Lank SM, Tuscher JJ, O'Connor DH.
Immunogenetics. 2009 Sep 24. [Epub ahead of print]


Direct RNA sequencing.
Ozsolak F, Platt AR, Jones DR, Reifenberger JG, Sass LE, McInerney P, Thompson JF, et al.
Nature. 2009 Oct 8;461(7265):814-8. Epub 2009 Sep 23.


Complete genome sequence of the sugarcane nitrogen-fixing endophyte Gluconacetobacter diazotrophicus PAL5.
Bertalan M, Albano R, Padua V, Rouws L, Rojas C, Hemerly A, Teixeira K, Schwab S, et al.
BMC Genomics. 2009 Sep 23;10(1):450. [Epub ahead of print]


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BayesPeak: Bayesian analysis of ChIP-seq data.
Spyrou C, Stark R, Lynch AG, Tavare S.
BMC Bioinformatics. 2009 Sep 21;10(1):299. [Epub ahead of print]


Computation of rank and select functions on hierarchical binary string and its application to genome mapping problems for short-read DNA sequences.
Kimura K, Suzuki Y, Sugano S, Koike A.
J Comput Biol. 2009 Sep 22. [Epub ahead of print]


The feasibility of using high resolution genome sequencing of influenza A viruses to detect mixed infections and quasispecies.
Ramakrishnan MA, Tu ZJ, Singh S, Chockalingam AK, Gramer MR, Wang P, et al.
PLoS One. 2009 Sep 22;4(9):e7105.


Tn-seq: high-throughput parallel sequencing for fitness and genetic interaction studies in microorganisms.
van Opijnen T, Bodi KL, Camilli A.
Nat Methods. 2009 Oct;6(10):767-72. Epub 2009 Sep 20.


Identifiability of isoform deconvolution from junction arrays and RNA-seq.
Hiller D, Jiang H, Xu W, Wong WH.
Bioinformatics. 2009 Sep 16. [Epub ahead of print]


Simultaneous alignment of short reads against multiple genomes.
Schneeberger K, Hagmann J, Ossowski S, Warthmann N, Gesing S, Kohlbacher O, Weigel D.
Genome Biol. 2009 Sep 17;10(9):R98. [Epub ahead of print]


Fast mapping of short sequences with mismatches, insertions and deletions using index structures.
Hoffmann S, Otto C, Kurtz S, Sharma CM, Khaitovich P, Vogel J, Stadler PF, Hackermüller J.
PLoS Comput Biol. 2009 Sep;5(9):e1000502. Epub 2009 Sep 11.


De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data.
Diguistini S, Liao NY, Platt D, Robertson G, Seidel M, Chan SK, Docking TR, Birol I, et al.
Genome Biol. 2009 Sep 11;10(9):R94. [Epub ahead of print]


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A pharmacogene database enhanced by the 1000 Genomes Project.
Gamazon ER, Zhang W, Huang RS, Dolan ME, Cox NJ.
Pharmacogenet Genomics. 2009 Sep 9. [Epub ahead of print]


Quantitative miRNA expression analysis: Comparing microarrays with next-generation sequencing.
Willenbrock H, Salomon J, Søkilde R, Barken KB, Hansen TN, Nielsen FC, Møller S, Litman T.
RNA. 2009 Sep 10. [Epub ahead of print]


The complete genome sequence of the algal symbiont Dinoroseobacter shibae: a hitchhiker's guide to life in the sea.
Wagner-Döbler I, Ballhausen B, Berger M, Brinkhoff T, Buchholz I, Bunk B, Cypionka H, et al.
ISME J. 2009 Sep 10. [Epub ahead of print]


Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans.
Haas BJ, Kamoun S, Zody MC, Jiang RH, Handsaker RE, Cano LM, Grabherr M, et al.
Nature. 2009 Sep 17;461(7262):393-8. Epub 2009 Sep 9.


Allele-specific expression assays using Solexa.
Main BJ, Bickel RD, McIntyre LM, Graze RM, Calabrese PP, Nuzhdin SV.
BMC Genomics. 2009 Sep 9;10:422.


TagDust — A program to eliminate artifacts from next generation sequencing data.
Lassmann T, Hayashizaki Y, Daub CO.
Bioinformatics. 2009 Sep 7. [Epub ahead of print]


Updates to the RMAP short-read mapping software.
Smith AD, Chung W, Hodges E, Kendall J, Hannon G, Hicks J, Xuan Z, Zhang MQ.
Bioinformatics. 2009 Sep 7. [Epub ahead of print]


Specific sequence selection and next generation resequencing of 68 E. coli genes using HybSelect.
Schracke N, Kornmeyer T, Kränzle M, Stähler PF, Summerer D, Beier M.
N Biotechnol. 2009 Sep 6. [Epub ahead of print]


Primer extension capture: targeted sequence retrieval from heavily degraded DNA sources.
Briggs AW, Good JM, Green RE, Krause J, Maricic T, Stenzel U, Pääbo S.
J Vis Exp. 2009 Sep 3;(31):1573. doi: 10.3791/1573.


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Whole genome amplification and de novo assembly of single bacterial cells.
Rodrigue S, Malmstrom RR, Berlin AM, Birren BW, Henn MR, Chisholm SW.
PLoS One. 2009 Sep 2;4(9):e6864.


Base dependent DNA-carbon nanotube interactions: activation enthalpies and assembly-disassembly control.
Albertorio F, Hughes ME, Golovchenko JA, Branton D.
Nanotechnology. 2009 Sep 30;20(39):395101. Epub 2009 Sep 2.


Discrimination of single base substitutions in a DNA strand immobilized in a biological nanopore.
Purnell RF, Schmidt JJ.
ACS Nano. 2009 Sep 22;3(9):2533-8.


LookSeq: A browser-based viewer for deep sequencing data.
Manske HM, Kwiatkowski DP.
Genome Res. 2009 Sep 29. [Epub ahead of print]


Translocation of RecA-coated double-stranded DNA through solid-state nanopores.
Smeets RM, Kowalczyk SW, Hall AR, Dekker NH, Dekker C.
Nano Lett. 2009 Sep;9(9):3089-96.

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