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Papers of Note: Jul 14, 2009


Sequencing-Related Papers of Note, June 2009

Formation of individual protein channels in lipid bilayers suspended in nanopores.
Studer A, Han X, Winkler FK, Tiefenauer LX.
Colloids Surf B Biointerfaces. 2009 Jun 10. [Epub ahead of print]

High-resolution profiling and discovery of planarian small RNAs.
Friedländer MR, Adamidi C, Han T, Lebedeva S, Isenbarger TA, et al.
Proc Natl Acad Sci U S A. 2009 Jun 29. [Epub ahead of print]

HAPLOWSER: a whole-genome haplotype browser for personal genome and metagenome.
Kim JH, Kim WC, Waterman MS, Park S, Li LM.
Bioinformatics. 2009 Jun 27. [Epub ahead of print]

A comparative study of species richness estimates obtained using nearly complete fragments and simulated pyrosequencing-generated fragments in 16S rRNA gene-based environmental surveys.
Youssef N, Sheik CS, Krumholz LR, Najar FZ, Roe BA, Elshahed MS.
Appl Environ Microbiol. 2009 Jun 26. [Epub ahead of print]

Comparative study on ChIP-seq data: normalization and binding pattern characterization.
Taslim C, Wu J, Yan P, Singer G, Parvin J, Huang T, Lin S, Huang K.
Bioinformatics. 2009 Jun 26. [Epub ahead of print]

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Genome analysis and genome-wide proteomics of Thermococcus gammatolerans, the most radioresistant organism known amongst the Archaea.
Zivanovic Y, Armengaud J, Lagorce A, Leplat C, et al.
Genome Biol. 2009 Jun 26;10(6):R70. [Epub ahead of print]

Large-scale parallel 454 sequencing reveals host ecological group specificity of arbuscular mycorrhizal fungi in a boreonemoral forest.
Opik M, Metsis M, Daniell TJ, Zobel M, Moora M.
New Phytol. 2009 Jun 24. [Epub ahead of print]

Deep sequencing identifies new and regulated microRNAs in Schmidtea mediterranea.
Lu YC, Smielewska M, Palakodeti D, Lovci MT, Aigner S, Yeo GW, Graveley BR.
RNA. 2009 Jun 24. [Epub ahead of print]

Extracting transcription factor targets from ChIP-seq data.
Tuteja G, White P, Schug J, Kaestner KH.
Nucleic Acids Res. 2009 Jun 24. [Epub ahead of print]

The Mycoplasma conjunctivae genome sequencing, annotation and analysis.
Calderon-Copete SP, Wigger G, Wunderlin C, Schmidheini T, Frey J, Quail MA, Falquet L.
BMC Bioinformatics. 2009 Jun 16;10 Suppl 6:S7.

A modified protocol for bisulfite genomic sequencing of difficult samples.
Pappas JJ, Toulouse A, Bradley WE.
Biol Proced Online. 2009 Jun 24. [Epub ahead of print]

Swift: primary data analysis for the Illumina Solexa sequencing platform.
Whiteford N, Skelly T, Curtis C, Ritchie ME, Löhr A, Zaranek AW, Abnizova I, Brown C.
Bioinformatics. 2009 Jun 23. [Epub ahead of print]

Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two base encoding.
McKernan KJ, Peckham HE, Costa G, McLaughlin S, Tsung E, Fu Y, et al.
Genome Res.
2009 Jun 22. [Epub ahead of print]

Filter-based hybridization capture of subgenomes enables resequencing and copy-number detection.
Herman DS, Hovingh GK, Iartchouk O, Rehm HL, Kucherlapati R, Seidman JG, Seidman CE.
Nat Methods. 2009 Jul;6(7):507-10. Epub 2009 Jun 21.

Genome sequence of the emerging pathogen Helicobacter canadensis.
Loman NJ, Snyder LA, Linton JD, Langdon R, Lawson AJ, Weinstock GW, Wren BW, Pallen MJ.
J Bacteriol. 2009 Jun 19. [Epub ahead of print]

Optical mapping reveals a large genetic inversion between two methicillin-resistant Staphylococcus aureus strains.
Shukla SK, Kislow J, Briska A, Henkhaus J, Dykes C.
J Bacteriol. 2009 Jun 19. [Epub ahead of print]

ISOLATE: A computational strategy for identifying the primary origin of cancers using high throughput sequencing.
Quon G, Morris Q.
Bioinformatics. 2009 Jun 19. [Epub ahead of print]

SHREC: A short-read error correction method.
Schröder J, Schröder H, Puglisi SJ, Sinja R, Schmidt B.
Bioinformatics. 2009 Jun 19. [Epub ahead of print]

VarScan: Variant detection in massively parallel sequencing of individual and pooled samples.
Koboldt DC, Chen K, Wylie T, Larson DE, McLellan MD, Mardis ER, Weinstock GM, Wilson RK, Ding L.
Bioinformatics. 2009 Jun 19. [Epub ahead of print]

Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly.
Dutilh BE, Huynen MA, Strous M.
Bioinformatics. 2009 Jun 19. [Epub ahead of print]

Profiling the T-cell receptor beta-chain repertoire by massively parallel sequencing.
Freeman JD, Warren RL, Webb JR, Nelson BH, Holt RA.
Genome Res. 2009 Jun 18. [Epub ahead of print]

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Next-generation tag sequencing for cancer gene expression profiling.
Morrissy AS, Morin RD, Delaney A, Zeng T, McDonald H, Jones SJ, Zhao Y, Hirst M, Marra MA.
Genome Res. 2009 Jun 18. [Epub ahead of print]

Distinguishing single- and double-stranded nucleic acid molecules using solid-state nanopores.
Skinner GM, van den Hout M, Broekmans O, Dekker C, Dekker NH.
Nano Lett. 2009 Jun 19. [Epub ahead of print]

A fast hybrid short read fragment assembly algorithm.
Schmidt B, Sinha R, Beresford-Smith B, Puglisi SJ.
Bioinformatics. 2009 Jun 17. [Epub ahead of print]

Using reads to annotate the genome: influence of length, background distribution, and sequence errors on prediction capacity.
Philippe N, Boureux A, Bréhélin L, Tarhio J, Commes T, Rivals E.
Nucleic Acids Res. 2009 Jun 16. [Epub ahead of print]

High-throughput multiplex sequencing to discover copy number variants in Drosophila.
Daines B, Wang H, Li Y, Han Y, Gibbs R, Chen R.
Genetics. 2009 Jun 15. [Epub ahead of print]
De novo transcriptome assembly with ABySS.
Birol I, Jackman SD, Nielsen C, Qian JQ, Varhol R, Stazyk G, et al.
Bioinformatics. 2009 Jun 15. [Epub ahead of print]
Detection of single nucleotide variations in expressed exons of the human genome using RNA-seq.
Chepelev I, Wei G, Tang Q, Zhao K.
Nucleic Acids Res. 2009 Jun 15. [Epub ahead of print]

Multiplex padlock capture and sequencing reveal human hypermutable CpG variations.
Li JB, Gao Y, Aach J, Zhang K, Kryukov G, Xie B, Ahlford A, et al.
Genome Res. 2009 Jun 12. [Epub ahead of print]

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Transcriptome sequencing of the Microarray Quality Control (MAQC) RNA reference samples using next generation sequencing.
Mane SP, Evans C, Cooper KL, Crasta OR, Folkerts O, et al.
BMC Genomics. 2009 Jun 12;10:264.

Statistical distributions of sequencing by synthesis with probabilistic nucleotide incorporation.
Kong Y.
J Comput Biol. 2009 Jun;16(6):817-27.
Mutation of FOXL2 in granulosa-cell tumors of the ovary.
Shah SP, Köbel M, Senz J, Morin RD, Clarke BA, Wiegand KC, et al.
N Engl J Med. 2009 Jun 25;360(26):2719-29. Epub 2009 Jun 10.

Ultra-deep pyrosequencing detects complex patterns of CD8+ T-lymphocyte escape in SIV-infected macaques.
Bimber BN, Burwitz BJ, O'Connor S, Detmer A, Gostick E, et al.
J Virol. 2009 Jun 10. [Epub ahead of print]

Local alignment of two-base encoded DNA sequence.
Homer N, Merriman B, Nelson SF.
BMC Bioinformatics. 2009 Jun 9;10(1):175. [Epub ahead of print]

Identification and analysis of miRNAs in human breast cancer and teratoma samples using deep sequencing.
Nygaard S, Jacobsen A, Lindow M, Eriksen J, Balslev E, et al.
BMC Med Genomics. 2009 Jun 9;2:35.

The Sequence Alignment/Map (SAM) format and SAMtools.
Li H, Handsaker B, Wysoker A, et al.; 1000 Genome Project Data Processing Subgroup.
Bioinformatics. 2009 Jun 8. [Epub ahead of print]

A clustering approach for identification of enriched domains from histone modification ChIP-seq data.
Zang C, Schones DE, Zeng C, Cui K, Zhao K, Peng W.
Bioinformatics. 2009 Jun 8. [Epub ahead of print]

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Soil pH as a predictor of soil bacterial community structure at the continental scale: a pyrosequencing-based assessment.
Lauber CL, Hamady M, Knight R, Fierer N.
Appl Environ Microbiol. 2009 Jun 5. [Epub ahead of print]

Characterization of airborne microbial communities at a high elevation site and their potential to act as atmospheric ice nuclei.
Bowers RM, Lauber CL, Wiedinmyer C, Hamady M, Hallar AG, Fall R, Knight R, Fierer N.
Appl Environ Microbiol. 2009 Jun 5. [Epub ahead of print]

Comparative profiling of the transcriptional response to infection in two species of Drosophila by short-read cDNA sequencing.
Sackton TB, Clark AG.
BMC Genomics. 2009 Jun 7;10:259.

A score system for quality evaluation of RNA sequence tags: an improvement for gene expression profiling.
Pinheiro DG, Galante PA, de Souza SJ, Zago MA, Silva WA Jr.
BMC Bioinformatics. 2009 Jun 6;10:170.

Novel microRNAs uncovered by deep sequencing of small RNA transcriptomes in bread wheat (Triticum aestivum L.) and Brachypodium distachyon (L.) Beauv.
Wei B, Cai T, Zhang R, Li A, Huo N, Li S, Gu YQ, Vogel J, Jia J, Qi Y, Mao L.
Funct Integr Genomics. 2009 Jun 5. [Epub ahead of print]

ABACAS: Algorithm Based Automatic Contiguation of Assembled Sequences.
Assefa S, Keane TM, Otto TD, Newbold C, Berriman M.
Bioinformatics. 2009 Jun 3. [Epub ahead of print]

Detecting SNPs and estimating allele frequencies in clonal bacterial populations by sequencing pooled DNA.
Holt KE, Teo YY, Li H, Nair S, Dougan G, Wain J, Parkhill J.
Bioinformatics. 2009 Jun 3. [Epub ahead of print]

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Genomic characterization of methanomicrobiales reveals three classes of methanogens.
Anderson I, Ulrich LE, Lupa B, Susanti D, Porat I, Hooper SD, Lykidis A, et al.
PLoS One. 2009 Jun 4;4(6):e5797.

Closing gaps in the human genome using sequencing by synthesis.
Garber M, Zody MC, Arachchi HM, Berlin A, Gnerre S, Green LM, Lennon N, Nusbaum C.
Genome Biol. 2009 Jun 2;10(6):R60. [Epub ahead of print]

Mapping the position of DNA polymerase-bound DNA templates in a nanopore at 5 Å resolution.
Gyarfas B, Olasagasti F, Benner S, Garalde D, Lieberman KR, Akeson M.
ACS Nano. 2009 Jun 23;3(6):1457-66.

The first Korean genome sequence and analysis: Full genome sequencing for a socio-ethnic group.
Ahn SM, Kim TH, Lee S, Kim D, Ghang H, Kim DS, Kim BC, et al.
Genome Res. 2009 Jun 24. [Epub ahead of print]

Addendum: Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing.
Pan Q, Shai O, Lee LJ, Frey BJ, Blencowe BJ.
Nat Genet. 2009 Jun;41(6):762. No abstract available.

Chemically labeled nucleotides and oligonucleotides encode DNA for sensing with nanopores.
Borsenberger V, Mitchell N, Howorka S.
J Am Chem Soc. 2009 Jun 10;131(22):7530-1.

Mobile elements create structural variation: Analysis of a complete human genome.
Xing J, Zhang Y, Han K, Salem AH, Sen SK, Huff CD, Zhou Q, Kirkness EF, Levy S, Batzer MA, Jorde LB.
Genome Res.
2009 Jun 9. [Epub ahead of print]

Detection of low-frequency pretherapy chemokine (CXC motif) receptor 4 (CXCR4)-using HIV-1 with ultra-deep pyrosequencing.
Archer J, Braverman MS, Taillon BE, Desany B, James I, Harrigan PR, Lewis M, Robertson DL.
AIDS. 2009 Jun 19;23(10):1209-18.

Electrophysiological study of single gold nanoparticle/alpha-hemolysin complex formation: a nanotool to slow down ssDNA through the alpha-hemolysin nanopore.
Astier Y, Uzun O, Stellacci F.
Small. 2009 Jun;5(11):1273-8. No abstract available.

On the use of ESI-QqTOF-MS/MS for the comparative sequencing of nucleic acids.
Oberacher H, Pitterl F.
Biopolymers. 2009 Jun;91(6):401-9.