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Papers of Note: Sep 21, 2010

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Quantitative comparison of genome-wide DNA methylation mapping technologies.
Bock C, Tomazou EM, Brinkman AB, Müller F, et al.
Nat Biotechnol. 2010 Sep 19. [Epub ahead of print]


Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications.
Harris RA, Wang T, Coarfa C, Nagarajan RP, et al.
Nat Biotechnol. 2010 Sep 19. [Epub ahead of print]


Validation of two ribosomal RNA removal methods for microbial metatranscriptomics.
He S, Wurtzel O, Singh K, Froula JL, et al.
Nat Methods. 2010 Sep 19. [Epub ahead of print]


Repetitive part of the banana (Musa acuminata) genome investigated by low-depth 454 sequencing.
Hribova E, Neumann P, Matsumoto T, Roux N, et al.
BMC Plant Biol. 2010 Sep 16;10(1):204.


Allele-specific and heritable chromatin signatures in humans.
Birney E, Lieb JD, Furey TS, Crawford GE, Iyer VR.
Hum Mol Genet. 2010 Sep 16. [Epub ahead of print]


By-passing in vitro screening — next generation sequencing technologies applied to antibody display and in silico candidate selection.
Ravn U, Gueneau F, Baerlocher L, Osteras M, et al.
Nucleic Acids Res. 2010 Sep 15. [Epub ahead of print]


Identification of rare DNA variants in mitochondrial disorders with improved array-based sequencing.
Wang W, Shen P, Thiyagarajan S, Lin S, et al.
Nucleic Acids Res. 2010 Sep 15. [Epub ahead of print]


Whole genome characterization of HIV/SIV intra-host diversity by ultra-deep pyrosequencing.
Bimber BN, Dudley DM, Lauck M, Becker EA, et al.
J Virol. 2010 Sep 15. [Epub ahead of print]


High-throughput, sensitive quantification of repopulating hematopoietic stem cell clones.
Kim S, Kim N, Presson AP, An DS, et al.
J Virol. 2010 Sep 15. [Epub ahead of print]


Quantitative analysis of a deeply sequenced marine microbial metatranscriptome.
Gifford SM, Sharma S, Rinta-Kanto JM, Moran MA.
ISME J. 2010 Sep 16. [Epub ahead of print]


Functional metagenomics to mine the human gut microbiome for dietary fiber catabolic enzymes.
Tasse L, Bercovici J, Pizzut-Serin S, Robe P, et al.
Genome Res. 2010 Sep 14. [Epub ahead of print]


The Characterization of Twenty Sequenced Human Genomes.
Pelak K, Shianna KV, Ge D, Maia JM, Zhu M, Smith JP, Cirulli ET, Fellay J, Dickson SP, Gumbs CE, Heinzen EL, Need AC, Ruzzo EK, Singh A, Campbell CR, Hong LK, Lornsen KA, McKenzie AM, Sobreira NL, Hoover-Fong JE, Milner JD, Ottman R, Haynes BF, Goedert JJ, Goldstein DB.
PLoS Genet. 2010 Sep 9;6(9). pii: e1001111.


Multi-Platform Next-Generation Sequencing of the Domestic Turkey (Meleagris gallopavo): Genome Assembly and Analysis.
Dalloul RA, Long JA, Zimin AV, Aslam L, Beal K, Ann Blomberg L, Bouffard P, Burt DW, Crasta O, Crooijmans RP, Cooper K, Coulombe RA, De S, Delany ME, Dodgson JB, Dong JJ, Evans C, Frederickson KM, Flicek P, Florea L, Folkerts O, Groenen MA, Harkins TT, Herrero J, Hoffmann S, Megens HJ, Jiang A, de Jong P, Kaiser P, Kim H, Kim KW, Kim S, Langenberger D, Lee MK, Lee T, Mane S, Marcais G, Marz M, McElroy AP, Modise T, Nefedov M, Notredame C, Paton IR, Payne WS, Pertea G, Prickett D, Puiu D, Qioa D, Raineri E, Ruffier M, Salzberg SL, Schatz MC, Scheuring C, Schmidt CJ, Schroeder S, Searle SM, Smith EJ, Smith J, Sonstegard TS, Stadler PF, Tafer H, Tu ZJ, Van Tassell CP, Vilella AJ, Williams KP, Yorke JA, Zhang L, Zhang HB, Zhang X, Zhang Y, Reed KM.
PLoS Biol. 2010 Sep 7;8(9). pii: e1000475.


A Polymer-Based Nanopore-Integrated Microfluidic Device for Generating Stable Bilayer Lipid Membranes.
Kawano R, Osaki T, Sasaki H, Takeuchi S.
Small. 2010 Sep 13. [Epub ahead of print]


An algorithm for automated closure during assembly.
Koren S, Miller JR, Walenz BP, Sutton G.
BMC Bioinformatics. 2010 Sep 10;11(1):457.
http://www.ncbi.nlm.nih.gov/pubmed/20831800


Pyrosequencing enhancement for better detection limit and sequencing homopolymers.
Gong M, Foo SH, Lin L, Liu ET, Gharizadeh B, Goel S.
Biochem Biophys Res Commun. 2010 Sep 9. [Epub ahead of print]


Reptile: Representative Tiling for Short Read Error Correction.
Yang X, Dorman KS, Aluru S.
Bioinformatics. 2010 Aug 16. [Epub ahead of print]


Candidate exome capture identifies mutation of SDCCAG8 as the cause of a retinal-renal ciliopathy.
Otto EA, Hurd TW, Airik R, Chaki M, Zhou W, Stoetzel C, Patil SB, Levy S, Ghosh AK, Murga-Zamalloa CA, van Reeuwijk J, Letteboer SJ, Sang L, Giles RH, Liu Q, Coene KL, Estrada-Cuzcano A, Collin RW, McLaughlin HM, Held S, Kasanuki JM, Ramaswami G, Conte J, Lopez I, Washburn J, Macdonald J, Hu J, Yamashita Y, Maher ER, Guay-Woodford LM, Neumann HP, Obermüller N, Koenekoop RK, Bergmann C, Bei X, Lewis RA, Katsanis N, Lopes V, Williams DS, Lyons RH, Dang CV, Brito DA, Dias MB, Zhang X, Cavalcoli JD, Nürnberg G, Nürnberg P, Pierce EA, Jackson PK, Antignac C, Saunier S, Roepman R, Dollfus H, Khanna H, Hildebrandt F.
Nat Genet. 2010 Sep 12. [Epub ahead of print]


Alternative expression analysis by RNA sequencing.
Griffith M, Griffith OL, Mwenifumbo J, Goya R, Morrissy AS, Morin RD, Corbett R, Tang MJ, Hou YC, Pugh TJ, Robertson G, Chittaranjan S, Ally A, Asano JK, Chan SY, Li HI, McDonald H, Teague K, Zhao Y, Zeng T, Delaney A, Hirst M, Morin GB, Jones SJ, Tai IT, Marra MA.
Nat Methods. 2010 Sep 12. [Epub ahead of print]


Coarse-grained simulations of stretching entangled DNA using oscillating electric fields.
Graham RS, Larson RG.
Chem Commun (Camb). 2010 Sep 8. [Epub ahead of print]


Construction of small-insert and large-insert metagenomic libraries.
Simon C, Daniel R.
Methods Mol Biol. 2010;668:39-50.


Metagenomic analysis of isotopically enriched DNA.
Chen Y, Neufeld JD, Dumont MG, Friedrich MW, Murrell JC.
Methods Mol Biol. 2010;668:67-75.


Bioinformatic tools for using whole genome sequencing as a rapid high resolution diagnostic typing tool when tracing bioterror organisms in the food and feed chain.
Segerman B, De Medici D, Ehling Schulz M, Fach P, Fenicia L, Fricker M, Wielinga P, Van Rotterdam B, Knutsson R.
Int J Food Microbiol. 2010 Sep 6. [Epub ahead of print]


High-resolution Whole-genome Sequencing Reveals Specific Chromatin Domains from Most Human Chromosomes Associate with Nucleoli.
van Koningsbruggen S, Gierlinski M, Schofield P, Martin D, Barton GJ, Ariyurek Y, den Dunnen JT, Lamond AI.
Mol Biol Cell. 2010 Sep 8. [Epub ahead of print]


Construction of small RNA cDNA libraries for deep sequencing.
Thomas MF, Ansel KM.
Methods Mol Biol. 2010;667:93-111.


Probabilistic Peak Calling and Controlling False Discovery Rate Estimations in Transcription Factor Binding Site Mapping from ChIP-seq.
Jiao S, Bailey CP, Zhang S, Ladunga I.
Methods Mol Biol. 2010;674:161-77.


Sequencing and analysis of an Irish human genome.
Tong P, Prendergast JG, Lohan AJ, Farrington SM, Cronin S, Friel N, Bradley DG, Hardiman O, Evans A, Wilson JF, Loftus BJ.
Genome Biol. 2010 Sep 7;11(9):R91.


Characteristics of 454 pyrosequencing data — enabling realistic simulation with flowsim.
Balzer S, Malde K, Lanzén A, Sharma A, Jonassen I.
Bioinformatics. 2010 Sep 15;26(18):i420-i425.


Sequencing bias: comparison of different protocols of microRNA library construction.
Tian G, Yin X, Luo H, Xu X, Bolund L, Zhang X.
BMC Biotechnol. 2010 Sep 6;10(1):64.


Classification of ncRNAs using position and size information in deep sequencing data.
Erhard F, Zimmer R.
Bioinformatics. 2010 Sep 15;26(18):i426-i432.


Sequencing and analysis of the giant panda genome.
Yang H.
Sci China Life Sci. 2010 Aug;53(8):1047-1048.


Molecular analysis of the diversity of vaginal microbiota associated with bacterial vaginosis.
Ling XZ, Kong MJ, Liu F, Zhu BH, Chen YX, Wang ZY, Li JL, Nelson KE, Xia XY, Xiang C.
BMC Genomics. 2010 Sep 7;11(1):488.


Contribution of genetic, epigenetic and transcriptomic differences to twin discordance in multiple sclerosis.
Handunnetthi L, Handel AE, Ramagopalan SV.
Expert Rev Neurother. 2010 Sep;10(9):1379-1381.


High-throughput, pooled sequencing identifies mutations in NUBPL and FOXRED1 in human complex I deficiency.
Calvo SE, Tucker EJ, Compton AG, Kirby DM, Crawford G, Burtt NP, Rivas M, Guiducci C, Bruno DL, Goldberger OA, Redman MC, Wiltshire E, Wilson CJ, Altshuler D, Gabriel SB, Daly MJ, Thorburn DR, Mootha VK.
Nat Genet. 2010 Sep 5. [Epub ahead of print]


Microbial community resemblance methods differ in their ability to detect biologically relevant patterns.
Kuczynski J, Liu Z, Lozupone C, McDonald D, Fierer N, Knight R.
Nat Methods. 2010 Sep 5. [Epub ahead of print]


A miRNA-tRNA mix-up: tRNA origin of proposed miRNA.
Schopman NC, Heynen S, Haasnoot J, Berkhout B.
RNA Biol. 2010 Sep 23;7(5).


Exome Sequencing Identifies WDR35 Variants Involved in Sensenbrenner Syndrome.
Gilissen C, Arts HH, Hoischen A, Spruijt L, Mans DA, Arts P, van Lier B, Steehouwer M, van Reeuwijk J, Kant SG, Roepman R, Knoers NV, Veltman JA, Brunner HG.
Am J Hum Genet. 2010 Sep 1. [Epub ahead of print]


A pyrosequencing study in twins shows that GI microbial profiles vary with inflammatory bowel disease phenotypes.
Willing B, Dicksved J, Halfvarson J, Andersson A, Lucio M, Zeng Z, Järnerot G, Tysk C, Jansson JK, Engstrand L.
Gastroenterology. 2010 Sep 2. [Epub ahead of print]


Deep sequencing of the innate immune transcriptomic response of zebrafish embryos to Salmonella infection.
Ordas A, Hegedus Z, Henkel CV, Stockhammer OW, Butler D, Jansen HJ, Racz P, Mink M, Spaink HP, Meijer AH.
Fish Shellfish Immunol. 2010 Aug 31. [Epub ahead of print]

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