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Items: 1 to 20 of 27

1.

The dynamics of the vaginal microbiome during infertility therapy with in vitro fertilization-embryo transfer.

Hyman RW, Herndon CN, Jiang H, Palm C, Fukushima M, Bernstein D, Vo KC, Zelenko Z, Davis RW, Giudice LC.

J Assist Reprod Genet. 2012 Feb;29(2):105-15. doi: 10.1007/s10815-011-9694-6. Epub 2012 Jan 6.

2.

NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy.

Pruitt KD, Tatusova T, Brown GR, Maglott DR.

Nucleic Acids Res. 2012 Jan;40(Database issue):D130-5. doi: 10.1093/nar/gkr1079. Epub 2011 Nov 24.

3.

A direct comparison of the KB™ Basecaller and phred for identifying the bases from DNA sequencing using chain termination chemistry.

Hyman RW, Jiang H, Fukushima M, Davis RW.

BMC Res Notes. 2010 Oct 8;3:257. doi: 10.1186/1756-0500-3-257.

4.

Semi-automated library preparation for high-throughput DNA sequencing platforms.

Farias-Hesson E, Erikson J, Atkins A, Shen P, Davis RW, Scharfe C, Pourmand N.

J Biomed Biotechnol. 2010;2010:617469. doi: 10.1155/2010/617469. Epub 2010 Jun 8.

5.

Highly-multiplexed barcode sequencing: an efficient method for parallel analysis of pooled samples.

Smith AM, Heisler LE, St Onge RP, Farias-Hesson E, Wallace IM, Bodeau J, Harris AN, Perry KM, Giaever G, Pourmand N, Nislow C.

Nucleic Acids Res. 2010 Jul;38(13):e142. doi: 10.1093/nar/gkq368. Epub 2010 May 11.

6.

Multiplex identification of microbes.

Hyman RW, St Onge RP, Allen EA, Miranda M, Aparicio AM, Fukushima M, Davis RW.

Appl Environ Microbiol. 2010 Jun;76(12):3904-10. doi: 10.1128/AEM.02785-09. Epub 2010 Apr 23.

7.

The NIH Human Microbiome Project.

NIH HMP Working Group, Peterson J, Garges S, Giovanni M, McInnes P, Wang L, Schloss JA, Bonazzi V, McEwen JE, Wetterstrand KA, Deal C, Baker CC, Di Francesco V, Howcroft TK, Karp RW, Lunsford RD, Wellington CR, Belachew T, Wright M, Giblin C, David H, Mills M, Salomon R, Mullins C, Akolkar B, Begg L, Davis C, Grandison L, Humble M, Khalsa J, Little AR, Peavy H, Pontzer C, Portnoy M, Sayre MH, Starke-Reed P, Zakhari S, Read J, Watson B, Guyer M.

Genome Res. 2009 Dec;19(12):2317-23. doi: 10.1101/gr.096651.109. Epub 2009 Oct 9.

8.

Multiplex detection of bacteria associated with normal microbiota and with bacterial vaginosis in vaginal swabs by use of oligonucleotide-coupled fluorescent microspheres.

Dumonceaux TJ, Schellenberg J, Goleski V, Hill JE, Jaoko W, Kimani J, Money D, Ball TB, Plummer FA, Severini A.

J Clin Microbiol. 2009 Dec;47(12):4067-77. doi: 10.1128/JCM.00112-09. Epub 2009 Sep 30.

9.

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 GL, McLaughlin SF, Fu Y, Tsung EF, Clouser CR, Duncan C, Ichikawa JK, Lee CC, Zhang Z, Ranade SS, Dimalanta ET, Hyland FC, Sokolsky TD, Zhang L, Sheridan A, Fu H, Hendrickson CL, Li B, Kotler L, Stuart JR, Malek JA, Manning JM, Antipova AA, Perez DS, Moore MP, Hayashibara KC, Lyons MR, Beaudoin RE, Coleman BE, Laptewicz MW, Sannicandro AE, Rhodes MD, Gottimukkala RK, Yang S, Bafna V, Bashir A, MacBride A, Alkan C, Kidd JM, Eichler EE, Reese MG, De La Vega FM, Blanchard AP.

Genome Res. 2009 Sep;19(9):1527-41. doi: 10.1101/gr.091868.109. Epub 2009 Jun 22.

10.

Insignia: a DNA signature search web server for diagnostic assay development.

Phillippy AM, Ayanbule K, Edwards NJ, Salzberg SL.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W229-34. doi: 10.1093/nar/gkp286. Epub 2009 May 5.

11.

The Ribosomal Database Project: improved alignments and new tools for rRNA analysis.

Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ, Kulam-Syed-Mohideen AS, McGarrell DM, Marsh T, Garrity GM, Tiedje JM.

Nucleic Acids Res. 2009 Jan;37(Database issue):D141-5. doi: 10.1093/nar/gkn879. Epub 2008 Nov 12.

12.

The lower genital tract microbiota in relation to cytokine-, SLPI- and endotoxin levels: application of checkerboard DNA-DNA hybridization (CDH).

Nikolaitchouk N, Andersch B, Falsen E, Strömbeck L, Mattsby-Baltzer I.

APMIS. 2008 Apr;116(4):263-77. doi: 10.1111/j.1600-0463.2008.00808.x.

PMID:
18397461
13.

Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes.

Frank JA, Reich CI, Sharma S, Weisbaum JS, Wilson BA, Olsen GJ.

Appl Environ Microbiol. 2008 Apr;74(8):2461-70. doi: 10.1128/AEM.02272-07. Epub 2008 Feb 22.

14.

Comprehensive DNA signature discovery and validation.

Phillippy AM, Mason JA, Ayanbule K, Sommer DD, Taviani E, Huq A, Colwell RR, Knight IT, Salzberg SL.

PLoS Comput Biol. 2007 May;3(5):e98. Epub 2007 Apr 20.

15.

Effect of primer mismatch, annealing temperature and PCR cycle number on 16S rRNA gene-targetting bacterial community analysis.

Sipos R, Székely AJ, Palatinszky M, Révész S, Márialigeti K, Nikolausz M.

FEMS Microbiol Ecol. 2007 May;60(2):341-50. Epub 2007 Mar 2.

16.

High-density universal 16S rRNA microarray analysis reveals broader diversity than typical clone library when sampling the environment.

DeSantis TZ, Brodie EL, Moberg JP, Zubieta IX, Piceno YM, Andersen GL.

Microb Ecol. 2007 Apr;53(3):371-83. Epub 2007 Mar 2.

PMID:
17334858
17.

Design of a seven-genome Escherichia coli microarray for comparative genomic profiling.

Willenbrock H, Petersen A, Sekse C, Kiil K, Wasteson Y, Ussery DW.

J Bacteriol. 2006 Nov;188(22):7713-21. Epub 2006 Sep 8.

18.

A unique and universal molecular barcode array.

Pierce SE, Fung EL, Jaramillo DF, Chu AM, Davis RW, Nislow C, Giaever G.

Nat Methods. 2006 Aug;3(8):601-3.

PMID:
16862133
19.

Microbes on the human vaginal epithelium.

Hyman RW, Fukushima M, Diamond L, Kumm J, Giudice LC, Davis RW.

Proc Natl Acad Sci U S A. 2005 May 31;102(22):7952-7. Epub 2005 May 23.

20.

Analysis of T-cell receptor V beta gene repertoires after immune stimulation and in malignancy by use of padlock probes and microarrays.

Banér J, Marits P, Nilsson M, Winqvist O, Landegren U.

Clin Chem. 2005 Apr;51(4):768-75. Epub 2005 Feb 3.

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