Microarray-based genomic selection for high-throughput resequencingDavid T Okou
Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Suite 301, Atlanta, Georgia 30322, USA
Nat Methods 4:907-9. 2007
..MGS, when combined with a next-generation resequencing technology, can enable large-scale resequencing in single-investigator laboratories...
Complete genome sequence of Treponema pallidum ssp. pallidum strain SS14 determined with oligonucleotide arraysPetra Matejková
Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Alkek N1619, Houston, TX 77030, USA
BMC Microbiol 8:76. 2008
..pallidum remains the enigmatic pathogen, since no virulence factors have been identified and the pathogenesis of the disease is poorly understood. Increasing rates of new syphilis cases per year have been observed recently...
- Light-directed 5'-->3' synthesis of complex oligonucleotide microarrays
Thomas J Albert
NimbleGen Systems Inc, One Science Court, Madison, WI 53711, USA
Nucleic Acids Res 31:e35. 2003
..998). We have also shown that the 3' ends of array probes are available for sequence-specific primer extension and ligation reactions...
- Direct selection of human genomic loci by microarray hybridization
Thomas J Albert
NimbleGen Systems Inc, 1 Science Court, Madison, Wisconsin 53711, USA
Nat Methods 4:903-5. 2007
..These direct selection methods supersede multiplex PCR for the large-scale analysis of genomic regions...
- Mutation discovery in bacterial genomes: metronidazole resistance in Helicobacter pylori
Thomas J Albert
NimbleGen Systems Inc, One Science Court, Madison, Wisconsin 53711, USA
Nat Methods 2:951-3. 2005
..We conclude that CGS identifies mutations in bacterial genomes efficiently, should enrich understanding of systems biology and genome evolution, and help track pathogens during outbreaks...
- Interrogating genomic diversity of E. coli O157:H7 using DNA tiling arrays
Scott A Jackson
Division of Molecular Biology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U S Food and Drug Administration, Laurel, MD 20708, USA
Forensic Sci Int 168:183-99. 2007
..coli O157:H7. The tiling DNA microarray system would be useful for the tracking and identification of individual strains of E. coli O157:H7 needed for forensic investigations...
- Genome-wide in situ exon capture for selective resequencing
Emily Hodges
Howard Hughes Medical Institute, Watson School of Biological Sciences, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
Nat Genet 39:1522-7. 2007
..This methodology provides an adaptable route toward rapid and efficient resequencing of any sizeable, non-repeat portion of the human genome...
- Identification of a nitroimidazo-oxazine-specific protein involved in PA-824 resistance in Mycobacterium tuberculosis
Ujjini H Manjunatha
Tuberculosis Research Section, National Institute of Allergy and Infectious Diseases, 12441 Parklawn Drive, Twinbrook II, Rockville, MD 20852, USA
Proc Natl Acad Sci U S A 103:431-6. 2006
..These results suggest that the sensitivity of Mtb to PA-824 and related compounds is mediated by a protein that is highly specific for subtle structural variations in these bicyclic nitroimidazoles...
- Nucleotide sequence changes between Streptococcus pneumoniae R6 and D39 strains determined by an oligonucleotide hybridization DNA sequencing technology
Suzanne P Williams
Translational Biomarkers and DNA Sequencing, Pfizer Global Research and Development, Eastern Point Road, Groton, CT 06340, United States
J Microbiol Methods 70:65-74. 2007
..We also discuss the potential impact of some of the amino acid changes found between these two widely used strains of pneumococci...
- SNP-specific array-based allele-specific expression analysis
Hans T Bjornsson
Department of Medicine and Center for Epigenetics, Institute of Basic Biomedical Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
Genome Res 18:771-9. 2008
..The approach is scalable to the whole genome and can be used for discovery of functional epigenetic modifications in patient samples...
- The UBX-regulated network in the haltere imaginal disc of D. melanogaster
Bradley M Hersh
Howard Hughes Medical Institute and University of Wisconsin Madison, 1525 Linden Drive, Madison, WI 53703, USA
Dev Biol 302:717-27. 2007
..The evolution of haltere morphology involved changes in UBX-regulated target genes, both positive and negative, throughout the wing genetic regulatory network...
- Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale
Christopher D Herring
Department of Bioengineering, University of California, San Diego, California 92093, USA
Nat Genet 38:1406-12. 2006
..The success of this new genome-scale approach indicates that real-time evolution studies will now be practical in a wide variety of contexts...
- Probing genomic diversity and evolution of Escherichia coli O157 by single nucleotide polymorphisms
Wei Zhang
Foodborne and Diarrheal Diseases Branch, National Center for Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
Genome Res 16:757-67. 2006
..Functional characterization of nucleotide polymorphisms should shed new insights on the evolution, epidemiology, and pathogenesis of STEC O157 and related pathogens...
- Tracking the evolution of the SARS coronavirus using high-throughput, high-density resequencing arrays
Christopher W Wong
Genome Institute of Singapore, Singapore 138672, Republic of Singapore
Genome Res 14:398-405. 2004
....
- Gene expression analysis using oligonucleotide arrays produced by maskless photolithography
Emile F Nuwaysir
NimbleGen Systems, Inc, Madison, Wisconsin 53711, USA
Genome Res 12:1749-55. 2002
..Custom gene expression arrays were manufactured and hybridized to Drosophila melanogaster and mouse samples. Quantitative PCR was used to validate the gene expression data from the mouse arrays...
