Oda, Mayumi, Glass, Jacob L., Thompson, Reid F., Mo, Yongkai, Olivier, Emmanuel N., Figueroa, Maria E., ...
Many genome-wide assays involve the generation of a subset (or representation) of the genome following restriction enzyme digestion. The use of enzymes sensitive to cytosine methylation allows...
Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. (2008)
Johnson, David S., Li, Wei, Gordon, D. Benjamin, Bhattacharjee, Arindam, Curry, Bo, Ghosh, Jayati, ...
The most widely used method for detecting genome-wide protein-DNA interactions is chromatin immunoprecipitation on tiling microarrays, commonly known as ChIP-chip. Here, we conducted the first...
SNP-specific array-based allele-specific expression analysis (2008)
Bjornsson, Hans T., Albert, Thomas J., Ladd-Acosta, Christine M., Green, Roland D., Rongione, Michael A., Middle, Christina M., ...
We have developed an optimized array-based approach for customizable allele-specific gene expression (ASE) analysis. The central features of the approach are the ability to select SNPs at will for...
Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets (2008)
Johnson, David S., Li, Wei, Gordon, D. Benjamin, Bhattacharjee, Arindam, Curry, Bo, Ghosh, Jayati, ...
The most widely used method for detecting genome-wide protein–DNA interactions is chromatin immunoprecipitation on tiling microarrays, commonly known as ChIP-chip. Here, we conducted the first...
Wen, Bo, Wu, Hao, Bjornsson, Hans, Green, Roland D., Irizarry, Rafael, Feinberg, Andrew P.
Most genome-level analysis treats the two parental alleles equivalently, yet diploid genomes contain two parental genomes that are often epigenetically distinct. While single nucleotide polymorphisms...
Cheng, Yong, King, David C., Dore, Louis C., Zhang, Xinmin, Zhou, Yuepin, Zhang, Ying, ...
Tissue development and function are exquisitely dependent on proper regulation of gene expression, but it remains controversial whether the genomic signals controlling this process are subject to...
Barrera, Leah O., Li, Zirong, Smith, Andrew D., Arden, Karen C., Cavenee, Webster K., Zhang, Michael Q., ...
By integrating genome-wide maps of RNA polymerase II (Polr2a) binding with gene expression data and H3ac and H3K4me3 profiles, we characterized promoters with enriched activity in mouse embryonic...
Dostie, Josee, Richmond, Joann M., Arnaout, Ramy A., Selzer, Rebecca R., Lee, William L., Honan, Tracey A., ...
Physical interactions between genetic elements located throughout the genome play important roles in gene regulation and can be identified with the Chromosome Conformation Capture (3C) methodology....
Dostie, Josée, Richmond, Todd A., Arnaout, Ramy A., Selzer, Rebecca R., Lee, William L., Honan, Tracey A., ...
Physical interactions between genetic elements located throughout the genome play important roles in gene regulation and can be identified with the Chromosome Conformation Capture (3C) methodology....
Comparative isoschizomer profiling of cytosine methylation: The HELP assay (2006)
Khulan, Batbayar, Thompson, Reid F., Ye, Kenny, Fazzari, Melissa J., Suzuki, Masako, Stasiek, Edyta, ...
The distribution of cytosine methylation in 6.2 Mb of the mouse genome was tested using cohybridization of genomic representations from a methylation-sensitive restriction enzyme and its...
Dostie, Josée, Richmond, Todd A., Arnaout, Ramy A., Selzer, Rebecca R., Lee, William L., Honan, Tracey A., ...
Physical interactions between genetic elements located throughout the genome play important roles in gene regulation and can be identified with the Chromosome Conformation Capture (3C) methodology....
Comparative isoschizomer profiling of cytosine methylation: The HELP assay (2006)
Khulan, Batbayar, Thompson, Reid F., Ye, Kenny, Fazzari, Melissa J., Suzuki, Masako, Stasiek, Edyta, ...
The distribution of cytosine methylation in 6.2 Mb of the mouse genome was tested using cohybridization of genomic representations from a methylation-sensitive restriction enzyme and its...
Triplet-Sensitized Photodeprotection of Oligonucleotides in Solution and on Microarray Chips (2004)
Wöll, Dominik, Walbert, Stefan, Stengele, Klaus-Peter, Albert, Tom J., Richmond, Todd, Norton, Jason, ...
Conditions and kinetics of triplet sensitization as a method for increasing the light sensitivity of photolabile protecting groups used for the photolithographic synthesis of oligonucleotide...
Light-directed 5'->3' synthesis of complex oligonucleotide microarrays (2003)
Albert, Thomas J., Norton, Jason, Ott, Markus, Richmond, Todd, Nuwaysir, Kate, Nuwaysir, Emile F., ...
Light‐directed synthesis of high‐density microarrays is currently performed in the 3′→5′ direction due to constraints in existing synthesis chemistry. This results in the probes being...
Light-directed 5′→3′ synthesis of complex oligonucleotide microarrays
Albert, Thomas J., Norton, Jason, Ott, Markus, Richmond, Todd, Nuwaysir, Kate, Nuwaysir, Emile F., ...
Light-directed synthesis of high-density microarrays is currently performed in the 3′→5′ direction due to constraints in existing synthesis chemistry. This results in the probes being...
Gene Expression Analysis Using Oligonucleotide Arrays Produced by Maskless Photolithography
Nuwaysir, Emile F., Huang, Wei, Albert, Thomas J., Singh, Jaz, Nuwaysir, Kate, Pitas, Alan, ...
Microarrays containing 195,000 in situ synthesized oligonucleotide features have been created using a benchtop, maskless photolithographic instrument. This instrument, the Maskless Array Synthesizer...
Light-directed 5′→3′ synthesis of complex oligonucleotide microarrays
Albert, Thomas J., Norton, Jason, Ott, Markus, Richmond, Todd, Nuwaysir, Kate, Nuwaysir, Emile F., ...
Light-directed synthesis of high-density microarrays is currently performed in the 3′→5′ direction due to constraints in existing synthesis chemistry. This results in the probes being...
Gene Expression Analysis Using Oligonucleotide Arrays Produced by Maskless Photolithography
Nuwaysir, Emile F., Huang, Wei, Albert, Thomas J., Singh, Jaz, Nuwaysir, Kate, Pitas, Alan, ...
Microarrays containing 195,000 in situ synthesized oligonucleotide features have been created using a benchtop, maskless photolithographic instrument. This instrument, the Maskless Array Synthesizer...
Comparative isoschizomer profiling of cytosine methylation: The HELP assay
Khulan, Batbayar, Thompson, Reid F., Ye, Kenny, Fazzari, Melissa J., Suzuki, Masako, Stasiek, Edyta, ...
The distribution of cytosine methylation in 6.2 Mb of the mouse genome was tested using cohybridization of genomic representations from a methylation-sensitive restriction enzyme and its...
Dostie, Josée, Richmond, Todd A., Arnaout, Ramy A., Selzer, Rebecca R., Lee, William L., Honan, Tracey A., ...
Physical interactions between genetic elements located throughout the genome play important roles in gene regulation and can be identified with the Chromosome Conformation Capture (3C) methodology....
An Integrative Genomic and Epigenomic Approach for the Study of Transcriptional Regulation
Figueroa, Maria E., Reimers, Mark, Thompson, Reid F., Ye, Kenny, Li, Yushan, Selzer, Rebecca R., ...
The molecular heterogeneity of acute leukemias and other tumors constitutes a major obstacle towards understanding disease pathogenesis and developing new targeted-therapies. Aberrant gene regulation...
Genome-wide mapping and analysis of active promoters in mouse embryonic stem cells and adult organs
Barrera, Leah O., Li, Zirong, Smith, Andrew D., Arden, Karen C., Cavenee, Webster K., Zhang, Michael Q., ...
By integrating genome-wide maps of RNA polymerase II (Polr2a) binding with gene expression data and H3ac and H3K4me3 profiles, we characterized promoters with enriched activity in mouse embryonic...
The Genomic Distribution and Function of Histone Variant HTZ-1 during C. elegans Embryogenesis
Whittle, Christina M., McClinic, Karissa N., Ercan, Sevinc, Zhang, Xinmin, Green, Roland D., Kelly, William G., ...
In all eukaryotes, histone variants are incorporated into a subset of nucleosomes to create functionally specialized regions of chromatin. One such variant, H2A.Z, replaces histone H2A and is...
Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets
Johnson, David S., Li, Wei, Gordon, D. Benjamin, Bhattacharjee, Arindam, Curry, Bo, Ghosh, Jayati, ...
The most widely used method for detecting genome-wide protein–DNA interactions is chromatin immunoprecipitation on tiling microarrays, commonly known as ChIP-chip. Here, we conducted the first...
SNP-specific array-based allele-specific expression analysis
Bjornsson, Hans T., Albert, Thomas J., Ladd-Acosta, Christine M., Green, Roland D., Rongione, Michael A., Middle, Christina M., ...
We have developed an optimized array-based approach for customizable allele-specific gene expression (ASE) analysis. The central features of the approach are the ability to select SNPs at will for...
Wen, Bo, Wu, Hao, Bjornsson, Hans, Green, Roland D., Irizarry, Rafael, Feinberg, Andrew P.
Most genome-level analysis treats the two parental alleles equivalently, yet diploid genomes contain two parental genomes that are often epigenetically distinct. While single nucleotide polymorphisms...
Cheng, Yong, King, David C., Dore, Louis C., Zhang, Xinmin, Zhou, Yuepin, Zhang, Ying, ...
Tissue development and function are exquisitely dependent on proper regulation of gene expression, but it remains controversial whether the genomic signals controlling this process are subject to...
Oda, Mayumi, Glass, Jacob L., Thompson, Reid F., Mo, Yongkai, Olivier, Emmanuel N., Figueroa, Maria E., ...
Many genome-wide assays involve the generation of a subset (or representation) of the genome following restriction enzyme digestion. The use of enzymes sensitive to cytosine methylation allows...