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The genome sequence of Drosophila melanogaster.
The fly Drosophila melanogaster is one of the most intensively studied organisms in biology and serves as a model system for the investigation of many developmental and cellular processes common to… Expand
Integrated Genomic Analyses of Ovarian Carcinoma
A catalogue of molecular aberrations that cause ovarian cancer is critical for developing and deploying therapies that will improve patients’ lives. The Cancer Genome Atlas project has analysed… Expand
Identification of a CpG island methylator phenotype that defines a distinct subgroup of glioma.
We have profiled promoter DNA methylation alterations in 272 glioblastoma tumors in the context of The Cancer Genome Atlas (TCGA). We found that a distinct subset of samples displays concerted… Expand
Comprehensive Molecular Characterization of Human Colon and Rectal Cancer
To characterize somatic alterations in colorectal carcinoma, we conducted a genome-scale analysis of 276 samples, analysing exome sequence, DNA copy number, promoter methylation and messenger RNA and… Expand
Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome
- B. Berman, Y. Nibu, +5 authors M. Eisen
- Biology, Medicine
- Proceedings of the National Academy of Sciences…
- 22 January 2002
A major challenge in interpreting genome sequences is understanding how the genome encodes the information that specifies when and where a gene will be expressed. The first step in this process is… Expand
Regions of focal DNA hypermethylation and long-range hypomethylation in colorectal cancer coincide with nuclear lamina–associated domains
Extensive changes in DNA methylation are common in cancer and may contribute to oncogenesis through transcriptional silencing of tumor-suppressor genes. Genome-scale studies have yielded important… Expand
Global analysis of patterns of gene expression during Drosophila embryogenesis
BackgroundCell and tissue specific gene expression is a defining feature of embryonic development in multi-cellular organisms. However, the range of gene expression patterns, the extent of the… Expand
Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules.
- T. Kelly, Y. Liu, F. Lay, G. Liang, B. Berman, P. Jones
- Biology, Medicine
- Genome research
- 1 December 2012
DNA methylation and nucleosome positioning work together to generate chromatin structures that regulate gene expression. Nucleosomes are typically mapped using nuclease digestion requiring… Expand
Annotation of the Drosophila melanogaster euchromatic genome: a systematic review
BackgroundThe recent completion of the Drosophila melanogaster genomic sequence to high quality and the availability of a greatly expanded set of Drosophila cDNA sequences, aligning to 78% of the… Expand
Comprehensive molecular portraits of human breast tumors
We analysed primary breast cancers by genomic DNA copy number arrays, DNA methylation, exome sequencing, messenger RNA arrays, microRNA sequencing and reverse-phase protein arrays. Our ability to… Expand