The purpose of the Bioinformatics Core (Core B) is to provide statistical and bioinformatics analysis of various high-throughput genomics data, primarily from sequencing applications such as ChlP-seq, RNA-seq, Hi-C, ChlA-PET, 4C-seq and replication timing experiments. Each of the three Projects utilize next generation sequencing technologies (NGS) to address questions relating to cell cycle control, chromosome architecture and cell fate decisions in pluripotent stem cells. Our core will provide comprehensive data analysis service to investigators of this Program Project. The PI and supporting staff of this Core have extensive experience in the analysis of high-throughput genomics data, especially NGS data. In addition to basic data analyses, we will work closely with investigators from the three Projects to identify emerging problems that are not addressed sufficiently by existing methods and software. This will involve the development of improved probability models, computer algorithms and analytical strategies to improve data analysis.
The proposed work is relevant to public health because the Core will support research projects that aim to understand the cytological correlation between chromosome structure and the pathogenesis of human diseases. Research devoted to understand the role of chromosome structure in gene regulation also helps the design of strategies for gene therapy.
|Sima, Jiao; Bartlett, Daniel A; Gordon, Molly R et al. (2018) Bacterial artificial chromosomes establish replication timing and sub-nuclear compartment de novo as extra-chromosomal vectors. Nucleic Acids Res 46:1810-1820|
|Singh, Amar M; Dalton, Stephen (2018) What Can 'Brown-ing' Do For You? Trends Endocrinol Metab 29:349-359|
|Dixon, Jesse R; Xu, Jie; Dileep, Vishnu et al. (2018) Integrative detection and analysis of structural variation in cancer genomes. Nat Genet 50:1388-1398|
|Xu, Chenhuan; Corces, Victor G (2018) Genome-Wide Mapping of Protein-DNA Interactions on Nascent Chromatin. Methods Mol Biol 1766:231-238|
|Dileep, Vishnu; Gilbert, David M (2018) Single-cell replication profiling to measure stochastic variation in mammalian replication timing. Nat Commun 9:427|
|Colunga, Thomas; Dalton, Stephen (2018) Building Blood Vessels with Vascular Progenitor Cells. Trends Mol Med 24:630-641|
|Wang, Tao; Holt, Matthew V; Young, Nicolas L (2018) The histone H4 proteoform dynamics in response to SUV4-20 inhibition reveals single molecule mechanisms of inhibitor resistance. Epigenetics Chromatin 11:29|
|Xu, Chenhuan; Corces, Victor G (2018) Nascent DNA methylome mapping reveals inheritance of hemimethylation at CTCF/cohesin sites. Science 359:1166-1170|
|Marchal, Claire; Sasaki, Takayo; Vera, Daniel et al. (2018) Genome-wide analysis of replication timing by next-generation sequencing with E/L Repli-seq. Nat Protoc 13:819-839|
|Rivera-Mulia, Juan Carlos; Schwerer, Hélène; Besnard, Emilie et al. (2018) Cellular senescence induces replication stress with almost no affect on DNA replication timing. Cell Cycle 17:1667-1681|
Showing the most recent 10 out of 118 publications