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.
|Tang, J; Li, Y; Lyon, K et al. (2014) Cancer driver-passenger distinction via sporadic human and dog cancer comparison: a proof-of-principle study with colorectal cancer. Oncogene 33:814-22|
|Sima, Jiao; Gilbert, David M (2014) Complex correlations: replication timing and mutational landscapes during cancer and genome evolution. Curr Opin Genet Dev 25:93-100|
|He, Yangqing; Peng, Jiangnan; Hamann, Mark T et al. (2014) An iridoid glucoside and the related aglycones from Cornus florida. J Nat Prod 77:2138-43|
|Pope, Benjamin D; Ryba, Tyrone; Dileep, Vishnu et al. (2014) Topologically associating domains are stable units of replication-timing regulation. Nature 515:402-5|
|Boccuto, Luigi; Aoki, Kazuhiro; Flanagan-Steet, Heather et al. (2014) A mutation in a ganglioside biosynthetic enzyme, ST3GAL5, results in salt & pepper syndrome, a neurocutaneous disorder with altered glycolipid and glycoprotein glycosylation. Hum Mol Genet 23:418-33|
|Kellis, Manolis; Wold, Barbara; Snyder, Michael P et al. (2014) Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease. Proc Natl Acad Sci U S A 111:E3366|
|Liu, Deli; Xiong, Huan; Ellis, Angela E et al. (2014) Molecular homology and difference between spontaneous canine mammary cancer and human breast cancer. Cancer Res 74:5045-56|
|Gasimli, Leyla; Hickey, Anne Marie; Yang, Bo et al. (2014) Changes in glycosaminoglycan structure on differentiation of human embryonic stem cells towards mesoderm and endoderm lineages. Biochim Biophys Acta 1840:1993-2003|
|Lu, Junjie; Li, Hu; Hu, Ming et al. (2014) The distribution of genomic variations in human iPSCs is related to replication-timing reorganization during reprogramming. Cell Rep 7:70-8|
|Yue, Feng; Cheng, Yong; Breschi, Alessandra et al. (2014) A comparative encyclopedia of DNA elements in the mouse genome. Nature 515:355-64|
Showing the most recent 10 out of 38 publications