All the single cells: single-cell transcriptomics/epigenomics experimental design and analysis considerations for glial biologists [PDF]
arXivSingle-cell transcriptomics, epigenomics, and other 'omics applied at single-cell resolution can significantly advance hypotheses and understanding of glial biology. Omics technologies are revealing a large and growing number of new glial cell subtypes, defined by their gene expression profile.
arxiv
A Statistical Model for the Analysis of Beta Values in DNA Methylation Studies [PDF]
arXiv, 2016 Background: The analysis of DNA methylation is a key component in the development of personalized treatment approaches. A common way to measure DNA methylation is the calculation of beta values, which are bounded variables of the form M = (M + U) that are generated by Illumina's 450k BeadChip array. The statistical analysis of beta values is considered
arxiv
The Dynamic Epigenome and its Implications in Toxicology [PDF]
, 2007 Moshe Szyf
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Reversibility of sex changes in the plant kingdom: more important than we thought?
Biological Reviews, EarlyView.ABSTRACT Compared to animals, plants show a wide range of reproductive strategies with different degrees of sex separation (e.g. dioecy, monoecy, hermaphroditism). While sex expression was previously thought to be genetically determined and fixed in plants, accumulating evidence suggests that sex expression can change reversibly even within one ...
Iris Sammarco +3 more
wiley +1 more source
Learning to Discover Regulatory Elements for Gene Expression Prediction [PDF]
arXivWe consider the problem of predicting gene expressions from DNA sequences. A key challenge of this task is to find the regulatory elements that control gene expressions. Here, we introduce Seq2Exp, a Sequence to Expression network explicitly designed to discover and extract regulatory elements that drive target gene expression, enhancing the accuracy ...
arxiv
A Noise-Filtering Approach for Cancer Drug Sensitivity Prediction [PDF]
arXiv, 2016 Accurately predicting drug responses to cancer is an important problem hindering oncologists' efforts to find the most effective drugs to treat cancer, which is a core goal in precision medicine. The scientific community has focused on improving this prediction based on genomic, epigenomic, and proteomic datasets measured in human cancer cell lines ...
arxiv
Perinatal Exposure to Oestradiol and Bisphenol A Alters the Prostate Epigenome and Increases Susceptibility to Carcinogenesis [PDF]
, 2008 Gail S. Prins +3 more
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Cancer‐Type‐Specific DNA Methylation Is a Source of Vulnerability in Liver Cancer Cells
Cancer Science, EarlyView.We profiled genome‐wide DNA methylation in 1165 human cancer cell lines representing 25 cancer types and identified 73 genes as potential liver cancer‐specific methylation‐silenced genes. We selected ASNS, BCAT2, FXYD5, and NQO1 genes for further experimental analysis and demonstrated that aberrant methylation of BCAT2 contributes to the vulnerability ...
Karen Minowa +3 more
wiley +1 more source
Multimodal 3D Genome Pre-training [PDF]
arXivDeep learning techniques have driven significant progress in various analytical tasks within 3D genomics in computational biology. However, a holistic understanding of 3D genomics knowledge remains underexplored. Here, we propose MIX-HIC, the first multimodal foundation model of 3D genome that integrates both 3D genome structure and epigenomic tracks ...
arxiv
Moving AHEAD with an international human epigenome project [PDF]
, 2008 Peter A. Jones +33 more
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