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Your search keyword '"Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory"' showing total 2 results
Start Over Author "Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory" Topic dna methylation Publication Type Academic Journals
2 results on '"Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory"'

1. FinaleMe: Predicting DNA methylation by the fragmentation patterns of plasma cell-free DNA.

Author

Liu Y, Reed SC, Lo C, Choudhury AD, Parsons HA, Stover DG, Ha G, Gydush G, Rhoades J, Rotem D, Freeman S, Katz DW, Bandaru R, Zheng H, Fu H, Adalsteinsson VA, and Kellis M

Subjects
Whole Genome Sequencing methods, Sulfites, Sequence Analysis, DNA methods, High-Throughput Nucleotide Sequencing, DNA Methylation genetics, Cell-Free Nucleic Acids genetics
Abstract

Analysis of DNA methylation in cell-free DNA reveals clinically relevant biomarkers but requires specialized protocols such as whole-genome bisulfite sequencing. Meanwhile, millions of cell-free DNA samples are being profiled by whole-genome sequencing. Here, we develop FinaleMe, a non-homogeneous Hidden Markov Model, to predict DNA methylation of cell-free DNA and, therefore, tissues-of-origin, directly from plasma whole-genome sequencing. We validate the performance with 80 pairs of deep and shallow-coverage whole-genome sequencing and whole-genome bisulfite sequencing data., (© 2024. The Author(s).)

Published
2024
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2. Joint profiling of DNA methylation and chromatin architecture in single cells.

Author

Li G, Liu Y, Zhang Y, Kubo N, Yu M, Fang R, Kellis M, and Ren B

Subjects
Animals, CpG Islands, Datasets as Topic, Humans, Mice, Mouse Embryonic Stem Cells cytology, Mouse Embryonic Stem Cells metabolism, Chromatin metabolism, DNA Methylation, Single-Cell Analysis methods
Abstract

We report a molecular assay, Methyl-HiC, that can simultaneously capture the chromosome conformation and DNA methylome in a cell. Methyl-HiC reveals coordinated DNA methylation status between distal genomic segments that are in spatial proximity in the nucleus, and delineates heterogeneity of both the chromatin architecture and DNA methylome in a mixed population. It enables simultaneous characterization of cell-type-specific chromatin organization and epigenome in complex tissues.

Published
2019
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