Deciphering the multi-scale, quantitative cis-regulatory code
S Kim, J Wysocka - Molecular cell, 2023 - cell.com
Uncovering the cis-regulatory code that governs when and how much each gene is
transcribed in a given genome and cellular state remains a central goal of biology. Here, we …
transcribed in a given genome and cellular state remains a central goal of biology. Here, we …
Making sense of the ageing methylome
Over time, the human DNA methylation landscape accrues substantial damage, which has
been associated with a broad range of age-related diseases, including cardiovascular …
been associated with a broad range of age-related diseases, including cardiovascular …
Single-molecule genome-wide mutation profiles of cell-free DNA for non-invasive detection of cancer
Somatic mutations are a hallmark of tumorigenesis and may be useful for non-invasive
diagnosis of cancer. We analyzed whole-genome sequencing data from 2,511 individuals in …
diagnosis of cancer. We analyzed whole-genome sequencing data from 2,511 individuals in …
Genome-wide cell-free DNA fragmentation in patients with cancer
Cell-free DNA in the blood provides a non-invasive diagnostic avenue for patients with
cancer. However, characteristics of the origins and molecular features of cell-free DNA are …
cancer. However, characteristics of the origins and molecular features of cell-free DNA are …
Detecting liver cancer using cell-free DNA fragmentomes
ZH Foda, AV Annapragada, K Boyapati, DC Bruhm… - Cancer discovery, 2023 - AACR
Liver cancer is a major cause of cancer mortality worldwide. Screening individuals at high
risk, including those with cirrhosis and viral hepatitis, provides an avenue for improved …
risk, including those with cirrhosis and viral hepatitis, provides an avenue for improved …
Cicero predicts cis-regulatory DNA interactions from single-cell chromatin accessibility data
Linking regulatory DNA elements to their target genes, which may be located hundreds of
kilobases away, remains challenging. Here, we introduce Cicero, an algorithm that identifies …
kilobases away, remains challenging. Here, we introduce Cicero, an algorithm that identifies …
Preprocessing, normalization and integration of the Illumina HumanMethylationEPIC array with minfi
The minfi package is widely used for analyzing Illumina DNA methylation array data. Here
we describe modifications to the minfi package required to support the …
we describe modifications to the minfi package required to support the …
Machine learning meets omics: applications and perspectives
The innovation of biotechnologies has allowed the accumulation of omics data at an
alarming rate, thus introducing the era of 'big data'. Extracting inherent valuable knowledge …
alarming rate, thus introducing the era of 'big data'. Extracting inherent valuable knowledge …
[HTML][HTML] Large-scale topological changes restrain malignant progression in colorectal cancer
SE Johnstone, A Reyes, Y Qi, C Adriaens, E Hegazi… - Cell, 2020 - cell.com
Widespread changes to DNA methylation and chromatin are well documented in cancer, but
the fate of higher-order chromosomal structure remains obscure. Here we integrated …
the fate of higher-order chromosomal structure remains obscure. Here we integrated …
Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer
Chromatin is folded into successive layers to organize linear DNA. Genes within the same
topologically associating domains (TADs) demonstrate similar expression and histone …
topologically associating domains (TADs) demonstrate similar expression and histone …