Machine learning for integrating data in biology and medicine: Principles, practice, and opportunities
New technologies have enabled the investigation of biology and human health at an
unprecedented scale and in multiple dimensions. These dimensions include a myriad of …
unprecedented scale and in multiple dimensions. These dimensions include a myriad of …
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 …
Managing the steady state chromatin landscape by nucleosome dynamics
Gene regulation arises out of dynamic competition between nucleosomes, transcription
factors, and other chromatin proteins for the opportunity to bind genomic DNA. The …
factors, and other chromatin proteins for the opportunity to bind genomic DNA. The …
Avocado: a multi-scale deep tensor factorization method learns a latent representation of the human epigenome
The human epigenome has been experimentally characterized by thousands of
measurements for every basepair in the human genome. We propose a deep neural …
measurements for every basepair in the human genome. We propose a deep neural …
FUN-LDA: a latent dirichlet allocation model for predicting tissue-specific functional effects of noncoding variation: methods and applications
We describe a method based on a latent Dirichlet allocation model for predicting functional
effects of noncoding genetic variants in a cell-type-and/or tissue-specific way (FUN-LDA) …
effects of noncoding genetic variants in a cell-type-and/or tissue-specific way (FUN-LDA) …
Robust chromatin state annotation
MF Shahraki, M Farahbod, MW Libbrecht - Genome Research, 2024 - genome.cshlp.org
With the goal of map** genomic activity, international projects have recently measured
epigenetic activity in hundreds of cell and tissue types. Chromatin state annotations …
epigenetic activity in hundreds of cell and tissue types. Chromatin state annotations …
A flexible repertoire of transcription factor binding sites and a diversity threshold determines enhancer activity in embryonic stem cells
Transcriptional enhancers are critical for development and phenotype evolution and are
often mutated in disease contexts; however, even in well-studied cell types, the sequence …
often mutated in disease contexts; however, even in well-studied cell types, the sequence …
Deregulated regulators: disease-causing cis variants in transcription factor genes
Whole-genome sequencing is accelerating identification of noncoding variants that disrupt
gene expression, although reports of such regulatory variants implicated in disease remain …
gene expression, although reports of such regulatory variants implicated in disease remain …
GREEN-DB: a framework for the annotation and prioritization of non-coding regulatory variants from whole-genome sequencing data
Non-coding variants have long been recognized as important contributors to common
disease risks, but with the expansion of clinical whole genome sequencing, examples of …
disease risks, but with the expansion of clinical whole genome sequencing, examples of …
Machine learning methods to model multicellular complexity and tissue specificity
Experimental approaches to study tissue specificity enable insight into the nature and
organization of the cell types and tissues that constitute complex multicellular organisms …
organization of the cell types and tissues that constitute complex multicellular organisms …