Emerging roles for endogenous retroviruses in immune epigenetic regulation
CA Buttler, EB Chuong - Immunological reviews, 2022 - Wiley Online Library
In recent years, there has been significant progress toward understanding the transcriptional
networks underlying mammalian immune responses, fueled by advances in regulatory …
networks underlying mammalian immune responses, fueled by advances in regulatory …
Critical evaluation of current hypotheses for the pathogenesis of hypertrophic cardiomyopathy
Hereditary hypertrophic cardiomyopathy (HCM), due to mutations in sarcomere proteins,
occurs in more than 1/500 individuals and is the leading cause of sudden cardiac death in …
occurs in more than 1/500 individuals and is the leading cause of sudden cardiac death in …
scTenifoldXct: a semi-supervised method for predicting cell-cell interactions and mapping cellular communication graphs
We present scTenifoldXct, a semi-supervised computational tool for detecting ligand-
receptor (LR)-mediated cell-cell interactions and mapping cellular communication graphs …
receptor (LR)-mediated cell-cell interactions and mapping cellular communication graphs …
Time-resolved transcriptomes reveal diverse B cell fate trajectories in the early response to Epstein-Barr virus infection
Epstein-Barr virus infection of B lymphocytes elicits diverse host responses via well-adapted
transcriptional control dynamics. Consequently, this host-pathogen interaction provides a …
transcriptional control dynamics. Consequently, this host-pathogen interaction provides a …
[PDF][PDF] Constrained disorder principle-based second-generation algorithms implement quantified variability signatures to improve the function of complex systems
T Sigawi, H Lehmann, N Hurvitz, Y Ilan - J. Bioinform. Syst. Biol, 2023 - fortunepublish.com
Improving the efficacy and overcoming the malfunctions of systems are significant
challenges. Variability characterizes all levels of complex biological systems. We reviewed …
challenges. Variability characterizes all levels of complex biological systems. We reviewed …
scTenifoldNet: a machine learning workflow for constructing and comparing transcriptome-wide gene regulatory networks from single-cell data
We present scTenifoldNet—a machine learning workflow built upon principal-component
regression, low-rank tensor approximation, and manifold alignment—for constructing and …
regression, low-rank tensor approximation, and manifold alignment—for constructing and …
Triku: a feature selection method based on nearest neighbors for single-cell data
Background Feature selection is a relevant step in the analysis of single-cell RNA
sequencing datasets. Most of the current feature selection methods are based on general …
sequencing datasets. Most of the current feature selection methods are based on general …
Controlled noise: evidence of epigenetic regulation of single-cell expression variability
Motivation Understanding single-cell expression variability (scEV) or gene expression noise
among cells of the same type and state is crucial for delineating population-level cellular …
among cells of the same type and state is crucial for delineating population-level cellular …
A comprehensive single cell data analysis of lymphoblastoid cells reveals the role of super‐enhancers in maintaining EBV latency
We probed the lifecycle of Epstein‐Barr virus (EBV) on a cell‐by‐cell basis using single cell
RNA sequencing (scRNA‐seq) data from nine publicly available lymphoblastoid cell lines …
RNA sequencing (scRNA‐seq) data from nine publicly available lymphoblastoid cell lines …
Enhanced transcriptional heterogeneity mediated by NF-κB super-enhancers
JN Wibisana, T Inaba, H Shinohara, N Yumoto… - PLoS …, 2022 - journals.plos.org
The transcription factor NF-κB, which plays an important role in cell fate determination, is
involved in the activation of super-enhancers (SEs). However, the biological functions of the …
involved in the activation of super-enhancers (SEs). However, the biological functions of the …