Integrating ChIP-seq with other functional genomics data

S Jiang, A Mortazavi - Briefings in functional genomics, 2018 - academic.oup.com
Transcription is regulated by transcription factor (TF) binding at promoters and distal
regulatory elements and histone modifications that control the accessibility of these …

Transcriptional determination and functional specificity of myeloid cells: making sense of diversity

S Monticelli, G Natoli - Nature Reviews Immunology, 2017 - nature.com
Early responses to invading pathogens and to non-microbial danger signals are mediated
by different innate immune and parenchymal tissue cells, which are able to respond to a …

Circadian entrainment triggers maturation of human in vitro islets

JR Alvarez-Dominguez, J Donaghey, N Rasouli… - Cell stem cell, 2020 - cell.com
Stem-cell-derived tissues could transform disease research and therapy, yet most methods
generate functionally immature products. We investigate how human pluripotent stem cells …

Leveraging chromatin accessibility for transcriptional regulatory network inference in T Helper 17 Cells

ER Miraldi, M Pokrovskii, A Watters, DM Castro… - Genome …, 2019 - genome.cshlp.org
Transcriptional regulatory networks (TRNs) provide insight into cellular behavior by
describing interactions between transcription factors (TFs) and their gene targets. The assay …

The accessible chromatin landscape of lipopolysaccharide-induced systemic inflammatory response identifying epigenome signatures and transcription regulatory …

Z Lv, H Fan, M Gao, X Zhang, G Li, Y Fan, Z Ning… - International Journal of …, 2024 - Elsevier
Lipopolysaccharide (LPS) can induce systemic inflammatory response (SIR) in animals.
Understanding the regulatory mechanism of SIR and therapies to ensure healthy growth is …

Integrated multi-omics reveals anaplerotic rewiring in methylmalonyl-CoA mutase deficiency

P Forny, X Bonilla, D Lamparter, W Shao, T Plessl… - Nature …, 2023 - nature.com
Methylmalonic aciduria (MMA) is an inborn error of metabolism with multiple monogenic
causes and a poorly understood pathogenesis, leading to the absence of effective causal …

Map** the developmental trajectory of human astrocytes reveals divergence in glioblastoma

C Sojka, HLV Wang, TN Bhatia, Y Li, P Chopra… - Nature Cell …, 2025 - nature.com
Glioblastoma (GBM) is defined by heterogeneous and resilient cell populations that closely
reflect neurodevelopmental cell types. Although it is clear that GBM echoes early and …

Epigenetic regulation of axon regeneration and glial activation in injury responses

S Wahane, D Halawani, X Zhou, H Zou - Frontiers in genetics, 2019 - frontiersin.org
Injury to the nervous system triggers a multicellular response in which epigenetic
mechanisms play an important role in regulating cell type-specific transcriptional changes …

Epigenetic regulation of immune cells in systemic lupus erythematosus: insight from chromatin accessibility

ZX Gao, T He, P Zhang, X Hu, M Ge, YQ Xu… - Expert Opinion on …, 2024 - Taylor & Francis
ABSTRACT Introduction Systemic Lupus Erythematosus (SLE) is a multi-dimensional
autoimmune disease involving numerous tissues throughout the body. The chromatin …

D evelopmental C hromatin R estriction of P ro‐G rowth G ene N etworks A cts as an E pigenetic B arrier to A xon R egeneration in C ortical N eurons

I Venkatesh, V Mehra, Z Wang, B Califf… - Developmental …, 2018 - Wiley Online Library
Axon regeneration in the central nervous system is prevented in part by a developmental
decline in the intrinsic regenerative ability of maturing neurons. This loss of axon growth …