[HTML][HTML] Best practices for single-cell analysis across modalities
Recent advances in single-cell technologies have enabled high-throughput molecular
profiling of cells across modalities and locations. Single-cell transcriptomics data can now …
profiling of cells across modalities and locations. Single-cell transcriptomics data can now …
Chromatin accessibility profiling methods
L Minnoye, GK Marinov, T Krausgruber, L Pan… - Nature Reviews …, 2021 - nature.com
Chromatin accessibility, or the physical access to chromatinized DNA, is a widely studied
characteristic of the eukaryotic genome. As active regulatory DNA elements are generally …
characteristic of the eukaryotic genome. As active regulatory DNA elements are generally …
[HTML][HTML] Liquid biopsy epigenomic profiling for cancer subtyping
SC Baca, JH Seo, MP Davidsohn, B Fortunato… - Nature medicine, 2023 - nature.com
Although circulating tumor DNA (ctDNA) assays are increasingly used to inform clinical
decisions in cancer care, they have limited ability to identify the transcriptional programs that …
decisions in cancer care, they have limited ability to identify the transcriptional programs that …
Cistrome Data Browser: expanded datasets and new tools for gene regulatory analysis
Abstract The Cistrome Data Browser (DB) is a resource of human and mouse cis-regulatory
information derived from ChIP-seq, DNase-seq and ATAC-seq chromatin profiling assays …
information derived from ChIP-seq, DNase-seq and ATAC-seq chromatin profiling assays …
Therapeutically increasing MHC-I expression potentiates immune checkpoint blockade
Immune checkpoint blockade (ICB) therapy revolutionized cancer treatment, but many
patients with impaired MHC-I expression remain refractory. Here, we combined FACS-based …
patients with impaired MHC-I expression remain refractory. Here, we combined FACS-based …
[HTML][HTML] Liver-fibrosis-activated transcriptional networks govern hepatocyte reprogramming and intra-hepatic communication
Liver fibrosis is a strong predictor of long-term mortality in individuals with metabolic-
associated fatty liver disease; yet, the mechanisms underlying the progression from the …
associated fatty liver disease; yet, the mechanisms underlying the progression from the …
[HTML][HTML] Integrative analyses of single-cell transcriptome and regulome using MAESTRO
Abstract We present Model-based AnalysEs of Transcriptome and RegulOme (MAESTRO),
a comprehensive open-source computational workflow (http://github. com/liulab …
a comprehensive open-source computational workflow (http://github. com/liulab …
[HTML][HTML] Stage-specific H3K9me3 occupancy ensures retrotransposon silencing in human pre-implantation embryos
R Xu, S Li, Q Wu, C Li, M Jiang, L Guo, M Chen, L Yang… - Cell Stem Cell, 2022 - cell.com
Summary H3K9me3, as a hallmark of heterochromatin, is important for cell-fate specification.
However, it remains unknown how H3K9me3 is reprogrammed during human early embryo …
However, it remains unknown how H3K9me3 is reprogrammed during human early embryo …
[HTML][HTML] Reprogramming of the FOXA1 cistrome in treatment-emergent neuroendocrine prostate cancer
Lineage plasticity, the ability of a cell to alter its identity, is an increasingly common
mechanism of adaptive resistance to targeted therapy in cancer. An archetypal example is …
mechanism of adaptive resistance to targeted therapy in cancer. An archetypal example is …
[HTML][HTML] Identification and functional characterization of transcriptional activators in human cells
Transcription is orchestrated by thousands of transcription factors (TFs) and chromatin-
associated proteins, but how these are causally connected to transcriptional activation is …
associated proteins, but how these are causally connected to transcriptional activation is …