Cargando…

Capturing cell type-specific chromatin compartment patterns by applying topic modeling to single-cell Hi-C data

Single-cell Hi-C (scHi-C) interrogates genome-wide chromatin interaction in individual cells, allowing us to gain insights into 3D genome organization. However, the extremely sparse nature of scHi-C data poses a significant barrier to analysis, limiting our ability to tease out hidden biological inf...

Descripción completa

Detalles Bibliográficos
Autores principales:	Kim, Hyeon-Jin, Yardımcı, Galip Gürkan, Bonora, Giancarlo, Ramani, Vijay, Liu, Jie, Qiu, Ruolan, Lee, Choli, Hesson, Jennifer, Ware, Carol B., Shendure, Jay, Duan, Zhijun, Noble, William Stafford
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Public Library of Science 2020
Materias:	Research Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7526900/ https://www.ncbi.nlm.nih.gov/pubmed/32946435 http://dx.doi.org/10.1371/journal.pcbi.1008173

Ejemplares similares

Software tools for visualizing Hi-C data
por: Yardımcı, Galip Gürkan, et al.
Publicado: (2017)

Unsupervised embedding of single-cell Hi-C data
por: Liu, Jie, et al.
Publicado: (2018)

HiC-spector: a matrix library for spectral and reproducibility analysis of Hi-C contact maps
por: Yan, Koon-Kiu, et al.
Publicado: (2017)

HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient
por: Yang, Tao, et al.
Publicado: (2017)

Massively multiplex single-cell Hi-C
por: Ramani, Vijay, et al.
Publicado: (2017)

Dynamics of genome reorganization during human cardiogenesis reveal an RBM20-dependent splicing factory
por: Bertero, Alessandro, et al.
Publicado: (2019)

Single-cell landscape of nuclear configuration and gene expression during stem cell differentiation and X inactivation
por: Bonora, Giancarlo, et al.
Publicado: (2021)

High Sensitivity Profiling of Chromatin Structure by MNase-SSP
por: Ramani, Vijay, et al.
Publicado: (2019)

Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of human lincRNA genes
por: Ma, Wenxiu, et al.
Publicado: (2014)

Predicting cell-type–specific gene expression from regions of open chromatin
por: Natarajan, Anirudh, et al.
Publicado: (2012)

Massively parallel characterization of transcriptional regulatory elements in three diverse human cell types
por: Agarwal, Vikram, et al.
Publicado: (2023)

Liquid chromatin Hi-C characterizes compartment-dependent chromatin interaction dynamics
por: Belaghzal, Houda, et al.
Publicado: (2021)

Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts
por: Ay, Ferhat, et al.
Publicado: (2014)

High-throughput determination of RNA structure by proximity ligation
por: Ramani, Vijay, et al.
Publicado: (2015)

Measuring the reproducibility and quality of Hi-C data
por: Yardımcı, Galip Gürkan, et al.
Publicado: (2019)

Fine mapping chromatin contacts in capture Hi-C data
por: Eijsbouts, Christiaan Q, et al.
Publicado: (2019)

Chromatin compartment dynamics in a haploinsufficient model of cardiac laminopathy
por: Bertero, Alessandro, et al.
Publicado: (2019)

HiCRep.py: fast comparison of Hi-C contact matrices in Python
por: Lin, Dejun, et al.
Publicado: (2021)

Capture Hi-C identifies the chromatin interactome of colorectal cancer risk loci
por: Jäger, Roland, et al.
Publicado: (2015)

MaxHiC: A robust background correction model to identify biologically relevant chromatin interactions in Hi-C and capture Hi-C experiments
por: Alinejad-Rokny, Hamid, et al.
Publicado: (2022)

Understanding Spatial Genome Organization: Methods and Insights
por: Ramani, Vijay, et al.
Publicado: (2016)

BL-Hi-C is an efficient and sensitive approach for capturing structural and regulatory chromatin interactions
por: Liang, Zhengyu, et al.
Publicado: (2017)

Correction: MaxHiC: A robust background correction model to identify biologically relevant chromatin interactions in Hi-C and capture Hi-C experiments
por: Alinejad-Rokny, Hamid, et al.
Publicado: (2022)

Pentad: a tool for distance-dependent analysis of Hi-C interactions within and between chromatin compartments
por: Magnitov, Mikhail D., et al.
Publicado: (2022)

Accessible high-throughput single-cell whole-genome sequencing with paired chromatin accessibility
por: Queitsch, Konstantin, et al.
Publicado: (2023)

Explicit DNase sequence bias modeling enables high-resolution transcription factor footprint detection
por: Yardımcı, Galip Gürkan, et al.
Publicado: (2014)

Graph embedding and unsupervised learning predict genomic sub-compartments from HiC chromatin interaction data
por: Ashoor, Haitham, et al.
Publicado: (2020)

Computational Processing and Quality Control of Hi-C, Capture Hi-C and Capture-C Data
por: Hansen, Peter, et al.
Publicado: (2019)

Chromatin accessibility reveals insights into androgen receptor activation and transcriptional specificity
por: Tewari, Alok K, et al.
Publicado: (2012)

ChiCMaxima: a robust and simple pipeline for detection and visualization of chromatin looping in Capture Hi-C
por: Ben Zouari, Yousra, et al.
Publicado: (2019)

dcHiC detects differential compartments across multiple Hi-C datasets
por: Chakraborty, Abhijit, et al.
Publicado: (2022)

Extracting multi-way chromatin contacts from Hi-C data
por: Liu, Lei, et al.
Publicado: (2021)

Statistical Evaluation of the Rodin–Ohno Hypothesis: Sense/Antisense Coding of Ancestral Class I and II Aminoacyl-tRNA Synthetases
por: Chandrasekaran, Srinivas Niranj, et al.
Publicado: (2013)

CTCF-mediated insulation and chromatin environment modulate Car5b escape from X inactivation
por: Fang, He, et al.
Publicado: (2023)

Capturing 3D Chromatin Maps of Human Primary Monocytes: Insights From High-Resolution Hi-C
por: Xia, Yu, et al.
Publicado: (2022)

scHiCDiff: detecting differential chromatin interactions in single-cell Hi-C data
por: Liu, Huiling, et al.
Publicado: (2023)

Accurate identification of centromere locations in yeast genomes using Hi-C
por: Varoquaux, Nelle, et al.
Publicado: (2015)

Smash and DASH with Cas9
por: Ramani, Vijay, et al.
Publicado: (2016)

Comprehensive characterization of tissue-specific chromatin accessibility in L2 Caenorhabditis elegans nematodes
por: Durham, Timothy J., et al.
Publicado: (2021)

Comparison of Capture Hi-C Analytical Pipelines
por: Aljogol, Dina, et al.
Publicado: (2022)

Cannot write session to /tmp/vufind_sessions/sess_od7ivd6u1e6lleb7t79aull817