Accurate Annotation for Differentiating and Imbalanced Cell Types in Single-Cell Chromatin Accessibility Data

Authors: Jia, Y., Li, S., Jiang, R., Chen, S.

Source: IEEE/ACM Transactions on Computational Biology and Bioinformatics IEEE/ACM Trans. Comput. Biol. and Bioinf. Computational Biology and Bioinformatics, IEEE/ACM Transactions on. 21(3):461-471 Jun, 2024

CTCF is selectively required for maintaining chromatin accessibility and gene expression in human erythropoiesis

Authors: Xue Yang, Li Cheng, Ye Xin, Jianxiang Zhang, Xinfeng Chen, Jinchao Xu, Mengli Zhang, Ruopeng Feng, Judith Hyle, Wenjie Qi, Wojciech Rosikiewicz, Beisi Xu, Chunliang Li, Peng Xu

Source: Genome Biology, Vol 26, Iss 1, Pp 1-23 (2025)

Subject Terms: CTCF, Chromatin accessibility, Transcription regulation, Hematopoiesis, Erythropoiesis, Genome editing, Biology (General), QH301-705.5, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1474-760X

Access URL: https://doaj.org/article/9e6655bced004107bd2a28205d03162d

scATAC-seq generates more accurate and complete regulatory maps than bulk ATAC-seq

Authors: E. Ravza Gur, Jim R. Hughes

Source: Scientific Reports, Vol 15, Iss 1, Pp 1-14 (2025)

Subject Terms: Bulk ATAC-seq, scATAC-seq, Gene regulation, Regulatory elements, Chromatin accessibility, Clustering, Medicine, Science

File Description: electronic resource

Relation: https://doaj.org/toc/2045-2322

Access URL: https://doaj.org/article/c86627e51ab34491836bd2512ea9c26f

IGN: Invariable gene set-based normalization for chromatin accessibility profile data analysis

Authors: Shengen Shawn Hu, Hai-Hui Xue, Chongzhi Zang

Source: Computational and Structural Biotechnology Journal, Vol 27, Iss , Pp 501-507 (2025)

Subject Terms: Chromatin accessibility, Normalization, Differential analysis, ATAC-seq, DNase-seq, Biotechnology, TP248.13-248.65

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2001037025000170; https://doaj.org/toc/2001-0370

Access URL: https://doaj.org/article/3b398231309743fc823aa516256269f6

Characteristics of transcriptome and chromatin accessibility in the peripheral blood after acute hypoxia exposure

Authors: Kuo Zeng, Pei-ru Yuan, Jin-feng Xuan, Lai-xi Zhao, Xiao-na Li, Jun Yao, Dong Zhao

Source: BMC Biology, Vol 23, Iss 1, Pp 1-12 (2025)

Subject Terms: Hypoxia, Transcriptome, Chromatin accessibility, High altitude, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://doaj.org/toc/1741-7007

Access URL: https://doaj.org/article/5619b5b2d7784c56ad9e8b41f069664f

HDI-STARR-seq: Condition-specific enhancer discovery in mouse liver in vivo

Authors: Ting-Ya Chang, David J. Waxman

Source: BMC Genomics, Vol 25, Iss 1, Pp 1-29 (2024)

Subject Terms: MPRA, DNase-seq, Chromatin accessibility, Hydrodynamic tail vein injection, Biotechnology, TP248.13-248.65, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1471-2164

Access URL: https://doaj.org/article/9f060d711c0d40f586c2e3c7cfee68d4

Predicting CTCF cell type active binding sites in human genome

Authors: Lu Chai, Jie Gao, Zihan Li, Hao Sun, Junjie Liu, Yong Wang, Lirong Zhang

Source: Scientific Reports, Vol 14, Iss 1, Pp 1-14 (2024)

Subject Terms: CTCF binding site, Convolutional neural networks, Chromatin accessibility, RAD21, SMC3, Medicine, Science

File Description: electronic resource

Relation: https://doaj.org/toc/2045-2322

Access URL: https://doaj.org/article/2f8037b674fe482eb230ed796a2e0790

Dynamic chromatin accessibility and transcriptome changes following PDGF-BB treatment of bone-marrow derived mesenchymal stem cells

Authors: Sheng Liu, Xiaona Chu, Jill L. Reiter, Xuhong Yu, Fang Fang, Patrick McGuire, Hongyu Gao, Yunlong Liu, Jun Wan, Yue Wang

Source: BMC Genomics, Vol 25, Iss 1, Pp 1-12 (2024)

Subject Terms: Mesenchymal stem cells, Platelet-derived growth factor (PDGF)-BB, Chromatin accessibility, Biotechnology, TP248.13-248.65, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1471-2164

Access URL: https://doaj.org/article/6b8dc3d28c0a48908c4edd90c47ea52a

Accelerating Deep Learning based Identification of Chromatin Accessibility from noisy ATAC-seq Data

Authors: Chaudhary, Narendra, Misra, Sanchit, Kalamkar, Dhiraj, Heinecke, Alexander, Georganas, Evangelos, Ziv, Barukh, Adelman, Menachem, Kaul, Bharat

Source: 2022 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW) IPDPSW Parallel and Distributed Processing Symposium Workshops (IPDPSW), 2022 IEEE International. :176-185 May, 2022

Relation: 2022 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW)

Detecting Protein-DNA Interactions Using CUT&RUN Analysis

Source: Journal of Visualized Experiments.

Availability: http://www.jove.com/video/202605

Emerging cooperativity between Oct4 and Sox2 governs the pluripotency network in early mouse embryos

Authors: Yanlin Hou, Zhengwen Nie, Qi Jiang, Sergiy Velychko, Sandra Heising, Ivan Bedzhov, Guangming Wu, Kenjiro Adachi, Hans R Scholer

Source: eLife, Vol 13 (2025)

Subject Terms: embryonic development, inner cell mass, chromatin accessibility, transcriptome, Oct4, Sox2, Medicine, Science, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://elifesciences.org/articles/100735; https://doaj.org/toc/2050-084X

Access URL: https://doaj.org/article/672b65bf1b9c417aa007e0ac2ee8e0b0

Matrix‐Rigidity Cooperates With Biochemical Cues in M2 Macrophage Activation Through Increased Nuclear Deformation and Chromatin Accessibility

Authors: Seung Jae Shin, Buuvee Bayarkhangai, Khaliunsarnai Tsogtbaatar, Meng Yuxuan, Sang‐Hyun Kim, Yong‐Jae Kim, Ali Taghizadeh, Daesan Kim, Dong‐Hwee Kim, Jung‐Hwan Lee, Jeongeun Hyun, Hae‐Won Kim

Source: Advanced Science, Vol 12, Iss 8, Pp n/a-n/a (2025)

Subject Terms: chromatin accessibility, macrophage activation, matrix rigidity, mechano‐chemical signaling, nuclear mechanosensing, Science

File Description: electronic resource

Relation: https://doaj.org/toc/2198-3844

Access URL: https://doaj.org/article/5dfe693628814db79f7b4e4acd406cce

Chromatin accessibility and differentially expressed genes profiling in large yellow croaker (Larimichthys crocea) head kidney cells following iridovirus infection

Authors: Chaowei Song, Ying Huang, Fang Han, Zhiyong Wang

Source: Frontiers in Immunology, Vol 16 (2025)

Subject Terms: chromatin accessibility, iridovirus infection, epigenetics, immune gene expression, ATAC-seq, Immunologic diseases. Allergy, RC581-607

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fimmu.2025.1513966/full; https://doaj.org/toc/1664-3224

Access URL: https://doaj.org/article/c408565580da4121a0691f66502920ce

A scATAC-seq atlas of stasis zone in rat skin burn injury wound process

Authors: Ruikang Li, Jiashan Li, Shuai Liu, Xinya Guo, Jianyu Lu, Tao Wang, Junjie Chen, Yue Zheng, Yue Yuan, Jiaxin Du, Bolin Zhu, Xiaoyu Wei, Pengcheng Guo, Longqi Liu, Xun Xu, Xi Dai, Runzhi Huang, Xin Liu, Xiaoyan Hu, Shiwei Wang, Shizhao Ji

Source: Frontiers in Cell and Developmental Biology, Vol 12 (2025)

Subject Terms: rat burn injuries, stasis zone, chromatin accessibility, wound healing, transcription factor, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fcell.2024.1519926/full; https://doaj.org/toc/2296-634X

Access URL: https://doaj.org/article/7a787f8d12cb46dea60e9d1fc6cf6645

Decoding the chromatin accessibility in Andrographis paniculata genome, a case study of genome-wide investigation of the cis-regulatory elements in medicinal plants

Authors: Mingkun Huang, Yufang Hu, Ling Zhang, Hua Yang, Chen Feng, Chunhong Jiang, Ning Xie, Difa Liu, Shilin Chen, Jihua Wang, Wei Sun

Source: Acta Pharmaceutica Sinica B, Vol 14, Iss 9, Pp 4179-4182 (2024)

Subject Terms: Andrographis paniculata, Chromatin accessibility, Medicinal plant, Epigenetics, ENCODE, cis-regulatory elements, Therapeutics. Pharmacology, RM1-950

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2211383524002430; https://doaj.org/toc/2211-3835

Access URL: https://doaj.org/article/8dda9583c8cc4c6988220deb0425e27b

Enhlink infers distal and context-specific enhancer–promoter linkages

Authors: Olivier B. Poirion, Wulin Zuo, Catrina Spruce, Candice N. Baker, Sandra L. Daigle, Ashley Olson, Daniel A. Skelly, Elissa J. Chesler, Christopher L. Baker, Brian S. White

Source: Genome Biology, Vol 25, Iss 1, Pp 1-32 (2024)

Subject Terms: Single-cell, Linkage analysis, Enhancers inference, Chromatin accessibility, Machine-learning, Biology (General), QH301-705.5, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1474-760X

Access URL: https://doaj.org/article/d0958acda13f4ce2a7cfa49c1a75dbc4

Current genomic deep learning models display decreased performance in cell type-specific accessible regions

Authors: Pooja Kathail, Richard W. Shuai, Ryan Chung, Chun Jimmie Ye, Gabriel B. Loeb, Nilah M. Ioannidis

Source: Genome Biology, Vol 25, Iss 1, Pp 1-22 (2024)

Subject Terms: Deep learning, Chromatin accessibility, Variant effect prediction, Biology (General), QH301-705.5, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1474-760X

Access URL: https://doaj.org/article/da295330cb0b4f5faec4822e64e910e6

ΔNp63 bookmarks and creates an accessible epigenetic environment for TGFβ-induced cancer cell stemness and invasiveness

Authors: Eleftheria Vasilaki, Yu Bai, Mohamad Moustafa Ali, Anders Sundqvist, Aristidis Moustakas, Carl-Henrik Heldin

Source: Cell Communication and Signaling, Vol 22, Iss 1, Pp 1-18 (2024)

Subject Terms: p63, Transforming growth factor β (TGFβ), Signal transduction, Transcription, Chromatin accessibility, Protein-protein interaction, Medicine, Cytology, QH573-671

File Description: electronic resource

Relation: https://doaj.org/toc/1478-811X

Access URL: https://doaj.org/article/c69b2398770746ad995d89ef0e1932d9

A Computational Approach to Demonstrate the Control of Gene Expression via Chromosomal Access in Colorectal Cancer

Authors: Caleb J. Pecka, Ishwor Thapa, Amar B. Singh, Dhundy Bastola

Source: BioMedInformatics, Vol 4, Iss 3, Pp 1822-1834 (2024)

Subject Terms: colorectal cancer, epigenetics, chromatin accessibility, snakemake, Neurosciences. Biological psychiatry. Neuropsychiatry, RC321-571, Computer applications to medicine. Medical informatics, R858-859.7

File Description: electronic resource

Relation: https://www.mdpi.com/2673-7426/4/3/100; https://doaj.org/toc/2673-7426

Access URL: https://doaj.org/article/7d88edf90f47413baa49811187c629b3

The chromatin accessibility and transcriptomic landscape of the aging mice cochlea and the identification of potential functional super-enhancers in age-related hearing loss

Authors: Chanyuan Zhang, Ting Yang, Xiaoqin Luo, Xiaoqing Zhou, Menglong Feng, Wei Yuan

Source: Clinical Epigenetics, Vol 16, Iss 1, Pp 1-22 (2024)

Subject Terms: Age-related hearing loss, Chromatin accessibility, Epigenetics, Senescence, Super-enhancer, Medicine, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1868-7083

Access URL: https://doaj.org/article/12bf5a9dd83945419c31d50a7b145a58