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2025	N-alpha-acetyltransferase 40 modulates ecdysteroid action through chromatin accessibility changes near the promoters of 20-hydroxyecdysone response genes in Tribolium Castaneum TcA cells Insect Biochemistry and Molecular Biology Surjeet Kumar Arya, Subba Reddy Palli
2025	HAND2 invades nucleolar condensates to pioneer lineage-specific cardiac pacemaker gene programs Nature Communications Kartik Kulkarni, Gabriella Quinn, Jared Dela Rosa, Sean Goetsch, Vrushali Pandit, Lin Wang, Akane Sakaguchi, Sushama Sivakumar, Nikhil V. Munshi
2024	Data-driven modeling of core gene regulatory network underlying leukemogenesis in IDH mutant AML npj Systems Biology and Applications Ataur Katebi, Xiaowen Chen, Daniel Ramirez, Sheng Li, Mingyang Lu
2023	ATAC-DEA: A Web-Based ATAC-Seq Data Differential Peak and Annotation Analysis Application Journal of Computational Biology Shilong Zhang, Sufang Wang
2022	Bibliometric review of ATAC-Seq and its application in gene expression Briefings in Bioinformatics Liheng Luo, Michael Gribskov, Sufang Wang
2022	Differential enrichment of H3K9me3 in intrahepatic cholangiocarcinoma BMC Medical Genomics Sheng Hu, Xuejun Wang, Tao Wang, Lianmin Wang, Lixin Liu, Wenjun Ren, Xiaoyong Liu, Weihan Zhang, Weiran Liao, Zhoujun Liao, Renchao Zou, Xiaowen Zhang
2022	Progress in Molecular Biology and Translational Science Zeeshan Ahmed
2022	Next-Generation Sequencing Applications for the Study of Fungal Pathogens Microorganisms Shiman Jiang, Yanfei Chen, Shengyi Han, Longxian Lv, Lanjuan Li
2022	Multi-omics strategies for personalized and predictive medicine: past, current, and future translational opportunities Emerging Topics in Life Sciences Zeeshan Ahmed
2021	ATACgraph: Profiling Genome-Wide Chromatin Accessibility From ATAC-seq Frontiers in Genetics Rita Jui-Hsien Lu, Yen-Ting Liu, Chih Wei Huang, Ming-Ren Yen, Chung-Yen Lin, Pao-Yang Chen
2021	PEPATAC: an optimized pipeline for ATAC-seq data analysis with serial alignments NAR Genomics and Bioinformatics Jason P Smith, M Ryan Corces, Jin Xu, Vincent P Reuter, Howard Y Chang, Nathan C Sheffield
2021	Genomics pipelines to investigate susceptibility in whole genome and exome sequenced data for variant discovery, annotation, prediction and genotyping PeerJ Zeeshan Ahmed, Eduard Gibert Renart, Saman Zeeshan
2020	Epigenetics Methods Anagha Joshi, Julia Romanowska
2020	100 Years of evolving gene–disease complexities and scientific debutants Briefings in Bioinformatics Saman Zeeshan, Ruoyun Xiong, Bruce T Liang, Zeeshan Ahmed
2020	ATAC-seq normalization method can significantly affect differential accessibility analysis and interpretation Epigenetics & Chromatin Jake J. Reske, Mike R. Wilson, Ronald L. Chandler
2020	Analytical Approaches for ATAC‐seq Data Analysis Current Protocols in Human Genetics Jason P. Smith, Nathan C. Sheffield
2019	Hand2 Selectively Reorganizes Chromatin Accessibility to Induce Pacemaker-like Transcriptional Reprogramming Cell Reports Antonio Fernandez-Perez, Adwait Amod Sathe, Minoti Bhakta, Kayla Leggett, Chao Xing, Nikhil Vilas Munshi
2019	PAN-INTACT enables direct isolation of lineage-specific nuclei from fibrous tissues PLOS ONE Samadrita Bhattacharyya, Adwait A. Sathe, Minoti Bhakta, Chao Xing, Nikhil V. Munshi
2018	GUAVA: A Graphical User Interface for the Analysis and Visualization of ATAC-seq Data Frontiers in Genetics Mayur Divate, Edwin Cheung
2018	ATACseqQC: a Bioconductor package for post-alignment quality assessment of ATAC-seq data BMC Genomics Jianhong Ou, Haibo Liu, Jun Yu, Michelle A. Kelliher, Lucio H. Castilla, Nathan D. Lawson, Lihua Julie Zhu
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