A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility
Cusanovich, Darren A., Hill, Andrew J., Aghamirzaie, Delasa, Daza, Riza M., Pliner, Hannah A., Berletch, Joel B., Filippova, Galina N., Huang, Xingfan +9 more·2018·Cell
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- Single nucleus multi-omics regulatory landscape of the murine pituitaryFrederique Murielle Ruf-Zamojski, Zidong Zhang, Michel Zamojski, Gregory R. Smith, Natalia Mendelev, Hanqing Liu, German Nudelman, Mika Moriwaki, Hanna Pinças, Rosa Castanon et al. · 2021 · Nature Communications
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- Perspectives on defining cell types in the brainMukamel, Eran A, Ngai, John · 2019 · Current Opinion in Neurobiology
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- DC3 is a method for deconvolution and coupled clustering from bulk and single-cell genomics dataWan-Wen Zeng, Xi Chen, Z. Duren, Yong Wang, Rui Jiang, Wing H Wong · 2019 · Nature Communications
- Spirits in the Material World: Enhancer RNAs in Transcriptional RegulationTim Y. Hou, W. Lee Kraus · 2020 · Trends in Biochemical Sciences
- The Role of De Novo Noncoding Regulatory Mutations in Neurodevelopmental DisordersTychele N. Turner, Evan E. Eichler · 2018 · Trends in Neurosciences
- A plate-based single-cell ATAC-seq workflow for fast and robust profiling of chromatin accessibilityXu, Wei, Wen, Yi, Liang, Yingying, Xu, Qiushi, Wang, Xuefei, Jin, Wenfei, Chen, Xi · 2021 · Nature Protocols
- Automatic cell type identification methods for single-cell RNA sequencingXie, Bingbing, Jiang, Qin, Mora, Antonio, Li, Xuri · 2021 · Computational and Structural Biotechnology Journal
- Applications of deep learning in understanding gene regulationZhongxiao Li, Elva Gao, Juexiao Zhou, Wenkai Han, Xiaopeng Xu, Xin Gao · 2023 · Cell Reports Methods
- Bi-order multimodal integration of single-cell dataJinzhuang Dou, Shaoheng Liang, Vakul Mohanty, Qi Miao, Yuefan Huang, Qingnan Liang, Xuesen Cheng, Sangbae Kim, Jongsu Choi, Yumei Li et al. · 2022 · Genome biology
- Single cell multiomic analysis reveals diabetes-associated β-cell heterogeneity driven by HNF1AChen Weng, Anniya Gu, Shanshan Zhang, Leina Lu, Luxin Ke, Peidong Gao, Xiaoxiao Liu, Yuntong Wang, Peinan Hu, Dylan Plummer et al. · 2023 · Nature Communications
- Classifying cells with Scasat, a single-cell ATAC-seq analysis toolSyed Murtuza Baker, Connor Rogerson, Andrew Hayes, Andrew D Sharrocks, Magnus Rattray · 2018 · Nucleic Acids Research
- RETRACTED ARTICLE: KDM4 orchestrates epigenomic remodeling of senescent cells and potentiates the senescence-associated secretory phenotype2021 · Retracted
- CUT&RUNTools 2.0: a pipeline for single-cell and bulk-level CUT&RUN and CUT&Tag data analysisFulong Yu, Vijay G. Sankaran, Guo‐Cheng Yuan · 2021 · Bioinformatics
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- Using single-cell technologies to map the human immune system — implications for nephrologyBenjamin J. Stewart, John R. Ferdinand, Menna Ruth Clatworthy · 2019 · Nature Reviews Nephrology
- The epigenetically-encoded memory of the innate immune systemSarah Sun, Luis Bruno Barreiro · 2020 · Current Opinion in Immunology
- scATAC-pro: a comprehensive workbench for single-cell chromatin accessibility sequencing dataWenbao Yu, Yasin Uzun, Qin Zhu, Changya Chen, Kai Tan · 2020 · Genome biology
- A multimodal cell census and atlas of the mammalian primary motor cortexBRAIN Initiative Cell Census Network (BICCN), Ricky S. Adkins, Andrew I. Aldridge, Shona W. Allen, Seth A. Ament, Xu An, Ethan J. Armand, Giorgio A. Ascoli, Trygve E. Bakken, Anita E. Bandrowski et al. · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
- Deep learning of cross-species single-cell landscapes identifies conserved regulatory programs underlying cell typesLi, Jiaqi, Wang, Jingjing, Zhang, Peijing, Wang, Renying, Mei, Yuqing, Sun, Zhongyi, Fei, Lijiang, Jiang, Mengmeng, Ma, Lifeng, E, Weigao et al. · 2022 · Nature Genetics
- Systematic benchmarking of single-cell ATAC-sequencing protocolsFlorian V. De Rop, Gert J. Hulselmans, Christopher Flerin, Paula Soler-Vila, Albert Rafels, Valerie Christiaens, Carmen Bravo González‐Blas, Doménica Marchese, Ginevra Caratù, Suresh Kumar Poovathingal et al. · 2023 · Nature Biotechnology
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- Single-cell joint profiling of multiple epigenetic proteins and gene transcriptionHaiqing Xiong, Qianhao Wang, Chen C. Li, Aibin He · 2024 · Science Advances
- Systems immunology: Integrating multi-omics data to infer regulatory networks and hidden drivers of immunityJiyang Yu, Junmin Peng, Hongbo Chi · 2019 · Current Opinion in Systems Biology
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- Perspectives on Bulk-Tissue RNA Sequencing and Single-Cell RNA Sequencing for Cardiac TranscriptomicsJana-Charlotte Hegenbarth, Giuliana Lezzoche, León J. De Windt, Monika Stoll · 2022 · Frontiers in Molecular Medicine
- NF-κB dynamics in the language of immune cellsMohammad Aqdas, Myong‐Hee Sung · 2022 · Trends in Immunology
- Enhancers Facilitate the Birth of De Novo Genes and Gene Integration into Regulatory NetworksPaco Majic, Joshua L. Payne · 2019 · Molecular Biology and Evolution
- Understanding the kidney one cell at a timeJihwan Park, Chang Liu, Junhyong Kim, Katalin Suszták · 2019 · Kidney International
- Enhancer RNAs: mechanisms in transcriptional regulation and functions in diseasesQianhui Li, Xin Liu, Jingtao Wen, Xi Chen, Bumin Xie, Yang Zhao · 2023 · Cell Communication and Signaling
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- A decade of molecular cell atlasesStephen R. Quake · 2022 · Trends in Genetics
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- Tracking cell-type-specific temporal dynamics in human and mouse brainsZi-Yu Lu, Melissa Zhang, Jasper Lee, András Sziráki, Sonya Anderson, Zehao Zhang, Zi-Han Xu, Weirong Jiang, Shaoyu Ge, Peter T. Nelson et al. · 2023 · Cell
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- The Role of Insulation in Patterning Gene ExpressionIsa Özdemir, Maria Cristina Gambetta · 2019 · Genes
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- Single-cell Hi-C data analysis: safety in numbersAleksandra A. Galitsyna, Mikhail Sergeevich Gelfand · 2021 · Briefings in Bioinformatics
- FoxP3 associates with enhancer-promoter loops to regulate Treg-specific gene expressionRicardo N. Ramírez, Kaitavjeet Chowdhary, Juliette Léon, Diane J. Mathis, Christophe O. Benoist · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
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