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
Cited by (789)
Items 501–600 of 789
- Genomic Architecture of Cells in Tissues (GeACT): Study of Human Mid-gestation FetusFeng Tian, Fan Zhou, Xiang Li, Wenping Ma, Honggui Wu, Ming Yang, Alec R. Chapman, David F. Lee, Longzhi Tan, Dong Xing et al. · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
- A map of bat virus receptors derived from single-cell multiomicsTianhang Lv, Xiaoshan Wang, Chao Yu, Zhifeng Wang, Rong Xiang, Linmiao Li, Yue Yuan, Yuhang Wang, Xiaoyu Wei, Yeya Yu et al. · 2022 · Scientific Data
- A generic reference defined by consensus peaks for scATAC-seq data analysisQiuchen Meng, Xinze Wu, Wen‐Chang Chen, Yubo Zhao, Chen Li, Wei Zheng, Jiaqi Li, Xi Xi, Sijie Chen, Catherine Zhang et al. · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
- Single-nucleus chromatin landscape dataset of mouse brain development and agingYuting Ma, Sicheng Guo, Yixi Chen, Yushan Peng, Xi Su, Hui Jiang, Xiumei Lin, Jianguo Zhang · 2024 · Scientific Data
- Genome-wide cancer-specific chromatin accessibility patterns derived from archival processed xenograft tumorsShelsa S. Marcel, Austin Quimby, Mélodie P. Noël, Oscar C. Jaimes, Marjan Mehrab‐Mohseni, Suud A. Ashur, Brian Velasco, James K. Tsuruta, Sandeep K. Kasoji, Charlene Santos et al. · 2021 · Genome Research
- A single-cell atlas of the murine limb skeleton integrating the developmental and adult stagesTim Herpelinck, Liesbeth Ory, Tom Verbraeken, Gabriele Nasello, Mojtaba Barzegari, Johanna Bolander, Frank P. Luyten, Przemko Tylżanowski, Liesbet Geris · 2025 · Scientific Reports
- Accurate cell type annotation for single‐cell chromatin accessibility data via contrastive learning and reference guidanceSiyu Li, Songming Tang, Yunchang Wang, Sijie Li, Yuhang Jia, Shengquan Chen · 2024 · Quantitative Biology
- Accurate Annotation for Differentiating and Imbalanced Cell Types in Single-Cell Chromatin Accessibility DataYuhang Jia, Siyu Li, Rui Jiang, Shengquan Chen · 2024 · IEEE Transactions on Computational Biology and Bioinformatics
- scBlood: A comprehensive single-cell accessible chromatin database of blood cellsYu Zhao, Zheng-min Yu, Ting Cui, Li-Dong Li, Yan-Yu Li, Fengcui Qian, Li-wei Zhou, Ye Li, Qiao-li Fang, Xue Huang et al. · 2024 · Computational and Structural Biotechnology Journal
- scPerb: Predict single-cell perturbation via style transfer-based variational autoencoderZhankui Tang, Minghao Zhou, Kai Zhang, Qianqian Song · 2024 · Journal of Advanced Research
- Integrating single-cell multi-omics data through self-supervised clusteringYuansong Zeng, Jianing Chen, Zixiang Pan, Weijiang Yu, Yuedong Yang · 2024 · Applied Soft Computing
- sCIN: a contrastive learning framework for single-cell multi-omics data integrationAmir Ebrahimi, Alireza Fotuhi Siahpirani, Hesam Montazeri · 2025 · Briefings in Bioinformatics
- ChromPolymerDB: a high-resolution database of single-cell 3D chromatin structures for functional genomicsMin Chen, Lin Du, Siyuan Zhao, Bowei Ye, Pourya Delafrouz, Hammad Farooq, Debaleena Chattopadhyay, G. Elisabeta Marai, Zhifeng Shao, Jie Liang et al. · 2025 · Nucleic Acids Research
- High-Resolution ATAC-Seq Analysis of Frozen Clinical TissuesPaloma Cejas, Henry W. Long · 2022 · Methods in molecular biology
- Representing and extracting knowledge from single-cell dataIonut Sebastian Mihai, Sarang Chafle, Johan Henriksson · 2023 · Biophysical Reviews
- Comparative Evaluation of Machine Learning Algorithms for Alzheimer’s Disease Classification using Synthetic Transcriptomics DatasetMohammad Abdullah, Yap Bee Wah, Abu Bakar Abdul Majeed, Yuslina Zakaria, Norshahida Shaadan, Mohamed Imran Mohamed Ariff, Jufiza A. Wahab, Samsiah Binti Ahmad, Mohd Sapuan Baharuddin, Wan Noor Hayatie Wan Abdul Aziz · 2023 · Trends in Sciences
- Single-cell sequencing: A promising approach for uncovering the characteristic of pancreatic islet cells in type 2 diabetesXinyi Fang, Yanjiao Zhang, Runyu Miao, Yuxin Zhang, Ruiyang Yin, Huifang Guan, Xinyue Huang, Jiaxing Tian · 2024 · Biomedicine & Pharmacotherapy
- Integration of single-cell transcriptome and chromatin accessibility and its application on tumor investigationChunyuan Yang, Yan Jin, Yuxin Yin · 2024 · Life Medicine
- The single-cell chromatin landscape in gonadal cell lineage specificationH. Suen, Fang-Hong Ou, Kai K. Miu, Zhang-Ting Wang, Wai-Yee Chan, J. Liao · 2024 · BMC Genomics
- Single-cell genomics to study developmental cell fate decisions in zebrafishRoberto Moreno-Ayala, Jan Philipp Junker · 2021 · Briefings in Functional Genomics
- Epigenetic Regulation of Endothelial Cell Lineages During Zebrafish Development—New Insights From Technical AdvancesVirginia Panara, Rui M. Monteiro, Katarzyna Koltowska · 2022 · Frontiers in Cell and Developmental Biology
- Evaluation of classification in single cell atac-seq data with machine learning methodsHongzhe Guo, Zhongbo Yang, Tao Jiang, Shiqi Liu, Yadong Wang, Zhe Cui · 2022 · BMC Bioinformatics
- scIBD: a self-supervised iterative-optimizing model for boosting the detection of heterotypic doublets in single-cell chromatin accessibility dataWenhao Zhang, Rui Jiang, Shengquan Chen, Ying Wang · 2023 · Genome biology
- Genome-Wide Screening Approaches for Biochemical Reactions Independent of Cell GrowthYuki Noguchi, Risa Matsui, Jaeyeon Suh, Yu Dou, Jun Suzuki · 2024 · Annual Review of Genomics and Human Genetics
- Accelerating Single-Cell Sequencing Data Analysis with SciDAP: A User-Friendly ApproachMichael Kotliar, Andrey V. Kartashov, Artem Barski · 2025 · Methods in molecular biology
- Improved mouse models and advanced genetic and genomic technologies for the study of neutrophilsVishnu Hosur, Daniel A. Skelly, Christopher Francis, Benjamin E. Low, Vivek Kohar, Lisa M. Burzenski, Mansoor M. Amiji, Leonard D. Shultz, Michael V. Wiles · 2020 · Drug Discovery Today
- Approximate distance correlation for selecting highly interrelated genes across datasetsQunlun Shen, Shihua Zhang · 2021 · PLoS Computational Biology
- Characterization of chromatin accessibility patterns in different mouse cell types using machine learning methods at single-cell resolutionYaochen Xu, FeiMing Huang, Wei Guo, Kaiyan Feng, Lin Zhu, Zhenbing Zeng, Tao Huang, Yu‐Dong Cai · 2023 · Frontiers in Genetics
- Spatial and temporal tools for building a human cell atlasJonah Cool, Richard Conroy, Sean E. Hanlon, Shannon K. Hughes, Ananda L. Roy · 2019 · Molecular Biology of the Cell
- Single-cell chromatin accessibility landscape of human umbilical cord blood in trisomy 18 syndromeXiaofen Qiu, Haiyan Yu, Hongwei Wu, Zhiyang Hu, Jun Zhou, Hua Lin, Wen Xue, Wanxia Cai, Jiejing Chen, Qiang Yan et al. · 2021 · Human Genomics
- A mouse tissue atlas of small non-coding RNAAlina Isakova, Tobias Fehlmann, Andreas Keller, Stephen R. Quake · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
- Single-cell multi-omic profiling of chromatin conformation and DNA methylationDong-Sung Lee, Chongyuan Luo, Jingtian Zhou, Sahaana Chandran, Angeline C. Rivkin, Anna Bartlett, Joseph R. Nery, Conor Fitzpatrick, Carolyn O’Connor, Jesse R. Dixon et al. · 2019
- Learning immune cell differentiationAlexandra Maslova, Ricardo N. Ramírez, Ke Ma, Hugo Schmutz, Chendi Wang, Curtis Fox, Bernard Ng, Christophe O. Benoist, Sara Mostafavi, the Immunological Genome Project · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
- Single Cell Epigenetics Reveal Cell-Cell Communication Networks in Normal and Abnormal Cardiac MorphogenesisSanjeev S. Ranade, Sean Whalen, Ivana Zlatanova, Tomohiro Nishino, Benjamin J. van Soldt, Lin Ye, Angelo Pelonero, Langley Grace Wallace, Yu Huang, Michael Alexanian et al. · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
- Flexible and scalable control of T cell memory by a reversible epigenetic switchKathleen Abadie, Elisa C. Clark, Obinna Ukogu, Wei Yang, Riza M. Daza, Kenneth K.H. Ng, Jumana Fathima, Allan L. Wang, Avinash Bhandoola, Armita Nourmohammad et al. · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
- Tutorial: guidelines for manual cell type annotation of single-cell multi-omics datasets using interactive softwareYang Joon Kim, Alexander J. Tarashansky, Karen Liang, Meghan Urisko, Leah C. Dorman, Michael Borja, Norma F Neff, Angela Oliveira Pisco, Alejandro A. Granados · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
- Extracellular matrix regulates lineage plasticity in prostate cancer through YAP/TEADTeng Han, Zhen Sun, Matthew Lange, Y Zoe Cho, Patrick D. McGillivray, Maren Büttner, Nathaniel R. Kastan, Subhiksha Nandakumar, HuiYong Zhao, Eralda Salataj et al. · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
- annATAC: automatic cell type annotation for scATAC-seq data based on language modelCui, Lingyu, Wang, Fang, Li, Hongfei, Liu, Qiaoming, Zhou, Murong, Wang, Guohua · 2025 · BMC Biology
- Should Artificial Intelligence Play a Durable Role in Biomedical Research and Practice?Pierre Bongrand · 2024 · International Journal of Molecular Sciences
- Quasi-spatial single-cell transcriptome based on physical tissue properties defines early aging associated niche in liverKwon Yong Tak, Ju‐Yeon Kim, Myungsun Park, Woo‐Seok Kim, Seoyeong Lee, Narae Park, Min Jeong Kim, Ju-Bin Kang, Yongjun Koh, Hae Young Yang et al. · 2025 · Nature Aging
- Developing a comprehensive database and search tool for single-cell ATAC-seq dataArrian Gibson-Khademi, Jonathan Wang, Erik Christensen, Parisa Shooshtari · 2026 · Scientific Reports
- An expanded role for single-cell chemical genomics profiling in drug discoveryAdeya Wyatt, Kevin Hoffer-Hawlik, Ross M. Giglio, Elham Azizi, José L. McFaline‐Figueroa · 2026 · Biochemical Journal
- RefTM: reference-guided topic modeling of single-cell chromatin accessibility dataZheng Zhang, Shengquan Chen, Zhixiang Lin · 2022 · Briefings in Bioinformatics
- HyGAnno: hybrid graph neural network–based cell type annotation for single-cell ATAC sequencing dataWeihang Zhang, Yang Cui, Bowen Liu, Martin Loza, Sung‐Joon Park, Kenta Nakai · 2024 · Briefings in Bioinformatics
- Computational modeling of aging-related gene networks: a reviewJosé Américo Nabuco Leva Ferreira de Freitas, Oliver Bischof · 2024 · Frontiers in Applied Mathematics and Statistics
- The Genomics of Aging at the Single-Cell ScaleWei You Zhou, Junyue Cao · 2025 · Annual Review of Genomics and Human Genetics
- PEAKQC: periodicity evaluation in single-cell ATAC-seq data for quality assessmentJan Detleffsen, Brenton Bruns, Mette Skou Bentsen, Carsten Tobias Kuenne, Mario Looso · 2025 · Briefings in Bioinformatics
- Decoding cnidarian cell type gene regulationAnamaria Elek, Marta Iglesias, Lukas Mahieu, Grygoriy Zolotarov, Xavier Grau‐Bové, Stein Aerts, Arnau Sebé-Pedrós · 2025 · Nature Ecology & Evolution
- A comprehensive benchmarking study on computational tools for cross-omics label transfer from single-cell RNA to ATAC dataYuge Wang, Hongyu Zhao · 2026 · G3 Genes Genomes Genetics
- A cutting-edge strategy for spinal cord injury treatment: resident cellular transdifferentiationYu-Ming Fang, Wei-can Chen, Wan-Jing Zheng, Yu-Shen Yang, Yan Zhang, Xin-Li Chen, Meng-Qin Pei, Shu Lin, He‐fan He · 2023 · Frontiers in Cellular Neuroscience
- Cofea: correlation-based feature selection for single-cell chromatin accessibility dataKeyi Li, Xiaoyang Chen, Shuang Song, Lin Hou, Shengquan Chen, Rui Jiang · 2023 · Briefings in Bioinformatics
- DECA: harnessing interpretable transformer model for cellular deconvolution of chromatin accessibility profileShijie Luo, Ming Zhu, Liquan Lin, Jiajing Xie, Shihao Lin, Ying Chen, Jiali Zhu, Jialiang Huang · 2024 · Briefings in Bioinformatics
- Decoding human cardiovascular development and disease through single-cell transcriptomic and epigenomic profilingLogan Dunkenberger, Daniel Yuhang Li, Ioannis Karakikes, Thomas Quertermous · 2025 · Trends in Cell Biology
- Epigenetic mechanisms in the regulation of lymphocyte differentiationNina Schmolka, Bruno Silva‐Santos, Anita Quintal Gomes · 2020 · Elsevier eBooks
- Analytics methods and tools for integration of biomedical data in medicineLin Zhang, Mehran Karimzadeh, Mattea L. Welch, Chris McIntosh, Bo Wang · 2020 · Elsevier eBooks
- Leveraging Novel Integrated Single-Cell Analyses to Define HIV-1 Latency ReversalSuhui Zhao, Athe M. N. Tsibris · 2021 · Viruses
- Kidney Development: Recent Insights from Technological AdvancesRuth Röck, Ludovica Rizzo, Soeren S. Lienkamp · 2022 · Physiology
- Learning single-cell chromatin accessibility profiles using meta-analytic marker genesRisa Karakida Kawaguchi, Ziqi Tang, Stephan Fischer, Chandana Rajesh, Rohit K. Tripathy, Peter K. Koo, Jesse Gillis · 2022 · Briefings in Bioinformatics
- A single cell framework for multi-omic analysis of disease identifies malignant regulatory signatures in mixed phenotype acute leukemiaJeffrey M. Granja, Sandy L. Klemm, Lisa M. McGinnis, Arwa S. Kathiria, Anja Mezger, Benjamin E. Parks, Eric J. Gars, Michaela Liedtke, Grace X. Y. Zheng, Howard Y. Chang et al. · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
- Spatially resolved gene regulatory and disease vulnerability map of the adult Macaque cortexYing Lei, Mengnan Cheng, Zihao Li, Zhenkun Zhuang, Liang Li Wu, Yunong Sun, Lei Han, Zhi‐Hao Huang, Yuzhou Wang, Zifei Wang et al. · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
- Single nucleus multi-omics regulatory atlas 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. · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
- Simultaneous deep generative modeling and clustering of single cell genomic dataQiao Liu, Shengquan Chen, Rui Jiang, Wing Hung Wong · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
- Profiling of transcribed cis -regulatory elements in single cellsJonathan Moody, Tsukasa Kouno, Akari Suzuki, Youtaro Shibayama, Chikashi C. Terao, Jen-Chien Chang, Fernando López-Redondo, Chi Wai Yip, Jessica Severin, Hiroyuki Suetsugu et al. · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
- Spatially resolved single-cell multiomics map of human trophoblast differentiation in early pregnancyAnna Arutyunyan, Kenny Roberts, Megan A. Sheridan, Ilia Kats, Luz García‐Alonso, Britta Velten, Regina Hoo, Kevin Troulé, Louis‐François Handfield, Luca Marconato et al. · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
- Matching queried single-cell open-chromatin profiles to large pools of single-cell transcriptomes and epigenomes for reference supported analysisShreya V. Mishra, Neetesh Pandey, Smriti Chawla, Madhu Sharma, Omkar Chandra, Indra Prakash Jha, Debarka Sengupta, Kedar Nath Natarajan, Vibhor Kumar · 2023 · Genome Research
- Going beyond cell clustering and feature aggregation: Is there single cell level information in single-cell ATAC-seq data?Aaron Wing Cheung Kwok, Heejung Shim, Davis James McCarthy · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
- Principled PCA separates signal from noise in omics count dataJay S. Stanley, Junchen Yang, Ruiqi Li, Ofir Lindenbaum, Dmitry Kobak, Boris Landa, Yuval Kluger · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
- Evolutionary transfer learning enables organism-wide inference of mammalian enhancer landscapesChengxiang Qiu, Riza M. Daza, Ian C. Welsh, Rupali P Patwardhan, Beth K. Martin, Tony W. Li, Shizhao Yang, Camiel C. A. Mannens, Seppe De Winter, Niklas Kempynck et al. · 2026
- SCITUNA: single-cell data integration tool using network alignmentAissa Houdjedj, Yacine Marouf, Mekan Myradov, Süleyman Onur Doğan, Burak Onur Erten, Öznur Taştan, Cesim Erten, Hilal Kazan · 2025 · BMC Bioinformatics
- Discovery of oligodendrocyte enhancers that regulate Sox10 expressionHongjoo An, Chuandong Fan, Dongkyeong Kim, Huy Bui, Yungki Park · 2025 · PLoS Genetics
- RelA Inhibits Embryonic Myogenesis by Coordinately Regulating a Novel Distal Enhancer of MyogeninMd Nazmul Hossain, Yao Gao, Sharmeen Islam, Li‐Wei Chen, Xinrui Li, Zhongyun Kou, Nathan C. Law, Jeanene Marie de Avila, Meijun J. Zhu, Min Du · 2025 · Advanced Science
- The Catsper3 promoter activity is regulated by the cAMP-Response Element Modulator tau (CREMτ) and the cAMP-Response Element Binding protein 1A (CREBA) transcription factorsDiego Eduardo Sánchez‐Jasso, Sergio Federico López‐Guzmán, Javier Hernández‐Sánchez, Rosa María Bermúdez‐Cruz, Norma Oviedo · 2025 · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms
- ArchVelo: archetypal velocity modeling for single-cell multi-omic trajectoriesMaria Avdeeva, Sarah K. Walker, Joris van der Veeken, Alexander Yu Rudensky, Yuri Pritykin · 2026 · Nature Communications
- How structural variation shapes the cancer epigenomeSigne MacLennan, Marco A. Marra · 2025 · Trends in cancer
- Branch-specific gene discovery in cell differentiation using multi-omics graph attentionYihao Yin, Linzhi Zhuang, Yulei Wang, Ya-Zhou Shi, Bengong Zhang · 2025 · PLoS Computational Biology
- Multimodal single cell analyses reveal gene networks of planarian stem cell differentiationAlberto Pérez-Posada, Helena García-Castro, Elena Emili, Anna Guixeras-Fontana, Virginia Vanni, David A. Salamanca-Díaz, Cirenia Arias-Baldrich, Siebren Frölich, Simon J. van Heeringen, Francesc Cebrià et al. · 2025 · Nature Communications
- MAPK14 converges on key transcriptional machinery to promote vascular smooth muscle cell degeneration in abdominal aortic aneurysmXiaoliang Wu, Chunhui Wang, Nestor Ishimwe, Wei Zhang, Jaser Doja, Shengshuai Shan, Chunyu Ge, Yong Sun, Jinjing Zhao, Micah B. Castillo et al. · 2026 · Signal Transduction and Targeted Therapy
- Single-nucleus multiple-organ chromatin accessibility landscape in the adult ratRonghai Li, Shanshan Duan, Qiuting Deng, Wen Ma, Chang Liu, Peng Gao, Lu Li, Yue Yuan · 2026 · GigaScience
- Chromatin accessibility landscapes define stromal cell identities across tissuesAmin Nooranikhojasteh, Ghazaleh Tavallaee, Nicholas Khuu, Shu Yi Shen, Shaida Ouladan, Ayush Raman, Elias Orouji · 2026 · Communications Biology
- EWS::WT1 isoform-dependent regulation of neogenes in desmoplastic small round cell tumorsDanh D. Truong, Justin W. Magrath, Kevin A. Murgas, Jiaqian Fan, Diana D. Shamsutdinova, Davis Ingram, Khalida Wani, Alexander J. Lazar, Sean Bong Lee, Joseph Aloysius Ludwig · 2026 · Communications Biology
- Advances in single-cell epigenomics of the immune systemJonas Schulte-Schrepping, Humberto J. Ferreira, Adem Saglam, Emily R. Hinkley, Joachim Ludwig Schultze · 2020 · Elsevier eBooks
- Destin2: Integrative and cross-modality analysis of single-cell chromatin accessibility dataPeter Yi Guan, Jin Seok Lee, Lihao Wang, Kevin Lin, Wenwen Mei, Li Chen, Yuchao Jiang · 2023 · Frontiers in Genetics
- Single-cell protein-DNA interactomics and multiomics tools for deciphering genome regulationHaiqing Xiong, Runyu Wang, Aibin He · 2023 · National Science Open
- Single-cell chromatin accessibility profiling of cell-state-specific gene regulatory programs during mouse organogenesisQiuting Deng, Shengpeng Wang, Zijie Huang, Qing Lan, Guangyao Lai, Jiangshan Xu, Yue Yuan, Chang Xin Liu, Xiumei Lin, Weimin Feng et al. · 2023 · Frontiers in Neuroscience
- Gene-regulation modules in nonalcoholic fatty liver disease revealed by single-nucleus ATAC-seqFumihiko Takeuchi, Yi-Qiang Liang, Hana Shimizu-Furusawa, Masato Isono, Mia Yang Ang, Kotaro Mori, Taizo Mori, Eiji Kakazu, Sachiyo Yoshio, Norihiro Kato · 2023 · Life Science Alliance
- scPipe: an extended preprocessing pipeline for comprehensive single-cell ATAC-Seq data integration in R/BioconductorShanika L. Amarasinghe, Phil Yang, Oliver Voogd, Haoyu Yang, Mei R. M. Du, Shian Su, Daniel V. Brown, Jafar S. Jabbari, Rory J. Bowden, Matthew E. Ritchie · 2023 · NAR Genomics and Bioinformatics
- Understanding single-cell multi-omics for high resolution cellular interactome mappingShubham Joshi, Anita Kumari, Rohit Joshi · 2025 · Elsevier eBooks
- scCorrect: Cross-modality label transfer from scRNA-seq to scATAC-seq using domain adaptationYan Liu, Wenyi Pei, Li Chen, Yu Xia, He Yan, Xiaohua Hu · 2025 · Analytical Biochemistry
- Gene2role: a role-based gene embedding method for comparative analysis of signed gene regulatory networksXin Zeng, Shu Liu, Bowen Liu, Weihang Zhang, Kang Xu, Fujio Toriumi, Kenta Nakai · 2025 · BMC Bioinformatics
- MINGLE: a mutual information-based interpretable framework for automatic cell type annotation in single-cell chromatin accessibility dataSiyu Li, Yifan Huang, Shengquan Chen · 2025 · Genome biology
- Multimodal-based analysis of single-cell ATAC-seq data enables highly accurate delineation of clinically relevant tumor cell subpopulationsKewei Xiong, Wei Wang, Ruofan Ding, Dinglin Luo, Yangmei Qin, Xudong Zou, Jiguang Wang, Chen Yu, Lei Li · 2026 · Genome Medicine
- Longitudinal analysis of body weight reveals homeostatic and adaptive traits linked to lifespan in diversity outbred miceG.V. Prateek, Zhenghao Chen, Kevin M. Wright, Andrea Di Francesco, Vladimir Jojic, Gary A. Churchill, Anil Raj · 2026 · Nature Communications
- Single-cell spatial map of cis-regulatory elements for disease-related genes in the macaque cortexJuan Meng, Cheng Chen, Zhiyong Zhu, Yongkang Sun, Yiming Huang, Jiqiang Fu, Luyan Wu, Ling Li, Ling Li, Yiqin Bai et al. · 2026 · Nature Communications
- GFETM: Genome foundation-based embedded topic model for scATAC-seq modelingYimin Fan, Adrien Osakwe, Shi Han, Yu Li, Jun Ding, Yue Li · 2026 · Cell Systems
- Genetic control of tumor development in malformation syndromesFloor A.M. Postema, Jan C. Oosterwijk, Raoul C. M. Hennekam · 2020 · American Journal of Medical Genetics Part A
- FITs: forest of imputation trees for recovering true signals in single-cell open chromatin profilesRachesh Sharma, Neetesh Pandey, Aanchal Mongia, Shreya V. Mishra, Angshul Majumdar, Vibhor Kumar · 2020 · NAR Genomics and Bioinformatics
- Endothelial cell heterogeneity and plasticity in health and disease—new insights from single-cell studiesLisa M. Becker, Alessandra Pasut, Anne Cuypers, Peter Carmeliet · 2022 · Elsevier eBooks
- HDAC inhibitors: A novel approach to hyperglycaemia management and treatmentMonapati Suchitra, Praveen Kumar Kusuma, Manjunatha S. Katagi, G. Venkateswarlu, Palani Mahalakshmi · 2023 · Health Sciences Review
- Expanding the single-cell genomics toolkitAnna Minkina, Jay Shendure · 2019 · Nature Genetics
- Tree-Based Co-Clustering Identifies Chromatin Accessibility Patterns Associated With Hematopoietic Lineage StructureThomas B. George, Nathaniel K. Strawn, Sivan Leviyang · 2021 · Frontiers in Genetics