The evolving concept of cell identity in the single cell era
Morris, Samantha A.·2019·Development
Cited by (153)
Items 101–153 of 153
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- Controlling cellular plasticity to improve in vitro models for kidney regenerationCarla Pou Casellas, Maarten B. Rookmaaker, Marianne Christina Verhaar · 2021 · Current Opinion in Biomedical Engineering
- Artificial Neural Networks for classification of single cell gene expressionJiahui Zhong, Minjie Lyu, Huan Jin, Zhiwei Cao, Lou T. Chitkushev, Guanglan Zhang, Derin B. Keskin, Vladimir Brusić · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
- H3.1 Cys96 oxidation by mitochondrial ROS promotes chromatin remodeling, breast cancer progression to metastasis and multi-drug resistanceFlávio Romero Palma, Fernando Toshio Ogata, Diego Rodrigues Coelho, Kirthi Pulakanti, Alison E. Meyer, Yunping Huang, Jeanne M. Danes, Matthew John Schipma, Cristina M. Furdui, Douglas R. Spitz et al. · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
- Unveiling stem cell induction mechanisms from spatiotemporal cell-type-specific gene regulatory networks in postembryonic root organogensisJavier Cabrera, Álvaro Sánchez-Corrionero, Angels de Luis Balaguer, Laura Serrano-Ron, Cristina del Barrio, Pilar Cubas, Pablo Pérez-García, Rosangela Sozzani, Miguel Á. Moreno-Risueno · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
- Divergence in cellular markers observed in single-cell transcriptomics datasets between cultured primary trabecular meshwork cells and tissuesAlice Tian, Sangbae Kim, Hasna Baidouri, Jin Li, Xuesen Cheng, Janice A. Vranka, Yumei Li, Rui Chen, Vijay Krishna Raghunathan · 2025 · Scientific Data
- Homebuilt Imaging-Based Spatial Transcriptomics: Tertiary Lymphoid Structures as a Case ExampleThomas Defard, Auxence Desrentes, Charles Fouillade, Florian Mueller · 2024 · Methods in molecular biology
- Diversification of dentate gyrus granule cell subtypes is regulated by Nrg1 nuclear back-signalingPrithviraj Rajebhosale, Li Jiang, Haylee J. Ressa, Kory R. Johnson, Niraj S. Desai, Alice Jone, Lorna W. Role, David A. Talmage · 2025 · Life Science Alliance
- Research advances in Raman imaging of single-cell phenotypes in fatty acid metabolism in cancersNing Xu, Saisai Yang, Qiwen Shi, Damei Sun, Hongwei Sun, Runa Wang, Zihang Zhou, Min Song Lin, Xiao'e Lou · 2026 · Spectrochimica Acta Part A Molecular and Biomolecular Spectroscopy
- Transitional cell states at the crossroads of development, disease, and repair-regenerationXiangyi Ke, Wellington Veras Cardoso · 2026 · Physiological Reviews
- Hooked hairs: A cellular key adaptation aiding seedling survival in nutrient-limited and drought conditionsSergio Alan Cervantes-Pérez, Ankita Roy, Addison K. Bralick, Peter Pietrzyk, Sandra Thibivilliers, Marc Libault, Alexander Bucksch · 2026 · Science Advances
- Protocol for Classification Single-Cell PBMC Types from Pathological Samples Using Supervised Machine LearningMinjie Lyu, Lin Xin, Huan Jin, Lou T. Chitkushev, Guanglan Zhang, Derin B. Keskin, Vladimir Brusić · 2023 · Methods in molecular biology
- Understanding Spondyloarthritis Pathogenesis: The Promise of Single-Cell ProfilingJoerg Ermann, Micah Lefton, Kevin S. Wei, María Gutiérrez‐Arcelus · 2024 · Current Rheumatology Reports
- Identification of type 2 diabetes- and obesity-associated human β-cells using deep transfer learningGitanjali Roy, Rameesha Syed, Olivia Lazaro, Sylvia Robertson, Sean McCabe, Daniela Rodriguez, Alex M. Mawla, Travis S. Johnson, Michael A. Kalwat · 2025 · eLife
- Endocrinology of a Single Cell: Tools and InsightsHanna Pinças, Frederique Murielle Ruf-Zamojski, Judith L. Turgeon, Stuart C. Sealfon · 2021 · Elsevier eBooks
- Cell Fate Analysis and Machine LearningShyamasree Ghosh, Rathi Dasgupta · 2022 · Springer eBooks
- Two distinct waves of transcriptome and translatome remodelling drive germline stem cell differentiationTamsin J. Samuels, Jinghua Gui, Daniel Gebert, Felipe Karam Teixeira · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
- Identification of type 2 diabetes- and obesity-associated human β-cells using deep transfer learningGitanjali Roy, Rameesha Syed, Olivia Lazaro, Sylvia Robertson, Sean McCabe, Daniela Rodriguez, Alex M. Mawla, Travis S. Johnson, Michael A. Kalwat · 2024 · eLife
- A DIY guide for image-based spatial transcriptomic: TLS as a case exampleThomas Defard, Auxence Desrentes, Charles Fouillade, Florian Mueller · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
- Hybrid Clustering of single-cell gene expression and cell spatial information via integrated NMF and k-meansSooyoun Oh, Haesun Park, Xiuwei Zhang · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
- Fostering a concept: Why cell identity mattersMihail Eugen Hinescu · 2020 · Journal of Cell Identity
- Single cell genomics for cellular phenotyping: applications in brain disorderAurora Arghir, Sorin Mihaela Papuc, Kenneth S. Kosik, Magdalena Budișteanu · 2020 · Journal of Cell Identity
- Assessment and Optimization of the Interpretability of Machine Learning Models Applied to Transcriptomic DataYongbing Zhao, Jinfeng Shao, Yan W. Asmann · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
- Activated-memory T cells influence naive T cell fate: A novel non-cytotoxic function of human CD8 T cellsKazuki Saski, Mouhamad Al Moussawy, Khodor I. Abou‐Daya, Camila Macedo, Amira Hosni-Ahmed, Silvia Liu, Mariam Juya, Alan F. Zahorchak, Diana Metes, Angus W. Thomson et al. · 2022 · Research Square
- Editorial: Machine Learning and Mathematical Models for Single-Cell Data AnalysisLe Ou-Yang, Xiao-Fei Zhang, Jiajun Zhang, Jin Chen, Min Wu · 2022 · Frontiers in Genetics
- Unraveling new mechanisms of postembryonic organ formation in Arabidopsis thaliana roots through computational and in vivo approachesLaura Serrano Ron · 2022
- Understanding Cell Differentiation Through Single-Cell Approaches: Conceptual Challenges of the Systemic ApproachLaëtitia Racine, Andràs Páldi · 2023 · Methods in molecular biology
- Glial Phenotype PlasticityWolfgang Walz · 2023 · Springer eBooks
- Author response: Identification of type 2 diabetes- and obesity-associated human β-cells using deep transfer learningGitanjali Roy, Rameesha Syed, Olivia Lazaro, Sylvia Robertson, Sean McCabe, Daniela Rodriguez, Alex M. Mawla, Travis S. Johnson, Michael A. Kalwat · 2024 · eLife
- Identification of type 2 diabetes- and obesity-associated human β-cells using deep transfer learningGitanjali Roy, Rameesha Syed, Olivia Lazaro, Sylvia Robertson, Sean McCabe, Daniela Rodriguez, Alex M. Mawla, Travis S. Johnson, Michael A. Kalwat · 2024 · eLife
- Reviewer #1 (Public Review): Identification of type 2 diabetes- and obesity-associated human β-cells using deep transfer learningGitanjali Roy, Rameesha Syed, Olivia Lazaro · 2024 · eLife
- eLife Assessment: Identification of type 2 diabetes- and obesity-associated human β-cells using deep transfer learningLori Sussel · 2024 · eLife
- Subcellular Region Morphology Reflects Cellular IdentityÁngel Román, Alba Díaz-Pizarro, Nuria Del Valle-Del Pino, Marcos Olivera-Gómez, Guadalupe Cumplido-Laso, Dixan A. Benitez, José María Carvajal-González, Sonia Mulero‐Navarro · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
- Contrastive Poincaré Maps: uncovering developmental lineages from single-cell data with scalable hyperbolic embeddingsNithya Bhasker, Hattie Chung, Louis Boucherie, Vladislav Kim, Stefanie Speidel, Melanie Weber · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
- Identification of type 2 diabetes- and obesity-associated human β-cells using deep transfer learningGitanjali Roy, Rameesha Syed, Olivia Lazaro, Sylvia Robertson, Sean McCabe, Daniela Rodriguez, Alex M. Mawla, Travis S. Johnson, Michael A. Kalwat · 2025 · eLife
- Rapid canalization of chromosome conformation-transcription fingerprints during embryogenesis revealed by fully-automated cell identity decoding with CeSCALEΚωνσταντίνος Ντέμος, Fei Xu, Nour-Zaynab Bazzi, Geoffrey Fucile, Hermina Petric Maretić, Ivan Dokmanić, Susan E. Mango, Ahilya N. Sawh · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
- Living Organs as Micro‐Factories: Material‐Producing OrganoidsQuentin Moana Perrin, Ali Miserez · 2026 · Wiley Interdisciplinary Reviews Nanomedicine and Nanobiotechnology
- MOSAIC: A Structured Multi-level Framework for Probabilistic and Interpretable Cell-type AnnotationMingyu Yang, Jing Qi, Minwen Lan, Jun Huang, Shuilin Jin · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
- Exploring cell diversity and fidelity in crustacean limb regeneration using single-nucleus RNA sequencingAlba Almazán · 2022
- Epigenetic characterization of cellular pliancy in breast cancerRahma Benhassoun · 2024 · theses.fr (ABES)
- Developmental stage dominates cell-type identity and reveals a chromatin regulatory function for Rad50 in DrosophilaThomas Boutet, Rosy Sakr, Marta Marzullo, Manisha Goyal, Pierre B. Cattenoz, Laura Ciapponi, Tina Mukherjee, Angela Giangrande · 2026 · Nucleic Acids Research
- Mechanisms of Cell Plasticity during Injury-Induced Epithelial ReprogrammingEvelyn Mazzarelli, Sara Lovisa · 2026 · Cells Tissues Organs
- Identity crisis: exploring the boundaries of cell type identification in the age of single-cell transcriptomicsSeulkee Yang, Sudeeksha Tyagi, Christian Rosenmund, Melissa A. Herman · 2026 · Frontiers in Cellular Neuroscience
- Single-cell chromatin landscapes visualize epigenetic barriers and reveal lineage-specific Polycomb-mediated repressionСергей Анатольевич Пирогов, Aleksander Purik, Artem Ilin, Jose Ramon Barcenas-Walls, Marek Bartošovič, Mattias Mannervik · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
- scFiLM: Dynamic Fusion of Gene Identity and Expression for Single-Cell AnalysisXingze Li, Xinghai Zeng, Tao Tang, Yingbo Cui · 2026 · Communications in computer and information science
- Cell-autonomous immunity model of aging and diseaseFei Wu, Daniel A. Winer, David Furman · 2026 · Trends Open
- Deep Mechanistic Models reveal pathway-extrinsic drivers of mammary MAPK signalling heterogeneityGiacomo Fabrini, Fabian Fröhlich · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
- Mural Lymphatic Endothelial Cells at CNS Borders: Endothelial Heterogeneity, Functional Specialization, and Cross-Species PerspectivesJunxiang Xu, Yijin Chang, Jiahao Lu, Dong Liu, Changsheng Chen · 2026 · Biology
- Analysis of Chromatin Structure Using Network Approaches: A Step-by-Step GuideBenoît Aliaga, Flavien Raynal, Véra Pancaldi · 2026 · Methods in molecular biology
- Quiescence as an Active and Dynamic Regulator of Neural Stem Cells in Adult Olfactory NeurogenesisJosé Manuel Morante‐Redolat, Isabel Fariñas · 2026 · European Journal of Neuroscience
- In Vivo Direct Reprogramming: Current Progress and Future Prospects from Mechanisms to Therapeutic ApplicationRishabh Deo Singh, Mauro Calvoli, Kyeong Kyu Kim · 2026 · Advanced Science
- Dynamic Modulation of Neural Cell Identity Maintenance via Lysine Acetyltransferase Type 3 Protein Targeted DegradationJuan Zaragoza-Lillo, Sergio Niñerola, Verónica Estefania Andrade-Montero, Francisco José López-Murcia, Tania López-Hernández, Ángel Barco, Rafael Alcalá‐Vida · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
- Defining early human developmental identity: A curated, cross-platform marker frameworkJochen Dobner, Alessandro Prigione, Andrea Rossi · 2026 · Stem Cell Reports