Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors
DOI 10.1038/nbt.4091
Cited by (1,014)
Items 301–400 of 1,014
- Reticular Fibroblasts Expressing the Transcription Factor WT1 Define a Stromal Niche that Maintains and Replenishes Splenic Red Pulp MacrophagesAlicia Bellomo, Isabelle Mondor, Lionel Spinelli, Marine Lagueyrie, Benjamin J. Stewart, Nicolas Brouilly, Bernard MALISSEN, Menna Ruth Clatworthy, Marc Bajénoff · 2020 · Immunity
- A unified computational framework for single-cell data integration with optimal transportKai Cao, Qiyu Gong, Yiguang Hong, Lin Wan · 2022 · Nature Communications
- Molecular mechanisms of lineage decisions in metabolite-specific T cellsFrancois P. Legoux, Jules Gilet, Emanuele Procopio, Klára Echasserieau, Karine Bernardeau, Olivier J Lantz · 2019 · Nature Immunology
- Deep generative model embedding of single-cell RNA-Seq profiles on hyperspheres and hyperbolic spacesJiarui Ding, Aviv Regev · 2021 · Nature Communications
- Manifold alignment for heterogeneous single-cell multi-omics data integration using PamonaKai Cao, Yiguang Hong, Lin Wan · 2021 · Bioinformatics
- A joint model of unpaired data from scRNA-seq and spatial transcriptomics for imputing missing gene expression measurementsLopez, Romain, Nazaret, Achille, Langevin, Maxime, Samaran, Jules, Regier, Jeffrey, Jordan, Michael I., Yosef, Nir · 2019 · arXiv
- Generative modeling of single-cell time series with PRESCIENT enables prediction of cell trajectories with interventionsYeo, Grace Hui Ting, Saksena, Sachit D., Gifford, David K. · 2021 · Nature Communications
- JAK–STAT Signaling in Inflammatory Breast Cancer Enables Chemotherapy-Resistant Cell StatesLaura E. Stevens, Guillermo Peluffo, Xintao Qiu, Daniel Temko, Anne Fassl, Zheqi Li, Anne C. Trinh, Marco Seehawer, Bojana Jovanović, Maša Alečković et al. · 2022 · Cancer Research
- Cellular plasticity balances the metabolic and proliferation dynamics of a regenerating liverChembazhi, Ullas V., Bangru, Sushant, Hernaez, Mikel, Kalsotra, Auinash · 2021 · Genome Research
- Presence of onco-fetal neighborhoods in hepatocellular carcinoma is associated with relapse and response to immunotherapyZiyi Li, Rhea Pai, Saurabh Gupta, Jennifer Currenti, Wei Guo, Anna Di Bartolomeo, Hao Feng, Zijie Zhang, Zhizhen Li, Longqi Liu et al. · 2024 · Nature Cancer
- Benchmarking clustering, alignment, and integration methods for spatial transcriptomicsYunfei Hu, Yikang Li, Manfei Xie, Mingxing Rao, Wenjun Shen, Can Luo, Haoran Qin, Jihoon Baek, Xin Zhou · 2024 · Genome biology
- scAlign: a tool for alignment, integration, and rare cell identification from scRNA-seq dataNelson Johansen, Gerald Quon · 2019 · Genome biology
- Cross-Species Analysis of Single-Cell Transcriptomic DataMaxwell E. R. Shafer · 2019 · Frontiers in Cell and Developmental Biology
- Single-cell transcriptomic analysis of endometriosis provides insights into fibroblast fates and immune cell heterogeneityJunyan Ma, Liqi Zhang, Hong Zhan, Yun Mo, Zuanjie Ren, Anwen Shao, Jun Lin · 2021 · Cell & Bioscience
- Modeling idiopathic autism in forebrain organoids reveals an imbalance of excitatory cortical neuron subtypes during early neurogenesisAlexandre Jourdon, Feinan Wu, Jessica Mariani, Davide Capauto, Scott Norton, Livia Tomasini, Anahita Amiri, Milovan Šuvakov, Jeremy D. Schreiner, Yeongjun Jang et al. · 2023 · Nature Neuroscience
- Spatiotemporal transcriptomic maps of whole mouse embryos at the onset of organogenesisAbhishek Sampath Kumar, Luyi Tian, Adriano Bolondi, Amèlia Aragonés Hernández, Robert R. Stickels, Helene Kretzmer, Evan M. Murray, Lars Wittler, Maria Walther, Gabriel Barakat et al. · 2023 · Nature Genetics
- A spatial human thymus cell atlas mapped to a continuous tissue axisNadav Yayon, Veronika R. Kedlian, Lena Boehme, Chenqu Suo, Brianna T. Wachter, Rebecca T. Beuschel, Oren Amsalem, Krzysztof Polański, Simon Koplev, Elizabeth J. Tuck et al. · 2024 · Nature
- Single-cell multi-omics in cancer immunotherapy: from tumor heterogeneity to personalized precision treatmentJiayuan Le, Yating Dian, Deze Zhao, Ziyu Guo, Zehao Luo, Xiang Chen, Furong Zeng, Guangtong Deng · 2025 · Molecular Cancer
- Evaluating and minimizing batch effects in metabolomicsHan, Wei, Li, Liang · 2022 · Mass Spectrometry Reviews
- Multi-omic evaluation of metabolic alterations in multiple sclerosis identifies shifts in aromatic amino acid metabolismKathryn C. Fitzgerald, Matthew D. Smith, Sol Kim, Elias S. Sotirchos, Michael D. Kornberg, Morgan Douglas, Bardia Nourbakhsh, Jennifer Graves, Ramandeep Rattan, Laila Poisson et al. · 2021 · Cell Reports Medicine
- Guidelines for bioinformatics of single-cell sequencing data analysis in Alzheimer’s disease: review, recommendation, implementation and applicationMinghui Wang, Won‐Min Song, Ming Chen, Qian Wang, Xianxiao Zhou, Peng Xu, Azra Krek, Yonejung Yoon, Lap Ho, Miranda E. Orr et al. · 2022 · Molecular Neurodegeneration
- Online single-cell data integration through projecting heterogeneous datasets into a common cell-embedding spaceLei Xiong, Kang Tian, Yuzhe Li, Weixi Ning, Xin Gao, Qiangfeng Cliff Zhang · 2022 · Nature Communications
- Single-cell RNA-seq of cultured human adipose-derived mesenchymal stem cellsXuanyu Liu, Qinqin Xiang, Fen Xu, Jiuzuo Huang, Nanze Yu, Qixu Zhang, Xiao Long, Zhou Zhou · 2019 · Scientific Data
- Evaluation of single-cell classifiers for single-cell RNA sequencing data setsXinlei Shelly Zhao, Shuang Wu, Nan Fang, Xiao Song Sun, Jue Fan · 2019 · Briefings in Bioinformatics
- Modeling human telencephalic development and autism-associated SHANK3 deficiency using organoids generated from single neural rosettesYueqi Wang, Simone Chiola, Guang Yang, Chad Russell, Celeste J. Armstrong, Yuanyuan Wu, Jay G. Spampanato, Paisley Tarboton, H. M. Arif Ullah, Nicolas Ulrich Edgar et al. · 2022 · Nature Communications
- CellTag Indexing: genetic barcode-based sample multiplexing for single-cell genomicsChuner Guo, Wenjun Kong, Kenji Kamimoto, Guillermo C. Rivera-Gonzalez, Xue Yang, Yuhei Kirita, Samantha A. Morris · 2019 · Genome biology
- Tumor vessel co-option probed by single-cell analysisLaure-Anne Marie Nicole Teuwen, Laura P. M. H. de Rooij, Anne Cuypers, Kateřina Rohlenová, Sébastien J. Dumas, Melissa García‐Caballero, Elda Meta, Jacob Amersfoort, Federico Taverna, Lisa M. Becker et al. · 2021 · Cell Reports
- Single-nuclei transcriptomes from human adrenal gland reveal distinct cellular identities of low and high-risk neuroblastoma tumorsOscar C. Bedoya-Reina, Wenyu Li, Maria Arceo, Monika Plescher, Petra Bullova, Han‐Pin Pui, Markéta Kaucká, Peter V. Kharchenko, Tommy Martinsson, Johan Holmberg et al. · 2021 · Nature Communications
- Data analysis guidelines for single-cell RNA-seq in biomedical studies and clinical applicationsMin‐Ying Su, Tao Pan, Qiu-Zhen Chen, Weiwei Zhou, Yi Gong, Gang Xu, Huan-Yu Yan, Si Li, Qiao-Zhen Shi, Ya Zhang et al. · 2022 · Military Medical Research
- Transcriptomic evidence that von Economo neurons are regionally specialized extratelencephalic-projecting excitatory neuronsRebecca D. Hodge, Jeremy A. Miller, Mark A. Novotny, Brian E. Kalmbach, Jonathan T. Ting, Trygve E. Bakken, Brian D. Aevermann, Eliza R. Barkan, Madeline L. Berkowitz-Cerasano, Charles Cobbs et al. · 2020 · Nature Communications
- Biologically indeterminate yet ordered promiscuous gene expression in single medullary thymic epithelial cellsFatima Dhalla, Jeanette Baran‐Gale, Stefano Maio, Lia Chappell, Georg A. Holländer, Chris Paul Ponting · 2019 · The EMBO Journal
- Co-varying neighborhood analysis identifies cell populations associated with phenotypes of interest from single-cell transcriptomicsYakir Reshef, Laurie Rumker, Joyce B. Kang, Aparna Nathan, Ilya Korsunsky, Samira Asgari, Megan B. Murray, David Branch Moody, Soumya Raychaudhuri · 2021 · Nature Biotechnology
- Stabilized mosaic single-cell data integration using unshared featuresShila Ghazanfar, Carolina Guibentif, John C. Marioni · 2023 · Nature Biotechnology
- Genome-wide In Vivo CNS Screening Identifies Genes that Modify CNS Neuronal Survival and mHTT ToxicityMary H. Wertz, Mollie R. Mitchem, Sergio Sebastian Pineda, Lea J. Hachigian, Hyeseung Lee, Vanessa Lau, Alex E. Powers, Ruth Kulicke, Gurrein K. Madan, Medina Colic et al. · 2020 · Neuron
- Flexible comparison of batch correction methods for single-cell RNA-seq using BatchBenchChazarra-Gil, Ruben, van Dongen, Stijn, Kiselev, Vladimir Yu, Hemberg, Martin · 2021 · Nucleic Acids Research
- Single-Cell Transcriptional Analyses Identify Lineage-Specific Epithelial Responses to Inflammation and Metaplastic Development in the Gastric CorpusKevin A. Bockerstett, Scott A. Lewis, Christine N. Noto, Eric L. Ford, José B. Sáenz, Nicholas M. Jackson, Tae-Hyuk Ahn, Jason C. Mills, Richard J. DiPaolo · 2020 · Gastroenterology
- Single-cell multiomics reveal the scale of multilayered adaptations enabling CLL relapse during venetoclax therapyRachel Thijssen, Luyi Tian, Mary Ann Anderson, Christoffer Flensburg, Andrew Jarratt, Alexandra L. Garnham, Jafar S. Jabbari, Hongke Peng, Thomas Eliot Lew, Charis E. Teh et al. · 2022 · Blood
- Modelling viral encephalitis caused by herpes simplex virus 1 infection in cerebral organoidsAgnieszka Rybak‐Wolf, Emanuel Wyler, Tancredi Massimo Pentimalli, Ivano Legnini, Anna Oliveras, Petar Glažar, Anna Loewa, Seung Joon Kim, Benedikt B. Kaufer, Andrew Woehler et al. · 2023 · Nature Microbiology
- Serglycin secreted by late-stage nucleus pulposus cells is a biomarker of intervertebral disc degenerationFan Chen, Linchuan Lei, Shunlun Chen, Zhuoyang Zhao, Yuming Huang, Guowei Jiang, Xingyu Guo, Zemin Li, Zhaomin Zheng, Jianru Wang · 2024 · Nature Communications
- Stabilized epithelial phenotype of cancer cells in primary tumors leads to increased colonization of liver metastasis in pancreatic cancerJulienne L. Carstens, Sujuan Yang, Pedro Corrêa de Sampaio, Xiaofeng Zheng, Souptik Barua, Kathleen M. McAndrews, Arvind U.K. Rao, Jared K. Burks, Andrew D. Rhim, Raghu Kalluri · 2021 · Cell Reports
- Learning interpretable cellular and gene signature embeddings from single-cell transcriptomic dataYifan Zhao, Huiyu Cai, Zuobai Zhang, Jian Tang, Yue Li · 2021 · Nature Communications
- Modeling human multi-lineage heart field development with pluripotent stem cellsDonghe Yang, Juliana Gomez-Garcia, Shunsuke Funakoshi, Thinh Ngoc Tran, Ian M. Fernandes, Gary D. Bader, Michael A. Laflamme, Gordon M. Keller · 2022 · Cell stem cell
- Evaluating batch correction methods for image-based cell profilingArevalo, John, Su, Ellen, van Dijk, Robert, Carpenter, Anne E., Singh, Shantanu · 2023
- Self-assembling manifolds in single-cell RNA sequencing dataAlexander J. Tarashansky, Yuan Xue, Pengyang Li, Stephen R. Quake, Bo Wang · 2019 · eLife
- Computational Methods for Single-Cell RNA SequencingBrian Hie, Joshua M. Peters, Sarah K. Nyquist, Alex K. Shalek, Bonnie Berger, Bryan D. Bryson · 2020 · Annual Review of Biomedical Data Science
- Identification and characterization of cellular heterogeneity within the developing renal interstitiumAlicia R. England, Christopher P. Chaney, Amrita Das, Mohita Patel, Alicia Malewska, Daniel A. Armendariz, Gary C. Hon, Douglas W. Strand, Keri A. Drake, Thomas J. Carroll · 2020 · Development
- Evaluating batch correction methods for image-based cell profilingJohn Arévalo, Ellen Su, Jessica Ewald, Robert van Dijk, Anne Elizabeth Carpenter, Shantanu Singh · 2024 · Nature Communications
- Integrative Multi-Omics Approaches for Identifying and Characterizing Biological Elements in Crop Traits: Current Progress and Future ProspectsBing-Liang Fan, Lin-Hua Chen, Lingling Chen, Hao Guo · 2025 · International Journal of Molecular Sciences
- Resistance to PD1 blockade in the absence of metalloprotease-mediated LAG3 sheddingLawrence Peter Andrews, Ashwin Somasundaram, Jessica M. Moskovitz, Andrea L. Szymczak-Workman, Chang Liu, Anthony Richard Cillo, Lin Huang, Daniel Paul Normolle, Kelly Dare Moynihan, Ichiro Taniuchi et al. · 2020 · Science Immunology
- Mapping human cell phenotypes to genotypes with single-cell genomicsJ. Gray Camp, Randall J. Platt, Barbara Treutlein · 2019 · Science
- Single-Cell Transcriptomics Reveals Early Emergence of Liver Parenchymal and Non-parenchymal Cell LineagesLotto, Jeremy, Drissler, Sibyl, Cullum, Rebecca, Wei, Wei, Setty, Manu, Bell, Erin M., Boutet, Stéphane C., Nowotschin, Sonja, Kuo, Ying-Yi, Garg, Vidur et al. · 2020 · Cell
- Large-scale reconstruction of cell lineages using single-cell readout of transcriptomes and CRISPR–Cas9 barcodes by scGESTALTBushra Raj, James A. Gagnon, Alexander F. Schier · 2018 · Nature Protocols
- Tempora: Cell trajectory inference using time-series single-cell RNA sequencing dataThinh Ngoc Tran, Gary D. Bader · 2020 · PLoS Computational Biology
- Time-resolved single-cell analysis of Brca1 associated mammary tumourigenesis reveals aberrant differentiation of luminal progenitorsKarsten Bach, Sara Pensa, Marija Zarocsinceva, Katarzyna Kania, Julie Stockis, Silvain Pinaud, Kyren A. Lazarus, Mona Shehata, Bruno M. Simões, Alice Greenhalgh et al. · 2021 · Nature Communications
- Single-cell and single-nucleus RNA-seq uncovers shared and distinct axes of variation in dorsal LGN neurons in mice, non-human primates, and humansTrygve E. Bakken, Cindy T. J. van Velthoven, Vilas Menon, Rebecca D. Hodge, Zizhen Yao, Thuc Nghi Nguyen, Lucas T. Graybuck, Gregory D. Horwitz, Darren Bertagnolli, Jeff Goldy et al. · 2021 · eLife
- Single-Cell RNA Sequencing Unifies Developmental Programs of Esophageal and Gastric Intestinal MetaplasiaKarol Nowicki-Osuch, Lizhe Zhuang, Tik Shing Cheung, Emily L. Black, Neus Masqué‐Soler, Ginny Devonshire, Aisling M. Redmond, Adam Freeman, Massimilliano di Pietro, Nastazja Pilonis et al. · 2023 · Cancer Discovery
- Distinct human Langerhans cell subsets orchestrate reciprocal functions and require different developmental regulationXiaochun Liu, Ronghui Zhu, Yang Luo, Shangshang Wang, Yi Zhao, Zhuoqiong Qiu, Yu Xin Zhang, Xiao Liu, Xu Yao, Xiao Li et al. · 2021 · Immunity
- Clustering by measuring local direction centrality for data with heterogeneous density and weak connectivityDehua Peng, Zhipeng Gui, Dehe Wang, Yuncheng Ma, Zichen Huang, Yu Zhou, Huayi Wu · 2022 · Nature Communications
- scCross: a deep generative model for unifying single-cell multi-omics with seamless integration, cross-modal generation, and in silico explorationXiuhui Yang, Koren Kathleen Mann, Hao Wu, Jun Ding · 2024 · Genome biology
- Single-cell analysis of mosquito hemocytes identifies signatures of immune cell subtypes and cell differentiationHyeogsun Kwon, Mubasher Mohammed, Oscar Franzén, Johan Ankarklev, Ryan C. Smith · 2021 · eLife
- Developmental landscape of human forebrain at a single-cell level identifies early waves of oligodendrogenesisDavid van Bruggen, Fabio Baldivia Pohl, Christoffer Mattsson Langseth, Petra Kukanja, Hower Lee, Alejandro Mossi Albiach, Mukund Kabbe, Mandy Meijer, Sten Linnarsson, Markus M. Hilscher et al. · 2022 · Developmental Cell
- Retinoic acid signaling is critical during the totipotency window in early mammalian developmentAne Iturbide, Mayra L. Ruiz Tejada Segura, Camille Noll, Kenji Schorpp, Ina Rothenaigner, Elias R. Ruiz-Morales, Gabriele Lubatti, Ahmed Agami, Kamyar Hadian, Antonio Scialdone et al. · 2021 · Nature Structural & Molecular Biology
- Single-Cell Analysis Reveals Distinct Immune and Smooth Muscle Cell Populations that Contribute to Chronic Thromboembolic Pulmonary HypertensionGayathri Viswanathan, Hèléne Fradin, Nour Nazo, Saba Ali, Asvin M. Ganapathi, Ian Cumming, Yonghua Zhuang, Issac Choi, Anmol Warman, Chanpreet Jassal et al. · 2023 · American Journal of Respiratory and Critical Care Medicine
- Molecular programs of regional specification and neural stem cell fate progression in macaque telencephalonNicola Micali, Shaojie Ma, Mingfeng Li, Suel–Kee Kim, Xoel Mato-Blanco, Suvimal Kumar Sindhu, Jon I. Arellano, Tianliuyun Gao, Mikihito Shibata, Kevin T. Gobeske et al. · 2023 · Science
- The implications of single-cell RNA-seq analysis in prostate cancer: unraveling tumor heterogeneity, therapeutic implications and pathways towards personalized therapyDechao Feng, Weizhen Zhu, Jie Wang, Dengxiong Li, Xu Shi, Qiao Xiong, Jia You, Ping Han, Shi Qiu, Qiang Wei et al. · 2024 · Military Medical Research
- Heterogeneity in endothelial cells and widespread venous arterialization during early vascular development in mammalsSiyuan Hou, Zongcheng Li, Ji Dong, Yun Gao, Zhilin Chang, Xiaochen Ding, Shuaili Li, Yunqiao Li, Yang Zeng, Xin Qian et al. · 2022 · Cell Research
- scDART: integrating unmatched scRNA-seq and scATAC-seq data and learning cross-modality relationship simultaneouslyZiqi Zhang, Chengkai Yang, Xiuwei Zhang · 2022 · Genome biology
- Multimodal single cell data integration challenge: results and lessons learnedLance, Christopher, Luecken, Malte D., Burkhardt, Daniel B., Cannoodt, Robrecht, Rautenstrauch, Pia, Laddach, Anna, Ubingazhibov, Aidyn, Cao, Zhi-Jie, Deng, Kaiwen, Khan, Sumeer et al. · 2022
- Targeting the Siglec–sialic acid axis promotes antitumor immune responses in preclinical models of glioblastomaPhilip Schmassmann, Julien Roux, Alicia Buck, Nazanin Tatari, Sabrina A. Hogan, Jinyu Wang, Natália Rodrigues Mantuano, Ronja Wieboldt, Sohyon Lee, Berend Snijder et al. · 2023 · Science Translational Medicine
- Microglia protect against age-associated brain pathologiesDavid A. D. Munro, Nadine Bestard-Cuche, Conor McQuaid, Audrey Chagnot, Sepideh Kiani Shabestari, Jean Paul Chadarevian, Upasana Maheshwari, Stefan Szymkowiak, Kim Morris, Mehreen Mohammad et al. · 2024 · Neuron
- Deep learning in single-cell and spatial transcriptomics data analysis: advances and challenges from a data science perspectiveShuang Ge, Shuqing Sun, Huan Xu, Qiang Shawn Cheng, Zhixiang Ren · 2025 · Briefings in Bioinformatics
- Single-cell sequencing and its applications in head and neck cancerZongtai Qi, Thomas F. Barrett, Anuraag S. Parikh, Itay Tirosh, Sidharth V. Puram · 2019 · Oral Oncology
- A fibroblast-dependent TGF-β1/sFRP2 noncanonical Wnt signaling axis promotes epithelial metaplasia in idiopathic pulmonary fibrosisMax Cohen, Alexis N. Brumwell, Tsung Che Ho, Kiana Garakani, Genevieve Montas, Darren Leong, Vivianne W. Ding, Jeffrey Alan Golden, Binh N. Trinh, David M. Jablons et al. · 2024 · Journal of Clinical Investigation
- Single-cell omics: experimental workflow, data analyses and applicationsFengying Sun, Haoyan Li, Dongqing Sun, Shaliu Fu, Lei Gu, Xin Shao, Qinqin Wang, Xin Dong, Bin Duan, Feiyang Xing et al. · 2024 · Science China Life Sciences
- Single-cell genomics to guide human stem cell and tissue engineeringJ. Gray Camp, Damian Wollny, Barbara Treutlein · 2018 · Nature Methods
- Coordinated changes in gene expression kinetics underlie both mouse and human erythroid maturationBarile, Melania, Imaz-Rosshandler, Ivan, Inzani, Isabella, Ghazanfar, Shila, Nichols, Jennifer, Marioni, John C., Guibentif, Carolina, Göttgens, Berthold · 2021 · Genome Biology
- A novel approach to remove the batch effect of single-cell dataFeng Zhang, Yu Wu, Weidong Tian · 2019 · Cell Discovery
- Batch alignment of single-cell transcriptomics data using deep metric learningXiaokang Yu, Xinyi Xu, Jingxiao Zhang, Xiangjie Li · 2023 · Nature Communications
- Single-cell resolution characterization of myeloid-derived cell states with implication in cancer outcomeGabriela Rapozo Guimarães, Giovanna Resk Maklouf, Cristiane Esteves Teixeira, Leandro de Oliveira Santos, Nayara Gusmão Tessarollo, Nayara Evelin de Toledo, Alessandra Freitas Serain, Cristóvão Antunes de Lanna, Marco Antônio M. Pretti, Jéssica Gonçalves Vieira da Cruz et al. · 2024 · Nature Communications
- scID Uses Discriminant Analysis to Identify Transcriptionally Equivalent Cell Types across Single-Cell RNA-Seq Data with Batch EffectKaterina Boufea, Sohan Seth, Nizar N. Batada · 2020 · iScience
- Computational methods for the integrative analysis of single-cell dataForcato, Mattia, Romano, Oriana, Bicciato, Silvio · 2021 · Briefings in Bioinformatics
- cellHarmony: cell-level matching and holistic comparison of single-cell transcriptomesDePasquale, Erica A K, Schnell, Daniel, Dexheimer, Phillip, Ferchen, Kyle, Hay, Stuart, Chetal, Kashish, Valiente-Alandí, Íñigo, Blaxall, Burns C, Grimes, H Leighton, Salomonis, Nathan · 2019 · Nucleic Acids Research
- An Integrated Epigenomic and Transcriptomic Map of Mouse and Human αβ T Cell DevelopmentLaura B. Chopp, Vishaka Gopalan, Thomas Ciucci, Allison J. Ruchinskas, Zachary Rae, Manon Lagarde, Yayi Gao, Caiyi Li, Marita Bosticardo, Francesca Pala et al. · 2020 · Immunity
- A time- and single-cell-resolved model of murine bone marrow hematopoiesisIwo Kuciński, Joana Campos, Melania Barile, Francesco Severi, Natacha Bohin, Pedro Nuno Moreira, Lewis Allen, Hannah Lawson, Myriam Luydmila Rachelle Haltalli, Sarah Kinston et al. · 2024 · Cell stem cell
- High‐throughput, microscope‐based sorting to dissect cellular heterogeneityNicholas Hasle, Anthony Cooke, Sanjay R Srivatsan, Heather Z Huang, Jason J. Stephany, Zachary Krieger, Dana L. Jackson, Weiliang Tang, Sriram Pendyala, Raymond J. Monnat et al. · 2020 · Molecular Systems Biology
- Single‐cell transcriptomes reveal heterogeneity of high‐grade serous ovarian carcinomaQian Hao, Jiajia Li, Qinghua Zhang, Fei Xu, Bangxiang Xie, Hua Lu, Xiaohua Wu, Xiang Yu Zhou · 2021 · Clinical and Translational Medicine
- Deciphering endothelial heterogeneity in health and disease at single-cell resolution: progress and perspectivesLisa M. Becker, Shiau-Haln Chen, Julie Rodor, Laura P. M. H. de Rooij, Andrew Howard Baker, Peter Carmeliet · 2022 · Cardiovascular Research
- Placental cell type deconvolution reveals that cell proportions drive preeclampsia gene expression differencesKyle A. Campbell, Justin A. Colacino, Muraly Puttabyatappa, John Dou, Elana R. Elkin, Saher Sue Hammoud, Steven E. Domino, Dana C. Dolinoy, Jaclyn M. Goodrich, Rita Karen Loch-Caruso et al. · 2023 · Communications Biology
- Benchmarking integration of single-cell differential expressionNguyen Cao Truong Hai, Bukyung Baik, Sora Yoon, Taesung Park, Dougu Nam · 2023 · Nature Communications
- Probabilistic Harmonization and Annotation of Single-cell Transcriptomics Data with Deep Generative ModelsChenling A. Xu, Romain Lopez, Edouard Mehlman, Jeffrey Regier, Michael I. Jordan, Nir Yosef · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
- BBrowser: Making single-cell data easily accessibleTri Le, Tan Phan, Minh Pham, Dat Tran, Loc Lam, Ngoc Tung Nguyen, Thao Truong, Hy Vuong, Tam Luu, Nam Phung et al. · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
- A statistical simulator scDesign for rational scRNA-seq experimental designWei Vivian Li, Jingyi Jessica Li · 2019 · Bioinformatics
- Variant to function mapping at single-cell resolution through network propagationFulong Yu, Liam D. Cato, Chen Weng, L. Alexander Liggett, Soyoung Jeon, Keren Xu, Charleston W. K. Chiang, Joseph Leo Wiemels, Jonathan S. Weissman, Adam J. de Smith et al. · 2022 · Nature Biotechnology
- Senescence-resistant human mesenchymal progenitor cells counter aging in primatesJinghui Lei, Zijuan Xin, Ning Liu, Taixin Ning, Ying Jing, Yicheng Qiao, Zan He, Mengmeng Jiang, Yuanhan Yang, Zhiyi Zhang et al. · 2025 · Cell
- Predicting Cell Populations in Single Cell Mass Cytometry DataTamim Abdelaal, Vincent van Unen, Thomas Höllt, Frits Koning, Marcel J. T. Reinders, Ahmed Essam Mahfouz · 2019 · Cytometry Part A
- Deep learning tackles single-cell analysis—a survey of deep learning for scRNA-seq analysisMario A. Flores, Zhentao Liu, Tinghe Zhang, Md Musaddaqui Hasib, Yu‐Chiao Chiu, Zhenqing Ye, Karla Paniagua, Sumin Jo, Jianqiu Zhang, Shou‐Jiang Gao et al. · 2021 · Briefings in Bioinformatics
- Single-cell RNA-seq clustering: datasets, models, and algorithmsLihong Peng, Xiongfei Tian, Geng Tian, Junlin Xu, Xin Huang, Yanbin Weng, Jialiang Yang, Liqian Zhou · 2020 · RNA Biology
- Thymic iNKT single cell analyses unmask the common developmental program of mouse innate T cellsSai Harsha Krovi, Jingjing Zhang, Mary Jessamine Michaels-Foster, Tonya M. Brunetti, Liyen Loh, James P Scott-Browne, Laurent Gapin · 2020 · Nature Communications
- Single-Nucleus RNA-Seq Reveals Dysregulation of Striatal Cell Identity Due to Huntington's Disease MutationsSonia Malaiya, Marcia Cortes-Gutierrez, Brian R. Herb, Sydney R. Coffey, Samuel R.W. Legg, Jeffrey P. Cantle, Carlo Colantuoni, Jeffrey B. Carroll, Seth A. Ament · 2021 · Journal of Neuroscience
- Mapping Phenotypic Plasticity upon the Cancer Cell State Landscape Using Manifold LearningDaniel B. Burkhardt, Beatriz P. San Juan, John George Lock, Smita Krishnaswamy, Christine Louise Chaffer · 2022 · Cancer Discovery