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 801–900 of 1,014
- Potential applications of deep learning in single-cell RNA sequencing analysis for cell therapy and regenerative medicineRuojin Yan, Chunmei Fan, Zi Yin, Tingzhang Wang, Xiao Chen · 2021 · Stem Cells
- Temporal Dynamic Methods for Bulk RNA-Seq Time Series DataSunghee Oh, Robert W. Li · 2021 · Genes
- Analysis of single-cell RNA sequencing data based on autoencodersAndrea Tangherloni, Federico Ricciuti, Daniela Besozzi, Píetro Lió, Ana Cvejic · 2021 · BMC Bioinformatics
- Progenitor translatome changes coordinated by Tsc1 increase perception of Wnt signals to end nephrogenesisAlison E. Jarmas, Eric W. Brunskill, Praneet Chaturvedi, Nathan Salomonis, Raphael Kopan · 2021 · Nature Communications
- Besca, a single-cell transcriptomics analysis toolkit to accelerate translational researchSophia Clara Mädler, Alice Julien-Laferrière, Luis Wyss, Miroslav Phan, Anthony Sonrel, Albert S. W. Kang, Eric Ulrich, Roland Schmucki, Jitao David Zhang, Martin Ebeling et al. · 2021 · NAR Genomics and Bioinformatics
- Single-Cell RNA Sequencing Reveals the Role of Phosphorylation-Related Genes in Hepatocellular Carcinoma Stem CellsFuwen Yao, Yongqiang Zhan, Changzheng Li, Ying Lu, Jiao Chen, Jing Deng, Zijing Wu, Qi Li, Yi’an Song, Binhua Chen et al. · 2022 · Frontiers in Cell and Developmental Biology
- Evidence for Multiple Subpopulations of Herpesvirus-Latently Infected CellsJustin T. Landis, Ryan H. Tuck, Yue Pan, Carson N. Mosso, Anthony B. Eason, Razia Moorad, James Stephen Marron, Dirk P. Dittmer · 2022 · mBio
- Identification of the central intermediate in the extra-embryonic to embryonic endoderm transition through single-cell transcriptomicsMichaela Rothová, Alexander Valentin Nielsen, Martin Proks, Yan Fung Wong, Alba Redó Riveiro, Madeleine Linneberg-Agerholm, Eyal David, Ido Amit, Ala Trusina, Joshua M. Brickman · 2022 · Nature Cell Biology
- Approaches in Gene Coexpression Analysis in EukaryotesVasileios L. Zogopoulos, Georgia Saxami, Apostolos Malatras, Konstantinos A. Papadopoulos, Ioanna Tsotra, Vassiliki A. Iconomidou, Ioannis Michalopoulos · 2022 · Biology
- Single-Cell Analysis of the Transcriptome and EpigenomeKrystyna Mazan-Mamczarz, Jisu Ha, Supriyo De, Payel Sen · 2022 · Methods in molecular biology
- Single cell transcriptomics identifies distinct profiles in pediatric acute respiratory distress syndromeTim Flerlage, Jeremy Chase Crawford, Emma Kaitlynn Allen, Danielle Severns, Shaoyuan Tan, Sherri L. Surman, Granger Ridout, Tanya Novak, Adrienne G. Randolph, Alina Nico West et al. · 2023 · Nature Communications
- Identification of female-enriched and disease-associated microglia (FDAMic) contributes to sexual dimorphism in late-onset Alzheimer’s diseaseDeng Wu, Xiaoman Bi, Hei‐Man Chow · 2024 · Journal of Neuroinflammation
- Novel insights into the protective effects of leonurine against acute kidney injury: Inhibition of ER stress-associated ferroptosis via regulating ATF4/CHOP/ACSL4 pathwayRan Cheng, Xiaowan Wang, Lihua Huang, Zhisheng Lu, WU Ai-jun, Shan Guo, Chuang Li, Wei Mao, Ying Xie, Peng Xu et al. · 2024 · Chemico-Biological Interactions
- Spatial analysis and predictive modeling of energy poverty: insights for policy implementationSidique Gawusu, Seidu Abdulai Jamatutu, Xiao-Bing Zhang, Solahudeen Tando Moomin, Abubakari Ahmed, Rhoda Afriyie Mensah, Oisik Das, Ishmael Ackah · 2024 · Environment Development and Sustainability
- scELMo: Embeddings from Language Models are Good Learners for Single-cell Data AnalysisLiu, Tianyu, Chen, Tianqi, Zheng, Wangjie, Luo, Xiao, Chen, Yiqun, Zhao, Hongyu · 2023
- Stem-cell states converge in multistage cutaneous squamous cell carcinoma developmentMark A. Taylor, Eve E. Kandyba, Kyle D. Halliwill, Reyno Delrosario, Matvei Khoroshkin, Hani Goodarzi, David Alan Quigley, Yun Rose Li, Di Wu, Saumya Bollam et al. · 2024 · Science
- Human yolk sac-derived innate lymphoid-biased multipotent progenitors emerge prior to hematopoietic stem cell formationYanli Ni, Guoju You, Yandong Gong, Xiaoyu Su, Yuan Du, Xiaoshuang Wang, Xiaochen Ding, Qingfeng Fu, Man Zhang, Tao Cheng et al. · 2024 · Developmental Cell
- MMP9High Neutrophils are Critical Mediators of Neutrophil Extracellular Traps Formation and Myocardial Ischemia/Reperfusion InjuryShiyu Hu, Feng Zhang, Jingpu Wang, Jian Zhang, Chenguang Li, Yang Lyu, Yiwen Wang, Rong Huang, Yang Gao, Hongbo Yang et al. · 2025 · Advanced Science
- Comparison of high-throughput single-cell RNA sequencing data processing pipelinesMingxuan Gao, Mingyi Ling, Xinwei Tang, Shun Wang, Xiao Xu, Ying Qiao, Wenxian Yang, Rongshan Yu · 2020 · Briefings in Bioinformatics
- Taming human brain organoids one cell at a timeAlexander Atamian, Lluís Cordón-Barris, Giorgia Quadrato · 2020 · Seminars in Cell and Developmental Biology
- Guidelines for biomarker discovery in endometrium: correcting for menstrual cycle bias reveals new genes associated with uterine disordersAlmudena Devesa-Peiró, Patricia Sebastián-León, António Pellicer, Patricia Díaz-Gimeno · 2021 · Molecular Human Reproduction
- Synthetic single cell RNA sequencing data from small pilot studies using deep generative modelsMartin Treppner, Adrián Salas-Bastos, Moritz Hess, Stefan Lenz, Tanja Vogel, Harald Binder · 2021 · Scientific Reports
- Integrating multiple references for single-cell assignmentBin Duan, Shaoqi Chen, Xiaohan Chen, Chenyu Zhu, Chen Tang, Shuguang Wang, Yicheng Gao, Shaliu Fu, Qi Liu · 2021 · Nucleic Acids Research
- RCA2: a scalable supervised clustering algorithm that reduces batch effects in scRNA-seq dataFlorian Schmidt, Bobby Ranjan, Quy Xiao Xuan Lin, Vaidehi Krishnan, Ignasius Joanito, Mohammad Amin Honardoost, Zahid Nawaz, Prasanna Nori Venkatesh, Joanna Hui Juan Tan, Nirmala Arul Rayan et al. · 2021 · Nucleic Acids Research
- RUV-III-NB: normalization of single cell RNA-seq dataAgus Salim, Ramyar Molania, Jianan Wang, Alysha Madhu De Livera, Rachel Thijssen, Terence Paul Speed · 2022 · Nucleic Acids Research
- Spatially Resolved Transcriptomes of Mammalian Kidneys Illustrate the Molecular Complexity and Interactions of Functional Nephron SegmentsArti M. Raghubar, Duy T. Pham, Xiao Tan, Laura F. Grice, Joanna Crawford, Pui Yeng Lam, Stacey B. Andersen, Sohye Yoon, Monica S.Y. Ng, Siok Min Teoh et al. · 2022 · Frontiers in Medicine
- Single-nucleus RNA sequencing and mRNA hybridization indicate key bud events and LcFT1 and LcTFL1-2 mRNA transportability during floral transition in litchiMingchao Yang, Zi-Chen Wu, Riyao Chen, Farhat Abbas, Guibing Hu, Xu‐Ming Huang, Wei-Song Guan, Yi-Song Xu, Huicong Wang · 2023 · Journal of Experimental Botany
- Atlas-scale single-cell multi-sample multi-condition data integration using scMerge2Yingxin Lin, Yue Cao, Elijah Willie, Ellis Patrick, Jean Yee Hwa Yang · 2023 · Nature Communications
- A single-cell transcriptional landscape of immune cells shows disease-specific changes of T cell and macrophage populations in human achalasiaZuqiang Liu, Hao Dai, Lu Yao, Weifeng Chen, Yun Wang, Liyun Ma, Xiaoqing Li, Shengli Lin, Meng‐Jiang He, Pingting Gao et al. · 2023 · Nature Communications
- An integrated approach identifies the molecular underpinnings of murine anterior visceral endoderm migrationShifaan Thowfeequ, Jonathan Fiorentino, Di Hu, Maria Solovey, Sharon Ruane, Maria A. Whitehead, Felix Zhou, Jonathan Godwin, Yentel Mateo‐Otero, Bart Vanhaesebroeck et al. · 2024 · Developmental Cell
- Integrative computational epigenomics to build data-driven gene regulation hypothesesTyrone Chen, Sonika Tyagi · 2020 · GigaScience
- Spatiotemporal transcriptomic atlas of rhizome formation in Oryza longistaminataXiaoping Lian, Liyuan Zhong, Yixuan Bai, Xuanmin Guang, Sijia Tang, Xing Guo, Tong Wei, Feng Ling Yang, Yujiao Zhang, Guangfu Huang et al. · 2024 · Plant Biotechnology Journal
- BERNN: Enhancing classification of Liquid Chromatography Mass Spectrometry data with batch effect removal neural networksSimon Pelletier, Mickaël Leclercq, Florence Roux‐Dalvai, Matthijs B. de Geus, Shannon N. Leslie, Weiwei Wang, TuKiet T. Lam, Angus Clark Nairn, Steven Edward Arnold, Becky Catherine Carlyle et al. · 2024 · Nature Communications
- Integrated single-cell RNA-seq analysis reveals mitochondrial calcium signaling as a modulator of endothelial-to-mesenchymal transitionMathilde Lebas, Giorgia Chinigò, Evan Courmont, Louay Bettaieb, Amani Machmouchi, Jermaine Goveia, Aleksandar Beatovic, Job Van Kerckhove, Cyril Robil, Fabiola Silva Angulo et al. · 2024 · Science Advances
- RANKL treatment restores thymic function and improves T cell–mediated immune responses in aged miceJérémy C. Santamaria, Jessica Chevallier, Léa Dutour, Amandine Picart, Camille Kergaravat, Agata Cieślak, Mourad Amrane, Renaud Vincentelli, Denis Puthier, Emmanuel Clave et al. · 2024 · Science Translational Medicine
- α-Ketoglutarate promotes trophectoderm induction and maturation from naive human embryonic stem cellsK. van Nerum, Anne Wenzel, Lidia Argemi‐Muntadas, Eleni Kafkia, Antar Drews, Ida Sophie Brun, Viktoria Lavro, Annina Roelofsen, Nikolaos Stamidis, Sandra Bagés‐Arnal et al. · 2025 · Nature Cell Biology
- Limitations of cell embedding metrics assessed using drifting islandsHanchen Wang, Jure Leskovec, Aviv Regev · 2025 · Nature Biotechnology
- Uncovering plaque-glia niches in human Alzheimer’s disease brains using spatial transcriptomicsDenis R. Avey, Bernard Ng, Ricardo A. Vialle, Nicola A. Kearns, Kátia de Paiva Lopes, Artemis Iatrou, Sashini L De Tissera, Himanshu Vyas, Devin M. Saunders, Daniel J. Flood et al. · 2025 · Molecular Neurodegeneration Advances
- Artificial intelligence in bioinformatics: a surveyJiyue Jiang, Yunke Li, Shiwei Cao, Yuheng Shan, Yuexing Liu, Tianyi Fei, Yule Yu, Yi Feng, Yu Li, Yixue Li et al. · 2025 · Briefings in Bioinformatics
- Impact of data preprocessing on cell-type clustering based on single-cell RNA-seq dataChunxiang Wang, Xin Gao, Juntao Liu · 2020 · BMC Bioinformatics
- Single-cell RNA sequencing of cultured human endometrial CD140b+CD146+ perivascular cells highlights the importance of in vivo microenvironmentDandan Cao, Rachel Chan, Ernest Hung Yu Ng, Kristina Gemzell‐Danielsson, William S.B. Yeung · 2021 · Stem Cell Research & Therapy
- Lef1 restricts ectopic crypt formation and tumor cell growth in intestinal adenomasSarika Heino, Shentong Fang, Marianne Lähde, Jenny Högström, Sina Nassiri, Andrew D. Campbell, Dustin James Flanagan, Alexander Raven, Michael C. Hodder, Nadia Nasreddin et al. · 2021 · Science Advances
- Molecular Signatures of Mitochondrial Complexes Involved in Alzheimer’s Disease via Oxidative Phosphorylation and Retrograde Endocannabinoid Signaling PathwaysFenqin Chen, Jun Bai, Shanshan Zhong, Rongwei Zhang, Xiaoqian Zhang, Ying Xu, Mei Zhao, Chuansheng Zhao, Zhike Zhou · 2022 · Oxidative Medicine and Cellular Longevity
- A gastruloid model of the interaction between embryonic and extra-embryonic cell typesNoémie M. L. P. Bérenger-Currias, Maria Mircea, Esmée Adegeest, Patrick R. van den Berg, Marleen Feliksik, Mazène Hochane, Timon Idema, Sander J. Tans, Stefan Semrau · 2022 · Journal of Tissue Engineering
- In vitro generation of mouse morula-like cellsHuanhuan Li, Litao Chang, Jinyi Wu, Jiahui Huang, Wei Guan, Lawrence E. Bates, Hannah T. Stuart, Mingyue Guo, Pengfei Zhang, Boyen Huang et al. · 2023 · Developmental Cell
- Multipotent progenitors instruct ontogeny of the superior colliculusGiselle Cheung, Florian M. Pauler, Peter Koppensteiner, Thomas Krausgruber, Carmen Streicher, Martin Schrammel, Natalie Gutmann-Özgen, Alexis E. Ivec, Christoph Bock, Ryuichi Shigemoto et al. · 2023 · Neuron
- Myeloid‐Mas Signaling Modulates Pathogenic Crosstalk among MYC + CD63 + Endothelial Cells, MMP12 + Macrophages, and Monocytes in Acetaminophen‐Induced Liver InjuryDaiwen Chen, Zhi Lü, Yudong Zhao, Lu Xia, Chun Liu, Siqing Zuo, Manchang Jin, Haoyu Jia, Shanshan Li, Shuo Zhang et al. · 2024 · Advanced Science
- FEATS: feature selection-based clustering of single-cell RNA-seq dataEdwin Vans, Ashwini Patil, Alok K. Sharma · 2020 · Briefings in Bioinformatics
- MS4A4A modifies the risk of Alzheimer disease by regulating lipid metabolism and immune response in a unique microglia stateShih‐Feng You, Logan Brase, Fabia Filipello, Abhirami Kannan Iyer, Jorge L. Del‐Aguila, June He, Ricardo D’Oliveira Albanus, John Budde, Joanne B. Norton, Jen Gentsch et al. · 2023 · medRxiv
- Uncovering Plaque-Glia Niches in Human Alzheimer’s Disease Brains Using Spatial TranscriptomicsAvey, Denis R., Ng, Bernard, Vialle, Ricardo A., Kearns, Nicola A., de Paiva Lopes, Katia, Iatrou, Artemis, De Tissera, Sashini, Vyas, Himanshu, Saunders, Devin M., Flood, Daniel J. et al. · 2024
- Leveraging neighborhood representations of single-cell data to achieve sensitive DE testing with miloDEAlsu Missarova, Emma Dann, Emma Dann, Rahul Satija, John C. Marioni · 2024 · Genome biology
- NiCo identifies extrinsic drivers of cell state modulation by niche covariation analysisAnkit Agrawal, Stefan Thomann, Sukanya Basu, Dominic Grün · 2024 · Nature Communications
- Single-cell transcriptomic and neuropathologic analysis reveals dysregulation of the integrated stress response in progressive supranuclear palsyKristen R. Whitney, Won‐Min Song, Abhijeet Sharma, Diana K. Dangoor, Kurt W. Farrell, Margaret M. Krassner, Hadley W. Ressler, Thomas D. Christie, Shrishtee Kandoi, Ruth Helen Walker et al. · 2024 · Acta Neuropathologica
- Direct specification of lymphatic endothelium from mesenchymal progenitorsIrina-Elena Lupu, David E. Grainger, Nils Kirschnick, Sarah Weischer, Eric Zhao, Inés Martínez‐Corral, Hans Schoofs, Marie Vanhollebeke, Grace Jones, Jonathan Godwin et al. · 2025 · Nature Cardiovascular Research
- Feature selection methods affect the performance of scRNA-seq data integration and queryingLuke Zappia, Sabrina Richter, Ciro Ramírez-Suástegui, Raphael Kfuri‐Rubens, Larsen Vornholz, Weixu Wang, Oliver Dietrich, Amit Frishberg, Malte D. Luecken, Fabian Joachim Theis · 2025 · Nature Methods
- Monocytic Myeloid-Derived Suppressor Cells Underpin Resistance to Adoptive T Cell Therapy in Nasopharyngeal CarcinomaRichard Hopkins, Wenwei Xiang, Damien Marlier, Veonice Bijin Au, Qian Ting Ching, Lynn Xue Wu, Rujun Guan, Bernett Teck Kwong Lee, Whay-Kuang John Chia, Who-Whong Wang et al. · 2020 · Molecular Therapy
- iSMNN: batch effect correction for single-cell RNA-seq data via iterative supervised mutual nearest neighbor refinementYuchen Yang, Gang Li, Yifang Xie, Li Wang, Taylor M. Lagler, Yingxi Yang, Jiandong Liu, Qian Li, Yun Li · 2021 · Briefings in Bioinformatics
- Evaluating microglial phenotypes using single-cell technologiesRoman Sankowski, Gianni Monaco, Marco Prinz · 2021 · Trends in Neurosciences
- Computational Methods for Single-Cell DNA Methylome AnalysisWaleed Iqbal, Wanding Zhou · 2022 · Genomics Proteomics & Bioinformatics
- Single cell RNA sequencing of the adult Drosophila eye reveals distinct clusters and novel marker genes for all major cell typesKelvin Yeung, Komal Kumar Bollepogu Raja, Yoon-Kyung Shim, Yumei Li, Rui Chen, Graeme Mardon · 2022 · Communications Biology
- Functional characterization of age-dependent p16 epimutation reveals biological drivers and therapeutic targets for colorectal cancerLi Yang, Xiaomin Chen, Christy Lee, Jiejun Shi, Emily B. Lawrence, Lanjing Zhang, Yumei Li, Nan Gao, Sung Yun Jung, Chad J. Creighton et al. · 2023 · Journal of Experimental & Clinical Cancer Research
- Dissociation protocols used for sarcoma tissues bias the transcriptome observed in single-cell and single-nucleus RNA sequencingDanh D. Truong, Salah-Eddine Lamhamedi-Cherradi, Robert W. Porter, Sandhya Krishnan, Jyothishmathi Swaminathan, Amber Gibson, Alexander J. Lazar, John Andrew Livingston, Vidya Gopalakrishnan, Nancy Beatriz Gordon et al. · 2023 · BMC Cancer
- Transposable elements regulate thymus development and functionJean‐David Larouche, Céline M. Laumont, Assya Trofimov, Krystel Vincent, Leslie Hesnard, Sylvie Brochu, Caroline Côté, Juliette Humeau, Éric Bonneil, Joël Lanoix et al. · 2023 · eLife
- Recent advances in endothelial colony-forming cells: from the transcriptomic perspectiveYaqiong Liu, Caomhán John Lyons, Christine Ayu Lagonda, Timothy O’Brien · 2024 · Journal of Translational Medicine
- An ancient apical patterning system sets the position of the forebrain in chordatesGiacomo Gattoni, Daniel Keitley, Ashley Sawle, Èlia Benito‐Gutiérrez · 2025 · Science Advances
- Single-cell multi-omics sequencing: application trends, COVID-19, data analysis issues and prospectsLu Huo, Jiao Jiao Li, Ling Chen, Zu‐Guo Yu, György Hutvágner, Jinyan Li · 2021 · Briefings in Bioinformatics
- Model-based prediction of spatial gene expression via generative linear mappingYasushi Okochi, Shunta Sakaguchi, Ken Nakae, Takefumi Kondo, Honda Naoki · 2021 · Nature Communications
- Complex hierarchical structures in single-cell genomics data unveiled by deep hyperbolic manifold learningTian Tian, Cheng Zhong, Xiang Lin, Zhi Wei, Hakon H. Hakonarson · 2023 · Genome Research
- scConfluence: single-cell diagonal integration with regularized Inverse Optimal Transport on weakly connected featuresJules Samaran, Gabriel Peyré A, Laura Cantini · 2024 · Nature Communications
- Single-cell RNA sequencing and machine learning provide candidate drugs against drug-tolerant persister cells in colorectal cancerYosui Nojima, Ryoji Yao, Takashi Suzuki · 2025 · Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease
- Neuroinflammation and Alzheimer's disease: Unravelling the molecular mechanismsAniket Kakkar, Harpreet Singh, Bhuvnesh Kumar Singh, Arvind Kumar, Arun Kumar Mishra, Hitesh Chopra · 2025 · Journal of Alzheimer s Disease
- Multi-omics approaches in plant biology: decoding agronomic traits for sustainable agricultureMuhammad Usama Younas, Shimin Zuo, Muhammad Qasim, Irshad Ahmad, Zhiming Feng, Shakal Khan Korai, Usman Zulfiqar, Feruza Tukhtaboeva, Ismoilov Ibrokhim, Tabarak Malik · 2025 · Plant Stress
- Integrated measurement of intracellular proteins and transcripts in single cellsAlexander M. Xu, Qianhe Liu, Kaitlyn Takata, Sarah Jeoung, Yapeng Su, Igor A. Antoshechkin, Sisi Chen, Matthew Thomson, James R. Heath · 2018 · Lab on a Chip
- Global and individualized community detection in inhomogeneous multilayer networksShuxiao Chen, Sifan Liu, Zongming Ma · 2022 · The Annals of Statistics
- NogoA-expressing astrocytes limit peripheral macrophage infiltration after ischemic brain injury in primatesAnthony G. Boghdadi, Joshua M. Spurrier, Leon Teo, Mingfeng Li, Mario Škarica, Benjamin Cao, William Chin Kwan, Tobias D. Merson, Susan K. Nilsson, Nenad Šestan et al. · 2021 · Nature Communications
- FIRM: Flexible integration of single-cell RNA-sequencing data for large-scale multi-tissue cell atlas datasetsJingsi Ming, Zhixiang Lin, Jia Zhao, Xiang Wan, Camille Ezran, Shixuan Liu, Can Yang, Angela Ruohao Wu · 2022 · Briefings in Bioinformatics
- An immunotherapy response prediction model derived from proliferative CD4+ T cells and antigen-presenting monocytes in ccRCCKun Chan Zheng, Lianchong Gao, Jie Hao, Xin Zou, Xiaoyong Hu · 2022 · Frontiers in Immunology
- Current insights in mouse iNKT and MAIT cell development using single cell transcriptomics dataSai Harsha Krovi, Liyen Loh, Andrea Spengler, Tonya M. Brunetti, Laurent Gapin · 2022 · Seminars in Immunology
- Single-cell analysis of chromatin and expression reveals age- and sex-associated alterations in the human heartDavid Fraser Read, Gregory T. Booth, Riza M. Daza, Dana L. Jackson, Rula Green Gladden, Sanjay R Srivatsan, Brent Ewing, Jennifer M. Franks, Cailyn H. Spurrell, Anne Roshella Gomes et al. · 2024 · Communications Biology
- Single-cell analysis reveals the implication of vascular endothelial cell-intrinsic ANGPT2 in human intracranial aneurysmYu Guo, Jia Li, Hongfei Zhang, Huaxing Zi, Mingjian Liu, Qingzhu An, Tianming Qiu, Peiliang Li, Jianping Song, Peixi Liu et al. · 2024 · Cardiovascular Research
- Generation of human region-specific brain organoids with medullary spinal trigeminal nucleiWei Pang, Jinkui Zhu, Kexin Yang, Xiaona Zhu, Wei Zhou, Linlin Jiang, Xuran Zhuang, Yantong Liu, Jianfeng Wei, Xiaoxiang Lu et al. · 2024 · Cell stem cell
- Quantitative single-cell interactomes in normal and virus-infected mouse lungsMargo P. Cain, Belinda J Hernandez, Jichao Chen · 2020 · Disease Models & Mechanisms
- Exploring dimension-reduced embeddings with SleepwalkSvetlana Ovchinnikova, Simon Anders · 2020 · Genome Research
- GLUER: integrative analysis of single-cell omics and imaging data by deep neural networkTao Peng, Gregory M. Chen, Kai Tan · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
- SEACells: Inference of transcriptional and epigenomic cellular states from single-cell genomics dataSitara Persad, Zi-Ning Choo, Christine Dien, Ignas Masilionis, Ronan Chaligné, Tal Nawy, Chrysothemis C. Brown, Itsik Pe’er, Manu N. Setty, Dana Pe’er · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
- Correspondence analysis for dimension reduction, batch integration, and visualization of single-cell RNA-seq dataLauren L. Hsu, Aedín C. Culhane · 2023 · Scientific Reports
- Generative modeling and latent space arithmetics predict single-cell perturbation response across cell types, studies and speciesLotfollahi, M., Wolf, F. Alexander, Theis, Fabian J. · 2018
- Practical bioinformatics pipelines for single-cell RNA-seq data analysisJiangping He, Lin Lihui, Chen Jiekai · 2022 · Biophysics Reports
- Principled and interpretable alignability testing and integration of single-cell dataRong Ma, Eric Sun, David L. Donoho, James Zou · 2024 · Proceedings of the National Academy of Sciences
- Mosaic integration of spatial multi-omics with SpaMosaicXuhua Yan, Kok Siong Ang, Kok Siong Ang, Lynn van Olst, Alex Edwards, Thomas Watson, Ruiqing Zheng, Di Zhang, Rong Fan, Min Li et al. · 2026 · Nature Genetics
- Regulatory T cell therapy is associated with distinct immune regulatory lymphocytic infiltrates in kidney transplantsOliver McCallion, Amy Rachael Cross, Matthew O. Brook, Conor Hennessy, Ricardo C. Ferreira, Dominik Trzupek, William R. Mulley, Sandeep Kumar, Maria Soares, Ian S D Roberts et al. · 2024 · Med
- Engineering Mice to Study Human ImmunityEsen Sefik, Tianli Xiao, Michael Chiorazzi, Ian D. Odell, Fengrui Zhang, Kriti Agrawal, Goran Micevic, Richard Anthony Flavell · 2025 · Annual Review of Immunology
- Single Cell Gene Expression to Understand the Dynamic Architecture of the HeartAndrea Massaia, Patricia Cháves, Sara Samari, Ricardo J. Miragaia, Kerstin B. Meyer, Sarah Amalia Teichmann, Michela Noseda · 2018 · Frontiers in Cardiovascular Medicine
- Modelling hereditary diffuse gastric cancer initiation using transgenic mouse‐derived gastric organoids and single‐cell sequencingKatherine Dixon, Tom P. Brew, David Farnell, Tanis D. Godwin, Simon Cheung, Christine Chow, Monica Ta, Germain Ho, Minh Bui, J. Maxwell Douglas et al. · 2021 · The Journal of Pathology
- Domain Adaptation Principal Component Analysis: Base Linear Method for Learning with Out-of-Distribution DataEvgeny M. Mirkes, Jonathan Bac, Aziz Fouché, Стасенко Сергей Викторович, Andrei Y. Zinovyev, Alexander N. Gorban · 2022 · Entropy
- Trajectory reconstruction identifies dysregulation of perinatal maturation programs in pluripotent stem cell-derived cardiomyocytesSuraj Kannan, Matthew Miyamoto, Renjun Zhu, Michaela R. Lynott, Jason Guo, Elaine Zhelan Chen, Alexandre R. Colas, Brian Leei Lin, Chulan Kwon · 2023 · Cell Reports
- Profiling the bloodstream form and procyclic form Trypanosoma brucei cell cycle using single-cell transcriptomicsEmma M. Briggs, Catarina A. Marques, Guy R Oldrieve, Jihua Hu, Thomas D. Otto, Keith R. Matthews · 2023 · eLife
- OPTIMAL : An OPTimized Imaging Mass cytometry AnaLysis framework for benchmarking segmentation and data explorationBethany Hunter, Ioana Nicorescu, Emma Foster, David McDonald, Gillian Hulme, Andrew Fuller, Amanda Thomson, Thibaut Goldsborough, Catharien M. U. Hilkens, Joaquim Majo et al. · 2023 · Cytometry Part A
- Opto-seq reveals input-specific immediate-early gene induction in ventral tegmental area cell typesRhiana C. Simon, Mary C. Loveless, Joshua X. Yee, Brandon Goh, Su G. Cho, Zainab Nasir, Koichi Hashikawa, Garret D. Stuber, Larry S. Zweifel, Marta E. Soden · 2024 · Neuron
- Detecting anomalous anatomic regions in spatial transcriptomics with STANDSKaichen Xu, Yan Lu, Suyang Hou, Kainan Liu, Yihang Du, Mengqian Huang, Hao Feng, Hao Wu, Xiaobo Sun · 2024 · Nature Communications