Cell2location maps fine-grained cell types in spatial transcriptomics

Comprehensive Integration of Single-Cell Data

Stuart, T., Butler, A., Hoffman, P., Hafemeister, C., Papalexi, E., Mauck, W. M., Hao, Y., Stoeckius, M., Smibert, P., & Satija, R. (2019) · Cell · doi:10.1016/j.cell.2019.05.031 · Cited by 15,453 · see citing works

SCANPY: large-scale single-cell gene expression data analysis

Wolf, F. A., Angerer, P., & Theis, F. J. (2018) · Genome Biology · doi:10.1186/s13059-017-1382-0 · Cited by 8,881 · see citing works

Solving Least Squares Problems

Lawson, C. L., & Hanson, R. J. (1995) · doi:10.1137/1.9781611971217 · Cited by 7,103 · see citing works

Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression

Hafemeister, C., & Satija, R. (2019) · Genome Biology · doi:10.1186/s13059-019-1874-1 · Cited by 4,479 · cited 1× · see citing works

Visualization and analysis of gene expression in tissue sections by spatial transcriptomics

Ståhl, P. L., Salmén, F., Vickovic, S., Lundmark, A., Navarro, J. F., Magnusson, J., Giacomello, S., Asp, M., Westholm, J. O., Huss, M., et al. (2016) · Science · doi:10.1126/science.aaf2403 · Cited by 3,834 · see citing works

ilastik: interactive machine learning for (bio)image analysis

Berg, S., Kutra, D., Kroeger, T., Straehle, C., Kausler, B. X., Haubold, C., Schiegg, M., Aleš, J., Beier, T., Rudy, M., et al. (2019) · Nature Methods · doi:10.1038/s41592-019-0582-9 · Cited by 3,277 · see citing works

Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq

Zeisel, A., Muñoz-Manchado, A. B., Codeluppi, S., Lönnerberg, P., La Manno, G., Juréus, A., Marques, S., Munguba, H., He, L., Betsholtz, C., et al. (2015) · Science · doi:10.1126/science.aaa1934 · Cited by 3,124 · see citing works

Molecular Architecture of the Mouse Nervous System

Zeisel, A., Hochgerner, H., Lönnerberg, P., Johnsson, A., Memic, F., van der Zwan, J., Häring, M., Braun, E., Borm, L. E., La Manno, G., et al. (2018) · Cell · doi:10.1016/j.cell.2018.06.021 · Cited by 2,995 · see citing works

Scrublet: computational identification of cell doublets in single-cell transcriptomic data

Wolock, S. L., Lopez, R., & Klein, A. M. (2019) · Cell Systems · doi:10.1016/j.cels.2018.11.005 · Cited by 2,758 · see citing works

Scrublet: computational identification of cell doublets in single-cell transcriptomic data

Wolock, S. L., Lopez, R., & Klein, A. M. (2018) · doi:10.1101/357368 · Cited by 2,758 · cited 1× · see citing works

Probabilistic programming in Python using PyMC3

Salvatier, J., Wiecki, T. V., & Fonnesbeck, C. (2016) · PeerJ Computer Science · doi:10.7717/peerj-cs.55 · Cited by 2,544 · see citing works

Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution

Rodriques, S. G., Stickels, R. R., Goeva, A., Martin, C. A., Murray, E., Vanderburg, C. R., Welch, J., Chen, L. M., Chen, F., & Macosko, E. Z. (2019) · Science · doi:10.1126/science.aaw1219 · Cited by 2,424 · see citing works

Single-cell reconstruction of the early maternal–fetal interface in humans

Vento-Tormo, R., Efremova, M., Botting, R. A., Turco, M. Y., Vento-Tormo, M., Meyer, K. B., Park, J.-E., Stephenson, E., Polański, K., Goncalves, A., et al. (2018) · Nature · doi:10.1038/s41586-018-0698-6 · Cited by 2,358 · see citing works

Shared and distinct transcriptomic cell types across neocortical areas

Tasic, B., Yao, Z., Graybuck, L. T., Smith, K. A., Nguyen, T. N., Bertagnolli, D., Goldy, J., Garren, E., Economo, M. N., Viswanathan, S., et al. (2018) · Nature · doi:10.1038/s41586-018-0654-5 · Cited by 1,746 · see citing works

Adult mouse cortical cell taxonomy revealed by single cell transcriptomics

Tasic, B., Menon, V., Nguyen, T. N., Kim, T. K., Jarsky, T., Yao, Z., Levi, B., Gray, L. T., Sorensen, S. A., Dolbeare, T., et al. (2016) · Nature Neuroscience · doi:10.1038/nn.4216 · Cited by 1,714 · see citing works

A molecular cell atlas of the human lung from single-cell RNA sequencing

Travaglini, K. J., Nabhan, A. N., Penland, L., Sinha, R., Gillich, A., Sit, R. V., Chang, S., Conley, S. D., Mori, Y., Seita, J., et al. (2020) · Nature · doi:10.1038/s41586-020-2922-4 · Cited by 1,657 · see citing works

Robust decomposition of cell type mixtures in spatial transcriptomics

Cable, D. M., Murray, E., Zou, L. S., Goeva, A., Macosko, E. Z., Chen, F., & Irizarry, R. A. (2022) · Nature Biotechnology · doi:10.1038/s41587-021-00830-w · Cited by 1,487 · see citing works

Highly sensitive spatial transcriptomics at near-cellular resolution with Slide-seqV2

Stickels, R. R., Murray, E., Kumar, P., Li, J., Marshall, J. L., Di Bella, D. J., Arlotta, P., Macosko, E. Z., & Chen, F. (2021) · Nature Biotechnology · doi:10.1038/s41587-020-0739-1 · Cited by 1,295 · see citing works

High-definition spatial transcriptomics for in situ tissue profiling

Vickovic, S., Eraslan, G., Salmén, F., Klughammer, J., Stenbeck, L., Schapiro, D., Äijö, T., Bonneau, R., Bergenstråhle, L., Navarro, J. F., et al. (2019) · Nature Methods · doi:10.1038/s41592-019-0548-y · Cited by 1,150 · see citing works

Multiplex digital spatial profiling of proteins and RNA in fixed tissue

Merritt, C. R., Ong, G. T., Church, S. E., Barker, K., Danaher, P., Geiss, G., Hoang, M., Jung, J., Liang, Y., McKay-Fleisch, J., et al. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-0472-9 · Cited by 1,072 · see citing works

A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation

Yao, Z., van Velthoven, C. T. J., Nguyen, T. N., Goldy, J., Sedeno-Cortes, A. E., Baftizadeh, F., Bertagnolli, D., Casper, T., Chiang, M., Crichton, K., et al. (2021) · Cell · doi:10.1016/j.cell.2021.04.021 · Cited by 1,065 · see citing works

A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation

(2020) · doi:10.1101/2020.03.30.015214 · Cited by 1,065 · see citing works

Single-cell spatial reconstruction reveals global division of labour in the mammalian liver

Halpern, K. B., Shenhav, R., Matcovitch-Natan, O., Tóth, B., Lemze, D., Golan, M., Massasa, E. E., Baydatch, S., Landen, S., Moor, A. E., et al. (2017) · Nature · doi:10.1038/nature21065 · Cited by 1,059 · see citing works

Integrating microarray-based spatial transcriptomics and single-cell RNA-seq reveals tissue architecture in pancreatic ductal adenocarcinomas

Moncada, R., Barkley, D., Wagner, F., Chiodin, M., Devlin, J. C., Baron, M., Hajdu, C. H., Simeone, D. M., & Yanai, I. (2020) · Nature Biotechnology · doi:10.1038/s41587-019-0392-8 · Cited by 1,045 · see citing works

BBKNN: fast batch alignment of single cell transcriptomes

Polański, K., Young, M. D., Miao, Z., Meyer, K. B., Teichmann, S. A., & Park, J.-E. (2020) · Bioinformatics · doi:10.1093/bioinformatics/btz625 · Cited by 932 · see citing works

Identification of region-specific astrocyte subtypes at single cell resolution

Batiuk, M. Y., Martirosyan, A., Wahis, J., de Vin, F., Marneffe, C., Kusserow, C., Koeppen, J., Viana, J. F., Oliveira, J. F., Voet, T., et al. (2020) · Nature Communications · doi:10.1038/s41467-019-14198-8 · Cited by 805 · see citing works

A Python library for probabilistic analysis of single-cell omics data

Gayoso, A., Lopez, R., Xing, G., Boyeau, P., Valiollah Pour Amiri, V., Hong, J., Wu, K., Jayasuriya, M., Mehlman, E., Langevin, M., et al. (2022) · Nature Biotechnology · doi:10.1038/s41587-021-01206-w · Cited by 789 · see citing works

Neural Circuit-Specialized Astrocytes: Transcriptomic, Proteomic, Morphological, and Functional Evidence

Chai, H., Diaz-Castro, B., Shigetomi, E., Monte, E., Octeau, J. C., Yu, X., Cohn, W., Rajendran, P. S., Vondriska, T. M., Whitelegge, J. P., et al. (2017) · Neuron · doi:10.1016/j.neuron.2017.06.029 · Cited by 769 · see citing works

Pyro: Deep Universal Probabilistic ProgrammingPreprint

Bingham, E., Chen, J. P., Jankowiak, M., Obermeyer, F. H., Pradhan, N., Karaletsos, T., Singh, R., Szerlip, P., Horsfall, P., & Goodman, N. D. (2018) · arXiv (Cornell University) · doi:10.48550/arxiv.1810.09538 · Cited by 767 · see citing works

SPOTlight: seeded NMF regression to deconvolute spatial transcriptomics spots with single-cell transcriptomes

Elosua-Bayes, M., Nieto, P., Mereu, E., Gut, I., & Heyn, H. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab043 · Cited by 732 · see citing works

Development and Functional Diversification of Cortical Interneurons

Lim, L., Mi, D., Llorca, A., & Marín, O. (2018) · Neuron · doi:10.1016/j.neuron.2018.10.009 · Cited by 714 · cited 2× · see citing works

Cells of the human intestinal tract mapped across space and time

Elmentaite, R., Kumasaka, N., Roberts, K., Fleming, A., Dann, E., King, H. W., Kleshchevnikov, V., Dabrowska, M. H., Pritchard, S., Bolt, L., et al. (2021) · Nature · doi:10.1038/s41586-021-03852-1 · Cited by 677 · see citing works

Mapping the temporal and spatial dynamics of the human endometrium in vivo and in vitro

(2021) · doi:10.1038/s41588-021-00972-2 · Cited by 662 · see citing works

Identifying gene expression programs of cell-type identity and cellular activity with single-cell RNA-Seq

Kotliar, D., Veres, A., Nagy, M. A., Tabrizi, S., Hodis, E., Melton, D. A., & Sabeti, P. C. (2019) · eLife · doi:10.7554/elife.43803 · Cited by 638 · see citing works

Functional diversity of astrocytes in neural circuit regulation

Haim, L. B., & Rowitch, D. H. (2017) · Nature Reviews Neuroscience · doi:10.1038/nrn.2016.159 · Cited by 618 · see citing works

Astroglial Kir4.1 in the lateral habenula drives neuronal bursts in depression

Cui, Y., Yang, Y., Ni, Z., Dong, Y., Cai, G., Foncelle, A., Ma, S., Sang, K., Tang, S., Li, Y., et al. (2018) · Nature · doi:10.1038/nature25752 · Cited by 597 · see citing works

Identification of diverse astrocyte populations and their malignant analogs

John Lin, C.-C., Yu, K., Hatcher, A., Huang, T.-W., Lee, H. K., Carlson, J., Weston, M. C., Chen, F., Zhang, Y., Zhu, W., et al. (2017) · Nature Neuroscience · doi:10.1038/nn.4493 · Cited by 525 · see citing works

Class-Switch Recombination Occurs Infrequently in Germinal Centers

Roco, J. A., Mesin, L., Binder, S. C., Nefzger, C. M., González-Figueroa, P., Cañete, P. F., Ellyard, J. I., Shen, Q., Robert, P. A., Cappello, J. Y., et al. (2019) · Immunity · doi:10.1016/j.immuni.2019.07.001 · Cited by 518 · see citing works

Spatiotemporal analysis of human intestinal development at single-cell resolution

Fawkner-Corbett, D., Antanaviciute, A., Parikh, K., Jagielowicz, M., Gerós, A. S., Gupta, T., Ashley, N., Khamis, D., Fowler, D. J., Morrissey, E. R., et al. (2021) · Cell · doi:10.1016/j.cell.2020.12.016 · Cited by 507 · see citing works

scRNA-seq assessment of the human lung, spleen, and esophagus tissue stability after cold preservation

Madissoon, E., Wilbrey-Clark, A., Miragaia, R. J., Saeb‐Parsy, K., Mahbubani, K. T. A., Georgakopoulos, N., Harding, P., Polański, K., Huang, N., Nowicki-Osuch, K., et al. (2019) · Genome biology · doi:10.1186/s13059-019-1906-x · Cited by 492 · see citing works

Astrocyte layers in the mammalian cerebral cortex revealed by a single-cell in situ transcriptomic map

Bayraktar, O. A., Bartels, T., Holmqvist, S., Kleshchevnikov, V., Martirosyan, A., Polioudakis, D., Ben Haim, L., Young, A. M. H., Batiuk, M. Y., Prakash, K., et al. (2020) · Nature Neuroscience · doi:10.1038/s41593-020-0602-1 · Cited by 489 · see citing works

Single-cell and spatial transcriptomics enables probabilistic inference of cell type topography

Andersson, A., Bergenstråhle, J., Asp, M., Bergenstråhle, L., Jurek, A., Navarro, J. F., & Lundeberg, J. (2020) · Communications Biology · doi:10.1038/s42003-020-01247-y · Cited by 463 · see citing works

Using single nuclei for RNA-seq to capture the transcriptome of postmortem neurons

Krishnaswami, S. R., Grindberg, R. V., Novotny, M., Venepally, P., Lacar, B., Bhutani, K., Linker, S. B., Pham, S., Erwin, J. A., Miller, J. A., et al. (2016) · Nature Protocols · doi:10.1038/nprot.2016.015 · Cited by 445 · see citing works

The promise of spatial transcriptomics for neuroscience in the era of molecular cell typing

Lein, E., Borm, L. E., & Linnarsson, S. (2017) · Science · doi:10.1126/science.aan6827 · Cited by 383 · see citing works

Laser capture microscopy coupled with Smart-seq2 for precise spatial transcriptomic profiling

Nichterwitz, S., Chen, G., Benitez, J. A., Yilmaz, M., Storvall, H., Cao, M., Sandberg, R., Deng, Q., & Hedlund, E. (2016) · Nature Communications · doi:10.1038/ncomms12139 · Cited by 331 · see citing works

Genome-wide RNA Tomography in the Zebrafish Embryo

Junker, J. P., Noël, E. S., Guryev, V., Peterson, K. A., Shah, G., Huisken, J., McMahon, A. P., Berezikov, E., Bakkers, J., & van Oudenaarden, A. (2014) · Cell · doi:10.1016/j.cell.2014.09.038 · Cited by 314 · see citing works

Layer-specific morphological and molecular differences in neocortical astrocytes and their dependence on neuronal layers

Lanjakornsiripan, D., Pior, B., Kawaguchi, D., Furutachi, S., Tahara, T., Katsuyama, Y., Suzuki, Y., Fukazawa, Y., & Gotoh, Y. (2018) · Nature Communications · doi:10.1038/s41467-018-03940-3 · Cited by 308 · see citing works

Human germinal centres engage memory and naive B cells after influenza vaccination

Turner, J. S., Zhou, J. Q., Han, J., Schmitz, A. J., Rizk, A. A., Alsoussi, W. B., Lei, T., Amor, M., McIntire, K. M., Meade, P., et al. (2020) · Nature · doi:10.1038/s41586-020-2711-0 · Cited by 304 · see citing works

Distinct microbial and immune niches of the human colon

James, K. R., Gomes, T., Elmentaite, R., Kumar, N., Gulliver, E. L., King, H. W., Stares, M. D., Bareham, B. R., Ferdinand, J. R., Petrova, V. N., et al. (2020) · Nature Immunology · doi:10.1038/s41590-020-0602-z · Cited by 301 · see citing works

Cellular and Molecular Probing of Intact Human Organs

Zhao, S., Todorov, M. I., Cai, R., -Maskari, R. A., Steinke, H., Kemter, E., Mai, H., Rong, Z., Warmer, M., Stanic, K., et al. (2020) · Cell · doi:10.1016/j.cell.2020.01.030 · Cited by 292 · see citing works

Single-cell analysis of human B cell maturation predicts how antibody class switching shapes selection dynamics

King, H. W., Orban, N. T., Riches, J. C., Clear, A. J., Warnes, G., Teichmann, S. A., & James, L. K. (2021) · Science Immunology · doi:10.1126/sciimmunol.abe6291 · Cited by 248 · see citing works

A molecular cell atlas of the human lung from single cell RNA sequencingPreprint

Travaglini, K. J., Nabhan, A. N., Penland, L., Sinha, R., Gillich, A., Sit, R. V., Chang, S., Conley, S. D., Mori, Y., Seita, J., et al. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/742320 · Cited by 216 · see citing works

A repeated molecular architecture across thalamic pathways

Phillips, J. W., Schulmann, A., Hara, E., Winnubst, J., Liu, C., Valakh, V., Wang, L., Shields, B. C., Korff, W. L., Chandrashekar, J. V., et al. (2019) · Nature Neuroscience · doi:10.1038/s41593-019-0483-3 · Cited by 191 · see citing works

A cell atlas of human thymic development defines T cell repertoire formationPreprint

Park, J.-E., Botting, R. A., Conde, C. D., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.01.28.911115 · Cited by 187 · see citing works

Shared and distinct transcriptomic cell types across neocortical areasPreprint

Tasic, B., Yao, Z., Smith, K. A., et al. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/229542 · Cited by 163 · see citing works

Region-Specific Transcriptional Control of Astrocyte Function Oversees Local Circuit Activities

Huang, A. Y.-S., Woo, J., Sardar, D., Lozzi, B., Huerta, N. A. B., Lin, C.-C. J., Felice, D., Jain, A., Paulucci-Holthauzen, A. A., & Deneen, B. (2020) · Neuron · doi:10.1016/j.neuron.2020.03.025 · Cited by 158 · see citing works

Gut‐associated lymphoid tissue, T cell trafficking, and chronic intestinal inflammation

Koboziev, I., Karlsson, F. J., & Grisham, M. B. (2010) · Annals of the New York Academy of Sciences · doi:10.1111/j.1749-6632.2010.05711.x · Cited by 150 · see citing works

The human intestinal B-cell response

Spencer, J., & Sollid, L. M. (2016) · Mucosal Immunology · doi:10.1038/mi.2016.59 · Cited by 126 · see citing works

The thalamus: gateway to the mind

Ward, L. M. (2013) · Wiley Interdisciplinary Reviews Cognitive Science · doi:10.1002/wcs.1256 · Cited by 111 · see citing works

De novo gene signature identification from single‐cell RNA‐seq with hierarchical Poisson factorization

Levitin, H. M., Yuan, J., Cheng, Y. L., Ruiz, F. J. R., Bush, E. C., Bruce, J. N., Canoll, P., Iavarone, A., Lasorella, A., Blei, D. M., et al. (2019) · Molecular Systems Biology · doi:10.15252/msb.20188557 · Cited by 107 · see citing works

AutoGeneS: Automatic gene selection using multi-objective optimization for RNA-seq deconvolution

Aliee, H., & Theis, F. J. (2021) · Cell Systems · doi:10.1016/j.cels.2021.05.006 · Cited by 103 · see citing works

scvi-tools: a library for deep probabilistic analysis of single-cell omics dataPreprint

Gayoso, A., Lopez, R., Xing, G. K., et al. (2021) · bioRxiv · doi:10.1101/2021.04.28.441833 · Cited by 66 · see citing works

T Helper Cell Differentiation and Their Function

Sun, B. (2014) · Advances in experimental medicine and biology · doi:10.1007/978-94-017-9487-9 · Cited by 24 · see citing works

Transcriptome-wide spatial RNA profiling maps the cellular architecture of the developing human neocortexPreprint

Roberts, K., Aivazidis, A., Kleshchevnikov, V., Li, T., Fropf, R., Rhodes, M., Beechem, J., Hemberg, M., & Bayraktar, O. A. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.03.20.436265 · Cited by 19 · see citing works

Single-cell roadmap of human gonadal developmentPreprint

Tormo, R. V., García‐Alonso, L., Lorenzi, V., et al. (2021) · Research Square · doi:10.21203/rs.3.rs-496470/v1 · Cited by 14 · see citing works

Automation of Multiplexed RNAscope Single-Molecule Fluorescent In Situ Hybridization and Immunohistochemistry for Spatial Tissue Mapping

Roberts, K., & Bayraktar, O. A. (2020) · Methods in molecular biology · doi:10.1007/978-1-0716-0623-0_15 · Cited by 11 · see citing works

chanzuckerberg/cellxgene: Release 0.15.0

Megill, C., Martin, B., Weaver, C., et al. (2020) · Zenodo (CERN European Organization for Nuclear Research) · doi:10.5281/zenodo.3710410 · Cited by 9 · see citing works

Methods and applications for single-cell and spatial multi-omics

Vandereyken, K., Sifrim, A., Thienpont, B., & Voet, T. (2023) · Nature Reviews Genetics · doi:10.1038/s41576-023-00580-2 · Cited by 1,244 · see citing works

Best practices for single-cell analysis across modalities

Heumos, L., Schaar, A. C., Lance, C., Litinetskaya, A., Drost, F., Zappia, L., Lücken, M. D., Strobl, D. C., Henao, J., Curion, F., et al. (2023) · Nature Reviews Genetics · doi:10.1038/s41576-023-00586-w · Cited by 1,051 · see citing works

Spatial multi-omic map of human myocardial infarction

Kuppe, C., Ramirez Flores, R. O., Li, Z., Hayat, S., Levinson, R. T., Liao, X., Hannani, M. T., Tanevski, J., Wünnemann, F., Nagai, J. S., et al. (2022) · Nature · doi:10.1038/s41586-022-05060-x · Cited by 772 · see citing works

Spatially informed clustering, integration, and deconvolution of spatial transcriptomics with GraphST

Long, Y., Ang, K. S., Li, M., Chong, K. L. K., Sethi, R., Zhong, C., Xu, H., Ong, Z., Sachaphibulkij, K., Chen, A., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-36796-3 · Cited by 700 · see citing works

The expanding vistas of spatial transcriptomics

Tian, L., Chen, F., & Macosko, E. Z. (2023) · Nature Biotechnology · doi:10.1038/s41587-022-01448-2 · Cited by 539 · see citing works

Benchmarking spatial and single-cell transcriptomics integration methods for transcript distribution prediction and cell type deconvolution

Li, B., Zhang, W., Guo, C., Xu, H., Li, L., Fang, M., Hu, Y., Zhang, X., Yao, X., Tang, M., et al. (2022) · Nature Methods · doi:10.1038/s41592-022-01480-9 · Cited by 459 · see citing works

Spatially resolved multiomics of human cardiac niches

Kanemaru, K., Cranley, J., Muraro, D., Miranda, A. M. A., Ho, S. Y., Wilbrey-Clark, A., Patrick Pett, J., Polanski, K., Richardson, L., Litvinukova, M., et al. (2023) · Nature · doi:10.1038/s41586-023-06311-1 · Cited by 425 · see citing works

Spatial profiling of chromatin accessibility in mouse and human tissues

Deng, Y., Bartosovic, M., Ma, S., Zhang, D., Kukanja, P., Xiao, Y., Su, G., Liu, Y., Qin, X., Rosoklija, G. B., et al. (2022) · Nature · doi:10.1038/s41586-022-05094-1 · Cited by 417 · see citing works

Single-cell and spatial transcriptomics: deciphering brain complexity in health and disease

Piwecka, M., Rajewsky, N., & Rybak-Wolf, A. (2023) · Nature Reviews Neurology · doi:10.1038/s41582-023-00809-y · Cited by 320 · see citing works

DestVI identifies continuums of cell types in spatial transcriptomics data

Lopez, R., Li, B., Keren-Shaul, H., Boyeau, P., Kedmi, M., Pilzer, D., Jelinski, A., Yofe, I., David, E., Wagner, A., et al. (2022) · Nature Biotechnology · doi:10.1038/s41587-022-01272-8 · Cited by 276 · see citing works

LIANA+ Provides an All-in-One Framework for Cell–Cell Communication Inference

Dimitrov, D., Schäfer, P. S. L., Farr, E., Rodriguez-Mier, P., Lobentanzer, S., Badia-i-Mompel, P., Dugourd, A., Tanevski, J., Ramirez Flores, R. O., & Saez-Rodriguez, J. (2024) · Nature Cell Biology · doi:10.1038/s41556-024-01469-w · Cited by 263 · see citing works

Impact of the Human Cell Atlas on medicine

Rood, J. E., Maartens, A., Hupalowska, A., Teichmann, S. A., & Regev, A. (2022) · Nature Medicine · doi:10.1038/s41591-022-02104-7 · Cited by 222 · see citing works

Slide-tags enables single-nucleus barcoding for multimodal spatial genomics

Russell, A. J. C., Weir, J. A., Nadaf, N. M., Shabet, M., Kumar, V., Kambhampati, S., Raichur, R., Marrero, G. J., Liu, S., Balderrama, K. S., et al. (2024) · Nature · doi:10.1038/s41586-023-06837-4 · Cited by 225 · see citing works

A spatially resolved atlas of the human lung characterizes a gland-associated immune niche

Madissoon, E., Oliver, A. J., Kleshchevnikov, V., Wilbrey-Clark, A., Polanski, K., Richoz, N., Ribeiro Orsi, A., Mamanova, L., Bolt, L., Elmentaite, R., et al. (2023) · Nature Genetics · doi:10.1038/s41588-022-01243-4 · Cited by 219 · see citing works

A human embryonic limb cell atlas resolved in space and time

Zhang, B., He, P., Lawrence, J. E. G., Wang, S., Tuck, E., Williams, B. A., Roberts, K., Kleshchevnikov, V., Mamanova, L., Bolt, L., et al. (2024) · Nature · doi:10.1038/s41586-023-06806-x · Cited by 143 · see citing works

Microglia-astrocyte crosstalk in the amyloid plaque niche of an Alzheimer’s disease mouse model, as revealed by spatial transcriptomics

Mallach, A., Zielonka, M., van Lieshout, V., An, Y., Khoo, J. H., Vanheusden, M., Chen, W.-T., Moechars, D., Arancibia-Carcamo, I. L., Fiers, M., et al. (2024) · Cell Reports · doi:10.1016/j.celrep.2024.114216 · Cited by 135 · see citing works

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Valdeolivas, A., Amberg, B., Giroud, N., Richardson, M., Gálvez, E. J. C., Badillo, S., Julien-Laferrière, A., Túrós, D., Voith von Voithenberg, L., Wells, I., et al. (2024) · npj Precision Oncology · doi:10.1038/s41698-023-00488-4 · Cited by 130 · see citing works

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Kukanja, P., Langseth, C. M., Rubio Rodríguez-Kirby, L. A., Agirre, E., Zheng, C., Raman, A., Yokota, C., Avenel, C., Tiklová, K., Guerreiro-Cacais, A. O., et al. (2024) · Cell · doi:10.1016/j.cell.2024.02.030 · Cited by 124 · see citing works

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Miranda, A. M. A., Janbandhu, V., Maatz, H., Kanemaru, K., Cranley, J., Teichmann, S. A., Hübner, N., Schneider, M. D., Harvey, R. P., & Noseda, M. (2023) · Nature Reviews Cardiology · doi:10.1038/s41569-022-00805-7 · Cited by 117 · see citing works

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Pullin, J. M., & McCarthy, D. J. (2022) · doi:10.1101/2022.05.09.490241 · Cited by 122 · see citing works

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Chen, W., Zhang, P., Tran, T. N., Xiao, Y., Li, S., Shah, V. V., Cheng, H., Brannan, K. W., Youker, K., Lai, L., et al. (2025) · Nature Methods · doi:10.1038/s41592-025-02707-1 · Cited by 118 · see citing works

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Gopee, N. H., Winheim, E., Olabi, B., Admane, C., Foster, A. R., Huang, N., Botting, R. A., Torabi, F., Sumanaweera, D., Le, A. P., et al. (2024) · Nature · doi:10.1038/s41586-024-08002-x · Cited by 108 · see citing works

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Lerma-Martin, C., Badia-i-Mompel, P., Ramirez Flores, R. O., Sekol, P., Schäfer, P. S. L., Riedl, C. J., Hofmann, A., Thäwel, T., Wünnemann, F., Ibarra-Arellano, M. A., et al. (2024) · Nature Neuroscience · doi:10.1038/s41593-024-01796-z · Cited by 76 · see citing works

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Mantri, M., Hinchman, M. M., McKellar, D. W., Wang, M. F. Z., Cross, S. T., Parker, J. S. L., & De Vlaminck, I. (2022) · Nature Cardiovascular Research · doi:10.1038/s44161-022-00138-1 · Cited by 74 · see citing works

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Lin, W., Li, Y., Qiu, C., Zou, B., Gong, Y., Zhang, X., Tian, D., Sherman, W., Sanchez, F., Wu, D., et al. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkae1298 · Cited by 46 · see citing works

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Heydari, A. A., & Sindi, S. S. (2023) · Biophysics Reviews · doi:10.1063/5.0091135 · Cited by 44 · see citing works

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Li, H., Chen, X., Wang, J. J., Shen, J., Abuduwufuer, K., Zhang, Z., Dong, Z., Wen, Z., He, J., Chen, S., et al. (2025) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-025-02143-9 · Cited by 40 · see citing works

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Sharma, A., Raut, S. S., Shukla, A., Gupta, S., Mishra, A., & Singh, A. (2025) · Seminars in Oncology · doi:10.1016/j.seminoncol.2025.152389 · Cited by 29 · see citing works

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Ma, C., Chitra, U., Zhang, S., & Raphael, B. J. (2022) · Cell Systems · doi:10.1016/j.cels.2022.09.002 · Cited by 27 · see citing works

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Marderstein, A. R., De Zuani, M., Moeller, R., Bezney, J., Padhi, E. M., Wong, S., Coorens, T. H. H., Xie, Y., Xue, H., Montgomery, S. B., et al. (2024) · Nature · doi:10.1038/s41586-024-07946-4 · Cited by 26 · see citing works

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Avey, D. R., Ng, B., Vialle, R. A., Kearns, N. A., de Paiva Lopes, K., Iatrou, A., De Tissera, S., Vyas, H., Saunders, D. M., Flood, D. J., et al. (2024) · doi:10.1101/2024.09.05.611566 · Cited by 24

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Petrescu, J., Gouveia Roque, C., Jackson, C. A., Daly, A. C., Butti, Z., Kang, K., Casel, O., Leung, M., Reilly, L., Eschbach, J., et al. (2026) · Cell · doi:10.1016/j.cell.2026.07.008 · Cited by 4 · see citing works

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Sloan, N. X., Mares, J., Daly, A. C., Grier, S., Haq, I., Jackson, C. A., Barretto, N., Casel, O., Kang, K., Khiste, S., et al. (2026) · Cell Genomics · doi:10.1016/j.xgen.2025.101127 · Cited by 2 · see citing works

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Mustafa, N. H., Kelesbayev, D., & Alibekova, Z. D. (2018) · The Journal of Economic Research & Business Administration · doi:10.26577/be-2018-2-2141

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Атабекова, Б. Б. (2024) · Habaršy. Pedagogika ġylymdary seriâsy · doi:10.51889/2959-5762.2023.80.4.019

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Ozaki, T., Hanaoka, E., Naka, M., et al. (1999) · DNA and Cell Biology · doi:10.1089/104454999315222 · Cited by 22 · see citing works

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Grimm, B. (2002) · Journal of Molluscan Studies · doi:10.1093/mollus/68.1.25 · Cited by 41 · see citing works