Impact of the Human Cell Atlas on medicine

Spatial reconstruction of single-cell gene expression data

Satija, R., Farrell, J. A., Gennert, D., Schier, A. F., & Regev, A. (2015) · Nature Biotechnology · doi:10.1038/nbt.3192 · Cited by 7,055 · see citing works

Oncology meets immunology: the cancer-immunity cycle.

Chen, D. S., & Mellman, I. (2013) · Immunity · doi:10.1016/j.immuni.2013.07.012 · Cited by 6,929 · see citing works

A Unique Microglia Type Associated with Restricting Development of Alzheimer’s Disease

Keren-Shaul, H., Spinrad, A., Weiner, A., Matcovitch-Natan, O., Dvir-Szternfeld, R., Ulland, T. K., David, E., Baruch, K., Lara-Astaiso, D., Toth, B., et al. (2017) · Cell · doi:10.1016/j.cell.2017.05.018 · Cited by 5,493 · see citing works

SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes

HCA Lung Biological Network, Sungnak, W., Huang, N., Bécavin, C., Berg, M., Queen, R., Litvinukova, M., Talavera-López, C., Maatz, H., Reichart, D., et al. (2020) · Nature Medicine · doi:10.1038/s41591-020-0868-6 · Cited by 2,501 · see citing works

Single-cell RNA-seq data analysis on the receptor ACE2 expression reveals the potential risk of different human organs vulnerable to 2019-nCoV infection

Zou, X., Chen, K., Zou, J., Han, P., Hao, J., & Han, Z. (2020) · Frontiers of Medicine · doi:10.1007/s11684-020-0754-0 · Cited by 2,287 · see citing works

SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across Tissues

Ziegler, C. G. K., Allon, S. J., Nyquist, S. K., Mbano, I. M., Miao, V. N., Tzouanas, C. N., Cao, Y., Yousif, A. S., Bals, J., Hauser, B. M., et al. (2020) · Cell · doi:10.1016/j.cell.2020.04.035 · Cited by 2,284 · see citing works

The human cell atlas

Regev, A., Teichmann, S. A., Lander, E. S., Amit, I., Benoist, C., Birney, E., Bodenmiller, B., Campbell, P., Carninci, P., Clatworthy, M., et al. (2017) · eLife · doi:10.7554/elife.27041 · Cited by 2,232 · see citing works

Complex cell-state changes revealed by single cell RNA sequencing of 76,149 microglia throughout the mouse lifespan and in the injured brain

Hammond, T. R., Dufort, C., Dissing-Olesen, L., Giera, S., Young, A., Wysoker, A., Walker, A. J., Segel, M., Nemesh, J., Saunders, A., et al. (2018) · doi:10.1101/406140 · Cited by 2,225 · see citing works

Defining T Cell States Associated with Response to Checkpoint Immunotherapy in Melanoma

Sade-Feldman, M., Yizhak, K., Bjorgaard, S. L., Ray, J. P., de Boer, C. G., Jenkins, R. W., Lieb, D. J., Chen, J. H., Frederick, D. T., Barzily-Rokni, M., et al. (2018) · Cell · doi:10.1016/j.cell.2018.10.038 · Cited by 2,053 · see citing works

Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens

Dixit, A., Parnas, O., Li, B., Chen, J., Fulco, C. P., Jerby-Arnon, L., Marjanovic, N. D., Dionne, D., Burks, T., Raychowdhury, R., et al. (2016) · Cell · doi:10.1016/j.cell.2016.11.038 · Cited by 1,863 · see citing works

A single-cell atlas of the peripheral immune response in patients with severe COVID-19

Wilk, A. J., Rustagi, A., Zhao, N. Q., Roque, J., Martínez-Colón, G. J., McKechnie, J. L., Ivison, G. T., Ranganath, T., Vergara, R., Hollis, T., et al. (2020) · Nature Medicine · doi:10.1038/s41591-020-0944-y · Cited by 1,493 · see citing works

A Cancer Cell Program Promotes T Cell Exclusion and Resistance to Checkpoint Blockade

Jerby-Arnon, L., Shah, P., Cuoco, M. S., Rodman, C., Su, M.-J., Melms, J. C., Leeson, R., Kanodia, A., Mei, S., Lin, J.-R., et al. (2018) · Cell · doi:10.1016/j.cell.2018.09.006 · Cited by 1,429 · see citing works

Single-cell RNA-seq reveals ectopic and aberrant lung-resident cell populations in idiopathic pulmonary fibrosis

Adams, T. S., Schupp, J. C., Poli, S., Ayaub, E. A., Neumark, N., Ahangari, F., Chu, S. G., Raby, B. A., DeIuliis, G., Januszyk, M., et al. (2020) · Science Advances · doi:10.1126/sciadv.aba1983 · Cited by 1,420 · see citing works

Intra- and Inter-cellular Rewiring of the Human Colon during Ulcerative Colitis

Smillie, C. S., Biton, M., Ordovás-Montañés, J., Sullivan, K. M., Burgin, G., Graham, D. B., Herbst, R. H., Rogel, N., Slyper, M., Waldman, J., et al. (2019) · Cell · doi:10.1016/j.cell.2019.06.029 · Cited by 1,386 · see citing works

Cell2location maps fine-grained cell types in spatial transcriptomics

Kleshchevnikov, V., Shmatko, A., Dann, E., Aivazidis, A., King, H. W., Li, T., Elmentaite, R., Lomakin, A., Kedlian, V., Gayoso, A., et al. (2022) · Nature Biotechnology · doi:10.1038/s41587-021-01139-4 · Cited by 1,279 · see citing works

Innate Immune Landscape in Early Lung Adenocarcinoma by Paired Single-Cell Analyses

Lavin, Y., Kobayashi, S., Leader, A., Amir, E.-A. D., Elefant, N., Bigenwald, C., Remark, R., Sweeney, R., Becker, C. D., Levine, J. H., et al. (2017) · Cell · doi:10.1016/j.cell.2017.04.014 · Cited by 1,209 · see citing works

A revised airway epithelial hierarchy includes CFTR-expressing ionocytes

Montoro, D. T., Haber, A. L., Biton, M., Vinarsky, V., Lin, B., Birket, S. E., Yuan, F., Chen, S., Leung, H. M., Villoria, J., et al. (2018) · Nature · doi:10.1038/s41586-018-0393-7 · Cited by 1,206 · see citing works

A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response

Adamson, B., Norman, T. M., Jost, M., Cho, M. Y., Nuñez, J. K., Chen, Y., Villalta, J. E., Gilbert, L. A., Horlbeck, M. A., Hein, M. Y., et al. (2016) · Cell · doi:10.1016/j.cell.2016.11.048 · Cited by 1,193 · see citing works

Cross-tissue immune cell analysis reveals tissue-specific features in humans

Conde, C. D., Xu, C., Jarvis, L. B., Rainbow, D. B., Wells, S. B., Gomes, T., Howlett, S. K., Suchánek, O., Polański, K., King, H. W., et al. (2022) · Science · doi:10.1126/science.abl5197 · Cited by 1,165 · see citing works

Altered TMPRSS2 usage by SARS-CoV-2 Omicron impacts infectivity and fusogenicity

Meng, B., Abdullahi, A., Ferreira, I. A. T. M., Goonawardane, N., Saito, A., Kimura, I., Yamasoba, D., Gerber, P. P., Fatihi, S., Rathore, S., et al. (2022) · Nature · doi:10.1038/s41586-022-04474-x · Cited by 1,146 · see citing works

Dysfunctional CD8 T cells form a proliferative, dynamically regulated compartment within human melanoma

Li, H., van der Leun, A. M., Yofe, I., Lubling, Y., Gelbard-Solodkin, D., van Akkooi, A. C. J., van den Braber, M., Rozeman, E. A., Haanen, J. B. A. G., Blank, C. U., et al. (2019) · Cell · doi:10.1016/j.cell.2018.11.043 · Cited by 1,101 · see citing works

Individual brain organoids reproducibly form cell diversity of the human cerebral cortex

Velasco, S., Kedaigle, A. J., Simmons, S. K., Nash, A., Rocha, M., Quadrato, G., Paulsen, B., Nguyen, L., Adiconis, X., Regev, A., et al. (2019) · Nature · doi:10.1038/s41586-019-1289-x · Cited by 1,094 · see citing works

SARS-CoV-2 receptor ACE2 and TMPRSS2 are primarily expressed in bronchial transient secretory cells

Lukassen, S., Chua, R. L., Trefzer, T. B., Kahn, N. C., Schneider, M. A., Muley, T., Winter, H., Meister, M. A., Veith, C., Boots, A. W., et al. (2020) · The EMBO Journal · doi:10.15252/embj.20105114 · Cited by 1,082 · see citing works

Cross-tissue organization of the fibroblast lineage

Buechler, M. B., Pradhan, R., Krishnamurty, A. T., Cox, C. B., Calviello, A. K., Wang, A. W., Yang, Y. A., Tam, L., Caothien, R. H., Roose‐Girma, M., et al. (2021) · Nature · doi:10.1038/s41586-021-03549-5 · Cited by 1,073 · see citing works

The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans

The Tabula Sapiens Consortium*, Jones, R. C., Karkanias, J., Krasnow, M. A., Pisco, A. O., Quake, S. R., Salzman, J., Yosef, N., Bulthaup, B., Brown, P., et al. (2022) · Science · doi:10.1126/science.abl4896 · Cited by 1,056 · see citing works

Interrogation of the Microenvironmental Landscape in Brain Tumors Reveals Disease-Specific Alterations of Immune Cells

Klemm, F., Maas, R. R., Bowman, R. L., Kornete, M., Soukup, K., Nassiri, S., Brouland, J., Iacobuzio–Donahue, C. A., Brennan, C. W., Tabar, V. S., et al. (2020) · Cell · doi:10.1016/j.cell.2020.05.007 · Cited by 1,050 · see citing works

A single-cell atlas of the airway epithelium reveals the CFTR-rich pulmonary ionocyte

Plasschaert, L. W., Žilionis, R., Choo-Wing, R., Savova, V., Knehr, J., Roma, G., Klein, A. M., & Jaffe, A. B. (2018) · Nature · doi:10.1038/s41586-018-0394-6 · Cited by 1,047 · 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

A conserved dendritic-cell regulatory program limits antitumour immunity

Maier, B. B., Leader, A. M., Chen, S. T., Tung, N., Chang, C., Bérichel, J. L., Chudnovskiy, A., Maskey, S., Walker, L. A., Finnigan, J. P., et al. (2020) · Nature · doi:10.1038/s41586-020-2134-y · Cited by 950 · see citing works

Deep learning and alignment of spatially resolved single-cell transcriptomes with Tangram

Biancalani, T., Scalia, G., Buffoni, L., Avasthi, R., Lu, Z., Sanger, A., Tokcan, N., Vanderburg, C. R., Segerstolpe, Å., Zhang, M., et al. (2021) · Nature Methods · doi:10.1038/s41592-021-01264-7 · Cited by 931 · see citing works

Single cell RNA sequencing of 13 human tissues identify cell types and receptors of human coronaviruses

Qi, F., Qian, S., Zhang, S., & Zhang, Z. (2020) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2020.03.044 · Cited by 905 · see citing works

Spatially organized multicellular immune hubs in human colorectal cancer

Pelka, K., Hofree, M., Chen, J. H., Sarkizova, S., Pirl, J. D., Jorgji, V., Bejnood, A., Dionne, D. A., Ge, W. H., Xu, K. H., et al. (2021) · Cell · doi:10.1016/j.cell.2021.08.003 · Cited by 902 · see citing works

A cellular census of human lungs identifies novel cell states in health and in asthma

Vieira Braga, F. A., Kar, G., Berg, M., Carpaij, O. A., Polanski, K., Simon, L. M., Brouwer, S., Gomes, T., Hesse, L., Jiang, J., et al. (2019) · Nature Medicine · doi:10.1038/s41591-019-0468-5 · Cited by 896 · see citing works

c-Jun overexpression in CAR T cells induces exhaustion resistance

Lynn, R. C., Weber, E. W., Sotillo, E., Gennert, D., Xu, P., Good, Z., Anbunathan, H., Lattin, J., Jones, R., Tieu, V., et al. (2019) · Nature · doi:10.1038/s41586-019-1805-z · Cited by 891 · see citing works

Single-Cell Analysis of Crohn’s Disease Lesions Identifies a Pathogenic Cellular Module Associated with Resistance to Anti-TNF Therapy

Martin, J. P. D., Chang, C., Boschetti, G., Ungaro, R. C., Giri, M., Grout, J. A., Gettler, K., Chuang, L.-S. F., Nayar, S., Greenstein, A. J., et al. (2019) · Cell · doi:10.1016/j.cell.2019.08.008 · Cited by 866 · see citing works

COVID-19 immune features revealed by a large-scale single-cell transcriptome atlas

Ren, X., Wen, W., Fan, X., Hou, W., Su, B., Cai, P., Li, J., Liu, Y., Tang, F., Zhang, F., et al. (2021) · Cell · doi:10.1016/j.cell.2021.01.053 · Cited by 865 · see citing works

Molecular diversity of midbrain development in mouse, human, and stem cells

La Manno, G., Gyllborg, D., Codeluppi, S., Nishimura, K., Salto, C., Zeisel, A., Borm, L. E., Stott, S. R. W., Toledo, E. M., Villaescusa, J. C., et al. (2016) · Cell · doi:10.1016/j.cell.2016.09.027 · Cited by 835 · see citing works

The immune cell landscape in kidneys of patients with lupus nephritis

the Accelerating Medicines Partnership in SLE network, Arazi, A., Rao, D. A., Berthier, C. C., Davidson, A., Liu, Y., Hoover, P., Chicoine, A. T., Eisenhaure, T., Jonsson, A. H., et al. (2019) · Nature Immunology · doi:10.1038/s41590-019-0398-x · Cited by 828 · see citing works

COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets

Delorey, T. M., Ziegler, C. G. K., Heimberg, G., Normand, R., Yang, Y., Segerstolpe, Å., Abbondanza, D., Fleming, S. J., Subramanian, A., Montoro, D. T., et al. (2021) · Nature · doi:10.1038/s41586-021-03570-8 · Cited by 809 · see citing works

SARS-CoV-2 infection of the oral cavity and saliva

Huang, N., Pérez, P., Kato, T., Mikami, Y., Okuda, K., Gilmore, R. C., Conde, C. D., Gasmi, B., Stein, S. R., Beach, M. E., et al. (2021) · Nature Medicine · doi:10.1038/s41591-021-01296-8 · Cited by 789 · see citing works

Peripheral T cell expansion predicts tumour infiltration and clinical response

Wu, T. D., Madireddi, S., de Almeida, P. E., Banchereau, R., Chen, Y.-J. J., Chitre, A. S., Chiang, E. Y., Iftikhar, H., O’Gorman, W. E., Au-Yeung, A., et al. (2020) · Nature · doi:10.1038/s41586-020-2056-8 · Cited by 770 · see citing works

Single-cell transcriptomes from human kidneys reveal the cellular identity of renal tumors

Young, M. D., Mitchell, T. J., Vieira Braga, F. A., Tran, M. G. B., Stewart, B. J., Ferdinand, J. R., Collord, G., Botting, R. A., Popescu, D.-M., Loudon, K. W., et al. (2018) · Science · doi:10.1126/science.aat1699 · Cited by 762 · see citing works

Mapping information-rich genotype-phenotype landscapes with genome-scale Perturb-seq

Replogle, J. M., Saunders, R. A., Pogson, A. N., Hussmann, J. A., Lenail, A., Guna, A., Mascibroda, L., Wagner, E. J., Adelman, K., Lithwick-Yanai, G., et al. (2022) · Cell · doi:10.1016/j.cell.2022.05.013 · Cited by 751 · see citing works

Single-cell multi-omics analysis of the immune response in COVID-19

Cambridge Institute of Therapeutic Immunology and Infectious Disease-National Institute of Health Research (CITIID-NIHR) COVID-19 BioResource Collaboration, Stephenson, E., Reynolds, G., Botting, R. A., Calero-Nieto, F. J., Morgan, M. D., Tuong, Z. K., Bach, K., Sungnak, W., Worlock, K. B., et al. (2021) · Nature Medicine · doi:10.1038/s41591-021-01329-2 · Cited by 742 · see citing works

Therapy-Induced Evolution of Human Lung Cancer Revealed by Single-Cell RNA Sequencing

Maynard, A., McCoach, C. E., Rotow, J. K., Harris, L., Haderk, F., Kerr, D. L., Yu, E. A., Schenk, E. L., Tan, W., Zee, A., et al. (2020) · Cell · doi:10.1016/j.cell.2020.07.017 · Cited by 697 · 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

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scGen predicts single-cell perturbation responses

Lotfollahi, M., Wolf, F. A., & Theis, F. J. (2019) · Nature Methods · doi:10.1038/s41592-019-0494-8 · Cited by 661 · see citing works

A molecular single-cell lung atlas of lethal COVID-19

Melms, J. C., Biermann, J., Huang, H., Wang, Y., Nair, A., Tagore, S., Katsyv, I., Rendeiro, A. F., Amin, A. D., Schapiro, D., et al. (2021) · Nature · doi:10.1038/s41586-021-03569-1 · Cited by 656 · see citing works

Pan-cancer computational histopathology reveals mutations, tumor composition and prognosis

Fu, Y., Jung, A. W., Viñas, R., González, S., Vöhringer, H. S., Shmatko, A., Yates, L. R., Jimenez‐Liñan, M., Moore, L., & Gerstung, M. (2020) · Nature Cancer · doi:10.1038/s43018-020-0085-8 · Cited by 636 · see citing works

A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens

Gasperini, M., Hill, A. J., McFaline-Figueroa, J. L., Martin, B., Kim, S., Zhang, M. D., Jackson, D., Leith, A., Schreiber, J., Noble, W. S., et al. (2019) · Cell · doi:10.1016/j.cell.2018.11.029 · Cited by 613 · see citing works

Tumor and immune reprogramming during immunotherapy in advanced renal cell carcinoma

Bi, K., He, M. X., Bakouny, Z., Kanodia, A., Napolitano, S., Wu, J., Grimaldi, G., Braun, D. A., Cuoco, M. S., Mayorga, A., et al. (2021) · Cancer Cell · doi:10.1016/j.ccell.2021.02.015 · Cited by 613 · see citing works

Non-coding genetic variants in human disease: Figure 1.

Zhang, F., & Lupski, J. R. (2015) · Human Molecular Genetics · doi:10.1093/hmg/ddv259 · Cited by 588 · see citing works

The Human and Mouse Enteric Nervous System at Single-Cell Resolution

Drokhlyansky, E., Smillie, C. S., Wittenberghe, N. V., Ericsson, M., Griffin, G. K., Eraslan, G., Dionne, D. A., Cuoco, M. S., Goder-Reiser, M. N., Sharova, T. Y., et al. (2020) · Cell · doi:10.1016/j.cell.2020.08.003 · Cited by 585 · see citing works

The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution

Rozenblatt–Rosen, O., Regev, A., Oberdoerffer, P., Nawy, T., Hupalowska, A., Rood, J., Ashenberg, O., Cerami, E. G., Coffey, R. J., Demir, E., et al. (2020) · Cell · doi:10.1016/j.cell.2020.03.053 · Cited by 557 · see citing works

Systems vaccinology of the BNT162b2 mRNA vaccine in humans

Arunachalam, P. S., Scott, M. K. D., Hagan, T., Li, C., Feng, Y., Wimmers, F., Grigoryan, L., Trisal, M., Edara, V. V., Lai, L., et al. (2021) · Nature · doi:10.1038/s41586-021-03791-x · Cited by 541 · see citing works

Notch signalling drives synovial fibroblast identity and arthritis pathology

Wei, K., Korsunsky, I., Marshall, J. L., Gao, A., Watts, G. F. M., Major, T., Croft, A. P., Watts, J., BLAZAR, P. E., Lange, J. K., et al. (2020) · Nature · doi:10.1038/s41586-020-2222-z · Cited by 538 · see citing works

Developmental cell programs are co-opted in inflammatory skin disease

Reynolds, G., Vegh, P., Fletcher, J., Poyner, E. F. M., Stephenson, E., Goh, I., Botting, R. A., Huang, N., Olabi, B., Dubois, A., et al. (2021) · Science · doi:10.1126/science.aba6500 · Cited by 529 · see citing works

Scalable, multimodal profiling of chromatin accessibility, gene expression and protein levels in single cells

Mimitou, E. P., Lareau, C. A., Chen, K. Y., Zorzetto-Fernandes, A. L., Hao, Y., Takeshima, Y., Luo, W., Huang, T.-S., Yeung, B. Z., Papalexi, E., et al. (2021) · Nature Biotechnology · doi:10.1038/s41587-021-00927-2 · Cited by 529 · see citing works

Single-cell transcriptome analysis of human skin identifies novel fibroblast subpopulation and enrichment of immune subsets in atopic dermatitis

He, H., Suryawanshi, H., Morozov, P. S., Gay-Mimbrera, J., DUCA, E. D., Kim, H. J., Kameyama, N., Estrada, Y. D., Der, E. B., Krueger, J. G., et al. (2020) · Journal of Allergy and Clinical Immunology · doi:10.1016/j.jaci.2020.01.042 · Cited by 510 · see citing works

A molecular network of the aging human brain provides insights into the pathology and cognitive decline of Alzheimer’s disease

Mostafavi, S., Gaiteri, C., Sullivan, S. E., White, C. C., Tasaki, S., Xu, J., Taga, M., Klein, H.-U., Patrick, E., Komashko, V., et al. (2018) · Nature Neuroscience · doi:10.1038/s41593-018-0154-9 · Cited by 509 · see citing works

Single-cell RNA-seq reveals cell type–specific molecular and genetic associations to lupus

Perez, R. K., Gordon, M. G., Subramaniam, M., Kim, M. C., Hartoularos, G. C., Targ, S., Sun, Y., Ogorodnikov, A., Bueno, R., Lu, A. C., et al. (2022) · Science · doi:10.1126/science.abf1970 · Cited by 507 · see citing works

Progressive immune dysfunction with advancing disease stage in renal cell carcinoma

Braun, D. A., Street, K., Burke, K. P., Cookmeyer, D. L., Denize, T., Pedersen, C. B., Gohil, S. H., Schindler, N. R., Pomerance, L., Hirsch, L., et al. (2021) · Cancer Cell · doi:10.1016/j.ccell.2021.02.013 · Cited by 502 · see citing works

Single-cell RNA-seq reveals fibroblast heterogeneity and increased mesenchymal fibroblasts in human fibrotic skin diseases

Deng, C., Hu, Y., Zhu, D., Cheng, Q., Gu, J., Feng, Q., Zhang, L.-X., Xu, Y., Wang, D., Rong, Z., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-24110-y · Cited by 492 · see citing works

Integrated Single-Cell Atlas of Endothelial Cells of the Human Lung

Schupp, J. C., Adams, T. S., Cosme, C., Raredon, M. S. B., Yuan, Y., Omote, N., Poli, S., Chioccioli, M., Rose, K.-A., Manning, E. P., et al. (2021) · Circulation · doi:10.1161/circulationaha.120.052318 · Cited by 453 · see citing works

Single-Cell Analyses Identify Brain Mural Cells Expressing CD19 as Potential Off-Tumor Targets for CAR-T Immunotherapies

Parker, K. R., Migliorini, D., Perkey, E., Yost, K. E., Bhaduri, A., Bagga, P., Haris, M., Wilson, N. E., Liu, F., Gabunia, K., et al. (2020) · Cell · doi:10.1016/j.cell.2020.08.022 · Cited by 451 · see citing works

Autism genes converge on asynchronous development of shared neuron classes

Paulsen, B., Velasco, S., Kedaigle, A. J., Pigoni, M., Quadrato, G., Deo, A. J., Adiconis, X., Uzquiano, A., Sartore, R., Yang, S. M., et al. (2022) · Nature · doi:10.1038/s41586-021-04358-6 · Cited by 439 · see citing works

High systemic and tumor-associated IL-8 correlates with reduced clinical benefit of PD-L1 blockade

Yuen, K. C. Y., Liu, L.-F., Gupta, V., Madireddi, S., Keerthivasan, S., Li, C., Rishipathak, D., Williams, P. T., Kadel, E. E., Koeppen, H., et al. (2020) · Nature Medicine · doi:10.1038/s41591-020-0860-1 · Cited by 433 · see citing works

Single-nucleus and spatial transcriptome profiling of pancreatic cancer identifies multicellular dynamics associated with neoadjuvant treatment

Hwang, W. L., Jagadeesh, K. A., Guo, J. A., Hoffman, H. I., Yadollahpour, P., Reeves, J. W., Mohan, R., Drokhlyansky, E., Van Wittenberghe, N., Ashenberg, O., et al. (2022) · Nature Genetics · doi:10.1038/s41588-022-01134-8 · Cited by 426 · see citing works

Gene regulatory networks controlling vertebrate retinal regeneration

Hoang, T. V., Wang, J., Boyd, P., Wang, F., Santiago, C. P., Jiang, L., Yoo, S., Lahne, M., Todd, L. J., Jia, M. X., et al. (2020) · Science · doi:10.1126/science.abb8598 · Cited by 422 · see citing works

The emerging landscape of spatial profiling technologies

Moffitt, J. R., Lundberg, E., & Heyn, H. (2022) · Nature Reviews Genetics · doi:10.1038/s41576-022-00515-3 · Cited by 419 · see citing works

Single-nucleus profiling of human dilated and hypertrophic cardiomyopathy

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SARS-CoV-2 receptor ACE2 and TMPRSS2 are primarily expressed in bronchial transient secretory cells

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Machine learning integrative approaches to advance computational immunology

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Towards systems immunology of critical illness at scale: from single cell ‘omics to digital twins

Yoram Vodovotz, B. (2023) · Trends in Immunology · doi:10.1016/j.it.2023.03.004 · Cited by 28 · see citing works

What is a cell type, really? The quest to categorize life’s myriad forms

Dance, A. (2024) · Nature · doi:10.1038/d41586-024-03073-2 · Cited by 27 · see citing works

Overcoming barriers to single-cell RNA sequencing adoption in low- and middle-income countries

Serebour, T. B., Cribbs, A. P., Baldwin, M. J., Masimirembwa, C. M., Chikwambi, Z., Kerasidou, A., & Snelling, S. J. B. (2024) · European Journal of Human Genetics · doi:10.1038/s41431-024-01564-4 · Cited by 26 · see citing works

A systematic overview of single-cell transcriptomics databases, their use cases, and limitations

Gondal, M. N., Shah, S. U. R., Chinnaiyan, A. M., & Cieslik, M. P. (2024) · Frontiers in Bioinformatics · doi:10.3389/fbinf.2024.1417428 · Cited by 26 · see citing works

Transcription factor networks disproportionately enrich for heritability of blood cell phenotypes

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Critical Challenges of Intravenous Nanomaterials Crossing the Blood‐Brain Barrier: from Blood to Brain

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The commitment of the human cell atlas to humanity

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Limitations of cell embedding metrics assessed using drifting islands

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Estimating the impact of single-cell RNA sequencing of human tissues on drug target validationPreprint

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Leveraging neighborhood representations of single-cell data to achieve sensitive DE testing with miloDE

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Rat Models of Hormone Receptor-Positive Breast Cancer

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Adapting systems biology to address the complexity of human disease in the single-cell era

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From single cell to spatial multi-omics: unveiling molecular mechanisms in dynamic and heterogeneous systems

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Artificial intelligence in tuberculosis: a new ally in disease control

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Single-cell transcriptomics identifies chondrocyte differentiation dynamics in vivo and in vitro

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Weakly supervised learning uncovers phenotypic signatures in single-cell dataPreprint

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Universal cell embedding provides a foundation model for cell biology

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Discovery and design of G protein-coupled receptor targeting antibodies

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Panpipes: a pipeline for multiomic single-cell and spatial transcriptomic data analysis

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Congenital Athymia: Unmet Needs and Practical Guidance

Howley, E., Davies, E. G., & Kreins, A. Y. (2023) · Therapeutics and Clinical Risk Management · doi:10.2147/tcrm.s379673 · Cited by 17 · see citing works

150 risk variants for diverticular disease of intestine prioritize cell types and enable polygenic prediction of disease susceptibility

Wu, Y., Goleva, S. B., Breidenbach, L. B., Kim, M., MacGregor, S., Gandal, M. J., Davis, L. K., & Wray, N. R. (2023) · Cell Genomics · doi:10.1016/j.xgen.2023.100326 · Cited by 17 · see citing works

Tackling neurodegeneration in vitro with omics: a path towards new targets and drugs

Carraro, C., Montgomery, J. V., Klimmt, J., Paquet, D., Schultze, J. L., & Beyer, M. (2024) · Frontiers in Molecular Neuroscience · doi:10.3389/fnmol.2024.1414886 · Cited by 15 · see citing works

Control of Cellular Differentiation Trajectories for Cancer Reversion

Gong, J., Lee, C., Kim, H., Kim, J., Jeon, J., Park, S., & Cho, K. (2024) · Advanced Science · doi:10.1002/advs.202402132 · Cited by 17 · see citing works

Disentangling cellular heterogeneity into interpretable biological factors through structured latent representationsPreprint

Moinfar, A. A., & Theis, F. J. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.11.06.622266 · Cited by 20 · see citing works

Modeling the dynamics of EMT reveals genes associated with pan-cancer intermediate states and plasticity

McDermott, M., Mehta, R., Torres, E. T. R., & MacLean, A. L. (2025) · npj Systems Biology and Applications · doi:10.1038/s41540-025-00512-2 · Cited by 15 · see citing works

Analysis of individual patient pathway coordination in a cross-species single-cell kidney atlas

Klötzer, K. A., Abedini, A., Shen, L., Balzer, M. S., Liang, X., Levinsohn, J. L., Ha, E., Dumoulin, B., Hogan, J., Quinn, G. Z., et al. (2025) · Nature Genetics · doi:10.1038/s41588-025-02285-0 · Cited by 16 · see citing works

Single‐Cell and Spatial Multiomics: Applications for Diseases

Li, W., Chen, C., Zhu, X., & Zhang, C. (2025) · MedComm · doi:10.1002/mco2.70553 · Cited by 16 · see citing works

Efficient profiling of total RNA in single cells with STORM-seqPreprint

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Construction of a prognostic model based on disulfidptosis-related genes and identification of CCNA2 as a novel biomarker for hepatocellular carcinoma

Wang, T., Li, W., Wu, Y., You, L., Zheng, C., Zhang, J., Qu, L., & Sun, X. (2024) · Biology Direct · doi:10.1186/s13062-024-00569-9 · Cited by 15 · see citing works

Insights, opportunities, and challenges provided by large cell atlases

Hemberg, M., Marini, F., Ghazanfar, S., Al-Ajami, A., Abassi, N., Anchang, B., Benayoun, B. A., Cao, Y., Chen, K., Cuesta-Astroz, Y., et al. (2025) · Genome biology · doi:10.1186/s13059-025-03771-8 · Cited by 15 · see citing works

Sensitive cluster-free differential expression testing.Preprint

Missarova, A. M., Rosen, L. U., Dann, E., Satija, R., & Marioni, J. C. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.03.08.531744 · Cited by 15 · see citing works

Scaling Dense Representations for Single Cell with Transcriptome-Scale ContextPreprint

Ho, N., Ellington, C. N., Hou, J., Addagudi, S., Mo, S., Tao, T., Li, D., Zhuang, Y., Wang, H., Cheng, X., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.11.28.625303 · Cited by 16 · see citing works

Metabolomics across scales: from single cells to population studies

Alexandrov, T., & Zamboni, N. (2026) · Nature · doi:10.1038/s41586-026-10277-1 · Cited by 14 · see citing works

Single-cell sequencing in diabetic retinopathy: progress and prospects

Yang, T., Zhang, N., & Yang, N. (2025) · Journal of Translational Medicine · doi:10.1186/s12967-024-06066-x · Cited by 15 · see citing works

Single-Cell Advances in Investigating and Understanding Chronic Kidney Disease and Diabetic Kidney Disease

Bhayana, S., Schytz, P. A., Olesen, E. T. B., Soh, K., & Das, V. (2024) · American Journal Of Pathology · doi:10.1016/j.ajpath.2024.07.007 · Cited by 13 · see citing works

Integrating Spatially‐Resolved Transcriptomics Data Across Tissues and Individuals: Challenges and Opportunities

Guo, B., Ling, W., Kwon, S. H., Panwar, P., Ghazanfar, S., Martinowich, K., & Hicks, S. C. (2025) · Small Methods · doi:10.1002/smtd.202401194 · Cited by 13 · see citing works

Initiative of clinical single‐cell biomedicine in clinical and translational medicine

Liu, F., Liu, X., Powell, C. A., Chen, C., Zeng, Y., Fang, H., & Wang, X. (2023) · Clinical and Translational Medicine · doi:10.1002/ctm2.1173 · Cited by 13 · see citing works

CELLama: Foundation Model for Single Cell and Spatial Transcriptomics by Cell Embedding Leveraging Language Model AbilitiesPreprint

Choi, H., Park, J., Kim, S., Kim, J., Lee, D., Bae, S., Shin, H., & Lee, D. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.05.08.593094 · Cited by 13 · see citing works

Cancer genomics and bioinformatics in Latin American countries: applications, challenges, and perspectives

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Chromatin accessibility profiling of targeted cell populations with laser capture microdissection coupled to ATAC-seq

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The Swedish initiative for the study of Primary sclerosing cholangitis (SUPRIM)

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The COVID-19 thrombus: distinguishing pathological, mechanistic, and phenotypic features and management

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Application of Single‐Cell Genomics to Animal Models of Periodontitis and Peri‐Implantitis

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Biomaterial-mediated Cell Atlas: an insight from single-cell and spatial transcriptomics

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Fast, flexible analysis of differences in cellular composition with crumblr

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Identification of drug candidates targeting monocyte reprogramming in people living with HIV

Knoll, R., Bonaguro, L., dos Santos, J. C., Warnat‐Herresthal, S., Cleophas, M. C. P., Blümel, E. P., Reusch, N., Horne, A., Herbert, M., Nuesch-Germano, M., et al. (2023) · Frontiers in Immunology · doi:10.3389/fimmu.2023.1275136 · Cited by 12 · see citing works

Cell fate simulation reveals cancer cell features in the tumor microenvironment

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Pan-cancer profiling of tumor-infiltrating natural killer cells through transcriptional reference mappingPreprint

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Novel dual gland GAN architecture improves human protein localization classification using salivary and pituitary gland inspired loss functions

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Mapping Cell Atlases at the Single‐Cell Level

Ye, F., Wang, J., Li, J., Mei, Y., & Guo, G. (2023) · Advanced Science · doi:10.1002/advs.202305449 · Cited by 11 · see citing works

Adversarial training improves model interpretability in single-cell RNA-seq analysis

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Cell Atlases as Roadmaps in Health and Disease

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The Human Cell Atlas from a cell census to a unified foundation model

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Human cross-tissue cell atlases: unprecedented resources towards systematic understanding of physiology and diseases

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Exploring cell-type associations of rare disease phenotypes using non-diseased cell atlases

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Mining single-cell data for cell type–disease associations

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