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

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

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

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

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

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

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

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

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

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

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

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

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

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 1,406

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

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

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

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

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 1,193

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

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

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 1,101

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 1,100

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

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

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

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

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., Tabar, V. S., et al. (2020) · Cell · doi:10.1016/j.cell.2020.05.007 · Cited by 1,030

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 939

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

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 917

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

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

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

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 890

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

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

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 835

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 823

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 805

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 795

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

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

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

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 715

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 691

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 671

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

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

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 655

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 627

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 616

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

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 601

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 572

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 566

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

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

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 525

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 520

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 517

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

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

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 506

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 462

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

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

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 436

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

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

Single-nucleus profiling of human dilated and hypertrophic cardiomyopathy

Chaffin, M., Papangeli, I., Simonson, B., Akkad, A.-D., Hill, M. C., Arduini, A., Fleming, S. J., Melanson, M., Hayat, S., Kost-Alimova, M., et al. (2022) · Nature · doi:10.1038/s41586-022-04817-8 · Cited by 418

Translocation of Viable Gut Microbiota to Mesenteric Adipose Drives Formation of Creeping Fat in Humans

Ha, C. W. Y., Martin, A., Sepich‐Poore, G. D., Shi, B., Wang, Y., Gouin, K. H., Humphrey, G., Sanders, K., Ratnayake, Y., Chan, K. S. L., et al. (2020) · Cell · doi:10.1016/j.cell.2020.09.009 · Cited by 415

Inhibitory CD161 receptor identified in glioma-infiltrating T cells by single-cell analysis

Mathewson, N. D., Ashenberg, O., Tirosh, I., Gritsch, S., Perez, E. M., Marx, S., Jerby‐Arnon, L., Chanoch-Myers, R., Hara, T., Richman, A. R., et al. (2021) · Cell · doi:10.1016/j.cell.2021.01.022 · Cited by 410

Single-nucleus cross-tissue molecular reference maps toward understanding disease gene function

Eraslan, G., Drokhlyansky, E., Anand, S. K., Fiškin, E., Subramanian, A., Slyper, M., Wang, J., Wittenberghe, N. V., Rouhana, J. M., Waldman, J., et al. (2022) · Science · doi:10.1126/science.abl4290 · Cited by 406

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 406

Massively multiplex chemical transcriptomics at single-cell resolution

Srivatsan, S. R., McFaline-Figueroa, J. L., Ramani, V., Saunders, L., Cao, J., Packer, J., Pliner, H. A., Jackson, D. L., Daza, R. M., Christiansen, L., et al. (2020) · Science · doi:10.1126/science.aax6234 · Cited by 401

Tissue-resident memory and circulating T cells are early responders to pre-surgical cancer immunotherapy

Luoma, A., Suo, S., Wang, Y., Gunasti, L., Porter, C. B. M., Nabilsi, N. H., Tadros, J., Ferretti, A. P., Liao, S., Gurer, C., et al. (2022) · Cell · doi:10.1016/j.cell.2022.06.018 · Cited by 398

High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin

Achim, K., Pettit, J.-B., Saraiva, L. R., Gavriouchkina, D., Larsson, T., Arendt, D., & Marioni, J. C. (2015) · Nature Biotechnology · doi:10.1038/nbt.3209 · Cited by 395

Genome-wide CRISPR screens of T cell exhaustion identify chromatin remodeling factors that limit T cell persistence

Belk, J. A., Yao, W., Ly, N., Freitas, K. A., Chen, Y.-T., Shi, Q., Valencia, A. M., Shifrut, E., Kale, N., Yost, K. E., et al. (2022) · Cancer Cell · doi:10.1016/j.ccell.2022.06.001 · Cited by 382

Longitudinal Multi-omics Analyses Identify Responses of Megakaryocytes, Erythroid Cells, and Plasmablasts as Hallmarks of Severe COVID-19

Bernardes, J. P., Mishra, N., Tran, F., Bahmer, T., Best, L., Blase, J. I., Bordoni, D., Franzenburg, J., Geisen, U. M., Josephs‐Spaulding, J., et al. (2020) · Immunity · doi:10.1016/j.immuni.2020.11.017 · Cited by 359

Impaired local intrinsic immunity to SARS-CoV-2 infection in severe COVID-19

Ziegler, C. G. K., Miao, V. N., Owings, A. H., Navia, A. W., Tang, Y., Bromley, J. D., Lotfy, P., Sloan, M., Laird, H., Williams, H. B., et al. (2021) · Cell · doi:10.1016/j.cell.2021.07.023 · Cited by 356

The spatial landscape of lung pathology during COVID-19 progression

Rendeiro, A. F., Ravichandran, H., Bram, Y., Chandar, V., Kim, J., Meydan, C., Park, J., Foox, J., HETHER, T. D., Warren, S. E., et al. (2021) · Nature · doi:10.1038/s41586-021-03475-6 · Cited by 353

Single-cell protein activity analysis identifies recurrence-associated renal tumor macrophages

Obradović, A., Chowdhury, N., Haake, S. M., Ager, C. R., Wang, V., Vlahos, L. J., Guo, X. V., Aggen, D. H., Rathmell, W. K., Jonasch, E. W., et al. (2021) · Cell · doi:10.1016/j.cell.2021.04.038 · Cited by 352

Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics

Muus, C., Luecken, M. D., Eraslan, G., Sikkema, L., Waghray, A., Heimberg, G., Kobayashi, Y., Vaishnav, E. D., Subramanian, A., Smillie, C. S., et al. (2021) · Nature Medicine · doi:10.1038/s41591-020-01227-z · Cited by 345

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. (2019) · Cell · doi:10.1016/j.cell.2018.12.034 · Cited by 344

Single-cell transcriptomic atlas of the human retina identifies cell types associated with age-related macular degeneration

Menon, M., Mohammadi, S., Davila-Velderrain, J., Goods, B. A., Cadwell, T. D., Xing, Y., Stemmer-Rachamimov, A., Shalek, A. K., Love, J. C., Kellis, M., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-12780-8 · Cited by 331

Expression Analysis and Significance of PD-1, LAG-3, and TIM-3 in Human Non–Small Cell Lung Cancer Using Spatially Resolved and Multiparametric Single-Cell Analysis

Datar, I. J., Sanmamed, M. F., Wang, J., Henick, B. S., Choi, J., Badri, T., Dong, W., Mani, N. L., Toki, M. I., Mejías, L. D., et al. (2019) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-18-4142 · Cited by 330

Mapping the developing human immune system across organs

Suo, C., Dann, E., Goh, I., Jardine, L., Kleshchevnikov, V., Park, J.-E., Botting, R. A., Stephenson, E., Engelbert, J., Tuong, Z. K., et al. (2022) · Science · doi:10.1126/science.abo0510 · Cited by 323

Spatial components of molecular tissue biology

Palla, G., Fischer, D. S., Regev, A., & Theis, F. J. (2022) · Nature Biotechnology · doi:10.1038/s41587-021-01182-1 · Cited by 318

In vivo Perturb-Seq reveals neuronal and glial abnormalities associated with autism risk genes

Jin, X., Simmons, S. K., Guo, A., Shetty, A. S., Ko, M., Nguyen, L., Jokhi, V., Robinson, E., Oyler, P., Curry, N., et al. (2020) · Science · doi:10.1126/science.aaz6063 · Cited by 317

Inferring and perturbing cell fate regulomes in human brain organoids

Fleck, J. S., Jansen, S. M. J., Wollny, D., Zenk, F., Seimiya, M., Jain, A., Okamoto, R., Santel, M., He, Z., Camp, J. G., et al. (2023) · Nature · doi:10.1038/s41586-022-05279-8 · Cited by 315

Lipid-Associated Macrophages Are Induced by Cancer-Associated Fibroblasts and Mediate Immune Suppression in Breast Cancer

Timperi, E., Gueguen, P., Molgora, M., Magagna, I., Kieffer, Y., Lopez‐Lastra, S., Sirven, P., Baudrin, L. G., Baulande, S., Nicolas, A., et al. (2022) · Cancer Research · doi:10.1158/0008-5472.can-22-1427 · Cited by 314

Impaired local intrinsic immunity to SARS-CoV-2 infection in severe COVID-19Preprint

Ziegler, C. G. K., Miao, V., Owings, A., Navia, A., Tang, Y., Bromley, J., Lotfy, P., Sloan, M., Laird, H., Williams, H., et al. (2021) · bioRxiv · doi:10.1101/2021.02.20.431155 · Cited by 298

Multimodal pooled Perturb-CITE-seq screens in patient models define mechanisms of cancer immune evasion

Frangieh, C. J., Melms, J. C., Thakore, P. I., Geiger-Schuller, K. R., Ho, P., Luoma, A. M., Cleary, B., Jerby-Arnon, L., Malu, S., Cuoco, M. S., et al. (2021) · Nature Genetics · doi:10.1038/s41588-021-00779-1 · Cited by 276

Mapping the single-cell transcriptomic response of murine diabetic kidney disease to therapies

Wu, H., González-Villalobos, R. A., Yao, X., Reilly, D. F., Chen, T., Rankin, M. M., Myshkin, E., Breyer, M. D., & Humphreys, B. D. (2022) · Cell Metabolism · doi:10.1016/j.cmet.2022.05.010 · Cited by 250

Cross-tissue, single-cell stromal atlas identifies shared pathological fibroblast phenotypes in four chronic inflammatory diseases

Korsunsky, I., Wei, K., Pohin, M., Kim, E. Y., Barone, F., Major, T., Taylor, E., Ravindran, R. P., Kemble, S., Watts, G. F. M., et al. (2022) · Med · doi:10.1016/j.medj.2022.05.002 · Cited by 249

Single-cell RNA sequencing reveals distinct tumor microenvironmental patterns in lung adenocarcinoma

Bischoff, P., Trinks, A., Obermayer, B., Pett, J. P., Wiederspahn, J., Uhlitz, F., Liang, X., Lehmann, A., Jurmeister, P. S., Elsner, A., et al. (2021) · Oncogene · doi:10.1038/s41388-021-02054-3 · Cited by 246

The Human Lung Cell Atlas: A High-Resolution Reference Map of the Human Lung in Health and Disease

Schiller, H. B., Montoro, D. T., Simon, L. M., Rawlins, E. L., Meyer, K. B., Strunz, M., Vieira Braga, F. A., Timens, W., Koppelman, G. H., Budinger, G. R. S., et al. (2019) · American Journal of Respiratory Cell and Molecular Biology · doi:10.1165/rcmb.2018-0416tr · Cited by 245

Single Cell RNA Sequencing Identifies Subsets of Hepatic Stellate Cells and Myofibroblasts in Liver Fibrosis

Krenkel, O., Hundertmark, J., Ritz, T., Weiskirchen, R., & Tacke, F. (2019) · Cells · doi:10.3390/cells8050503 · Cited by 241

Identifying disease-critical cell types and cellular processes by integrating single-cell RNA-sequencing and human genetics

Jagadeesh, K. A., Dey, K. K., Montoro, D. T., Mohan, R., Gazal, S., Engreitz, J. M., Xavier, R. J., Price, A. L., & Regev, A. (2022) · Nature Genetics · doi:10.1038/s41588-022-01187-9 · Cited by 239

Lymph nodes are innervated by a unique population of sensory neurons with immunomodulatory potential

Huang, S., Ziegler, C. G. K., Austin, J., Mannoun, N., Vukovic, M., Ordovás-Montañés, J., Shalek, A. K., & von Andrian, U. H. (2020) · Cell · doi:10.1016/j.cell.2020.11.028 · Cited by 234

High-Resolution mRNA and Secretome Atlas of Human Enteroendocrine Cells

Beumer, J., Puschhof, J., Bauzá‐Martinez, J., Martínez-Silgado, A., Elmentaite, R., James, K. R., Ross, A., Hendriks, D. F. G., Artegiani, B., Busslinger, G. A., et al. (2020) · Cell · doi:10.1016/j.cell.2020.04.036 · Cited by 229

Modeling intercellular communication in tissues using spatial graphs of cells

Fischer, D. S., Schaar, A. C., & Theis, F. J. (2022) · Nature Biotechnology · doi:10.1038/s41587-022-01467-z · Cited by 224

Skin-resident innate lymphoid cells converge on a pathogenic effector state

Bielecki, P., Riesenfeld, S. J., Hütter, J.-C., Triglia, E. T., Kowalczyk, M. S., Ricardo-González, R. R., Lian, M., Vesely, M. C. A., Kroehling, L., Xu, H. Y., et al. (2021) · Nature · doi:10.1038/s41586-021-03188-w · Cited by 223

Single-cell eQTL models reveal dynamic T cell state dependence of disease loci

Nathan, A., Asgari, S., Ishigaki, K., Valencia, C., Amariuta, T., Luo, Y., Beynor, J. I., Baglaenko, Y., Suliman, S., Price, A. L., et al. (2022) · Nature · doi:10.1038/s41586-022-04713-1 · Cited by 221

Cross-tissue, single-cell stromal atlas identifies shared pathological fibroblast phenotypes in four chronic inflammatory diseasesPreprint

Korsunsky, I., Wei, K., Pohin, M., et al. (2021) · bioRxiv · doi:10.1101/2021.01.11.426253 · Cited by 218

Cell transcriptomic atlas of the non-human primate Macaca fascicularis

Han, L., Wei, X., Liu, C., Volpe, G., Zhuang, Z., Zou, X., Wang, Z., Pan, T., Yuan, Y., Zhang, X., et al. (2022) · Nature · doi:10.1038/s41586-022-04587-3 · Cited by 211

Single-Cell RNA Sequencing to Dissect the Immunological Network of Autoimmune Myocarditis.

Hua, X., Hu, G., Hu, Q., Chang, Y., Hu, Y., Gao, L., Chen, X., Yang, P.-C., Zhang, Y., Li, M., et al. (2020) · Circulation · doi:10.1161/circulationaha.119.043545 · Cited by 201

Classification of human chronic inflammatory skin disease based on single-cell immune profiling

Liu, Y., Wang, H., Taylor, M. A., Cook, C. P., Martínez‐Berdeja, A., North, J. P., Harirchian, P., Hailer, A., Zhao, Z., Ghadially, R., et al. (2022) · Science Immunology · doi:10.1126/sciimmunol.abl9165 · Cited by 179

Mapping Development of the Human Intestinal Niche at Single-Cell Resolution

Holloway, E. M., Czerwinski, M. J., Tsai, Y.-H., Wu, J. H., Wu, A., Childs, C. J., Walton, K. D., Sweet, C. W., Yu, Q., Glass, I. A., et al. (2020) · Cell stem cell · doi:10.1016/j.stem.2020.11.008 · Cited by 176

Multiplexed single-cell transcriptional response profiling to define cancer vulnerabilities and therapeutic mechanism of action

McFarland, J. M., Paolella, B. R., Warren, A., Geiger-Schuller, K., Shibue, T., Rothberg, M., Kuksenko, O., Colgan, W. N., Jones, A., Chambers, E., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-17440-w · Cited by 173

Hypertension delays viral clearance and exacerbates airway hyperinflammation in patients with COVID-19

Trump, S., Lukassen, S., Anker, M. S., Chua, R. L., Liebig, J., Thürmann, L., Corman, V. M., Binder, M., Loske, J., Klasa, C., et al. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-00796-1 · Cited by 172

The organoid cell atlas

the Human Cell Atlas ‘Biological Network’ Organoids, Bock, C., Boutros, M., Camp, J. G., Clarke, L., Clevers, H., Knoblich, J. A., Liberali, P., Regev, A., Rios, A. C., et al. (2021) · Nature Biotechnology · doi:10.1038/s41587-020-00762-x · Cited by 171

Spatially and cell-type resolved quantitative proteomic atlas of healthy human skin

Dyring‐Andersen, B., Løvendorf, M. B., Coscia, F., Santos, A., Møller, L. B. P., Colaço, A. R., Niu, L., Bzorek, M., Doll, S., Andersen, J. L., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-19383-8 · Cited by 162

Blood and immune development in human fetal bone marrow and Down syndrome

Jardine, L., Webb, S., Goh, I., Londoño, M. Q., Reynolds, G., Mather, M. W., Olabi, B., Stephenson, E., Botting, R. A., Horsfall, D., et al. (2021) · Nature · doi:10.1038/s41586-021-03929-x · Cited by 162

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

Gasperini, M. J., Hill, A. J., McFaline‐Figueroa, J. L., Martin, B., Kim, S., Zhang, M. D., Jackson, D., Leith, A., Schreiber, J. M., Noble, W. S., et al. (2019) · Cell · doi:10.1016/j.cell.2019.02.027 · Cited by 150

Integrated multi-omic characterization of congenital heart disease

Hill, M. C., Kadow, Z. A., Long, H., Morikawa, Y., Martin, T. J., Birks, E. J., Campbell, K. S., Nerbonne, J. M., Lavine, K. J., Wadhwa, L., et al. (2022) · Nature · doi:10.1038/s41586-022-04989-3 · Cited by 150

Efficient stimulation of retinal regeneration from Müller glia in adult mice using combinations of proneural bHLH transcription factors

Todd, L. J., Hooper, M. J., Haugan, A. K., Finkbeiner, C., Jorstad, N. L., Radulovich, N. P., Wong, C. K., Donaldson, P. C., Jenkins, W., Chen, Q., et al. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.109857 · Cited by 147

Single-cell RNA sequencing of psoriatic skin identifies pathogenic Tc17 cell subsets and reveals distinctions between CD8+ T cells in autoimmunity and cancer

Liu, J., Chang, H.-W., Huang, Z., Nakamura, M., Sekhon, S., Ahn, R. S., Muñoz-Sandoval, P., Bhattarai, S., Beck, K. M., Sanchez, I. M., et al. (2020) · Journal of Allergy and Clinical Immunology · doi:10.1016/j.jaci.2020.11.028 · Cited by 147

Resolving the Spatial and Cellular Architecture of Lung Adenocarcinoma by Multiregion Single-Cell Sequencing

Sinjab, A. F., Han, G., Treekitkarnmongkol, W., Hara, K., Brennan, P. M., Dang, M., Hao, D., Wang, R., Dai, E., Dejima, H., et al. (2021) · Cancer Discovery · doi:10.1158/2159-8290.cd-20-1285 · Cited by 140

Single Cell RNA-seq reveals ectopic and aberrant lung resident cell populations in Idiopathic Pulmonary FibrosisPreprint

Adams, T. S., Schupp, J. C., Poli, S., et al. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/759902 · Cited by 138

Machine learning for perturbational single-cell omics

Ji, Y., Lotfollahi, M., Wolf, F. A., & Theis, F. J. (2021) · Cell Systems · doi:10.1016/j.cels.2021.05.016 · Cited by 137

Distinct epigenetic features of tumor-reactive CD8+ T cells in colorectal cancer patients revealed by genome-wide DNA methylation analysis

Yang, R., Cheng, S., Luo, N., Gao, R., Yu, K., Kang, B., Wang, L., Zhang, Q., Fang, Q., Zhang, L., et al. (2019) · Genome biology · doi:10.1186/s13059-019-1921-y · Cited by 129

Opposing immune and genetic mechanisms shape oncogenic programs in synovial sarcoma

Jerby‐Arnon, L., Neftel, C., Shore, M. E., Weisman, H. R., Mathewson, N. D., McBride, M. J., Haas, B. J., Izar, B., Volorio, A., Boulay, G., et al. (2021) · Nature Medicine · doi:10.1038/s41591-020-01212-6 · Cited by 129

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. (2020) · Cell · doi:10.1016/j.cell.2020.04.017 · Cited by 122

DIALOGUE maps multicellular programs in tissue from single-cell or spatial transcriptomics data

Jerby‐Arnon, L., & Regev, A. (2022) · Nature Biotechnology · doi:10.1038/s41587-022-01288-0 · Cited by 119

Single-nucleus transcriptome analysis of human brain immune response in patients with severe COVID-19

Fullard, J. F., Lee, H.-C., Voloudakis, G., Suo, S., Javidfar, B., Shao, Z., Peter, C. J., Zhang, W., Jiang, S., Corvelo, A., et al. (2021) · Genome Medicine · doi:10.1186/s13073-021-00933-8 · Cited by 108

Single-cell multiome of the human retina and deep learning nominate causal variants in complex eye diseases

Wang, S. K., Nair, S., Li, R., Kraft, K., Pampari, A., Patel, A., Kang, J. B., Luong, C., Kundaje, A., & Chang, H. Y. (2022) · bioRxiv · doi:10.1016/j.xgen.2022.100164 · Cited by 101

An Integrated Taxonomy for Monogenic Inflammatory Bowel Disease

Bolton, C., Smillie, C. S., Pandey, S., Elmentaite, R., Wei, G., Argmann, C., Aschenbrenner, D., James, K. R., McGovern, D. P. B., Macchi, M., et al. (2021) · Gastroenterology · doi:10.1053/j.gastro.2021.11.014 · Cited by 99

Systematic discovery and perturbation of regulatory genes in human T cells reveals the architecture of immune networks

Freimer, J. W., Shaked, O., Naqvi, S., Sinnott-Armstrong, N., Kathiria, A. S., Garrido, C. M., Chen, A. F., Cortez, J. T., Greenleaf, W. J., Pritchard, J. K., et al. (2022) · Nature Genetics · doi:10.1038/s41588-022-01106-y · Cited by 98

Massively parallel phenotyping of coding variants in cancer with Perturb-seq

Ursu, O., Neal, J. T., Shea, E., Thakore, P. I., Jerby-Arnon, L., Nguyen, L., Dionne, D., Diaz, C., Bauman, J., Mosaad, M. M., et al. (2022) · Nature Biotechnology · doi:10.1038/s41587-021-01160-7 · Cited by 96

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

Fu, Y., Jung, A. W., Viñas, R., et al. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/813543 · Cited by 95

Functional CRISPR dissection of gene networks controlling human regulatory T cell identity

Schumann, K., Raju, S. S., Lauber, M., Kolb, S., Shifrut, E., Cortez, J. T., Skartsis, N., Nguyen, V. Q., Woo, J. M., Roth, T. L., et al. (2020) · Nature Immunology · doi:10.1038/s41590-020-0784-4 · Cited by 93

B cell genomics behind cross-neutralization of SARS-CoV-2 variants and SARS-CoV

Scheid, J. F., Barnes, C. O., Eraslan, B., Hudak, A., Keeffe, J. R., Cosimi, L. A., Brown, E., Muecksch, F., Weisblum, Y., Zhang, S., et al. (2021) · Cell · doi:10.1016/j.cell.2021.04.032 · Cited by 91

The Human Cell Atlas White PaperPreprint

Regev, A., Teichmann, S. A., Rozenblatt–Rosen, O., Stubbington, M. J. T., Ardlie, K., Amit, I., Arlotta, P., Bader, G. D., Benoist, C. O., Biton, M., et al. (2018) · arXiv (Cornell University) · doi:10.17863/cam.40032 · Cited by 88

Three-dimensional spatial transcriptomics uncovers cell type localizations in the human rheumatoid arthritis synovium

Vicković, S., Schapiro, D., Carlberg, K., Lötstedt, B., Larsson, L., Hildebrandt, F., Korotkova, M., Hensvold, A. H., Catrina, A. I., Sorger, P. K., et al. (2022) · Communications Biology · doi:10.1038/s42003-022-03050-3 · Cited by 87

High-resolution Slide-seqV2 spatial transcriptomics enables discovery of disease-specific cell neighborhoods and pathways

Marshall, J. L., Noel, T., Wang, Q. S., Chen, H., Murray, E. M., Subramanian, A., Vernon, K. A., Bazúa‐Valenti, S., Liguori, K., Keller, K. H., et al. (2022) · iScience · doi:10.1016/j.isci.2022.104097 · Cited by 87

Single-cell analysis of Crohn’s disease lesions identifies a pathogenic cellular module associated with resistance to anti-TNF therapyPreprint

Martin, J., Boschetti, G., Chang, C., et al. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/503102 · Cited by 80

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

Replogle, J. M., Saunders, R. A., Pogson, A. N., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.12.16.473013 · Cited by 79

Epithelial plasticity can generate multi-lineage phenotypes in human and murine bladder cancers

Sfakianos, J. P., Daza, J., Hu, Y., Anastos, H., Bryant, G., Bareja, R., Badani, K. K., Galsky, M. D., Elemento, O., Faltas, B. M., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-16162-3 · Cited by 68

Global Characterization of Peripheral B Cells in Parkinson’s Disease by Single-Cell RNA and BCR Sequencing

Wang, P., Luo, M., Zhou, W., Jin, X., Xu, Z., Yan, S., Li, Y., Xu, C., Cheng, R., Huang, Y., et al. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.814239 · Cited by 68

Single cell derived mRNA signals across human kidney tumors

Young, M. D., Mitchell, T. J., Custers, L., Margaritis, T., Morales-Rodriguez, F., Kwakwa, K., Khabirova, E., Kildisiute, G., Oliver, T. R. W., de Krijger, R. R., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-23949-5 · Cited by 63

Screening for modulators of the cellular composition of gut epithelia via organoid models of intestinal stem cell differentiation

Mead, B. E., Hattori, K., Levy, L. E., Imada, S., Goto, N., Vukovic, M., Sze, D., Kummerlowe, C., Matute, J. D., Duan, J., et al. (2022) · Nature Biomedical Engineering · doi:10.1038/s41551-022-00863-9 · Cited by 60

Single-cell multiomics dissection of basal and antigen-specific activation states of CD19-targeted CAR T cells

Bai, Z., Lundh, S. M., Kim, D., Woodhouse, S., Barrett, D. M., Myers, R. M., Grupp, S. A., Maus, M. V., June, C. H., Cámara, P. G., et al. (2021) · Journal for ImmunoTherapy of Cancer · doi:10.1136/jitc-2020-002328 · Cited by 57

Single-Cell Multiomics Techniques: From Conception to Applications

Dimitriu, M. A., Lazar-Contes, I., Roszkowski, M., & Mansuy, I. M. (2022) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2022.854317 · Cited by 55

Mostly natural sequencing-by-synthesis for scRNA-seq using Ultima sequencing

Simmons, S., Lithwick‐Yanai, G., Adiconis, X., Oberstrass, F. C., Iremadze, N., Geiger-Schuller, K., Thakore, P. I., Frangieh, C. J., Barad, O., Almogy, G., et al. (2022) · Nature Biotechnology · doi:10.1038/s41587-022-01452-6 · Cited by 54

Case-control analysis of single-cell RNA-seq studiesPreprint

Petukhov, V., Igolkina, A. A., Rydbirk, R., Mei, S., Christoffersen, L., Khodosevich, K., & Kharchenko, P. V. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.03.15.484475 · Cited by 52

A bird’s eye view of fibroblast heterogeneity: A pan‐disease, pan‐cancer perspective

Pradhan, R., Krishnamurty, A. T., Fletcher, A. L., Turley, S. J., & Müller, S. (2021) · Immunological Reviews · doi:10.1111/imr.12990 · Cited by 51

Learning interpretable cellular responses to complex perturbations in high-throughput screensPreprint

Lotfollahi, M., Klimovskaia, A., Donno, C. D., Ji, Y., Ibarra, I. L., Wolf, F. A., Yakubova, N., Theis, F. J., & López-Paz, D. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.04.14.439903 · Cited by 49

Single-Cell RNA-Seq Analysis of Olfactory Mucosal Cells of Alzheimer’s Disease Patients

Lampinen, R., Fazaludeen, M. F., Avesani, S., Örd, T., Penttilä, E., Lehtola, J.-M., Saari, T. T., Hannonen, S., Saveleva, L., Kaartinen, E., et al. (2022) · Cells · doi:10.3390/cells11040676 · Cited by 49

Identification of Variants in Genes Associated with Single-gene Inflammatory Bowel Disease by Whole-exome Sequencing

Ashton, J. J., Andreoletti, G., Coelho, T. A. F., Haggarty, R., Batra, A., Afzal, N. A., Beattie, R. M., & Ennis, S. (2016) · Inflammatory Bowel Diseases · doi:10.1097/mib.0000000000000890 · Cited by 44

snPATHO-seq: unlocking the FFPE archives for single nucleus RNA profilingPreprint

Vallejo, A. F., Harvey, K., Wang, T., Wise, K., Butler, L. M., Polo, J. M., Plummer, J., Swarbrick, A., & Martelotto, L. G. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.08.23.505054 · Cited by 41

Single-cell RNA sequencing reveals ex vivo signatures of SARS-CoV-2-reactive T cells through ‘reverse phenotyping’

Fischer, D. S., Ansari, M., Wagner, K. I., Jarosch, S., Huang, Y., Mayr, C. H., Strunz, M., Lang, N. J., D’Ippolito, E., Hammel, M., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-24730-4 · Cited by 40

Mapping the developing human immune system across organsPreprint

Suo, C., Dann, E., Goh, I., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.01.17.476665 · Cited by 40

GEARS: Predicting transcriptional outcomes of novel multi-gene perturbationsPreprint

Roohani, Y., Huang, K., & Leskovec, J. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.07.12.499735 · Cited by 40

Integrated bulk and single-cell RNA-sequencing identified disease-relevant monocytes and a gene network module underlying systemic sclerosis

Kobayashi, S., Nagafuchi, Y., Okubo, M., Sugimori, Y., Shirai, H., Hatano, H., Maeda, J., Yanaoka, H., Takeshima, Y., Ota, M., et al. (2020) · Journal of Autoimmunity · doi:10.1016/j.jaut.2020.102547 · Cited by 39

Genome-wide CRISPR screens of T cell exhaustion identify chromatin remodeling factors that limit T cell persistencePreprint

Belk, J. A., Yao, W., Ly, N., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.04.20.488974 · Cited by 36

Integrated Single Cell Atlas of Endothelial Cells of the Human LungPreprint

Schupp, J. C., Adams, T. S., Cosme, C., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.10.21.347914 · Cited by 32

Transcriptome-wide prediction of prostate cancer gene expression from histopathology images using co-expression-based convolutional neural networks

Weitz, P., Wang, Y., Kartasalo, K., Egevad, L., Lindberg, J., Grönberg, H., Eklund, M., & Rantalainen, M. (2022) · Bioinformatics · doi:10.1093/bioinformatics/btac343 · Cited by 30

SnFFPE-Seq: towards scalable single nucleus RNA-Seq of formalin-fixed paraffin-embedded (FFPE) tissuePreprint

Chung, H., Melnikov, A., Aubin, C., Drokhlyansky, E., Wittenberghe, N. V., Magee, E. M., Waldman, J., Spira, A. E., Chen, F., Mazzilli, S. A., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.08.25.505257 · Cited by 29

Systematic discovery and perturbation of regulatory genes in human T cells reveals the architecture of immune networksPreprint

Freimer, J. W., Shaked, O., Naqvi, S., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.04.18.440363 · Cited by 29

The legacy of the Human Genome Project

Rood, J., & Regev, A. (2021) · Science · doi:10.1126/science.abl5403 · Cited by 28

Single-cell multiome of the human retina and deep learning nominate causal variants in complex eye diseasesPreprint

Wang, S. K., Nair, S., Li, R., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.03.09.483684 · Cited by 27

Single-cell RNA sequencing reveals distinct tumor microenvironmental patterns in lung adenocarcinomaPreprint

Bischoff, P., Trinks, A., Obermayer, B., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.12.11.419606 · Cited by 20

Molecular Profiling of Coronavirus Disease 2019 (COVID-19) Autopsies Uncovers Novel Disease Mechanisms

Pujadas, E., Beaumont, M. A., Shah, H., Schrode, N., Francoeur, N. J., Shroff, S., Bryce, C., Grimes, Z., Gregory, J. K., Donnelly, R. F., et al. (2021) · American Journal Of Pathology · doi:10.1016/j.ajpath.2021.08.009 · Cited by 20

The network effect: studying COVID-19 pathology with the Human Cell Atlas

Teichmann, S. A., & Regev, A. (2020) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-020-0267-3 · Cited by 19

Resolving the spatial and cellular architecture of lung adenocarcinoma by multi-region single-cell sequencingPreprint

Sinjab, A. F., Han, G., Treekitkarnmongkol, W., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.09.04.283739 · Cited by 19

The Human Cell Atlas & Equity: Lessons LearnedPreprint

Majumder, P. P., Mhlanga, M. M., & Shalek, A. K. (2020) · DSpace@MIT (Massachusetts Institute of Technology) · doi:10.48550/arxiv.2010.16154 · Cited by 18

The Human Cell Atlas and equity: lessons learned

Majumder, P. P., Mhlanga, M. M., & Shalek, A. K. (2020) · Nature Medicine · doi:10.1038/s41591-020-1100-4 · Cited by 15

Bioinformatics Analysis of Publicly Available Single-Nuclei Transcriptomics Alzheimer’s Disease Datasets Reveals APOE Genotype-Specific Changes Across Cell Types in Two Brain Regions

Belonwu, S., Li, Y., Bunis, D. G., Rao, A. A., Solsberg, C. W., Oskotsky, T., Taubes, A. L., Grone, B. P., Zalocusky, K. A., Fragiadakis, G. K., et al. (2022) · Frontiers in Aging Neuroscience · doi:10.3389/fnagi.2022.749991 · Cited by 13

Spatially and cell-type resolved quantitative proteomic atlas of healthy human skin

Dyring-Andersen, B., Løvendorf, M. B., Coscia, F., et al. (2020) · doi:10.1101/2020.06.22.163717 · Cited by 11

How to ensure the Human Cell Atlas benefits humanity

Majumder, P. P., Mhlanga, M. M., Shalek, A. K., Guigó, R., Knoppers, B. M., & Wold, B. J. (2022) · Nature · doi:10.1038/d41586-022-01186-0 · Cited by 5

Multi-regional characterisation of renal cell carcinoma and microenvironment at single cell resolutionPreprint

Li, R., Ferdinand, J. R., Loudon, K. W., Bowyer, G., Mamanova, L., Neves, J. B., Bolt, L., Fasouli, E. S., Lawson, A. R. J., Young, M. D., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.11.12.468373 · Cited by 2

Molecular Profiling of COVID-19 Autopsies Uncovers Novel Disease MechanismsPreprint

Pujadas, E., Beaumont, M. A., Shah, H., et al. (2021) · medRxiv · doi:10.1101/2021.04.04.21253205 · Cited by 1

Large-scale foundation model on single-cell transcriptomics

Hao, M., Gong, J., Zeng, X., Liu, C., Guo, Y., Cheng, X., Wang, T., Ma, J., Zhang, X., & Song, L. (2024) · Nature Methods · doi:10.1038/s41592-024-02305-7 · Cited by 628

Profiling cell identity and tissue architecture with single-cell and spatial transcriptomics

Gulati, G. S., D'Silva, J. P., Liu, Y., Wang, L., & Newman, A. M. (2024) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-024-00768-2 · Cited by 335

Automatic cell-type harmonization and integration across Human Cell Atlas datasets

Xu, C., Prete, M., Webb, S., Jardine, L., Stewart, B. J., Hoo, R., He, P., Meyer, K. B., & Teichmann, S. A. (2023) · Cell · doi:10.1016/j.cell.2023.11.026 · Cited by 299

Regulation of phospholipid distribution in the lipid bilayer by flippases and scramblases

Sakuragi, T., & Nagata, S. (2023) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-023-00604-z · Cited by 278

Single-cell sequencing to multi-omics: technologies and applications

Wu, X., Yang, X., Dai, Y., Zhao, Z., Zhu, J., Guo, H., & Yang, R. (2024) · Biomarker Research · doi:10.1186/s40364-024-00643-4 · Cited by 222

Cell Atlases as Roadmaps in Health and Disease

Regev, A. (2020) · The Keio Journal of Medicine · doi:10.2302/kjm.69-002-abst

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

Rood, J., Wynne, S., Robson, L., Hupalowska, A., Randell, J., Teichmann, S. A., & Regev, A. (2024) · Nature · doi:10.1038/s41586-024-08338-4 · Cited by 173

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

Zhang, P., & Li, S. (2022) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-022-01201-w · Cited by 13

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

Novoa, J., Pazos, F., & Chagoyen, M. (2026) · Briefings in Bioinformatics · doi:10.1093/bib/bbag426 · Cited by 1

Mining single-cell data for cell type–disease associations

Chen, K., Farley, K. O., & Lassmann, T. (2024) · NAR Genomics and Bioinformatics · doi:10.1093/nargab/lqae180