The DOI matches its Crossref record; 32 of the 32 references it cites were found in a registry or an index.
Computational methods for single-cell omics across modalities
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“Increasingly sophisticated experimental approaches have allowed discovery of significant diversity and functional heterogeneity within the fibroblast population during organ fibrosis22–25 .”
From Fibrosis: from mechanisms to medicines (2020) · cites this paper as [24]
In the citing paper
“Correlated transcriptomic and epigenomic signatures can allow computational methods to integrate independent datasets despite batch effects and systematic differences (Efremova and Teichmann, 2020).”
From Single-Cell Sequencing of Brain Cell Transcriptomes and Epigenomes (2021) · cites this paper as Efremova and Teichmann, 2020
Citations
Cites
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
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
Scenic: single-cell regulatory network inference and clustering.
Aibar, S., González-Blas, C. B., Moerman, T., Huynh-Thu, V. A., Imrichova, H., Hulselmans, G., Rambow, F., Marine, J.-C., Geurts, P., Aerts, J., et al. (2017) · Nature Methods · doi:10.1038/nmeth.4463 · Cited by 6,520
Efremova, M., Vento-Tormo, M., Teichmann, S. A., & Vento-Tormo, R. (2020) · Nature Protocols · doi:10.1038/s41596-020-0292-x · Cited by 3,449
Self-citationSimultaneous epitope and transcriptome measurement in single cells
Stoeckius, M., Hafemeister, C., Stephenson, W., Houck-Loomis, B., Chattopadhyay, P. K., Swerdlow, H., Satija, R., & Smibert, P. (2017) · Nature Methods · doi:10.1038/nmeth.4380 · Cited by 3,098
Single-Cell Multi-omic Integration Compares and Contrasts Features of Brain Cell Identity
Welch, J. D., Kozareva, V., Ferreira, A., Vanderburg, C., Martin, C., & Macosko, E. Z. (2019) · Cell · doi:10.1016/j.cell.2019.05.006 · Cited by 1,193
MOFA+: a statistical framework for comprehensive integration of multi-modal single-cell data
Argelaguet, R., Arnol, D., Bredikhin, D., Deloro, Y., Velten, B., Marioni, J. C., & Stegle, O. (2020) · Genome Biology · doi:10.1186/s13059-020-02015-1 · Cited by 1,091
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
Multiplexed quantification of proteins and transcripts in single cells
Peterson, V. M., Zhang, K. X., Kumar, N., Wong, J., Li, L., Wilson, D. C., Moore, R., McClanahan, T. K., Sadekova, S., & Klappenbach, J. A. (2017) · Nature Biotechnology · doi:10.1038/nbt.3973 · Cited by 832
Lineage Tracing in Humans Enabled by Mitochondrial Mutations and Single-Cell Genomics
Ludwig, L. S., Lareau, C. A., Ulirsch, J. C., Christian, E., Muus, C., Li, L. H., Pelka, K., Ge, W. H., Oren, Y., Brack, A., et al. (2019) · Cell · doi:10.1016/j.cell.2019.01.022 · Cited by 554
Research works printed but not linked: 1
- Burdziak, C., Azizi, E., Prabhakaran, S. & Pe’er, D. A nonparametric multi-view model for estimating cell type-specific gene regulatory networks. Preprint at arXiv https://arxiv.org/abs/1902.08138 (2019). · arXiv
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Items 201–211 of 211
Modeling Dynamics, Cell Type Specificity, and Perturbations in Gene Regulatory Networks
Shin, J., Halberg, S., Liu, Y., Hazra, S., Lee, E. D.-I., & Roy, S. (2026) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-120922-103729
Outissint, I., Pan, H., Lu, P., Tang, M., & Gong, X. (2026) · Pathology - Research and Practice · doi:10.1016/j.prp.2026.156485
CellPulse: A Foundation Model of Coordinated Gene Dynamics Simulating Viral Infectious DiseasesPreprint
Liu, D., Zhu, X., Zhang, L., Xu, D., Lou, J., Xiong, X., Ren, Y., Wu, Y. N., & Zhou, X. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.04.22.720078
Robust semi-supervised scRNA-seq integration from virtual adversarial learningPreprint
He, C., Filippidis, P., Xing, J., Kleinstein, S., & Guan, L. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.06.07.730754
Wang, C., Chen, Y., Feng, X., Yan, C., Ma, Y., Tian, X., Ji, X., Xue, L., Wang, H., Zhang, J., et al. (2026) · Food Bioscience · doi:10.1016/j.fbio.2026.109261
Intraclonal heterogeneity in mature B-cell malignancies: The perspective of immunogenetics
Iatrou, A., Roussos, A., Chatzikonstantinou, T., Chatzidimitriou, A., Stamatopoulos, K., & Agathangelidis, A. (2026) · Seminars in Cancer Biology · doi:10.1016/j.semcancer.2026.102616
Waqas, W., Dildar, T., Shafiq, M., Ullah, A., Shah, S. A. U. R., Ikhwanuddin, M., & Ma, H. (2026) · Journal of Environmental Sciences · doi:10.1016/j.jes.2026.105796
SingPro 2.0: a proteomics-centric knowledge base for single-cell multimodal profiling
Zhou, Y., Deng, J., Zhu, Z., Kou, Y., Pan, Z., Zhang, Y., Jiang, Y., Sun, X., Lian, X., Mou, M., et al. (2026) · Nucleic Acids Research · doi:10.1093/nar/gkag933
Sethi, R., & Chen, J. (2024) · Zenodo (CERN European Organization for Nuclear Research) · doi:10.5281/zenodo.10609309
Disentangling Over-Integration of Single-Cell and Spatial Multiomics Data with Transfer Learning
Lu, R., Zhang, S., & Gao, L. (2026) · Big Data Mining and Analytics · doi:10.26599/bdma.2025.9020112
Wan, J., Zhao, D., Li, S., Gao, X., & Shao, Y. (2026) · Biomolecules · doi:10.3390/biom16111578
Metadata
- Authors
- Efremova, M., & Teichmann, S. A.
- Affiliations
- Wellcome Sanger Institute (GB)
- University of Cambridge (GB)
- Corresponding author
- Teichmann, Sarah A.
- Venue
- Nature Methods
- Published
- 2020-01
- Volume
- 17
- Issue
- 1
- Pages
- 14-17
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- OpenAlex
- W2998127407
- Cited by
- 201
- References
- 31
- Citations by year
- 2026: 14 · 2025: 20 · 2024: 28 · 2023: 41 · 2022: 28 · 2021: 48 · 2020: 22
- FWCI
- 11.29
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Nature Methods (publishedVersion)
- PubMed (publishedVersion)
- Queen Mary Research Online (Queen Mary University of London) (submittedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Keywords
- single-cell omics, multi-omics integration, single-cell genomics, single-cell epigenomics, single-cell transcriptomics, single-cell proteomics, gene regulatory networks, signaling networks, cell identity, computational methods
- MeSH terms
- Epigenome, Humans, Computational Biology, Proteome, Gene Expression Profiling, Gene Regulatory Networks, Metabolic Networks and Pathways, Single-Cell Analysis
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