The DOI matches its Crossref record; 70 of the 70 references it cites were found in a registry or an index.
Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq
Open accessAbstract
Single-cell expression profiles of melanoma: Tumors harbor multiple cell types that are thought to play a role in the development of resistance to drug treatments. Tirosh et al. used single-cell sequencing to investigate the distribution of these differing genetic profiles within melanomas. Many cells harbored heterogeneous genetic programs that reflected two different states of genetic expression, one of which was linked to resistance development. Following drug treatment, the resistance-linked expression state was found at a much higher level. Furthermore, the environment of the melanoma cells affected their gene expression programs. Science , this issue p. 189
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“SALL4-regulated genes showed a significant enrichment and positive correlation with published invasiveness signatures40–42, while they significantly anti-correlated with their corresponding proliferation signatures40–42”
From Epigenetic control of melanoma cell invasiveness by the stem cell factor SALL4 (2021) · cites this paper as [42]
Experimental — accuracy not yet measuredThe check wasn’t confident either way, so it gives no verdict — never disputed.
In the citing paper
“among the SALL4-HDAC2 targets upregulated upon SALL4 knockdown, we found integrins (ITGB1, ITGA6, ITGA4), N-cadherin (CDH2), TGFBR2, VEGFR-1, PDGFC, LOXL2, MAPK8, and many others which are associated with invasive melanoma phenotypes40–42”
From Epigenetic control of melanoma cell invasiveness by the stem cell factor SALL4 (2021) · cites this paper as [42]
Experimental — accuracy not yet measuredThe check wasn’t confident either way, so it gives no verdict — never disputed.
In the citing paper
“Consistent with previous reports in mice 43 , the proportions of HSCs expressing G2/M/S-phase genes were enhanced upon IFNa treatment ( Fig. 2h,i) .”
From Type 1 interferon perturbates clonal competition by reshaping human blood development (2026) · cites this paper as [43]
Experimental — accuracy not yet measuredThe check wasn’t confident either way, so it gives no verdict — never disputed.
In the citing paper
“As IFNa has been shown to induce HSC and progenitors into cell cycle entry 43 , we posited that differential induction of progenitor subtypes into proliferation may underlie the shifts in differentiation.”
From Type 1 interferon perturbates clonal competition by reshaping human blood development (2026) · cites this paper as [43]
Experimental — accuracy not yet measuredIn the citing paper
“Almost all previous work quantifying differences between single-cell datasets relies on discrete partitioning of the data before downstream analysis9–16.”
From Quantifying the effect of experimental perturbations at single-cell resolution (2021) · cites this paper as [11]
In the citing paper
“Cell cycle genes56 were excluded from this feature set and the dataset was subsetted to the resulting gene set.”
From Inferring and perturbing cell fate regulomes in human brain organoids (2023) · cites this paper as [56]
In the citing paper
“We used the union of the selected genes and TFs and further excluded cell-cycle-related genes56 from the set.”
From Inferring and perturbing cell fate regulomes in human brain organoids (2023) · cites this paper as [56]
In the citing paper
“Through deconvolution of complex samples30, such as tumor biopsies35, one may infer their cellular milieu, and characterize the rare5, functionally important1, and unknown36 cell types they contain.”
From Revealing the vectors of cellular identity with single-cell genomics (2016) · cites this paper as [35]
In the citing paper
“Several studies inferred the cell cycle phase of individual cells from single-cell RNA-seq data30,35,97,99, relying on transcriptional signatures of discrete phases from earlier bulk profiling experiments146.”
From Revealing the vectors of cellular identity with single-cell genomics (2016) · cites this paper as [35]
In the citing paper
“We performed latent variable regression to mitigate heterogeneity resulting from cell-cycle state10,11 (Extended Data Fig. 1), preventing subsequent analysis from being dominated by mitotic phase-specific gene expression”
From Developmental diversification of cortical inhibitory interneurons (2018) · cites this paper as [11]
In the citing paper
“In parallel, methods to measure the transcriptomes of single cells have been used to discover new cell types11 and new functional cell states12,13, and provide additional motivation for the development of tools to measure chromatin regulation at single-cell resolution14.”
From Droplet-based combinatorial indexing for massive-scale single-cell chromatin accessibility (2019) · cites this paper as [12]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Hallmarks of Cancer: The Next Generation
Hanahan, D., & Weinberg, R. A. (2011) · Cell · doi:10.1016/j.cell.2011.02.013 · Cited by 66,590
Fast and accurate short read alignment with Burrows-Wheeler transform
Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607
(2008) · Journal of Machine Learning Research · Cited by 33,051
PD-1 and PD-L1 Immune Checkpoint Blockade to Treat Breast Cancer
Hartkopf, A. D., Taran, F., Wallwiener, M., Walter, C. B., Krämer, B., Grischke, E., & Brucker, S. Y. (2016) · Breast Care · doi:10.1159/000453569 · Cited by 30,989
New response evaluation criteria in solid tumours: revised RECIST guideline (version 1.1)
Eisenhauer, E. A., Therasse, P., Bogaerts, J., Schwartz, L. H., Sargent, D., Ford, R., Dancey, J., Arbuck, S., Gwyther, S., Mooney, M., et al. (2009) · European Journal of Cancer · doi:10.1016/j.ejca.2008.10.026 · Cited by 29,534
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M., et al. (2010) · Genome Research · doi:10.1101/gr.107524.110 · Cited by 27,895
RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
Li, B., & Dewey, C. N. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-323 · Cited by 22,179
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009) · Genome Biology · doi:10.1186/gb-2009-10-3-r25 · Cited by 21,849
(1996) · Cited by 20,179
Adverse Renal Effects of Immune Checkpoint Inhibitors: A Narrative Review
Wanchoo, R., Karam, S., Uppal, N. N., Barta, V. S., Deray, G., Devoe, C., Launay‐Vacher, V., Jhaveri, K. D., & on behalf of Cancer and Kidney International Network Workgroup on Immune Checkpoint Inhibitors (2017) · American Journal of Nephrology · doi:10.1159/000455014 · Cited by 15,320
Flagged first, then by citations
Cited by
Sorted by citations
Items 501–600 of 1,033
Mapping the genetic landscape of DNA double-strand break repair
Hussmann, J. A., Jia, L., Ravisankar, P., Yan, J., Cirincione, A., Xu, A., Simpson, D., Yang, D., Bothmer, A., Cotta‐Ramusino, C., et al. (2021) · Cell · doi:10.1016/j.cell.2021.10.002 · Cited by 188
Murine single-cell RNA-seq reveals cell-identity- and tissue-specific trajectories of aging
Kimmel, J. C., Penland, L., Rubinstein, N. D., Hendrickson, D. G., Kelley, D. R., & Rosenthal, A. Z. (2019) · Genome Research · doi:10.1101/gr.253880.119 · Cited by 184
“To investigate changes in cell cycle frequency in our data, we evaluated cell cycle activity by scoring the expression of S phase–associated genes andG2M-associated genes (Methods; Tirosh et al. 2016).”
MethodInitiation of Antiviral B Cell Immunity Relies on Innate Signals from Spatially Positioned NKT Cells
Gaya, M., Barral, P., Burbage, M., Aggarwal, S., Montaner, B., Navia, A. W., Aïd, M., Tsui, C., Villavicencio, P. M., Nair, U., et al. (2017) · Cell · doi:10.1016/j.cell.2017.11.036 · Cited by 184
Self-citationCurrent Advances in the Treatment of BRAF-Mutant Melanoma
Patel, H. M., Yacoub, N., Mishra, R., White, A., Yuan, L., Alanazi, S., & Garrett, J. T. (2020) · Cancers · doi:10.3390/cancers12020482 · Cited by 184
Olalekan, S. A., Xie, B., Back, R., Eckart, H., & Basu, A. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.109165 · Cited by 184
Zywitza, V., Misios, A., Bunatyan, L., Willnow, T. E., & Rajewsky, N. (2018) · Cell Reports · doi:10.1016/j.celrep.2018.11.003 · Cited by 183
IFNγ-Dependent Tissue-Immune Homeostasis Is Co-opted in the Tumor Microenvironment
Nirschl, C. J., Suárez‐Fariñas, M., Izar, B., Prakadan, S. M., Dannenfelser, R., Tirosh, I., Liu, Y., Zhu, Q., Devi, K. S. P., Carroll, S. L., et al. (2017) · Cell · doi:10.1016/j.cell.2017.06.016 · Cited by 183
Self-citationPei, W., Shang, F., Wang, X., Fanti, A.-K., Greco, A., Busch, K., Klapproth, K., Zhang, Q., Quedenau, C., Sauer, S., et al. (2020) · Cell stem cell · doi:10.1016/j.stem.2020.07.018 · Cited by 183
An atlas of cells in the human tonsil
Massoni-Badosa, R., Aguilar-Fernández, S., Nieto, J. C., Soler-Vila, P., Elosua-Bayés, M., Marchese, D., Kulis, M., Vilas‐Zornoza, A., Bühler, M. M., Rashmi, S., et al. (2024) · Immunity · doi:10.1016/j.immuni.2024.01.006 · Cited by 188
Crespo-Garcia, S., Tsuruda, P. R., Dejda, A., Ryan, R. D., Fournier, F., Chaney, S. Y., Pilon, F., Dogan, T., Cagnone, G., Patel, P., et al. (2021) · Cell Metabolism · doi:10.1016/j.cmet.2021.01.011 · Cited by 182
Discrete limbal epithelial stem cell populations mediate corneal homeostasis and wound healing
Altshuler, A., Amitai-Lange, A., Tarazi, N., Dey, S., Strinkovsky, L., Hadad-Porat, S., Bhattacharya, S., Nasser, W., Imeri, J., Ben-David, G., et al. (2021) · Cell stem cell · doi:10.1016/j.stem.2021.04.003 · Cited by 181
Characterizing dedifferentiation of thyroid cancer by integrated analysis
Luo, H., Xia, X., Kim, G. D., Liu, Y., Xue, Z., Zhang, L., Shu, Y., Yang, T., Chen, Y., Zhang, S., et al. (2021) · Science Advances · doi:10.1126/sciadv.abf3657 · Cited by 181
B-cell-specific checkpoint molecules that regulate anti-tumour immunity
Bod, L., Kye, Y.-C., Shi, J., Triglia, E. T., Schnell, A., Fessler, J., Ostrowski, S. M., von Franque, M., Kuchroo, J. R., Barilla, R., et al. (2023) · Nature · doi:10.1038/s41586-023-06231-0 · Cited by 188
Self-citationSingle-cell CRISPR screens in vivo map T cell fate regulomes in cancer
Zhou, P., Shi, H., Huang, H., Sun, X., Yuan, S., Chapman, N. M., Connelly, J. P., Lim, S. A., Saravia, J., Anil, K. C., et al. (2023) · Nature · doi:10.1038/s41586-023-06733-x · Cited by 190
Heming, M., Li, X., Räuber, S. J., Mausberg, A. K., Börsch, A., Hartlehnert, M., Singhal, A., Lu, I., Fleischer, M., Szepanowski, F., et al. (2020) · Immunity · doi:10.1016/j.immuni.2020.12.011 · Cited by 181
Basement membrane stiffness determines metastases formation
Reuten, R., Zendehroud, S., Nicolau, M., Fleischhauer, L., Laitala, A., Kiderlen, S., Nikodemus, D., Wullkopf, L., Nielsen, S. R., McNeilly, S., et al. (2021) · Nature Materials · doi:10.1038/s41563-020-00894-0 · Cited by 181
Anadon, C. M., Yu, X., Hänggi, K., Biswas, S., Chaurio, R. A., Martin, A., Payne, K. K., Mandal, G., Innamarato, P., Harro, C. M., et al. (2022) · Cancer Cell · doi:10.1016/j.ccell.2022.03.008 · Cited by 185
Targeting minimal residual disease: a path to cure?
Luskin, M. R., Murakami, M. A., Manalis, S. R., & Weinstock, D. M. (2018) · Nature reviews. Cancer · doi:10.1038/nrc.2017.125 · Cited by 179
Generation of hypothalamic arcuate organoids from human induced pluripotent stem cells
Huang, W., Wong, S. Z. H., Pather, S. R., Nguyen, P. T., Zhang, F., Zhang, D. Y., Zhang, Z., Lu, L., Fang, W., Chen, L., et al. (2021) · Cell stem cell · doi:10.1016/j.stem.2021.04.006 · Cited by 179
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
Optimized human intestinal organoid model reveals interleukin-22-dependency of paneth cell formation
He, G.-W., Lin, L., DeMartino, J., Zheng, X., Staliarova, N., Dayton, T., Begthel, H., van de Wetering, W. J., Bodewes, E., van Zon, J., et al. (2022) · Cell Stem Cell · doi:10.1016/j.stem.2022.08.002 · Cited by 178
Genomic Approaches to Understanding Response and Resistance to Immunotherapy
Braun, D. A., Burke, K. P., & Allen, E. M. V. (2016) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-16-0066 · Cited by 178
Gueguen, P., Metoikidou, C., Dupic, T., Lawand, M., Goudot, C., Baulande, S., Lameiras, S., Lantz, O. J., Girard, N., Seguin‐Givelet, A., et al. (2021) · Science Immunology · doi:10.1126/sciimmunol.abd5778 · Cited by 181
Zhang, X., Zhang, C., Qiao, M., Cheng, C., Tang, N., Lu, S., Sun, W. C., Xu, B., Cao, Y., Wei, X., et al. (2022) · Cancer Cell · doi:10.1016/j.ccell.2022.09.013 · Cited by 176
The Receptor Tyrosine Kinase AXL in Cancer Progression
Rankin, E. B., & Giaccia, A. J. (2016) · Cancers · doi:10.3390/cancers8110103 · Cited by 174
Linking genome structures to functions by simultaneous single-cell Hi-C and RNA-seq
Liu, Z., Chen, Y., Xia, Q., Liu, M., Xu, H., Chi, Y., Deng, Y., & Xing, D. (2023) · Science · doi:10.1126/science.adg3797 · Cited by 174
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
Self-citationLightbody, G., Haberland, V., Browne, F., Taggart, L., Zheng, H., Parkes, E., & Blayney, J. K. (2019) · Briefings in Bioinformatics · doi:10.1093/bib/bby051 · Cited by 173
An integrative ENCODE resource for cancer genomics
Zhang, J., Lee, D., Dhiman, V., Jiang, P., Xu, J., McGillivray, P., Yang, H., Liu, J., Meyerson, W., Clarke, D., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-14743-w · Cited by 172
Raman-guided subcellular pharmaco-metabolomics for metastatic melanoma cells
Du, J., Su, Y., Qian, C., Yuan, D., Miao, K., Lee, D., Ng, A. H. C., Wijker, R. S., Ribas, A., Levine, R. D., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-18376-x · Cited by 171
Heterogeneity within molecular subtypes of breast cancer
Turner, K. M., Yeo, S. K., Holm, T. M., Shaughnessy, E., & Guan, J. (2021) · American Journal of Physiology-Cell Physiology · doi:10.1152/ajpcell.00109.2021 · Cited by 171
Experimental Considerations for Single-Cell RNA Sequencing Approaches
Nguyen, Q. H., Pervolarakis, N., Nee, K., & Kessenbrock, K. (2018) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2018.00108 · Cited by 170
A single-cell tumor immune atlas for precision oncologyPreprint
Nieto, P., Elosua-Bayés, M., Trincado, J. L., Marchese, D., Massoni-Badosa, R., Salvany, M., Henriques, A. R., Nieto, J. C., Aguilar-Fernández, S., Mereu, E., et al. (2021) · Genome Research · doi:10.1101/gr.273300.120 · Cited by 171
Single cell transcriptomic analysis of human pluripotent stem cell chondrogenesis
Wu, C., Dicks, A. R., Steward, N. S., Tang, R., Katz, D. B., Choi, Y., & Guilak, F. (2021) · Nature Communications · doi:10.1038/s41467-020-20598-y · Cited by 169
Reconstruction of the tumor spatial microenvironment along the malignant-boundary-nonmalignant axis
Xun, Z., Ding, X., Zhang, Y., Zhang, B., Lai, S., Zou, D., Zheng, J., Chen, G., Su, B., Han, L., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-36560-7 · Cited by 169
Dissecting intratumoral myeloid cell plasticity by single cell RNA-seq
Song, Q., Hawkins, G. A., Wudel, L., Chou, P., Forbes, E., Pullikuth, A. K., Liu, L., Jin, G., Craddock, L., Topaloglu, U., et al. (2019) · Cancer Medicine · doi:10.1002/cam4.2113 · Cited by 168
Single-Cell Genomics: A Stepping Stone for Future Immunology Discoveries
Giladi, A., & Amit, I. (2018) · Cell · doi:10.1016/j.cell.2017.11.011 · Cited by 168
Reinhardt, J., Landsberg, J., Schmid-Burgk, J. L., Ramis, B. B., Bald, T., Glodde, N., Lopez-Ramos, D., Young, A., Ngiow, S. F., Nettersheim, D., et al. (2017) · Cancer Research · doi:10.1158/0008-5472.can-17-0395 · Cited by 167
Decoding Human Megakaryocyte Development
Wang, H., He, J., Xu, Z., Chen, X., Yang, H. Q., Shi, S., Liu, C., Zeng, Y., Wu, D., Bai, Z., et al. (2020) · Cell stem cell · doi:10.1016/j.stem.2020.11.006 · Cited by 170
Ma, L., Heinrich, S., Wang, L., Keggenhoff, F. L., Khatib, S. A., Forgues, M., Kelly, M. C., Hewitt, S. M., Saif, A., Hernandez, J. M., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-35291-5 · Cited by 178
Cancer cells impair monocyte-mediated T cell stimulation to evade immunity
Elewaut, A., Estivill, G., Bayerl, F., Castillon, L., Novatchkova, M., Pottendorfer, E., Hoffmann-Haas, L., Schönlein, M., Nguyễn, T. C. B., Lauss, M., et al. (2024) · Nature · doi:10.1038/s41586-024-08257-4 · Cited by 167
Integrated single-cell analysis of multicellular immune dynamics during hyperacute HIV-1 infection
Kazer, S. W., Aicher, T. P., Muema, D., Carroll, S. L., Ordovás-Montañés, J., Miao, V. N., Tu, A. A., Ziegler, C. G. K., Nyquist, S. K., Wong, E. B., et al. (2020) · Nature Medicine · doi:10.1038/s41591-020-0799-2 · Cited by 168
Self-citationSCSA: A Cell Type Annotation Tool for Single-Cell RNA-seq Data
Cao, Y., Wang, X., & Peng, G. (2020) · Frontiers in Genetics · doi:10.3389/fgene.2020.00490 · Cited by 166
Dost, A. F. M., Moye, A. L., Vedaie, M., Tran, L. M., Fung, E., Heinze, D. M., Villacorta-Martín, C., Huang, J., Hekman, R. M., Kwan, J., et al. (2020) · Cell stem cell · doi:10.1016/j.stem.2020.07.022 · Cited by 166
A single cell atlas of the human liver tumor microenvironment
Massalha, H., Halpern, K. B., Abu‐Gazala, S., Jana, T., Massasa, E. E., Moor, A. E., Buchauer, L., Rozenberg, M., Pikarsky, E., Amit, I., et al. (2020) · Molecular Systems Biology · doi:10.15252/msb.20209682 · Cited by 167
Single-Cell Transcriptomic Map of the Human and Mouse Bladders
Yu, Z., Liao, J., Chen, Y., Zou, C., Zhang, H., Cheng, J., Liu, D., Li, T., Zhang, Q., Li, J., et al. (2019) · Journal of the American Society of Nephrology · doi:10.1681/asn.2019040335 · Cited by 164
Kim, K.-S., Park, S., Park, S. Y., Kim, G., Park, S. M., Cho, J.-W., Kim, D., Park, Y. M., Koh, Y. W., Kim, H. R., et al. (2020) · Genome Medicine · doi:10.1186/s13073-020-00722-9 · Cited by 164
Shao, X., Lu, X., Liao, J., Chen, H., & Fan, X. (2020) · Protein & Cell · doi:10.1007/s13238-020-00727-5 · Cited by 164
Single-cell multiomics reveals persistence of HIV-1 in expanded cytotoxic T cell clones
Collora, J. A., Liu, R., Pinto-Santini, D., Ravindra, N. G., Ganoza, C., Lama, J. R., Alfaro, R., Chiarella, J., Spudich, S., Mounzer, K., et al. (2022) · Immunity · doi:10.1016/j.immuni.2022.03.004 · Cited by 164
Xu, Y., Su, G.-H., Ma, D., Xiao, Y., Shao, Z.-M., & Jiang, Y.-Z. (2021) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-021-00729-7 · Cited by 163
Cancer Stem Cells and Epithelial-to-Mesenchymal Transition in Cancer Metastasis
Celià-Terrassa, T., & Jolly, M. K. (2020) · Cold Spring Harbor Perspectives in Medicine · doi:10.1101/cshperspect.a036905 · Cited by 163
Single-cell analyses to tailor treatments
Shalek, A. K., & Benson, M. (2017) · Science Translational Medicine · doi:10.1126/scitranslmed.aan4730 · Cited by 163
Self-citationCombating subclonal evolution of resistant cancer phenotypes
Brady, S. W., McQuerry, J. A., Qiao, Y., Piccolo, S., Shrestha, G., Jenkins, D. F., Layer, R. M., Pedersen, B. S., Miller, R. H., Esch, A. M., et al. (2017) · Nature Communications · doi:10.1038/s41467-017-01174-3 · Cited by 163
A NOTCH feed-forward loop drives reprogramming from adrenergic to mesenchymal state in neuroblastoma
van Groningen, T., Akogul, N., Westerhout, E. M., Chan, A., Hasselt, N. E., Zwijnenburg, D. A., Broekmans, M. E. C., Stroeken, P. J. M., Haneveld, F., Hooijer, G. K. J., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-09470-w · Cited by 163
Cell-type-specific resolution epigenetics without the need for cell sorting or single-cell biology
Rahmani, E., Schweiger, R., Rhead, B., Criswell, L. A., Barcellos, L. F., Eskin, E., Rosset, S., Sankararaman, S., & Halperin, E. (2019) · Nature Communications · doi:10.1038/s41467-019-11052-9 · Cited by 163
Fan, X., Fu, Y., Zhou, X., Sun, L., Yang, M., Wang, M., Chen, R., Wu, Q., Yong, J., Dong, J., et al. (2020) · Science Advances · doi:10.1126/sciadv.aaz2978 · Cited by 163
Midkine rewires the melanoma microenvironment toward a tolerogenic and immune-resistant state
Cerezo‐Wallis, D., Contreras-Alcalde, M., Troulé, K., Catena, X., Mucientes, C., Calvo, T. G., Cañón, E., Tejedo, C., Pennacchi, P. C., Hogan, S. A., et al. (2020) · Nature Medicine · doi:10.1038/s41591-020-1073-3 · Cited by 168
Haas, Q., Boligan, K. F., Jandus, C., Schneider, C., Simillion, C., Stanczak, M. A., Haubitz, M., Jafari, S. M. S., Zippelius, A., Baerlocher, G. M., et al. (2019) · Cancer Immunology Research · doi:10.1158/2326-6066.cir-18-0505 · Cited by 164
Reconstructing cell cycle pseudo time-series via single-cell transcriptome data
Liu, Z., Lou, H., Xie, K., Wang, H. E., Chen, N., Aparicio, O. M., Zhang, M. Q., Jiang, R., & Chen, T. (2017) · Nature Communications · doi:10.1038/s41467-017-00039-z · Cited by 160
Song, C., Piva, M., Sun, L., Hong, A., Moriceau, G., Kong, X., Zhang, H., Lomeli, S. H., Qian, J., Yu, C. C., et al. (2017) · Cancer Discovery · doi:10.1158/2159-8290.cd-17-0401 · Cited by 160
Targeting the Warburg effect via LDHA inhibition engages ATF4 signaling for cancer cell survival
Pathria, G., Scott, D. A., Feng, Y., Lee, J. S., Fujita, Y., Zhang, G., Sahu, A. D., Ruppin, E., Herlyn, M., Osterman, A. L., et al. (2018) · The EMBO Journal · doi:10.15252/embj.201899735 · Cited by 163
MiT/TFE Family of Transcription Factors, Lysosomes, and Cancer
Perera, R. M., Malta, C. D., & Ballabio, A. (2018) · Annual Review of Cancer Biology · doi:10.1146/annurev-cancerbio-030518-055835 · Cited by 162
Role of Radiation Therapy in Modulation of the Tumor Stroma and Microenvironment
Menon, H., Ramapriyan, R., Cushman, T. R., Verma, V., Kim, H. H., Schoenhals, J. E., Atalar, S. C., Selek, U., Chun, S. G., Chang, J. Y., et al. (2019) · Frontiers in Immunology · doi:10.3389/fimmu.2019.00193 · Cited by 160
Next-generation computational tools for interrogating cancer immunity
Finotello, F., Rieder, D., Hackl, H., & Trajanoski, Z. (2019) · Nature Reviews Genetics · doi:10.1038/s41576-019-0166-7 · Cited by 161
Xi, H., Langerman, J., Sabri, S., Chien, P., Young, C. S., Younesi, S., Hicks, M. R., Gonzalez, K. M., Fujiwara, W., Marzi, J., et al. (2020) · Cell stem cell · doi:10.1016/j.stem.2020.04.017 · Cited by 160
Song, G., Shi, Y., Lu, M., Ma, J., Huang, S., Zhang, J., Wu, Y. C., Li, J., Lin, Y., Yang, S., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-29164-0 · Cited by 160
Self-citationSmalley, I., Chen, Z., Phadke, M. A., Li, J., Yu, X., Wyatt, C. J., Evernden, B. R., Messina, J. L., Sarnaik, A. A., Sondak, V. K., et al. (2021) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-21-1694 · Cited by 159
FOXM1 drives proximal tubule proliferation during repair from acute ischemic kidney injury
Chang-Panesso, M., Kadyrov, F. F., Lalli, M., Wu, H., Ikeda, S., Kefaloyianni, E., Abdelmageed, M. M., Herrlich, A., Kobayashi, A., & Humphreys, B. D. (2019) · Journal of Clinical Investigation · doi:10.1172/jci125519 · Cited by 158
Yang, H. H., & Lin, P. C. (2017) · Seminars in Cancer Biology · doi:10.1016/j.semcancer.2017.08.001 · Cited by 157
The Influence of Tumor Microenvironment on Immune Escape of Melanoma
Simiczyjew, A., Dratkiewicz, E., Mazurkiewicz, J., Ziętek, M., Matkowski, R., & Nowak, D. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21218359 · Cited by 157
Atherosclerosis Is a Smooth Muscle Cell–Driven Tumor-Like Disease
Pan, H., Ho, S. E., Xue, C., Cui, J. G., Johanson, Q., Sachs, N., Ross, L. S., Li, F., Solomon, R. A., Connolly, E. S., et al. (2024) · Circulation · doi:10.1161/circulationaha.123.067587 · Cited by 157
The bone-marrow niche in MDS and MGUS: implications for AML and MM
Ghobrial, I. M., Detappe, A., Anderson, K. C., & Steensma, D. P. (2018) · Nature Reviews Clinical Oncology · doi:10.1038/nrclinonc.2017.197 · Cited by 156
Durães, F. D. V., Lafont, A., Beibel, M., Martin, K., Darribat, K., Cuttat, R., Waldt, A., Naumann, U., Wieczorek, G., Gaulis, S., et al. (2020) · JCI Insight · doi:10.1172/jci.insight.130651 · Cited by 156
LifeTime and improving European healthcare through cell-based interceptive medicine
Rajewsky, N., Almouzni, G., Gorski, S. A., Aerts, S., Amit, I., Bertero, M. G., Bock, C., Bredenoord, A. L., Cavalli, G., Chiocca, S., et al. (2020) · Nature · doi:10.1038/s41586-020-2715-9 · Cited by 157
Jeong, H. Y., Ham, I.-H., Lee, S. H., Ryu, D., Son, S.-Y., Han, S.-U., Kim, T.-M., & Hur, H. (2021) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-21-0792 · Cited by 156
Antigen Dominance Hierarchies Shape TCF1+ Progenitor CD8 T Cell Phenotypes in Tumors
Burger, M. L., Cruz, A. M., Crossland, G. E., Gaglia, G., Ritch, C. C., Blatt, S. E., Bhutkar, A. J., Canner, D. A., Kienka, T., Tavana, S. Z., et al. (2021) · Cell · doi:10.1016/j.cell.2021.08.020 · Cited by 158
Self-citationSpatial landscapes of cancers: insights and opportunities
Chen, J., Larsson, L., Swarbrick, A., & Lundeberg, J. (2024) · Nature Reviews Clinical Oncology · doi:10.1038/s41571-024-00926-7 · Cited by 156
Pan-Peptide Meta Learning for T-cell receptor–antigen binding recognition
Gao, Y., Gao, Y., Fan, Y., Zhu, C., Wei, Z., Zhou, C., Chuai, G., Chen, Q., Zhang, H., & Liu, Q. (2023) · Nature Machine Intelligence · doi:10.1038/s42256-023-00619-3 · Cited by 155
Molecular transitions in early progenitors during human cord blood hematopoiesis
Zheng, S., Papalexi, E., Butler, A., Stephenson, W., & Satija, R. (2018) · Molecular Systems Biology · doi:10.15252/msb.20178041 · Cited by 155
High-throughput single-сell sequencing in cancer research
Jia, Q., Chu, H., Jin, Z., Long, H., & Zhu, B. (2022) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-022-00990-4 · Cited by 157
A single-cell analysis reveals tumor heterogeneity and immune environment of acral melanoma
Zhang, C., Shen, H., Yang, T., Li, T., Liu, X., Wang, J., Liao, Z., Wei, J., Lu, J., Liu, H., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-34877-3 · Cited by 163
Neutralizing IL-8 potentiates immune checkpoint blockade efficacy for glioma
Liu, H., Zhao, Q., Tan, L., Wu, X., Huang, R., Zuo, Y., Chen, L., Yang, J.-G., Zhang, Z., Ruan, W., et al. (2023) · Cancer Cell · doi:10.1016/j.ccell.2023.03.004 · Cited by 156
Ahmed, F., & Haass, N. K. (2018) · Frontiers in Oncology · doi:10.3389/fonc.2018.00173 · Cited by 153
Harmancı, A. S., Harmanci, A. O., & Zhou, X. (2020) · Nature Communications · doi:10.1038/s41467-019-13779-x · Cited by 153
Zhu, B., Wu, Y., Huang, S., Zhang, R., Son, Y. M., Li, C., Cheon, I. S., Gao, X., Wang, M., Yao, C., et al. (2021) · Immunity · doi:10.1016/j.immuni.2021.04.001 · Cited by 153
Single-cell transcriptomic profiling reveals the tumor heterogeneity of small-cell lung cancer
Tian, Y., Li, Q., Yang, Z., Zhang, S., Xu, J., Wang, Z., Bai, H., Duan, J., Zheng, B. J., Li, W., et al. (2022) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-022-01150-4 · Cited by 153
Transcript-indexed ATAC-seq for precision immune profiling
Satpathy, A. T., Saligrama, N., Buenrostro, J. D., Wei, Y., Wu, B., Rubin, A. J., Granja, J. M., Lareau, C. A., Li, R., Qi, Y., et al. (2018) · Nature Medicine · doi:10.1038/s41591-018-0008-8 · Cited by 152
Intratumoral CD103+ CD8+ T cells predict response to PD-L1 blockade
Banchereau, R., Chitre, A. S., Scherl, A., Wu, T. D., Patil, N. S., de Almeida, P. E., Kadel, E. E., Madireddi, S., Au‐Yeung, A., Takahashi, C., et al. (2021) · Journal for ImmunoTherapy of Cancer · doi:10.1136/jitc-2020-002231 · Cited by 153
Mirabella, F., Desiato, G., Mancinelli, S., Fossati, G., Rasile, M., Morini, R., Markicevic, M., Grimm, C., Amegandjin, C. A., Termanini, A., et al. (2021) · Immunity · doi:10.1016/j.immuni.2021.10.006 · Cited by 152
Ferrarotto, R., Mitani, Y., McGrail, D. J., Li, K., Karpinets, T. V., Bell, D., Frank, S. J., Song, X., Kupferman, M. E., Liu, B., et al. (2020) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-20-1192 · Cited by 151
Hsu, C., Ou, D., Bai, L., Chen, C., Lin, L., Huang, S.-F. K., Cheng, A., Jeng, Y., & Hsu, C. (2021) · Liver Cancer · doi:10.1159/000515305 · Cited by 151
Lane, K. M., Valen, D. V., DeFelice, M. M., Macklin, D. N., Kudo, T., Jaimovich, A., Carr, A., Meyer, T., Pe’er, D., Boutet, S. C., et al. (2017) · Cell Systems · doi:10.1016/j.cels.2017.03.010 · Cited by 150
Distinct modes of cell competition shape mammalian tissue morphogenesis
Ellis, S. J., Gomez, N. C., Levorse, J. M., Mertz, A. F., Ge, Y., & Fuchs, E. V. (2019) · Nature · doi:10.1038/s41586-019-1199-y · Cited by 150
Zeng, Y., Liu, C., Gong, Y., Bai, Z., Hou, S., He, J., Bian, Z., Li, Z., Ni, Y., Yan, J., et al. (2019) · Immunity · doi:10.1016/j.immuni.2019.09.008 · Cited by 150
Ren, X., Zhong, G., Zhang, Q., Zhang, L., Sun, Y., & Zhang, Z. (2020) · Cell Research · doi:10.1038/s41422-020-0353-2 · Cited by 152
Zhu, G., Su, H., Johnson, C. H., Khan, S. A., Kluger, H. M., & Lu, L. (2021) · European Journal of Cancer · doi:10.1016/j.ejca.2021.03.053 · 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
Jessa, S., Mohammadnia, A., Harutyunyan, A. S., Hulswit, M., Varadharajan, S., Lakkis, H., Kabir, N., Bashardanesh, Z., Hébert, S., Faury, D., et al. (2022) · Nature Genetics · doi:10.1038/s41588-022-01205-w · Cited by 150
Cebrián‐Silla, A., Nascimento, M. A., Redmond, S., Mansky, B., Wu, D., Obernier, K., Rodriguez, R. R., González-Granero, S., García‐Verdugo, J. M., Lim, D. A., et al. (2021) · eLife · doi:10.7554/elife.67436 · Cited by 148
Transcriptomic profiles of neoantigen-reactive T cells in human gastrointestinal cancers
Zheng, C., Fass, J. N., Shih, Y.-P., Gunderson, A. J., Silva, N. S., Huang, H., Bernard, B. M., Rajamanickam, V., Slagel, J., Bifulco, C. B., et al. (2022) · Cancer Cell · doi:10.1016/j.ccell.2022.03.005 · Cited by 151
Metadata
- Authors
- Tirosh, I., Izar, B., Prakadan, S. M., Wadsworth, M. H., Treacy, D., Trombetta, J. J., Rotem, A., Rodman, C., Lian, C., Murphy, G., Fallahi-Sichani, M., Dutton-Regester, K., Lin, J.-R., Cohen, O., Shah, P., Lu, D., Genshaft, A. S., Hughes, T. K., Ziegler, C. G. K., Kazer, S. W., Gaillard, A., Kolb, K. E., Villani, A.-C., Johannessen, C. M., Andreev, A. Y., Van Allen, E. M., Bertagnolli, M., Sorger, P. K., Sullivan, R. J., Flaherty, K. T., Frederick, D. T., Jané-Valbuena, J., Yoon, C. H., Rozenblatt-Rosen, O., Shalek, A. K., Regev, A., & Garraway, L. A.
- Affiliations
- Broad Institute (US)
- Brigham and Women's Hospital (US)
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA.
- Program in Therapeutic Sciences, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
- Harvard University (US)
- Massachusetts General Hospital (US)
- Corresponding author
- Tirosh, Itay
- Izar, Benjamin
- Yoon, Charles H.
- Shalek, Alex K.
- Regev, Aviv
- Garraway, Levi A.
- ORCID
- Tirosh, Itay
- Izar, Benjamin
- Prakadan, Sanjay M.
- Wadsworth, Marc H.
- Rotem, Asaf
- Rodman, Christopher
- Lian, Christine
- Lin, Jia-Ren
- Cohen, Ofir
- Shah, Parin
- Genshaft, Alex S.
- Hughes, Travis K.
- Ziegler, Carly G. K.
- Kazer, Samuel W.
- Kolb, Kellie E.
- Villani, Alexandra-Chloé
- Johannessen, Cory M.
- Bertagnolli, Monica
- Sorger, Peter K.
- Sullivan, Ryan J.
- Flaherty, Keith T.
- Frederick, Dennie T.
- Yoon, Charles H.
- Shalek, Alex K.
- Regev, Aviv
- Garraway, Levi A.
- Venue
- Science
- Published
- 2016-04-08
- Volume
- 352
- Issue
- 6282
- Pages
- 189-196
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- PMC
- PMC4944528
- OpenAlex
- W2332292689
- Cited by
- 4,944
- References
- 70
- Citations by year
- 2026: 546 · 2025: 629 · 2024: 633 · 2023: 606 · 2022: 582 · 2021: 608 · 2020: 486 · 2019: 336 · 2018: 265 · 2017: 195 · 2016: 41
- FWCI
- 145.13
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc-sa)
- PMC
- Funders
- National Cancer Institute (NCI) (P01CA163222, R35CA197737)
- Dr. Miriam and Sheldon Adelson Medical Research Foundation
- Melanoma Research Alliance
- Ludwig Center at Harvard Medical School
- Howard Hughes Medicine Institute
- Klarman Cell Observatory
- STARR Cancer Consortium
- Broad Institute
- Searle Scholars Program
- Beckman Young Investigator Program
- Dana-Farber Cancer Institute
- Human Frontier Science Program
- Integrative Cancer Biology Program (U54CA112962)
- NCI (1U24CA180922, P30-CA14051, K99CA194163)
- NIH (DP2 OD020839, P50GM107618)
- Ludwig Center at Harvard
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Health Sciences › Medicine › Oncology › Cancer Immunotherapy and Biomarkers
- Health Sciences › Medicine › Oncology › Cutaneous Melanoma Detection and Management
- Keywords
- metastatic melanoma, tumor microenvironment, tumor heterogeneity, MITF, AXL kinase, drug resistance, tumor-infiltrating T cells, T cell exhaustion, clonal expansion, tumor stroma, endothelial cells, cell-cell interactions, immunotherapy
- MeSH terms
- Base Sequence, Cell Communication, Cell Cycle, Humans, Immunotherapy, Lymphocyte Activation, Melanoma, Neoplasm Metastasis, RNA, Skin Neoplasms, T-Lymphocytes, Stromal Cells, Sequence Analysis, RNA, Drug Resistance, Neoplasm, Genomics, Endothelial Cells, Microphthalmia-Associated Transcription Factor, Single-Cell Analysis, Tumor Microenvironment, Transcriptome
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
