The DOI matches its Crossref record; 90 of the 90 references it cites were found in a registry or an index.
Single-Cell Sequencing of Developing Human Gut Reveals Transcriptional Links to Childhood Crohn’s Disease
Open accessAbstract
Human gut development requires the orchestrated interaction of differentiating cell types. Here, we generate an in-depth single-cell map of the developing human intestine at 6-10 weeks post-conception. Our analysis reveals the transcriptional profile of cycling epithelial precursor cells; distinct from LGR5-expressing cells. We propose that these cells may contribute to differentiated cell subsets via the generation of LGR5-expressing stem cells and receive signals from surrounding mesenchymal cells. Furthermore, we draw parallels between the transcriptomes of ex vivo tissues and in vitro fetal organoids, revealing the maturation of organoid cultures in a dish. Lastly, we compare scRNA-seq profiles from pediatric Crohn's disease epithelium alongside matched healthy controls to reveal disease-associated changes in the epithelial composition. Contrasting these with the fetal profiles reveals the re-activation of fetal transcription factors in Crohn's disease. Our study provides a resource available at www.gutcellatlas.org, and underscores the importance of unraveling fetal development in understanding disease.
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.
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
Scikit-learn: Machine Learning in Python
Pedregosa, F., Varoquaux, G., Gramfort, A., Michel, V., Thirion, B., Grisel, O., Blondel, M., Müller, A., Nothman, J., Louppe, G., et al. (2012) · arXiv · doi:10.48550/arxiv.1201.0490 · Cited by 71,016
SCANPY: large-scale single-cell gene expression data analysis
Wolf, F. A., Angerer, P., & Theis, F. J. (2018) · Genome Biology · doi:10.1186/s13059-017-1382-0 · Cited by 8,881
Massively parallel digital transcriptional profiling of single cells
Zheng, G. X. Y., Terry, J. M., Belgrader, P., Ryvkin, P., Bent, Z. W., Wilson, R., Ziraldo, S. B., Wheeler, T. D., McDermott, G. P., Zhu, J., et al. (2017) · Nature Communications · doi:10.1038/ncomms14049 · Cited by 7,353
Identification of stem cells in small intestine and colon by marker gene Lgr5
Barker, N., van Es, J. H., Kuipers, J., Kujala, P., van den Born, M., Cozijnsen, M., Haegebarth, A., Korving, J., Begthel, H., Peters, P. J., et al. (2007) · Nature · doi:10.1038/nature06196 · Cited by 5,687
From Louvain to Leiden: guaranteeing well-connected communities
Traag, V. A., Waltman, L., & van Eck, N. J. (2019) · Scientific Reports · doi:10.1038/s41598-019-41695-z · Cited by 5,635
Dimensionality reduction for visualizing single-cell data using UMAP
Becht, E., McInnes, L., Healy, J., Dutertre, C.-A., Kwok, I. W. H., Ng, L. G., Ginhoux, F., & Newell, E. W. (2019) · Nature Biotechnology · doi:10.1038/nbt.4314 · Cited by 5,358
Sato, T., Stange, D. E., Ferrante, M., Vries, R. G. J., van Es, J. H., van den Brink, S., van Houdt, W. J., Pronk, A., van Gorp, J., Siersema, P. D., et al. (2011) · Gastroenterology · doi:10.1053/j.gastro.2011.07.050 · Cited by 3,753
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-citationGeneralizing RNA velocity to transient cell states through dynamical modeling
Bergen, V., Lange, M., Peidli, S., Wolf, F. A., & Theis, F. J. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-0591-3 · Cited by 2,951
Scrublet: computational identification of cell doublets in single-cell transcriptomic data
Wolock, S. L., Lopez, R., & Klein, A. M. (2019) · Cell Systems · doi:10.1016/j.cels.2018.11.005 · Cited by 2,758
Paneth cells constitute the niche for Lgr5 stem cells in intestinal crypts
Sato, T., van Es, J. H., Snippert, H. J., Stange, D. E., Vries, R. G., van den Born, M., Barker, N., Shroyer, N. F., van de Wetering, M., & Clevers, H. (2011) · Nature · doi:10.1038/nature09637 · Cited by 2,510
Single-cell reconstruction of the early maternal–fetal interface in humans
Vento-Tormo, R., Efremova, M., Botting, R. A., Turco, M. Y., Vento-Tormo, M., Meyer, K. B., Park, J.-E., Stephenson, E., Polański, K., Goncalves, A., et al. (2018) · Nature · doi:10.1038/s41586-018-0698-6 · Cited by 2,358
Self-citationWolf, F. A., Hamey, F. K., Plass, M., Solana, J., Dahlin, J. S., Göttgens, B., Rajewsky, N., Simon, L., & Theis, F. J. (2019) · Genome Biology · doi:10.1186/s13059-019-1663-x · Cited by 1,698
Depletion of epithelial stem-cell compartments in the small intestine of mice lacking Tcf-4
Korinek, V., Barker, N., Moerer, P., van Donselaar, E., Huls, G., Peters, P. J., & Clevers, H. (1998) · Nature Genetics · doi:10.1038/1270 · Cited by 1,581
de Lange, K. M., Moutsianas, L., Lee, J. C., Lamb, C. A., Luo, Y., Kennedy, N. A., Jostins, L., Rice, D. L., Gutierrez-Achury, J., Ji, S.-G., et al. (2017) · Nature Genetics · doi:10.1038/ng.3760 · Cited by 1,445
Intra- and Inter-cellular Rewiring of the Human Colon during Ulcerative Colitis
Smillie, C. S., Biton, M., Ordovas-Montanes, 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 1,394
BBKNN: fast batch alignment of single cell transcriptomes
Polański, K., Young, M. D., Miao, Z., Meyer, K. B., Teichmann, S. A., & Park, J.-E. (2020) · Bioinformatics · doi:10.1093/bioinformatics/btz625 · Cited by 932
Self-citationMartin, J. C., Chang, C., Boschetti, G., Ungaro, R., Giri, M., Grout, J. A., Gettler, K., Chuang, L.-S., Nayar, S., Greenstein, A. J., et al. (2019) · Cell · doi:10.1016/j.cell.2019.08.008 · Cited by 872
Colonic epithelial cell diversity in health and inflammatory bowel disease
Parikh, K., Antanaviciute, A., Fawkner-Corbett, D., Jagielowicz, M., Aulicino, A., Lagerholm, C., Davis, S., Kinchen, J., Chen, H. H., Alham, N. K., et al. (2019) · Nature · doi:10.1038/s41586-019-0992-y · Cited by 860
Structural Remodeling of the Human Colonic Mesenchyme in Inflammatory Bowel Disease
Kinchen, J., Chen, H. H., Parikh, K., Antanaviciute, A., Jagielowicz, M., Fawkner-Corbett, D., Ashley, N., Cubitt, L., Mellado-Gomez, E., Attar, M., et al. (2018) · Cell · doi:10.1016/j.cell.2018.08.067 · Cited by 745
fdrtool: a versatile R package for estimating local and tail area-based false discovery rates
Strimmer, K. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btn209 · Cited by 737
YAP/TAZ-Dependent Reprogramming of Colonic Epithelium Links ECM Remodeling to Tissue Regeneration
Yui, S., Azzolin, L., Maimets, M., Pedersen, M. T., Fordham, R. P., Hansen, S. L., Larsen, H. L., Guiu, J., Alves, M. R. P., Rundsten, C. F., et al. (2018) · Cell Stem Cell · doi:10.1016/j.stem.2017.11.001 · Cited by 681
Villification: How the Gut Gets Its Villi
Shyer, A. E., Tallinen, T., Nerurkar, N. L., Wei, Z., Gil, E. S., Kaplan, D. L., Tabin, C. J., & Mahadevan, L. (2013) · Science · doi:10.1126/science.1238842 · Cited by 562
Subepithelial telocytes are an important source of Wnts that supports intestinal crypts
Shoshkes-Carmel, M., Wang, Y. J., Wangensteen, K. J., Tóth, B., Kondo, A., Massasa, E. E., Itzkovitz, S., & Kaestner, K. H. (2018) · Nature · doi:10.1038/s41586-018-0084-4 · Cited by 516
Bayraktar, O. A., Bartels, T., Holmqvist, S., Kleshchevnikov, V., Martirosyan, A., Polioudakis, D., Ben Haim, L., Young, A. M. H., Batiuk, M. Y., Prakash, K., et al. (2020) · Nature Neuroscience · doi:10.1038/s41593-020-0602-1 · Cited by 489
Self-citationMoor, A. E., Harnik, Y., Ben-Moshe, S., Massasa, E. E., Rozenberg, M., Eilam, R., Bahar Halpern, K., & Itzkovitz, S. (2018) · Cell · doi:10.1016/j.cell.2018.08.063 · Cited by 480
Computational assignment of cell-cycle stage from single-cell transcriptome data
Scialdone, A., Natarajan, K. N., Saraiva, L. R., Proserpio, V., Teichmann, S. A., Stegle, O., Marioni, J. C., & Buettner, F. (2015) · Methods · doi:10.1016/j.ymeth.2015.06.021 · Cited by 409
Self-citationFordham, R. P., Yui, S., Hannan, N. R. F., Soendergaard, C., Madgwick, A., Schweiger, P. J., Nielsen, O. H., Vallier, L., Pedersen, R. A., Nakamura, T., et al. (2013) · Cell Stem Cell · doi:10.1016/j.stem.2013.09.015 · Cited by 399
Self-citationThe emergent landscape of the mouse gut endoderm at single-cell resolution
Nowotschin, S., Setty, M., Kuo, Y.-Y., Liu, V., Garg, V., Sharma, R., Simon, C. S., Saiz, N., Gardner, R., Boutet, S. C., et al. (2019) · Nature · doi:10.1038/s41586-019-1127-1 · Cited by 383
Epithelial hedgehog signals pattern the intestinal crypt-villus axis
Madison, B. B., Braunstein, K., Kuizon, E., Portman, K., Qiao, X. T., & Gumucio, D. L. (2005) · Development · doi:10.1242/dev.01576 · Cited by 377
Distinct Mesenchymal Cell Populations Generate the Essential Intestinal BMP Signaling Gradient
McCarthy, N., Manieri, E., Storm, E. E., Saadatpour, A., Luoma, A. M., Kapoor, V. N., Madha, S., Gaynor, L. T., Cox, C., Keerthivasan, S., et al. (2020) · Cell Stem Cell · doi:10.1016/j.stem.2020.01.008 · Cited by 361
Ye, H., Kelly, T. F., Samadani, U., Lim, L., Rubio, S., Overdier, D. G., Roebuck, K. A., & Costa, R. H. (1997) · Molecular and Cellular Biology · doi:10.1128/mcb.17.3.1626 · Cited by 359
Karlsson, L., Lindahl, P., Heath, J. K., & Betsholtz, C. (2000) · Development · doi:10.1242/dev.127.16.3457 · Cited by 316
Mallow, E. B., Harris, A., Salzman, N., Russell, J. P., DeBerardinis, R. J., Ruchelli, E., & Bevins, C. L. (1996) · Journal of Biological Chemistry · doi:10.1074/jbc.271.8.4038 · Cited by 296
Mustata, R. C., Vasile, G., Fernandez-Vallone, V., Strollo, S., Lefort, A., Libert, F., Monteyne, D., Pérez-Morga, D., Vassart, G., & Garcia, M.-I. (2013) · Cell Reports · doi:10.1016/j.celrep.2013.09.005 · Cited by 295
Bending Gradients: How the Intestinal Stem Cell Gets Its Home
Shyer, A. E., Huycke, T. R., Lee, C., Mahadevan, L., & Tabin, C. J. (2015) · Cell · doi:10.1016/j.cell.2015.03.041 · Cited by 292
Differences in goblet cell differentiation between Crohn's disease and ulcerative colitis
Gersemann, M., Becker, S., Kübler, I., Koslowski, M., Wang, G., Herrlinger, K. R., Griger, J., Fritz, P., Fellermann, K., Schwab, M., et al. (2009) · Differentiation · doi:10.1016/j.diff.2008.09.008 · Cited by 288
The Paneth Cell α-Defensin Deficiency of Ileal Crohn’s Disease Is Linked to Wnt/Tcf-4
Wehkamp, J., Wang, G., Kübler, I., Nuding, S., Gregorieff, A., Schnabel, A., Kays, R. J., Fellermann, K., Burk, O., Schwab, M., et al. (2007) · The Journal of Immunology · doi:10.4049/jimmunol.179.5.3109 · Cited by 286
Morphogenesis and maturation of the embryonic and postnatal intestine
Chin, A. M., Hill, D. R., Aurora, M., & Spence, J. R. (2017) · Seminars in Cell & Developmental Biology · doi:10.1016/j.semcdb.2017.01.011 · Cited by 226
Vertebrate intestinal endoderm development
Spence, J. R., Lauf, R., & Shroyer, N. F. (2011) · Developmental Dynamics · doi:10.1002/dvdy.22540 · Cited by 219
Kaestner, K. H., Silberg, D. G., Traber, P. G., & Schütz, G. (1997) · Genes & Development · doi:10.1101/gad.11.12.1583 · Cited by 211
Somatic Evolution in Non-neoplastic IBD-Affected Colon
Olafsson, S., McIntyre, R. E., Coorens, T., Butler, T., Jung, H., Robinson, P. S., Lee-Six, H., Sanders, M. A., Arestang, K., Dawson, C., et al. (2020) · Cell · doi:10.1016/j.cell.2020.06.036 · Cited by 206
Schreurs, R. R. C. E., Baumdick, M. E., Sagebiel, A. F., Kaufmann, M., Mokry, M., Klarenbeek, P. L., Schaltenberg, N., Steinert, F. L., van Rijn, J. M., Drewniak, A., et al. (2019) · Immunity · doi:10.1016/j.immuni.2018.12.010 · Cited by 205
Long-Term Culture Captures Injury-Repair Cycles of Colonic Stem Cells
Wang, Y., Chiang, I.-L., Ohara, T. E., Fujii, S., Cheng, J., Muegge, B. D., Ver Heul, A., Han, N. D., Lu, Q., Xiong, S., et al. (2019) · Cell · doi:10.1016/j.cell.2019.10.015 · Cited by 200
Mapping Development of the Human Intestinal Niche at Single-Cell Resolution
Holloway, E. M., Czerwinski, M., Tsai, Y.-H., Wu, J. H., Wu, A., Childs, C. J., Walton, K. D., Sweet, C. W., Yu, Q., Glass, I., et al. (2021) · Cell Stem Cell · doi:10.1016/j.stem.2020.11.008 · Cited by 182
Lin, C.-C., Bradstreet, T. R., Schwarzkopf, E. A., Sim, J., Carrero, J. A., Chou, C., Cook, L. E., Egawa, T., Taneja, R., Murphy, T. L., et al. (2014) · Nature Communications · doi:10.1038/ncomms4551 · Cited by 178
Kraiczy, J., Nayak, K. M., Howell, K. J., Ross, A., Forbester, J., Salvestrini, C., Mustata, R., Perkins, S., Andersson-Rolf, A., Leenen, E., et al. (2019) · Gut · doi:10.1136/gutjnl-2017-314817 · Cited by 178
Self-citationKolterud, Å., Grosse, A. S., Zacharias, W. J., Walton, K. D., Kretovich, K. E., Madison, B. B., Waghray, M., Ferris, J. E., Hu, C., Merchant, J. L., et al. (2009) · Gastroenterology · doi:10.1053/j.gastro.2009.05.002 · Cited by 170
Memory CD4+ T cells are generated in the human fetal intestine
Li, N., van Unen, V., Abdelaal, T., Guo, N., Kasatskaya, S. A., Ladell, K., McLaren, J. E., Egorov, E. S., Izraelson, M., Chuva de Sousa Lopes, S. M., et al. (2019) · Nature Immunology · doi:10.1038/s41590-018-0294-9 · Cited by 168
Hedgehog-responsive mesenchymal clusters direct patterning and emergence of intestinal villi
Walton, K. D., Kolterud, Å., Czerwinski, M. J., Bell, M. J., Prakash, A., Kushwaha, J., Grosse, A. S., Schnell, S., & Gumucio, D. L. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1205669109 · Cited by 167
CDH2 and CDH11 act as regulators of stem cell fate decisions
Alimperti, S., & Andreadis, S. T. (2015) · Stem Cell Research · doi:10.1016/j.scr.2015.02.002 · Cited by 166
Blimp1 regulates the transition of neonatal to adult intestinal epithelium
Muncan, V., Heijmans, J., Krasinski, S. D., Büller, N. V., Wildenberg, M. E., Meisner, S., Radonjic, M., Stapleton, K. A., Lamers, W. H., Biemond, I., et al. (2011) · Nature Communications · doi:10.1038/ncomms1463 · Cited by 165
Generation of intestinal surface: an absorbing tale
Walton, K. D., Freddo, A. M., Wang, S., & Gumucio, D. L. (2016) · Development · doi:10.1242/dev.135400 · Cited by 161
Lgr5+ telocytes are a signaling source at the intestinal villus tip
Halpern, K. B., Massalha, H., Zwick, R. K., Moor, A. E., Castillo‐Azofeifa, D., Rozenberg, M., Farack, L., Egozi, A., Miller, D. R., Averbukh, I., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-15714-x · Cited by 160
Ellinghaus, D., Zhang, H., Zeißig, S., Lipinski, S., Till, A., Jiang, T., Stade, B., Bromberg, Y., Ellinghaus, E., Keller, A., et al. (2013) · Gastroenterology · doi:10.1053/j.gastro.2013.04.040 · Cited by 158
Tracing the origin of adult intestinal stem cells
Guiu, J., Hannezo, É., Yui, S., Demharter, S., Ulyanchenko, S., Maimets, M., Jørgensen, A., Perlman, S., Lundvall, L., Mamsen, L. S., et al. (2019) · Nature · doi:10.1038/s41586-019-1212-5 · Cited by 158
Villification in the mouse: Bmp signals control intestinal villus patterning
Walton, K. D., Whidden, M., Kolterud, Å., Shoffner, S. K., Czerwinski, M. J., Kushwaha, J. S., Parmar, N., Chandhrasekhar, D., Freddo, A. M., Schnell, S. D., et al. (2015) · Development · doi:10.1242/dev.130112 · Cited by 153
Bettess, M. D., Dubois, N. C., Murphy, M., Dubey, C., Roger, C., Robine, S., & Trumpp, A. (2005) · Molecular and Cellular Biology · doi:10.1128/mcb.25.17.7868-7878.2005 · Cited by 152
Restricted High Level Expression of Tcf-4 Protein in Intestinal and Mammary Gland Epithelium
Barker, N., Huls, G. A., Kořínek, V., & Clevers, H. C. (1999) · American Journal Of Pathology · doi:10.1016/s0002-9440(10)65247-9 · Cited by 149
Harper, J. A., Mould, A. W., Andrews, R., Bikoff, E. K., & Robertson, E. J. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1105852108 · Cited by 148
YY1 mediates TGF-β1-induced EMT and pro-fibrogenesis in alveolar epithelial cells
Chuyi, Z., Zhu, X., Hua, Y., Zhao, Q., Wang, K., Zhen, L., Wang, G., Lü, J., Luo, A., Cho, W. C. S., et al. (2019) · Respiratory Research · doi:10.1186/s12931-019-1223-7 · Cited by 141
Implication of TNF-Related Apoptosis-Inducing Ligand in Inflammatory Intestinal Epithelial Lesions
Bègue, B., Wajant, H., Bambou, J., Dubuquoy, L., Siegmund, D., Beaulieu, J., Canioni, D., Berrebi, D. D., Brousse, N., Desreumaux, P., et al. (2006) · Gastroenterology · doi:10.1053/j.gastro.2006.03.022 · Cited by 135
Bacterial colonization and gut development in preterm neonates
Cilieborg, M. S., Boyé, M., & Sangild, P. T. (2012) · Early Human Development · doi:10.1016/j.earlhumdev.2011.12.027 · Cited by 134
Cell dynamics in fetal intestinal epithelium: implications for intestinal growth and morphogenesis
Grosse, A. S., Pressprich, M. F., Curley, L. B., Hamilton, K. L., Margolis, B. L., Hildebrand, J. D., & Gumucio, D. L. (2011) · Development · doi:10.1242/dev.065789 · Cited by 131
Yu, F., Sharma, S., Jankovic, D. L., Gurram, R. K., Su, P., Hu, G., Li, R., Rieder, S. A., Zhao, K., Sun, B., et al. (2018) · The Journal of Experimental Medicine · doi:10.1084/jem.20170155 · Cited by 131
Vitali, R., Stronati, L., Negroni, A., Nardo, G. D., Pierdomenico, M., Giudice, E. D., Rossi, P., & Cucchiara, S. (2011) · The American Journal of Gastroenterology · doi:10.1038/ajg.2011.231 · Cited by 117
Kim, J., Fei, L., Yin, W.-C., Coquenlorge, S., Rao‐Bhatia, A., Zhang, X., Shi, S. S. W., Lee, J. H., Hahn, N. A., Rizvi, W., et al. (2020) · Nature Communications · doi:10.1038/s41467-019-14058-5 · Cited by 114
Kaestner, K. H., Bleckmann, S. C., Monaghan, A. P., et al. (1996) · Development · doi:10.1242/dev.122.6.1751 · Cited by 99
Fgf9 signaling regulates small intestinal elongation and mesenchymal development
Geske, M. J., Zhang, X.-Q., Patel, K. K., Ornitz, D., & Stappenbeck, T. (2008) · Development · doi:10.1242/dev.020453 · Cited by 93
Tsai, Y.-H., Nattiv, R., Dedhia, P. H., Nagy, M. S., Chin, A. M., Thomson, M., Klein, O. D., & Spence, J. R. (2016) · Development · doi:10.1242/dev.138453 · Cited by 87
Xian, L., Georgess, D., Huso, T. H., Cope, L., Belton, A., Chang, Y.-T., Kuang, W., Gu, Q.-H., Zhang, X., Senger, S., et al. (2017) · Nature Communications · doi:10.1038/ncomms15008 · Cited by 85
The Intestinal Stem Cell Niche: A Central Role for Foxl1-Expressing Subepithelial Telocytes
Kaestner, K. H. (2019) · Cellular and Molecular Gastroenterology and Hepatology · doi:10.1016/j.jcmgh.2019.04.001 · Cited by 84
Kraiczy, J., Nayak, K., Ross, A., Raine, T., Mak, T. N., Gasparetto, M., Cario, E., Rakyan, V. K., Heuschkel, R. B., & Zilbauer, M. (2015) · Mucosal Immunology · doi:10.1038/mi.2015.88 · Cited by 79
Self-citationSonntag, B., Stolze, B., Heinecke, A., Luegering, A., Heidemann, J., Lebiedz, P., Rijcken, E. J. M., Kiesel, L., Domschke, W., Kucharzik, T. F., et al. (2007) · Inflammatory Bowel Diseases · doi:10.1002/ibd.20206 · Cited by 71
KRAS and TP53 mutations in inflammatory bowel disease-associated colorectal cancer: a meta-analysis
Du, L., Kim, J. J., Shen, J., Chen, B., & Dai, N. (2017) · Oncotarget · doi:10.18632/oncotarget.14549 · Cited by 71
Dupaul-Chicoine, J., Dagenais, M., & Saleh, M. (2013) · Inflammatory Bowel Diseases · doi:10.1097/mib.0b013e31828dcac7 · Cited by 68
Rao‐Bhatia, A., Zhu, M. S., Yin, W.-C., Coquenlorge, S., Zhang, X., Woo, J., Sun, Y., Dean, C. H., Liu, A., Hui, C., et al. (2020) · Developmental Cell · doi:10.1016/j.devcel.2020.02.003 · Cited by 65
RNA Velocity: Molecular Kinetics from Single-Cell RNA-Seq
Svensson, V., & Pachter, L. S. (2018) · Molecular Cell · doi:10.1016/j.molcel.2018.09.026 · Cited by 62
Epithelial inactivation of Yy1 abrogates lung branching morphogenesis
Boucherat, O., Landry‐Truchon, K., Bérubé‐Simard, F., Houde, N., Beuret, L., Lezmi, G., Foulkes, W. D., Delacourt, C., Charron, J., & Jeannotte, L. (2015) · Development · doi:10.1242/dev.120469 · Cited by 57
Horvath, B., Liu, G., Wu, X., Lai, K., Shen, B., & Liu, X. (2015) · Gastroenterology report · doi:10.1093/gastro/gov022 · Cited by 43
Chin, A. M., Tsai, Y.-H., Finkbeiner, S. R., Nagy, M. S., Walker, E. M., Ethen, N. J., Williams, B. O., Battle, M. A., & Spence, J. R. (2016) · Stem Cell Reports · doi:10.1016/j.stemcr.2016.09.004 · Cited by 33
Takaishi, H., Kanai∥, T., Nakazawa, A., et al. (2012) · Journal of Gastroenterology · doi:10.1007/s00535-012-0566-3 · Cited by 31
Ito, K., Yamazaki, S., Yamamoto, R., Tajima, Y., Yanagida, A., Kobayashi, T., Kato‐Itoh, M., Kakuta, S., Iwakura, Y., Nakauchi, H., et al. (2014) · Journal of Biological Chemistry · doi:10.1074/jbc.m114.580084 · Cited by 27
Matthews, S. M., Eshelman, M. A., Berg, A. S., Koltun, W. A., & Yochum, G. S. (2019) · PLoS ONE · doi:10.1371/journal.pone.0212850 · Cited by 25
Yanai, H., Atsumi, N., Tanaka, T., Nakamura, N., Komai, Y., Omachi, T., Tanaka, K., Ishigaki, K., Saiga, K., Ohsugi, H., et al. (2017) · Scientific Reports · doi:10.1038/s41598-017-09927-2 · Cited by 21
Wu, Y. L., Kimura, Y., Okamoto, T., Matsuhisa, K., Asada, R., Saito, A., Sakaue, F., Imaizumi, K., & Kaneko, M. (2019) · Scientific Reports · doi:10.1038/s41598-019-56748-6 · Cited by 18
Single-cell in situ transcriptomic map of astrocyte cortical layer diversityPreprint
Bayraktar, O. A., Bartels, T., Polioudakis, D., Holmqvist, S., Haim, L. B., Young, A. M. H., Prakash, K., Brown, A. P. Y., Paredes, M. F., Kawaguchi, R., et al. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/432104 · Cited by 16
Self-citationPublisher Correction: Single-cell multi-omics sequencing of human early embryos
Li, L., Guo, F., Gao, Y., Ren, Y., Yuan, P., Yan, L., Li, R., Lian, Y., Li, J., Hu, B., et al. (2018) · Nature Cell Biology · doi:10.1038/s41556-018-0166-4 · Cited by 14
Yu, Q., Kilik, U., Holloway, E. M., Tsai, Y.-H., Wu, A., Wu, J. H., Czerwinski, M. J., Childs, C. J., He, Z., Glass, I. A., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.07.24.219147 · Cited by 12
Bo, L., Fu, H., & Yang, J. (2018) · Molecular Medicine Reports · doi:10.3892/mmr.2018.9267 · Cited by 9
Cited by
Cross-tissue immune cell analysis reveals tissue-specific features in humans
Domínguez Conde, C., Xu, C., Jarvis, L. B., Rainbow, D. B., Wells, S. B., Gomes, T., Howlett, S. K., Suchanek, O., Polanski, K., King, H. W., et al. (2022) · Science · doi:10.1126/science.abl5197 · Cited by 1,159
Self-citationSpatially 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., Ge, W. H., Xu, K. H., et al. (2021) · Cell · doi:10.1016/j.cell.2021.08.003 · Cited by 874
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., Pritchard, S., Bolt, L., et al. (2021) · Nature · doi:10.1038/s41586-021-03852-1 · Cited by 699
Self-citationMacrophages in intestinal homeostasis and inflammatory bowel disease
Hegarty, L. M., Jones, G.-R., & Bain, C. C. (2023) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/s41575-023-00769-0 · Cited by 355
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 340
Self-citation
Metadata
- Authors
- Elmentaite, R., Ross, A. D. B., Roberts, K., James, K. R., Ortmann, D., Gomes, T., Nayak, K., Tuck, L., Pritchard, S., Bayraktar, O. A., Heuschkel, R., Vallier, L., Teichmann, S. A., & Zilbauer, M.
- Venue
- Developmental Cell
- Publisher
- Elsevier BV
- Published
- 2020-12
- Volume
- 55
- Issue
- 6
- Pages
- 771-783.e5
- ISSN
- 1534-5807 (ISSN-L)
- OpenAlex
- W3110852430
- Cited by
- 316
- References
- 90
- FWCI
- 12.03
- Type
- journal article
- Language
- en
- Open access
- hybrid
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
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.