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A single-cell Arabidopsis root atlas reveals developmental trajectories in wild-type and cell identity mutants
Open accessAbstract
In all multicellular organisms, transcriptional networks orchestrate organ development. The Arabidopsis root, with its simple structure and indeterminate growth, is an ideal model for investigating the spatiotemporal transcriptional signatures underlying developmental trajectories. To map gene expression dynamics across root cell types and developmental time, we built a comprehensive, organ-scale atlas at single-cell resolution. In addition to estimating developmental progressions in pseudotime, we employed the mathematical concept of optimal transport to infer developmental trajectories and identify their underlying regulators. To demonstrate the utility of the atlas to interpret new datasets, we profiled mutants for two key transcriptional regulators at single-cell resolution, shortroot and scarecrow. We report transcriptomic and in vivo evidence for tissue trans-differentiation underlying a mixed cell identity phenotype in scarecrow. Our results support the atlas as a rich community resource for unraveling the transcriptional programs that specify and maintain cell identity to regulate spatiotemporal organ development.
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Cites
Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing
Benjamini, Y., & Hochberg, Y. (1995) · Journal of the Royal Statistical Society Series B: Statistical Methodology · doi:10.1111/j.2517-6161.1995.tb02031.x · Cited by 109,482
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
Love, M. I., Huber, W., & Anders, S. (2014) · Genome Biology · doi:10.1186/s13059-014-0550-8 · Cited by 95,106
Trimmomatic: a flexible trimmer for Illumina sequence data
Bolger, A. M., Lohse, M., & Usadel, B. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu170 · Cited by 65,548
Regression shrinkage and selection via the lasso
Tibshirani, R. (1996) · Journal of the Royal Statistical Society Series B: Statistical Methodology · doi:10.1111/j.2517-6161.1996.tb02080.x · Cited by 51,482
Robinson, M. D., McCarthy, D. J., & Smyth, G. K. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btp616 · Cited by 41,364
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
Integrating single-cell transcriptomic data across different conditions, technologies, and species
Butler, A., Hoffman, P., Smibert, P., Papalexi, E., & Satija, R. (2018) · Nature Biotechnology · doi:10.1038/nbt.4096 · Cited by 13,174
Complex heatmaps reveal patterns and correlations in multidimensional genomic data
Gu, Z., Eils, R., & Schlesner, M. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btw313 · Cited by 10,034
Near-optimal probabilistic RNA-seq quantification
Bray, N. L., Pimentel, H., Melsted, P., & Pachter, L. (2016) · Nature Biotechnology · doi:10.1038/nbt.3519 · Cited by 9,723
McCarthy, D. J., Chen, Y., & Smyth, G. K. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks042 · Cited by 5,195
McGinnis, C. S., Murrow, L. M., & Gartner, Z. J. (2019) · Cell Systems · doi:10.1016/j.cels.2019.03.003 · Cited by 4,521
The single-cell transcriptional landscape of mammalian organogenesis
Cao, J., Spielmann, M., Qiu, X., Huang, X., Ibrahim, D. M., Hill, A. J., Zhang, F., Mundlos, S., Christiansen, L., Steemers, F. J., et al. (2019) · Nature · doi:10.1038/s41586-019-0969-x · Cited by 4,490
Hafemeister, C., & Satija, R. (2019) · Genome Biology · doi:10.1186/s13059-019-1874-1 · Cited by 4,479 · cited 2×
“Plotted gene expression values ‘Log-normalized’ indicates expression values extracted from the slot ‘data’ of a Seurat object’s ‘SCT’ assay, which contains the lognormalized, ‘corrected’ counts produced by the SCTransform function (Hafemeister and Satija, 2019).”
MethodGeneralizing 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
Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape
O’Malley, R. C., Huang, S.-S. C., Song, L., Lewsey, M. G., Bartlett, A., Nery, J. R., Galli, M., Gallavotti, A., & Ecker, J. R. (2016) · Cell · doi:10.1016/j.cell.2016.04.038 · Cited by 1,608
Single-cell transcriptional diversity is a hallmark of developmental potential
Gulati, G. S., Sikandar, S. S., Wesche, D. J., Manjunath, A., Bharadwaj, A., Berger, M. J., Ilagan, F., Kuo, A. H., Hsieh, R. W., Cai, S., et al. (2020) · Science · doi:10.1126/science.aax0249 · Cited by 1,571
Cellular organisation of the Arabidopsis thaliana root
Dolan, L., Janmaat, K., Willemsen, V., Linstead, P., Poethig, S., Roberts, K., & Scheres, B. (1993) · Development · doi:10.1242/dev.119.1.71 · Cited by 1,462
Integrative single-cell analysis
Stuart, T., & Satija, R. (2019) · Nature Reviews Genetics · doi:10.1038/s41576-019-0093-7 · Cited by 1,460
Cao, J., Packer, J. S., Ramani, V., Cusanovich, D. A., Huynh, C., Daza, R., Qiu, X., Lee, C., Furlan, S. N., Steemers, F. J., et al. (2017) · doi:10.1101/104844 · Cited by 1,402
A Gene Expression Map of the Arabidopsis Root
Birnbaum, K., Shasha, D. E., Wang, J. Y., Jung, J. W., Lambert, G. M., Galbraith, D. W., & Benfey, P. N. (2003) · Science · doi:10.1126/science.1090022 · Cited by 1,258
Self-citationThe PLETHORA Genes Mediate Patterning of the Arabidopsis Root Stem Cell Niche
Aida, M., Beis, D., Heidstra, R., Willemsen, V., Blilou, I., Galinha, C., Nussaume, L., Noh, Y.-S., Amasino, R., & Scheres, B. (2004) · Cell · doi:10.1016/j.cell.2004.09.018 · Cited by 1,213
A High-Resolution Root Spatiotemporal Map Reveals Dominant Expression Patterns
Brady, S. M., Orlando, D. A., Lee, J.-Y., Wang, J. Y., Koch, J., Dinneny, J. R., Mace, D., Ohler, U., & Benfey, P. N. (2007) · Science · doi:10.1126/science.1146265 · Cited by 1,182
Self-citationTranscription switches for protoxylem and metaxylem vessel formation
Kubo, M., Udagawa, M., Nishikubo, N., Horiguchi, G., Yamaguchi, M., Ito, J., Mimura, T., Fukuda, H., & Demura, T. (2005) · Genes & Development · doi:10.1101/gad.1331305 · Cited by 1,177
Di Laurenzio, L., Wysocka-Diller, J., Malamy, J. E., Pysh, L., Helariutta, Y., Freshour, G., Hahn, M. G., Feldmann, K. A., & Benfey, P. N. (1996) · Cell · doi:10.1016/s0092-8674(00)80115-4 · Cited by 1,124
Self-citationKolberg, L., Raudvere, U., Kuzmin, I., Vilo, J., & Peterson, H. (2020) · F1000Research · doi:10.12688/f1000research.24956.2 · Cited by 1,098
Orchestrating single-cell analysis with Bioconductor
Amezquita, R. A., Lun, A. T. L., Becht, E., Carey, V. J., Carpp, L. N., Geistlinger, L., Marini, F., Rue-Albrecht, K., Risso, D., Soneson, C., et al. (2020) · Nature Methods · doi:10.1038/s41592-019-0654-x · Cited by 945
Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis
Farrell, J. A., Wang, Y., Riesenfeld, S. J., Shekhar, K., Regev, A., & Schier, A. F. (2018) · Science · doi:10.1126/science.aar3131 · Cited by 876
Cell Signalling by MicroRNA165/6 Directs Gene Dose-Dependent Root Cell Fate
Carlsbecker, A., Lee, J.-Y., Roberts, C. J., Dettmer, J., Lehesranta, S., Zhou, J., Lindgren, O., Moreno-Risueno, M. A., Vatén, A., Thitamadee, S., et al. (2010) · Nature · doi:10.1038/nature08977 · Cited by 861
Self-citationSchiebinger, G., Shu, J., Tabaka, M., Cleary, B., Subramanian, V., Solomon, A., Gould, J., Liu, S., Lin, S., Berube, P., et al. (2019) · Cell · doi:10.1016/j.cell.2019.01.006 · Cited by 829
Self-citationCell Identity Mediates the Response of Arabidopsis Roots to Abiotic Stress
Dinneny, J. R., Long, T. A., Wang, J. Y., Jung, J. W., Mace, D., Pointer, S., Barron, C., Brady, S. M., Schiefelbein, J., & Benfey, P. N. (2008) · Science · doi:10.1126/science.1153795 · Cited by 739
Self-citationDissecting cell identity via network inference and in silico gene perturbation
Kamimoto, K., Stringa, B., Hoffmann, C. M., Jindal, K., Solnica-Krezel, L., & Morris, S. A. (2023) · Nature · doi:10.1038/s41586-022-05688-9 · Cited by 677
Cell-specific nitrogen responses mediate developmental plasticity
Gifford, M. L., Dean, A., Gutierrez, R. A., Coruzzi, G. M., & Birnbaum, K. D. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0709559105 · Cited by 615
Denyer, T., Ma, X., Klesen, S., Scacchi, E., Nieselt, K., & Timmermans, M. C. P. (2019) · Developmental Cell · doi:10.1016/j.devcel.2019.02.022 · Cited by 608
Lee, M. M., & Schiefelbein, J. (1999) · Cell · doi:10.1016/s0092-8674(00)81536-6 · Cited by 584
The dynamics of gene expression in vertebrate embryogenesis at single-cell resolution
Briggs, J. A., Weinreb, C., Wagner, D. E., Megason, S., Peshkin, L., Kirschner, M. W., & Klein, A. M. (2018) · Science · doi:10.1126/science.aar5780 · Cited by 565
Root development in Arabidopsis: four mutants with dramatically altered root morphogenesis
Benfey, P. N., Linstead, P. J., Roberts, K., Schiefelbein, J. W., Hauser, M.-T., & Aeschbacher, R. A. (1993) · Development · doi:10.1242/dev.119.1.57 · Cited by 558
Self-citationSingle-Cell RNA Sequencing Resolves Molecular Relationships Among Individual Plant Cells
Ryu, K. H., Huang, L., Kang, H. M., & Schiefelbein, J. (2019) · Plant Physiology · doi:10.1104/pp.18.01482 · Cited by 545
A Single-Cell RNA Sequencing Profiles the Developmental Landscape of Arabidopsis Root
Zhang, T.-Q., Xu, Z.-G., Shang, G.-D., & Wang, J.-W. (2019) · Molecular Plant · doi:10.1016/j.molp.2019.04.004 · Cited by 505
APL regulates vascular tissue identity in Arabidopsis
Bonke, M., Thitamadee, S., Mähönen, A. P., Hauser, M.-T., & Helariutta, Y. (2003) · Nature · doi:10.1038/nature02100 · Cited by 504
Benchmarking single-cell RNA-sequencing protocols for cell atlas projects
Mereu, E., Lafzi, A., Moutinho, C., Ziegenhain, C., McCarthy, D. J., Álvarez-Varela, A., Batlle, E., Sagar, Grün, D., Lau, J. K., et al. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-0469-4 · Cited by 499
Secreted Peptide Signals Required for Maintenance of Root Stem Cell Niche in Arabidopsis
Matsuzaki, Y., Ogawa-Ohnishi, M., Mori, A., & Matsubayashi, Y. (2010) · Science · doi:10.1126/science.1191132 · Cited by 495
An Ancient Mechanism Controls the Development of Cells with a Rooting Function in Land Plants
Menand, B., Yi, K., Jouannic, S., Hoffmann, L., Ryan, E., Linstead, P., Schaefer, D. G., & Dolan, L. (2007) · Science · doi:10.1126/science.1142618 · Cited by 464
Dynamics of Gene Expression in Single Root Cells of Arabidopsis thaliana
Jean-Baptiste, K., McFaline-Figueroa, J. L., Alexandre, C. M., Dorrity, M. W., Saunders, L., Bubb, K. L., Trapnell, C., Fields, S., Queitsch, C., & Cuperus, J. T. (2019) · The Plant Cell · doi:10.1105/tpc.18.00785 · Cited by 433
High-Throughput Single-Cell Transcriptome Profiling of Plant Cell Types
Shulse, C. N., Cole, B. J., Ciobanu, D., Lin, J., Yoshinaga, Y., Gouran, M., Turco, G. M., Zhu, Y., O’Malley, R. C., Brady, S. M., et al. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.04.054 · Cited by 432
Self-citationEmergence of a High-Plasticity Cell State during Lung Cancer Evolution
Marjanovic, N. D., Hofree, M., Chan, J. E., Canner, D., Wu, K., Trakala, M., Hartmann, G. G., Smith, O. C., Kim, J. Y., Evans, K. V., et al. (2020) · Cancer Cell · doi:10.1016/j.ccell.2020.06.012 · Cited by 405
Genetic evidence that the endodermis is essential for shoot gravitropism in Arabidopsis thaliana
Fukaki, H., Wysocka‐Diller, J., Kato, T., Fujisawa, H., Benfey, P. N., & Tasaka, M. (1998) · The Plant Journal · doi:10.1046/j.1365-313x.1998.00137.x · Cited by 365
Self-citationTranscriptional Profile of the Arabidopsis Root Quiescent Center
Nawy, T., Lee, J.-Y., Colinas, J., Wang, J. Y., Thongrod, S. C., Malamy, J. E., Birnbaum, K., & Benfey, P. N. (2005) · The Plant Cell · doi:10.1105/tpc.105.031724 · Cited by 359
Self-citationWhole-Genome Analysis of the SHORT-ROOT Developmental Pathway in Arabidopsis
Levesque, M. P., Vernoux, T., Busch, W., Cui, H., Wang, J. Y., Blilou, I., Hassan, H., Nakajima, K., Matsumoto, N., Lohmann, J. U., et al. (2006) · PLoS Biology · doi:10.1371/journal.pbio.0040143 · Cited by 349
Self-citationVascular transcription factors guide plant epidermal responses to limiting phosphate conditions
Wendrich, J. R., Yang, B., Vandamme, N., Verstaen, K., Smet, W., Van de Velde, C., Minne, M., Wybouw, B., Mor, E., Arents, H. E., et al. (2020) · Science · doi:10.1126/science.aay4970 · Cited by 317
Farmer, A., Thibivilliers, S., Ryu, K. H., Schiefelbein, J., & Libault, M. (2021) · Molecular Plant · doi:10.1016/j.molp.2021.01.001 · Cited by 317
Li, S., Yamada, M., Han, X., Ohler, U., & Benfey, P. N. (2016) · Developmental Cell · doi:10.1016/j.devcel.2016.10.012 · Cited by 311
Self-citationHeidstra, R., Welch, D., & Scheres, B. (2004) · Genes & Development · doi:10.1101/gad.305504 · Cited by 306
The MYB36 transcription factor orchestrates Casparian strip formation
Kamiya, T., Borghi, M., Wang, P., Danku, J., Kalmbach, L., Hosmani, P. S., Naseer, S., Fujiwara, T., Geldner, N., & Salt, D. E. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1507691112 · Cited by 303
De Rybel, B., Möller, B., Yoshida, S., Grabowicz, I., Barbier de Reuille, P., Boeren, S., Smith, R. S., Borst, J. W., & Weijers, D. (2013) · Developmental Cell · doi:10.1016/j.devcel.2012.12.013 · Cited by 301
Lee, J.-Y., Colinas, J., Wang, J. Y., Mace, D., Ohler, U., & Benfey, P. N. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0510607103 · Cited by 292
Self-citationNitzan, M., Karaiskos, N., Friedman, N., & Rajewsky, N. (2019) · Nature · doi:10.1038/s41586-019-1773-3 · Cited by 284
Mobile PEAR transcription factors integrate positional cues to prime cambial growth
Miyashima, S., Roszak, P., Sevilem, I., Toyokura, K., Blob, B., Heo, J.-O., Mellor, N., Help-Rinta-Rahko, H., Otero, S., Smet, W., et al. (2019) · Nature · doi:10.1038/s41586-018-0839-y · Cited by 264
Optimizing RNA-Seq Mapping with STAR
Dobin, A., & Gingeras, T. R. (2016) · Methods in Molecular Biology · doi:10.1007/978-1-4939-3572-7_13 · Cited by 248
Cell Pattern in the Arabidopsis Root Epidermis Determined by Lateral Inhibition with Feedback
Lee, M. M., & Schiefelbein, J. (2002) · The Plant Cell · doi:10.1105/tpc.010434 · Cited by 219
SUMO E3 Ligase HIGH PLOIDY2 Regulates Endocycle Onset and Meristem Maintenance in Arabidopsis
Ishida, T., Fujiwara, S., Miura, K., Stacey, N., Yoshimura, M., Schneider, K., Adachi, S., Minamisawa, K., Umeda, M., & Sugimoto, K. (2009) · The Plant Cell · doi:10.1105/tpc.109.068072 · Cited by 204
The regulatory landscape of Arabidopsis thaliana roots at single-cell resolution
Dorrity, M. W., Alexandre, C. M., Hamm, M. O., Vigil, A.-L., Fields, S., Queitsch, C., & Cuperus, J. T. (2021) · Nature Communications · doi:10.1038/s41467-021-23675-y · Cited by 184
A Genome-Scale Resource for the Functional Characterization of Arabidopsis Transcription Factors
Pruneda-Paz, J. L., Breton, G., Nagel, D. H., Kang, S. E., Bonaldi, K., Doherty, C. J., Ravelo, S., Galli, M., Ecker, J. R., & Kay, S. A. (2014) · Cell Reports · doi:10.1016/j.celrep.2014.06.033 · Cited by 183
MYB36 regulates the transition from proliferation to differentiation in the Arabidopsis root
Liberman, L. M., Sparks, E. E., Moreno-Risueno, M. A., Petricka, J. J., & Benfey, P. N. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1515576112 · Cited by 179
Self-citationA map of cell type‐specific auxin responses
Bargmann, B. O. R., Vanneste, S., Krouk, G., Nawy, T., Efroni, I., Shani, E., Choe, G., Friml, J., Bergmann, D. C., Estelle, M., et al. (2013) · Molecular Systems Biology · doi:10.1038/msb.2013.40 · Cited by 176
Berger, F., Haseloff, J., Schiefelbein, J., & Dolan, L. (1998) · Current Biology · doi:10.1016/s0960-9822(98)70176-9 · Cited by 168
ACAULIS5 controls Arabidopsis xylem specification through the prevention of premature cell death
Muñiz, L., Minguet, E. G., Singh, S. K., Pesquet, E., Vera-Sirera, F., Moreau-Courtois, C. L., Carbonell, J., Blázquez, M. A., & Tuominen, H. (2008) · Development · doi:10.1242/dev.019349 · Cited by 166
The barcode, UMI, set format and BUStools
Melsted, P., Ntranos, V., & Pachter, L. (2019) · Bioinformatics · doi:10.1093/bioinformatics/btz279 · Cited by 165
Quantification of cell identity from single-cell gene expression profiles
Efroni, I., Ip, P.-L., Nawy, T., Mello, A., & Birnbaum, K. D. (2015) · Genome Biology · doi:10.1186/s13059-015-0580-x · Cited by 163
Strigolactone- and Karrikin-Independent SMXL Proteins Are Central Regulators of Phloem Formation
Wallner, E.-S., López-Salmerón, V., Belevich, I., Poschet, G., Jung, I., Grünwald, K., Sevilem, I., Jokitalo, E., Hell, R., Helariutta, Y., et al. (2017) · Current Biology · doi:10.1016/j.cub.2017.03.014 · Cited by 160
SHORT-ROOT Regulates Primary, Lateral, and Adventitious Root Development in Arabidopsis
Lucas, M., Swarup, R., Paponov, I. A., Swarup, K., Casimiro, I., Lake, D., Péret, B., Zappala, S., Mairhofer, S., Whitworth, M., et al. (2010) · PLANT PHYSIOLOGY · doi:10.1104/pp.110.165126 · Cited by 155
Rules and Self-Organizing Properties of Post-embryonic Plant Organ Cell Division Patterns
von Wangenheim, D., Fangerau, J., Schmitz, A., Smith, R. S., Leitte, H., Stelzer, E. H. K., & Maizel, A. (2016) · Current Biology · doi:10.1016/j.cub.2015.12.047 · Cited by 152
Combining Expression and Comparative Evolutionary Analysis. The COBRA Gene Family
Brady, S. M., Song, S., Dhugga, K. S., Rafalski, J. A., & Benfey, P. N. (2006) · PLANT PHYSIOLOGY · doi:10.1104/pp.106.087262 · Cited by 149
Self-citationClay, N. K., & Nelson, T. M. (2005) · PLANT PHYSIOLOGY · doi:10.1104/pp.104.055756 · Cited by 140
A single-cell view of the transcriptome during lateral root initiation in Arabidopsis thaliana
Gala, H., Lanctot, A., Jean-Baptiste, K., Guiziou, S., Chu, J. C., Zemke, J. E., George, W., Queitsch, C., Cuperus, J. T., & Nemhauser, J. L. (2021) · The Plant Cell · doi:10.1093/plcell/koab101 · Cited by 136
A high-resolution gene expression map of the Arabidopsis shoot meristem stem cell niche
Yadav, R. K., Tavakkoli, M., Xie, M., Girke, T., & Reddy, G. V. (2014) · Development · doi:10.1242/dev.106104 · Cited by 127
Regulation of epidermal cell fate in Arabidopsis roots: the importance of multiple feedback loops
Schiefelbein, J., Huang, L., & Zheng, X. (2014) · Frontiers in Plant Science · doi:10.3389/fpls.2014.00047 · Cited by 123
Power in Numbers: Single-Cell RNA-Seq Strategies to Dissect Complex Tissues
Birnbaum, K. D. (2018) · Annual Review of Genetics · doi:10.1146/annurev-genet-120417-031247 · Cited by 117
The potential of single-cell profiling in plants
Efroni, I., & Birnbaum, K. D. (2016) · Genome biology · doi:10.1186/s13059-016-0931-2 · Cited by 109
A Comprehensive Toolkit for Inducible, Cell Type-Specific Gene Expression in Arabidopsis
Schürholz, A.-K., Lopéz-Salmerón, V., Li, Z., Forner, J., Wenzl, C., Gaillochet, C., Augustin, S., Barro, A. V., Fuchs, M., Gebert, M., et al. (2018) · PLANT PHYSIOLOGY · doi:10.1104/pp.18.00463 · Cited by 109
Franks, J. M., Cai, G., & Whitfield, M. L. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty026 · Cited by 101
Bhosale, R., Boudolf, V., Cuevas, F., Lu, R., Eekhout, T., Hu, Z., Isterdael, G. V., Lambert, G. M., Xu, F., Nowack, M. K., et al. (2018) · The Plant Cell · doi:10.1105/tpc.17.00983 · Cited by 101
Week-long imaging of cell divisions in the Arabidopsis root meristem
Rahni, R., & Birnbaum, K. D. (2019) · Plant Methods · doi:10.1186/s13007-019-0417-9 · Cited by 86
Developmental single-cell transcriptomics in the Lytechinus variegatus sea urchin embryo
Massri, A. J., Greenstreet, L., Afanassiev, A., Berrío, A., Wray, G. A., Schiebinger, G. R., & McClay, D. R. (2021) · Development · doi:10.1242/dev.198614 · Cited by 84
Self-citationCellOracle: Dissecting cell identity via network inference and in silico gene perturbation
Kamimoto, K., Hoffmann, C. M., & Morris, S. A. (2020) · doi:10.1101/2020.02.17.947416 · Cited by 81
The iRoCS T oolbox – 3 D analysis of the plant root apical meristem at cellular resolution
Schmidt, T., Pasternak, T. P., Liu, K., et al. (2014) · The Plant Journal · doi:10.1111/tpj.12429 · Cited by 75
Cui, H., Hao, Y., Kovtun, M., Štolc, V., Deng, X., Sakakibara, H., & Kojima, M. (2011) · PLANT PHYSIOLOGY · doi:10.1104/pp.111.183178 · Cited by 69
Clark, N. M., Buckner, E., Fisher, A., Nelson, E. C., Nguyen, T. T., Simmons, A. R., Balaguer, M. A. D. L., Butler-Smith, T., Sheldon, P. J., Bergmann, D. C., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-13132-2 · Cited by 63
Framework for gradual progression of cell ontogeny in the Arabidopsis root meristem
Wendrich, J. R., Möller, B. K., Li, S., et al. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1707400114 · Cited by 54
Uncovering Gene Regulatory Networks Controlling Plant Cell Differentiation
Drapek, C., Sparks, E. E., & Benfey, P. N. (2017) · Trends in Genetics · doi:10.1016/j.tig.2017.05.002 · Cited by 51
Self-citationIntricacies of single-cell multi-omics data integration
Rautenstrauch, P., Vlot, A. H. C., Saran, S., & Ohler, U. (2021) · Trends in Genetics · doi:10.1016/j.tig.2021.08.012 · Cited by 48
Self-citationMinimum requirements for changing and maintaining endodermis cell identity in the Arabidopsis root
Drapek, C., Sparks, E. E., Marhavý, P., Taylor, I. W., Andersen, T. G., Hennacy, J. H., Geldner, N., & Benfey, P. N. (2018) · Nature Plants · doi:10.1038/s41477-018-0213-y · Cited by 46
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Metadata
- Authors
- Shahan, R., Hsu, C.-W., Nolan, T. M., Cole, B. J., Taylor, I. W., Greenstreet, L., Zhang, S., Afanassiev, A., Vlot, A. H. C., Schiebinger, G., Benfey, P. N., & Ohler, U.
- Venue
- Developmental Cell
- Publisher
- Elsevier BV
- Published
- 2022-02
- Volume
- 57
- Issue
- 4
- Pages
- 543-560.e9
- ISSN
- 1534-5807 (ISSN-L)
- OpenAlex
- W4220835023
- Cited by
- 363
- References
- 102
- FWCI
- 18.71
- 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 ›
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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.
