The DOI matches its Crossref record; 164 of the 164 references it cites were found in a registry or an index.
Metabolic modeling of single Th17 cells reveals regulators of autoimmunity
Open accessPublished version of a preprint
Abstract
Metabolism is a major regulator of immune cell function, but it remains difficult to study the metabolic status of individual cells. Here, we present Compass, an algorithm to characterize cellular metabolic states based on single-cell RNA sequencing and flux balance analysis. We applied Compass to associate metabolic states with T helper 17 (Th17) functional variability (pathogenic potential) and recovered a metabolic switch between glycolysis and fatty acid oxidation, akin to known Th17/regulatory T cell (Treg) differences, which we validated by metabolic assays. Compass also predicted that Th17 pathogenicity was associated with arginine and downstream polyamine metabolism. Indeed, polyamine-related enzyme expression was enhanced in pathogenic Th17 and suppressed in Treg cells. Chemical and genetic perturbation of polyamine metabolism inhibited Th17 cytokines, promoted Foxp3 expression, and remodeled the transcriptome and epigenome of Th17 cells toward a Treg-like state. In vivo perturbations of the polyamine pathway altered the phenotype of encephalitogenic T cells and attenuated tissue inflammation in CNS autoimmunity.
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?
In the citing paper
“the non-pathogenic/homeostatic and pathogenic Th17 cell phenotypes studied in the mouse models may mirror the physiological roles of human Th17 cell subsets that are important for immunity against distinct bacteria and fungi”
From TH17 cell heterogeneity and its role in tissue inflammation (2023) · cites this paper as [65]
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
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
Fast gapped-read alignment with Bowtie 2
Langmead, B., & Salzberg, S. L. (2012) · Nature Methods · doi:10.1038/nmeth.1923 · Cited by 56,400
Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L., Gillette, M. A., Paulovich, A., Pomeroy, S. L., Golub, T. R., Lander, E. S., et al. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0506580102 · Cited by 53,625
limma powers differential expression analyses for RNA-sequencing and microarray studies
Ritchie, M. E., Phipson, B., Wu, D., Hu, Y., Law, C. W., Shi, W., & Smyth, G. K. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv007 · Cited by 40,458
Model-based Analysis of ChIP-Seq (MACS)
Zhang, Y., Liu, T., Meyer, C. A., Eeckhoute, J., Johnson, D. S., Bernstein, B. E., Nusbaum, C., Myers, R. M., Brown, M., Li, W., et al. (2008) · Genome Biology · doi:10.1186/gb-2008-9-9-r137 · Cited by 18,386
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
KEGG: new perspectives on genomes, pathways, diseases and drugs
Kanehisa, M., Furumichi, M., Tanabe, M., Sato, Y., & Morishima, K. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkw1092 · Cited by 8,865
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
Self-citationBettelli, E., Carrier, Y., Gao, W., Korn, T., Strom, T. B., Oukka, M., Weiner, H. L., & Kuchroo, V. K. (2006) · Nature · doi:10.1038/nature04753 · Cited by 6,992
Self-citationBuenrostro, J. D., Giresi, P. G., Zaba, L. C., Chang, H. Y., & Greenleaf, W. J. (2013) · Nature Methods · doi:10.1038/nmeth.2688 · Cited by 6,422
voom: precision weights unlock linear model analysis tools for RNA-seq read counts
Law, C. W., Chen, Y., Shi, W., & Smyth, G. K. (2014) · Genome Biology · doi:10.1186/gb-2014-15-2-r29 · Cited by 6,155
A Unique Microglia Type Associated with Restricting Development of Alzheimer’s Disease
Keren-Shaul, H., Spinrad, A., Weiner, A., Matcovitch-Natan, O., Dvir-Szternfeld, R., Ulland, T. K., David, E., Baruch, K., Lara-Astaiso, D., Toth, B., et al. (2017) · Cell · doi:10.1016/j.cell.2017.05.018 · Cited by 5,493
Korn, T., Bettelli, E., Oukka, M., & Kuchroo, V. K. (2009) · Annual Review of Immunology · doi:10.1146/annurev.immunol.021908.132710 · Cited by 4,873
Self-citationGREAT improves functional interpretation of cis-regulatory regions
McLean, C. Y., Bristor, D., Hiller, M., Clarke, S. L., Schaar, B. T., Lowe, C. B., Wenger, A. M., & Bejerano, G. (2010) · Nature Biotechnology · doi:10.1038/nbt.1630 · Cited by 4,502
FIMO: scanning for occurrences of a given motif
Grant, C. E., Bailey, T. L., & Noble, W. S. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr064 · Cited by 4,247
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
Siepel, A., Bejerano, G., Pedersen, J. S., Hinrichs, A. S., Hou, M., Rosenbloom, K., Clawson, H., Spieth, J., Hillier, L. W., Richards, S., et al. (2005) · Genome Research · doi:10.1101/gr.3715005 · Cited by 3,971
What is flux balance analysis?
Orth, J. D., Thiele, I., & Palsson, B. Ø. (2010) · Nature Biotechnology · doi:10.1038/nbt.1614 · Cited by 3,903
Veldhoen, M., Hocking, R. J., Atkins, C. J., Locksley, R. M., & Stockinger, B. (2006) · Immunity · doi:10.1016/j.immuni.2006.01.001 · Cited by 3,605
A guide to immunometabolism for immunologists
O'Neill, L. A. J., Kishton, R. J., & Rathmell, J. (2016) · Nature Reviews Immunology · doi:10.1038/nri.2016.70 · Cited by 3,315
Transforming growth factor-β induces development of the TH17 lineage
Mangan, P. R., Harrington, L. E., O'Quinn, D. B., Helms, W. S., Bullard, D. C., Elson, C. O., Hatton, R. D., Wahl, S. M., Schoeb, T. R., & Weaver, C. T. (2006) · Nature · doi:10.1038/nature04754 · Cited by 3,087
Cua, D. J., Sherlock, J., Chen, Y., Murphy, C. A., Joyce, B., Seymour, B., Lucian, L., To, W., Kwan, S., Churakova, T., et al. (2003) · Nature · doi:10.1038/nature01355 · Cited by 2,906
The Reactome Pathway Knowledgebase
Fabregat, A., Jupe, S., Matthews, L. R., Sidiropoulos, K., Gillespie, M. E., Garapati, P. V., Haw, R., Jassal, B., Korninger, F., May, B., et al. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx1132 · Cited by 2,862
Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors
Haghverdi, L., Lun, A. T. L., Morgan, M. D., & Marioni, J. C. (2018) · Nature Biotechnology · doi:10.1038/nbt.4091 · Cited by 2,416
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
Mills, E. L., Kelly, B., Logan, A., Costa, A. S. H., Varma, M., Bryant, C. E., Tourlomousis, P., Däbritz, J. H. M., Gottlieb, E., Latorre, I., et al. (2016) · Cell · doi:10.1016/j.cell.2016.08.064 · Cited by 2,291
Regev, A., Teichmann, S. A., Lander, E. S., Amit, I., Benoist, C., Birney, E., Bodenmiller, B., Campbell, P., Carninci, P., Clatworthy, M., et al. (2017) · eLife · doi:10.7554/elife.27041 · Cited by 2,232
Self-citationZhou, L., Ivanov, I. I., Spolski, R. J., Min, R., Shenderov, K., Egawa, T., Levy, D. E., Leonard, W. J., & Littman, D. R. (2007) · Nature Immunology · doi:10.1038/ni1488 · Cited by 2,210
Posttranscriptional Control of T Cell Effector Function by Aerobic Glycolysis
Chang, C.-H., Curtis, J. D., Maggi, L. B., Faubert, B., Villarino, A. V., O’Sullivan, D., Huang, S. C.-C., van der Windt, G. J. W., Blagih, J., Qiu, J., et al. (2013) · Cell · doi:10.1016/j.cell.2013.05.016 · Cited by 2,204
Self-citationMichalek, R. D., Gerriets, V. A., Jacobs, S. R., Macintyre, A. N., MacIver, N. J., Mason, E. F., Sullivan, S. A., Nichols, A. G., & Rathmell, J. C. (2011) · The Journal of Immunology · doi:10.4049/jimmunol.1003613 · Cited by 2,091
Jha, A. K., Huang, S. C.-C., Sergushichev, A., Lampropoulou, V., Ivanova, Y., Loginicheva, E., Chmielewski, K., Stewart, K. M., Ashall, J., Everts, B., et al. (2015) · Immunity · doi:10.1016/j.immuni.2015.02.005 · Cited by 2,066
Self-citationDefining T Cell States Associated with Response to Checkpoint Immunotherapy in Melanoma
Sade-Feldman, M., Yizhak, K., Bjorgaard, S. L., Ray, J. P., de Boer, C. G., Jenkins, R. W., Lieb, D. J., Chen, J. H., Frederick, D. T., Barzily-Rokni, M., et al. (2018) · Cell · doi:10.1016/j.cell.2018.10.038 · Cited by 2,053
Single-Cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment
Azizi, E., Carr, A. J., Plitas, G., Cornish, A. E., Konopacki, C., Prabhakaran, S., Nainys, J., Wu, K., Kiseliovas, V., Setty, M., et al. (2018) · Cell · doi:10.1016/j.cell.2018.05.060 · Cited by 1,976
Ancient DNA and the rewriting of human history: be sparing with Occam’s razor
Haber, M., Mezzavilla, M., Xue, Y., & Tyler-Smith, C. (2016) · Genome Biology · doi:10.1186/s13059-015-0866-z · Cited by 1,924
Aggarwal, S., Ghilardi, N., Xie, M.-H., de Sauvage, F. J., & Gurney, A. L. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m207577200 · Cited by 1,848
Recovering Gene Interactions from Single-Cell Data Using Data Diffusion
van Dijk, D., Sharma, R., Nainys, J., Yim, K., Kathail, P., Carr, A. J., Burdziak, C., Moon, K. R., Chaffer, C. L., Pattabiraman, D., et al. (2018) · Cell · doi:10.1016/j.cell.2018.05.061 · Cited by 1,829
Shi, L. Z., Wang, R., Huang, G., Vogel, P., Neale, G., Green, D. R., & Chi, H. (2011) · Journal of Experimental Medicine · doi:10.1084/jem.20110278 · Cited by 1,803
Romani, L. (2011) · Nature Reviews Immunology · doi:10.1038/nri2939 · Cited by 1,793
Immunometabolism governs dendritic cell and macrophage function
O'Neill, L. A. J., & Pearce, E. J. (2015) · The Journal of Experimental Medicine · doi:10.1084/jem.20151570 · Cited by 1,779
Self-citationThe Biological Functions of T Helper 17 Cell Effector Cytokines in Inflammation
Ouyang, W., Kolls, J. K., & Zheng, Y. (2008) · Immunity · doi:10.1016/j.immuni.2008.03.004 · Cited by 1,750
McGeachy, M. J., Bak-Jensen, K. S., Chen, Y., Tato, C. M., Blumenschein, W., McClanahan, T., & Cua, D. J. (2007) · Nature Immunology · doi:10.1038/ni1539 · Cited by 1,520
Phosphoenolpyruvate Is a Metabolic Checkpoint of Anti-tumor T Cell Responses
Ho, P.-C., Bihuniak, J. D., Macintyre, A. N., Staron, M., Liu, X., Amezquita, R., Tsui, Y.-C., Cui, G., Micevic, G., Perales, J. C., et al. (2015) · Cell · doi:10.1016/j.cell.2015.08.012 · Cited by 1,462
Khan, A., Fornés, O., Stigliani, A., Gheorghe, M., Castro-Mondragon, J. A., van der Lee, R., Bessy, A., Chèneby, J., Kulkarni, S. R., Tan, G., et al. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx1126 · Cited by 1,457
Regev, A., Teichmann, S. A., Lander, E. S., Amit, I., Benoist, C. O., Birney, E., Bodenmiller, B., & al, E. (2017) · Zurich Open Repository and Archive (University of Zurich) · doi:10.5167/uzh-162597 · Cited by 1,457
Self-citationGeneration of pathogenic TH17 cells in the absence of TGF-β signalling
Ghoreschi, K., Laurence, A., Yang, X.-P., Tato, C. M., McGeachy, M. J., Konkel, J. E., Ramos, H. L., Wei, L., Davidson, T. S., Bouladoux, N., et al. (2010) · Nature · doi:10.1038/nature09447 · Cited by 1,388
Fueling Immunity: Insights into Metabolism and Lymphocyte Function
Pearce, E. L., Poffenberger, M. C., Chang, C.-H., & Jones, R. G. (2013) · Science · doi:10.1126/science.1242454 · Cited by 1,363
Self-citationMetabolic Instruction of Immunity
Buck, M. D., Sowell, R., Kaech, S. M., & Pearce, E. L. (2017) · Cell · doi:10.1016/j.cell.2017.04.004 · Cited by 1,270
Self-citationCritical Regulation of Early Th17 Cell Differentiation by Interleukin-1 Signaling
Chung, Y., Chang, S. H., Martínez, G., Yang, X. O., Nurieva, R., Kang, H. S., Ma, L., Watowich, S. S., Jetten, A. M., Tian, Q., et al. (2009) · Immunity · doi:10.1016/j.immuni.2009.02.007 · Cited by 1,247
Metabolic Regulation of T Lymphocytes
MacIver, N. J., Michalek, R. D., & Rathmell, J. C. (2013) · Annual Review of Immunology · doi:10.1146/annurev-immunol-032712-095956 · Cited by 1,244
Induction and effector functions of TH17 cells
Bettelli, E., Korn, T., Oukka, M., & Kuchroo, V. K. (2008) · Nature · doi:10.1038/nature07036 · Cited by 1,243
Self-citationCreation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0
Heirendt, L., Arreckx, S., Pfau, T., Mendoza, S. N., Richelle, A., Heinken, A., Haraldsdóttir, H. S., Wachowiak, J., Keating, S., Vlasov, V., et al. (2019) · Nature Protocols · doi:10.1038/s41596-018-0098-2 · Cited by 1,222
Macrophage Immunometabolism: Where Are We (Going)?
den Bossche, J. V., O'Neill, L. A. J., & Menon, D. (2017) · Trends in Immunology · doi:10.1016/j.it.2017.03.001 · Cited by 1,187
Induction and molecular signature of pathogenic TH17 cells
Lee, Y., Awasthi, A., Yosef, N., Quintana, F. J., Xiao, S., Peters, A., Wu, C., Kleinewietfeld, M., Kunder, S., Hafler, D. A., et al. (2012) · Nature Immunology · doi:10.1038/ni.2416 · Cited by 1,174
Self-citationMacintyre, A. N., Gerriets, V. A., Nichols, A., Michalek, R. D., Rudolph, M. C., Deoliveira, D., Anderson, S. M., Abel, E. D., Chen, B. J., Hale, L. P., et al. (2014) · Cell Metabolism · doi:10.1016/j.cmet.2014.05.004 · Cited by 1,169
A Validated Regulatory Network for Th17 Cell Specification
Ciofani, M., Madar, A., Galan, C., Sellars, M., Mace, K., Pauli, F., Agarwal, A., Huang, W., Parkurst, C. N., Muratet, M., et al. (2012) · Cell · doi:10.1016/j.cell.2012.09.016 · Cited by 1,160
Corces, M. R., Buenrostro, J. D., Wu, B., Greenside, P. G., Chan, S. M., Koenig, J. L., Snyder, M. P., Pritchard, J. K., Kundaje, A., Greenleaf, W. J., et al. (2016) · Nature Genetics · doi:10.1038/ng.3646 · Cited by 1,151
Tesmer, L. A., Lundy, S. K., Sarkar, S., & Fox, D. A. (2008) · Immunological Reviews · doi:10.1111/j.1600-065x.2008.00628.x · Cited by 1,132
Pooling across cells to normalize single-cell RNA sequencing data with many zero counts
L. Lun, A. T., Bach, K., & Marioni, J. C. (2016) · Genome Biology · doi:10.1186/s13059-016-0947-7 · Cited by 1,108
Transcriptional Heterogeneity and Lineage Commitment in Myeloid Progenitors
Paul, F., Arkin, Y., Giladi, A., Jaitin, D. A., Kenigsberg, E., Keren-Shaul, H., Winter, D., Lara-Astiaso, D., Gury, M., Weiner, A., et al. (2015) · Cell · doi:10.1016/j.cell.2015.11.013 · Cited by 1,082
Van Hove, H., Martens, L., Scheyltjens, I., De Vlaminck, K., Pombo Antunes, A. R., De Prijck, S., Vandamme, N., De Schepper, S., Van Isterdael, G., Scott, C. L., et al. (2019) · Nature Neuroscience · doi:10.1038/s41593-019-0393-4 · Cited by 1,074
McGeachy, M. J., Chen, Y., Tato, C. M., Laurence, A., Joyce-Shaikh, B., Blumenschein, W. M., McClanahan, T. K., O'Shea, J. J., & Cua, D. J. (2009) · Nature Immunology · doi:10.1038/ni.1698 · Cited by 1,074
Exponential scaling of single-cell RNA-seq in the past decade
Svensson, V., Vento-Tormo, R., & Teichmann, S. A. (2018) · Nature Protocols · doi:10.1038/nprot.2017.149 · Cited by 1,034
A community-driven global reconstruction of human metabolism
Thiele, I., Swainston, N., Fleming, R. M. T., Hoppe, A., Sahoo, S., Aurich, M. K., Haraldsdottir, H., Mo, M. L., Rolfsson, O., Stobbe, M. D., et al. (2013) · Nature Biotechnology · doi:10.1038/nbt.2488 · Cited by 1,019
Khan, A., Fornes, O., Stigliani, A., Gheorghe, M., Castro-Mondragon, J., van der Lee, R., Bessy, A., Chèneby, J., Kulkarni, S. R., Tan, G., et al. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx1188 · Cited by 973
Metabolic Flux Balancing: Basic Concepts, Scientific and Practical Use
Varma, A., & Palsson, B. Ø. (1994) · Nature Biotechnology · doi:10.1038/nbt1094-994 · Cited by 945
De novo fatty acid synthesis controls the fate between regulatory T and T helper 17 cells
Berod, L., Friedrich, C., Nandan, A., Freitag, J., Hagemann, S., Harmrolfs, K., Sandouk, A., Hesse, C., Castro, C. N., Bähre, H., et al. (2014) · Nature Medicine · doi:10.1038/nm.3704 · Cited by 927
Lactate modulation of immune responses in inflammatory versus tumour microenvironments
Certo, M., Tsai, C.-H., Pucino, V., Ho, P.-C., & Mauro, C. (2021) · Nature Reviews Immunology · doi:10.1038/s41577-020-0406-2 · Cited by 924
Pathogen-induced human TH17 cells produce IFN-γ or IL-10 and are regulated by IL-1β
Zielinski, C. E., Mele, F., Aschenbrenner, D., Jarrossay, D., Ronchi, F., Gattorno, M., Monticelli, S., Lanzavecchia, A., & Sallusto, F. (2012) · Nature · doi:10.1038/nature10957 · Cited by 919
A cellular census of human lungs identifies novel cell states in health and in asthma
Vieira Braga, F. A., Kar, G., Berg, M., Carpaij, O. A., Polanski, K., Simon, L. M., Brouwer, S., Gomes, T., Hesse, L., Jiang, J., et al. (2019) · Nature Medicine · doi:10.1038/s41591-019-0468-5 · Cited by 896
Unraveling the Complex Interplay Between T Cell Metabolism and Function
Geltink, R. I. K., Kyle, R. L., & Pearce, E. L. (2018) · Annual Review of Immunology · doi:10.1146/annurev-immunol-042617-053019 · Cited by 849
Self-citationConstraint-based models predict metabolic and associated cellular functions
Bordbar, A., Monk, J. M., King, Z. A., & Palsson, B. Ø. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3643 · Cited by 844
Polyamine metabolism and cancer: treatments, challenges and opportunities
Casero, R. A., Stewart, T. M., & Pegg, A. E. (2018) · Nature reviews. Cancer · doi:10.1038/s41568-018-0050-3 · Cited by 826
Metabolic coordination of T cell quiescence and activation
Chapman, N. M., Boothby, M. R., & Chi, H. (2019) · Nature reviews. Immunology · doi:10.1038/s41577-019-0203-y · Cited by 793
Scaling single-cell genomics from phenomenology to mechanism
Tanay, A., & Regev, A. (2017) · Nature · doi:10.1038/nature21350 · Cited by 792
Self-citationAerobic glycolysis promotes T helper 1 cell differentiation through an epigenetic mechanism
Peng, M., Yin, N., Chhangawala, S., Xu, K., Leslie, C. S., & Li, M. O. (2016) · Science · doi:10.1126/science.aaf6284 · Cited by 787
Jäger, A., Dardalhon, V., Sobel, R. A., Bettelli, E., & Kuchroo, V. K. (2009) · The Journal of Immunology · doi:10.4049/jimmunol.0901906 · Cited by 783
Self-citationConstraining the metabolic genotype–phenotype relationship using a phylogeny of in silico methods
Lewis, N. E., Nagarajan, H., & Palsson, B. O. (2012) · Nature Reviews Microbiology · doi:10.1038/nrmicro2737 · Cited by 779
Omic data from evolved E. coli are consistent with computed optimal growth from genome‐scale models
Lewis, N. E., Hixson, K. K., Conrad, T. M., Lerman, J. A., Charusanti, P., Polpitiya, A. D., Adkins, J., Schramm, G., Purvine, S. O., López‐Ferrer, D., et al. (2010) · Molecular Systems Biology · doi:10.1038/msb.2010.47 · Cited by 748
Metabolic programming and PDHK1 control CD4+ T cell subsets and inflammation
Gerriets, V. A., Kishton, R. J., Nichols, A., Macintyre, A. N., Inoue, M., Ilkayeva, O., Winter, P. S., Liu, X., Priyadharshini, B., Slawinska, M. E., et al. (2014) · Journal of Clinical Investigation · doi:10.1172/jci76012 · Cited by 747
Succinate: a metabolic signal in inflammation
Mills, E., & O’Neill, L. A. J. (2014) · Trends in Cell Biology · doi:10.1016/j.tcb.2013.11.008 · Cited by 741
SAVER: gene expression recovery for single-cell RNA sequencing
Huang, M. C., Wang, J., Torre, E. A., Dueck, H., Shaffer, S. M., Bonasio, R., Murray, J. I., Raj, A., Li, M., & Zhang, N. R. (2018) · Nature Methods · doi:10.1038/s41592-018-0033-z · Cited by 739
Using Genome-scale Models to Predict Biological Capabilities
O’Brien, E. J., Monk, J. M., & Palsson, B. Ø. (2015) · Cell · doi:10.1016/j.cell.2015.05.019 · Cited by 732
Distinct Regulation of Th17 and Th1 Cell Differentiation by Glutaminase-Dependent Metabolism
Johnson, M. O., Wolf, M. M., Madden, M. Z., Andrejeva, G., Sugiura, A., Contreras, D. C., Maseda, D., Liberti, M. V., Paz, K. G., Kishton, R. J., et al. (2018) · Cell · doi:10.1016/j.cell.2018.10.001 · Cited by 729
Th17 Cell Differentiation: The Long and Winding Road
McGeachy, M. J., & Cua, D. J. (2008) · Immunity · doi:10.1016/j.immuni.2008.03.001 · Cited by 712
Dynamic regulatory network controlling TH17 cell differentiation
Yosef, N., Shalek, A. K., Gaublomme, J. T., Jin, H., Lee, Y., Awasthi, A., Wu, C., Karwacz, K., Xiao, S., Jorgolli, M., et al. (2013) · Nature · doi:10.1038/nature11981 · Cited by 682
Self-citationMetabolic control of cell death
Green, D. R., Galluzzi, L., & Kroemer, G. (2014) · Science · doi:10.1126/science.1250256 · Cited by 678
Hypoxia-inducible factors enhance the effector responses of CD8(+) T cells to persistent antigen
Doedens, A. L., Phan, A. T., Stradner, M. H., Fujimoto, J. K., Nguyen, J. V., Yang, E., Johnson, R. S., & Goldrath, A. W. (2013) · Nature Immunology · doi:10.1038/ni.2714 · Cited by 660
Metabolites and the Tumour Microenvironment: From Cellular Mechanisms to Systemic Metabolism
Elia, I., & Haigis, M. C. (2021) · Nature Metabolism · doi:10.1038/s42255-020-00317-z · Cited by 651
Self-citationNetwork-based prediction of human tissue-specific metabolism
Shlomi, T., Cabili, M. N., Herrgård, M. J., Palsson, B. Ø., & Ruppin, E. (2008) · Nature Biotechnology · doi:10.1038/nbt.1487 · Cited by 637
Revealing the vectors of cellular identity with single-cell genomics
Wagner, A., Regev, A., & Yosef, N. (2016) · Nature Biotechnology · doi:10.1038/nbt.3711 · Cited by 632
Self-citationContext-Specific Metabolic Networks Are Consistent with Experiments
Becker, S. A., & Palsson, B. Ø. (2008) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000082 · Cited by 606
Transcriptional Basis of Mouse and Human Dendritic Cell Heterogeneity
Brown, C. C., Gudjonson, H., Pritykin, Y., Deep, D., Lavallée, V., Mendoza, A., Fromme, R. M., Mažutis, L., Ariyan, C. E., Leslie, C. S., et al. (2019) · Cell · doi:10.1016/j.cell.2019.09.035 · Cited by 601
Finlay, D. K., Rosenzweig, E., Sinclair, L. V., Feijoo-Carnero, C., Hukelmann, J. L., Rolf, J., Panteleyev, A. A., Okkenhaug, K., & Cantrell, D. A. (2012) · Journal of Experimental Medicine · doi:10.1084/jem.20112607 · Cited by 596
Single-cell genomics unveils critical regulators of Th17 cell pathogenicity
Gaublomme, J. T., Yosef, N., Lee, Y., Gertner, R. S., Yang, L. V., Wu, C., Pandolfi, P. P., Mak, T., Satija, R., Shalek, A. K., et al. (2015) · Cell · doi:10.1016/j.cell.2015.11.009 · Cited by 575
Self-citationPucino, V., Certo, M., Bulusu, V., Cucchi, D., Goldmann, K., Pontarini, E., Haas, R., Smith, J., Headland, S. E., Blighe, K., et al. (2019) · Cell Metabolism · doi:10.1016/j.cmet.2019.10.004 · Cited by 555
Spatiotemporal structure of cell fate decisions in murine neural crest
Soldatov, R., Kaucka, M., Kastriti, M. E., Petersen, J., Chontorotzea, T., Englmaier, L., Akkuratova, N., Yang, Y., Häring, M., Dyachuk, V., et al. (2019) · Science · doi:10.1126/science.aas9536 · Cited by 546
The Treg/Th17 Axis: A Dynamic Balance Regulated by the Gut Microbiome
Omenetti, S., & Pizarro, T. T. (2015) · Frontiers in Immunology · doi:10.3389/fimmu.2015.00639 · Cited by 545
Foundations of Immunometabolism and Implications for Metabolic Health and Disease
Hotamışlıgil, G. S. (2017) · Immunity · doi:10.1016/j.immuni.2017.08.009 · Cited by 534
Focused specificity of intestinal TH17 cells towards commensal bacterial antigens
Yang, Y., Torchinsky, M. B., Gobert, M., Xiong, H., Xu, M., Linehan, J. L., Alonzo, F., Ng, C., Chen, A., Lin, X., et al. (2014) · Nature · doi:10.1038/nature13279 · Cited by 520
Pearce, E. J., & Everts, B. (2014) · Nature reviews. Immunology · doi:10.1038/nri3771 · Cited by 500
Self-citationSingle-Cell Transcriptomics of Regulatory T Cells Reveals Trajectories of Tissue Adaptation
Miragaia, R. J., Gomes, T., Chomka, A., Jardine, L., Riedel, A., Hegazy, A. N., Whibley, N., Tucci, A., Chen, X., Lindeman, I., et al. (2019) · Immunity · doi:10.1016/j.immuni.2019.01.001 · Cited by 499
Immunometabolism at the interface between macrophages and pathogens
Russell, D. G., Huang, L., & VanderVen, B. C. (2019) · Nature reviews. Immunology · doi:10.1038/s41577-019-0124-9 · Cited by 470
Immunometabolism and natural killer cell responses
O’Brien, K., & Finlay, D. K. (2019) · Nature reviews. Immunology · doi:10.1038/s41577-019-0139-2 · Cited by 452
Halofuginone Inhibits T H 17 Cell Differentiation by Activating the Amino Acid Starvation Response
Sundrud, M. S., Koralov, S. B., Feuerer, M., Calado, D. P., Kozhaya, A. E., Rhule-Smith, A., Lefebvre, R. E., Unutmaz, D., Mazitschek, R., Waldner, H., et al. (2009) · Science · doi:10.1126/science.1172638 · Cited by 447
A Distinct Gene Module for Dysfunction Uncoupled from Activation in Tumor-Infiltrating T Cells
Singer, M., Wang, C., Cong, L., Marjanovic, N. D., Kowalczyk, M. S., Zhang, H., Nyman, J., Sakuishi, K., Kurtuluş, S., Gennert, D. G., et al. (2016) · Cell · doi:10.1016/j.cell.2016.08.052 · Cited by 422
Self-citationThe dichotomous nature of T helper 17 cells
Stockinger, B., & Omenetti, S. (2017) · Nature reviews. Immunology · doi:10.1038/nri.2017.50 · Cited by 419
CD5L/AIM Regulates Lipid Biosynthesis and Restrains Th17 Cell Pathogenicity
Wang, C., Yosef, N., Gaublomme, J. T., Wu, C., Lee, Y., Clish, C. B., Kaminski, J., Xiao, S., zu Hörste, G. M., Pawlak, M., et al. (2015) · Cell · doi:10.1016/j.cell.2015.10.068 · Cited by 405
Self-citationRaud, B., Roy, D. G., Divakaruni, A. S., Tarasenko, T. N., Franke, R., Ma, E. H., Samborska, B., Hsieh, W. Y., Wong, A., Stüve, P., et al. (2018) · Cell Metabolism · doi:10.1016/j.cmet.2018.06.002 · Cited by 401
MetaCell: analysis of single-cell RNA-seq data using K-nn graph partitions
Baran, Y., Bercovich, A., Sebé-Pedrós, A., Lubling, Y., Giladi, A., Chomsky, E., Meir, Z., Hoichman, M., Lifshitz, A., & Tanay, A. (2019) · Genome biology · doi:10.1186/s13059-019-1812-2 · Cited by 392
Immunometabolism: From basic mechanisms to translation
Makowski, L., Chaib, M., & Rathmell, J. C. (2020) · Immunological Reviews · doi:10.1111/imr.12858 · Cited by 386
Cutting Edge: IL-23 Receptor GFP Reporter Mice Reveal Distinct Populations of IL-17-Producing Cells
Awasthi, A., Riol‐Blanco, L., Jäger, A., Korn, T., Pot, C., Galileos, G., Bettelli, E., Kuchroo, V. K., & Oukka, M. (2009) · The Journal of Immunology · doi:10.4049/jimmunol.0900732 · Cited by 365
Self-citationEtomoxir Inhibits Macrophage Polarization by Disrupting CoA Homeostasis
Divakaruni, A. S., Hsieh, W. Y., Minarrieta, L., Duong, T., Kim, K. K. O., Desousa, B. R., Andreyev, A. Y., Bowman, C. E., Caradonna, K. L., Dranka, B. P., et al. (2018) · Cell Metabolism · doi:10.1016/j.cmet.2018.06.001 · Cited by 364
Spermidine/spermine- N 1 -acetyltransferase: a key metabolic regulator
Pegg, A. E. (2008) · American Journal of Physiology-Endocrinology and Metabolism · doi:10.1152/ajpendo.90217.2008 · Cited by 360
Metabolism as a guiding force for immunity
Jung, J., Zeng, H., & Horng, T. (2018) · Nature Cell Biology · doi:10.1038/s41556-018-0217-x · Cited by 354
Immunometabolism of regulatory T cells
Newton, R. H., Priyadharshini, B., & Turka, L. A. (2016) · Nature Immunology · doi:10.1038/ni.3466 · Cited by 338
BASiCS: Bayesian Analysis of Single-Cell Sequencing Data
Vallejos, C. A., Marioni, J. C., & Richardson, S. (2015) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1004333 · Cited by 302
Xiao, S., Yosef, N., Yang, J., Wang, Y., Zhou, L., Zhu, C. Y., Wu, C., Baloglu, E., Schmidt, D. R., Ramesh, R., et al. (2014) · Immunity · doi:10.1016/j.immuni.2014.04.004 · Cited by 283
Self-citationFunctional interpretation of single cell similarity maps
DeTomaso, D., Jones, M. G., Subramaniam, M., Ashuach, T., Ye, C., & Yosef, N. (2019) · Nature Communications · doi:10.1038/s41467-019-12235-0 · Cited by 259
Self-citationOral-resident natural Th17 cells and γδ T cells control opportunistic Candida albicans infections
Conti, H. R., Peterson, A. C., Brane, L., Huppler, A. R., Hernández-Santos, N., Whibley, N., Garg, A. V., Simpson-Abelson, M. R., Gibson, G. A., Mamo, A. J., et al. (2014) · Journal of Experimental Medicine · doi:10.1084/jem.20130877 · Cited by 254
The Treg/Th17 Cell Balance: A New Paradigm for Autoimmunity
Eisenstein, E. M., & Williams, C. B. (2009) · Pediatric Research · doi:10.1203/pdr.0b013e31819e76c7 · Cited by 235
Deconstructing Olfactory Stem Cell Trajectories at Single-Cell Resolution
Fletcher, R. B., Das, D., Gadye, L., Street, K., Baudhuin, A., Wagner, A., Cole, M. B., Flores-Ramirez, Q., Choi, Y. G., Yosef, N., et al. (2017) · Cell stem cell · doi:10.1016/j.stem.2017.04.003 · Cited by 235
Self-citationMetabolic control of the Treg/Th17 axis
Barbi, J. J., Pardoll, D. M., & Pan, F. (2013) · Immunological Reviews · doi:10.1111/imr.12029 · Cited by 227
Elimination of Thermodynamically Infeasible Loops in Steady-State Metabolic Models
Schellenberger, J., Lewis, N. E., & Palsson, B. Ø. (2011) · Biophysical Journal · doi:10.1016/j.bpj.2010.12.3707 · Cited by 220
A Systematic Evaluation of Methods for Tailoring Genome-Scale Metabolic Models
Opdam, S., Richelle, A., Kellman, B. P., Li, S., Zielinski, D. C., & Lewis, N. E. (2017) · Cell Systems · doi:10.1016/j.cels.2017.01.010 · Cited by 219
Metabolic heterogeneity underlies reciprocal fates of TH17 cell stemness and plasticity
Karmaus, P. W. F., Chen, X., Lim, S. A., Herrada, A. A., Nguyen, T.-L. M., Xu, B., Dhungana, Y., Rankin, S., Chen, W., Rosencrance, C., et al. (2019) · Nature · doi:10.1038/s41586-018-0806-7 · Cited by 215
Modification of Proteins by Metabolites in Immunity
Diskin, C., Ryan, T. A. J., & O'Neill, L. A. J. (2020) · Immunity · doi:10.1016/j.immuni.2020.09.014 · Cited by 215
Systems Biology: Constraint-based Reconstruction and Analysis
Palsson, B. Ø. (2015) · doi:10.1017/cbo9781139854610 · Cited by 210
Wu, P., Peters, J. M., & Harris, R. A. (2001) · Biochemical and Biophysical Research Communications · doi:10.1006/bbrc.2001.5608 · Cited by 206
ORegAnno 3.0: a community-driven resource for curated regulatory annotation
Lesurf, R., Cotto, K. C., Wang, G., Griffith, M., Kasaian, K., Jones, S. J. M., Montgomery, S. B., Griffith, O. L., & The Open Regulatory Annotation Consortium (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1203 · Cited by 201
Optimizing genome-scale network reconstructions
Monk, J. M., Nogales, J., & Palsson, B. Ø. (2014) · Nature Biotechnology · doi:10.1038/nbt.2870 · Cited by 200
Th17 cytokines in mucosal immunity and inflammation
Guglani, L., & Khader, S. A. (2010) · Current Opinion in HIV and AIDS · doi:10.1097/coh.0b013e328335c2f6 · Cited by 199
Starvation Increases the Amount of Pyruvate Dehydrogenase Kinase in Several Mammalian Tissues
Wu, P., Blair, P. V., Sato, J., Jaskiewicz, J. A., Popov, K. M., & Harris, R. A. (2000) · Archives of Biochemistry and Biophysics · doi:10.1006/abbi.2000.1946 · Cited by 181
Biphasic Dynamics of Macrophage Immunometabolism during Mycobacterium tuberculosis Infection
Shi, L., Jiang, Q., Bushkin, Y., Subbian, S., & Tyagi, S. (2019) · mBio · doi:10.1128/mbio.02550-18 · Cited by 173
Performance Assessment and Selection of Normalization Procedures for Single-Cell RNA-Seq
Cole, M. B., Risso, D., Wagner, A., DeTomaso, D., Ngai, J., Purdom, E., Dudoit, S., & Yosef, N. (2019) · Cell Systems · doi:10.1016/j.cels.2019.03.010 · Cited by 173
Self-citationDysfunctional T cell metabolism in the tumor microenvironment
Beckermann, K. E., Dudzinski, S. O., & Rathmell, J. C. (2017) · Cytokine & Growth Factor Reviews · doi:10.1016/j.cytogfr.2017.04.003 · Cited by 165
Zanini, F., Robinson, M., Croote, D., Sahoo, M. K., Sanz, A. M., Ortiz-Lasso, E., Albornóz, L. L., Rosso, F., Montoya, J. G., Goo, L., et al. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1813819115 · Cited by 160
Gemta, L. F., Siska, P. J., Nelson, M. E., Gao, X., Liu, X., Locasale, J. W., Yagita∥, H., Slingluff, C. L., Hoehn, K. L., Rathmell, J. C., et al. (2019) · Science Immunology · doi:10.1126/sciimmunol.aap9520 · Cited by 158
Critical role of histone demethylase Jmjd3 in the regulation of CD4+ T-cell differentiation
Li, Q., Zou, J., Wang, M., Ding, X., Chepelev, I., Zhou, X., Zhao, W., Wei, G., Cui, J., Zhao, K., et al. (2014) · Nature Communications · doi:10.1038/ncomms6780 · Cited by 152
Ancillary Activity: Beyond Core Metabolism in Immune Cells
Puleston, D. J., Villa, M., & Pearce, E. L. (2017) · Cell Metabolism · doi:10.1016/j.cmet.2017.06.019 · Cited by 150
Self-citationInsight Into Non-Pathogenic Th17 Cells in Autoimmune Diseases
Wu, X., Tian, J., & Wang, S. (2018) · Frontiers in Immunology · doi:10.3389/fimmu.2018.01112 · Cited by 148
Wang, Q., Liberti, M. V., Liu, P., Deng, X., Liu, Y., Locasale, J. W., & Lai, L. (2017) · Cell Chemical Biology · doi:10.1016/j.chembiol.2016.11.013 · Cited by 147
Jell, J., Merali, S., Hensen, M. L., Mazurchuk, R. V., Spernyak, J. A., Diegelman, P., Kisiel, N. D., Barrero, C. A., Deeb, K. K., Alhonen, L. I., et al. (2006) · Journal of Biological Chemistry · doi:10.1074/jbc.m610265200 · Cited by 136
K-nearest neighbor smoothing for high-throughput single-cell RNA-Seq dataPreprint
Wagner, F., Yan, Y., & Yanai, I. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/217737 · Cited by 134
Karouzakis, E., Gay, R. E., Gay, S., & Neidhart, M. (2011) · Arthritis & Rheumatism · doi:10.1002/art.34340 · Cited by 133
Mounce, B. C., Poirier, E. Z., Passoni, G., Simon‐Lorière, E., Cesaro, T., Prot, M., Stapleford, K. A., Moratorio, G., Sakuntabhai, A., Levraud, J., et al. (2016) · Cell Host & Microbe · doi:10.1016/j.chom.2016.06.011 · Cited by 128
IL-17 signaling in host defense against Candida albicans
Gaffen, S. L., Hernández‐Santos, N., & Peterson, A. (2011) · Immunologic Research · doi:10.1007/s12026-011-8226-x · Cited by 125
Liu, Z., Cao, W., Xu, L., Chen, X., Zhan, Y., Yang, Q., Liu, S., Chen, P., Jiang, Y., Sun, X., et al. (2015) · Journal of Molecular Cell Biology · doi:10.1093/jmcb/mjv022 · Cited by 121
Pompura, S. L., Wagner, A., Kitz, A., Laperche, J. M., Yosef, N., Dominguez‐Villar, M., & Hafler, D. A. (2020) · Journal of Clinical Investigation · doi:10.1172/jci138519 · Cited by 121
Self-citationSystems biology constraint-based reconstruction and analysis
Palsson, B. Ø. (2015) · Cited by 120
Integration of single-cell RNA-seq data into population models to characterize cancer metabolism
Damiani, C., Maspero, D., Filippo, M. D., Colombo, R., Pescini, D., Graudenzi, A., Westerhoff, H. V., Alberghina, L., Vanoni, M., & Mauri, G. (2019) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1006733 · Cited by 114
Pyruvate kinase M2 is requisite for Th1 and Th17 differentiation
Kono, M., Maeda, K., Stocton-Gavanescu, I., Pan, W., Umeda, M., Katsuyama, E., Burbano, C., Orite, S. Y. K., Vukelic, M., Tsokos, M., et al. (2019) · JCI Insight · doi:10.1172/jci.insight.127395 · Cited by 103
From Network Analysis to Functional Metabolic Modeling of the Human Gut Microbiota
Bauer, E., & Thiele, I. (2018) · mSystems · doi:10.1128/msystems.00209-17 · Cited by 88
Moshe, N. B. B., Hen‐Avivi, S., Levitin, N., Yehezkel, D., Oosting, M., Joosten, L. A. B., Netea, M. G., & Avraham, R. (2019) · Nature Communications · doi:10.1038/s41467-019-11257-y · Cited by 88
Revealing dynamics of gene expression variability in cell state space
Grün, D. (2019) · Nature Methods · doi:10.1038/s41592-019-0632-3 · Cited by 85
Fine tuning of immunometabolism for the treatment of rheumatic diseases
Rhoads, J. P., Major, A. S., & Rathmell, J. C. (2017) · Nature Reviews Rheumatology · doi:10.1038/nrrheum.2017.54 · Cited by 81
Pyruvate dehydrogenase phosphatase catalytic subunit 2 limits Th17 differentiation
Kono, M., Yoshida, N., Maeda, K., Skinner, N., Pan, W., Kyttaris, V. C., Tsokos, M., & Tsokos, G. C. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1805717115 · Cited by 79
Adler, M., Kohanim, Y. K., Tendler, A., Mayo, A., & Alon, U. S. (2019) · Cell Systems · doi:10.1016/j.cels.2018.12.008 · Cited by 72
Increased Polyamines Alter Chromatin and Stabilize Autoantigens in Autoimmune Diseases
Brooks, W. H. (2013) · Frontiers in Immunology · doi:10.3389/fimmu.2013.00091 · Cited by 66
Reenergizing T cell anti-tumor immunity by harnessing immunometabolic checkpoints and machineries
Ho, P., & Kaech, S. M. (2017) · Current Opinion in Immunology · doi:10.1016/j.coi.2017.04.003 · Cited by 62
Determinants of Tissue-Specific Metabolic Adaptation of T Cells
Varanasi, S. K., Kumar, S. V., & Rouse, B. T. (2020) · Cell Metabolism · doi:10.1016/j.cmet.2020.10.013 · Cited by 49
Immunometabolism in the Tumor Microenvironment
Roy, D. G., Kaymak, I., Williams, K. S., Ma, E. H., & Jones, R. G. (2020) · Annual Review of Cancer Biology · doi:10.1146/annurev-cancerbio-030518-055817 · Cited by 49
Bowlin, T. L., McKown, B. J., & Sunkara, P. S. (1987) · Immunopharmacology · doi:10.1016/0162-3109(87)90051-8 · Cited by 26
Unexpected Targets and Triggers of Autoimmunity
Lee, Y., Collins, M. A., & Kuchroo, V. K. (2014) · Journal of Clinical Immunology · doi:10.1007/s10875-014-0040-5 · Cited by 15
Self-citationRegulation of Ornithine Decarboxylase in the Kidney of Autoimmune Mice with the lpr Gene
Hsu, H., Seibold, J. R., & Thomas, T. (1994) · Autoimmunity · doi:10.3109/08916939409071351 · Cited by 12
Flagged first, then by citations
Cited by
Sorted by citations
Polyamines in cancer: integrating organismal metabolism and antitumour immunity
Holbert, C. E., Cullen, M., Casero, R. A., & Stewart, T. M. (2022) · Nature reviews. Cancer · doi:10.1038/s41568-022-00473-2 · Cited by 378
Principles and therapeutic applications of adaptive immunity
Chi, H., Pepper, M., & Thomas, P. G. (2024) · Cell · doi:10.1016/j.cell.2024.03.037 · Cited by 394
Metabolic adaptation of lymphocytes in immunity and disease
Chapman, N. M., & Chi, H. (2022) · Immunity · doi:10.1016/j.immuni.2021.12.012 · Cited by 317
TH17 cell heterogeneity and its role in tissue inflammation
Schnell, A., Littman, D. R., & Kuchroo, V. K. (2023) · Nature Immunology · doi:10.1038/s41590-022-01387-9 · Cited by 286
Self-citationStem-like intestinal Th17 cells give rise to pathogenic effector T cells during autoimmunity
Schnell, A., Huang, L., Singer, M., Singaraju, A., Barilla, R. M., Regan, B. M. L., Bollhagen, A., Thakore, P. I., Dionne, D., Delorey, T. M., et al. (2021) · Cell · doi:10.1016/j.cell.2021.11.018 · Cited by 268
Self-citation
Metadata
- Authors
- Wagner, A., Wang, C., Fessler, J., DeTomaso, D., Avila-Pacheco, J., Kaminski, J., Zaghouani, S., Christian, E., Thakore, P., Schellhaass, B., Akama-Garren, E., Pierce, K., Singh, V., Ron-Harel, N., Douglas, V. P., Bod, L., Schnell, A., Puleston, D., Sobel, R. A., Haigis, M., Pearce, E. L., Soleimani, M., Clish, C., Regev, A., Kuchroo, V. K., & Yosef, N.
- Affiliations
- University of California, Berkeley (US)
- Broad Institute (US)
- Brigham and Women's Hospital (US)
- Massachusetts Eye and Ear Infirmary (US)
- Max Planck Institute of Immunobiology and Epigenetics (DE)
- VA Palo Alto Health Care System (US)
- Harvard University (US)
- University of New Mexico (US)
- Ragon Institute of MGH, MIT and Harvard (US)
- Corresponding author
- Wang, Chao
- Kuchroo, Vijay K.
- Yosef, Nir
- ORCID
- Wagner, Allon
- Wang, Chao
- Fessler, Johannes
- DeTomaso, David
- Zaghouani, Sarah
- Christian, Elena
- Pierce, Kerry
- Singh, Vasundhara
- Douglas, Vivian Paraskevi
- Bod, Lloyd
- Schnell, Alexandra
- Puleston, Daniel
- Sobel, Raymond A.
- Haigis, Marcia
- Pearce, Erika L.
- Soleimani, Manoocher
- Clish, Clary
- Regev, Aviv
- Kuchroo, Vijay K.
- Yosef, Nir
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2021-08
- Volume
- 184
- Issue
- 16
- Pages
- 4168-4185.e21
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC8621950
- OpenAlex
- W3174064560
- Cited by
- 524
- References
- 163
- Citations by year
- 2026: 105 · 2025: 118 · 2024: 111 · 2023: 92 · 2022: 75 · 2021: 18
- FWCI
- 27.61
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- www.elsevier.com/tdm/userlicense/1.0/ (tdm)
- www.elsevier.com/legal/tdmrep-license (tdm)
- www.elsevier.com/open-access/userlicense/1.0/ (vor, 369 d)
- doi.org/10.15223/policy-017 (stm-asf)
- doi.org/10.15223/policy-037 (stm-asf)
- doi.org/10.15223/policy-012 (stm-asf)
- doi.org/10.15223/policy-029 (stm-asf)
- doi.org/10.15223/policy-004 (stm-asf)
- Locations
- Cell (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- Chan Zuckerberg Initiative
- Australian Academy of Science
- Österreichischen Akademie der Wissenschaften
- NIH
- Canada First Research Excellence Fund (P01AI039671, P01AI056299, P01AI073748, R01AI144166, R01NS045937, RO1NS30843, TA-1605-08590)
- National Multiple Sclerosis Society
- National Institute of Mental Health (NIH5U19MH114821)
- Topics
- Life Sciences › Immunology and Microbiology › Immunology › T-cell and B-cell Immunology
- Life Sciences › Immunology and Microbiology › Immunology › Psoriasis: Treatment and Pathogenesis
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Keywords
- Th17 cells, cellular metabolism, flux balance analysis, glycolysis, fatty acid oxidation, regulatory T cells, polyamine metabolism, arginine metabolism, Foxp3, central nervous system autoimmunity, multiple sclerosis, encephalitogenic T cells
- MeSH terms
- Epigenome, Diamine N-Acetyltransferase, Acetyltransferases, Adenosine Triphosphate, Aerobiosis, Algorithms, Eflornithine, Animals, Chromatin, Citric Acid Cycle, Encephalomyelitis, Autoimmune, Experimental, Fatty Acids, Glycolysis, Mice, Inbred C57BL, Models, Biological, Oxidation-Reduction, Putrescine, Autoimmunity, Cytokines, Mitochondrial Membrane Transport Proteins, T-Lymphocytes, Regulatory, Mice, Jumonji Domain-Containing Histone Demethylases, Th17 Cells, Single-Cell Analysis, 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
