Densely Interconnected Transcriptional Circuits Control Cell States in Human Hematopoiesis
Open accessAbstract
Though many individual transcription factors are known to regulate hematopoietic differentiation, major aspects of the global architecture of hematopoiesis remain unknown. Here, we profiled gene expression in 38 distinct purified populations of human hematopoietic cells and used probabilistic models of gene expression and analysis of cis-elements in gene promoters to decipher the general organization of their regulatory circuitry. We identified modules of highly coexpressed genes, some of which are restricted to a single lineage but most of which are expressed at variable levels across multiple lineages. We found densely interconnected cis-regulatory circuits and a large number of transcription factors that are differentially expressed across hematopoietic states. These findings suggest a more complex regulatory system for hematopoiesis than previously assumed.
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Myeloid clusters were identified by checking canonical myeloid marker gene expression and by automated annotation with SingleR based on the Novershtern immune reference dataset.
“To identify myeloid clusters, we checked the expression of canonical myeloid marker genes (Supplementary Data 3). Furthermore, we used SingleR v2.0.074 for automated annotation based on the Novershtern immune reference dataset75 from the celldex v1.8.0 package74.”
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Because cells are unsynchronized, single cells captured at any time point stochastically include cells at different instantaneous points along a temporal trajectory.
“Since cells are unsynchronized, the set of single cells captured at any time point will stochastically contain cells positioned in different instantaneous time points along the temporal trajectory59,135,136 (Fig. 1b).”
From Revealing the vectors of cellular identity with single-cell genomics (2016) · cites this paper as [135]
Several studies have analyzed the covariation structure between transcripts or proteins across single cells to infer regulatory relations.
“Leveraging this insight, several studies have analyzed the covariation structure between transcripts or proteins across single cells to infer regulatory relations1–3,41,135,137,168–172.”
From Revealing the vectors of cellular identity with single-cell genomics (2016) · cites this paper as [135]
Similar approaches have been used in other biological settings, and enhanced resolution, for example from pseudotemporal ordering, has helped recover such dependencies.
“Similar approaches have been used in other biological settings1, and enhanced resolution, for example from pseudotemporal ordering, has helped recover such dependencies135,137.”
From Revealing the vectors of cellular identity with single-cell genomics (2016) · cites this paper as [135]
Most prior mammalian regulatory circuit reconstruction studies assumed a single fixed network.
“Most of these studies have relied upon computational circuit-reconstruction algorithms that assume one ‘fixed’ network.”
From Dynamic regulatory network controlling TH17 cell differentiation (2013) · cites this paper as [7]
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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 · see citing works
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 · see citing works
Self-citationUltrafast and memory-efficient alignment of short DNA sequences to the human genome.
Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009) · Genome Biology · doi:10.1186/gb-2009-10-3-r25 · Cited by 21,849 · see citing works
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 · see citing works
Bioconductor: open software development for computational biology and bioinformatics
Gentleman, R., Carey, V., Bates, D., Bolstad, B., Dettling, M., Dudoit, S., Ellis, B., Gautier, L., Ge, Y., Gentry, J., et al. (2004) · Genome Biology · doi:10.1186/gb-2004-5-10-r80 · Cited by 13,133 · see citing works
Exploration, normalization, and summaries of high density oligonucleotide array probe level data
Irizarry, R. A. (2003) · Biostatistics · doi:10.1093/biostatistics/4.2.249 · Cited by 10,603 · see citing works
Adjusting batch effects in microarray expression data using empirical Bayes methods
Johnson, W. E., Li, C., & Rabinovic, A. (2007) · Biostatistics · doi:10.1093/biostatistics/kxj037 · Cited by 8,658 · see citing works
Core Transcriptional Regulatory Circuitry in Human Embryonic Stem Cells
Boyer, L. A., Lee, T. I., Cole, M. F., Johnstone, S. E., Levine, S. S., Zucker, J. P., Guenther, M. G., Kumar, R. M., Murray, H. L., Jenner, R. G., et al. (2005) · Cell · doi:10.1016/j.cell.2005.08.020 · Cited by 4,505 · see citing works
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 · see citing works
Recurrent Fusion of <i>TMPRSS2</i> and ETS Transcription Factor Genes in Prostate Cancer
Tomlins, S. A., Rhodes, D. R., Perner, S., Dhanasekaran, S. M., Mehra, R., Sun, X.-W., Varambally, S., Cao, X., Tchinda, J., Kuefer, R., et al. (2005) · Science · doi:10.1126/science.1117679 · Cited by 3,846 · see citing works
A gene atlas of the mouse and human protein-encoding transcriptomes
Su, A. I., Wiltshire, T., Batalov, S., Lapp, H., Ching, K. A., Block, D., Zhang, J., Soden, R., Hayakawa, M., Kreiman, G., et al. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0400782101 · Cited by 3,475 · see citing works
Hematopoiesis: An Evolving Paradigm for Stem Cell Biology
Orkin, S. H., & Zon, L. I. (2008) · Cell · doi:10.1016/j.cell.2008.01.025 · Cited by 2,570 · see citing works
Bhattacharjee, A., Richards, W. G., Staunton, J. E., Li, C., Monti, S., Vasa, P. P., Ladd, C., Beheshti, J., Bueno, R., Gillette, M. A., et al. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.191502998 · Cited by 2,540 · see citing works
Self-citationMetagenes and molecular pattern discovery using matrix factorization
Brunet, J.-P., Tamayo, P., Golub, T. R., & Mesirov, J. P. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0308531101 · Cited by 2,183 · see citing works
Self-citationMonti, S., Tamayo, P., Mesirov, J., & Golub, T. (2003) · Machine Learning · doi:10.1023/a:1023949509487 · Cited by 2,116 · see citing works
Self-citationReich, M. M., Liefeld, T., Gould, J., Lerner, J., Tamayo, P., & Mesirov, J. P. (2006) · Nature Genetics · doi:10.1038/ng0506-500 · Cited by 2,035 · see citing works
Self-citationTRANSFAC(R): transcriptional regulation, from patterns to profiles
Matys, V. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg108 · Cited by 1,985 · see citing works
A Lentiviral RNAi Library for Human and Mouse Genes Applied to an Arrayed Viral High-Content Screen
Moffat, J., Grueneberg, D. A., Yang, X., Kim, S. Y., Kloepfer, A. M., Hinkle, G., Piqani, B., Eisenhaure, T., Luo, B., Grenier, J. K., et al. (2006) · Cell · doi:10.1016/j.cell.2006.01.040 · Cited by 1,803 · see citing works
JASPAR: an open-access database for eukaryotic transcription factor binding profiles
Sandelin, A. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkh012 · Cited by 1,763 · see citing works
Teoria Statistica Delle Classi e Calcolo Delle Probabilità
(2010) · Sage eBooks · doi:10.4135/9781412961288.n455 · Cited by 1,702 · see citing works
Segal, E., Shapira, M., Regev, A., Pe’er, D., Botstein, D., Koller, D., & Friedman, N. (2003) · Nature Genetics · doi:10.1038/ng1165 · Cited by 1,686 · see citing works
Self-citationA Stem Cell Molecular Signature
Ivanova, N. B., Dimos, J. T., Schaniel, C., Hackney, J. A., Moore, K. A., & Lemischka, I. R. (2002) · Science · doi:10.1126/science.1073823 · Cited by 1,543 · see citing works
Requirement of transcription factor PU.1 in the development of multiple hematopoietic lineages
Scott, E. W., Simon, M. C., Anastasi, J., & Singh, H. (1994) · Science · doi:10.1126/science.8079170 · Cited by 1,532 · see citing works
Transformation from committed progenitor to leukaemia stem cell initiated by MLL–AF9
Krivtsov, A. V., Twomey, D., Feng, Z., Stubbs, M. C., Wang, Y., Faber, J., Levine, J. E., Wang, J., Hahn, W. C., Gilliland, D. G., et al. (2006) · Nature · doi:10.1038/nature04980 · Cited by 1,513 · cited 2× · see citing works
“However, human leukemias often express more complex combinations of modules that are not observed in normal samples, including HSPC modules, as has been reported in murine models of leukemia (Krivtsov et al., 2006).”
Self-citationPrognostically Useful Gene-Expression Profiles in Acute Myeloid Leukemia
Valk, P. J. M., Verhaak, R. G. W., Beijen, M. A., Erpelinck, C. A. J., van Doorn-Khosrovani, S. B. V. W., Boer, J. M., Beverloo, H. B., Moorhouse, M. J., van der Spek, P. J., Löwenberg, B., et al. (2004) · New England Journal of Medicine · doi:10.1056/nejmoa040465 · Cited by 1,370 · see citing works
Pevny, L., Simon, M. C., Robertson, E., Klein, W. H., Tsai, S.-F., D'Agati, V., Orkin, S. H., & Costantini, F. (1991) · Nature · doi:10.1038/349257a0 · Cited by 1,308 · see citing works
Genomic and transcriptional aberrations linked to breast cancer pathophysiologies
Chin, K., DeVries, S., Fridlyand, J., Spellman, P. T., Roydasgupta, R., Kuo, W.-L., Lapuk, A. V., Neve, R. M., Qian, Z., Ryder, T., et al. (2006) · Cancer Cell · doi:10.1016/j.ccr.2006.10.009 · Cited by 1,288 · see citing works
Oncogenic Transcription Factors in the Human Acute Leukemias
Look, A. T. (1997) · Science · doi:10.1126/science.278.5340.1059 · Cited by 1,206 · see citing works
Diversity and Complexity in DNA Recognition by Transcription Factors
Badis, G., Berger, M., Philippakis, A. A., Talukder, S., Gehrke, A. R., Jaeger, S., Chan, E. T., Metzler, G., Vedenko, A., Chen, X., et al. (2009) · Science · doi:10.1126/science.1162327 · Cited by 1,031 · see citing works
Hughes, J. D., Estep, P. W., Tavazoie, S., & Church, G. M. (2000) · Journal of Molecular Biology · doi:10.1006/jmbi.2000.3519 · Cited by 1,008 · see citing works
Use of Gene-Expression Profiling to Identify Prognostic Subclasses in Adult Acute Myeloid Leukemia
Bullinger, L., Döhner, K., Bair, E., Fröhling, S., Schlenk, R. F., Tibshirani, R. J., Döhner, H., & Pollack, J. R. (2004) · New England Journal of Medicine · doi:10.1056/nejmoa031046 · Cited by 990 · see citing works
Liu, M., Lee, M., Cohen, M. B., Bommakanti, M., & Freedman, L. P. (1996) · Genes & Development · doi:10.1101/gad.10.2.142 · Cited by 889 · see citing works
Statistical Methods for Research Workers.
Anscombe, F. J., & Fisher, R. A. (1955) · Journal of the Royal Statistical Society Series A (General) · doi:10.2307/2342720 · Cited by 840 · see citing works
Chromatin immunoprecipitation and microarray-based analysis of protein location
Lee, T. I., Johnstone, S. E., & Young, R. A. (2006) · Nature Protocols · doi:10.1038/nprot.2006.98 · Cited by 743 · see citing works
Self-citationWilson, N. K., Foster, S. D., Wang, X., Knezevic, K., Schütte, J., Kaimakis, P., Chilarska, P. M., Kinston, S., Ouwehand, W. H., Dzierzak, E., et al. (2010) · Cell stem cell · doi:10.1016/j.stem.2010.07.016 · Cited by 728 · see citing works
The hardwiring of development: organization and function of genomic regulatory systems
Arnone, M. I., & Davidson, E. H. (1997) · Development · doi:10.1242/dev.124.10.1851 · Cited by 700 · see citing works
Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data
Valouev, A., Johnson, D. S., Sundquist, A., Medina, C., Anton, E., Batzoglou, S., Myers, R. M., & Sidow, A. (2008) · Nature Methods · doi:10.1038/nmeth.1246 · Cited by 695 · see citing works
Genomic Regulatory Systems: Development and Evolution
Davidson, E. H. (2005) · Thammasat University Digital Collections · Cited by 690 · see citing works
Liu, X. S., Brutlag, D. L., & Liu, J. S. (2002) · Nature Biotechnology · doi:10.1038/nbt717 · Cited by 670 · see citing works
The value of prior knowledge in discovering motifs with MEME.
Bailey, T. L., & Elkan, C. (1995) · PubMed · Cited by 665 · see citing works
Transcription factors in myeloid development: balancing differentiation with transformation
Rosenbauer, F., & Tenen, D. G. (2007) · Nature Reviews Immunology · doi:10.1038/nri2024 · Cited by 606 · cited 1× · see citing works
“These results support the role of chosen regulators in differentiation and are consistent with a broader paradigm in which lineage-specific promoters can dysregulate key TFs to disrupt differentiation (Rosenbauer and Tenen, 2007; Tomlins et al., 2005).”
Variation in Homeodomain DNA Binding Revealed by High-Resolution Analysis of Sequence Preferences
Berger, M. F., Badis, G., Gehrke, A. R., Talukder, S., Philippakis, A. A., Peña-Castillo, L., Alleyne, T. M., Mnaimneh, S., Botvinnik, O. B., Chan, E. T., et al. (2008) · Cell · doi:10.1016/j.cell.2008.05.024 · Cited by 606 · see citing works
Transcriptional regulation of erythropoiesis: an affair involving multiple partners
Cantor, A. B., & Orkin, S. H. (2002) · Oncogene · doi:10.1038/sj.onc.1205326 · Cited by 584 · see citing works
NANOG Is a Direct Target of TGFβ/Activin-Mediated SMAD Signaling in Human ESCs
Xu, R., Sampsell-Barron, T. L., Gu, F., Root, S. H., Peck, R. M., Pan, G., Yu, J., Antosiewicz‐Bourget, J., Tian, S., Stewart, R. M., et al. (2008) · Cell stem cell · doi:10.1016/j.stem.2008.07.001 · Cited by 512 · see citing works
Unbiased Reconstruction of a Mammalian Transcriptional Network Mediating Pathogen Responses
Amit, I., Garber, M., Chevrier, N., Leite, A. P., Donner, Y., Eisenhaure, T., Guttman, M., Grenier, J. K., Li, W., Zuk, O., et al. (2009) · Science · doi:10.1126/science.1179050 · Cited by 488 · see citing works
Self-citationThe FANTOM Consortium, & Riken Omics Science Center (2009) · Nature Genetics · doi:10.1038/ng.375 · Cited by 427 · see citing works
C/EBPβ is required for 'emergency' granulopoiesis
Hirai, H., Zhang, P., Dayaram, T., Hetherington, C. J., Mizuno, S.-I., Imanishi, J., Akashi, K., & Tenen, D. G. (2006) · Nature Immunology · doi:10.1038/ni1354 · Cited by 425 · see citing works
Global regulation of erythroid gene expression by transcription factor GATA-1
Welch, J. J. (2004) · Blood · doi:10.1182/blood-2004-04-1603 · Cited by 408 · see citing works
Regulatory networks define phenotypic classes of human stem cell lines
Müller, F.-J., Laurent, L. C., Kostka, D., Ulitsky, I., Williams, R., Lu, C., Park, I.-H., Rao, M. S., Shamir, R., Schwartz, P. H., et al. (2008) · Nature · doi:10.1038/nature07213 · Cited by 343 · see citing works
A Common Set of Gene Regulatory Networks Links Metabolism and Growth Inhibition
Cam, H., Balciunaite, E., Blais, A., Spektor, A., Scarpulla, R. C., Young, R., Kluger, Y., & Dynlacht, B. D. (2004) · Molecular Cell · doi:10.1016/j.molcel.2004.09.037 · Cited by 322 · see citing works
Self-citation(2001) · Elsevier eBooks · doi:10.1016/b978-0-12-205351-1.x5000-9 · Cited by 314 · see citing works
A Universal Framework for Regulatory Element Discovery across All Genomes and Data Types
Elemento, O., Slonim, N., & Tavazoie, S. (2007) · Molecular Cell · doi:10.1016/j.molcel.2007.09.027 · Cited by 309 · see citing works
Systems-level dynamic analyses of fate change in murine embryonic stem cells
Lu, R., Markowetz, F. M., Unwin, R. D., Leek, J. T., Airoldi, E. M., MacArthur, B. D., Lachmann, A., Rozov, R., Ma’ayan, A., Boyer, L. A., et al. (2009) · Nature · doi:10.1038/nature08575 · Cited by 291 · see citing works
Positive regulation of immune cell function and inflammatory responses by phosphatase PAC-1
Jeffrey, K. L., Brummer, T., Rolph, M. S., Liu, S. M., Callejas, N. A., Grumont, R. J., Gilliéron, C., Mackay, F., Grey, S. T., Camps, M., et al. (2006) · Nature Immunology · doi:10.1038/ni1310 · Cited by 270 · see citing works
Hahm, K., Cobb, B. S., McCarty, A., Brown, K. E., Klug, C. A., Lee, R., Akashi, K., Weissman, I. L., Fisher, A. G., & Smale, S. T. (1998) · Genes & Development · doi:10.1101/gad.12.6.782 · Cited by 253 · see citing works
The SCL gene product: a positive regulator of erythroid differentiation.
Aplan, P. D., Nakahara, K., Orkin, S. H., & Kirsch, I. R. (1992) · The EMBO Journal · doi:10.1002/j.1460-2075.1992.tb05500.x · Cited by 230 · see citing works
Tarte, K., Zhan, F., Vos, J. D., Klein, B., & Shaughnessy, J. D. (2003) · Blood · doi:10.1182/blood-2002-10-3161 · Cited by 215 · see citing works
A method for high-throughput gene expression signature analysis
Peck, D., Crawford, E. D., Ross, K. N., Stegmaier, K., Golub, T. R., & Lamb, J. (2006) · Genome biology · doi:10.1186/gb-2006-7-7-r61 · Cited by 205 · see citing works
Self-citationLinhart, C., Halperin, Y., & Ron Shamir, A. (2008) · Genome Research · doi:10.1101/gr.076117.108 · Cited by 188 · see citing works
Transcriptional Regulatory Circuits: Predicting Numbers from Alphabets
Kim, H. D., Shay, T., O’Shea, E. K., & Regev, A. (2009) · Science · doi:10.1126/science.1171347 · Cited by 179 · see citing works
Self-citationOutlier sums for differential gene expression analysis
Tibshirani, R., & Hastie, T. J. (2006) · Biostatistics · doi:10.1093/biostatistics/kxl005 · Cited by 175 · see citing works
Macaulay, I. C., Tijssen, M. R., Thijssen‐Timmer, D. C., Gusnanto, A., Steward, M., Burns, P., Langford, C. F., Ellis, P. D., Dudbridge, F., Zwaginga, J. J., et al. (2006) · Blood · doi:10.1182/blood-2006-07-036269 · Cited by 168 · see citing works
Tamayo, P., Scanfeld, D., Ebert, B., Gillette, M., Roberts, C., & Mesirov, J. (2007) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.0701068104 · Cited by 163 · see citing works
Self-citationSCL: From the origin of hematopoiesis to stem cells and leukemia
Lécuyer, É., & Hoang, T. (2004) · Experimental Hematology · doi:10.1016/j.exphem.2003.10.010 · Cited by 154 · see citing works
Aramburu, J. F., Azzoni, L., Rao, A., & PERUSSIA, B. (1995) · The Journal of Experimental Medicine · doi:10.1084/jem.182.3.801 · Cited by 138 · see citing works
Hematopoietic developmental pathways: on cellular basis
Iwasaki, H., & Akashi, K. (2007) · Oncogene · doi:10.1038/sj.onc.1210754 · Cited by 132 · see citing works
Learning Module NetworksPreprint
Segal, E., Pe’er, D., Regev, A., Koller, D., & Friedman, N. (2012) · arXiv (Cornell University) · doi:10.48550/arxiv.1212.2517 · Cited by 131 · see citing works
Self-citationGenomic approaches to hematologic malignancies
Ebert, B. L., & Golub, T. R. (2004) · Blood · doi:10.1182/blood-2004-01-0274 · Cited by 130 · see citing works
Self-citationGeorgantas, R. W., Tanavde, V., Malehorn, M., Heimfeld, S., Chen, C., Carr, L., Martínez-Murillo, F., Riggins, G., Kowalski, J., & Civin, C. I. (2004) · Cancer Research · doi:10.1158/0008-5472.can-03-3247 · Cited by 127 · see citing works
Chen, J., & Sadowski, I. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0407069102 · Cited by 111 · see citing works
Self-citationChen, M. L., Logan, T. D., Hochberg, M. L., Shelat, S. G., Yu, X., Wilding, G. E., Tan, W., Kujoth, G. C., Prolla, T. A., Selak, M. A., et al. (2009) · Blood · doi:10.1182/blood-2008-08-169474 · Cited by 108 · see citing works
Unraveling the crucial roles of <i>Meis1</i> in leukemogenesis and normal hematopoiesis
Argiropoulos, B., Yung, E., & Humphries, R. K. (2007) · Genes & Development · doi:10.1101/gad.1619407 · Cited by 101 · see citing works
Gene expression profiles during human CD4+ T cell differentiation
Lee, M. S., Hanspers, K., Barker, C. S., Korn, A. P., & McCune, J. M. (2004) · International Immunology · doi:10.1093/intimm/dxh112 · Cited by 98 · see citing works
Brx Mediates the Response of Lymphocytes to Osmotic Stress Through the Activation of NFAT5
Kino, T., Takatori, H., Manoli, I., Wang, Y., Tiulpakov, A. N., Blackman, M. R., Su, Y. A., Chrousos, G. P., DeCherney, A. H., & Segars, J. H. (2009) · Science Signaling · doi:10.1126/scisignal.2000081 · Cited by 95 · see citing works
A Simple Hyper-Geometric Approach for Discovering Putative Transcription Factor Binding Sites
Barash, Y., Bejerano, G., & Friedman, N. (2001) · Lecture notes in computer science · doi:10.1007/3-540-44696-6_22 · Cited by 94 · see citing works
Self-citationEbert, B. L., Lee, M. D., Pretz, J. L., Subramanian, A., Mak, R. H., Golub, T. R., & Sieff, C. A. (2005) · Blood · doi:10.1182/blood-2004-08-3313 · Cited by 93 · see citing works
Self-citationMitochondria in hematopoiesis and hematological diseases
Fontenay, M., Cathelin, S., Amiot, M., Gyan, E., & Solary, É. (2006) · Oncogene · doi:10.1038/sj.onc.1209606 · Cited by 92 · see citing works
Funnell, A. P. W., Maloney, C., Thompson, L. J., Keys, J. R., Tallack, M. R., Perkins, A. C., & Crossley, M. (2007) · Molecular and Cellular Biology · doi:10.1128/mcb.01658-06 · Cited by 88 · see citing works
Gordon, D. B., Nekludova, L., McCallum, S., & Fraenkel, E. (2005) · Computer applications in the biosciences · doi:10.1093/bioinformatics/bti481 · Cited by 87 · see citing works
The Mouse Genome Database: enhancements and updates
Bult, C. J., Kadin, J. A., Richardson, J. E., Blake, J. A., Eppig, J. T., & the Mouse Genome Database Group (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp880 · Cited by 84 · see citing works
Differential Regulation of Foxo3a Target Genes in Erythropoiesis
Bakker, W. J., van Dijk, T. B., Amelsvoort, M. P.-V., Kolbus, A., Yamamoto, K., Steinlein, P., Verhaak, R. G. W., Mak, T. W., Beug, H., Löwenberg, B., et al. (2007) · Molecular and Cellular Biology · doi:10.1128/mcb.01662-06 · Cited by 81 · see citing works
Haining, W., Ebert, B., Subrmanian, A., Wherry, E., Eichbaum, Q., Evans, J. W., Mak, R., Rivoli, S., Pretz, J., Angelosanto, J. M., et al. (2008) · Journal of Immunology · doi:10.4049/jimmunol.181.3.1859 · Cited by 77 · see citing works
Self-citationIkaros and chromatin regulation in early hematopoiesis
Ng, S. Y., Yoshida, T., & Georgopoulos, K. (2007) · Current Opinion in Immunology · doi:10.1016/j.coi.2007.02.014 · Cited by 67 · see citing works
PU.1, a Shared Transcriptional Regulator of Lymphoid and Myeloid Cell Fates
SINGH, H., DEKOTER, R. P., & WALSH, J. C. (1999) · Cold Spring Harbor Symposia on Quantitative Biology · doi:10.1101/sqb.1999.64.13 · Cited by 66 · see citing works
A Novel Bayesian DNA Motif Comparison Method for Clustering and Retrieval
Habib, N., Kaplan, T., Margalit, H., & Friedman, N. (2008) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000010 · Cited by 48 · see citing works
Self-citationTanay, A., Steinfeld, I., Kupiec, M., & Ron Shamir, A. (2005) · Molecular Systems Biology · doi:10.1038/msb4100005 · Cited by 48 · see citing works
Downstream targets of HOXB4 in a cell line model of primitive hematopoietic progenitor cells
Lee, H. M., Zhang, H., Schulz, V., Tuck, D. P., & Forget, B. G. (2010) · Blood · doi:10.1182/blood-2009-11-253872 · Cited by 43 · see citing works
Astier, A., Xu, R., Svoboda, M., Hinds, E., Olivier, M., de Beaumont, R., Crean, C., Gabig, T. G., & Freedman, A. S. (2003) · Blood · doi:10.1182/blood-2002-05-1519 · Cited by 40 · see citing works
YY1 and GATA-1 Interaction Modulate the Chicken 3′-Side α-Globin Enhancer Activity
Rincón‐Arano, H., Valadéz-Graham, V., Guerrero, G., Escamilla-Del-Arenal, M., & Targa, F. R. (2005) · Journal of Molecular Biology · doi:10.1016/j.jmb.2005.04.040 · Cited by 38 · see citing works
Lineage Promiscuity and Plasticity in Hematopoietic Development
Akashi, K. (2005) · Annals of the New York Academy of Sciences · doi:10.1196/annals.1349.016 · Cited by 38 · see citing works
Li, Q., Frestedt, J. L., & Kersey, J. H. (1998) · Blood · doi:10.1182/blood.v92.10.3841 · Cited by 33 · see citing works
Chang, L. W., Payton, J. E., Yuan, W., Ley, T. J., Nagarajan, R., & Stormo, G. D. (2008) · Genome biology · doi:10.1186/gb-2008-9-2-r38 · Cited by 27 · see citing works
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- Quesenberry PJ Colvin GA 2005 Hematopoietic stem cells, progenitor cells, and cytokines Williams Hematology (McGraw-Hill) 153 174
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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 · see citing works
Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma
Patel, A. P., Tirosh, I., Trombetta, J. J., Shalek, A. K., Gillespie, S. M., Wakimoto, H., Cahill, D. P., Nahed, B. V., Curry, W. T., Martuza, R. L., et al. (2014) · Science · doi:10.1126/science.1254257 · Cited by 5,063 · see citing works
Self-citationxCell: digitally portraying the tissue cellular heterogeneity landscape
Aran, D., Hu, Z., & Butte, A. J. (2017) · Genome Biology · doi:10.1186/s13059-017-1349-1 · Cited by 4,397 · see citing works
Molecular and genetic properties of tumors associated with local immune cytolytic activity
Rooney, M. S., Shukla, S. A., Wu, C. J., Getz, G., & Hacohen, N. (2015) · Cell · doi:10.1016/j.cell.2014.12.033 · Cited by 3,825 · see citing works
Annotation of functional variation in personal genomes using RegulomeDB
Boyle, A. P., Hong, E. L., Hariharan, M., Cheng, Y., Schaub, M. A., Kasowski, M., Karczewski, K. J., Park, J., Hitz, B. C., Weng, S., et al. (2012) · Genome Research · doi:10.1101/gr.137323.112 · Cited by 2,722 · see citing works
Merad, M., Sathe, P., Helft, J., Miller, J., & Mortha, A. (2013) · Annual Review of Immunology · doi:10.1146/annurev-immunol-020711-074950 · Cited by 2,309 · see citing works
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 · see citing works
Böttcher, J. P., Bonavita, E., Chakravarty, P., Blees, H., Cabeza-Cabrerizo, M., Sammicheli, S., Rogers, N. C., Sahai, E., Zelenay, S., & Reis e Sousa, C. (2018) · Cell · doi:10.1016/j.cell.2018.01.004 · Cited by 1,857 · see citing works
Single-cell RNA sequencing to explore immune cell heterogeneity
Papalexi, E., & Satija, R. (2018) · Nature Reviews Immunology · doi:10.1038/nri.2017.76 · Cited by 1,806 · see citing works
The genetic basis of early T-cell precursor acute lymphoblastic leukaemia
Zhang, J., Ding, L., Holmfeldt, L., Wu, G., Heatley, S. L., Payne-Turner, D., Easton, J., Chen, X., Wang, J., Rusch, M., et al. (2012) · Nature · doi:10.1038/nature10725 · Cited by 1,596 · see citing works
“Comparison of the gene expression profile of ETP ALL with those of purified norma”
ResultArchitecture of the human regulatory network derived from ENCODE data
Gerstein, M., Kundaje, A. B., Hariharan, M., Landt, S. G., Yan, K., Cheng, C., Mu, X. J., Khurana, E., Rozowsky, J. S., Alexander, R. P., et al. (2012) · Nature · doi:10.1038/nature11245 · Cited by 1,418 · see citing works
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 · see citing works
Chromatin Potential Identified by Shared Single-Cell Profiling of RNA and Chromatin
Ma, S., Zhang, B., LaFave, L. M., Earl, A. S., Chiang, Z., Hu, Y., Ding, J., Brack, A., Kartha, V. K., Tay, T., et al. (2020) · Cell · doi:10.1016/j.cell.2020.09.056 · Cited by 1,146 · see citing works
Self-citationSingle-Cell RNA-Seq Reveals AML Hierarchies Relevant to Disease Progression and Immunity
van Galen, P., Hovestadt, V., Wadsworth II, M. H., Hughes, T. K., Griffin, G. K., Battaglia, S., Verga, J. A., Stephansky, J., Pastika, T. J., Lombardi Story, J., et al. (2019) · Cell · doi:10.1016/j.cell.2019.01.031 · Cited by 1,164 · see citing works
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 · see citing works
Variants in ELL2 influencing immunoglobulin levels associate with multiple myeloma
Swaminathan, B., Þorleifsson, G., Jöud, M., Ali, M., Johnsson, E., Ajore, R., Sulem, P., Halvarsson, B.-M., Eyjolfsson, G. I., Haraldsdóttir, V., et al. (2015) · Nature Communications · doi:10.1038/ncomms8213 · Cited by 1,211 · see citing works
Self-citationModulation of Myelopoiesis Progenitors Is an Integral Component of Trained Immunity
Mitroulis, I., Ruppova, K., Wang, B., Chen, L.-S., Grzybek, M., Grinenko, T., Eugster, A., Troullinaki, M., Palladini, A., Kourtzelis, I., et al. (2018) · Cell · doi:10.1016/j.cell.2017.11.034 · Cited by 1,100 · see citing works
Stem cell gene expression programs influence clinical outcome in human leukemia
Eppert, K., Takenaka, K., Lechman, E. R., Waldron, L., Nilsson, B., van Galen, P., Metzeler, K. H., Poeppl, A. G., Ling, V., Beyene, J., et al. (2011) · Nature Medicine · doi:10.1038/nm.2415 · Cited by 1,032 · see citing works
Self-citationHuman haematopoietic stem cell lineage commitment is a continuous process
Velten, L., Haas, S. F., Raffel, S., Blaszkiewicz, S., Islam, S., Hennig, B. P., Hirche, C., Lutz, C., Buss, E. C., Nowak, D., et al. (2017) · Nature Cell Biology · doi:10.1038/ncb3493 · Cited by 925 · see citing works
Monaco, G., Lee, B., Xu, W., Mustafah, S., Hwang, Y. Y., Carré, C., Burdin, N., Visan, L., Ceccarelli, M., Poidinger, M., et al. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.01.041 · Cited by 958 · see citing works
Hematopoiesis: a human perspective
Doulatov, S., Notta, F., Laurenti, E., & Dick, J. E. (2012) · Cell stem cell · doi:10.1016/j.stem.2012.01.006 · Cited by 895 · see citing works
A 17-gene stemness score for rapid determination of risk in acute leukaemia
Ng, S. W. K., Mitchell, A., Kennedy, J. A., Chen, W. C., McLeod, J., Ibrahimova, N., Arruda, A., Popescu, A., Gupta, V., Schimmer, A. D., et al. (2016) · Nature · doi:10.1038/nature20598 · Cited by 912 · see citing works
From haematopoietic stem cells to complex differentiation landscapes
Laurenti, E., & Göttgens, B. (2018) · Nature · doi:10.1038/nature25022 · Cited by 830 · see citing works
Characterization of cell fate probabilities in single-cell data with Palantir
Setty, M., Kiseliovas, V., Levine, J., Gayoso, A., Mazutis, L., & Pe’er, D. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0068-4 · Cited by 833 · see citing works
Buenrostro, J. D., Corces, M. R., Lareau, C. A., Wu, B., Schep, A. N., Aryee, M. J., Majeti, R., Chang, H. Y., & Greenleaf, W. J. (2018) · Cell · doi:10.1016/j.cell.2018.03.074 · Cited by 670 · see citing works
Deciphering the transcriptional network of the dendritic cell lineage
Miller, J. C., Brown, B. D., Shay, T., Gautier, E. L., Jojic, V., Cohain, A. T., Pandey, G. S., Leboeuf, M., Elpek, K. G., Helft, J., et al. (2012) · Nature Immunology · doi:10.1038/ni.2370 · Cited by 779 · see citing works
Self-citationA single-cell resolution map of mouse hematopoietic stem and progenitor cell differentiation
Nestorowa, S., Hamey, F. K., Pijuan Sala, B., Diamanti, E., Shepherd, M., Laurenti, E., Wilson, N. K., Kent, D. G., & Göttgens, B. (2016) · Blood · doi:10.1182/blood-2016-05-716480 · Cited by 768 · see citing works
Personalized Immunomonitoring Uncovers Molecular Networks that Stratify Lupus Patients
Banchereau, R., Hong, S., Cantarel, B. L., Baldwin, N. E., Baisch, J. M., Edens, M., Cepika, A., Acs, P., Turner, J., Anguiano, E., et al. (2016) · Cell · doi:10.1016/j.cell.2016.03.008 · Cited by 739 · see citing works
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 · see citing works
Self-citationMicroRNAs as regulatory elements in immune system logic
Mehta, A., & Baltimore, D. (2016) · Nature Reviews Immunology · doi:10.1038/nri.2016.40 · Cited by 704 · see citing works
Mendillo, M. L., Santagata, S., Koeva, M., Bell, G. W., Hu, R., Tamimi, R. M., Fraenkel, E., Ince, T. A., Whitesell, L. J., & Lindquist, S. L. (2012) · Cell · doi:10.1016/j.cell.2012.06.031 · Cited by 696 · see citing works
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 · see citing works
Self-citationPAX5-driven subtypes of B-progenitor acute lymphoblastic leukemia
Gu, Z., Churchman, M. L., Roberts, K. G., Moore, I., Zhou, X., Nakitandwe, J., Hagiwara, K., Pelletier, S. W., Gingras, S., Berns, H., et al. (2019) · Nature Genetics · doi:10.1038/s41588-018-0315-5 · Cited by 596 · see citing works
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 582 · see citing works
Tracing the origins of relapse in acute myeloid leukaemia to stem cells
Shlush, L. I., Mitchell, A., Heisler, L. E., Abelson, S., Ng, S., Trotman-Grant, A. C., Medeiros, J. J. F., Rao‐Bhatia, A., Jaciw-Zurakowsky, I., Marke, R., et al. (2017) · Nature · doi:10.1038/nature22993 · Cited by 598 · see citing works
Monocytic Subclones Confer Resistance to Venetoclax-Based Therapy in Acute Myeloid Leukemia Patients
Pei, S.-S., Pollyea, D., Gustafson, A. L., Stevens, B. M., Minhajuddin, M., Fu, R., Riemondy, K., Gillen, A. E., Sheridan, R. M., Kim, J., et al. (2020) · Cancer Discovery · doi:10.1158/2159-8290.cd-19-0710 · Cited by 281 · see citing works
A clinically meaningful metric of immune age derived from high-dimensional longitudinal monitoring
Alpert, A., Pickman, Y., Leipold, M., Rosenberg-Hasson, Y., Ji, X., Gaujoux, R., Rabani, H., Starosvetsky, E., Kveler, K., Schaffert, S., et al. (2019) · Nature Medicine · doi:10.1038/s41591-019-0381-y · Cited by 513 · see citing works
Doering, T. A., Crawford, A., Angelosanto, J., Paley, M., Ziegler, C. G. K., & Wherry, E. J. (2012) · Immunity · doi:10.1016/j.immuni.2012.08.021 · Cited by 542 · see citing works
Multiplexed mass cytometry profiling of cellular states perturbed by small-molecule regulators
Bodenmiller, B., Zunder, E. R., Finck, R., Chen, T. J., Savig, E. S., Bruggner, R. V., Simonds, E. F., Bendall, S. C., Sachs, K., Krutzik, P. O., et al. (2012) · Nature Biotechnology · doi:10.1038/nbt.2317 · Cited by 546 · see citing works
Pluripotency Factors in Embryonic Stem Cells Regulate Differentiation into Germ Layers
Thomson, M. W., Liu, S. J., Zou, L.-N., Smith, Z., Meissner, A., & Ramanathan, S. (2011) · Cell · doi:10.1016/j.cell.2011.05.017 · Cited by 533 · see citing works
CellNet: Network Biology Applied to Stem Cell Engineering
Cahan, P., Li, H., Morris, S. A., da Rocha, E. L., Daley, G. Q., & Collins, J. J. (2014) · Cell · doi:10.1016/j.cell.2014.07.020 · Cited by 522 · see citing works
Sykes, D. B., Kfoury, Y. S., Mercier, F. E., Wawer, M. J., Law, J. M., Haynes, M. K., Lewis, T. A., Schajnovitz, A., Jain, E., Lee, D., et al. (2016) · Cell · doi:10.1016/j.cell.2016.08.057 · Cited by 500 · see citing works
Oxysterols direct immune cell migration via EBI2
Hannedouche, S., Zhang, J., Yi, T., Shen, W., Nguyen, D. G., Pereira, J. P., Guerini, D., Baumgarten, B. U., Roggo, S. P., Wen, B. G., et al. (2011) · Nature · doi:10.1038/nature10280 · Cited by 489 · see citing works
Chen, S., Zhu, G., Yang, Y., Wang, F., Xiao, Y., Zhang, N., Bian, X., Zhu, Y., Yu, Y., Liu, F., et al. (2021) · Nature Cell Biology · doi:10.1038/s41556-020-00613-6 · Cited by 504 · see citing works
Haematopoietic stem and progenitor cells from human pluripotent stem cells
Sugimura, R., Jha, D., Han, A., Soria-Valles, C., da Rocha, E. D., Lu, Y.-F., Goettel, J., Serrao, E., Rowe, R. G., Malleshaiah, M., et al. (2017) · Nature · doi:10.1038/nature22370 · Cited by 459 · see citing works
Regenerative lineages and immune-mediated pruning in lung cancer metastasis
Laughney, A. M., Hu, J., Campbell, N. R., Bakhoum, S. F. W., Setty, M. N., Lavallée, V., Xie, Y., Masilionis, I., Carr, A., Kottapalli, S., et al. (2020) · Nature Medicine · doi:10.1038/s41591-019-0750-6 · Cited by 470 · see citing works
Pal, B., Chen, Y., Vaillant, F., Capaldo, B. D., Joyce, R., Song, X., Bryant, V. L., Penington, J. S., Stefano, L. D., Ribera, N. T., et al. (2021) · The EMBO Journal · doi:10.15252/embj.2020107333 · Cited by 476 · see citing works
Orchestrated Intron Retention Regulates Normal Granulocyte Differentiation
Wong, J. J.-L., Ritchie, W., Ebner, O. A., Selbach, M., Wong, J. W. H., Huang, Y., Gao, D., Pinello, N., Gonzalez, M., Baidya, K., et al. (2013) · Cell · doi:10.1016/j.cell.2013.06.052 · Cited by 462 · see citing works
Quantifying tumor-infiltrating immune cells from transcriptomics data
Finotello, F., & Trajanoski, Z. (2018) · Cancer Immunology Immunotherapy · doi:10.1007/s00262-018-2150-z · Cited by 402 · see citing works
Social network architecture of human immune cells unveiled by quantitative proteomics
Rieckmann, J. C., Geiger, R., Hornburg, D., Wolf, T., Kveler, K., Jarrossay, D., Sallusto, F., Shen-Orr, S. S., Lanzavecchia, A., Mann, M., et al. (2017) · Nature Immunology · doi:10.1038/ni.3693 · Cited by 376 · see citing works
DNA Methylation Dynamics during In Vivo Differentiation of Blood and Skin Stem Cells
Bock, C., Beerman, I., Lien, W., Smith, Z. D., Gu, H., Boyle, P., Gnirke, A., Fuchs, E. V., Rossi, D. J., & Meissner, A. (2012) · Molecular Cell · doi:10.1016/j.molcel.2012.06.019 · Cited by 378 · see citing works
Conservation and divergence in the transcriptional programs of the human and mouse immune systems
Shay, T., Jojic, V., Zuk, O., Rothamel, K., Puyraimond-Zemmour, D., Feng, T., Wakamatsu, E., Benoist, C., Koller, D., Regev, A., et al. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1222738110 · Cited by 359 · see citing works
Self-citationThe genetic basis and cell of origin of mixed phenotype acute leukaemia
Alexander, T., Gu, Z., Iacobucci, I., Dickerson, K. M., Choi, J. K., Xu, B., Payne-Turner, D., Yoshihara, H., Loh, M. L., Horan, J., et al. (2018) · Nature · doi:10.1038/s41586-018-0436-0 · Cited by 360 · see citing works
Germline ETV6 mutations in familial thrombocytopenia and hematologic malignancy
Zhang, M. Y., Churpek, J. E., Keel, S., Walsh, T., Lee, M. K., Loeb, K. R., Gülsüner, S., Pritchard, C. C., Sánchez-Bonilla, M., Delrow, J. J., et al. (2015) · Nature Genetics · doi:10.1038/ng.3177 · Cited by 368 · see citing works
Global transcriptome analyses of human and murine terminal erythroid differentiation
An, X., Schulz, V., Li, J., Wu, K., Liu, J., Xue, F., Hu, J., Mohandas, N., & Gallagher, P. G. (2014) · Blood · doi:10.1182/blood-2014-01-548305 · Cited by 361 · see citing works
Transcription factor binding dynamics during human ES cell differentiation
Tsankov, A. M., Gu, H., Akopian, V., Ziller, M. J., Donaghey, J., Amit, I., Gnirke, A., & Meissner, A. (2015) · Nature · doi:10.1038/nature14233 · Cited by 349 · see citing works
DPP8/DPP9 inhibitor-induced pyroptosis for treatment of acute myeloid leukemia
Johnson, D. C., Taabazuing, C. Y., Okondo, M. C., Chui, A. J., Rao, S. D., Brown, F. C., Reed, C., Peguero, E., de Stanchina, E., Kentsis, A., et al. (2018) · Nature Medicine · doi:10.1038/s41591-018-0082-y · Cited by 342 · see citing works
Ram, O., Goren, A., Amit, I., Shoresh, N., Yosef, N., Ernst, J., Kellis, M., Gymrek, M., Issner, R., Coyne, M., et al. (2011) · Cell · doi:10.1016/j.cell.2011.09.057 · Cited by 331 · see citing works
Self-citationSweeney, T. E., Shidham, A., Wong, H. R., & Khatri, P. (2015) · Science Translational Medicine · doi:10.1126/scitranslmed.aaa5993 · Cited by 338 · see citing works
Zhang, J. A., Mortazavi, A., Williams, B. A., Wold, B. J., & Rothenberg, E. V. (2012) · Cell · doi:10.1016/j.cell.2012.01.056 · Cited by 337 · see citing works
Systematic Functional Dissection of Common Genetic Variation Affecting Red Blood Cell Traits
Ulirsch, J. C., Nandakumar, S. K., Wang, L., Giani, F. C., Zhang, X., Rogov, P., Melnikov, A., McDonel, P., Do, R., Mikkelsen, T. S., et al. (2016) · Cell · doi:10.1016/j.cell.2016.04.048 · Cited by 328 · see citing works
Sanda, T., Lawton, L. N., Barrasa, M. I., Fan, Z. P., Kohlhammer, H., Gutiérrez, A., Ma, W., Tatarek, J., Ahn, Y., Kelliher, M. A., et al. (2012) · Cancer Cell · doi:10.1016/j.ccr.2012.06.007 · Cited by 333 · see citing works
Self-citationSomatic mutations and cell identity linked by Genotyping of Transcriptomes
Nam, A. S., Kim, K.-T., Chaligne, R., Izzo, F., Ang, C., Taylor, J., Myers, R. M., Abu-Zeinah, G., Brand, R., Omans, N. D., et al. (2019) · Nature · doi:10.1038/s41586-019-1367-0 · Cited by 333 · see citing works
A Myc enhancer cluster regulates normal and leukaemic haematopoietic stem cell hierarchies
Bahr, C., von Paleske, L., Uslu, V. V., Remeseiro, S., Takayama, N., Ng, S. W., Murison, A., Langenfeld, K., Petretich, M., Scognamiglio, R., et al. (2018) · Nature · doi:10.1038/nature25193 · Cited by 328 · see citing works
Bagger, F. O., Sasivarevic, D., Sohi, S. H., Laursen, L. G., Pundhir, S., Sønderby, C. K., Winther, O., Rapin, N., & Porse, B. T. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv1101 · Cited by 330 · see citing works
Single-cell transcriptional profiles in human skeletal muscle
Rubenstein, A. B., Smith, G. R., Raue, U., Begue, G., Minchev, K., Ruf-Zamojski, F., Nair, V. D., Wang, X., Zhou, L., Zaslavsky, E., et al. (2020) · Scientific Reports · doi:10.1038/s41598-019-57110-6 · Cited by 323 · see citing works
Seventy-five genetic loci influencing the human red blood cell
van der Harst, P., Zhang, W., Leach, I. M., Rendon, A., Verweij, N., Sehmi, J., Paul, D. S., Elling, U., Allayee, H., Li, X., et al. (2012) · Nature · doi:10.1038/nature11677 · Cited by 306 · see citing works
Trompouki, E., Bowman, T. V., Lawton, L. N., Fan, Z. P., Wu, D.-C., DiBiase, A., Martin, C., Cech, J. N., Sessa, A. K., LeBlanc, J., et al. (2011) · Cell · doi:10.1016/j.cell.2011.09.044 · Cited by 303 · see citing works
Self-citationISMARA: automated modeling of genomic signals as a democracy of regulatory motifsPreprint
Balwierz, P. J., Pachkov, M. V., Arnold, P., Gruber, A. J., Zavolan, M., & van Nimwegen, E. (2014) · Genome Research · doi:10.1101/gr.169508.113 · Cited by 299 · see citing works
Weng, N.-P., Araki, Y., & Subedi, K. (2012) · Nature Reviews Immunology · doi:10.1038/nri3173 · Cited by 290 · see citing works
AMPK/FIS1-Mediated Mitophagy Is Required for Self-Renewal of Human AML Stem Cells
Pei, S., Minhajuddin, M., Adane, B., Khan, N., Stevens, B. M., Mack, S. C., Lai, S., Rich, J. N., Sheth, A. I., Shannon, K., et al. (2018) · Cell stem cell · doi:10.1016/j.stem.2018.05.021 · Cited by 300 · see citing works
Transcriptional diversity during lineage commitment of human blood progenitors
Chen, L., Kostadima, M. A., Martens, J. H. A., Canu, G., Garcia, S. P., Turro, E., Downes, K., Macaulay, I. C., Bielczyk-Maczyńska, E., Coe, S., et al. (2014) · Science · doi:10.1126/science.1251033 · Cited by 296 · see citing works
Hodges, E., Molaro, A., dos Santos, C. O., Thekkat, P. U., Song, Q., Uren, P. J., Park, J., Butler, J., Rafii, S., McCombie, W., et al. (2011) · Molecules and Cells · doi:10.1016/j.molcel.2011.08.026 · Cited by 304 · see citing works
Models of human core transcriptional regulatory circuitriesPreprint
Saint‐André, V., Alexander Joel Federation, Lin, C. Y., Abraham, B. J., Reddy, J., Lee, T. I., Bradner, J. E., & Young, R. A. (2016) · Genome Research · doi:10.1101/gr.197590.115 · Cited by 290 · see citing works
Self-citationCursons, J., Souza-Fonseca-Guimarães, F., Foroutan, M., Anderson, A., Hollande, F., Hediyeh-zadeh, S., Behren, A., Huntington, N. D., & Davis, M. J. (2019) · Cancer Immunology Research · doi:10.1158/2326-6066.cir-18-0500 · Cited by 298 · see citing works
Khan, N., Downey, J., Sanz, J., Kaufmann, E., Blankenhaus, B., Pacis, A., Pernet, E., Ahmed, E. A., Cardoso, S., Nijnik, A., et al. (2020) · Cell · doi:10.1016/j.cell.2020.09.062 · Cited by 296 · see citing works
Vitamin D Receptor Signaling Mechanisms: Integrated Actions of a Well-Defined Transcription Factor
Carlberg, C., & Campbell, M. J. (2013) · Steroids · doi:10.1016/j.steroids.2012.10.019 · Cited by 293 · see citing works
Core circadian clock genes regulate leukemia stem cells in AML
Puram, R. V., Kowalczyk, M. S., de Boer, C. G., Schneider, R. K., Miller, P. G., McConkey, M., Tothova, Z., Tejero, H., Heckl, D., Järås, M., et al. (2016) · Cell · doi:10.1016/j.cell.2016.03.015 · Cited by 274 · see citing works
Self-citationGodec, J., Tan, Y. Q., Liberzon, A., Tamayo, P., Bhattacharya, S., Butte, A. J., Mesirov, J. P., & Haining, W. N. (2016) · Immunity · doi:10.1016/j.immuni.2015.12.006 · Cited by 289 · see citing works
Self-citationAn update on vitamin D signaling and cancer
Carlberg, C., & Múñoz, A. (2020) · Seminars in Cancer Biology · doi:10.1016/j.semcancer.2020.05.018 · Cited by 290 · see citing works
Computational deconvolution: extracting cell type-specific information from heterogeneous samples
Shen-Orr, S. S., & Gaujoux, R. (2013) · Current Opinion in Immunology · doi:10.1016/j.coi.2013.09.015 · Cited by 280 · see citing works
Doulatov, S. R., Vo, L. T., Chou, S. S., Kim, P. G., Arora, N., Li, H., Hadland, B., Bernstein, I. D., Collins, J. J., Zon, L. I., et al. (2013) · Cell stem cell · doi:10.1016/j.stem.2013.09.002 · Cited by 278 · see citing works
DNA Methylation Dynamics of Human Hematopoietic Stem Cell Differentiation
Farlik, M., Halbritter, F., Müller, F., Choudry, F., Ebert, P., Klughammer, J., Farrow, S., Santoro, A., Ciaurro, V., Mathur, A., et al. (2016) · Cell stem cell · doi:10.1016/j.stem.2016.10.019 · Cited by 263 · see citing works
AP-1 imprints a reversible transcriptional programme of senescent cells.
Martínez-Zamudio, R. I., Roux, P.-F., de Freitas, J. A. N. L. F., Robinson, L., Doré, G., Sun, B., Belenki, D., Milanovic, M., Herbig, U., Schmitt, C. A., et al. (2020) · Nature Cell Biology · doi:10.1038/s41556-020-0529-5 · Cited by 236 · see citing works
Single-cell analysis reveals the continuum of human lympho-myeloid progenitor cells
Karamitros, D., Stoilova, B., Aboukhalil, Z., Hamey, F., Reinisch, A., Samitsch, M., Quek, L. S., Otto, G., Repapi, E., Doondeea, J. B., et al. (2017) · Nature Immunology · doi:10.1038/s41590-017-0001-2 · Cited by 263 · see citing works
Partial exhaustion of CD8 T cells and clinical response to teplizumab in new-onset type 1 diabetes
Long, S. A., Thorpe, J., DeBerg, H. A., Gersuk, V., Eddy, J. A., Harris, K. M., Ehlers, M., Herold, K. C., Nepom, G. T., & Linsley, P. S. (2016) · Science Immunology · doi:10.1126/sciimmunol.aai7793 · Cited by 250 · see citing works
Transcription factor networks in erythroid cell and megakaryocyte development
Doré, L. C., & Crispino, J. D. (2011) · Blood · doi:10.1182/blood-2011-04-285981 · Cited by 238 · see citing works
Laurenti, E., Doulatov, S. R., Zandi, S., Plumb, I., Chen, J., April, C., Fan, J., & Dick, J. E. (2013) · Nature Immunology · doi:10.1038/ni.2615 · Cited by 224 · see citing works
Self-citationBagger, F. O., Kinalis, S., & Rapin, N. (2019) · Nucleic Acids Research · doi:10.1093/nar/gky1076 · Cited by 229 · see citing works
Aoki, T., Chong, L. C., Takata, K., Milne, K., Hav, M., Colombo, A., Chavez, E. A., Nissen, M. D., Wang, X., Miyata‐Takata, T., et al. (2019) · Cancer Discovery · doi:10.1158/2159-8290.cd-19-0680 · Cited by 226 · see citing works
A general approach for detecting expressed mutations in AML cells using single cell RNA-sequencing
Petti, A. A., Williams, S. R., Miller, C. A., Fiddes, I. T., Srivatsan, S. N., Chen, D. Y., Fronick, C. C., Fulton, R. S., Church, D. M., & Ley, T. J. (2019) · Nature Communications · doi:10.1038/s41467-019-11591-1 · Cited by 215 · see citing works
Democratizing systems immunology with modular transcriptional repertoire analyses
Chaussabel, D., & Baldwin, N. E. (2014) · Nature reviews. Immunology · doi:10.1038/nri3642 · Cited by 213 · see citing works
A LncRNA-MAF:MAFB transcription factor network regulates epidermal differentiation
Lopez-Pajares, V., Qu, K., Zhang, J., Webster, D. E., Barajas, B. C., Siprashvili, Z., Zarnegar, B. J., Boxer, L. D., Rios, E. J., Tao, S., et al. (2015) · Developmental Cell · doi:10.1016/j.devcel.2015.01.028 · Cited by 194 · see citing works
Redefinition of the human mast cell transcriptome by deep-CAGE sequencing
Motakis, E., Guhl, S., Ishizu, Y., Itoh, M., Kawaji, H., de Hoon, M., Lassmann, T., Carninci, P., Hayashizaki, Y., Zuberbier, T., et al. (2014) · Blood · doi:10.1182/blood-2013-02-483792 · Cited by 211 · see citing works
ETV6 mutations in early immature human T cell leukemias
Vlierberghe, P. V., Ambesi‐Impiombato, A., Pérez-García, A., Haydu, J. E., Rigo, I., Hadler, M., Tosello, V., Gatta, G. D., Paietta, E. M., Racevskis, J., et al. (2011) · The Journal of Experimental Medicine · doi:10.1084/jem.20112239 · Cited by 210 · see citing works
Linsley, P. S., Speake, C., Whalen, E., & Chaussabel, D. (2014) · PLoS ONE · doi:10.1371/journal.pone.0109760 · Cited by 210 · see citing works
Computational methods for trajectory inference from single‐cell transcriptomics
Cannoodt, R., Saelens, W., & Saeys, Y. (2016) · European Journal of Immunology · doi:10.1002/eji.201646347 · Cited by 206 · see citing works
Ng, E. S., Azzola, L., Bruveris, F., Calvanese, V., Phipson, B., Vlahos, K., Hirst, C. E., Jokubaitis, V. J., Yu, Q. C., Maksimovic, J., et al. (2016) · Nature Biotechnology · doi:10.1038/nbt.3702 · Cited by 196 · see citing works
Efficacy of Retinoids in IKZF1-Mutated BCR-ABL1 Acute Lymphoblastic Leukemia
Churchman, M. L., Low, J. A., Qu, C., Paietta, E. M., Kasper, L. H., Chang, Y., Payne-Turner, D., Althoff, M. J., Song, G., Chen, S.-C., et al. (2015) · Cancer Cell · doi:10.1016/j.ccell.2015.07.016 · Cited by 203 · see citing works
Lien, W.-H., Guo, X., Polak, L., Lawton, L. N., Young, R. A., Zheng, D., & Fuchs, E. (2011) · Cell Stem Cell · doi:10.1016/j.stem.2011.07.015 · Cited by 199 · see citing works
Self-citation
- Authors
- Novershtern, N., Subramanian, A., Lawton, L. N., Mak, R. H., Haining, W. N., McConkey, M. E., Habib, N., Yosef, N., Chang, C. Y., Shay, T., Frampton, G. M., Drake, A. C. B., Leskov, I., Nilsson, B., Preffer, F., Dombkowski, D., Evans, J. W., Liefeld, T., Smutko, J. S., Chen, J., Friedman, N., Young, R. A., Golub, T. R., Regev, A., & Ebert, B. L.
- Affiliations
- Broad Institute (US)
- Whitehead Institute for Biomedical Research (US)
- Dana-Farber Cancer Institute (US)
- Brigham and Women's Hospital (US)
- Hebrew University of Jerusalem (IL)
- Koch Institute for Integrative Cancer Research At MIT (US)
- Massachusetts General Hospital (US)
- Corresponding author
- Regev, Aviv
- Ebert, Benjamin L.
- ORCID
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2011-01
- Volume
- 144
- Issue
- 2
- Pages
- 296-309
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC3049864
- OpenAlex
- W2150892663
- Cited by
- 942
- References
- 94
- Citations by year
- 2026: 18 · 2025: 40 · 2024: 51 · 2023: 46 · 2022: 66 · 2021: 57 · 2020: 90 · 2019: 66 · 2018: 66 · 2017: 63 · 2016: 78 · 2015: 71 · 2014: 64 · 2013: 72 · 2012: 70
- FWCI
- 29.71
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- other-oa
- www.elsevier.com/tdm/userlicense/1.0/ (tdm)
- www.elsevier.com/legal/tdmrep-license (tdm)
- www.elsevier.com/open-access/userlicense/1.0/ (vor, 928 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, other-oa)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
- DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc)
- Lund University Publications (Lund University) (submittedVersion)
- Elsevier eBooks
- Funders
- Wellcome Trust
- National Institutes of Health (DP1OD003958)
- National Heart, Lung, and Blood Institute (R01HL082945)
- National Human Genome Research Institute (R01HG002668)
- National Cancer Institute (RC1CA145229, P01CA108631, P01CA066996)
- National Institute of General Medical Sciences (T32GM007753)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Health Sciences › Medicine › Hematology › Hematopoietic Stem Cell Transplantation
- Keywords
- hematopoiesis, transcriptional circuits, cis-regulatory elements, gene regulatory networks, hematopoietic lineage, transcription factors, gene co-expression modules, promoter analysis, cell states
- MeSH terms
- Gene Expression Regulation, Hematopoiesis, Humans, Transcription Factors, Gene Expression Profiling, Gene Regulatory Networks
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.
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