from CaltechAUTHORS

• Schulte, Samuel J.; Shin, Boyoung; et el. (2024) Multiplex, Quantitative, High-Resolution Imaging of Protein:Protein Complexes via Hybridization Chain Reaction; ACS Chemical Biology; Vol. 19; No. 2; 280-288; PMCID PMC10877569; 10.1021/acschembio.3c00431
• Schulte, Samuel J.; Shin, Boyoung; et el. (2024) Multiplex, Quantitative, High-Resolution Imaging of Protein:Protein Complexes via Hybridization Chain Reaction; ACS Chemical Biology; 10.1021/acschembio.3c00431
• Spolski, Rosanne; Li, Peng; et el. (2023) Distinct use of super-enhancer elements controls cell type–specific CD25 transcription and function; Science Immunology; Vol. 8; No. 89; eadi8217; 10.1126/sciimmunol.adi8217
• Shin, Boyoung; Zhou, Wen; et el. (2023) Runx factors launch T cell and innate lymphoid programs via direct and gene network-based mechanisms; Nature Immunology; Vol. 24; 1458–1472; 10.1038/s41590-023-01585-z
• MacNabb, Brendan W. and Rothenberg, Ellen V. (2023) Speed and navigation control of thymocyte development by the fetal T-cell gene regulatory network; Immunological Reviews; 10.1111/imr.13190
• Kagan, Jonathan C.; Rothenberg, Ellen V.; et el. (2023) Cold Spring Harbor Laboratory 2022: emerging insights and viewpoints in immunology; Trends in Immunology; Vol. 44; No. 4; 248-255; 10.1016/j.it.2023.02.003
• Shin, Boyoung and Rothenberg, Ellen V. (2023) Multi-modular structure of the gene regulatory network for specification and commitment of murine T cells; Frontiers in Immunology; Vol. 14; Art. No. 1108368; PMCID PMC9928580; 10.3389/fimmu.2023.1108368
• Rothenberg, Ellen V. (2022) Transcription factors specifically control change; Genes and Development; Vol. 36; No. 21-24; 1097-1099; PMCID PMC9851400; 10.1101/gad.350308.122
• Rothenberg, Ellen V. (2022) The Heart of the Machine: Construction of T Cell Identity, Made Accessible; Journal of Immunology; Vol. 209; No. 7; 1235-1236; 10.4049/jimmunol.2200264
• Zhou, Wen; Gao, Fan; et el. (2022) Single-cell deletion analyses show control of pro–T cell developmental speed and pathways by Tcf7, Spi1, Gata3, Bcl11a, Erg, and Bcl11b; Science Immunology; Vol. 7; No. 71; eabm1920; PMCID PMC9273332; 10.1126/sciimmunol.abm1920
• Rothenberg, Ellen V. (2021) Logic and lineage impacts on functional transcription factor deployment for T-cell fate commitment; Biophysical Journal; Vol. 120; No. 19; 4162-4181; 10.1016/j.bpj.2021.04.002
• Hosokawa, Hiroyuki; Koizumi, Maria; et el. (2021) Stage-specific action of Runx1 and GATA3 controls silencing of PU.1 expression in mouse pro-T cells; Journal of Experimental Medicine; Vol. 218; No. 8; Art. No. e20202648; PMCID PMC8241539; 10.1084/jem.20202648
• Sidwell, Tom and Rothenberg, Ellen V. (2021) Epigenetic Dynamics in the Function of T-Lineage Regulatory Factor Bcl11b; Frontiers in Immunology; Vol. 12; Art. No. 669498; PMCID PMC8079813; 10.3389/fimmu.2021.669498
• Hosokawa, Hiroyuki and Rothenberg, Ellen V. (2021) How transcription factors drive choice of the T cell fate; Nature Reviews. Immunology; Vol. 21; No. 3; 162-176; 10.1038/s41577-020-00426-6
• Rothenberg, Ellen V. (2021) Single-cell insights into the hematopoietic generation of T-lymphocyte precursors in mouse and human; Experimental Hematology; Vol. 95; 1-12; PMCID PMC8018899; 10.1016/j.exphem.2020.12.005
• Shin, Boyoung; Hosokawa, Hiroyuki; et el. (2021) Runx1 and Runx3 drive progenitor to T-lineage transcriptome conversion in mouse T cell commitment via dynamic genomic site switching; Proceedings of the National Academy of Sciences of the United States of America; Vol. 118; No. 4; Art. No. e2019655118; PMCID PMC7848575; 10.1073/pnas.2019655118
• Olariu, Victor; Yui, Mary A.; et el. (2021) Multi-scale Dynamical Modeling of T Cell Development from an Early Thymic Progenitor State to Lineage Commitment; Cell Reports; Vol. 34; No. 2; Art. No. 108622; PMCID PMC7943435; 10.1016/j.celrep.2020.108622
• Rothenberg, Ellen V. and Göttgens, Berthold (2021) How haematopoiesis research became a fertile ground for regulatory network biology as pioneered by Eric Davidson; Current Opinion in Hematology; Vol. 28; No. 1; 1-10; PMCID PMC7755131; 10.1097/moh.0000000000000628
• Romero-Wolf, Maile; Shin, Boyoung; et el. (2020) Notch2 complements Notch1 to mediate inductive signaling that initiates early T cell development; Journal of Cell Biology; Vol. 219; No. 10; Art. No. e202005093; PMCID PMC7659720; 10.1083/jcb.202005093
• Wang, Xun and Rothenberg, Ellen V. (2020) Illuminating the core of adaptive immunity—how the regulatory genome controls Rag chromatin dynamics; Science Immunology; Vol. 5; No. 51; Art. No. eabd6427; 10.1126/sciimmunol.abd6427
• Spolski, Rosanne; Li, Peng; et el. (2020) Functional dissection of the Il2ra superenhancer reveals developmentally regulated and cell type specific elements; Journal of Immunology; Vol. 204; No. S1; Art. No. 78.16
• Hosokawa, Hiroyuki; Romero-Wolf, Maile; et el. (2020) Cell type–specific actions of Bcl11b in early T-lineage and group 2 innate lymphoid cells; Journal of Experimental Medicine; Vol. 217; No. 1; Art. No. e20190972; PMCID PMC7037248; 10.1084/jem.20190972
• Rothenberg, Ellen V. (2019) Dynamic control of the T-cell specification gene regulatory network; Current Opinion in Systems Biology; Vol. 18; 62-76; PMCID PMC7015151; 10.1016/j.coisb.2019.10.012
• Zhou, Wen and Rothenberg, Ellen V. (2019) Building a Human Thymus: A Pointillist View; Immunity; Vol. 51; No. 5; 788-790; 10.1016/j.immuni.2019.10.003
• Zhou, Wen; Yui, Mary A.; et el. (2019) Single-Cell Analysis Reveals Regulatory Gene Expression Dynamics Leading to Lineage Commitment in Early T Cell Development; Cell Systems; Vol. 9; No. 4; 321-337; PMCID PMC6932747; 10.1016/j.cels.2019.09.008
• Sashital, Dipali; Blanpain, Cedric; et el. (2019) Advice from Cell Press Reviewers; Cell; Vol. 179; No. 1; 40-45; 10.1016/j.cell.2019.08.044
• Rothenberg, Ellen V. (2019) Programming for T-lymphocyte fates: modularity and mechanisms; Genes and Development; Vol. 33; No. 17-18; 1117-1135; PMCID PMC6719619; 10.1101/gad.327163.119
• Rothenberg, Ellen V. (2019) Causal Gene Regulatory Network Modeling and Genomics: Second-Generation Challenges; Journal of Computational Biology; Vol. 26; No. 7; 703-718; PMCID PMC6661971; 10.1089/cmb.2019.0098
• Rothenberg, Ellen V. (2019) Encounters across networks: Windows into principles of genomic regulation; Marine Genomics; Vol. 44; 3-12; PMCID PMC6431589; 10.1016/j.margen.2019.01.003
• Rothenberg, Ellen V.; Hosokawa, Hiroyuki; et el. (2019) Mechanisms of Action of Hematopoietic Transcription Factor PU.1 in Initiation of T-Cell Development; Frontiers in Immunology; Vol. 10; Art. No. 228; PMCID PMC6391351; 10.3389/fimmu.2019.00228
• Hosokawa, Hiroyuki; Romero-Wolf, Maile; et el. (2018) Bcl11b sets pro-T cell fate by site-specific cofactor recruitment and by repressing Id2 and Zbtb16; Nature Immunology; Vol. 19; No. 12; 1427-1440; PMCID PMC6240390; 10.1038/s41590-018-0238-4
• Ng, Kenneth K. N.; Yui, Mary A.; et el. (2018) A stochastic epigenetic switch controls the dynamics of T-cell lineage commitment; eLife; Vol. 7; Art. No. e37851; PMCID PMC6245732; 10.7554/eLife.37851
• Ungerbäck, Jonas; Hosokawa, Hiroyuki; et el. (2018) Pioneering, chromatin remodeling, and epigenetic constraint in early T-cell gene regulation by SPI1 (PU.1); Genome Research; Vol. 28; No. 10; 1508-1519; PMCID PMC6169891; 10.1101/gr.231423.117
• Hosokawa, Hiroyuki; Ungerbäck, Jonas; et el. (2018) Transcription Factor PU.1 Represses and Activates Gene Expression in Early T Cells by Redirecting Partner Transcription Factor Binding; Immunity; Vol. 48; No. 6; 1119-1134; PMCID PMC6063530; 10.1016/j.immuni.2018.04.024
• Hosokawa, Hiroyuki and Rothenberg, Ellen V. (2018) Cytokines, Transcription Factors, and the Initiation of T-Cell Development; Cold Spring Harbor Perspectives in Biology; Vol. 10; No. 5; 1-19; PMCID PMC5876153; 10.1101/cshperspect.a028621
• Hu, Gangqing; Cui, Kairong; et el. (2018) Transformation of Accessible Chromatin and 3D Nucleome Underlies Lineage Commitment of Early T Cells; Immunity; Vol. 48; No. 2; 227-242; PMCID PMC5847274; 10.1016/j.immuni.2018.01.013
• Rothenberg, Ellen V. (2017) Fitting structure to function in gene regulatory networks; History and Philosophy of the Life Sciences; Vol. 39; No. 4; Art. No. 37; PMCID PMC5660880; 10.1007/s40656-017-0164-z
• He, Zhiheng; Ma, Jian; et el. (2017) A two-amino-acid substitution in the transcription factor RORγt disrupts its function in T_H17 differentiation but not in thymocyte development; Nature Immunology; Vol. 18; No. 10; 1128-1138; PMCID PMC5678981; 10.1038/ni.3832
• Longabaugh, William J. R.; Zeng, Weihua; et el. (2017) Bcl11b and combinatorial resolution of cell fate in the T-cell gene regulatory network; Proceedings of the National Academy of Sciences of the United States of America; Vol. 114; No. 23; 5800-5807; PMCID PMC5468679; 10.1073/pnas.1610617114
• Tsagaratou, Ageliki; González-Avalos, Edahí; et el. (2017) TET proteins regulate the lineage specification and TCR-mediated expansion of iNKT cells; Nature Immunology; Vol. 18; No. 1; 45-53; PMCID PMC5376256; 10.1038/ni.3630
• Rothenberg, Ellen V. (2016) Multiple Curricula for B Cell Developmental Programming; Immunity; Vol. 45; No. 3; 457-458; 10.1016/j.immuni.2016.09.005
• Manesso, Erica; Kueh, Hao Yuan; et el. (2016) Irreversibility of T-cell specification: insights from computational modelling of a minimal network architecture; PLoS ONE; Vol. 11; No. 8; Art. No. e0161260; PMCID PMC4995000; 10.1371/journal.pone.0161260
• Kueh, Hao Yuan; Yui, Mary A.; et el. (2016) Asynchronous combinatorial action of four regulatory factors activates Bcl11b for T cell commitment; Nature Immunology; Vol. 17; No. 8; 956-965; PMCID PMC4955789; 10.1038/ni.3514
• Rothenberg, E.; Kueh, H. Y.; et el. (2016) Dissecting the transcriptional regulatory network for early T-cell commitment; European Journal of Immunology; Vol. 46; No. S1; 797; 10.1002/eji.201670200
• Rothenberg, Ellen V.; Kueh, Hao Yuan; et el. (2016) Hematopoiesis and T-cell specification as a model developmental system; Immunological Reviews; Vol. 271; No. 1; 72-97; PMCID PMC4837658; 10.1111/imr.12417
• Rothenberg, Ellen V. (2016) Eric Davidson: Steps to A Gene Regulatory Network for Development; Developmental Biology; Vol. 412; No. 2; S7-S19; PMCID PMC4828313; 10.1016/j.ydbio.2016.01.020
• Van de Walle, Inge; Dolens, Anne-Catherine; et el. (2016) GATA3 induces human T-cell commitment by restraining Notch activity and repressing NK-cell fate; Nature Communications; Vol. 7; Art. No. 11171; PMCID PMC4823830; 10.1038/ncomms11171
• Rothenberg, Ellen V.; Ungerbäck, Jonas; et el. (2016) Forging T-Lymphocyte Identity: Intersecting Networks of Transcriptional Control; Advances in Immunology; Vol. 129; 109-174; PMCID PMC4747653; 10.1016/bs.ai.2015.09.002
• Hood, Leroy and Rothenberg, Ellen V. (2015) Developmental biologist Eric H. Davidson, 1937–2015; Proceedings of the National Academy of Sciences of the United States of America; Vol. 112; No. 44; 13423-13425; PMCID PMC4640791; 10.1073/pnas.1518876112
• Champhekar, Ameya; Damle, Sagar S.; et el. (2015) Regulation of early T-lineage gene expression and developmental progression by the progenitor cell transcription factor PU.1; Genes and Development; Vol. 29; No. 8; 832-848; PMCID PMC4403259; 10.1101/gad.259879.115
• Rothenberg, Ellen V. (2015) Immune Cell Identity: Perspective from a Palimpsest; Perspectives in Biology and Medicine; Vol. 58; No. 2; 205-228; PMCID PMC4747652; 10.1353/pbm.2015.0020
• Scripture-Adams, Deirdre D.; Damle, Sagar S.; et el. (2014) GATA-3 Dose-Dependent Checkpoints in Early T Cell Commitment; Journal of Immunology; Vol. 193; No. 7; 3470-3491; PMCID PMC4170028; 10.4049/jimmunol.1301663
• Yui, Mary A. and Rothenberg, Ellen V. (2014) Developmental gene networks: a triathlon on the course to T cell identity; Nature Reviews. Immunology; Vol. 14; No. 8; 529-545; PMCID PMC4153685; 10.1038/nri3702
• Kueh, Hao Yuan; Elowitz, Michael B.; et el. (2014) Macrophage and T-cell fate control: Insights from tracking transcription factor dynamics in single cells; Experimental Hematology; Vol. 42; No. 8; S16; 10.1016/j.exphem.2014.07.054
• Rothenberg, Ellen V. (2014) The chromatin landscape and transcription factors in T cell programming; Trends in Immunology; Vol. 35; No. 5; 195-204; PMCID PMC4039984; 10.1016/j.it.2014.03.001
• Rothenberg, Ellen V. (2014) Transcriptional Control of Early T and B Cell Developmental Choices; Annual Review of Immunology; Vol. 32; 283-321; PMCID PMC3994230; 10.1146/annurev-immunol-032712-100024
• Rothenberg, Ellen V. (2013) Epigenetic mechanisms and developmental choice hierarchies in T-lymphocyte development; Briefings in Functional Genomics; Vol. 12; No. 6; 512-524; PMCID PMC3838197; 10.1093/bfgp/elt027
• Rothenberg, Ellen V.; Champhekar, Ameya; et el. (2013) Transcriptional Establishment of Cell-Type Identity: Dynamics and Causal Mechanisms of T-Cell Lineage Commitment; Cold Spring Harbor Symposia on Quantitative Biology; Vol. 78; 1-11; PMCID PMC3990665; 10.1101/sqb.2013.78.020271
• Kueh, Hao Yuan; Champhekhar, Ameya; et el. (2013) Positive Feedback Between PU.1 and the Cell Cycle Controls Myeloid Differentiation; Science; Vol. 341; No. 6146; 670-673; PMCID PMC3913367; 10.1126/science.1240831
• Li, Long; Zhang, Jingli A.; et el. (2013) A far downstream enhancer for murine Bcl11b controls its T-cell specific expression; Blood; Vol. 122; No. 6; 902-911; PMCID PMC3739036; 10.1182/blood-2012-08-447839
• Rothenberg, Ellen (2013) Transcriptional and epigenetic thresholds for entry to the T-cell developmental program; Experimental Hematology; Vol. 41; No. 8; S8
• Yui, Mary A.; Feng, Ni; et el. (2013) Loss of T Cell Progenitor Checkpoint Control Underlies Leukemia Initiation in Rag1-Deficient Nonobese Diabetic Mice; Journal of Immunology; Vol. 190; No. 7; 3276-3288; PMCID PMC3608698; 10.4049/jimmunol.1202970
• Del Real, Marissa Morales and Rothenberg, Ellen

22. 2013. Architecture of a lymphomyeloid developmental switch controlled by PU.1, Notch and Gata3; Development; Vol. 140; No. 6; 1207-1219; PMCID PMC3585658; 10.1242/dev.088559

• Rothenberg, Ellen V. (2013) GATA-3 locks the door to the B-cell option; Blood; Vol. 121; No. 10; 1673-1674; PMCID PMC3591792; 10.1182/blood-2013-01-477737
• Manesso, Erica; Chickarmane, Vijay; et el. (2013) Computational modelling of T-cell formation kinetics: output regulated by initial proliferation-linked deferral of developmental competence; Journal of the Royal Society Interface; Vol. 10; No. 78; Art. No. 20120774; PMCID PMC3565808; 10.1098/rsif.2012.0774
• Zarnegar, M. A. and Rothenberg, E. V. (2012) Ikaros represses and activates PU.1 cell-type-specifically through the multifunctional Sfpi1 URE and a myeloid specific enhancer; Oncogene; Vol. 31; No. 43; 4647-4654; PMCID PMC3679182; 10.1038/onc.2011.597
• Zhang, Jingli A.; Mortazavi, Ali; et el. (2012) Dynamic Transformations of Genome-wide Epigenetic Marking and Transcriptional Control Establish T Cell Identity; Cell; Vol. 149; No. 2; 467-482; PMCID PMC3336965; 10.1016/j.cell.2012.01.056
• Rothenberg, Ellen V. (2012) Transcriptional drivers of the T-cell lineage program; Current Opinion in Immunology; Vol. 24; No. 2; 132-138; PMCID PMC3319509; 10.1016/j.coi.2011.12.012
• Kueh, Hao Yuan and Rothenberg, Ellen V. (2012) Regulatory gene network circuits underlying T cell development from multipotent progenitors; Wiley Interdisciplinary Reviews. Systems Biology and Medicine; Vol. 4; No. 1; 79-102; PMCID PMC3242926; 10.1002/wsbm.162
• Rothenberg, Ellen V. (2011) T Cell Lineage Commitment: Identity and Renunciation; Journal of Immunology; Vol. 186; No. 12; 6649-6655; PMCID PMC3111953; 10.4049/jimmunol.1003703
• Feng, Ni; Vegh, Patricia; et el. (2011) Lineage Divergence at the First TCR-Dependent Checkpoint: Preferential γδ and Impaired αβ T Cell Development in Nonobese Diabetic Mice; Journal of Immunology; Vol. 186; No. 2; 826-837; PMCID PMC4087166; 10.4049/jimmunol.1002630
• Rothenberg, Ellen V. (2010) Lineage determination in the immune system; Immunological Reviews; Vol. 238; No. 1; 5-11; PMCID PMC3058842; 10.1111/j.1600-065X.2010.00965.x
• Rothenberg, Ellen V.; Zhang, Jingli; et el. (2010) Multilayered specification of the T-cell lineage fate; Immunological Reviews; Vol. 238; No. 1; 150-168; PMCID PMC2965335; 10.1111/j.1600-065X.2010.00964.x
• Zarnegar, Mark A.; Chen, Jing; et el. (2010) Cell-Type-Specific Activation and Repression of PU.1 by a Complex of Discrete, Functionally Specialized cis-Regulatory Elements; Molecular and Cellular Biology; Vol. 30; No. 20; 4922-1939; PMCID PMC2950536; 10.1128/MCB.00354-10
• Li, Long; Leid, Mark; et el. (2010) An Early T Cell Lineage Commitment Checkpoint Dependent on the Transcription Factor Bcl11b; Science; Vol. 329; No. 5987; 89-93; PMCID PMC2935300; 10.1126/science.1188989
• Rothenberg, Ellen V. (2010) B cell specification from the genome up; Nature Immunology; Vol. 11; No. 7; 572-574; 10.1038/ni0710-572
• Yui, Mary A.; Feng, Ni; et el. (2010) Fine-Scale Staging of T Cell Lineage Commitment in Adult Mouse Thymus; Journal of Immunology; Vol. 185; No. 1; 284-293; PMCID PMC4091773; 10.4049/jimmunol.1000679
• Rothenberg, Ellen V. and Murre, Cornelis (2010) Editorial overview; Current Opinion in Immunology; Vol. 22; No. 2; 145-147; 10.1016/j.coi.2010.03.002
• Rothenberg, Ellen V. and Murre, Cornelis (2010) Lymphocyte development; Current Opinion in Immunology; Vol. 22; No. 2; 145-147; 10.1016/j.coi.2010.03.002
• Novak, Thomas J. and Rothenberg, Ellen V. (2009) Differential Transient and Long-Term Expression of DNA Sequences Introduced into T-Lymphocyte Lines; DNA; Vol. 5; No. 6; 439-451; 10.1089/dna.1.1986.5.439
• Rothenberg, Ellen V. (2009) Decision by committee: new light on the CD4/CD8-lineage choice; Immunology and Cell Biology; Vol. 87; No. 2; 109-112; 10.1038/icb.2008.100
• David-Fung, Elizabeth-Sharon; Butler, Robert; et el. (2009) Transcription factor expression dynamics of early T-lymphocyte specification and commitment; Developmental Biology; Vol. 325; No. 2; 444-467; PMCID PMC2663971; 10.1016/j.ydbio.2008.10.021
• Georgescu, Constantin; Longabaugh, William J. R.; et el. (2008) A gene regulatory network armature for T lymphocyte specification; Proceedings of the National Academy of Sciences of the United States of America; Vol. 105; No. 51; 20100-20105; PMCID PMC2629331; 10.1073/pnas.0806501105
• Taghon, Tom and Rothenberg, Ellen V. (2008) Molecular mechanisms that control mouse and human TCR-αβ and TCR-γδ T cell development; Seminars In Immunopathology; Vol. 30; No. 4; 383-398; 10.1007/s00281-008-0134-3
• Guo, Yalin; Maillard, Ivan; et el. (2008) Core binding factors are necessary for natural killer cell development, and cooperate with Notch signaling during T cell specification; Blood; Vol. 112; No. 3; 480-492; PMCID PMC2481540; 10.1182/blood-2007-10-120261
• Rothenberg, Ellen V. and Scripture-Adams, Deirdre

4. 2008. Competition and collaboration: GATA-3, PU.1, and Notch signaling in early T-cell fate determination; Seminars in Immunology; Vol. 20; No. 4; 236-246; PMCID PMC2634812; 10.1016/j.smim.2008.07.006

• Rothenberg, Ellen V. (2008) Erg in stem cells: a function emerges; Nature Immunology; Vol. 9; No. 7; 714-716; 10.1038/ni0708-714
• Rothenberg, Ellen V.; Moore, Jonathan E.; et el. (2008) Launching the T-cell-lineage developmental programme; Nature Reviews. Immunology; Vol. 8; No. 1; 9-21; PMCID PMC3131407; 10.1038/nri2232
• Taghon, Tom; Yui, Mary A.; et el. (2007) Mast cell lineage diversion of T lineage precursors by the essential T cell transcription factor GATA-3; Nature Immunology; Vol. 8; No. 8; 845-855; PMCID PMC3140173; 10.1038/ni1486
• Tydell, C. C.; David-Fung, Elizabeth-Sharon; et el. (2007) Molecular Dissection of Prethymic Progenitor Entry into the T Lymphocyte Developmental Pathway; Journal of Immunology; Vol. 179; No. 1; 421-438; 10.4049/jimmunol.179.1.421
• Rothenberg, Ellen V. (2007) Regulatory factors for initial T lymphocyte lineage specification; Current Opinion in Hematology; Vol. 14; No. 4; 322-329; 10.1097/MOH.0b013e3281de72a8
• Rothenberg, Ellen V. (2007) Negotiation of the T Lineage Fate Decision by Transcription-Factor Interplay and Microenvironmental Signals; Immunity; Vol. 26; No. 6; 690-702; 10.1016/j.immuni.2007.06.005
• Rothenberg, Ellen V. (2007) Cell lineage regulators in B and T cell development; Nature Immunology; Vol. 8; No. 5; 441-444; 10.1038/ni1461
• Franco, Christopher B.; Scripture-Adams, Dierdre D.; et el. (2006) Notch/Delta signaling constrains reengineering of pro-T cells by PU.1; Proceedings of the National Academy of Sciences of the United States of America; Vol. 103; No. 32; 11993-11998; PMCID PMC1567686; 10.1073/pnas.0601188103
• Wang, Duncheng; Claus, Carol L.; et el. (2006) The Basic Helix-Loop-Helix Transcription Factor HEBAlt Is Expressed in Pro-T Cells and Enhances the Generation of T Cell Precursors; Journal of Immunology; Vol. 177; No. 1; 109-119; 10.4049/jimmunol.177.1.109
• David-Fung, Elizabeth-Sharon; Yui, Mary A.; et el. (2006) Progression of regulatory gene expression states in fetal and adult pro-T-cell development; Immunological Reviews; Vol. 209; No. 1; 212-236; PMCID PMC4157939; 10.1111/j.0105-2896.2006.00355.x
• Taghon, Tom; Yui, Mary A.; et el. (2006) Developmental and Molecular Characterization of Emerging β- and γδ-Selected Pre-T Cells in the Adult Mouse Thymus; Immunity; Vol. 24; No. 1; 53-64; 10.1016/j.immuni.2005.11.012
• Adachi, Satoko and Rothenberg, Ellen V. (2005) Cell-type-specific epigenetic marking of the IL2 gene at a distal cis-regulatory region in competent, nontranscribing T-cells; Nucleic Acids Research; Vol. 33; No. 10; 3200-3210; PMCID PMC1142491; 10.1093/nar/gki637
• Taghon, Tom N.; David, Elizabeth-Sharon; et el. (2005) Delayed, asynchronous, and reversible T-lineage specification induced by Notch/Delta signaling; Genes and Development; Vol. 19; No. 8; 965-978; PMCID PMC1080135; 10.1101/gad.1298305
• Dionne, Christopher J.; Tse, Kevin Y.; et el. (2005) Subversion of T lineage commitment by PU.1 in a clonal cell line system; Developmental Biology; Vol. 280; No. 2; 448-466; 10.1016/j.ydbio.2005.01.027
• Rothenberg, Ellen V. and Taghon, Tom (2005) Molecular Genetics of T Cell Development; Annual Review of Immunology; Vol. 23; 601-649; 10.1146/annurev.immunol.23.021704.115737
• Rothenberg, Ellen V. (2005) Thymic Regulation–Hidden in Plain Sight; Science; Vol. 307; No. 5711; 858-859; 10.1126/science.1109501
• Yui, Mary A. and Rothenberg, Ellen V. (2004) Deranged Early T Cell Development in Immunodeficient Strains of Nonobese Diabetic Mice; Journal of Immunology; Vol. 173; No. 9; 5381-5391; 10.4049/jimmunol.173.9.5381
• Rothenberg, Ellen V. and Pant, Rashmi (2004) Origins of lymphocyte developmental programs: transcription factor evidence; Seminars in Immunology; Vol. 16; No. 4; 227-238; 10.1016/j.smim.2004.08.002
• Anderson, Michele K.; Pant, Rashmi; et el. (2004) Evolutionary Origins of Lymphocytes: Ensembles of T Cell and B Cell Transcriptional Regulators in a Cartilaginous Fish; Journal of Immunology; Vol. 172; No. 10; 5851-5860; 10.4049/jimmunol.172.10.5851
• Yui, Mary A.; Sharp, Leslie L.; et el. (2004) Preferential Activation of an IL-2 Regulatory Sequence Transgene in TCRγδ and NKT Cells: Subset-Specific Differences in IL-2 Regulation; Journal of Immunology; Vol. 172; No. 8; 4691-4699; 10.4049/jimmunol.172.8.4691
• Telfer, J. C.; Hedblom, E. E.; et el. (2004) Localization of the Domains in Runx Transcription Factors Required for the Repression of CD4 in Thymocytes; Journal of Immunology; Vol. 172; No. 7; 4359-4370; 10.4049/jimmunol.172.7.4359
• Rothenberg, Ellen V. (2004) From totipotency to T in a dish; Nature Immunology; Vol. 5; No. 4; 359-360; 10.1038/ni0404-359
• Hernández-Hoyos, Gabriela; Anderson, Michele K.; et el. (2003) GATA-3 Expression Is Controlled by TCR Signals and Regulates CD4/CD8 Differentiation; Immunity; Vol. 19; No. 1; 83-94; 10.1016/S1074-7613(03)00176-6
• Warren, Luigi A. and Rothenberg, Ellen V. (2003) Regulatory coding of lymphoid lineage choice by hematopoietic transcription factors; Current Opinion in Immunology; Vol. 15; No. 2; 166-175; 10.1016/S0952-7915(03)00011-6
• Rothenberg, Ellen V. (2002) T-lineage specification and commitment: a gene regulation perspective; Seminars in Immunology; Vol. 14; No. 6; 431-440; 10.1016/S1044532302000787
• Rothenberg, Ellen V. and Dionne, Christopher J. (2002) Lineage plasticity and commitment in T-cell development; Immunological Reviews; Vol. 187; No. 1; 96-115; 10.1034/j.1600-065X.2002.18709.x
• Anderson, Michele K.; Hernandez-Hoyos, Gabriela; et el. (2002) Definition of Regulatory Network Elements for T Cell Development by Perturbation Analysis with PU.1 and GATA-3; Developmental Biology; Vol. 246; No. 1; 103-121; 10.1006/dbio.2002.0674
• Rothenberg, Ellen V. and Anderson, Michele K. (2002) Elements of Transcription Factor Network Design for T-Lineage Specification; Developmental Biology; Vol. 246; No. 1; 29-44; 10.1006/dbio.2002.0667
• Anderson, Michele K.; Weiss, Angela H.; et el. (2002) Constitutive Expression of PU.1 in Fetal Hematopoietic Progenitors Blocks T Cell Development at the Pro-T Cell Stage; Immunity; Vol. 16; No. 2; 285-296; 10.1016/S1074-7613(02)00277-7
• Rothenberg, Ellen V. (2001) Mapping of complex regulatory elements by pufferfish/zebrafish transgenesis; Proceedings of the National Academy of Sciences of the United States of America; Vol. 98; No. 12; 6540-6542; PMCID PMC34387
• Makita, Takako; Hernandez-Hoyos, Gabriela; et el. (2001) A developmental transition in definitive erythropoiesis: erythropoietin expression is sequentially regulated by retinoic acid receptors and HNF4; Genes and Development; Vol. 15; No. 7; 889-901; PMCID PMC312661; 10.1101/gad.871601
• Miracle, Ann L.; Anderson, Michele K.; et el. (2001) Complex expression patterns of lymphocyte-specific genes during the development of cartilaginous fish implicate unique lymphoid tissues in generating an immune repertoire; International Immunology; Vol. 13; No. 4; 567-580; 10.1093/intimm/13.4.567
• Rothenberg, Ellen V. (2001) Notchless T cell maturation?; Nature Immunology; Vol. 2; No. 3; 189-190; 10.1038/85231
• Yui, Mary A.; Hernández-Hoyos, Gabriela; et el. (2001) A New Regulatory Region of the IL-2 Locus That Confers Position-Independent Transgene Expression; Journal of Immunology; Vol. 166; No. 3; 1730-1739; 10.4049/jimmunol.166.3.1730
• Chen, Fei; Rowen, Lee; et el. (2001) Differential Transcriptional Regulation of Individual TCR V Segments Before Gene Rearrangement; Journal of Immunology; Vol. 166; No. 3; 1771-1780; 10.4049/jimmunol.166.3.1771
• Anderson, Michele K.; Sun, Xiao; et el. (2001) Evolution of hematopoiesis: Three members of the PU.1 transcription factor family in a cartilaginous fish, Raja eglanteria; Proceedings of the National Academy of Sciences of the United States of America; Vol. 98; No. 2; 553-558; PMCID PMC14625; 10.1073/pnas.021478998
• Telfer, Janice C. and Rothenberg, Ellen V. (2001) Expression and Function of a Stem Cell Promoter for the Murine CBFα2 Gene: Distinct Roles and Regulation in Natural Killer and T Cell Development; Developmental Biology; Vol. 229; No. 2; 363-382; 10.1006/dbio.2000.9991
• Rothenberg, Ellen V. (2000) Stepwise specification of lymphocyte developmental lineages; Current Opinion in Genetics and Development; Vol. 10; No. 4; 370-379; 10.1016/S0959-437X(00)00098-8
• Hernández-Hoyos, Gabriela; Sohn, Sue J.; et el. (2000) Lck Activity Controls CD4/CD8 T Cell Lineage Commitment; Immunity; Vol. 12; No. 3; 313-322; 10.1016/S1074-7613(00)80184-3
• Rothenberg, Ellen V.; Telfer, Janice C.; et el. (1999) Transcriptional regulation of lymphocyte lineage commitment; Bioessays; Vol. 21; No. 9; 726-742; 10.1002/(SICI)1521-1878(199909)21:9<726::AID-BIES4>3.0.CO;2-S
• Anderson, Michele K.; Hernandez-Hoyos, Gabriela; et el. (1999) Precise developmental regulation of Ets family transcription factors during specification and commitment to the T cell lineage; Development; Vol. 126; No. 14; 3131-3148
• Chen, Fei; Chen, Dan; et el. (1999) Specific regulation of Fos family transcription factors in thymocytes at two developmental checkpoints; International Immunology; Vol. 11; No. 5; 677-688; 10.1093/intimm/11.5.677
• Wang, Hua; Diamond, Rochelle A.; et el. (1998) Precocious expression of T cell functional response genes in vivo in primitive thymocytes before T lineage commitment; International Immunology; Vol. 10; No. 11; 1623-1635; 10.1093/intimm/10.11.1623
• Ward, Susan B.; Hernandez-Hoyos, Gabriela; et el. (1998) Chromatin remodeling of the interleukin-2 gene: distinct alterations in the proximal versus distal enhancer regions; Nucleic Acids Research; Vol. 26; No. 12; 2923-2934; PMCID PMC147656
• Wang, Hua; Diamond, Rochelle A.; et el. (1998) Cross-lineage expression of Ig-beta (B29) in thymocytes: Positive and negative gene regulation to establish T cell identity; Proceedings of the National Academy of Sciences of the United States of America; Vol. 95; No. 12; 6831-6836; PMCID PMC22652
• Yang-Snyder, Julia A. and Rothenberg, Ellen V. (1998) Spontaneous Expression of Interleukin-2 In Vivo in Specific Tissues of Young Mice; Developmental Immunology; Vol. 5; No. 4; 223-245; PMCID PMC2275993; 10.1155/1998/12421
• Diamond, Rochelle A.; Ward, Susan B.; et el. (1997) Different Developmental Arrest Points in RAG-2 -/- and SCID Thymocytes on Two Genetic Backgrounds Developmental Choices and Cell Death Mechanisms before TCR Gene Rearrangement; Journal of Immunology; Vol. 158; No. 9; 4052-4064
• Diamond, Rochelle A.; Ward, Susan B.; et el. (1997) Different Developmental Arrest Points in RAG-2 -/- and SCID Thymocytes on Two Genetic Backgrounds Developmental Choices and Cell Death Mechanisms before TCR Gene Rearrangement; Journal of Immunology; Vol. 158; No. 9; 4052-4064
• Rothenberg, Ellen V. and Ward, Susan B. (1996) A dynamic assembly of diverse transcription factors integrates activation and cell-type information for interleukin 2 gene regulation; Proceedings of the National Academy of Sciences of the United States of America; Vol. 93; No. 18; 9358-9365; PMCID PMC38432
• Rothenberg, Ellen V. (1996) How T Cells Count; Science; Vol. 273; No. 5271; 78-79; 10.1126/science.273.5271.78
• Reya, Tannishtha; Yang-Snyder, Julia A.; et el. (1996) Regulated expression and function of CD122 (interleukin-2/interleukin-15R-β) during lymphoid development; Blood; Vol. 87; No. 1; 190-201
• Lindenboim, Liora; Diamond, Rochelle; et el. (1995) Apoptosis Induced by Serum Deprivation of PC12 Cells Is Not Preceded by Growth Arrest and Can Occur at Each Phase of the Cell Cycle; Cancer Research; Vol. 55; No. 6; 1242-1247
• Rothenberg, Ellen V. (1994) Signaling mechanisms in thymocyte selection; Current Opinion in Immunology; Vol. 6; No. 2; 257-265; 10.1016/0952-7915(94)90099-X
• Chen, Dan and Rothenberg, Ellen V. (1994) Interleukin 2 transcription factors as molecular targets of cAMP inhibition: delayed inhibition kinetics and combinatorial transcription roles; Journal of Experimental Medicine; Vol. 179; No. 3; 931-942; PMCID PMC2191402; 10.1084/jem.179.3.931
• Garrity, Paul A.; Chen, Dan; et el. (1994) Interleukin-2 transcription is regulated in vivo at the level of coordinated binding of both constitutive and regulated factors; Molecular and Cellular Biology; Vol. 14; No. 3; 2159-2169; PMCID PMC358576; 10.1128/MCB.14.3.2159
• Rothenberg, Ellen V. and Diamond, Rochelle A. (1994) Costimulation by interleukin-1 of multiple activation responses in a developmentally restricted subset of immature thymocytes; European Journal of Immunology; Vol. 24; No. 1; 24-33; 10.1002/eji.1830240105
• Rothenberg, Ellen V.; Chen, Dan; et el. (1993) Functional and phenotypic analysis of thymocytes in SCID mice. Evidence for functional response transitions before and after the SCID arrest point; Journal of Immunology; Vol. 151; No. 7; 3530-3546
• Chen, Dan and Rothenberg, Ellen V. (1993) Molecular basis for developmental changes in interleukin-2 gene inducibility; Molecular and Cellular Biology; Vol. 13; No. 1; 228-237; PMCID PMC358902
• Yang-Snyder, Julia A. and Rothenberg, Ellen V. (1993) Developmental and Anatomical Patterns Of IL-2 Gene Expression in Vivo in The Murine Thymus; Developmental Immunology; Vol. 3; No. 2; 85-102; PMCID PMC2275923; 10.1155/1993/86096
• Novak, Thomas J.; Yoshimura, Fayth K.; et el. (1992) In vitro transfection of fresh thymocytes and T cells shows subset-specific expression of viral promoters; Molecular and Cellular Biology; Vol. 12; No. 4; 1515-1527; PMCID PMC369593
• Novak, Thomas J. and Rothenberg, Ellen V. (1990) cAMP inhibits induction of interleukin 2 but not of interleukin 4 in T cells; Proceedings of the National Academy of Sciences of the United States of America; Vol. 87; No. 23; 9353-9357; PMCID PMC55163; 10.1073/pnas.87.23.9353
• Novak, Thomas J.; Chen, Dan; et el. (1990) Interleukin-1 Synergy with Phosphoinositide Pathway Agonists for Induction of Interleukin-2 Gene Expression: Molecular Basis of Costimulation; Molecular and Cellular Biology; Vol. 10; No. 12; 6325-6334; PMCID PMC362908
• Novak, Thomas J.; White, Patricia M.; et el. (1990) Regulatory anatomy of the murine interleukin-2 gene; Nucleic Acids Research; Vol. 18; No. 15; 4523-4533; PMCID PMC331273; 10.1093/nar/18.15.4523
• Rothenberg, Ellen V. (1990) Death and transfiguration of cortical thymocytes: a reconsideration; Immunology Today; Vol. 11; No. 4; 116-119; 10.1016/0167-5699(90)90047-D
• Rothenberg, Ellen V.; Diamond, Rochelle A.; et el. (1990) IL-2 gene inducibility in T cells before T cell receptor expression. Changes in signaling pathways and gene expression requirements during intrathymic maturation; Journal of Immunology; Vol. 144; No. 5; 1614-1624
• Boyer, Paul D.; Diamond, Rochelle A.; et el. (1989) Changes in inducibility of IL-2 receptor alpha-chain and T cell-receptor expression during thymocyte differentiation in the mouse; Journal of Immunology; Vol. 142; No. 12; 4124-4130
• Rothenberg, Ellen V. (1989) The long road to functional maturity for developing T cells; Immunology Today; Vol. 10; No. 4; 116-117; 10.1016/0167-5699(89)90243-0
• McGuire, Kathleen L.; Yang, Julia A.; et el. (1988) Influence of activating stimulus on functional phenotype: Interleukin 2 mRNA accumulation differentially induced by ionophore and receptor ligands in subsets of murine T cells; Proceedings of the National Academy of Sciences of the United States of America; Vol. 85; No. 17; 6503-6507; PMCID PMC282001
• Rothenberg, Ellen V.; McGuire, Kathleen L.; et el. (1988) Molecular Indices of Functional Competence in Developing T Cells; Immunological Reviews; Vol. 104; No. 1; 29-53; 10.1111/j.1600-065X.1988.tb00758.x
• Boyer, Paul D. and Rothenberg, Ellen V. (1988) IL-2 receptor inducibility is blocked in cortical-type thymocytes; Journal of Immunology; Vol. 140; No. 9; 2886-2892
• Kinnon, Christine; McGuire, Kathleen L.; et el. (1987) Differential regulation of T cell receptor gamma genes in immature thymocyte populations; European Journal of Immunology; Vol. 17; No. 9; 1265-1269; 10.1002/eji.1830170908
• McGuire, Kathleen L. and Rothenberg, Ellen V. (1987) Inducibility of interleukin-2 RNA expression in individual mature and immature T lymphocytes; EMBO Journal; Vol. 6; No. 4; 939-946; PMCID PMC553486
• Haas, Martin; Altman, Amnon; et el. (1987) Radiation leukemia virus and X-irradiation induce in C57BL/6 mice two distinct T-cell neoplasms: A growth factor-dependent lymphoma and a growth factor-independent lymphoma; Leukemia Research; Vol. 11; No. 3; 223-239; 10.1016/0145-2126(87)90046-4
• Kinnon, Christine; Diamond, Rochelle A.; et el. (1986) Activation of T cell antigen receptor alpha- and beta-chain genes in the thymus: implications for the lineages of developing cortical thymocytes; Journal of Immunology; Vol. 137; No. 12; 4010-4015
• Lugo, James P.; Krishnan, Santosh N.; et el. (1986) Early Precursor Thymocytes Can Produce Interleukin 2 upon Stimulation with Calcium Ionophore and Phorbol Ester; Proceedings of the National Academy of Sciences of the United States of America; Vol. 83; No. 6; 1862-1866; PMCID PMC323184
• Rothenberg, Ellen and Lugo, James P. (1985) Differentiation and cell division in the mammalian thymus; Developmental Biology; Vol. 112; No. 1; 1-17; 10.1016/0012-1606(85)90114-9
• Lugo, J. P.; Krishnan, S. N.; et el. (1985) Proliferation of thymic stem cells with and without receptors for interleukin 2. Implications for intrathymic antigen recognition; Journal of Experimental Medicine; Vol. 161; No. 5; 1048-1062; PMCID PMC2187600; 10.1084/jem.161.5.1048
• Caplan, Barry and Rothenberg, Ellen (1984) High-level secretion of interleukin 2 by a subset of proliferating thymic lymphoblasts; Journal of Immunology; Vol. 133; No. 4; 1983-1991
• Haas, Martin; Altman, Amnon; et el. (1984) Mechanism of T-Cell Lymphomagenesis: Transformation of Growth-Factor-Dependent T-Lymphoblastoma Cells to Growth-Factor-Independent T-Lymphoma Cells; Proceedings of the National Academy of Sciences of the United States of America; Vol. 81; No. 6; 1742-1746; PMCID PMC344995
• Rothenberg, Ellen and Triglia, Dennis (1983) Clonal proliferation unlinked to terminal deoxynucleotidyl transferase synthesis in thymocytes of young mice; Journal of Immunology; Vol. 130; No. 4; 1627-1633
• Rothenberg, E. and Triglia, D. (1983) Lyt-2 glycoprotein is synthesized as a single molecular species; Journal of Experimental Medicine; Vol. 157; No. 1; 365-370; PMCID PMC2186898; 10.1084/jem.157.1.365
• Rothenberg, Ellen (1982) What is the role of T-lymphocyte surveillance in neoplastic disease?; American Journal of Surgery; Vol. 143; No. 6; 664-669; 10.1016/0002-9610(82)90032-0
• Rothenberg, Ellen (1982) A specific biosynthetic marker for immature thymic lymphoblasts. Active synthesis of thymus-leukemia antigen restricted to proliferating cells; Journal of Experimental Medicine; Vol. 155; No. 1; 140-154; PMCID PMC2186575; 10.1084/jem.155.1.140
• Rothenberg, Ellen and Triglia, Dennis (1981) Structure and expression of glycoproteins controlled by the Qa-1^a allele; Immunogenetics; Vol. 14; No. 6; 455-468; 10.1007/BF00350118
• Triglia, Dennis and Rothenberg, Ellen V. (1981) “Mature” thymocytes are not glucocorticoid-resistant in vitro; Journal of Immunology; Vol. 127; No. 1; 64-68
• Michaelson, James; Rothenberg, Ellen; et el. (1980) Genetic polymorphism of murineβ_2-microglobulin detected biochemically; Immunogenetics; Vol. 11-11; No. 1; 93-95; 10.1007/BF01567773
• Rothenberg, Ellen (1980) Expression of Differentiation Antigens in Subpopulations of Mouse Thymocytes: Regulation at the Level of de Novo Synthesis; Cell; Vol. 20; No. 1; 1-9; 10.1016/0092-8674(80)90228-7
• Rothenberg, Ellen and Triglia, Dennis (1980) In vitro maintenance of differentiation marker synthesis by subpopulations of mouse thymocytes; Journal of Supramolecular Structure; Vol. 14; No. 3; 371-382; 10.1002/jss.400140310
• Rothenberg, E. and Boyser, Edward A. (1979) Synthesis and processing of molecules bearing thymus leukemia antigen; Journal of Experimental Medicine; Vol. 150; No. 4; 777-791; PMCID PMC2185687; 10.1084/jem.150.4.777
• Baltimore, D.; Gilboa, E.; et el. (1979) Production of a Discrete, Infectious, Double-stranded DNA by Reverse Transcription in Virions of Moloney Murine Leukemia Virus; Cold Spring Harbor Symposia on Quantitative Biology; Vol. 43; No. 0; 869-874; 10.1101/SQB.1979.043.01.093
• Donoghue, Daniel J.; Rothenberg, Ellen; et el. (1978) Heteroduplex Analysis of the Nonhomology Region between Moloney MuLV and the Dual Host Range Derivative HIX Virus; Cell; Vol. 14; No. 4; 959-970; 10.1016/0092-8674(78)90350-1
• Shields, Anthony; Witte, Owen N.; et el. (1978) High frequency of aberrant expression of moloney murine leukemia virus in clonal infections; Cell; Vol. 14; No. 3; 601-609; 10.1016/0092-8674(78)90245-3
• Rothenberg, Ellen; Donoghue, Daniel J.; et el. (1978) Analysis of a 5’ Leader Sequence on Murine Leukemia Virus 21S RNA: Heteroduplex Mapping with Long Reverse Transcriptase Products; Cell; Vol. 13; No. 3; 435-451; 10.1016/0092-8674(78)90318-5
• Rothenberg, Ellen; Smotkin, David; et el. (1977) In vitro synthesis of infectious DNA of murine leukaemia virus; Nature; Vol. 269; No. 5624; 122-126; 10.1038/269122a0
• Rothenberg, Ellen and Baltimore, David (1977) Increased Length of DNA Made by Virions of Murine Leukemia Virus at Limiting Magnesium Ion Concentration; Journal of Virology; Vol. 21; No. 1; 168-178; PMCID PMC353803
• Haseltine, William A.; Kleid, Dennis G.; et el. (1976) Ordered transcription of RNA tumor virus genomes; Journal of Molecular Biology; Vol. 106; No. 1; 109-131; 10.1016/0022-2836(76)90303-X
• Rothenberg, Ellen and Baltimore, David (1976) Synthesis of Long, Representative DNA Copies of the Murine RNA Tumor Virus Genome; Journal of Virology; Vol. 17; No. 1; 168-174; PMCID PMC515400