Stephen Smale

Title(s)Professor, MIMG
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    Title(s)Professor, Medicine

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    University of California, Berkeley, Berkeley, CaliforniaPh.D. 1986Biochemistry
    Cornell University, Ithaca, New YorkA.B.1981Chemistry
    Collapse Awards and Honors
    American Association for the Advancement of Science 2020Fellow
    Keystone Symposium, “Transcription and RNA Regulation in Inflammation and Immunity,” Tahoe City, CA2019Keynote Speaker
    The 28th Annual Molecular Biology Retreat, University of Colorado, Denver, Snow Mountain Ranch, CO2017Keynote Speaker
    UCLA2016Life Sciences Excellence Award in Educational Innovation

    Collapse Overview 
    Collapse Overview
    Stephen T. Smale is a molecular immunologist and biochemist who arrived at UCLA in 1990 as an Assistant Professor in the Department of Microbiology and Immunology within the UCLA School of Medicine. In 1999, he was promoted to Professor and, in 2014, to Distinguished Professor, in the Department of Microbiology, Immunology, and Molecular Genetics, which spans the UCLA College of Letters and Science and the David Geffen School of Medicine. From 1990 to 2007, he was also a Howard Hughes Medical Institute Investigator. Dr. Smale graduated Magna Cum Laude from Cornell University, with Honors and Distinction in Chemistry. He received his Ph.D. in Biochemistry from the University of California, Berkeley under the mentorship of Dr. Robert Tjian. He then was a Helen Hay Whitney Foundation postdoctoral fellow with Nobelist Dr. David Baltimore at the Whitehead Institute, MIT. At UCLA, Dr. Smale previously served as Vice Chair of the Department of Microbiology, Immunology, and Molecular Genetics, Director of Basic and Translational Research for the UCLA Jonsson Comprehensive Cancer Center, Director of the Howard Hughes Medical Institute Science Education Program, Co-Director of the UCLA-Caltech Medical Scientist Training Program, and founding Chair of the School of Medicine's Research Initiative in Immunity, Inflammation, infection, and Transplantation (I3T). He currently serves as Vice Dean for Research in the David Geffen School of Medicine. The research in Dr. Smale's laboratory focuses on gene regulation during inflammatory and innate immune responses and during lymphocyte development and leukemogenesis.

    Collapse Research 
    Collapse Research Activities and Funding
    State-of-the-art GMP facility for the development of lifesaving gene and cell therapies
    NIH C06OD030144Sep 25, 2020 - Mar 31, 2024
    Role: Principal Investigator
    FASEB Summer Research Conference on Molecular Mechanisms of Immune Cell Development and Function
    NIH R13AI118112May 1, 2015 - Apr 30, 2016
    Role: Principal Investigator
    Ribonomics of Gene Regulation to predict Innate Immune Responses
    NIH U01HG007912Jan 5, 2015 - Nov 30, 2018
    Role: Co-Investigator
    FASEB SRC on Molecular Mechanisms of Immune Cell Development and Function
    NIH R13AI106088Jun 1, 2013 - May 31, 2014
    Role: Co-Principal Investigator
    Immunobiology of Leprosy
    NIH P50AR063020Aug 16, 2012 - Jul 31, 2017
    Role: Co-Investigator
    High throughput screens for modulators of inflammatory cytakine gene expression
    NIH R21AI076921May 15, 2009 - Apr 30, 2011
    Role: Principal Investigator
    Pioneer factor interactions in embryonic stem cells
    NIH R21CA137278May 1, 2009 - Apr 30, 2011
    Role: Principal Investigator
    Selective regulation of pro-inflammatory genes in macrophages
    NIH R01GM086372Sep 30, 2008 - Jul 31, 2017
    Role: Principal Investigator
    Pro-inflammatory gene regulation in a native chromatin environment
    NIH R01CA127279Jun 1, 2008 - Apr 30, 2012
    Role: Principal Investigator
    Cytokines in Health and Disease: 15th Annual Meeting of the International Cytokin
    NIH R13AI077292Oct 24, 2007 - Oct 23, 2008
    Role: Principal Investigator
    Selective gene activation by the NF-kappaB family of transcription factors
    NIH R01AI073868Feb 1, 2007 - Jan 31, 2012
    Role: Principal Investigator
    The UCLA Center for Medical Countermeasures Against Radiation
    NIH U19AI067769Aug 31, 2005 - Jul 31, 2021
    Role: Co-Investigator
    Biological functions and mechanisms of action of Ikaros proteins
    NIH R01DK043726Aug 1, 1996 - Jul 31, 2016
    Role: Principal Investigator
    NIH R29DK043726May 1, 1991 - Jul 31, 1996
    Role: Principal Investigator
    UCLA-Caltech Medical Scientist Training Program
    NIH T32GM008042Jul 1, 1983 - Jun 30, 2024
    Role: Co-Principal Investigator

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    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Allogeneic hematopoietic stem cell transplantation: lessons learned by a molecular immunologist/transplant patient. Trends Immunol. 2022 06; 43(6):459-465. Smale ST. PMID: 35490132.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    2. Suppressing fatty acid synthase by type I interferon and chemical inhibitors as a broad spectrum anti-viral strategy against SARS-CoV-2. Acta Pharm Sin B. 2022 Apr; 12(4):1624-1635. Aliyari SR, Ghaffari AA, Pernet O, Parvatiyar K, Wang Y, Gerami H, Tong AJ, Vergnes L, Takallou A, Zhang A, Wei X, Chilin LD, Wu Y, Semenkovich CF, Reue K, Smale ST, Lee B, Cheng G. PMID: 35251918; PMCID: PMC8883762.
      View in: PubMed   Mentions: 2  
    3. TPL-2 Inhibits IFN-β Expression via an ERK1/2-TCF-FOS Axis in TLR4-Stimulated Macrophages. J Immunol. 2022 02 15; 208(4):941-954. Blair L, Pattison MJ, Chakravarty P, Papoutsopoulou S, Bakiri L, Wagner EF, Smale S, Ley SC. PMID: 35082159; PMCID: PMC9012084.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    4. Species-Specific Relationships between DNA and Chromatin Properties of CpG Islands in Embryonic Stem Cells and Differentiated Cells. Stem Cell Reports. 2021 04 13; 16(4):899-912. Langerman J, Lopez D, Pellegrini M, Smale ST. PMID: 33770494; PMCID: PMC8072027.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansAnimalsCells
    5. Interferon-mediated reprogramming of membrane cholesterol to evade bacterial toxins. Nat Immunol. 2020 07; 21(7):746-755. Zhou QD, Chi X, Lee MS, Hsieh WY, Mkrtchyan JJ, Feng AC, He C, York AG, Bui VL, Kronenberger EB, Ferrari A, Xiao X, Daly AE, Tarling EJ, Damoiseaux R, Scumpia PO, Smale ST, Williams KJ, Tontonoz P, Bensinger SJ. PMID: 32514064; PMCID: PMC7778040.
      View in: PubMed   Mentions: 20     Fields:    Translation:HumansAnimalsCells
    6. Toll-Like Receptors Induce Signal-Specific Reprogramming of the Macrophage Lipidome. Cell Metab. 2020 07 07; 32(1):128-143.e5. Hsieh WY, Zhou QD, York AG, Williams KJ, Scumpia PO, Kronenberger EB, Hoi XP, Su B, Chi X, Bui VL, Khialeeva E, Kaplan A, Son YM, Divakaruni AS, Sun J, Smale ST, Flavell RA, Bensinger SJ. PMID: 32516576; PMCID: PMC7891175.
      View in: PubMed   Mentions: 21     Fields:    Translation:AnimalsCells
    7. A Future Outlook on Molecular Mechanisms of Immunity. Trends Immunol. 2020 07; 41(7):549-555. Weinmann AS, Youngblood BA, Smale ST, Brink R, Schatz DG, McHeyzer-Williams M. PMID: 32507312.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    8. Single cell analysis reveals immune cell-adipocyte crosstalk regulating the transcription of thermogenic adipocytes. Elife. 2019 10 23; 8. Rajbhandari P, Arneson D, Hart SK, Ahn IS, Diamante G, Santos LC, Zaghari N, Feng AC, Thomas BJ, Vergnes L, Lee SD, Rajbhandari AK, Reue K, Smale ST, Yang X, Tontonoz P. PMID: 31644425; PMCID: PMC6837845.
      View in: PubMed   Mentions: 51     Fields:    Translation:AnimalsCells
    9. Dissection of acute stimulus-inducible nucleosome remodeling in mammalian cells. Genes Dev. 2019 09 01; 33(17-18):1159-1174. Comoglio F, Simonatto M, Polletti S, Liu X, Smale ST, Barozzi I, Natoli G. PMID: 31371436; PMCID: PMC6719622.
      View in: PubMed   Mentions: 13     Fields:    Translation:AnimalsCells
    10. Comparison of reprogramming factor targets reveals both species-specific and conserved mechanisms in early iPSC reprogramming. BMC Genomics. 2018 Dec 22; 19(1):956. Fu K, Chronis C, Soufi A, Bonora G, Edwards M, Smale ST, Zaret KS, Plath K, Pellegrini M. PMID: 30577748; PMCID: PMC6303873.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansAnimalsCells
    11. Transcriptional regulation of macrophage cholesterol efflux and atherogenesis by a long noncoding RNA. Nat Med. 2018 03; 24(3):304-312. Sallam T, Jones M, Thomas BJ, Wu X, Gilliland T, Qian K, Eskin A, Casero D, Zhang Z, Sandhu J, Salisbury D, Rajbhandari P, Civelek M, Hong C, Ito A, Liu X, Daniel B, Lusis AJ, Whitelegge J, Nagy L, Castrillo A, Smale S, Tontonoz P. PMID: 29431742; PMCID: PMC5839972.
      View in: PubMed   Mentions: 90     Fields:    Translation:HumansAnimalsCells
    12. IL-10 Signaling Remodels Adipose Chromatin Architecture to Limit Thermogenesis and Energy Expenditure. Cell. 2018 01 11; 172(1-2):218-233.e17. Rajbhandari P, Thomas BJ, Feng AC, Hong C, Wang J, Vergnes L, Sallam T, Wang B, Sandhu J, Seldin MM, Lusis AJ, Fong LG, Katz M, Lee R, Young SG, Reue K, Smale ST, Tontonoz P. PMID: 29249357; PMCID: PMC5766418.
      View in: PubMed   Mentions: 54     Fields:    Translation:AnimalsCells
    13. Defined Sensing Mechanisms and Signaling Pathways Contribute to the Global Inflammatory Gene Expression Output Elicited by Ionizing Radiation. Immunity. 2017 09 19; 47(3):421-434.e3. Purbey PK, Scumpia PO, Kim PJ, Tong AJ, Iwamoto KS, McBride WH, Smale ST. PMID: 28930658; PMCID: PMC5661954.
      View in: PubMed   Mentions: 20     Fields:    Translation:HumansAnimalsCells
    14. A Macrophage Response to Mycobacterium leprae Phenolic Glycolipid Initiates Nerve Damage in Leprosy. Cell. 2017 Aug 24; 170(5):973-985.e10. Madigan CA, Cambier CJ, Kelly-Scumpia KM, Scumpia PO, Cheng TY, Zailaa J, Bloom BR, Moody DB, Smale ST, Sagasti A, Modlin RL, Ramakrishnan L. PMID: 28841420; PMCID: PMC5848073.
      View in: PubMed   Mentions: 43     Fields:    Translation:AnimalsCells
    15. Opposing roles of Toll-like receptor and cytosolic DNA-STING signaling pathways for Staphylococcus aureus cutaneous host defense. PLoS Pathog. 2017 Jul; 13(7):e1006496. Scumpia PO, Botten GA, Norman JS, Kelly-Scumpia KM, Spreafico R, Ruccia AR, Purbey PK, Thomas BJ, Modlin RL, Smale ST. PMID: 28704551; PMCID: PMC5526579.
      View in: PubMed   Mentions: 28     Fields:    Translation:HumansAnimalsCells
    16. Genetic analysis of Ikaros target genes and tumor suppressor function in BCR-ABL1+ pre-B ALL. J Exp Med. 2017 03 06; 214(3):793-814. Schjerven H, Ayongaba EF, Aghajanirefah A, McLaughlin J, Cheng D, Geng H, Boyd JR, Eggesbø LM, Lindeman I, Heath JL, Park E, Witte ON, Smale ST, Frietze S, Müschen M. PMID: 28190001; PMCID: PMC5339667.
      View in: PubMed   Mentions: 13     Fields:    Translation:HumansAnimalsCells
    17. The Ly6C(lo)-Down: Targeting Developmental Enhancers for Cell Subset Depletion. Immunity. 2016 11 15; 45(5):949-951. Thomas BJ, Smale ST. PMID: 27851919.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    18. A Stringent Systems Approach Uncovers Gene-Specific Mechanisms Regulating Inflammation. Cell. 2016 Mar 24; 165(1):165-179. Tong AJ, Liu X, Thomas BJ, Lissner MM, Baker MR, Senagolage MD, Allred AL, Barish GD, Smale ST. PMID: 26924576; PMCID: PMC4808443.
      View in: PubMed   Mentions: 76     Fields:    Translation:AnimalsCells
    19. Type I and Type II Interferon Coordinately Regulate Suppressive Dendritic Cell Fate and Function during Viral Persistence. PLoS Pathog. 2016 Jan; 12(1):e1005356. Cunningham CR, Champhekar A, Tullius MV, Dillon BJ, Zhen A, de la Fuente JR, Herskovitz J, Elsaesser H, Snell LM, Wilson EB, de la Torre JC, Kitchen SG, Horwitz MA, Bensinger SJ, Smale ST, Brooks DG. PMID: 26808628; PMCID: PMC4726812.
      View in: PubMed   Mentions: 36     Fields:    Translation:AnimalsCells
    20. Class-specific regulation of pro-inflammatory genes by MyD88 pathways and IκBζ. J Biol Chem. 2015 Sep 11; 290(37):22446. Kayama H, Ramirez-Carrozzi VR, Yamamoto M, Mizutani T, Kuwata H, Iba H, Matsumoto M, Honda K, Smale ST, Takeda K. PMID: 26362542; PMCID: PMC4566219.
      View in: PubMed   Mentions: 2     Fields:    
    21. Regulation of gene expression dynamics during developmental transitions by the Ikaros transcription factor. Genes Dev. 2015 Sep 01; 29(17):1801-16. Arenzana TL, Schjerven H, Smale ST. PMID: 26314708; PMCID: PMC4573854.
      View in: PubMed   Mentions: 16     Fields:    Translation:AnimalsCells
    22. Age-Related Gene Expression Differences in Monocytes from Human Neonates, Young Adults, and Older Adults. PLoS One. 2015; 10(7):e0132061. Lissner MM, Thomas BJ, Wee K, Tong AJ, Kollmann TR, Smale ST. PMID: 26147648; PMCID: PMC4493075.
      View in: PubMed   Mentions: 21     Fields:    Translation:HumansCells
    23. Divergence of transcriptional landscape occurs early in B cell activation. Epigenetics Chromatin. 2015; 8:20. Fowler T, Garruss AS, Ghosh A, De S, Becker KG, Wood WH, Weirauch MT, Smale ST, Aronow B, Sen R, Roy AL. PMID: 25987903; PMCID: PMC4434543.
      View in: PubMed   Mentions: 15     Fields:    
    24. Class-specific regulation of pro-inflammatory genes by MyD88 pathways and IκBζ. J Biol Chem. 2015 Feb 20; 290(8):4815. Kayama H, Ramirez-Carrozzi VR, Yamamoto M, Mizutani T, Kuwata H, Iba H, Matsumoto M, Honda K, Smale ST, Takeda K. PMID: 25713407; PMCID: PMC4335220.
      View in: PubMed   Mentions: 1     Fields:    
    25. Transcriptional control of inflammatory responses. Cold Spring Harb Perspect Biol. 2014 Sep 11; 6(11):a016261. Smale ST, Natoli G. PMID: 25213094; PMCID: PMC4413233.
      View in: PubMed   Mentions: 54     Fields:    Translation:Cells
    26. Restriction of IL-22-producing T cell responses and differential regulation of regulatory T cell compartments by zinc finger transcription factor Ikaros. J Immunol. 2014 Oct 15; 193(8):3934-46. Heller JJ, Schjerven H, Li S, Lee A, Qiu J, Chen ZM, Smale ST, Zhou L. PMID: 25194055; PMCID: PMC4185244.
      View in: PubMed   Mentions: 10     Fields:    Translation:AnimalsCells
    27. Toward an understanding of the gene-specific and global logic of inducible gene transcription. Cold Spring Harb Symp Quant Biol. 2013; 78:61-8. Smale ST, Plevy SE, Weinmann AS, Zhou L, Ramirez-Carrozzi VR, Pope SD, Bhatt DM, Tong AJ. PMID: 24747344.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansAnimalsCells
    28. Transcriptional regulation in the immune system: a status report. Trends Immunol. 2014 May; 35(5):190-4. Smale ST. PMID: 24703179; PMCID: PMC4041609.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansCells
    29. Pten null prostate epithelium promotes localized myeloid-derived suppressor cell expansion and immune suppression during tumor initiation and progression. Mol Cell Biol. 2014 Jun; 34(11):2017-28. Garcia AJ, Ruscetti M, Arenzana TL, Tran LM, Bianci-Frias D, Sybert E, Priceman SJ, Wu L, Nelson PS, Smale ST, Wu H. PMID: 24662052; PMCID: PMC4019050.
      View in: PubMed   Mentions: 55     Fields:    Translation:AnimalsCells
    30. MHC binding prediction with KernelRLSpan and its variations. J Immunol Methods. 2014 Apr; 406:10-20. Shen WJ, Wei YT, Guo X, Smale S, Wong HS, Li SC. PMID: 24603003.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansAnimalsCells
    31. Chromatin contributions to the regulation of innate immunity. Annu Rev Immunol. 2014; 32:489-511. Smale ST, Tarakhovsky A, Natoli G. PMID: 24555473.
      View in: PubMed   Mentions: 73     Fields:    Translation:HumansAnimalsCells
    32. Selective regulation of lymphopoiesis and leukemogenesis by individual zinc fingers of Ikaros. Nat Immunol. 2013 Oct; 14(10):1073-83. Schjerven H, McLaughlin J, Arenzana TL, Frietze S, Cheng D, Wadsworth SE, Lawson GW, Bensinger SJ, Farnham PJ, Witte ON, Smale ST. PMID: 24013668; PMCID: PMC3800053.
      View in: PubMed   Mentions: 57     Fields:    Translation:AnimalsCells
    33. PCR-mediated site-directed mutagenesis. Cold Spring Harb Protoc. 2013 Aug 01; 2013(8):738-42. Carey MF, Peterson CL, Smale ST. PMID: 23906918.
      View in: PubMed   Mentions: 18     Fields:    Translation:Cells
    34. Electrophoretic mobility-shift assays. Cold Spring Harb Protoc. 2013 Jul 01; 2013(7):636-9. Carey MF, Peterson CL, Smale ST. PMID: 23818676.
      View in: PubMed   Mentions: 6     Fields:    Translation:Cells
    35. DNase I footprinting. Cold Spring Harb Protoc. 2013 May 01; 2013(5):469-78. Carey MF, Peterson CL, Smale ST. PMID: 23637368.
      View in: PubMed   Mentions: 7     Fields:    Translation:Cells
    36. Preparation of (32)P-end-labeled DNA fragments for performing DNA-binding experiments. Cold Spring Harb Protoc. 2013 May 01; 2013(5):464-8. Carey MF, Peterson CL, Smale ST. PMID: 23637369.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    37. Splicing kinetics and transcript release from the chromatin compartment limit the rate of Lipid A-induced gene expression. RNA. 2013 Jun; 19(6):811-27. Pandya-Jones A, Bhatt DM, Lin CH, Tong AJ, Smale ST, Black DL. PMID: 23616639; PMCID: PMC3683915.
      View in: PubMed   Mentions: 56     Fields:    Translation:AnimalsCells
    38. The RNase protection assay. Cold Spring Harb Protoc. 2013 Mar 01; 2013(3). Carey MF, Peterson CL, Smale ST. PMID: 23457339.
      View in: PubMed   Mentions: 8     Fields:    Translation:Cells
    39. The primer extension assay. Cold Spring Harb Protoc. 2013 Feb 01; 2013(2):164-73. Carey MF, Peterson CL, Smale ST. PMID: 23378648.
      View in: PubMed   Mentions: 12     Fields:    Translation:Cells
    40. Genome-wide identification of Ikaros targets elucidates its contribution to mouse B-cell lineage specification and pre-B-cell differentiation. Blood. 2013 Mar 07; 121(10):1769-82. Ferreirós-Vidal I, Carroll T, Taylor B, Terry A, Liang Z, Bruno L, Dharmalingam G, Khadayate S, Cobb BS, Smale ST, Spivakov M, Srivastava P, Petretto E, Fisher AG, Merkenschlager M. PMID: 23303821.
      View in: PubMed   Mentions: 62     Fields:    Translation:AnimalsCells
    41. Designing an enhancer landscape. Cell. 2012 Nov 21; 151(5):929-31. Xu J, Smale ST. PMID: 23178114; PMCID: PMC3732118.
      View in: PubMed   Mentions: 8     Fields:    
    42. Regulation of cooperative function of the Il12b enhancer and promoter by the interferon regulatory factors 3 and 5. Biochem Biophys Res Commun. 2013 Jan 04; 430(1):95-100. Koshiba R, Yanai H, Matsuda A, Goto A, Nakajima A, Negishi H, Nishio J, Smale ST, Taniguchi T. PMID: 23154183.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansCells
    43. Restraint of inflammatory signaling by interdependent strata of negative regulatory pathways. Nat Immunol. 2012 Oct; 13(10):916-24. Murray PJ, Smale ST. PMID: 22990889; PMCID: PMC4893774.
      View in: PubMed   Mentions: 85     Fields:    Translation:HumansAnimalsCells
    44. Transcript dynamics of proinflammatory genes revealed by sequence analysis of subcellular RNA fractions. Cell. 2012 Jul 20; 150(2):279-90. Bhatt DM, Pandya-Jones A, Tong AJ, Barozzi I, Lissner MM, Natoli G, Black DL, Smale ST. PMID: 22817891; PMCID: PMC3405548.
      View in: PubMed   Mentions: 242     Fields:    Translation:AnimalsCells
    45. Confirming the functional importance of a protein-DNA interaction. Cold Spring Harb Protoc. 2012 Jul 01; 2012(7):733-57. Carey MF, Peterson CL, Smale ST. PMID: 22753608.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
    46. Cross-interference of RLR and TLR signaling pathways modulates antibacterial T cell responses. Nat Immunol. 2012 May 20; 13(7):659-66. Negishi H, Yanai H, Nakajima A, Koshiba R, Atarashi K, Matsuda A, Matsuki K, Miki S, Doi T, Aderem A, Nishio J, Smale ST, Honda K, Taniguchi T. PMID: 22610141.
      View in: PubMed   Mentions: 69     Fields:    Translation:AnimalsCells
    47. Dimer-specific regulatory mechanisms within the NF-κB family of transcription factors. Immunol Rev. 2012 Mar; 246(1):193-204. Smale ST. PMID: 22435556.
      View in: PubMed   Mentions: 83     Fields:    Translation:HumansAnimalsCells
    48. Identifying cis-acting DNA elements within a control region. Cold Spring Harb Protoc. 2012 Mar 01; 2012(3):279-96. Carey MF, Peterson CL, Smale ST. PMID: 22383646.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    49. Experimental strategies for cloning or identifying genes encoding DNA-binding proteins. Cold Spring Harb Protoc. 2012 Feb 01; 2012(2):183-92. Carey MF, Peterson CL, Smale ST. PMID: 22301659.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    50. Transcriptional regulation in the innate immune system. Curr Opin Immunol. 2012 Feb; 24(1):51-7. Smale ST. PMID: 22230561; PMCID: PMC3288296.
      View in: PubMed   Mentions: 46     Fields:    Translation:HumansAnimalsCells
    51. Experimental strategies for the identification of DNA-binding proteins. Cold Spring Harb Protoc. 2012 Jan 01; 2012(1):18-33. Carey MF, Peterson CL, Smale ST. PMID: 22194258.
      View in: PubMed   Mentions: 13     Fields:    Translation:Cells
    52. Principles of dimer-specific gene regulation revealed by a comprehensive characterization of NF-κB family DNA binding. Nat Immunol. 2011 Nov 20; 13(1):95-102. Siggers T, Chang AB, Teixeira A, Wong D, Williams KJ, Ahmed B, Ragoussis J, Udalova IA, Smale ST, Bulyk ML. PMID: 22101729; PMCID: PMC3242931.
      View in: PubMed   Mentions: 110     Fields:    Translation:HumansAnimalsCells
    53. Hierarchies of NF-κB target-gene regulation. Nat Immunol. 2011 Jul 19; 12(8):689-94. Smale ST. PMID: 21772277; PMCID: PMC3169328.
      View in: PubMed   Mentions: 124     Fields:    Translation:HumansAnimalsCells
    54. A distal enhancer in Il12b is the target of transcriptional repression by the STAT3 pathway and requires the basic leucine zipper (B-ZIP) protein NFIL3. J Biol Chem. 2011 Jul 01; 286(26):23582-90. Smith AM, Qualls JE, O'Brien K, Balouzian L, Johnson PF, Schultz-Cherry S, Smale ST, Murray PJ. PMID: 21566115; PMCID: PMC3123121.
      View in: PubMed   Mentions: 35     Fields:    Translation:AnimalsCells
    55. NFIL3 is a regulator of IL-12 p40 in macrophages and mucosal immunity. J Immunol. 2011 Apr 15; 186(8):4649-55. Kobayashi T, Matsuoka K, Sheikh SZ, Elloumi HZ, Kamada N, Hisamatsu T, Hansen JJ, Doty KR, Pope SD, Smale ST, Hibi T, Rothman PB, Kashiwada M, Plevy SE. PMID: 21383239; PMCID: PMC3172700.
      View in: PubMed   Mentions: 48     Fields:    Translation:HumansAnimalsCells
    56. Magnesium-agarose electrophoretic mobility shift assay (EMSA) of transcription factor IID binding to DNA. Cold Spring Harb Protoc. 2010 Nov 01; 2010(11):pdb.prot5514. Carey MF, Peterson CL, Smale ST. PMID: 21041387.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    57. Immune inhibitory ligand CD200 induction by TLRs and NLRs limits macrophage activation to protect the host from meningococcal septicemia. Cell Host Microbe. 2010 Sep 16; 8(3):236-47. Mukhopadhyay S, Plüddemann A, Hoe JC, Williams KJ, Varin A, Makepeace K, Aknin ML, Bowdish DM, Smale ST, Barclay AN, Gordon S. PMID: 20833375.
      View in: PubMed   Mentions: 38     Fields:    Translation:HumansAnimalsCells
    58. Protein complex binding to promoter DNA: immobilized template assay. Cold Spring Harb Protoc. 2010 Aug 01; 2010(8):pdb.prot5465. Carey MF, Peterson CL, Smale ST. PMID: 20679374.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    59. Potassium permanganate probing of Pol II open complexes. Cold Spring Harb Protoc. 2010 Aug 01; 2010(8):pdb.prot5479. Carey MF, Peterson CL, Smale ST. PMID: 20679388.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    60. Pioneer factors in embryonic stem cells and differentiation. Curr Opin Genet Dev. 2010 Oct; 20(5):519-26. Smale ST. PMID: 20638836; PMCID: PMC2943026.
      View in: PubMed   Mentions: 41     Fields:    Translation:AnimalsCells
    61. Purification of epitope-tagged transcription factor IID. Cold Spring Harb Protoc. 2010 Jul 01; 2010(7):pdb.prot5450. Carey MF, Peterson CL, Smale ST. PMID: 20647354.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    62. Purification of mediator from HeLa cell lines expressing a flag-tagged mediator subunit. Cold Spring Harb Protoc. 2010 Jul 01; 2010(7):pdb.prot5451. Carey MF, Peterson CL, Smale ST. PMID: 20647355.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    63. Luciferase assay. Cold Spring Harb Protoc. 2010 May; 2010(5):pdb.prot5421. Smale ST. PMID: 20439408.
      View in: PubMed   Mentions: 20     Fields:    Translation:AnimalsCells
    64. Chloramphenicol acetyltransferase assay. Cold Spring Harb Protoc. 2010 May; 2010(5):pdb.prot5422. Smale ST. PMID: 20439409.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    65. Beta-galactosidase assay. Cold Spring Harb Protoc. 2010 May; 2010(5):pdb.prot5423. Smale ST. PMID: 20439410.
      View in: PubMed   Mentions: 27     Fields:    Translation:Cells
    66. Seq-ing LPS-induced enhancers. Immunity. 2010 Mar 26; 32(3):296-8. Smale ST. PMID: 20346768.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansAnimalsCells
    67. Selective transcription in response to an inflammatory stimulus. Cell. 2010 Mar 19; 140(6):833-44. Smale ST. PMID: 20303874; PMCID: PMC2847629.
      View in: PubMed   Mentions: 153     Fields:    Translation:HumansAnimalsCells
    68. G-less cassette in vitro transcription using HeLa cell nuclear extracts. Cold Spring Harb Protoc. 2010 Mar; 2010(3):pdb.prot5387. Carey MF, Peterson CL, Smale ST. PMID: 20194456.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    69. Calcium phosphate transfection of 3T3 fibroblasts. Cold Spring Harb Protoc. 2010 Feb; 2010(2):pdb.prot5372. Smale ST. PMID: 20150135.
      View in: PubMed   Mentions: 3     Fields:    Translation:AnimalsCells
    70. DEAE-dextran transfection of lymphocyte cell lines. Cold Spring Harb Protoc. 2010 Feb; 2010(2):pdb.prot5373. Smale ST. PMID: 20150136.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansAnimalsCells
    71. Transfection by electroporation of RAW 264.7 macrophages. Cold Spring Harb Protoc. 2010 Feb; 2010(2):pdb.prot5374. Smale ST. PMID: 20150137.
      View in: PubMed   Mentions: 2     Fields:    Translation:AnimalsCells
    72. Transcriptional competence and the active marking of tissue-specific enhancers by defined transcription factors in embryonic and induced pluripotent stem cells. Genes Dev. 2009 Dec 15; 23(24):2824-38. Xu J, Watts JA, Pope SD, Gadue P, Kamps M, Plath K, Zaret KS, Smale ST. PMID: 20008934; PMCID: PMC2800090.
      View in: PubMed   Mentions: 100     Fields:    Translation:AnimalsCells
    73. Dignam and Roeder nuclear extract preparation. Cold Spring Harb Protoc. 2009 Dec; 2009(12):pdb.prot5330. Carey MF, Peterson CL, Smale ST. PMID: 20150077.
      View in: PubMed   Mentions: 26     Fields:    Translation:HumansCells
    74. In vitro transcription using HeLa cell extracts and primer extension. Cold Spring Harb Protoc. 2009 Dec; 2009(12):pdb.prot5331. Carey MF, Peterson CL, Smale ST. PMID: 20150078.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    75. Self-renewal of the long-term reconstituting subset of hematopoietic stem cells is regulated by Ikaros. Stem Cells. 2009 Dec; 27(12):3082-92. Papathanasiou P, Attema JL, Karsunky H, Hosen N, Sontani Y, Hoyne GF, Tunningley R, Smale ST, Weissman IL. PMID: 19816952; PMCID: PMC3401049.
      View in: PubMed   Mentions: 20     Fields:    Translation:AnimalsCells
    76. Nuclear run-on assay. Cold Spring Harb Protoc. 2009 Nov; 2009(11):pdb.prot5329. Smale ST. PMID: 20150068.
      View in: PubMed   Mentions: 22     Fields:    Translation:Cells
    77. Selectivity of the NF-{kappa}B response. Cold Spring Harb Perspect Biol. 2010 Apr; 2(4):a000257. Sen R, Smale ST. PMID: 20452937; PMCID: PMC2845200.
      View in: PubMed   Mentions: 66     Fields:    Translation:Animals
    78. Evaluation of the long-term reconstituting subset of hematopoietic stem cells with CD150. Stem Cells. 2009 Oct; 27(10):2498-508. Papathanasiou P, Attema JL, Karsunky H, Xu J, Smale ST, Weissman IL. PMID: 19593793; PMCID: PMC2783507.
      View in: PubMed   Mentions: 21     Fields:    Translation:AnimalsCells
    79. In vivo dimethyl sulfate (DMS) footprinting via ligation-mediated polymerase chain reaction (LM-PCR). Cold Spring Harb Protoc. 2009 Sep; 2009(9):pdb.prot5278. Carey MF, Peterson CL, Smale ST. PMID: 20147263.
      View in: PubMed   Mentions: 1     Fields:    Translation:Animals
    80. Chromatin immunoprecipitation (ChIP). Cold Spring Harb Protoc. 2009 Sep; 2009(9):pdb.prot5279. Carey MF, Peterson CL, Smale ST. PMID: 20147264.
      View in: PubMed   Mentions: 110     Fields:    Translation:AnimalsCells
    81. In vivo DNase I, MNase, and restriction enzyme footprinting via ligation-mediated polymerase chain reaction (LM-PCR). Cold Spring Harb Protoc. 2009 Sep; 2009(9):pdb.prot5277. Carey MF, Peterson CL, Smale ST. PMID: 20147262.
      View in: PubMed   Mentions: 5     Fields:    Translation:AnimalsCells
    82. A unifying model for the selective regulation of inducible transcription by CpG islands and nucleosome remodeling. Cell. 2009 Jul 10; 138(1):114-28. Ramirez-Carrozzi VR, Braas D, Bhatt DM, Cheng CS, Hong C, Doty KR, Black JC, Hoffmann A, Carey M, Smale ST. PMID: 19596239; PMCID: PMC2712736.
      View in: PubMed   Mentions: 303     Fields:    Translation:HumansAnimalsCells
    83. Regulation of B cell fate commitment and immunoglobulin heavy-chain gene rearrangements by Ikaros. Nat Immunol. 2008 Aug; 9(8):927-36. Reynaud D, Demarco IA, Reddy KL, Schjerven H, Bertolino E, Chen Z, Smale ST, Winandy S, Singh H. PMID: 18568028; PMCID: PMC2699484.
      View in: PubMed   Mentions: 134     Fields:    Translation:AnimalsCells
    84. Class-specific regulation of pro-inflammatory genes by MyD88 pathways and IkappaBzeta. J Biol Chem. 2008 May 02; 283(18):12468-77. Kayama H, Ramirez-Carrozzi VR, Yamamoto M, Mizutani T, Kuwata H, Iba H, Matsumoto M, Honda K, Smale ST, Takeda K. PMID: 18319258.
      View in: PubMed   Mentions: 41     Fields:    Translation:AnimalsCells
    85. Hydroxyl-radical footprinting. CSH Protoc. 2007 Dec 01; 2007:pdb.prot4810. Carey M, Smale ST. PMID: 21356993.
      View in: PubMed   Mentions: 2  
    86. Phosphate ethylation interference assay. CSH Protoc. 2007 Dec 01; 2007:pdb.prot4811. Carey M, Smale ST. PMID: 21356994.
      View in: PubMed   Mentions:
    87. Methylation interference assay. CSH Protoc. 2007 Dec 01; 2007:pdb.prot4812. Carey M, Smale ST. PMID: 21356995.
      View in: PubMed   Mentions:
    88. Micrococcal Nuclease-Southern Blot Assay: I. MNase and Restriction Digestions. CSH Protoc. 2007 Nov 01; 2007:pdb.prot4890. Carey M, Smale ST. PMID: 21356981.
      View in: PubMed   Mentions: 11  
    89. Micrococcal Nuclease-Southern Blot Assay: II. Capillary Transfer and Hybridization. CSH Protoc. 2007 Nov 01; 2007:pdb.prot4891. Carey M, Smale ST. PMID: 21356982.
      View in: PubMed   Mentions:
    90. Predominant interaction of both Ikaros and Helios with the NuRD complex in immature thymocytes. J Biol Chem. 2007 Oct 12; 282(41):30227-38. Sridharan R, Smale ST. PMID: 17681952.
      View in: PubMed   Mentions: 75     Fields:    Translation:HumansAnimalsCells
    91. Pioneer factor interactions and unmethylated CpG dinucleotides mark silent tissue-specific enhancers in embryonic stem cells. Proc Natl Acad Sci U S A. 2007 Jul 24; 104(30):12377-82. Xu J, Pope SD, Jazirehi AR, Attema JL, Papathanasiou P, Watts JA, Zaret KS, Weissman IL, Smale ST. PMID: 17640912; PMCID: PMC1941477.
      View in: PubMed   Mentions: 64     Fields:    Translation:HumansAnimalsCells
    92. Epigenetic characterization of hematopoietic stem cell differentiation using miniChIP and bisulfite sequencing analysis. Proc Natl Acad Sci U S A. 2007 Jul 24; 104(30):12371-6. Attema JL, Papathanasiou P, Forsberg EC, Xu J, Smale ST, Weissman IL. PMID: 17640913; PMCID: PMC1924790.
      View in: PubMed   Mentions: 65     Fields:    Translation:Cells
    93. Ikaros DNA-binding proteins as integral components of B cell developmental-stage-specific regulatory circuits. Immunity. 2007 Mar; 26(3):335-44. Thompson EC, Cobb BS, Sabbattini P, Meixlsperger S, Parelho V, Liberg D, Taylor B, Dillon N, Georgopoulos K, Jumaa H, Smale ST, Fisher AG, Merkenschlager M. PMID: 17363301.
      View in: PubMed   Mentions: 83     Fields:    Translation:AnimalsCells
    94. An inducible enhancer required for Il12b promoter activity in an insulated chromatin environment. Mol Cell Biol. 2007 Apr; 27(7):2698-712. Zhou L, Nazarian AA, Xu J, Tantin D, Corcoran LM, Smale ST. PMID: 17242186; PMCID: PMC1899891.
      View in: PubMed   Mentions: 29     Fields:    Translation:AnimalsCells
    95. A role for Dicer in immune regulation. J Exp Med. 2006 Oct 30; 203(11):2519-27. Cobb BS, Hertweck A, Smith J, O'Connor E, Graf D, Cook T, Smale ST, Sakaguchi S, Livesey FJ, Fisher AG, Merkenschlager M. PMID: 17060477; PMCID: PMC2118134.
      View in: PubMed   Mentions: 272     Fields:    Translation:AnimalsCells
    96. Pursuing gene regulation 'logic' via RNA interference and chromatin immunoprecipitation. Nat Immunol. 2006 Jul; 7(7):692-7. Li CC, Ramirez-Carrozzi VR, Smale ST. PMID: 16785883.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansAnimalsCells
    97. Hematopoiesis flies high with Ikaros. Nat Immunol. 2006 Apr; 7(4):367-9. Smale ST, Dorshkind K. PMID: 16550201.
      View in: PubMed   Mentions: 2     Fields:    Translation:AnimalsCells
    98. Selective and antagonistic functions of SWI/SNF and Mi-2beta nucleosome remodeling complexes during an inflammatory response. Genes Dev. 2006 Feb 01; 20(3):282-96. Ramirez-Carrozzi VR, Nazarian AA, Li CC, Gore SL, Sridharan R, Imbalzano AN, Smale ST. PMID: 16452502; PMCID: PMC1361700.
      View in: PubMed   Mentions: 212     Fields:    Translation:AnimalsCells
    99. A c-Rel subdomain responsible for enhanced DNA-binding affinity and selective gene activation. Genes Dev. 2005 Sep 15; 19(18):2138-51. Sanjabi S, Williams KJ, Saccani S, Zhou L, Hoffmann A, Ghosh G, Gerondakis S, Natoli G, Smale ST. PMID: 16166378; PMCID: PMC1221885.
      View in: PubMed   Mentions: 61     Fields:    Translation:AnimalsCells
    100. Transgenic expression of Helios in B lineage cells alters B cell properties and promotes lymphomagenesis. J Immunol. 2005 Sep 15; 175(6):3508-15. Dovat S, Montecino-Rodriguez E, Schuman V, Teitell MA, Dorshkind K, Smale ST. PMID: 16148093.
      View in: PubMed   Mentions: 16     Fields:    Translation:AnimalsCells
    101. T cell lineage choice and differentiation in the absence of the RNase III enzyme Dicer. J Exp Med. 2005 May 02; 201(9):1367-73. Cobb BS, Nesterova TB, Thompson E, Hertweck A, O'Connor E, Godwin J, Wilson CB, Brockdorff N, Fisher AG, Smale ST, Merkenschlager M. PMID: 15867090; PMCID: PMC2213187.
      View in: PubMed   Mentions: 250     Fields:    Translation:AnimalsCells
    102. Assembly of silent chromatin during thymocyte development. Semin Immunol. 2005 Apr; 17(2):129-40. Su RC, Sridharan R, Smale ST. PMID: 15737574.
      View in: PubMed   Mentions: 13     Fields:    Translation:AnimalsCells
    103. Dynamic assembly of silent chromatin during thymocyte maturation. Nat Genet. 2004 May; 36(5):502-6. Su RC, Brown KE, Saaber S, Fisher AG, Merkenschlager M, Smale ST. PMID: 15098035.
      View in: PubMed   Mentions: 59     Fields:    Translation:AnimalsCells
    104. Interleukin-10 inhibits interleukin-12 p40 gene transcription by targeting a late event in the activation pathway. Mol Cell Biol. 2004 Mar; 24(6):2385-96. Zhou L, Nazarian AA, Smale ST. PMID: 14993278; PMCID: PMC355839.
      View in: PubMed   Mentions: 42     Fields:    Translation:AnimalsCells
    105. Ikaros family members from the agnathan Myxine glutinosa and the urochordate Oikopleura dioica: emergence of an essential transcription factor for adaptive immunity. J Immunol. 2003 Dec 01; 171(11):6006-13. Cupit PM, Hansen JD, McCarty AS, White G, Chioda M, Spada F, Smale ST, Cunningham C. PMID: 14634112.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansAnimalsCells
    106. Upstream of Ikaros. Trends Immunol. 2003 Nov; 24(11):567-70. Liberg D, Smale ST, Merkenschlager M. PMID: 14596876.
      View in: PubMed   Mentions: 12     Fields:    Translation:AnimalsCells
    107. C/EBPbeta regulation in lipopolysaccharide-stimulated macrophages. Mol Cell Biol. 2003 Jul; 23(14):4841-58. Bradley MN, Zhou L, Smale ST. PMID: 12832471; PMCID: PMC162211.
      View in: PubMed   Mentions: 54     Fields:    Translation:HumansAnimalsCells
    108. The establishment and maintenance of lymphocyte identity through gene silencing. Nat Immunol. 2003 Jul; 4(7):607-15. Smale ST. PMID: 12830135.
      View in: PubMed   Mentions: 23     Fields:    Translation:HumansAnimalsCells
    109. Widespread failure of hematolymphoid differentiation caused by a recessive niche-filling allele of the Ikaros transcription factor. Immunity. 2003 Jul; 19(1):131-44. Papathanasiou P, Perkins AC, Cobb BS, Ferrini R, Sridharan R, Hoyne GF, Nelms KA, Smale ST, Goodnow CC. PMID: 12871645.
      View in: PubMed   Mentions: 52     Fields:    Translation:AnimalsCells
    110. A Th2 cytokine LCR. Adding a new piece to the regulatory puzzle. Immunity. 2003 Jul; 19(1):1-2. Smale ST. PMID: 12871632.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    111. Common interaction surfaces of the toll-like receptor 4 cytoplasmic domain stimulate multiple nuclear targets. Mol Cell Biol. 2003 Apr; 23(7):2543-55. Ronni T, Agarwal V, Haykinson M, Haberland ME, Cheng G, Smale ST. PMID: 12640135; PMCID: PMC150739.
      View in: PubMed   Mentions: 26     Fields:    Translation:HumansAnimalsCells
    112. The RNA polymerase II core promoter. Annu Rev Biochem. 2003; 72:449-79. Smale ST, Kadonaga JT. PMID: 12651739.
      View in: PubMed   Mentions: 428     Fields:    Translation:HumansAnimalsCells
    113. Selective dimerization of a C2H2 zinc finger subfamily. Mol Cell. 2003 Feb; 11(2):459-70. McCarty AS, Kleiger G, Eisenberg D, Smale ST. PMID: 12620233.
      View in: PubMed   Mentions: 42     Fields:    Translation:HumansAnimalsCells
    114. A common mechanism for mitotic inactivation of C2H2 zinc finger DNA-binding domains. Genes Dev. 2002 Dec 01; 16(23):2985-90. Dovat S, Ronni T, Russell D, Ferrini R, Cobb BS, Smale ST. PMID: 12464629; PMCID: PMC187490.
      View in: PubMed   Mentions: 57     Fields:    Translation:AnimalsCells
    115. Chromatin structure and gene regulation in the immune system. Annu Rev Immunol. 2002; 20:427-62. Smale ST, Fisher AG. PMID: 11861609.
      View in: PubMed   Mentions: 48     Fields:    Translation:HumansAnimalsCells
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