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  1. 1.   Deletion of a single CTCF motif at the boundary of a chromatin domain with three FGF genes disrupts gene expression and embryonic development
  2. Chakraborty, Shreeta; Wenzlitschke, Nina; Anderson,Matthew; Eraso, Ariel; Baudic, Manon; Thompson, Joyce J; Evans, Alicia A; Shatford-Adams, Lilly M; Chari,Raj; Awasthi,Roackie; Dale, Ryan K; Lewandoski,Mark; Petros, Timothy J; Rocha, Pedro P
  3. Developmental Cell. 2025, Feb 24;
  1. 2.   African ancestry-derived APOL1 risk genotypes show proximal epigenetic associations
  2. Breeze, Charles E; Lin, Bridget M; Winkler,Cheryl; Franceschini, Nora
  3. BMC Genomics. 2024, May 08; 25(1): 452.
  1. 3.   Crystal Structure of an i-Motif from the HRAS Oncogene Promoter
  2. Li, Kevin S; Jordan, Deondre; Lin, Linda Y; McCarthy, Sawyer E; Schneekloth,Jay; Yatsunyk, Liliya A
  3. Angewandte Chemie (International ed. in English). 2023, Mar 30; e202301666.
  1. 4.   Matrin3 regulates mitotic spindle dynamics by controlling alternative splicing of CDC14B
  2. Muys, Bruna R; Shrestha, Roshan L; Anastasakis, Dimitrios G; Pongor, Lorinc; Li, Xiao Ling; Grammatikakis, Ioannis; Polash, Ahsan; Chari,Raj; Gorospe, Myriam; Harris, Curtis C; Aladjem, Mirit I; Basrai, Munira A; Hafner, Markus; Lal, Ashish
  3. Cell Reports. 2023, Mar 15; 42(3): 112260.
  1. 5.   hRpn13 shapes the proteome and transcriptome through epigenetic factors HDAC8, PADI4, and transcription factor NF-kB p50
  2. Osei Amponsa,Vasty; Chandravanshi,Monika; Lu,Xiuxiu; Magidson,Valentin; Das,Sudipto; Andresson,Thorkell; Dyba,Marzena; Sabbasani, Venkata R; Swenson, Rolf E; Fromont, Caroline; Shrestha,Biraj; Zhao,Yongmei; Clapp,Michelle; Chari,Raj; Walters,Kylie
  3. Molecular Cell. 2023, Feb 1; 84(3): 522-537.
  1. 6.   Systematic exploration of dynamic splicing networks reveals conserved multistage regulators of neurogenesis
  2. Han, Hong; Best, Andrew J; Braunschweig, Ulrich; Mikolajewicz, Nicholas; Li, Jack Daiyang; Roth, Jonathan; Chowdhury, Fuad; Mantica, Federica; Nabeel-Shah, Syed; Parada, Guillermo; Brown, Kevin R; O'Hanlon, Dave; Wei, Jiarun; Yao, Yuxi; Zid, Abdelrahman Abou; Comsa, Lim Caden; Jen, Mark; Wang, Jenny; Datti, Alessandro; Gonatopoulos Pournatzis,Thomas; Weatheritt, Robert J; Greenblatt, Jack F; Wrana, Jeffrey L; Irimia, Manuel; Gingras, Anne-Claude; Moffat, Jason; Blencowe, Benjamin J
  3. Molecular Cell. 2022, Jul 31; 82(16): 2982-2999.
  1. 7.   Transcriptome-Wide Effects of NusA on RNA Polymerase Pausing in Bacillus subtilis
  2. Jayasinghe, Oshadhi T; Mandell, Zachary F; Yakhnin,Alex; Kashlev,Mikhail; Babitzke, Paul
  3. Journal of Bacteriology. 2022, Mar 08; e0053421.
  1. 8.   Tying the knot in the tetrahydrofolate (THF) riboswitch: A molecular basis for gene regulation
  2. Wilt,Haley; Yu,Ping; Tan, Kemin; Wang, Yun-Xing; Stagno,Jason
  3. Journal of Structural Biology. 2021, Mar; 213(1):
  1. 9.   NusG-dependent RNA polymerase pausing is a frequent function of this universally conserved transcription elongation factor
  2. Yakhnin, Alexander V; Kashlev,Mikhail; Babitzke, Paul
  3. Critical reviews in biochemistry and molecular biology. 2020, Oct 02; 1-13.
  1. 10.   Improved Retinal Organoid Differentiation by Modulating Signaling Pathways Revealed by Comparative Transcriptome Analyses with Development In Vivo
  2. Brooks, Matthew J; Chen, Holly Y; Kelley, Ryan A; Mondal, Anupam K; Nagashima,Kunio; De Val Alda,Natalia; Li, Tiansen; Chaitankar, Vijender; Swaroop, Anand
  3. Stem cell reports. 2019, Nov 12; 13(5): 891-905.
  1. 11.   POGZ Is Required for Silencing Mouse Embryonic ß-like Hemoglobin and Human Fetal Hemoglobin Expression
  2. Gudmundsdottir, Bjorg; Gudmundsson, Kristbjorn O; Klarmann, Kimberly; Singh, Satyendra K; Sun, Lei; Singh, Shweta; Du, Yang; Coppola, Vincenzo; Stockwin, Luke; Nguyen, Nhu; Tessarollo, Lino; Thorsteinsson, Leifur; Sigurjonsson, Olafur E; Gudmundsson, Sveinn; Rafnar, Thorunn; Tisdale, John F; Keller, Jonathan
  3. Cell Reports. 2018, Jun 12; 23(11): 3236-3248.
  1. 12.   Short- and long-term changes in gene expression mediated by the activation of TLR9
  2. Klaschik, S.; Tross, D.; Shirota, H.; Klinman, D. M.
  3. Molecular Immunology. 2010, Mar; 47(6): 1317-1324.
  1. 13.   Global changes in gene expression and synergistic interactions induced by TLR9 and TLR3
  2. Tross, D.; Petrenko, L.; Klaschik, S.; Zhu, Q.; Klinman, D. M.
  3. Molecular Immunology. 2009 46(13): 2557-2564.
  1. 14.   Differential roles of C/EBP beta regulatory domains in specifviuy MCP-1 and IL-6 transcription
  2. Spooner, C. J.; Guo, X. R.; Johnson, P. F.; Schwartz, R. C.
  3. Molecular Immunology. 2007, Feb; 44(6): 1384-1392.
  1. 15.   C/EBP beta serine 64, a phosphoacceptor site, has a critical role in LPS-induced IL-6 and MCP-1 transcription
  2. Spooner, C. J.; Sebastian, T.; Shuman, J. D.; Durairaj, S.; Guo, X. R.; Johnson, P. F.; Schwartz, R. C.
  3. Cytokine. 2007, Feb; 37(2): 119-127.
  1. 16.   Coupling the distribution of RNA polymerase to global gene regulation and the dynamic structure of the bacterial nucleoid in Escherichia coli
  2. Jin, D. J.; Cabrera, J. E.
  3. Journal of Structural Biology. 2006, Nov; 156(2): 284-291.
  1. 17.   Analysis of transcription factor AP-2 expression and function during mouse preimplantation development
  2. Winger, Q.; Huang, J.; Auman, H. J.; Lewandoski, M.; Williams, T.
  3. Biology of Reproduction. 2006, Sep; 75(3): 324-333.
  1. 18.   The regulation of acetylcholinesterase by cis-elements within intron I in cultured contracting myotubes
  2. Cohen, T. V.; R, all
  3. Journal of Neurochemistry. 2006, Aug; 98(3): 723-734.
  1. 19.   Unraveling the pros and cons of interferon-gamma gene regulation
  2. Young, H. A.
  3. Immunity. 2006, MAY; 24(5): 506-507.
  1. 20.   Comprehensive analysis of pathway or functionally related gene expression in the National Cancer Institute's anticancer screen
  2. Huang, R.; Wallqvist, A.; Covell, D. G.
  3. Genomics. 2006, MAR; 87(3): 315-328.
  1. 21.   WholePathwayScope: a comprehensive pathway-based analysis tool for high-throughput data
  2. Yi, M.; Horton, J. D.; Cohen, J. C.; Hobbs, H. H.; Stephens, R. M.
  3. Bmc Bioinformatics. 2006, JAN 19; 7
  1. 22.   Comparison of the protein-protein interfaces in the p53-DNA crystal structures: Towards elucidation of the biological interface
  2. Ma, B. Y.; Pan, Y. P.; Gunasekaran, K.; Venkataraghavan, R. B.; Levine, A. J.; Nussinov, R.
  3. Proceedings of the National Academy of Sciences of the United States of America. 2005, MAR 15; 102(11): 3988-3993.
  1. 23.   IFN-gamma gene expression is controlled by the architectural transcription factor HMGA1
  2. Chau, K. Y.; Keane-Myers, A. M.; Fedele, M.; Ikeda, Y.; Creusot, R. J.; Menozzi, L.; Cousins, D. J.; Manfioletti, G.; Feigenbaum, L.; Fusco, A.; Ono, S. J.
  3. International Immunology. 2005, MAR; 17(3): 297-306.
  1. 24.   Histone deacetylase inhibition down-regulates cyclin D1 transcription by inhibiting nuclear factor-kappa B/p65 DNA binding
  2. Hu, J.; Colburn, N. H.
  3. Molecular Cancer Research. 2005, FEB; 3(2): 100-109.
  1. 25.   Quantitative kinetic analysis of the bacteriophage lambda genetic network
  2. Kobiler, O.; Rokney, A.; Friedman, N.; Court, D. L.; Stavans, J.; Oppenheim, A. B.
  3. Proceedings of the National Academy of Sciences of the United States of America. 2005 102(12): 4470-4475.
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