 Connection
Co-Authors
This is a "connection" page, showing publications co-authored by James Goodrich and Jennifer Kugel.
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Connection Strength |
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9.048 |
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Kugel JF, Goodrich JA. Finding the start site: redefining the human initiator element. Genes Dev. 2017 01 01; 31(1):1-2.
Score: 0.578
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Goodrich JA, Kugel JF. Studying the affinity, kinetic stability, and specificity of RNA/protein interactions: SINE ncRNA/Pol II complexes as a model system. Methods Mol Biol. 2015; 1206:165-78.
Score: 0.503
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Kugel JF, Goodrich JA. The regulation of mammalian mRNA transcription by lncRNAs: recent discoveries and current concepts. Epigenomics. 2013 Feb; 5(1):95-102.
Score: 0.441
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Kugel JF, Goodrich JA. Non-coding RNAs: key regulators of mammalian transcription. Trends Biochem Sci. 2012 Apr; 37(4):144-51.
Score: 0.411
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Goodrich JA, Kugel JF. Genome-wide insights into eukaryotic transcriptional control. Genome Biol. 2010; 11(6):305.
Score: 0.367
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Goodrich JA, Kugel JF. Dampening DNA binding: a common mechanism of transcriptional repression for both ncRNAs and protein domains. RNA Biol. 2010 May-Jun; 7(3):305-9.
Score: 0.366
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Kugel JF, Goodrich JA. In new company: U1 snRNA associates with TAF15. EMBO Rep. 2009 May; 10(5):454-6.
Score: 0.339
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Goodrich JA, Kugel JF. From bacteria to humans, chromatin to elongation, and activation to repression: The expanding roles of noncoding RNAs in regulating transcription. Crit Rev Biochem Mol Biol. 2009 Jan-Feb; 44(1):3-15.
Score: 0.332
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Goodrich JA, Kugel JF. Non-coding-RNA regulators of RNA polymerase II transcription. Nat Rev Mol Cell Biol. 2006 Aug; 7(8):612-6.
Score: 0.277
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Kugel JF, Goodrich JA. Beating the heat: A translation factor and an RNA mobilize the heat shock transcription factor HSF1. Mol Cell. 2006 Apr 21; 22(2):153-4.
Score: 0.275
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Miller GM, Brant TS, Goodrich JA, Kugel JF. Short-term exposure to ethanol induces transcriptional changes in nontumorigenic breast cells. FEBS Open Bio. 2023 10; 13(10):1941-1952.
Score: 0.229
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Suwita JP, Voong CK, Ly E, Goodrich JA, Kugel JF. Single molecule studies characterize the kinetic mechanism of tetrameric p53 binding to different native response elements. PLoS One. 2023; 18(8):e0286193.
Score: 0.229
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Kugel JF, Goodrich JA. In vitro studies of the early steps of RNA synthesis by human RNA polymerase II. Methods Enzymol. 2003; 370:687-701.
Score: 0.219
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Kugel JF, Goodrich JA. Translocation after synthesis of a four-nucleotide RNA commits RNA polymerase II to promoter escape. Mol Cell Biol. 2002 Feb; 22(3):762-73.
Score: 0.206
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Voong CK, Goodrich JA, Kugel JF. Interactions of HMGB Proteins with the Genome and the Impact on Disease. Biomolecules. 2021 10 02; 11(10).
Score: 0.201
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Rivas T, Goodrich JA, Kugel JF. The Herpes Simplex Virus 1 Protein ICP4 Acts as both an Activator and a Repressor of Host Genome Transcription during Infection. Mol Cell Biol. 2021 09 24; 41(10):e0017121.
Score: 0.198
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Ly E, Kugel JF, Goodrich JA. Single molecule studies reveal that p53 tetramers dynamically bind response elements containing one or two half sites. Sci Rep. 2020 09 30; 10(1):16176.
Score: 0.187
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Ly E, Powell AE, Goodrich JA, Kugel JF. Release of Human TFIIB from Actively Transcribing Complexes Is Triggered upon Synthesis of 7- and 9-nt RNAs. J Mol Biol. 2020 06 26; 432(14):4049-4060.
Score: 0.183
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Salant GM, Tat KL, Goodrich JA, Kugel JF. miR-206 knockout shows it is critical for myogenesis and directly regulates newly identified target mRNAs. RNA Biol. 2020 07; 17(7):956-965.
Score: 0.180
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Ly E, Goodrich JA, Kugel JF. Monitoring transcriptional activity by RNA polymerase II in vitro using single molecule co-localization. Methods. 2019 04 15; 159-160:45-50.
Score: 0.168
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Cardiello JF, Goodrich JA, Kugel JF. Heat Shock Causes a Reversible Increase in RNA Polymerase II Occupancy Downstream of mRNA Genes, Consistent with a Global Loss in Transcriptional Termination. Mol Cell Biol. 2018 09 15; 38(18).
Score: 0.162
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Abrisch RG, Eidem TM, Yakovchuk P, Kugel JF, Goodrich JA. Correction for Abrisch et al., Infection by Herpes Simplex Virus 1 Causes Near-Complete Loss of RNA Polymerase II Occupancy on the Host Cell Genome. J Virol. 2016 12 15; 90(24):11279.
Score: 0.144
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Blair RH, Horn AE, Pazhani Y, Grado L, Goodrich JA, Kugel JF. The HMGB1 C-Terminal Tail Regulates DNA Bending. J Mol Biol. 2016 10 09; 428(20):4060-4072.
Score: 0.141
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Horn AE, Kugel JF, Goodrich JA. Single molecule microscopy reveals mechanistic insight into RNA polymerase II preinitiation complex assembly and transcriptional activity. Nucleic Acids Res. 2016 09 06; 44(15):7132-43.
Score: 0.138
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Eidem TM, Kugel JF, Goodrich JA. Noncoding RNAs: Regulators of the Mammalian Transcription Machinery. J Mol Biol. 2016 06 19; 428(12):2652-2659.
Score: 0.136
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Abrisch RG, Eidem TM, Yakovchuk P, Kugel JF, Goodrich JA. Infection by Herpes Simplex Virus 1 Causes Near-Complete Loss of RNA Polymerase II Occupancy on the Host Cell Genome. J Virol. 2015 12 16; 90(5):2503-13.
Score: 0.134
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Ponicsan SL, Kugel JF, Goodrich JA. Repression of RNA Polymerase II Transcription by B2 RNA Depends on a Specific Pattern of Structural Regions in the RNA. Noncoding RNA. 2015 Jun; 1:4-16.
Score: 0.130
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Walters RD, McSwiggen DT, Goodrich JA, Kugel JF. Selection and characterization of a DNA aptamer that can discriminate between cJun/cJun and cJun/cFos. PLoS One. 2014; 9(6):e101015.
Score: 0.121
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Cardiello JF, Kugel JF, Goodrich JA. A new twist on cell growth control. Cell Cycle. 2014; 13(22):3474-5.
Score: 0.117
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Horn AE, Goodrich JA, Kugel JF. Single molecule studies of RNA polymerase II transcription in vitro. Transcription. 2014; 5(1):e27608.
Score: 0.117
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Walters RD, Drullinger LF, Kugel JF, Goodrich JA. NFATc2 recruits cJun homodimers to an NFAT site to synergistically activate interleukin-2 transcription. Mol Immunol. 2013 Nov; 56(1-2):48-56.
Score: 0.112
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Ponicsan SL, Houel S, Old WM, Ahn NG, Goodrich JA, Kugel JF. The non-coding B2 RNA binds to the DNA cleft and active-site region of RNA polymerase II. J Mol Biol. 2013 Oct 09; 425(19):3625-38.
Score: 0.110
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Wagner SD, Yakovchuk P, Gilman B, Ponicsan SL, Drullinger LF, Kugel JF, Goodrich JA. RNA polymerase II acts as an RNA-dependent RNA polymerase to extend and destabilize a non-coding RNA. EMBO J. 2013 Mar 20; 32(6):781-90.
Score: 0.110
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Blair RH, Goodrich JA, Kugel JF. Using FRET to monitor protein-induced DNA bending: the TBP-TATA complex as a model system. Methods Mol Biol. 2013; 977:203-15.
Score: 0.110
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Blair RH, Goodrich JA, Kugel JF. Single-molecule fluorescence resonance energy transfer shows uniformity in TATA binding protein-induced DNA bending and heterogeneity in bending kinetics. Biochemistry. 2012 Sep 25; 51(38):7444-55.
Score: 0.107
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Yakovchuk P, Goodrich JA, Kugel JF. B2 RNA represses TFIIH phosphorylation of RNA polymerase II. Transcription. 2011 Jan-Feb; 2(1):45-9.
Score: 0.095
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Nguyen TN, Kim LJ, Walters RD, Drullinger LF, Lively TN, Kugel JF, Goodrich JA. The C-terminal region of human NFATc2 binds cJun to synergistically activate interleukin-2 transcription. Mol Immunol. 2010 Aug; 47(14):2314-22.
Score: 0.092
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Ponicsan SL, Kugel JF, Goodrich JA. Genomic gems: SINE RNAs regulate mRNA production. Curr Opin Genet Dev. 2010 Apr; 20(2):149-55.
Score: 0.090
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Yakovchuk P, Gilman B, Goodrich JA, Kugel JF. RNA polymerase II and TAFs undergo a slow isomerization after the polymerase is recruited to promoter-bound TFIID. J Mol Biol. 2010 Mar 19; 397(1):57-68.
Score: 0.089
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Wagner SD, Kugel JF, Goodrich JA. TFIIF facilitates dissociation of RNA polymerase II from noncoding RNAs that lack a repression domain. Mol Cell Biol. 2010 Jan; 30(1):91-7.
Score: 0.089
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Walters RD, Kugel JF, Goodrich JA. InvAluable junk: the cellular impact and function of Alu and B2 RNAs. IUBMB Life. 2009 Aug; 61(8):831-7.
Score: 0.086
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Yakovchuk P, Goodrich JA, Kugel JF. B2 RNA and Alu RNA repress transcription by disrupting contacts between RNA polymerase II and promoter DNA within assembled complexes. Proc Natl Acad Sci U S A. 2009 Apr 07; 106(14):5569-74.
Score: 0.084
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Gilman B, Drullinger LF, Kugel JF, Goodrich JA. TATA-binding protein and transcription factor IIB induce transcript slipping during early transcription by RNA polymerase II. J Biol Chem. 2009 Apr 03; 284(14):9093-8.
Score: 0.084
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Mariner PD, Walters RD, Espinoza CA, Drullinger LF, Wagner SD, Kugel JF, Goodrich JA. Human Alu RNA is a modular transacting repressor of mRNA transcription during heat shock. Mol Cell. 2008 Feb 29; 29(4):499-509.
Score: 0.078
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Hieb AR, Halsey WA, Betterton MD, Perkins TT, Kugel JF, Goodrich JA. TFIIA changes the conformation of the DNA in TBP/TATA complexes and increases their kinetic stability. J Mol Biol. 2007 Sep 21; 372(3):619-32.
Score: 0.075
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Weaver JR, Good K, Walters RD, Kugel JF, Goodrich JA. Characterization of the sequence and architectural constraints of the regulatory and core regions of the human interleukin-2 promoter. Mol Immunol. 2007 Apr; 44(11):2813-9.
Score: 0.073
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Espinoza CA, Goodrich JA, Kugel JF. Characterization of the structure, function, and mechanism of B2 RNA, an ncRNA repressor of RNA polymerase II transcription. RNA. 2007 Apr; 13(4):583-96.
Score: 0.073
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Hieb AR, Baran S, Goodrich JA, Kugel JF. An 8 nt RNA triggers a rate-limiting shift of RNA polymerase II complexes into elongation. EMBO J. 2006 Jul 12; 25(13):3100-9.
Score: 0.070
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Weaver JR, Kugel JF, Goodrich JA. The sequence at specific positions in the early transcribed region sets the rate of transcript synthesis by RNA polymerase II in vitro. J Biol Chem. 2005 Dec 02; 280(48):39860-9.
Score: 0.066
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Espinoza CA, Allen TA, Hieb AR, Kugel JF, Goodrich JA. B2 RNA binds directly to RNA polymerase II to repress transcript synthesis. Nat Struct Mol Biol. 2004 Sep; 11(9):822-9.
Score: 0.061
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Allen TA, Von Kaenel S, Goodrich JA, Kugel JF. The SINE-encoded mouse B2 RNA represses mRNA transcription in response to heat shock. Nat Struct Mol Biol. 2004 Sep; 11(9):816-21.
Score: 0.061
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Connection Strength
The connection strength for concepts is the sum of the scores for each matching publication.
Publication scores are based on many factors, including how long ago they were written and whether the person is a first or senior author.
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