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The Silent Sway of Splicing by Synonymous Substitutions. J Biol Chem. 2015 Nov 13; 290(46):27700-11.
Mueller WF, Larsen LS, Garibaldi A, Hatfield GW, Hertel KJ. PMID: 26424794; PMCID: PMC4646019.
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PubMed Mentions:
30 Fields:
Translation:
HumansAnimalsCells
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Directed DNA shuffling of retrovirus and retrotransposon integrase protein domains. PLoS One. 2013; 8(5):e63957.
Qi X, Vargas E, Larsen L, Knapp W, Hatfield GW, Lathrop R, Sandmeyer S. PMID: 23691126; PMCID: PMC3656877.
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PubMed Mentions:
2 Fields:
Translation:
Cells
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Computational identification of a transiently open L1/S3 pocket for reactivation of mutant p53. Nat Commun. 2013; 4:1407.
Wassman CD, Baronio R, Demir Ö, Wallentine BD, Chen CK, Hall LV, Salehi F, Lin DW, Chung BP, Hatfield GW, Richard Chamberlin A, Luecke H, Lathrop RH, Kaiser P, Amaro RE. PMID: 23360998; PMCID: PMC3562459.
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PubMed Mentions:
111 Fields:
Translation:
HumansCells
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Ensemble-based computational approach discriminates functional activity of p53 cancer and rescue mutants. PLoS Comput Biol. 2011 Oct; 7(10):e1002238.
Demir Ö, Baronio R, Salehi F, Wassman CD, Hall L, Hatfield GW, Chamberlin R, Kaiser P, Lathrop RH, Amaro RE. PMID: 22028641; PMCID: PMC3197647.
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PubMed Mentions:
22 Fields:
Translation:
HumansCells
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A vector set for systematic metabolic engineering in Saccharomyces cerevisiae. Yeast. 2011 Feb; 28(2):123-36.
Fang F, Salmon K, Shen MW, Aeling KA, Ito E, Irwin B, Tran UP, Hatfield GW, Da Silva NA, Sandmeyer S. PMID: 20936606; PMCID: PMC3070743.
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PubMed Mentions:
30 Fields:
Translation:
Animals
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All-codon scanning identifies p53 cancer rescue mutations. Nucleic Acids Res. 2010 Nov; 38(20):7079-88.
Baronio R, Danziger SA, Hall LV, Salmon K, Hatfield GW, Lathrop RH, Kaiser P. PMID: 20581117; PMCID: PMC2978351.
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PubMed Mentions:
12 Fields:
Translation:
HumansCells
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Recombinant human collagen and biomimetic variants using a de novo gene optimized for modular assembly. Biomacromolecules. 2010 Jun 14; 11(6):1460-9.
Chan SW, Hung SP, Raman SK, Hatfield GW, Lathrop RH, Da Silva NA, Wang SW. PMID: 20481478.
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PubMed Mentions:
7 Fields:
Translation:
HumansAnimals
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Mechanism of U insertion RNA editing in trypanosome mitochondria: the bimodal TUTase activity of the core complex. J Mol Biol. 2010 Jun 25; 399(5):680-95.
Ringpis GE, Aphasizheva I, Wang X, Huang L, Lathrop RH, Hatfield GW, Aphasizhev R. PMID: 20362585; PMCID: PMC2885523.
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PubMed Mentions:
15 Fields:
Translation:
AnimalsCells
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A 'random steady-state' model for the pyruvate dehydrogenase and alpha-ketoglutarate dehydrogenase enzyme complexes. Phys Biol. 2010 Mar 12; 7:16016.
Najdi TS, Hatfield GW, Mjolsness ED. PMID: 20228444.
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PubMed Mentions:
2 Fields:
Translation:
Cells
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Predicting positive p53 cancer rescue regions using Most Informative Positive (MIP) active learning. PLoS Comput Biol. 2009 Sep; 5(9):e1000498.
Danziger SA, Baronio R, Ho L, Hall L, Salmon K, Hatfield GW, Kaiser P, Lathrop RH. PMID: 19756158; PMCID: PMC2742196.
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PubMed Mentions:
17 Fields:
Translation:
HumansAnimals
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Computationally Optimised DNA Assembly of synthetic genes. Int J Bioinform Res Appl. 2008; 4(3):324-36.
Larsen LS, Wassman CD, Hatfield GW, Lathrop RH. PMID: 18640907; PMCID: PMC2668710.
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PubMed Mentions:
10 Fields:
Translation:
Cells
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Ty3 nucleocapsid controls localization of particle assembly. J Virol. 2008 Mar; 82(5):2501-14.
Larsen LS, Beliakova-Bethell N, Bilanchone V, Zhang M, Lamsa A, Dasilva R, Hatfield GW, Nagashima K, Sandmeyer S. PMID: 18094177; PMCID: PMC2258933.
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PubMed Mentions:
25 Fields:
Translation:
AnimalsCells
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TY3 GAG3 protein forms ordered particles in Escherichia coli. Virology. 2008 Jan 20; 370(2):223-7.
Larsen LS, Kuznetsov Y, McPherson A, Hatfield GW, Sandmeyer S. PMID: 17964628; PMCID: PMC2701475.
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PubMed Mentions:
5 Fields:
Translation:
AnimalsCells
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Ty3 capsid mutations reveal early and late functions of the amino-terminal domain. J Virol. 2007 Jul; 81(13):6957-72.
Larsen LS, Zhang M, Beliakova-Bethell N, Bilanchone V, Lamsa A, Nagashima K, Najdi R, Kosaka K, Kovacevic V, Cheng J, Baldi P, Hatfield GW, Sandmeyer S. PMID: 17442718; PMCID: PMC1933270.
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PubMed Mentions:
23 Fields:
Translation:
AnimalsCells
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Pressure dissociation of integration host factor-DNA complexes reveals flexibility-dependent structural variation at the protein-DNA interface. Nucleic Acids Res. 2007; 35(6):1761-72.
Senear DF, Tretyachenko-Ladokhina V, Opel ML, Aeling KA, Hatfield GW, Franklin LM, Darlington RC, Alexander Ross JB. PMID: 17324943; PMCID: PMC1874591.
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PubMed Mentions:
1 Fields:
Translation:
Cells
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Optimizing scaleup yield for protein production: Computationally Optimized DNA Assembly (CODA) and Translation Engineering. Biotechnol Annu Rev. 2007; 13:27-42.
Hatfield GW, Roth DA. PMID: 17875472.
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PubMed Mentions:
19 Fields:
Translation:
Cells
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DNA deformation energy as an indirect recognition mechanism in protein-DNA interactions. IEEE/ACM Trans Comput Biol Bioinform. 2007 Jan-Mar; 4(1):117-25.
Aeling KA, Steffen NR, Johnson M, Hatfield GW, Lathrop RH, Senear DF. PMID: 17277419.
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PubMed Mentions:
3 Fields:
Translation:
HumansAnimalsCells
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GRA1 protein vaccine confers better immune response compared to codon-optimized GRA1 DNA vaccine. Vaccine. 2007 Feb 26; 25(10):1824-37.
Döskaya M, Kalantari-Dehaghi M, Walsh CM, Hiszczynska-Sawicka E, Davies DH, Felgner PL, Larsen LS, Lathrop RH, Hatfield GW, Schulz JR, Gürüz Y, Jurnak F. PMID: 17234306.
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PubMed Mentions:
11 Fields:
Translation:
AnimalsCells
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Indirect recognition in sequence-specific DNA binding by Escherichia coli integration host factor: the role of DNA deformation energy. J Biol Chem. 2006 Dec 22; 281(51):39236-48.
Aeling KA, Opel ML, Steffen NR, Tretyachenko-Ladokhina V, Hatfield GW, Lathrop RH, Senear DF. PMID: 17035240.
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PubMed Mentions:
23 Fields:
Translation:
Cells
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HB tag modules for PCR-based gene tagging and tandem affinity purification in Saccharomyces cerevisiae. Yeast. 2006 Jun; 23(8):623-32.
Tagwerker C, Zhang H, Wang X, Larsen LS, Lathrop RH, Hatfield GW, Auer B, Huang L, Kaiser P. PMID: 16823883.
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PubMed Mentions:
35 Fields:
Translation:
AnimalsCells
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Application of a generalized MWC model for the mathematical simulation of metabolic pathways regulated by allosteric enzymes. J Bioinform Comput Biol. 2006 Apr; 4(2):335-55.
Najdi TS, Yang CR, Shapiro BE, Hatfield GW, Mjolsness ED. PMID: 16819787.
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PubMed Mentions:
9 Fields:
Translation:
Cells
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Biosynthesis and Regulation of the Branched-Chain Amino Acids†. EcoSal Plus. 2006 Jan; 2(1).
Salmon KA, Yang CR, Hatfield GW. PMID: 26443574.
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PubMed Mentions:
9 Fields:
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Global gene expression profiling in Escherichia coli K12: effects of oxygen availability and ArcA. J Biol Chem. 2005 Apr 15; 280(15):15084-96.
Salmon KA, Hung SP, Steffen NR, Krupp R, Baldi P, Hatfield GW, Gunsalus RP. PMID: 15699038.
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PubMed Mentions:
100 Fields:
Translation:
Cells
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A mathematical model for the branched chain amino acid biosynthetic pathways of Escherichia coli K12. J Biol Chem. 2005 Mar 25; 280(12):11224-32.
Yang CR, Shapiro BE, Hung SP, Mjolsness ED, Hatfield GW. PMID: 15657047.
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PubMed Mentions:
17 Fields:
Translation:
Cells
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Application of a generalized MWC model for the mathematical simulation of metabolic pathways regulated by allosteric enzymes. Proc IEEE Comput Syst Bioinform Conf. 2005; 279-88.
Najdi TS, Yang CR, Shapiro BE, Hatfield GW, Mjolsness ED. PMID: 16447985.
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PubMed Mentions:
1 Fields:
Translation:
Cells
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How noisy and replicable are DNA microarry data? Int J Bioinform Res Appl. 2005; 1(1):31-50.
Sundaresh S, Hung SP, Hatfield GW, Baldi P. PMID: 18048120.
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PubMed Mentions:
1 Fields:
Translation:
Humans
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Identification of hair cycle-associated genes from time-course gene expression profile data by using replicate variance. Proc Natl Acad Sci U S A. 2004 Nov 09; 101(45):15955-60.
Lin KK, Chudova D, Hatfield GW, Smyth P, Andersen B. PMID: 15520371; PMCID: PMC524696.
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PubMed Mentions:
37 Fields:
Translation:
Animals
-
An enzyme mechanism language for the mathematical modeling of metabolic pathways. Bioinformatics. 2005 Mar; 21(6):774-80.
Yang CR, Shapiro BE, Mjolsness ED, Hatfield GW. PMID: 15509612.
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PubMed Mentions:
12 Fields:
Translation:
Cells
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Activation of transcription initiation from a stable RNA promoter by a Fis protein-mediated DNA structural transmission mechanism. Mol Microbiol. 2004 Jul; 53(2):665-74.
Opel ML, Aeling KA, Holmes WM, Johnson RC, Benham CJ, Hatfield GW. PMID: 15228542.
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PubMed Mentions:
22 Fields:
Translation:
Cells
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Effects of exercise on gene expression in human peripheral blood mononuclear cells. J Appl Physiol (1985). 2004 Oct; 97(4):1461-9.
Connolly PH, Caiozzo VJ, Zaldivar F, Nemet D, Larson J, Hung SP, Heck JD, Hatfield GW, Cooper DM. PMID: 15194674.
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PubMed Mentions:
74 Fields:
Translation:
HumansCellsCTClinical Trials
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Global gene expression profiling in Escherichia coli K12. The effects of oxygen availability and FNR. J Biol Chem. 2003 Aug 08; 278(32):29837-55.
Salmon K, Hung SP, Mekjian K, Baldi P, Hatfield GW, Gunsalus RP. PMID: 12754220.
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PubMed Mentions:
117 Fields:
Translation:
Cells
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Differential analysis of DNA microarray gene expression data. Mol Microbiol. 2003 Feb; 47(4):871-7.
Hatfield GW, Hung SP, Baldi P. PMID: 12581345.
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PubMed Mentions:
28 Fields:
Translation:
HumansCells
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Global gene expression profiling in Escherichia coli K12. The effects of leucine-responsive regulatory protein. J Biol Chem. 2002 Oct 25; 277(43):40309-23.
Hung SP, Baldi P, Hatfield GW. PMID: 12130640.
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PubMed Mentions:
55 Fields:
Translation:
Cells
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DNA topology-mediated control of global gene expression in Escherichia coli. Annu Rev Genet. 2002; 36:175-203.
Hatfield GW, Benham CJ. PMID: 12429691.
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PubMed Mentions:
97 Fields:
Translation:
Cells
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The role of DNA deformation energy at individual base steps for the identification of DNA-protein binding sites. Genome Inform. 2002; 13:153-62.
Steffen NR, Murphy SD, Lathrop RH, Opel ML, Tolleri L, Hatfield GW. PMID: 14571384.
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PubMed Mentions:
6 Fields:
Translation:
Cells
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DNA sequence and structure: direct and indirect recognition in protein-DNA binding. Bioinformatics. 2002; 18 Suppl 1:S22-30.
Steffen NR, Murphy SD, Tolleri L, Hatfield GW, Lathrop RH. PMID: 12169527.
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PubMed Mentions:
22 Fields:
Translation:
Cells
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Activation and repression of transcription initiation by a distant DNA structural transition. Mol Microbiol. 2001 May; 40(3):684-90.
Sheridan SD, Opel ML, Hatfield GW. PMID: 11359573.
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PubMed Mentions:
3 Fields:
Translation:
Cells
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Improved statistical inference from DNA microarray data using analysis of variance and a Bayesian statistical framework. Analysis of global gene expression in Escherichia coli K12. J Biol Chem. 2001 Jun 08; 276(23):19937-44.
Long AD, Mangalam HJ, Chan BY, Tolleri L, Hatfield GW, Baldi P. PMID: 11259426.
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PubMed Mentions:
150 Fields:
Translation:
Cells
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The effects of DNA supercoiling on the expression of operons of the ilv regulon of Escherichia coli suggest a physiological rationale for divergently transcribed operons. Mol Microbiol. 2001 Mar; 39(5):1109-15.
Opel ML, Arfin SM, Hatfield GW. PMID: 11251829.
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PubMed Mentions:
6 Fields:
Translation:
Cells
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DNA supercoiling-dependent transcriptional coupling between the divergently transcribed promoters of the ilvYC operon of Escherichia coli is proportional to promoter strengths and transcript lengths. Mol Microbiol. 2001 Jan; 39(1):191-8.
Opel ML, Hatfield GW. PMID: 11123701.
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PubMed Mentions:
25 Fields:
Translation:
Cells
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Global gene expression profiling in Escherichia coli K12. The effects of integration host factor. J Biol Chem. 2000 Sep 22; 275(38):29672-84.
Arfin SM, Long AD, Ito ET, Tolleri L, Riehle MM, Paegle ES, Hatfield GW. PMID: 10871608.
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PubMed Mentions:
81 Fields:
Translation:
Cells
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Transcriptional coupling between the divergent promoters of a prototypic LysR-type regulatory system, the ilvYC operon of Escherichia coli. Proc Natl Acad Sci U S A. 1999 Dec 07; 96(25):14294-9.
Rhee KY, Opel M, Ito E, Hung Sp, Arfin SM, Hatfield GW. PMID: 10588699; PMCID: PMC24430.
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PubMed Mentions:
34 Fields:
Translation:
Cells
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Inhibition of DNA supercoiling-dependent transcriptional activation by a distant B-DNA to Z-DNA transition. J Biol Chem. 1999 Mar 19; 274(12):8169-74.
Sheridan SD, Benham CJ, Hatfield GW. PMID: 10075720.
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PubMed Mentions:
15 Fields:
Translation:
AnimalsCells
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Activation of gene expression by a novel DNA structural transmission mechanism that requires supercoiling-induced DNA duplex destabilization in an upstream activating sequence. J Biol Chem. 1998 Aug 14; 273(33):21298-308.
Sheridan SD, Benham CJ, Hatfield GW. PMID: 9694890.
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PubMed Mentions:
32 Fields:
Translation:
Cells
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Activation of gene expression by a ligand-induced conformational change of a protein-DNA complex. J Biol Chem. 1998 May 01; 273(18):11257-66.
Rhee KY, Senear DF, Hatfield GW. PMID: 9556617.
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PubMed Mentions:
15 Fields:
Translation:
Cells
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Growth rate-related regulation of the ilvGMEDA operon of Escherichia coli K-12 is a consequence of the polar frameshift mutation in the ilvG gene of this strain. J Bacteriol. 1997 Mar; 179(6):2086-8.
Parekh BS, Hatfield GW. PMID: 9068661; PMCID: PMC178939.
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PubMed Mentions:
6 Fields:
Translation:
Cells
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Leucine-responsive regulatory protein-DNA interactions in the leader region of the ilvGMEDA operon of Escherichia coli. J Biol Chem. 1996 Oct 25; 271(43):26499-507.
Rhee KY, Parekh BS, Hatfield GW. PMID: 8900118.
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PubMed Mentions:
15 Fields:
Translation:
Cells
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Effects of integration host factor and DNA supercoiling on transcription from the ilvPG promoter of Escherichia coli. J Biol Chem. 1996 Aug 23; 271(34):20258-64.
Parekh BS, Sheridan SD, Hatfield GW. PMID: 8702758.
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PubMed Mentions:
9 Fields:
Translation:
Cells
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Transcriptional activation by protein-induced DNA bending: evidence for a DNA structural transmission model. Proc Natl Acad Sci U S A. 1996 Feb 06; 93(3):1173-7.
Parekh BS, Hatfield GW. PMID: 8577735; PMCID: PMC40051.
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PubMed Mentions:
35 Fields:
Translation:
Cells
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Codon pair utilization biases influence translational elongation step times. J Biol Chem. 1995 Sep 29; 270(39):22801-6.
Irwin B, Heck JD, Hatfield GW. PMID: 7559409.
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PubMed Mentions:
79 Fields:
Translation:
Cells
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DNA topology-mediated regulation of transcription initiation from the tandem promoters of the ilvGMEDA operon of Escherichia coli. J Mol Biol. 1992 Apr 20; 224(4):919-35.
Pagel JM, Winkelman JW, Adams CW, Hatfield GW. PMID: 1569580.
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PubMed Mentions:
18 Fields:
Translation:
Cells
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Integration host factor-mediated expression of the ilvGMEDA operon of Escherichia coli. J Biol Chem. 1991 Jan 25; 266(3):1985-96.
Pagel JM, Hatfield GW. PMID: 1703160.
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PubMed Mentions:
11 Fields:
Translation:
Cells
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Characterization of the integration host factor binding site in the ilvPG1 promoter region of the ilvGMEDA operon of Escherichia coli. J Biol Chem. 1990 Jun 15; 265(17):10055-60.
Winkelman JW, Hatfield GW. PMID: 2190979.
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PubMed Mentions:
7 Fields:
Translation:
Cells
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The primary structure of a halorhodopsin from Natronobacterium pharaonis. Structural, functional and evolutionary implications for bacterial rhodopsins and halorhodopsins. J Biol Chem. 1990 Jan 25; 265(3):1253-60.
Lanyi JK, Duschl A, Hatfield GW, May K, Oesterhelt D. PMID: 2104837.
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PubMed Mentions:
29 Fields:
Translation:
Cells
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Nonrandom utilization of codon pairs in Escherichia coli. Proc Natl Acad Sci U S A. 1989 May; 86(10):3699-703.
Gutman GA, Hatfield GW. PMID: 2657727; PMCID: PMC287207.
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PubMed Mentions:
129 Fields:
Translation:
Cells
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Overlapping transcription and termination of the convergent ilvA and ilvY genes of Escherichia coli. J Biol Chem. 1989 Jan 15; 264(2):1224-31.
Sameshima JH, Wek RC, Hatfield GW. PMID: 2642900.
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PubMed Mentions:
8 Fields:
Translation:
Cells
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Transcriptional activation at adjacent operators in the divergent-overlapping ilvY and ilvC promoters of Escherichia coli. J Mol Biol. 1988 Oct 05; 203(3):643-63.
Wek RC, Hatfield GW. PMID: 3062177.
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PubMed Mentions:
52 Fields:
Translation:
Cells
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Valyl-tRNA synthetase gene of Escherichia coli K12. Molecular genetic characterization. J Biol Chem. 1988 Jan 15; 263(2):857-67.
Heck JD, Hatfield GW. PMID: 3275659.
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PubMed Mentions:
9 Fields:
Translation:
Cells
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Valyl-tRNA synthetase gene of Escherichia coli K12. Primary structure and homology within a family of aminoacyl-TRNA synthetases. J Biol Chem. 1988 Jan 15; 263(2):868-77.
Heck JD, Hatfield GW. PMID: 3275660.
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PubMed Mentions:
21 Fields:
Translation:
Cells
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Rho-dependent transcriptional polarity in the ilvGMEDA operon of wild-type Escherichia coli K12. J Biol Chem. 1987 Nov 05; 262(31):15256-61.
Wek RC, Sameshima JH, Hatfield GW. PMID: 2822718.
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PubMed Mentions:
17 Fields:
Translation:
Cells