Quantitative model for genome-wide cyclic AMP receptor protein binding site identification and characteristic analysis
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Hsi-Yuan Huang | Yang-Chi-Dung Lin | Yi-Gang Chen | Xiao-Xuan Cai | Hsien-Da Huang | Shidong Cui | Yijun Luo | Peng Qiu | Zhe Wang
[1] OUP accepted manuscript , 2021, Briefings In Bioinformatics.
[2] Jinwei Zhu,et al. Characterizing the Binding Sites for GK Domain of DLG1 and DLG4 via Molecular Dynamics Simulation , 2020, Frontiers in Molecular Biosciences.
[3] De-Shuang Huang,et al. High-Order Convolutional Neural Network Architecture for Predicting DNA-Protein Binding Sites , 2019, IEEE/ACM Transactions on Computational Biology and Bioinformatics.
[4] Mohamed Chaabane,et al. Comprehensive evaluation of deep learning architectures for prediction of DNA/RNA sequence binding specificities , 2019, Bioinform..
[5] Julio Collado-Vides,et al. RegulonDB v 10.5: tackling challenges to unify classic and high throughput knowledge of gene regulation in E. coli K-12 , 2018, Nucleic Acids Res..
[6] Gabriela Bitencourt-Ferreira,et al. Development of a machine-learning model to predict Gibbs free energy of binding for protein-ligand complexes. , 2018, Biophysical chemistry.
[7] B. Palsson,et al. ChIP-exo interrogation of Crp, DNA, and RNAP holoenzyme interactions , 2018, PloS one.
[8] Hsi-Yuan Huang,et al. PredCRP: predicting and analysing the regulatory roles of CRP from its binding sites in Escherichia coli , 2018, Scientific Reports.
[9] Hsi-Yuan Huang,et al. PredCRP: predicting and analysing the regulatory roles of CRP from its binding sites in Escherichia coli , 2018, Scientific Reports.
[10] Peter D. Karp,et al. The EcoCyc database: reflecting new knowledge about Escherichia coli K-12 , 2016, Nucleic Acids Res..
[11] Minoru Kanehisa,et al. KEGG: new perspectives on genomes, pathways, diseases and drugs , 2016, Nucleic Acids Res..
[12] N. Jayaram,et al. Evaluating tools for transcription factor binding site prediction , 2016, BMC Bioinformatics.
[13] Michael Y. Galperin,et al. Expanded microbial genome coverage and improved protein family annotation in the COG database , 2014, Nucleic Acids Res..
[14] Prudence Mutowo-Meullenet,et al. The GOA database: Gene Ontology annotation updates for 2015 , 2014, Nucleic Acids Res..
[15] Hsi-Yuan Huang,et al. CRP represses the CRISPR/Cas system in Escherichia coli: evidence that endogenous CRISPR spacers impede phage P1 replication , 2014, Molecular microbiology.
[16] Hans V. Westerhoff,et al. Nitrogen Assimilation in Escherichia coli: Putting Molecular Data into a Systems Perspective , 2013, Microbiology and Molecular Reviews.
[17] Wyeth W. Wasserman,et al. The Next Generation of Transcription Factor Binding Site Prediction , 2013, PLoS Comput. Biol..
[18] Chien-Yu Chen,et al. PiDNA: predicting protein–DNA interactions with structural models , 2013, Nucleic Acids Res..
[19] N. Fujita,et al. Novel Roles of cAMP Receptor Protein (CRP) in Regulation of Transport and Metabolism of Carbon Sources , 2011, PloS one.
[20] Robert D. Finn,et al. HMMER web server: interactive sequence similarity searching , 2011, Nucleic Acids Res..
[21] Narmada Thanki,et al. CDD: a Conserved Domain Database for the functional annotation of proteins , 2010, Nucleic Acids Res..
[22] A. Ishihama. Prokaryotic genome regulation: multifactor promoters, multitarget regulators and hierarchic networks. , 2010, FEMS microbiology reviews.
[23] H. Won,et al. Structural overview on the allosteric activation of cyclic AMP receptor protein. , 2009, Biochimica et biophysica acta.
[24] Mikael Bodén,et al. MEME Suite: tools for motif discovery and searching , 2009, Nucleic Acids Res..
[25] Zhengchang Su,et al. Computational prediction of cAMP receptor protein (CRP) binding sites in cyanobacterial genomes , 2009, BMC Genomics.
[26] S. Kędracka-Krok,et al. cAMP Receptor Protein from Escherichia coli as a Model of Signal Transduction in Proteins – A Review , 2008, Journal of Molecular Microbiology and Biotechnology.
[27] Rodrigo Lopez,et al. Clustal W and Clustal X version 2.0 , 2007, Bioinform..
[28] David Bryant,et al. DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists , 2007, Nucleic Acids Res..
[29] Jolyon Holdstock,et al. Studies of the distribution of Escherichia coli cAMP-receptor protein and RNA polymerase along the E. coli chromosome. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[30] T. Inada,et al. Implication of membrane localization of target mRNA in the action of a small RNA: mechanism of post-transcriptional regulation of glucose transporter in Escherichia coli. , 2005, Genes & development.
[31] Milton H. Saier,et al. Transcriptome Analysis of Crp-Dependent Catabolite Control of Gene Expression in Escherichia coli , 2004, Journal of bacteriology.
[32] G. Crooks,et al. WebLogo: a sequence logo generator. , 2004, Genome research.
[33] D. Swigon,et al. Catabolite activator protein: DNA binding and transcription activation. , 2004, Current opinion in structural biology.
[34] Chrystala Constantinidou,et al. Identification of the CRP regulon using in vitro and in vivo transcriptional profiling. , 2004, Nucleic acids research.
[35] Heidi J Sofia,et al. Phylogeny of the bacterial superfamily of Crp-Fnr transcription regulators: exploiting the metabolic spectrum by controlling alternative gene programs. , 2003, FEMS microbiology reviews.
[36] P. Shannon,et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.
[37] J. Collado-Vides,et al. Identifying global regulators in transcriptional regulatory networks in bacteria. , 2003, Current opinion in microbiology.
[38] Alexander E. Kel,et al. MATCHTM: a tool for searching transcription factor binding sites in DNA sequences , 2003, Nucleic Acids Res..
[39] T. Inada,et al. Expression of the glucose transporter gene, ptsG, is regulated at the mRNA degradation step in response to glycolytic flux in Escherichia coli , 2001, The EMBO journal.
[40] J G Harman,et al. Allosteric regulation of the cAMP receptor protein. , 2001, Biochimica et biophysica acta.
[41] M. Ashburner,et al. Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.
[42] T. N. Bhat,et al. The Protein Data Bank , 2000, Nucleic Acids Res..
[43] R. Ebright,et al. Transcription activation by catabolite activator protein (CAP). , 1999, Journal of molecular biology.
[44] M. Saier,et al. Multiple mechanisms controlling carbon metabolism in bacteria. , 1998, Biotechnology and bioengineering.
[45] H. Aiba,et al. A common role of CRP in transcription activation: CRP acts transiently to stimulate events leading to open complex formation at a diverse set of promoters , 1998, The EMBO journal.
[46] R. Ebright,et al. Transcription Activation at Class II CAP-Dependent Promoters: Two Interactions between CAP and RNA Polymerase , 1996, Cell.
[47] J. Lee,et al. Mode of selectivity in cyclic AMP receptor protein-dependent promoters in Escherichia coli. , 1996, Biochemistry.
[48] S. Adhya,et al. The galactose regulon of Escherichia coli , 1993, Molecular microbiology.
[49] H. Buc,et al. Transcriptional regulation by cAMP and its receptor protein. , 1993, Annual review of biochemistry.
[50] D. Crothers,et al. Sequence-dependent contribution of distal binding domains to CAP protein-DNA binding affinity. , 1991, Nucleic acids research.
[51] R. Utsumi,et al. Control mechanism of the Escherichia coli K-12 cell cycle is triggered by the cyclic AMP-cyclic AMP receptor protein complex , 1989, Journal of bacteriology.
[52] A. Gronenborn,et al. The binding of the cyclic AMP receptor protein to synthetic DNA sites containing permutations in the consensus sequence TGTGA. , 1987, The Biochemical journal.
[53] M. E. Gent,et al. Probing the sequence-specific interaction of the cyclic AMP receptor protein with DNA by site-directed mutagenesis. , 1987, The Biochemical journal.
[54] Thomas A. Steitz,et al. Structure of catabolite gene activator protein at 2.9 Å resolution suggests binding to left-handed B-DNA , 1981, Nature.
[55] J. Beckwith,et al. Mechanism of activation of catabolite-sensitive genes: a positive control system. , 1970, Proceedings of the National Academy of Sciences of the United States of America.