• In this work, we identified whole-genome and metagenomic operons via MetaRon (Metagenome and whole-genome opeRon prediction pipeline). (biomedcentral.com)
  • MetaRon consistently achieved high operon prediction sensitivity, specificity and accuracy across E. coli whole-genome (97.8, 94.1 and 92.4%), simulated genome (93.7, 75.5 and 88.1%) and E. coli c20 (87, 91 and 88%,), respectively. (biomedcentral.com)
  • With MetaRon, we were able to remove two notable limitations of existing whole-genome operon prediction methods: (1) generalizability (ability to predict operons in unrelated bacterial genomes), and (2) whole-genome and metagenomic data management. (biomedcentral.com)
  • GSEL version 2, an online genome-wide query system of operon organization and regulatory sequence elements of Geobacter sulfurreducens. (umass.edu)
  • While the concept has been long and widely used in bacterial studies since it was first proposed in 1964, very little is known about how its component operons are arranged in a bacterial genome. (niu.edu)
  • We present a computational study to elucidate of the organizational principles of regulons in a bacterial genome, based on the experimentally validated regulons of E. coli and B. subtilis. (niu.edu)
  • and (3) the global arrangement of the component operons of all the regulons in a genome tends to minimize a simple scoring function, indicating that the global arrangement of regulons follows simple organizational principles. (niu.edu)
  • It is estimated that about 60% of the Mycobacterium tuberculosis genome is arranged into operons, which makes them interesting drug targets in the face of emerging drug resistance. (researchgate.net)
  • We demonstrate the power of the method by uncovering several novel features of an iconic gene regulatory program: the induction of Escherichia coli 's lac operon in response to a switch from glucose to lactose. (nature.com)
  • The leucine operon leader is an RNA element that was found upstream of some leucine biosynthesis leuABCD operons in Escherichia coli and related bacteria and that is involved in the amino acid dependent attenuation of their transcription [ 6186194 ]. (lbl.gov)
  • Insightful directed evolution of Escherichia coli quorum sensing promoter region of the lsrACDBFG operon: a tool for synthetic biology systems and protein expression. (umd.edu)
  • His Escherichia coli study combines topics from a wide range of disciplines, such as Gene expression, Computational biology and Growth medium. (research.com)
  • In this project, I will employ biochemical, cell, systems biology and computational approaches to study the relevance of post-transcriptional regulators such as RNA-binding proteins and microRNAs in DDR. (europa.eu)
  • The research programs in the Im group focus on the applications of theoretical/computational methods to chemical and physical problems in biology and material science. (kcbioinformatics.org)
  • Journal of Computational Biology , 6:343-360, 1999. (uiuc.edu)
  • To address the many current challenges in the field - from developing more predictive computational design methods to determining the requirements for function in cells - we combine concepts from computer science, physics, chemistry, mathematics, engineering and biology. (ucsf.edu)
  • Predicting and designing the structures of proteins with biologically useful accuracy has been a key challenge in computational structural biology and molecular engineering. (ucsf.edu)
  • Journal of bioinformatics and computational biology 15(1): 1650039. (umd.edu)
  • His studies in Gene integrate themes in fields like Synechococcus, Computational biology and Cell biology. (research.com)
  • Biochemistry, Flux, Metabolic engineering, Computational biology and Gene are his primary areas of study. (research.com)
  • Brian F. Pfleger combines subjects such as Amino acid substitution, Protein engineering and Strain engineering with his study of Computational biology. (research.com)
  • Candidate gene is closely connected to Computational biology in his research, which is encompassed under the umbrella topic of Transposable element. (research.com)
  • PLoS Computational Biology. (ista.ac.at)
  • These two functions can be easily applied to the 2,072 prokaryotic genomes supported by the DOOR2 operon database (PMID: 24214966) (Function V) . These two new methods along with a network analysis and visualization function (Function IV) were implemented and connected with all the existing functions of DMINDA (Functions VI-VII) , giving rise to this 2nd-generation web server: DMINDA 2 . (osumc.edu)
  • We welcome enthusiastic masters students on our computational voyages of discovery into genomes. (lu.se)
  • Efficient regulation of bacterial genes in response to the environmental stimulus results in unique gene clusters known as operons. (biomedcentral.com)
  • Here, the function of regulation is quite clear: expressing energy and carbon, that a number around 0.2% would be the right genes at the right time will enable the cell to make the expected, and that the difference is more or less specific to the lac most of the resources within its reach, by maximizing the uptake operon [7]. (lu.se)
  • An operon is a set of adjacent genes which are transcribed into a single messenger RNA. (researchgate.net)
  • Genes are transcriptional units, and include bacterial operons. (yeastgenome.org)
  • Operons aiding microbial survival are crucial in understanding the gene regulation, identification of new pathways and novel products in diverse environmental settings. (biomedcentral.com)
  • human gut microbiome, data repositories, large-scale and integrative computational tools, modelling, immunomodulation, drug screening Background The human gastrointestinal tract is a complex ecosystem in which eukaryotic cells continuously interact with nutrients and with the complex microbial population of the gut microbiota [1]. (deepdyve.com)
  • Computational and Structural Biotechnology Journal (2022). (cd-genomics.com)
  • Metagenomic operon prediction thus remains an understudied plane. (biomedcentral.com)
  • Computational prediction of RpoS and RpoD regulatory sites in Geobacter sulfurreducens using sequence and gene expression information. (umass.edu)
  • Computational prediction of conserved operons and phylogenetic footprinting of transcription regulatory elements in the metal-reducing bacterial family Geobacteraceae. (umass.edu)
  • This paper presents the results of a theoretical and numerical study on the analysis of bistable behavior of the most studied gene regulatory network, the lac operon, in terms of the model parameters. (yasar.edu.tr)
  • To achieve such a goal, strategies that combine the different theoretical and computational methods to identify proteins and generate a set of plausible alternative network topologies for the process of interest are needed. (biomedcentral.com)
  • I. Develop computational methods for modeling & design of proteins, in the program Rosetta ( www.rosettacommons.org ). (ucsf.edu)
  • They then measured the level of the sigE operon proteins being produced in the cell. (fieldofscience.com)
  • As a result, the life sciences have become increasingly computational in nature, and bioinformatics has taken on a central role in research studies. (researchgate.net)
  • Operons allow prokaryotes to efficiently circumvent environmental stresses. (researchgate.net)
  • This page displays every known transcription unit of this operon and their known regulation. (unam.mx)
  • Here you might use a short transcription terminator sequence (e.g., a T0 terminator) to substitute over nucleotides early in the operon of interest, effectively blocking downstream mRNA synthesis across the operon as well. (inscripta.com)
  • For organisms with active experimental communities, ongoing efforts are required to update those annotations to reflect new computational inferences, and new gene identifications and pathways reported in the experimental literature. (sri.com)
  • In the case of the lac operon of E. coli, a well-studied system for whether a gene is regulated. (lu.se)
  • In each sentence, the event (triggered by the verb activate ) and its participants ( narL gene product as the CAUSE and nitrate reductase operon as the THEME) are identical. (nactem.ac.uk)
  • MetaRon identifies operons without any experimental or functional information. (biomedcentral.com)
  • however, experimental/functional information about operons is absent in metagenomic data. (biomedcentral.com)
  • Experimental identification of metagenomic operons is an intensive and challenging process due to everchanging formulation of operons with respect to environmental stimulus. (biomedcentral.com)
  • In particular we use tightly integrated computational and experimental, multi-omic approaches to discover the processes underlying how cells behave (or misbehave) and accordingly how cancers develop and grow. (stanford.edu)
  • By building new functions through a combination of computational design and experimental engineering, I also hope to learn how molecular design principles shape systems-level properties of biological functions. (ucsf.edu)
  • In the Center, both computational and experimental approaches are used to understand the mechanism of these pumps on cellular and molecular levels. (oucreate.com)
  • Computational searches for similar RNA structures in the leader regions of various bacteria have identified the conserved Leu attenuators in various Gammaproteobacteria, and in some bacteria from the Firmicutes and Thermotogales phyla [ 15135544 ]. (lbl.gov)
  • SMRT-Cappable-seq reveals complex operon variants in bacteria. (cd-genomics.com)
  • Monitoring lineages of growing and dividing bacteria reveals an inducible memory of mar operon expression. (ista.ac.at)
  • The proposed project explores a previously uncharacterized link between post-transcriptional RNA operons and DDR. (europa.eu)
  • There are plentiful computational methods which focus on integrative data analysis of humans, and model organisms, like mouse and drosophila. (uni-frankfurt.de)
  • Dr. Deed's research focuses on using computational modeling to understand how macromolecular structures assemble from their component parts. (kcbioinformatics.org)
  • Extended Data Fig. 1 Compound and Operon structures. (thebrighterside.news)
  • Our goal is the development of a new approach based on the use and combination of mathematical, theoretical and computational methods to identify the topology of a target network. (biomedcentral.com)
  • Trained in organic chemistry at University of Bergen (MSc 1983), including using computer-based expert system (SECS) and computational methods for strategies in organic synthesis. (ntnu.edu)
  • In addition, the effect of identified candidate mutations on protein stability and interactions was assessed quantitatively with well-established computational methods. (biomedcentral.com)
  • The lac operon of E. coli is but one example of how enzyme and transporter production can be made conditional on the presence of a nutrient to catabolize. (lu.se)
  • Presumably, this study is the first organized effort to predict metagenomic operons and perform a detailed analysis in association with a disease, in this case type 2 diabetes . (biomedcentral.com)
  • We selected a subset of 245 isolates for further genomic analysis to more evenly sample across outbreaks and to reduce computational demands. (cdc.gov)
  • An international team of researchers including scientists at the University of Basel, has now discovered a new antibiotic by computational analysis and deciphered its mode of action. (thebrighterside.news)
  • Rockhopper is a comprehensive and user-friendly system for computational analysis of bacterial RNA-seq data. (multiqc.info)
  • Most recently, we have focused on application of computational protein design to endow cells with the ability to sense and respond to new molecular signals and orchestrate desired biological responses, one of the most fundamental capabilities of living systems (Glasgow*, Huang*, Mandell* et al. (ucsf.edu)
  • These efforts demonstrate the power of standardized and reproducible computational workflows for integrating and analysing varied omics data and gaining deeper insights into microbe community structure and function as well as host-microbe interactions. (deepdyve.com)
  • We also demonstrate the use of operons as a subset to represent the trends of secondary metabolites in whole-metagenome data and the role of secondary metabolites in the occurrence of disease condition. (biomedcentral.com)
  • In order to test that this operon was involved in cell membrane responses to antibiotics the lab carried out a variety of experiments, all producing evidence that lead towards this conclusion. (fieldofscience.com)
  • The InscriptaDesigner software utilizes a powerful computational approach for optimal CRISPR-based editing, which includes a scoring system for each individual design. (inscripta.com)
  • We present a computational model for calculating the yield of radiation-induced chromosomal aberrations in human cells based on a stochastic Monte Carlo approach and calibrated using the relative frequencies and distributions of chromosomal aberrations reported in the literature. (bioone.org)
  • Regulons, as groups of transcriptionally co-regulated operons, are the basic units of cellular response systems in bacterial cells. (niu.edu)
  • P. aeruginosa chromosome contains multiple operons encoding multidrug efflux transporters. (oucreate.com)
  • Finally, we identified 1,232,407 unique operons from 145 paired-end human gut metagenome samples. (biomedcentral.com)
  • IEEE Computational Science & Engineering , 2:56-59, 2000. (uiuc.edu)