Fangping Mu

Summary

Affiliation: Los Alamos National Laboratory
Country: USA

Publications

  1. pmc Prediction of metabolic reactions based on atomic and molecular properties of small-molecule compounds
    Fangping Mu
    Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    Bioinformatics 27:1537-45. 2011
  2. pmc Using sequence-specific chemical and structural properties of DNA to predict transcription factor binding sites
    Amy L Bauer
    Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
    PLoS Comput Biol 6:e1001007. 2010
  3. pmc Binding of nucleoid-associated protein fis to DNA is regulated by DNA breathing dynamics
    Kristy Nowak-Lovato
    Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
    PLoS Comput Biol 9:e1002881. 2013
  4. ncbi request reprint Carbon-fate maps for metabolic reactions
    Fangping Mu
    Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    Bioinformatics 23:3193-9. 2007
  5. ncbi request reprint Prediction of oxidoreductase-catalyzed reactions based on atomic properties of metabolites
    Fangping Mu
    Theoretical Biology and Biophysics Group, Theoretical Division Los Alamos, NM 87545, USA
    Bioinformatics 22:3082-8. 2006
  6. pmc Automated genomic context analysis and experimental validation platform for discovery of prokaryote transcriptional regulator functions
    Ricardo Marti-Arbona
    Bioscience Division, Los Alamos National Laboratory, PO Box 1663, Los Alamos, NM 87545, USA
    BMC Genomics 15:1142. 2014
  7. pmc Improved predictions of transcription factor binding sites using physicochemical features of DNA
    Mark Maienschein-Cline
    Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
    Nucleic Acids Res 40:e175. 2012

Collaborators

  • Amy L Bauer
  • Anny Usheva
  • Elizabeth Hong-Geller
  • Ricardo Marti-Arbona
  • Kristy Nowak-Lovato
  • William S Hlavacek
  • Mark Maienschein-Cline
  • Pat J Unkefer
  • Clifford J Unkefer
  • Kristy L Nowak-Lovato
  • Melinda S Wren
  • Ludmil B Alexandrov
  • Afsheen Banisadr
  • Alan R Bishop
  • Kim Ø Rasmussen
  • Boian S Alexandrov
  • Aaron R Dinner

Detail Information

Publications7

  1. pmc Prediction of metabolic reactions based on atomic and molecular properties of small-molecule compounds
    Fangping Mu
    Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    Bioinformatics 27:1537-45. 2011
    ..Here, we develop an approach for predicting the reactivity of small-molecule metabolites in enzyme-catalyzed reactions that combines expert knowledge, computational chemistry and machine learning...
  2. pmc Using sequence-specific chemical and structural properties of DNA to predict transcription factor binding sites
    Amy L Bauer
    Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
    PLoS Comput Biol 6:e1001007. 2010
    ..SiteSleuth also outperforms QPMEME, a method similar to SiteSleuth in that it involves a learning algorithm. The main advantage of SiteSleuth is a lower false positive rate...
  3. pmc Binding of nucleoid-associated protein fis to DNA is regulated by DNA breathing dynamics
    Kristy Nowak-Lovato
    Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
    PLoS Comput Biol 9:e1002881. 2013
    ..We conclude that Fis binding is associated with DNA breathing dynamics, which in turn may be regulated by various nucleotide modifications...
  4. ncbi request reprint Carbon-fate maps for metabolic reactions
    Fangping Mu
    Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    Bioinformatics 23:3193-9. 2007
    ..Analysis of isotope labeling patterns requires knowledge of the fates of individual atoms and moieties in reactions, which can be difficult to collect in a useful form when considering a large number of enzymatic reactions...
  5. ncbi request reprint Prediction of oxidoreductase-catalyzed reactions based on atomic properties of metabolites
    Fangping Mu
    Theoretical Biology and Biophysics Group, Theoretical Division Los Alamos, NM 87545, USA
    Bioinformatics 22:3082-8. 2006
    ..To address this challenge, we investigate how machine learning can be used to predict potential substrates and products of oxidoreductase-catalyzed reactions...
  6. pmc Automated genomic context analysis and experimental validation platform for discovery of prokaryote transcriptional regulator functions
    Ricardo Marti-Arbona
    Bioscience Division, Los Alamos National Laboratory, PO Box 1663, Los Alamos, NM 87545, USA
    BMC Genomics 15:1142. 2014
    ..We used these characteristics to predict the metabolic involvement for a Transcriptional Regulator (TR) of unknown function, identified and confirmed its biological activity...
  7. pmc Improved predictions of transcription factor binding sites using physicochemical features of DNA
    Mark Maienschein-Cline
    Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
    Nucleic Acids Res 40:e175. 2012
    ....