Affiliation: Los Alamos National Laboratory
- Using sequence-specific chemical and structural properties of DNA to predict transcription factor binding sitesAmy 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...
- Prediction of metabolic reactions based on atomic and molecular properties of small-molecule compoundsFangping 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...
- Binding of nucleoid-associated protein fis to DNA is regulated by DNA breathing dynamicsKristy 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...
- Prediction of oxidoreductase-catalyzed reactions based on atomic properties of metabolitesFangping 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...
- Carbon-fate maps for metabolic reactionsFangping 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...
- Improved predictions of transcription factor binding sites using physicochemical features of DNAMark Maienschein-Cline
Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
Nucleic Acids Res 40:e175. 2012....