452 citations · 656 across the 7 of their papers we have counts for
7 papers
Inferring the shape of data: A probabilistic framework for analyzing experiments in the natural sciences
Korak Kumar Ray, Anjali R. Verma, Ruben L. Gonzalez +1
A critical step in data analysis for many different types of experiments is the identification of features with theoretically defined shapes in N-dimensional datasets; examples of…
Fidelity of bacterial translation initiation: a stochastic kinetic model
Dipanwita Ghanti, Kelvin Caban, Joachim Frank +2
During the initiation stage of protein synthesis, a ribosomal initiation complex (IC) is assembled on a messenger RNA (mRNA) template. In bacteria, the speed and accuracy of this a…
Quantitative Connection Between Ensemble Thermodynamics and Single-Molecule Kinetics: A Case Study Using Cryogenic Electron Microscopy and Single-Molecule Fluorescence Resonance Energy Transfer Investigations of the Ribosome
Colin D. Kinz-Thompson, Ajeet K. Sharma, Joachim Frank +2
At equilibrium, thermodynamic and kinetic information can be extracted from biomolecular energy landscapes by many techniques. However, while static, ensemble techniques yield ther…
Hierarchically-coupled hidden Markov models for learning kinetic rates from single-molecule data
Jan-Willem van de Meent, Jonathan E. Bronson, Frank Wood +2
We address the problem of analyzing sets of noisy time-varying signals that all report on the same process but confound straightforward analyses due to complex inter-signal heterog…
Graphical models for inferring single molecule dynamics
Jonathan E. Bronson, Jake M. Hofman, Jingyi Fei +2
Background: The recent explosion of experimental techniques in single molecule biophysics has generated a variety of novel time series data requiring equally novel computational to…
Allosteric collaboration between elongation factor G and the ribosomal L1 stalk directs tRNA movements during translation
Jingyi Fei, Jonathan E. Bronson, Jake M. Hofman +3
Determining the mechanism by which transfer RNAs (tRNAs) rapidly and precisely transit through the ribosomal A, P and E sites during translation remains a major goal in the study o…
Learning Rates and States from Biophysical Time Series: A Bayesian Approach to Model Selection and Single-Molecule FRET Data
Jonathan E. Bronson, Jingyi Fei, Jake M. Hofman +2
Time series data provided by single-molecule Forster resonance energy transfer (sm-FRET) experiments offer the opportunity to infer not only model parameters describing molecular c…