Publications
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2023
Santos, Fox, Mohan, O’Malley, Viswanathan, Lubbers. Development of the Senseiver for efficient field reconstruction from sparse observations. Nature Machine Intelligence.
Blanchard, Bhowmik, Fox, Gounley, Glaser, Akpa, Irle. Adaptive language model training for molecular design. Journal of Cheminformatics.
Fox, English, Akpa. Targeting tissues via dynamic human systems modelin in generative design.GenBio Workshop, NeurIPS.
Fox, Ghosh. Active Causal Machine Learning for Molecular Property Prediction. AI4Mat Workshop, NeurIPS.
Fox, Batt, Ruess. Bayesian filtering for model predictive control of stochastic gene expression in single cells. Physical Biology.
Santos, Fox, Lubbers, Lin. Blackout Diffusion: Generative Diffusion Models in Discrete-State Spaces. ICML.
Spannaus, Gounley, Chandra Shekar, Fox, Mohd-Yusof, Schaefferkoetter, Hanson. FrESCO: Framework for Exploring Scalable Computational Oncology. Journal of Open Source Software.
Raymond, Ghaffari, Aguilera, Ron, Morisaki, Fox, May, Stasevich, Munsky. Using Mechanistic Models and Machine Learning to Design Single-Color Multiplexed Nascent Chain Tracking Experiments. Frontiers in Cell Dev. Bio.
2022
(Fox, Fletcher), Fraisse, Aditya, Sosa-Carrilo, Petit, Gilles, Bertaux, Ruess, Batt. Enabling reactive microscopy with MicroMator. Nature Communications.
Santos, Fox, Mohan, Viswanathan, Lubbers. The Senseiver: attention-based global field reconstruction from sparse observations. Neurips workshop on Machine Learning and the Physical Sciences.
Fox. Extracting Information from Stochastic Trajectories of Gene Expression. arXiv preprint.
2021
Fox, Barkai, Krapf. Aging power spectrum of membrane protein transport and other subordinated random walks. Nature Communications.
Jashnsaz, Fox, Munsky, Neuert. Building predictive signaling models by perturbing yeast cells with time-varying stimulations resulting in distinct signaling responses. STAR Protocols.
2020
Jashnsaz, Fox, Hughes, Li, Munsky, Neuert. Diverse cell stimulation kinetics identify predictive signal transduction models. iScience.
Fox, Neuert, Munsky. Optimal Design of Single-Cell Experiments within Temporally Fluctuating Environments. Complexity.
2019
Aguilera, Raymond, Fox, May, Djokic, Morisaki, Stasevich, Munsky. Computational design and interpretation of single-RNA translation experiments. PloS Computational Biology.
Fox and Munsky. The finite state projection based Fisher information matrix approach to estimate and maximize the information in single-cell experiments. PloS Computational Biology.
Vo, Fox, Baetica, Munsky. Bayesian estimation for stochastic gene expression using multifidelity models. Journal of Physical Chemistry B.
2018
Munsky, Li, Fox, Shepherd, Neuert. Distribution shapes govern the discovery of predictive models for gene regulation. Proceedings of the National Academy of Sciences.
2017
Fox and Munsky. Stochasticity or Noise in Biochemical Reactions. arXiv preprint.
2016
Fox, Neuert, Munsky. Finite state projection based bounds to compare chemical equation models using single-cell data. Journal of Chemical Physics.
2015
Munsky, Fox, Neuert. Integrating single-molecule experiments and discrete stochastic models to understand heterogeneous gene trancsription dynamics. Elsevier Methods .
Soltani, Bokes, Fox, Singh. Nonspecific transcription factor binding can reduce noise in the expression of downstream proteins. Physical biology.
N Rangarajan, Fox, Singh, Kulkami, G Rangarajan. Disorder, oscillatory dynamics and state switching: the role of c-Myc. Journal of Theoretical Biology.
2014
Fox and Singh. Stochastic analysis of protein-mediated and microRNA-mediated feedback circuits in HIV. IFAC Proceedings Volumes 47.