Publications

2024

Razo-Mejia, M.. AutoEncoderToolkit.jl: A Julia package for training (Variational) Autoencoders. Journal of Open Source Software (2024). open-access PDF | github repository | AutoEncoderToolkit.jl documentation
Razo-Mejia, M., Mani, M. & Petrov, D. Bayesian inference of relative fitness on high-throughput pooled competition assays. PLoS Comp. Bio. (2024). open-access PDF | paper website | github repository | BarBay.jl documentation

2021

Morrison, M. J., Razo-Mejia, M. & Phillips, R. Reconciling kinetic and thermodynamic models of bacterial transcription. PLoS Comp. Bio. (2021). open-access PDF | github repository

2020

Razo-Mejia, M. et al. First-principles prediction of the information processing capacity of a simple genetic circuit. Phys. Rev. E 102, 022404 (2020). open-access PDF | paper website | github repository

2019

Chure, G., Razo-Mejia, M., et al. Predictive shifts in free energy couple mutations to their phenotypic consequences. PNAS 201907869 (2019) doi:10.1073/pnas.1907869116. open-access PDF | paper website | github repository
Phillips, R. Belliveau, N., Chure, G., Garcia, H., Razo-Mejia, M., & Scholes, Clarissa. Figure 1 Theory Meets Figure 2 Experiments in the Study of Gene Expression. Annu. Rev. Biophys. 48, 121–163 (2019). link
Foster, P. J., Razo-Mejia, M. & Phillips, R. Measuring the Energetic Costs of Embryonic Development. Dev. Cell 48, 591–592 (2019). link

2018

Razo-Mejia, M. et al. Tuning Transcriptional Regulation through Signaling: A Predictive Theory of Allosteric Induction. Cell Syst. 6, 456-469.e10 (2018). open-access PDF | paper website | github repository

2015

Zelcbuch, L., Razo-Mejia, M., et al. An In Vivo Metabolic Approach for Deciphering the Product Specificity of Glycerate Kinase Proves that Both E. coli’s Glycerate Kinases Generate 2-Phosphoglycerate. PLoS One 10, e0122957 (2015). open-access PDF

2014

Razo-Mejia, M. et al. Comparison of the theoretical and real-world evolutionary potential of a genetic circuit. Phys. Biol. 11, 026005 (2014). link