86 citations · 134 across the 11 of their papers we have counts for
12 papers
Multitask Bayesian Neural Networks for Multiparameter Protein Engineering
Fabio Herrera-Rocha, David Medina-Ortiz, Desiree Wyrzykala +2
Simultaneously engineering multiple protein properties remains a major challenge. Existing machine learning-based pipelines for protein engineering often model properties separatel…
Quaternionic Response Geometry for Proteins: Toward a Noncommutative Theory of Ordered Deformations
Xiaoting Chen, Chon-Fai Kam, Yu Li +6
Protein function may depend not only on endpoint conformations but also on the ordered deformation histories through which they are reached. This distinction is relevant to alloste…
Machine Learning-Driven Enzyme Mining: Opportunities, Challenges, and Future Perspectives
Yanzi Zhang, Felix Moorhoff, Sizhe Qiu +4
Enzyme mining is rapidly evolving as a data-driven strategy to identify biocatalysts with tailored functions from the vast landscape of uncharacterized proteins. The integration of…
Best Practices for Machine Learning-Assisted Protein Engineering
Fabio Herrera-Rocha, David Medina-Ortiz, Fabian Mauz +2
Data-driven modeling based on Machine Learning (ML) is becoming a central component of protein engineering workflows. This perspective presents the elements necessary to develop ef…
Geometric deep learning assists protein engineering. Opportunities and Challenges
Julián García-Vinuesa, Jorge Rojas, Nicole Soto-García +7
Protein engineering is experiencing a paradigmatic shift through the integration of geometric deep learning into computational design workflows. While traditional strategies, such…
From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering
Wen-ran Li, Xavier F. Cadet, David Medina-Ortiz +6
Protein design with desirable properties has been a significant challenge for many decades. Generative artificial intelligence is a promising approach and has achieved great succes…
Model-based assessment of sampling protocols for infectious disease genomic surveillance
Sebastian Contreras, Karen Y. Oróstica, Anamaria Daza-Sanchez +8
Genomic surveillance of infectious diseases allows monitoring circulating and emerging variants and quantifying their epidemic potential. However, due to the high costs associated…
Mutational signatures and transmissibility of SARS-CoV-2 Gamma and Lambda variants
Karen Y. Oróstica, Sebastian Contreras, Sebastian B. Mohr +12
The emergence of SARS-CoV-2 variants of concern endangers the long-term control of COVID-19, especially in countries with limited genomic surveillance. In this work, we explored ge…
Peptipedia: a comprehensive database for peptide research supported by Assembled predictive models and Data Mining approaches
Cristofer Quiroz, Yasna Barrera Saavedra, Benjamín Armijo-Galdames +4
Motivation: Peptides have attracted the attention in this century due to their remarkable therapeutic properties. Computational tools are being developed to take advantage of exist…
Combination of digital signal processing and assembled predictive models facilitates the rational design of proteins
David Medina-Ortiz, Sebastian Contreras, Juan Amado-Hinojosa +4
Predicting the effect of mutations in proteins is one of the most critical challenges in protein engineering; by knowing the effect a substitution of one (or several) residues in t…
Statistically-based methodology for revealing real contagion trends and correcting delay-induced errors in the assessment of COVID-19 pandemic
Sebastián Contreras, Juan Pablo Biron-Lattes, H. Andrés Villavicencio +3
COVID-19 pandemic has reshaped our world in a timescale much shorter than what we can understand. Particularities of SARS-CoV-2, such as its persistence in surfaces and the lack of…
A multi-group SEIRA model for the spread of COVID-19 among heterogeneous populations
Sebastian Contreras, H. Andres Villavicencio, David Medina-Ortiz +2
The outbreak and propagation of COVID-19 have posed a considerable challenge to modern society. In particular, the different restrictive actions taken by governments to prevent the…