PLOS Computational Biology

by Matthew S. Woodstock, Jann Paul Mattern, Zhen Wu, Gregory L. Britten

Because they are based on established theory, mechanistic models are essential for projecting ecological responses to novel conditions. Yet mechanistic agent-based model (ABM) applications have often been limited by computational constraints. This paper introduces SwimmingIndividuals, an open-...

by Miguel Fernandez-Martin, Camila Pontes, Victoria Ruiz-Serra, Alfonso Valencia

Evolutionarily conserved protein-protein interactions (PPIs) reveal fundamental biological processes. However, predicting protein function solely from these interactions provides an incomplete picture of biological systems. Computational methods for predicting PPIs often struggle due to limi...

by Rana A. Barghout, Lya Chiñas Serrano, Benjamin Sanchez-Lengeling, Radhakrishnan Mahadevan

The construction of accurate enzyme-constrained genome-scale models (ecGEMs) remains a critical challenge in systems biology, limited by sparse kinetic data and the need for biologically meaningful representations. This work presents an integrated framework combining CPI-Pred, a ...

by Louis Fostier, Manon Lesage, Violette Thermes, Frédérique Clément, Romain Yvinec

Early oogenesis in juvenile fish establishes the ovarian reserve, which conditions lifelong reproductive capacity. This process is regulated by local hormonal feedback mechanisms, mainly involving Anti-Müllerian Hormone (AMH). In this work, we develop a mechanistic size-structured populat...

by Lubomir Tomaska

Department chairs occupy a pivotal position in the university. Teaching, research, graduate education, and much of the academic community's professional and administrative activity are organized at the departmental level. Yet, despite the importance of the position and the considerable challenges it entails, many scientists assume the role with little ...