Quantitative Biology
Semi-directed networks are partially directed graphs that model evolution where the directed edges represent reticulate evolutionary events. We present an algorithm that reconstructs binary $n$-leaf semi-directed level-1 networks in $O(…
Similarly to gear systems in vehicles, most chemical reaction networks (CRNs) involved in energy transduction have at their disposal multiple transduction pathways, each characterized by distinct efficiencies. We conceptualize these…
Over the past decades, cognitive neuroscientists and behavioral economists have recognized the value of describing the process of decision making in detail and modeling the emergence of decisions over time. For example, the time it takes to…
Major depressive disorder persistently stands as a major public health problem. While some progress has been made toward effective treatments, the neural mechanisms that give rise to the disorder remain poorly understood. In this…
Complexity is a ubiquitous concept in contemporary science and everyday life. A complex dynamical system is usually characterized by a blend of order and disorder, as well as emergent phenomena that often span multiple temporal and spatial…
Designing structurally stable RNA sequences with specific motifs and other desirable properties is an important challenge in bioinformatics. The potential design space increases exponentially with the length of the RNA to be engineered,…
Social anxiety disorder (SAD) is associated with heightened physiological arousal in social-evaluative contexts, but it remains unclear whether such autonomic reactivity extends to non-evaluative cognitive stressors. This study investigated…
Combinatorial optimization algorithm is essential in computer-aided drug design by progressively exploring chemical space to design lead compounds with high affinity to target protein. However current methods face inherent challenges in…
The accurate prediction of chromosomal instability from the morphology of circulating tumor cells (CTCs) enables real-time detection of CTCs with high metastatic potential in the context of liquid biopsy diagnostics. However, it presents a…
The Antibiotic Resistance Microbiology Dataset (ARMD) is a de-identified resource derived from electronic health records (EHR) that facilitates research in antimicrobial resistance (AMR). ARMD encompasses big data from adult patients…
Large-scale crises, including wars and pandemics, have repeatedly shaped human history, and their simultaneous occurrence presents profound challenges to societies. Understanding the dynamics of epidemic spread during warfare is essential…
We propose to analyze dynamically changing brain networks by decomposing them into three orthogonal components through the Hodge decomposition. We propose to quantify the magnitude and relative strength of each component. We performed…
Semi-directed networks provide a graphical structure for describing the evolutionary history of organisms in the presence of hybridization. We introduce two algorithms for reconstructing semi-directed level-1 phylogenetic networks from…
Endowing brain anatomy, dynamics, and function with a network structure is becoming standard in neuroscience. In its simplest form, a network is a collection of units and relationships between them. The pattern of relations among the units…
Parr et al., 2025 examines how auto-regressive and deep temporal models differ in their treatment of non-Markovian sequence modelling. Building on this, we highlight the need for dissociating model architectures, i.e., how the predictive…
We demonstrate that final-state uncertainty is ubiquitous in multistable systems of coupled neuronal maps, meaning that predicting whether one such system will eventually be chaotic or nonchaotic is often nearly impossible. We propose a…
Accurately annotating and controlling protein function from sequence data remains a major challenge, particularly within homologous families where annotated sequences are scarce and structural variation is minimal. We present a two-stage…
Brain rhythms seem central to understanding the neurophysiological basis of human cognition. Yet, despite significant advances, key questions remain unresolved. In this comprehensive position paper, we review the current state of the art on…
Autocatalysis underlies the ability of chemical and biochemical systems to replicate. Autocatalysis was recently defined stoichiometrically for reaction networks; five types of minimal autocatalytic networks, termed autocatalytic cores were…
Neuronal networks alternate between high- and low-activity regimes, known as up and down states. They also display rhythmic patterns essential for perception, memory consolidation, and sensory processing. Despite their importance, the…