Quantitative Biology
There is strong and diverse evidence for mental rotation (MR) abilities in adults. However, current evidence for MR in children rests on just a few behavioral paradigms adapted from the adult literature. Here, we leverage recent…
This work presents a new framework for procedural generation of dynamic 3D plant model geometries, which has been implemented in the Helios modeling system. Key goals of this work were to develop a model that 1) has a generalized set of…
Bone marrow cell cytomorphology analysis is critical for the diagnosis of hematological malignancies but remains a labor-intensive process subject to significant inter-observer variability. While recent foundation models have shown promise…
DNA language models have advanced genomics, but their downstream performance varies widely due to differences in tokenization, pretraining data, and architecture. We argue that a major bottleneck lies in tokenizing sparse and unevenly…
In this work, we integrate theoretical modeling, molecular simulation, and empirical analysis to identify and characterize evolutionary hysteresis. We first show how epistatic interactions create bistable fitness landscapes and structural…
This overview of integrated information theory (IIT) emphasizes IIT's "consciousness-first" approach to what exists. Consciousness demonstrates to each of us that something exists--experience--and reveals its essential properties--the…
Networks constitute fundamental organizational structures across biological systems, although conventional graph-theoretic analyses capture exclusively pairwise interactions, thereby omitting the intricate higher-order relationships that…
The origin of life on Earth via the spontaneous emergence of a protocell prior to Darwinian evolution remains a fundamental open question in physics and chemistry. Here, we develop a conceptual framework based on information theory and…
Chemical reaction network theory provides powerful tools for rigorously understanding chemical reactions and the dynamical systems and differential equations that represent them. A frequent issue with mathematical analyses of these networks…
Trajectory inference is used to order single-cell omics data along a path that reflects a continuous transition between cells. This approach is useful for studying processes like cell differentiation, where a stem cell matures into a…
Spike sorting is an essential process in neural recording, which identifies and separates electrical signals from individual neurons recorded by electrodes in the brain, enabling researchers to study how specific neurons communicate and…
Emotion and fairness play a key role in mediating socioeconomic decisions in humans; however, the underlying neurocognitive mechanism remains largely unknown. This exploratory study unraveled the interplay between agents' emotions and the…
This article considers the problem of 3-dimensional genome reconstruction for single-cell data, and the uniqueness of such reconstructions in the setting of haploid organisms. We consider multiple graph models as representations of this…
Cell biologists study in parallel the morphology of cells with the regulation mechanisms that modify this morphology. Such studies are complicated by the inherent heterogeneity present in the cell population. It remains difficult to define…
Detecting walking pattern abnormalities in dairy cows early on holds the potential to reduce the occurrence of clinical lameness. This study aimed to predict gait scores in non-clinically lame dairy cows by using gait attributes based on…
We propose and analyze a model for antibiotic resistance transfer in a bacterial biofilm and examine antibiotic dosing strategies that are effective in bacterial elimination. In particular, we consider a 1-D model of a biofilm with…
Working memory is a promising paradigm for assessing cognitive ergonomics of brain states in brain-computer interfaces(BCIs). This study decodes these states with a focus on environmental illumination effects via two distinct working memory…
Accurate interception of moving objects, such as catching a ball, requires the nervous system to overcome sensory delays, noise, and environmental dynamics. One key challenge is predicting future object motion in the presence of sensory…
ATPases cyclically convert chemical energy in the form of ATP gradients into directed motion inside cells. To function, ATPases rely on allosteric communication between at least two binding sites, an internal signaling mechanism that is not…
We investigate a type of lunar calendar known as lists of the 'nights of the moon', found throughout East Polynesia, including Rapa Nui (Easter Island). Using computational methods, we analyzed the lexical and structural divergence of 49…