Quantitative Biology
Biological systems exhibit marked molecular asymmetry, with proteins based predominantly on L-amino acids and nucleic acids and carbohydrates largely composed of D-sugars. Explanations for homochirality include asymmetric photochemistry,…
Missense variant interpretation remains challenging because pathogenicity depends on heterogeneous evidence from population frequency, evolutionary conservation, transcript context, amino acid substitution severity, prior pathogenicity…
Animal behavior unfolds across many timescales, from fast movement patterns to slow changes in internal states such as hunger, arousal, and circadian phase. These slow variables are rarely measured directly and must instead be inferred from…
Chromatin regulators can alter transcriptional programs by modifying the accessibility of regulatory DNA elements. Understanding how regulatory sequences differ between wild-type (WT) and knockout (KO) conditions is crucial for deciphering…
Generative AI research increasingly confronts a shared problem: systems must sustain yet govern their own generative activity when uncertainty is high, evidence is missing, or context is insufficient. This position paper argues that…
In biological systems, sensing is not performed by the brain alone: the body deforms, vibrates, and filters external stimuli before they are transduced into neural signals. In engineered systems, this processing burden is placed largely on…
The design of RNA molecules that interact with specific proteins is a critical challenge in experimental and computational biology. Despite recent progress in natural language modeling and deep learning-based protein design, there remains…
Proteins encode diverse functions within complex three-dimensional structures, yet most deep learning representations remain highly entangled, obscuring the biophysical signals that underlie function. Here we introduce ProtDiS, a…
Long non-coding RNAs (lncRNAs) are emerging regulatory molecules implicated in chronic disease pathogenesis, including Type 2 Diabetes Mellitus (T2D). We investigated ten literature reported lncRNAs associated with T2D: MALAT1, MEG3, MIAT,…
Multicellular self-organization drives development in biological organisms, yet a comprehensive theory is lacking as basic properties of cells can complicate common approaches. Framing such properties by dynamic graphs led to new…
Although obtaining deep brain activity from non-invasive scalp electroencephalography (sEEG) is crucial for neuroscience and clinical diagnosis, directly generating high-fidelity intracranial electroencephalography (iEEG) signals remains a…
Achieving advanced machine intelligence remains a central challenge in AI research, often approached through scaling neural architectures and generative models. However, biological systems offer a broader repertoire of strategies for…
Understanding how the brain integrates motor suppression with motivational processes remains a fundamental question in neuroscience. The rostral Pedunculopontine nucleus, a brainstem structure involved in motor control, has been shown to…
Allometric scaling laws, such as Kleiber's law for metabolic rate, highlight how efficiency emerges with size across living systems. The brain, with its characteristic sublinear scaling of activity, has long posed a puzzle: why do larger…
Identifying enzymes that catalyze target biochemical reactions is a key step in computational enzyme discovery and biocatalyst design. Recent representation-learning methods formulate this problem as enzyme--reaction matching, where paired…
Menopause fundamentally reshapes female physiology, yet current understanding is limited by small longitudinal cohorts that characterize it as a gradual transition. Large-scale biomedical datasets remain underutilized because the age of the…
Extracellular matrix (ECM) remodeling is central to a wide variety of healthy and diseased tissue processes. Unfortunately, predicting ECM remodeling under various chemical and mechanical conditions has proven to be excessively challenging,…
Inferring the biophysical parameters of conductance-based models (CBMs) from experimentally accessible recordings remains a central challenge in computational neuroscience. Spike times are the most widely available data, yet they reveal…
The regularity of ecosystem size spectra is one of the most intriguing and relevant phenomena on our planet. Pelagic size spectra generally show a log-linearly downtrending shape, following a power-law distribution. A constant log-linear…
Hydrogen cations, or protons, provide the medium by which energy is stored and converted in biological systems. Such pre-eminence relies on the interplay between interfacial and bulk chemical transformations, according to mechanisms that…