Quantitative Biology
Paediatric Acute Myeloid Leukemia is a complex adaptive ecosystem with high morbidity. Current trajectory inference algorithms struggle to predict causal dynamics in AML progression, including relapse and recurrence risk. We propose a…
Pre-training large language models on genomic sequences is a powerful approach for learning biologically meaningful representations. Masked language modeling (MLM) methods, such as DNABERT and Nucleotide Transformer (NT), achieve strong…
The world of beauty is deeply connected to the visual cortex, as perception often begins with vision in both humans and marmosets. In this study, to investigate their functional correspondences, we used 13 healthy human volunteers (9 males…
Tree balance plays an important role in various research areas in phylogenetics and computer science. Typically, it is measured with the help of a balance index or imbalance index. There are more than 25 such indices available, recently…
The vigor of potato plants, defined as the canopy area at the end of the exponential growth stage, depends on the origin and physiological state of the seed tuber. Experiments carried out with six potato varieties in three test fields over…
Functional ultrasound imaging (fUSI) is a cutting-edge technology that measures changes in cerebral blood volume (CBV) by detecting backscattered echoes from red blood cells moving within its field of view (FOV). It offers high…
Understanding the rules underlying organismal development is a major unsolved problem in biology. Each cell in a developing organism responds to signals in its local environment by dividing, excreting, consuming, or reorganizing, yet how…
We present QUBODock, a pip-installable tool that formulates ligand pose generation as a Quadratic Unconstrained Binary Optimization (QUBO) problem and solves it efficiently on CPU or GPU. QUBODock focuses exclusively on pose generation and…
Recent studies have shown how spiking networks can learn complex functionality through error-correcting plasticity, but the resulting structures and dynamics remain poorly studied. To elucidate how these models may link to observed dynamics…
The Eigen model is a prototypical toy model of evolution that is synonymous with the so-called error catastrophe: when mutation rates are sufficiently high, the genetic variant with the largest replication rate does not occupy the largest…
Phytophagous mites in the genus Brevipalpus (Tenuipalpidae) can be major pests, causing direct damage to their host plants or vectoring viruses. However, a phylogeny-based classification to understand their evolution and predict their…
There is a tradeoff between attaining statistical power with large, difficult to gather data sets, and producing highly scalable assays that register brief data samples. Often, as grand-averaging techniques a priori assume…
Robust information representation and its persistent maintenance are fundamental for higher cognitive functions. Existing models employ distinct neural mechanisms to separately address noise-resistant processing or information maintenance,…
Schistosomiasis, a neglected tropical disease caused by Schistosoma parasites, remains a major global health challenge. The Schistosoma mansoni thioredoxin glutathione reductase (SmTGR) is essential for parasite redox balance and immune…
Insight into how information can propagate within cortical networks is essential for a more complete understanding of neural dynamics and computation in complex networks. Networks with clustered connections have previously been shown to…
Highly pathogenic avian influenza (HPAI), especially the H5N1 strain, remains a major threat to animal health, food security, and public health. Recent spillover events in dairy cattle in the United States, linked to wild birds, highlight…
Transcriptomic assays such as the PAM50-based ROR-P score guide recurrence risk stratification in non-metastatic, ER-positive, HER2-negative breast cancer but are not universally accessible. Histopathology is routinely available and may…
Biological organisms are simple at heart: cells, their basic units, perform a variety of behaviors by expressing proteins from DNA-encoded genes. Gene expression though depends on sets of often-convoluted regulatory interactions known as…
Dynamic brain data, teeming with biological and functional insights, are becoming increasingly accessible through advanced measurements, providing a gateway to understanding the inner workings of the brain in living subjects. However, the…
We propose a topological framework for memory and inference grounded in the structure of spike-timing dynamics, persistent homology, and the Context-Content Uncertainty Principle (CCUP). Starting from the observation that polychronous…