Quantitative Biology
Exposure to psychoactive substances during pregnancy, such as cannabis, can disrupt neurodevelopment and alter large-scale brain networks, yet identifying their neural signatures remains challenging. We introduced KOCOBrain: KuramotO…
Lattice-based random walk models are widely used to study populations of migrating cells with motility bias and proliferation. Crowding is typically represented by volume exclusion, where each lattice site can be occupied by at most one…
The ethical and legal imperative to share research data without causing harm requires careful attention to privacy risks. While mounting evidence demonstrates that data sharing benefits science, legitimate concerns persist regarding the…
A central idea in understanding brains and building artificial intelligence is that structure determines function. Yet, how the brain's complex structure arises from a limited set of genetic instructions remains a key question. The ultra…
On broadly Copernican grounds, we are entitled to assume that apparently behaviorally sophisticated extraterrestrial entities ("aliens") would be conscious. Otherwise, we humans would be inexplicably, implausibly lucky to have…
Mathematical modeling allows us to better understand myeloproliferative neoplasms (MPN), a group of blood cancers, emergence and development. We test different mathematical models on an initial cohort to determine the emergence and…
Cancer is a complex genetic disease involving uncontrolled cell growth and proliferation, and necessitates effective targeting of dysregulated cellular pathways underlying cancer progression. Multiple genetic and epigenetic alterations…
Cells of diatoms and related algae with complex plastids of red algal origin are highly compartmentalized. These plastids are surrounded by four envelope membranes, which also define the periplastidic compartment (PPC), the space between…
Structural dynamics of macromolecules is critical to their structural-function relationship. Cryogenic electron microscopy (CryoEM) provides snapshots of vitrified protein at different compositional and conformational states, and the…
Partial differential equation (PDE) models for infectious diseases, while less common than their ordinary differential equation (ODE) counterparts, have found successful applications for many years. Such models are typically of…
Rationale: Transcranial magnetic stimulation (TMS)-based measures such as resting motor threshold (RMT) and short interval intracortical inhibition (SICI) are widely employed to study motor cortical and corticospinal tract function, and…
In the context of global warming, tree populations rely on two primary mechanisms of adaptation: phenotypic plasticity, which enables individuals to adjust their behavior in response to environmental stress, and genetic evolution, driven by…
While large neural nets perform impressively on specific tasks, they are unreliable and unsafe, as is shown by the persistent hallucinations of large language models. This paper shows that large neural nets are intrinsically unreliable,…
Infectious disease superspreading caused by heterogeneity in contact behavior has been observed to be an important determinant of epidemic dynamics and size in both empirical and theoretical settings. However, it has also been observed that…
The incidence of advanced renal cell carcinoma(RCC) has been rising, presenting significant challenges due to the limited efficacy and severe side effects of traditional radiotherapy and chemotherapy. While combination immunotherapies show…
Wolbachia, a maternally transmitted endosymbiont, offers a powerful biological control strategy for mosquito-borne diseases such as dengue, Zika, and malaria. We develop an integro-difference equation (IDE) model that integrates Wolbachia's…
Sleep is thought to support memory consolidation and the recovery of optimal energetic regime by reorganizing synaptic connectivity, yet how plasticity across hierarchical brain circuits contributes to abstraction and energy efficiency…
We suggest a new approach to $\beta$-diversity in ecological systems, based on the energy of the graph sheaf Laplacian associated with the sample data. This scalar quantity is easily computable using methods of linear algebra. We show using…
Motivation: High-throughput sequencing (HTS) enables population-scale genomics but generates massive datasets, creating bottlenecks in storage, transfer, and analysis. FASTQ, the standard format for over two decades, stores one byte per…
The accurate prediction of protein-ligand binding affinity is important for drug discovery yet remains challenging for multi-domain proteins, where inter-domain dynamics and flexible linkers govern molecular recognition. Current geometric…