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Genomic Foundation Models (GFMs), such as Evolutionary Scale Modeling (ESM), have demonstrated significant success in variant effect prediction. However, their adversarial robustness remains largely unexplored. To address this gap, we…
The stability of model proteins with designed sequences is assessed in terms of the number of sequences (obtained from the designed sequence through mutations), which fold into 5the ``native'' conformation. By a complete enumeration of the…
Recent advances in generative modeling have enabled significant progress in structure-based drug design (SBDD). Existing methods typically condition molecule generation on empty binding pockets from holo complexes, overlooking informative…
Extended vector meson dominance model, that allows to describe the electromagnetic form factors of nucleons obeying the asymptotic quark counting rule prescriptions and contains the minimal number of free parameters, is presented. We get a…
With the fast evolution of high-throughput technology, longitudinal gene expression experiments have become affordable and increasingly common in biomedical fields. Generalized estimating equation (GEE) approach is a widely used statistical…
Protein contacts contain important information for protein structure and functional study, but contact prediction from sequence information remains very challenging. Recently evolutionary coupling (EC) analysis, which predicts contacts by…
Cancer cell mutations occur when cells undergo multiple cell divisions, and these mutations can be spontaneous or environmentally-induced. The mechanisms that promote and sustain these mutations are still not fully understood. This study…
Cancer is a primary cause of human death, but discovering drugs and tailoring cancer therapies are expensive and time-consuming. We seek to facilitate the discovery of new drugs and treatment strategies for cancer using variational…
Genetic variants in cis-regulatory elements or trans-acting regulators commonly influence the quantity and spatiotemporal distribution of gene transcription. Recent interest in expression quantitative trait locus (eQTL) mapping has…
The prediction modeling of drug-target interactions is crucial to drug discovery and design, which has seen rapid advancements owing to deep learning technologies. Recently developed methods, such as those based on graph neural networks…
Non-genetic forms of antimicrobial drug resistance can result from cell-to-cell variability that is not encoded in the genetic material. Data from recent studies also suggest that non-genetic mechanisms can facilitate the development of…
Antimicrobial resistance is an important public health concern that has implications in the practice of medicine worldwide. Accurately predicting resistance phenotypes from genome sequences shows great promise in promoting better use of…
Among countless channels of hard exclusive reactions, the kaon electromagnetic form factors (EMFFs) are of special interest, which have been measured up to $Q^2 \sim 50\;{\rm GeV}^2$ in the timelike domain. The kaon EMFFs thereby serve an…
${\bf Background}$ Knowledge of nucleon structure is today ever more of a precision science, with heightened theoretical and experimental activity expected in coming years. At the same time, a persistent gap lingers between theoretical…
Drug optimization has become increasingly crucial in light of fast-mutating virus strains and drug-resistant cancer cells. Nevertheless, it remains challenging as it necessitates retaining the beneficial properties of the original drug…
Stochastic models of sequential mutation acquisition are widely used to quantify cancer and bacterial evolution. Across manifold scenarios, recurrent research questions are: how many cells are there with $n$ alterations, and how long will…
Graph Contrastive Learning (GCL) is a powerful self-supervised learning framework that performs data augmentation through graph perturbations, with growing applications in the analysis of biological networks such as Gene Regulatory Networks…
We report on the near edge X-ray absorption fine structure (NEXAFS) spectroscopy of hybrid organic-inorganic resists. These materials are nonchemically amplified systems based on Si, Zr, and Ti oxides, synthesized from organically modified…
The recent expansion of multidrug-resistant (MDR) pathogens poses significant challenges in treating healthcare-associated infections. Although antibacterial resistance occurs by numerous mechanisms, active efflux of the drugs is a critical…
Can we understand and predict the evolutionary pathways by which bacteria acquire multi-drug resistance (MDR)? These questions have substantial potential impact in basic biology and in applied approaches to address the global health…