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Hypertension is a highly prevalent condition and a major risk factor for cardiovascular disease. The landmark Systolic Blood Pressure Intervention Trial (SPRINT) showed that lowering systolic blood pressure (BP) goals from 140 mmHg to 120…
Excitatory synaptic connections in the adult neocortex consist of multiple synaptic contacts, almost exclusively formed on dendritic spines. Changes of dendritic spine shape and volume, a correlate of synaptic strength, can be tracked in…
Living systems rely on coordinated molecular interactions, especially those related to gene expression and protein activity. The Unfolded Protein Response is a crucial mechanism in eukaryotic cells, activated when unfolded proteins exceed a…
A salient feature of prefrontal cortex organization is the vast diversity of cell types that support the temporal integration of events required for sculpting future responses. A major obstacle in understanding the routing of information…
Vehicle Routing Problems (VRPs) can model many real-world scenarios and often involve complex constraints. While recent neural methods excel in constructing solutions based on feasibility masking, they struggle with handling complex…
Neurodegenerative diseases are characterized as the progressive loss of neural cells, e.g. neurons, glial cells. Ageing, monogenic variations, viral infections, and many other factors are determined and speculated as causes for them. While…
Understanding how small molecules perturb gene expression is essential for uncovering drug mechanisms, predicting off-target effects, and identifying repurposing opportunities. While prior deep learning frameworks have integrated multimodal…
Predicting protein-protein interactions (PPIs) by learning informative representations from amino acid sequences is a challenging yet important problem in biology. Although various deep learning models in Siamese architecture have been…
Massive molecular simulations of drug-target proteins have been used as a tool to understand disease mechanism and develop therapeutics. This work focuses on learning a generative neural network on a structural ensemble of a drug-target…
New cells are generated throughout life and integrate into the hippocampus via the process of adult neurogenesis. Epileptogenic brain injury induces many structural changes in the hippocampus, including the death of interneurons and altered…
Protein-ligand binding prediction is central to virtual screening and affinity ranking, two fundamental tasks in drug discovery. While recent retrieval-based methods embed ligands and protein pockets into Euclidean space for…
Liquid liquid phase separation (LLPS) of proteins is an intracellular process that is widely used by cells for many purposes. In living cells (in vivo), LLPS occurs in complex and crowded environments. Amino acids (AAs) are vital components…
The ability to accurately infer cardiac electrophysiological (EP) properties is key to improving arrhythmia diagnosis and treatment. In this work, we developed a physics-informed neural networks (PINNs) framework to predict how different…
Prediction of protein-ligand interactions (PLI) plays a crucial role in drug discovery as it guides the identification and optimization of molecules that effectively bind to target proteins. Despite remarkable advances in deep…
Computationally predicting protein-protein interactions (PPIs) is challenging due to the lack of integrated, multimodal protein representations. DPEB is a curated collection of 22,043 human proteins that integrates four embedding types:…
Models of protein energetics which neglect interactions between amino acids that are not adjacent in the native state, such as the Go model, encode or underlie many influential ideas on protein folding. Implicit in this simplification is a…
The interaction between Ribonucleic Acids (RNAs) and proteins, also called RNA Protein Interaction (RPI), plays an important role in the life activities of organisms, including in various regulatory processes, such as gene splicing, gene…
We present a new method for the detection of gene pathways associated with a multivariate quantitative trait, and use it to identify causal pathways associated with an imaging endophenotype characteristic of longitudinal structural change…
Prion diseases are invariably fatal and highly infectious neurodegenerative diseases affecting humans and animals. The neurodegenerative diseases such as Creutzfeldt-Jakob disease, variant Creutzfeldt-Jakob diseases,…
We provide a visualization model that targets the visualization of Protein-Protein Interactions(PPI) and combines it with a super view based on publications and methods to extract interactions. Although there are several existing tools, our…