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Biomarker subpopulations have become increasingly important for drug development in targeted therapies. The use of biomarkers has the potential to facilitate more effective outcomes by guiding patient selection appropriately, thus enhancing…
We study the computational complexity of decomposing finite discrete dynamical systems (FDDSs) in terms of the semiring operations of alternative and synchronous execution, which is useful for the analysis of discrete phenomena in science…
The protein-protein interactions (PPIs) are crucial for understanding the majority of cellular processes. PPIs play important role in gene transcription regulation, cellular signaling, molecular basis of immune response and more. Moreover,…
Next-generation sequencing technologies now constitute a method of choice to measure gene expression. Data to analyze are read counts, commonly modeled using Negative Binomial distributions. A relevant issue associated with this…
Computer-Aided Drug Discovery research has proven to be a promising direction in drug discovery. In recent years, Deep Learning approaches have been applied to problems in the domain such as Drug-Target Interaction Prediction and have shown…
Bifurcations leading to complex dynamical behaviour of non-linear systems are often encountered when the characteristics of feedback circuits in the system are varied. In systems with many unknown or varying parameters, it is an…
Understanding the origins of collective, fluid-like behavior in ultrarelativistic nuclear collisions constitutes one of the biggest open challenges in the field. In this Letter, it is argued that certain features in the multiplicity…
The prediction of the three-dimensional native structure of proteins from the knowledge of their amino acid sequence, known as the protein folding problem, is one of the most important yet unsolved issues of modern science. Since the…
We devise an approach for targeted molecular design, a problem of interest in computational drug discovery: given a target protein site, we wish to generate a chemical with both high binding affinity to the target and satisfactory…
Proteins are the fundamental macromolecules that play diverse and crucial roles in all living matter and have tremendous implications in healthcare, manufacturing, and biotechnology. Their functions are largely determined by the sequences…
We study theoretically a novel drug delivery system that utilizes the overexpression of certain proteins in cancerous cells for cell specific chemotherapy. The system consists of dendrimers conjugated with "keys" (ex: folic acid) which…
Complex fluids subjected to localized microscopic energy inputs, typical of active microrheology setups, exhibit poorly understood nonequilibrium behaviors because of the intricate self-organization of their mesoscopic constituents. In this…
Inside a cell, heterotypic proteins assemble in inhomogeneous, crowded systems where the abundance of these proteins vary with cell types. While some protein complexes form putative structures that can be visualized with imaging, there are…
Several sub-diffusive stochastic processes in nature, e.g., motion of tagged monomer in polymers, height fluctuation of interfaces and particle dynamics in single-file diffusion etc. can be described rigorously or approximately by the…
The remarkable structural diversity of modern proteins reflects millions of years of evolution, during which sequence space has expanded while many structural features remain conserved. This conservation is evident not only among homologous…
Bidirectional typechecking, in which terms either synthesize a type or are checked against a known type, has become popular for its scalability (unlike Damas-Milner type inference, bidirectional typing remains decidable even for very…
When analyzing complex networks a key target is to uncover their modular structure, which means searching for a family of modules, namely node subsets spanning each a subnetwork more densely connected than the average. This work proposes a…
Motivation: Drug combination is a sensible strategy for disease treatment by improving the efficacy and reducing concomitant side effects. Due to the large number of possible combinations among candidate compounds, exhaustive screening is…
Modeling potential alloys requires the exploration of all possible configurations of atoms. Additionally, modeling the thermal properties of materials requires knowledge of the possible ways of displacing the atoms. One solution to finding…
The analysis of the three-dimensional structure of proteins is an important topic in molecular biochemistry. Structure plays a critical role in defining the function of proteins and is more strongly conserved than amino acid sequence over…