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We propose a general formulation for continuous treatment recommendation problems in settings with clinical survival data, which we call the Deep Survival Dose Response Function (DeepSDRF). That is, we consider the problem of learning the…
Predicting clinical outcomes to anti-cancer drugs on a personalized basis is challenging in cancer treatment due to the heterogeneity of tumors. Traditional computational efforts have been made to model the effect of drug response on…
Interactions of polyelectrolytes (PEs) with proteins play a crucial role in numerous biological processes, such as the internalization of virus particles into host cells. Although docking, machine learning methods, and molecular dynamics…
Antimicrobial resistance (AMR) poses a mounting global health crisis, requiring rapid and reliable prediction frameworks that capture its complex evolutionary dynamics. Traditional antimicrobial susceptibility testing (AST), while accurate,…
CXCR7, a G-protein-coupled chemokine receptor, has recently emerged as a key player in cancer progression, particularly in driving angiogenesis and metastasis. Despite its significance, currently, few effective inhibitors exist for…
Recent advances in protein function prediction exploit graph-based deep learning approaches to correlate the structural and topological features of proteins with their molecular functions. However, proteins in vivo are not static but…
The Coronavirus Disease (COVID-19) pandemic caused by the SARS-coronavirus 2 (SARS-CoV-2) urgently calls for the design of drugs directed against this new virus. Given its essential role in proteolytic processing, the main protease Mpro has…
The COVID-19 pandemic caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has spurred unprecedented and concerted worldwide research to curtail and eradicate this pathogen. SARS-CoV-2 has four structural proteins:…
Virtual screening of phytochemicals was performed through molecular docking, simulation, in silico ADMET and drug-likeness prediction to identify the potential hits that can inhibit the effects of SARS-CoV-2. Considering the published…
In this perspective article, a clinically inspired phenotype-driven experimental approach is put forward to address the challenge of the adaptive response of solid cancers to small-molecule targeted therapies. A list of conditions is…
We investigate the rates of drug resistance acquisition in a natural population using molecular epidemiological data from Bolivia. First, we study the rate of direct acquisition of double resistance from the double sensitive state within…
COVID-19 has affected the world tremendously. It is critical that biological experiments and clinical designs are informed by computational approaches for time- and cost-effective solutions. Comparative analyses particularly can play a key…
Antibiotic resistance is a worldwide challenge. A potential approach to block resistance is to simultaneously inhibit WT and known escape variants of the target bacterial protein. Here we applied an integrated computational and experimental…
Accurately predicting drug-drug interactions (DDIs) is crucial for pharmaceutical research and clinical safety. Recent deep learning models often suffer from high computational costs and limited generalization across datasets. In this…
Multiplex and multi-directional control of metabolic pathways is crucial for metabolic engineering to improve product yield of fuels, chemicals, and pharmaceuticals. To achieve this goal, artificial transcriptional regulators such as…
Adapting Deep Learning (DL) techniques to automate non-trivial coding activities, such as code documentation and defect detection, has been intensively studied recently. Learning to predict code changes is one of the popular and essential…
The understanding of the mechanisms of SARS-CoV-2 evolution and transmission is one of the greatest challenges of our time. By integrating artificial intelligence (AI), viral genomes isolated from patients, tens of thousands of mutational…
Aerial robotics for transporting suspended payloads as the form of freely-floating manipulator are growing great interest in recent years. However, the force/torque caused by payload and residual dynamics will introduce unmodeled…
The seasonal human influenza virus undergoes rapid evolution, leading to significant changes in circulating viral strains from year to year. These changes are typically driven by adaptive mutations, particularly in the antigenic epitopes,…
Colorectal cancer liver metastasis (CRLM) exhibits high postoperative recurrence and pronounced prognostic heterogeneity, challenging individualized management. Existing prognostic approaches often rely on static representations from a…