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Subclasses of lymphocytes carry different functional roles to work together to produce an immune response and lasting immunity. Additionally to these functional roles, T and B-cell lymphocytes rely on the diversity of their receptor chains…
Recently exciting progress has been made on protein contact prediction, but the predicted contacts for proteins without many sequence homologs is still of low quality and not very useful for de novo structure prediction. This paper presents…
Epitope vaccines are a promising direction to enable precision treatment for cancer, autoimmune diseases, and allergies. Effectively designing such vaccines requires accurate prediction of proteasomal cleavage in order to ensure that the…
Identification of the influential clinical symptoms and laboratory features that help in the diagnosis of dengue fever in early phase of the illness would aid in designing effective public health management and virological surveillance…
Many people die from lung-related diseases every year. X-ray is an effective way to test if one is diagnosed with a lung-related disease or not. This study concentrates on categorizing three distinct types of lung X-rays: those depicting…
Epilepsy is a neurological brain disorder which life threatening and gives rise to recurrent seizures that are unprovoked. It occurs due to the abnormal chemical changes in our brain. Over the course of many years, studies have been…
Lineage tracing, the determination and mapping of progeny arising from single cells, is an important approach enabling the elucidation of mechanisms underlying diverse biological processes ranging from development to disease. We developed a…
Background: Over the past few decades, numerous forecasting methods have been proposed in the field of epidemic forecasting. Such methods can be classified into different categories such as deterministic vs. probabilistic, comparative…
We present BEEP (Biomedical Evidence-Enhanced Predictions), a novel approach for clinical outcome prediction that retrieves patient-specific medical literature and incorporates it into predictive models. Based on each individual patient's…
Isochores are long genome segments relatively homogeneous in G+C. A heuristic algorithm based on entropic segmentation has been developed by our group, and a web server implementing all the required components is available. However, a…
Which of your team's possible lineups has the best chances against each of your opponents possible lineups? In order to answer this question we develop LinNet. LinNet exploits the dynamics of a directed network that captures the performance…
The human immune system depends on a highly diverse collection of antibody-making B cells. B cell receptor sequence diversity is generated by a random recombination process called "rearrangement" forming progenitor B cells, then a Darwinian…
Personalized drug response has received public awareness in recent years. How to combine gene test result and drug sensitivity records is regarded as essential in the real-world implementation. Research articles are good sources to train…
Breast cancer cell lines are indispensable tools for unraveling disease mechanisms, enabling drug discovery, and developing personalized treatments, yet their heterogeneity and inconsistent classification pose significant challenges in…
Accurate in silico modeling of the antigen processing pathway is crucial to enable personalized epitope vaccine design for cancer. An important step of such pathway is the degradation of the vaccine into smaller peptides by the proteasome,…
Data-enabled predictive control (DeePC) for linear systems utilizes data matrices of recorded trajectories to directly predict new system trajectories, which is very appealing for real-life applications. In this paper we leverage the…
CNN-based deep learning models for disease detection have become popular recently. We compared the binary classification performance of eight prominent deep learning models: DenseNet 121, DenseNet 169, DenseNet 201, EffecientNet b0,…
We consider cell line classification using multivariate time series data obtained from electric cell-substrate impedance sensing (ECIS) technology. The ECIS device, which monitors the attachment and spreading of mammalian cells in real time…
Human immune system contains white blood cells (WBC) that are good indicator of many diseases like bacterial infections, AIDS, cancer, spleen, etc. White blood cells have been sub classified into four types: monocytes, lymphocytes,…
Personalized cancer treatment requires a thorough understanding of complex interactions between drugs and cancer cell lines in varying genetic and molecular contexts. To address this, high-throughput screening has been used to generate…