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The enormous diversity of life forms thriving in drastically different environmental milieus involves a complex interplay among constituent proteins interacting with each other. However, the organizational principles characterizing the…
Understanding the intricate interplay among sequence, structure, and function remains a fundamental challenge in proteomics. The sequence-structure-function paradigm posits that biological roles are governed by the tertiary geometric…
Protein-Protein Interaction Networks aim to model the interactome, providing a powerful tool for understanding the complex relationships governing cellular processes. These networks have numerous applications, including functional…
Biological information processing as implemented by regulatory and signaling networks in living cells requires sufficient specificity of molecular interaction to distinguish signals from one another, but much of regulation and signaling…
Composed of amino acid chains that influence how they fold and thus dictating their function and features, proteins are a class of macromolecules that play a central role in major biological processes and are required for the structure,…
The promise of discovering a functional blueprint of a cellular system from large-scale and high-throughput sequence and experimental data is predicated on the belief that the same top-down investigative approach that proved successful in…
How DNA-binding proteins locate specific genomic targets remains a central challenge in molecular biology. Traditional protein-centric approaches, which rely on wet-lab experiments and visualization techniques, often lack genome-wide…
Just as physicists strive to develop a TOE (theory of everything), which explains and unifies the physical laws of the universe, the life-scientist wishes to uncover the TOE as it relates to cellular systems. This can only be achieved with…
Multi-omics studies often rely on pathway enrichment to interpret heterogeneous molecular changes, but pathway enrichment (PE)-based workflows inherit structural limitations of pathway resources, including curation lag, functional…
Genome organization in eukaryotes during interphase stems from the delicate balance between non-random correlations present in the DNA polynucleotide linear sequence and the physico/chemical reactions which shape continuously the form and…
Understanding functional organization of genetic information is a major challenge in modern biology. Following the initial publication of the human genome sequence in 2001, advances in high-throughput measurement technologies and efficient…
Quantum effects are mainly used for the determination of molecular shapes in molecular biology, but quantum information theory may be a more useful tool to understand the physics of life. Organic molecules and quantum circuits/protocols can…
Cells with the same genome can exist in different phenotypes. and can change between distinct phenotypes when subject to specific stimuli and microenvironments. Some examples include cell differentiation during development, reprogramming…
Automated medical coding, an essential task for healthcare operation and delivery, makes unstructured data manageable by predicting medical codes from clinical documents. Recent advances in deep learning and natural language processing have…
Recently, data-centric AI methodology has been a dominant paradigm in single-cell transcriptomics analysis, which treats data representation rather than model complexity as the fundamental bottleneck. In the review of current studies,…
Predicting gene function from its DNA sequence is a fundamental challenge in biology. Many deep learning models have been proposed to embed DNA sequences and predict their enzymatic function, leveraging information in public databases…
The interaction between proteins and DNA is a key driving force in a significant number of biological processes such as transcriptional regulation, repair, recombination, splicing, and DNA modification. The identification of DNA-binding…
The modeling of genomic sequences presents unique challenges due to their length and structural complexity. Traditional sequence models struggle to capture long-range dependencies and biological features inherent in DNA. In this work, we…
Proteins are macromolecules responsible for essential functions in almost all living organisms. Designing reasonable proteins with desired functions is crucial. A protein's sequence and structure are strongly correlated and they together…
DNA sequence encoding is fundamental to gene function prediction, protein synthesis, and diverse downstream biological tasks. Despite the substantial progress achieved by large-scale DNA sequence pretraining, existing studies have…