Related papers: PhaGO: Protein function annotation for bacteriopha…
Transcription factors (TFs), the key players in transcriptional regulation, have attracted great experimental attention, yet the functions of most human TFs remain poorly understood. Recent capabilities in genome-wide protein binding…
The ejection of DNA from a bacterial virus (``phage'') into its host cell is a biologically important example of the translocation of a macromolecular chain along its length through a membrane. The simplest mechanism for this motion is…
The Integration Host Factor (IHF) is a nucleoid-associated protein critical for both DNA compaction and biofilm stability. While its role in DNA packaging within the cell is well understood, its structural role in scaffolding biofilms is…
The remarkable success of AlphaFold2 in providing accurate atomic-level prediction of protein structures from their amino acid sequence has transformed approaches to the protein folding problem. However, its core paradigm of mapping one…
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…
Current metagenomic analysis algorithms require significant computing resources, can report excessive false positives (type I errors), may miss organisms (type II errors / false negatives), or scale poorly on large datasets. This paper…
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:…
Protein function prediction is currently achieved by encoding its sequence or structure, where the sequence-to-function transcendence and high-quality structural data scarcity lead to obvious performance bottlenecks. Protein domains are…
Annotating the structure of protein-coding genes represents a major challenge in the analysis of eukaryotic genomes. This task sets the groundwork for subsequent genomic studies aimed at understanding the functions of individual genes.…
With the astonishing rate that the genomic and metagenomic sequence data sets are accumulating, there are many reasons to constrain the data analyses. One approach to such constrained analyses is to focus on select subsets of gene families…
Multibillion-clone landscape phage display libraries were prepared by the fusion of the phage major coat protein pVIII with foreign random peptides. Phage particles and their proteins specific for cancer and bacterial cells were selected…
Generative Adversarial Networks (GANs) represent an attractive and novel approach to generate realistic data, such as genes, proteins, or drugs, in synthetic biology. Here, we apply GANs to generate synthetic DNA sequences encoding for…
Background: Phage therapy shows promise for treating antibiotic-resistant Klebsiella infections. Identifying phage depolymerases that target Klebsiella capsular polysaccharides is crucial, as these capsules contribute to biofilm formation…
As protein informatics advances rapidly, the demand for enhanced predictive accuracy, structural analysis, and functional understanding has intensified. Transformer models, as powerful deep learning architectures, have demonstrated…
Motivation: Receptor-binding proteins (RBPs) initiate viral infection and determine host specificity, serving as key targets for phage engineering and therapy. However, the identification of RBPs is complicated by their extreme sequence…
Biological data sets are often high-dimensional, noisy, and governed by complex interactions among sparse signals. This poses major challenges for interpretability and reliable feature selection. Tasks such as identifying motif interactions…
Proteins are the main workhorses of biological functions in a cell, a tissue, or an organism. Identification and quantification of proteins in a given sample, e.g. a cell type under normal/disease conditions, are fundamental tasks for the…
When planktonic bacteria adhere together to a surface, they begin to form biofilms, or communities of bacteria. Biofilm formation in a host can be extremely problematic if left untreated, especially since antibiotics can be ineffective in…
Noncoding RNAs are integral to a wide range of biological processes, including translation, gene regulation, host-pathogen interactions and environmental sensing. While genomics is now a mature field, our capacity to identify noncoding RNA…
Motivation: DNA methylation is an intensely studied epigenetic mark, yet its functional role is incompletely understood. Attempts to quantitatively associate average DNA methylation to gene expression yield poor correlations outside of the…