相关论文: RAId DbS: A Mass-Spectrometry Based Peptide Identi…
Statistically meaningful comparison/combination of peptide identification results from various search methods is impeded by the lack of a universal statistical standard. Providing an E-value calibration protocol, we demonstrated earlier the…
Summary: The advent of Web-based tools that assist in the analysis and visualization of macromolecules require application programming interfaces (APIs) designed for modern web frameworks. To this end, we have developed a Node.js module…
Tandem repeats in proteins identification, classification and curation is a complex process that requires manual processing from experts, processing power and time. There are recent and relevant advances applying machine learning for…
By coupling peptides with DNA tags (i.e., 'barcodes'), it is now possible to harness high-throughput sequencing (HTS) technologies to enable highly multiplexed peptide-based assays, which have a variety of potential applications including…
Motivation: Peptides have attracted the attention in this century due to their remarkable therapeutic properties. Computational tools are being developed to take advantage of existing information, encapsulating knowledge and making it…
Motivation: Assigning statistical significance accurately has become increasingly important as meta data of many types, often assembled in hierarchies, are constructed and combined for further biological analyses. Statistical inaccuracy of…
Peptide identification in mass spectrometry-based proteomics is crucial for understanding protein function and dynamics. Traditional database search methods, though widely used, rely on heuristic scoring functions and statistical…
Data sharing is a key factor for ensuring reproducibility and transparency of scientific experiments, and neuroimaging is no exception. The vast heterogeneity of data formats and imaging modalities utilised in the field makes it a very…
Diffusion weighted imaging techniques permit us to infer microstructural detail in biological tissue in vivo and noninvasively. Modern sequences are based on advanced diffusion encoding schemes, allowing probing of more revealing measures…
Peptides offer great biomedical potential and serve as promising drug candidates. Currently, the majority of approved peptide drugs are directly derived from well-explored natural human peptides. It is quite necessary to utilize advanced…
We have established an RNA Mapping Database (RMDB) to enable a new generation of structural, thermodynamic, and kinetic studies from quantitative single-nucleotide-resolution RNA structure mapping (freely available at…
The increasingly collaborative, globalized nature of scientific research combined with the need to share data and the explosion in data volumes present an urgent need for a scientific data management system (SDMS). An SDMS presents a…
Liquid chromatography with tandem mass spectrometry (LC-MS/MS) based proteomics is a well-established research field with major applications such as identification of disease biomarkers, drug discovery, drug design and development. In…
Motivation: Digitization of pathology laboratories through digital slide scanners and advances in deep learning approaches for objective histological assessment have resulted in rapid progress in the field of computational pathology (CPath)…
Peptide microarrays have emerged as a powerful technology in immunoproteomics as they provide a tool to measure the abundance of different antibodies in patient serum samples. The high dimensionality and small sample size of many…
Nanobodies are small antibody fragments derived from camelids that selectively bind to antigens. These proteins have marked physicochemical properties that support advanced therapeutics, including treatments for SARS-CoV-2. To realize their…
Maintaining or improving the performance of Deep Neural Networks (DNNs) through fine-tuning requires labeling newly collected inputs, a process that is often costly and time-consuming. To alleviate this problem, input selection approaches…
Summary: PDBImages is an innovative, open-source Node.js package that harnesses the power of the popular macromolecule structure visualization software Mol*. Designed for use by the scientific community, PDBImages provides a means to…
We propose a novel approach for predicting protein-peptide interactions using a bi-modal transformer architecture that learns an inter-facial joint distribution of residual contacts. The current data sets for crystallized protein-peptide…
While state-of-the-art models for breast cancer detection leverage multi-view mammograms for enhanced diagnostic accuracy, they often focus solely on visual mammography data. However, radiologists document valuable lesion descriptors that…