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Statistical Shape Models (SSMs) excel at identifying population level anatomical variations, which is at the core of various clinical and biomedical applications, including morphology-based diagnostics and surgical planning. However, the…
Proteins perform much of the work in living organisms, and consequently the development of efficient computational methods for protein representation is essential for advancing large-scale biological research. Most current approaches…
Protein quantification and analysis are well-accepted approaches for biomarker discovery but are limited to identification without structural information. High-throughput omics data (i.e., genomics, transcriptomics, and proteomics) have…
The evolution, regulation and sustenance of biological complexity is determined by protein-protein interaction network that is filled with dynamic events. Recent experimental evidences point out that clustering of proteins has a vital role…
Detecting weak clustered signal in spatial data is important but challenging in applications such as medical image and epidemiology. A more efficient detection algorithm can provide more precise early warning, and effectively reduce the…
Protein function is inherently linked to its localization within the cell, and fluorescent microscopy data is an indispensable resource for learning representations of proteins. Despite major developments in molecular representation…
An approach that combines Self-Organizing maps, hierarchical clustering and network components is presented, aimed at comparing protein conformational ensembles obtained from multiple Molecular Dynamic simulations. As a first result the…
Understanding the structural and functional characteristics of proteins are crucial for developing preventative and curative strategies that impact fields from drug discovery to policy development. An important and popular technique for…
Crosslinking Mass Spectrometry (MS) can uncover protein-protein interactions and provide structural information on proteins in their native cellular environments. Despite its promise, the field remains hampered by inconsistent data formats,…
Inferring the structural properties of a protein from its amino acid sequence is a challenging yet important problem in biology. Structures are not known for the vast majority of protein sequences, but structure is critical for…
Classification of proteins based on their structure provides a valuable resource for studying protein structure, function and evolutionary relationships. With the rapidly increasing number of known protein structures, manual and…
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…
We theorize that phylogenetic profiles provide a quantitative method that can relate the structural and functional properties of proteins, as well as their evolutionary relationships. A key feature of phylogenetic profiles is the…
The study of biological processes can greatly benefit from tools that automatically predict gene functions or directly cluster genes based on shared functionality. Existing data mining methods predict protein functionality by exploiting…
Proteins move and deform to ensure their biological functions. Despite significant progress in protein structure prediction, approximating conformational ensembles at physiological conditions remains a fundamental open problem. This paper…
Cellular identity and function are linked to both their intrinsic genomic makeup and extrinsic spatial context within the tissue microenvironment. Spatial transcriptomics (ST) offers an unprecedented opportunity to study this, providing in…
Proteomics will celebrate its 20th year in 2014. In this relatively short period of time, it has invaded most areas of biology and its use will probably continue to spread in the future. These two decades have seen a considerable increase…
The ultimate target of proteomics identification is to identify and quantify the protein in the organism. Mass spectrometry (MS) based on label-free protein quantitation has mainly focused on analysis of peptide spectral counts and ion peak…
Structural assessment of biomolecular complexes is vital for translating molecular models into functional insights, shaping our understanding of biology and aiding drug discovery. However, current structure-based scoring functions often…
Nuclear magnetic resonance (NMR) spectroscopy is one of the leading techniques for protein studies. The method features a number of properties, allowing to explain macromolecular interactions mechanistically and resolve structures with…