Related papers: Progress in the definition of a reference human mi…
Several processes in the cell, such as gene regulation, start when key proteins recognise and bind to short DNA sequences. However, as these sequences can be hundreds of million times shorter than the genome, they are hard to find by simple…
We observe that human poses exhibit strong group-wise structural correlation and spatial coupling between keypoints due to the biological constraints of different body parts. This group-wise structural correlation can be explored to improve…
Proteins perform critical processes in all living systems: converting solar energy into chemical energy, replicating DNA, as the basis of highly performant materials, sensing and much more. While an incredible range of functionality has…
In multicellular organisms, relations among parts and between parts and the whole are contextual and interdependent. These organisms and their cells are ontogenetically linked: an organism starts as a cell that divides producing…
Understanding protein solubility is essential for their functional applications. Computational methods for predicting protein solubility are crucial for reducing experimental costs and enhancing the efficiency and success rates of protein…
Protein language models are increasingly used to guide experimental and clinical decisions, yet it is often unclear whether a confident prediction reflects recognition of biological evidence or retrieval of a statistical default. We examine…
Protein representation learning plays a crucial role in understanding the structure and function of proteins, which are essential biomolecules involved in various biological processes. In recent years, deep learning has emerged as a…
Cell-to-cell heterogeneity drives a range of (patho)physiologically important phenomena, such as cell fate and chemotherapeutic resistance. The role of metabolism, and particularly mitochondria, is increasingly being recognised as an…
Learning by imitation is one of the most significant abilities of human beings and plays a vital role in human's computational neural system. In medical image analysis, given several exemplars (anchors), experienced radiologist has the…
Motivation: Understanding functions of proteins in specific human tissues is essential for insights into disease diagnostics and therapeutics, yet prediction of tissue-specific cellular function remains a critical challenge for biomedicine.…
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…
Numerous cellular functions rely on protein$\unicode{x2013}$protein interactions. Efforts to comprehensively characterize them remain challenged however by the diversity of molecular recognition mechanisms employed within the proteome. Deep…
Protein structures are important for understanding their functions and interactions. Currently, many protein structure prediction methods are enriching the structure database. Discriminating the origin of structures is crucial for…
Organoids are self-organized 3D cell clusters that closely mimic the architecture and function of in vivo tissues and organs. Quantification of organoid morphology helps in studying organ development, drug discovery, and toxicity…
As I compress on the canvas of a few pages here major results of my research on the retinoblastoma tumor suppressor protein (RB) spreading over the past 15 years, an exciting picture emerges on this unique host molecule which surpasses in…
Protein structure prediction can be shown to be an NP-hard problem; the number of conformations grows exponentially with the number of residues. The native conformations of proteins occupy a very small subset of these, hence an exploratory,…
Linguistic analysis of protein sequences is an underexploited technique. Here, we capitalize on the concept of the lipogram to characterize sequences at the proteome levels. A lipogram is a literary composition which omits one or more…
Identifying the entire set of complexes is essential not only to understand complex formations, but also to map the high level organisation of the cell. Computational prediction of protein complexes faces several challenges including the…
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…
Current protein forcefields like the ones seen in CHARMM or Xplor-NIH have many terms that include bonded and non-bonded terms. Yet the forcefields do not take into account the use of hydrogen bonds which are important for secondary…