Related papers: Microarrays for Amino Acid Analysis and Protein Se…
Microarray technology is a process that allows thousands of genes simultaneously monitor to various experimental conditions. It is used to identify the co-expressed genes in specific cells or tissues that are actively used to make proteins,…
Motivation: The design of enzymes is as challenging as it is consequential for making chemical synthesis in medical and industrial applications more efficient, cost-effective and environmentally friendly. While several aspects of this…
Single particle, cryogenic electron microscopy (cryo-EM) experiments now routinely produce high-resolution data for large proteins and their complexes. Building an atomic model into a cryo-EM density map is challenging, particularly when no…
This paper considers the problem of decentralized analysis and control synthesis to verify and ensure properties like stability and dissipativity of a large-scale networked system comprised of linear subsystems interconnected in an…
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…
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…
Classification and identification of amino acids in aqueous solutions is important in the study of biomacromolecules. Laser Induced Breakdown Spectroscopy (LIBS) uses high energy laser-pulses for ablation of chemical compounds whose…
High throughput screening of small molecules and natural products is costly, requiring significant amounts of time, reagents, and operating space. Although microarrays have proven effective in the miniaturization of screening for certain…
Protein-protein interactions (protein functionalities) are mediated by water, which compacts individual proteins and promotes close and temporarily stable large-area protein-protein interfaces. Proteins are peptide chains decorated by amino…
Multiple sequence alignment (MSA) has been one of the most important problems in bioinformatics for more decades and it is still heavily examined by many mathematicians and biologists. However, mostly because of the practical motivation of…
The stochastic kinetics of BRN are described by a chemical master equation (CME) and the underlying laws of mass action. The CME must be usually solved numerically by generating enough traces of random reaction events. The resulting…
Tokenization is a crucial step in processing protein sequences for machine learning models, as proteins are complex sequences of amino acids that require meaningful segmentation to capture their functional and structural properties.…
Frequency tagging is a powerful approach to investigate the neural processing of sensory features, and is recently adapted to study the neural correlates of superordinate structures, i.e., chunks, in complex sequences such as speech and…
The "large p, small n" paradigm arises in microarray studies, where expression levels of thousands of genes are monitored for a small number of subjects. There has been an increasing demand for study of asymptotics for the various…
Motivation: Microarray data has been recently been shown to be efficacious in distinguishing closely related cell types that often appear in the diagnosis of cancer. It is useful to determine the minimum number of genes needed to do such a…
Transcript enumeration methods such as SAGE, MPSS, and sequencing-by-synthesis EST ``digital northern'', are important high-throughput techniques for digital gene expression measurement. As other counting or voting processes, these…
Aligning multiple protein structures can yield valuable information about structural similarities among related proteins, as well as provide insight into evolutionary relationships between proteins in a family. We have developed an…
The processes, resulting in the transcription of RNA, are intrinsically noisy. It was observed experimentally that the synthesis of mRNA molecules is driven by short, burst-like, events. An accurate prediction of the protein level often…
The expression levels of many thousands of genes can be measured simultaneously by DNA microarrays (chips). This novel experimental tool has revolutionized research in molecular biology and generated considerable excitement. A typical…
Proposing beneficial amino acid substitutions, whether for mutational effect prediction or protein engineering, remains a central challenge in structural biology. Recent inverse folding models, trained to reconstruct sequences from…