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Recent advances in single cell sequencing and multi-omics techniques have significantly improved our understanding of biological phenomena and our capacity to model them. Despite combined capture of data modalities showing similar progress,…
Intrinsically disordered proteins and regions are increasingly appreciated for their abundance in the proteome and the many functional roles they play in the cell. In this short review, we describe a variety of approaches used to obtain…
Introduced more than fifty years ago, dynamic light scattering is routinely used to determine the size distribution of colloidal suspensions, as well as of macromolecules in solution, such as proteins, nucleic acids, and their complexes.…
Understanding and predicting the phase behavior of intrinsically disordered proteins (IDPs) is of significant interest due to their role in many biological processes. However, effectively characterizing phase behavior and its complex…
Biomarker discovery for clinical purposes is one of the major areas in which proteomics is used. However, despite considerable effort, the successes have been relatively scarce. In this perspective paper, we try to highlight and analyze the…
The primary step in search of the gene prediction is an identification of the coding region from genomic DNA sequence. Gene structure in the case of a eukaryotic organism is composed of promoter, intron, start codon, exons, stop codon, etc.…
DNA sequencing is the basic workhorse of modern day biology and medicine. Shotgun sequencing is the dominant technique used: many randomly located short fragments called reads are extracted from the DNA sequence, and these reads are…
Human physiology and pathology arise from the coordinated interactions of diverse single cells. However, analyzing single cells has been limited by the low sensitivity and throughput of analytical methods. DNA sequencing has recently made…
Lattice models, for their coarse-grained nature, are best suited for the study of the ``designability problem'', the phenomenon in which most of the about 16,000 proteins of known structure have their native conformations concentrated in a…
Current protein language models (PLMs) learn protein representations mainly based on their sequences, thereby well capturing co-evolutionary information, but they are unable to explicitly acquire protein functions, which is the end goal of…
Electrical impedance tomography is an imaging modality for extracting information on the conductivity distribution inside a physical body from boundary measurements of current and voltage. In many practical applications, it is a priori…
Inverse protein folding, the process of designing sequences that fold into a specific 3D structure, is crucial in bio-engineering and drug discovery. Traditional methods rely on experimentally resolved structures, but these cover only a…
Monitoring structures of elastic materials for defect detection by means of ultrasound waves (Structural Health Monitoring, SHM) demands for an efficient computation of parameters which characterize their mechanical behavior.…
Food protein digestibility and bioavailability are critical aspects in addressing human nutritional demands, particularly when seeking sustainable alternatives to animal-based proteins. In this study, we propose a machine learning approach…
Two-dimensional electrophoresis of proteins has preceded, and accompanied, the birth of proteomics. Although it is no longer the only experimental scheme used in modern proteomics, it still has distinct features and advantages. The purpose…
In recent years, there has been an explosion of research on the application of deep learning to the prediction of various peptide properties, due to the significant development and market potential of peptides. Molecular dynamics has…
A plethora of protein language models have been released in recent years. Yet comparatively little work has addressed how to best sample from them to optimize desired biological properties. We fill this gap by proposing a flexible,…
Spectroscopic ellipsometry is a powerful method with high surface sensitivity that can be used to monitor the growth of even sub-monolayer film. However, the analysis of ultrathin films is complicated by the correlation of the dielectric…
Automated segmentation of cancer on medical images can aid targeted diagnostic and therapeutic procedures. However, its adoption is limited by the high cost of expert annotations required for training and inter-observer variability in…
Biologists frequently desire protein inhibitors for a variety of reasons, including use as research tools for understanding biological processes and application to societal problems in agriculture, healthcare, etc. Immunotherapy, for…