Related papers: PASS: De novo assembler for short peptide sequence…
Proteins are macromolecules that perform essential functions in all living organisms. Designing novel proteins with specific structures and desired functions has been a long-standing challenge in the field of bioengineering. Existing…
The alignment of biological sequences such as DNA, RNA, and proteins, is one of the basic tools that allow to detect evolutionary patterns, as well as functional/structural characterizations between homologous sequences in different…
Background: The inception of next generations sequencing technologies have exponentially increased the volume of biological sequence data. Protein sequences, being quoted as the `language of life', has been analyzed for a multitude of…
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…
Background: High-throughput proteomics techniques, such as mass spectrometry (MS)-based approaches, produce very high-dimensional data-sets. In a clinical setting one is often interested in how mass spectra differ between patients of…
Probabilistic Amplitude Shaping (PAS) is a coded-modulation scheme in which the encoder is a concatenation of a distribution matcher with a systematic Forward Error Correction (FEC) code. For reduced computational complexity the decoder can…
Mass spectrometry (MS) stands as a cornerstone analytical technique for molecular identification, yet de novo structure elucidation from spectra remains challenging due to the combinatorial complexity of chemical space and the inherent…
Label-free optical absorption microscopy techniques continue to evolve as promising tools for label-free histopathological imaging of cells and tissues. However, critical challenges relating to specificity and contrast, as compared to…
The structure of proteins is essential for its function. The determination of protein structures is possible by experimental or predicted by computational methods, but also a combination of both approaches is possible. Here, first an…
Liquid Chromatography coupled to Mass Spectrometry (LC-MS) based methods are commonly used for high-throughput, quantitative measurements of the proteome (i.e. the set of all proteins in a sample at a given time). Targeted LC-MS produces…
Peptide de novo sequencing is a method used to reconstruct amino acid sequences from tandem mass spectrometry data without relying on existing protein sequence databases. Traditional deep learning approaches, such as Casanovo, mainly…
The Precision Proton Spectrometer (PPS) is a new subdetector of CMS that provides a powerful tool for the advancement of beyond standard model searches. We present recent results obtained with the PPS subdetector illustrating the unique…
Most end-to-end speech recognition systems model text directly as a sequence of characters or sub-words. Current approaches to sub-word extraction only consider character sequence frequencies, which at times produce inferior sub-word…
The tandem mass spectrometry fragments a large number of molecules of the same peptide sequence into charged prefix and suffix subsequences, and then measures mass/charge ratios of these ions. The de novo peptide sequencing problem is to…
Tandem Mass Spectrometry is a cornerstone technique for identifying unknown small molecules in fields such as metabolomics, natural product discovery and environmental analysis. However, certain aspects, such as the probabilistic…
Mass spectrometry (MS) is used widely in biomolecular structural analysis and is particularly dominant in the study of proteins. Despite its considerable power, state-of-the-art protein MS frequently suffers from limited reliability of…
Protein language models have excelled in a variety of tasks, ranging from structure prediction to protein engineering. However, proteins are highly diverse in functions and structures, and current state-of-the-art models including the…
New computing paradigms are required to solve the most challenging computational problems where no exact polynomial time solution exists.Probabilistic Ising Accelerators has gained promise on these problems with the ability to model complex…
Protein structure similarity search (PSSS), which tries to search proteins with similar structures, plays a crucial role across diverse domains from drug design to protein function prediction and molecular evolution. Traditional…
Recent emergence of next-generation DNA sequencing technology has enabled acquisition of genetic information at unprecedented scales. In order to determine the genetic blueprint of an organism, sequencing platforms typically employ…