Related papers: Protein Sequencing with an Adaptive Genetic Algori…
DNA sequence alignment is important today as it is usually the first step in finding gene mutation, evolutionary similarities, protein structure, drug development and cancer treatment. Covid-19 is one recent example. There are many…
Metabolomics complements investigation of the genome, transcriptome, and proteome of an organism. Today, the vast majority of metabolites remain unknown, in particular for non-model organisms. Mass spectrometry is one of the predominant…
Engineering new molecules with desirable functions and properties has the potential to extend our ability to engineer proteins beyond what nature has so far evolved. Advances in the so-called "de novo" design problem have recently been…
Motivation: Gene set testing is typically performed in a supervised context to quantify the association between groups of genes and a clinical phenotype. In many cases, however, a gene set-based interpretation of genomic data is desired in…
Biological functions stem from coordinated interactions among proteins, nucleic acids and small molecules. Mass spectrometry technologies for reliable, high throughput single-cell proteomics will add a new modality to genomics and enable…
High throughput sequencing techniques have highly impactedon modern biology, widening the gap between sequenced andannotated data. Automatic annotation tools are thereforeof the foremost importance to guide biologists' experiments. However,…
Representation learning for proteins has primarily focused on the global understanding of protein sequences regardless of their length. However, shorter proteins (known as peptides) take on distinct structures and functions compared to…
Next Generation Sequencing can sample the whole genome (WGS) or the 1-2% of the genome that codes for proteins called the whole exome (WES). Machine learning approaches to variant calling achieve high accuracy in WGS data, but the reduced…
Breast cancer's complexity and variability pose significant challenges in understanding its progression and guiding effective treatment. This study aims to integrate protein sequence data with expression levels to improve the molecular…
Protein is linked to almost every life process. Therefore, analyzing the biological structure and property of protein sequences is critical to the exploration of life, as well as disease detection and drug discovery. Traditional protein…
Metagenomics is the study of environments through genetic sampling of their microbiota. Metagenomic studies produce large datasets that are estimated to grow at a faster rate than the available computational capacity. A key step in the…
Recent developments in next generation sequencing technology have led to the creation of extensive, open-source protein databases consisting of hundreds of millions of sequences. To render these sequences applicable in biomedical…
Mapping human genetic variation is fundamentally interesting in fields such as anthropology and forensic inference. At the same time patterns of genetic diversity confound efforts to determine the genetic basis of complex disease. Due to…
What are proteins made from, as the working parts of the living cells protein machines? To answer this question, we need a technology to disassemble proteins onto elementary func-tional details and to prepare lumped description of such…
Systematic identification of protein function is a key problem in current biology. Most traditional methods fail to identify functionally equivalent proteins if they lack similar sequences, structural data or extensive manual annotations.…
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…
Deep learning has advanced mass spectrometry data interpretation, yet most models remain feature extractors rather than unified scoring frameworks. We present pUniFind, the first large-scale multimodal pre-trained model in proteomics that…
Pre-trained models have been successful in many protein engineering tasks. Most notably, sequence-based models have achieved state-of-the-art performance on protein fitness prediction while structure-based models have been used…
Sequencing by synthesis is used in many next-generation DNA sequencing technologies. Some of the technologies, especially those exploring the principle of single-molecule sequencing, allow incomplete nucleotide incorporation in each cycle.…
Compound identification from tandem mass spectrometry (MS/MS) data is a critical step in the analysis of complex mixtures. Typical solutions for the MS/MS spectrum to compound (MS2C) problem involve comparing the unknown spectrum against a…