Related papers: Top-down proteomics on a microfluidic platform
Proteins are biomolecules of life. They fold into a great variety of three-dimensional (3D) shapes. Underlying these folding patterns are many recurrent structural fragments or building blocks (analogous to `LEGO bricks'). This paper…
The quality and ease of proteomics analysis depends on the performance of the analytical tools used, and thus of the performances of the protein separation tools used to deconvolute complex protein samples. Among protein samples, membrane…
Proteomic matrix-assisted laser desorption/ionisation (MALDI) linear time-of-flight (TOF) mass spectrometry (MS) may be used to produce protein profiles from biological samples with the aim of discovering biomarkers for disease. However,…
In this paper, we propose a data-driven method to learn interpretable topological features of biomolecular data and demonstrate the efficacy of parsimonious models trained on topological features in predicting the stability of synthetic…
A fundamental goal of research in molecular biology is to understand protein structure. Protein crystallography is currently the most successful method for determining the three-dimensional (3D) conformation of a protein, yet it remains…
Persistent homology has been devised as a promising tool for the topological simplification of complex data. However, it is computationally intractable for large data sets. In this work, we introduce multiresolution persistent homology for…
Accurate localization of proteins from fluorescence microscopy images is challenging due to the inter-class similarities and intra-class disparities introducing grave concerns in addressing multi-class classification problems. Conventional…
Protein quantification and analysis are well-accepted approaches for biomarker discovery but are limited to identification without structural information. High-throughput omics data (i.e., genomics, transcriptomics, and proteomics) have…
Identification and alignment of three-dimensional folding of proteins may yield useful information about relationships too remote to be detected by conventional methods, such as sequence comparison, and may potentially lead to prediction of…
Shotgun proteomics is a high-throughput technology used to identify unknown proteins in a complex mixture. At the heart of this process is a prediction task, the spectrum identification problem, in which each fragmentation spectrum produced…
Mass spectrometry provides a high-throughput way to identify proteins in biological samples. In a typical experiment, proteins in a sample are first broken into their constituent peptides. The resulting mixture of peptides is then subjected…
Reliable hardware connectivity is vital in heterogeneous integrated systems. For example, in digital microfluidics lab-on-a-chip systems, there are hundreds of physical connections required between a micro-electro-mechanical fabricated…
Unbiased, label-free proteomics is becoming a powerful technique for measuring protein expression in almost any biological sample. The output of these measurements after preprocessing is a collection of features and their associated…
We put forward the idea of establishing a novel interdisciplinary field of research at the interface between quantum mechanics and proteomics. The new field, called quantum proteomics, is defined as the large-scale study of the electronic…
Protein representation learning is a challenging task that aims to capture the structure and function of proteins from their amino acid sequences. Previous methods largely ignored the fact that not all amino acids are equally important for…
Protein representation learning (PRL) is crucial for understanding structure-function relationships, yet current sequence- and graph-based methods fail to capture the hierarchical organization inherent in protein structures. We introduce…
Rapid identification of microparticles in liquid is an important problem in environmental and biomedical applications such as for microplastic detection in water sources and physiological fluids. Existing spectro-scopic techniques are…
We demonstrate a multipurpose microwave frequency identification solution that is implemented based on a photonic integrated chip and is able to identify different types of microwave signals, including single-frequency, multiple-frequency,…
The three dimensional structure of a protein is an outcome of the interactions of its constituent amino acids in 3D space. Considering the amino acids as nodes and the interactions among them as edges we have constructed and analyzed…
Proteins are essential macromolecules of life and thus understanding their function is of great importance. The number of functionally unclassified proteins is large even for simple and well studied organisms such as baker's yeast. Methods…