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The predictive accuracy of Machine Learning (ML) models of molecular properties depends on the choice of the molecular representation. Based on the postulates of quantum mechanics, we introduce a hierarchy of representations which meet…
Molecular simulations and biophysical experiments can be used to provide independent and complementary insights into the molecular origin of biological processes. A particularly useful strategy is to use molecular simulations as a modelling…
Single-molecule spectroscopy (SMS) is an exceptionally sensitive technique, but its inherently limited photon budget produces noisy data that can readily lead to subjective analyses, fitting errors, and reduced statistical power, obscuring…
One of the central challenges in the computational analysis of liquid chromatography-tandem mass spectrometry (LC-MS/MS) data is to identify the compounds underlying the output spectra. In recent years, this problem is increasingly tackled…
Single-cell technologies offer insights into molecular feature distributions, but comparing them poses challenges. We propose a kernel-testing framework for non-linear cell-wise distribution comparison, analyzing gene expression and…
The folding dynamics of proteins at the single molecule level has been studied with single-molecule force spectroscopy (SMFS) experiments for twenty years, but a common standardized method for the analysis of the collected data and for the…
Meta-analysis is routinely performed in many scientific disciplines. This analysis is attractive since discoveries are possible even when all the individual studies are underpowered. However, the meta-analytic discoveries may be entirely…
One of the challenges of the proteomic analysis by 2D-gel is to visualize the low abundance proteins, particularly those localized in organelles. An additional problem with nuclear proteins lies in their strong interaction with nuclear…
Time course measurement of single molecules on a cell surface provides detailed information on the dynamics of the molecules, which is otherwise inaccessible. To extract the quantitative information, single particle tracking (SPT) is…
Motivation: With the development of droplet based systems, massive single cell transcriptome data has become available, which enables analysis of cellular and molecular processes at single cell resolution and is instrumental to…
Understanding protein solubility is essential for their functional applications. Computational methods for predicting protein solubility are crucial for reducing experimental costs and enhancing the efficiency and success rates of protein…
Authors of biomedical publications often use gel images to report experimental results such as protein-protein interactions or protein expressions under different conditions. Gel images offer a way to concisely communicate such findings,…
New technologies have enabled the investigation of biology and human health at an unprecedented scale and in multiple dimensions. These dimensions include a myriad of properties describing genome, epigenome, transcriptome, microbiome,…
The current capacity of computers makes it possible to perform simulations of small systems with portable, explicit-solvent potentials achieving high degree of accuracy. However, simplified models must be employed to exploit the behaviour…
Considerable interest has recently been focused on studying multiple phenotypes simultaneously in both epidemiological and genomic studies, either to capture the multidimensionality of complex disorders or to understand shared etiology of…
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…
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…
In the present work, we review the fundamental methods which have been developed in the last few years for classifying into families and clans the distribution of amino acids in protein databases. This is done through functions of random…
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…
The production processes of proteins in prokaryotic cells are investigated. Most of the mathematical models in the literature study the production of {\em one} fixed type of proteins. When several classes of proteins are considered, an…