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Analysis of multi-source dataset, where data on the same objects are collected from multiple sources, is of rising importance in many fields, most notably in multi-omics biology. A novel framework and algorithms for integrative…
Methods for alignment of protein sequences typically measure similarity by using substitution matrix with scores for all possible exchanges of one amino acid with another. Although widely used, the matrices derived from homologous sequence…
Window profiles of amino acids in protein sequences are taken as a description of the amino acid environment. The relative entropy or Kullback-Leibler distance derived from profiles is used as a measure of dissimilarity for comparison of…
Proteins are regularly described with some general indices (mass fractal dimension, surface fractal dimension, entropy, enthalpy, free energies, hydrophobicity, denaturation temperature etc..), which are inherently statistical in nature.…
Background: The increasing volume and variety of genotypic and phenotypic data is a major defining characteristic of modern biomedical sciences. At the same time, the limitations in technology for generating data and the inherently…
A contact map is a simple representation of the structure of proteins and other chain-like macromolecules. This representation is quite amenable to numerical studies of folding. We show that the number of contact maps corresponding to the…
Present study is dedicated to the problem of electrochemical analysis of multicomponent mixtures such as milk. A combination of cyclic voltammetry facilities and machine learning technique made it possible to create a pattern recognition…
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…
An analysis of the network defined by the potential energy minima of multi-atomic systems and their connectivity via reaction pathways that go through transition states allows to understand important characteristics like thermodynamic,…
Quantitative evidence synthesis methods aim to combine data from multiple medical trials to infer relative effects of different interventions. A challenge arises when trials report continuous outcomes on different measurement scales. To…
Integrated nanophotonic biosensors offer a promising route toward future biomedical detection applications that may enable inexpensive, portable, and sensitive diagnosis of diseases with a small amount of biological samples for convenient…
In the context of biometrics, matching confidence refers to the confidence that a given matching decision is correct. Since many biometric systems operate in critical decision-making processes, such as in forensics investigations,…
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,…
A problem studied in Systems Biology is how to find shortest paths in metabolic networks. Unfortunately, simple (i.e., graph theoretic) shortest paths do not properly reflect biochemical facts. An approach to overcome this issue is to use…
Interactive segmentation is a crucial research area in medical image analysis aiming to boost the efficiency of costly annotations by incorporating human feedback. This feedback takes the form of clicks, scribbles, or masks and allows for…
Timely and accurate lymphoma diagnosis is essential for guiding cancer treatment. Standard diagnostic practice combines hematoxylin and eosin (HE)-stained whole slide images with immunohistochemistry, flow cytometry, and molecular genetic…
We combine the standard 1992 20x20 substitution matrix based on block alignment, BLOSUM62, with the standard 1982 amino acid hydropathicity scale KD as well as the modern 2007 hydropathicity scale MZ, and compare the results. The…
Capturing intricate biological phenomena often requires multiscale modeling where coarse and inexpensive models are developed using limited components of expensive and high-fidelity models. Here, we consider such a multiscale framework in…
The primitive data for deducing the Miyazawa-Jernigan contact energy or BLOSUM score metrix are the pair frequency counts. Each amino acid corresponds to a distribution. Taking the Kullback-Leibler distance of two probability distributions…
All known terrestrial proteins are coded as continuous strings of ~20 amino acids. The patterns formed by the repetitions of elements in groups of finite sequences describes the natural architectures of protein families. We present a method…