An Automated Analysis of Homocoupling Defects Using MALDI-MS and Open-Source Computer Software.

Conjugated organic polymers have substantial potential for multiple applications but their properties are strongly influenced by structural defects such as homocoupling of monomer units and unexpected end-groups. Detecting and/or quantifying these defects requires complex experimental techniques, which hinder the optimization of synthesis protocols and fundamental studies on the influence of structural defects. Mass spectrometry offers a simple way to detect these defects but a manual analysis of many complex spectra is tedious and provides only approximate results.

Magnetstein: An Open-Source Tool for Quantitative NMR Mixture Analysis Robust to Low Resolution, Distorted Lineshapes, and Peak Shifts.

H NMR spectroscopy is a powerful tool for analyzing mixtures including determining the concentrations of individual components. When signals from multiple compounds overlap, this task requires computational solutions. They are typically based on peak-picking and the comparison of obtained peak lists with libraries of individual components.

Critical assessment of synthetic accessibility scores in computer-assisted synthesis planning.

Modern computer-assisted synthesis planning tools provide strong support for this problem. However, they are still limited by computational complexity. This limitation may be overcome by scoring the synthetic accessibility as a pre-retrosynthesis heuristic.

National and subnational short-term forecasting of COVID-19 in Germany and Poland during early 2021.

Background: During the COVID-19 pandemic there has been a strong interest in forecasts of the short-term development of epidemiological indicators to inform decision makers. In this study we evaluate probabilistic real-time predictions of confirmed cases and deaths from COVID-19 in Germany and Poland for the period from January through April 2021.

Methods: We evaluate probabilistic real-time predictions of confirmed cases and deaths from COVID-19 in Germany and Poland.

Alignstein: Optimal transport for improved LC-MS retention time alignment.

Background: Reproducibility of liquid chromatography separation is limited by retention time drift. As a result, measured signals lack correspondence over replicates of the liquid chromatography-mass spectrometry (LC-MS) experiments. Correction of these errors is named retention time alignment and needs to be performed before further quantitative analysis.

CONET: copy number event tree model of evolutionary tumor history for single-cell data.

Copy number alterations constitute important phenomena in tumor evolution. Whole genome single-cell sequencing gives insight into copy number profiles of individual cells, but is highly noisy. Here, we propose CONET, a probabilistic model for joint inference of the evolutionary tree on copy number events and copy number calling.

Data-driven case fatality rate estimation for the primary lineage of SARS-CoV-2 in Poland.

After more than one and a half year since the COVID-19 pandemics outbreak the scientific world is constantly trying to understand its dynamics. In this paper of the case fatality rates (CFR) for COVID-19 we study the historic data regarding mortality in Poland during the first six months of pandemic, when no SARS-CoV-2 variants of concern were present among infected. To this end, we apply competing risk models to perform both uni- and multivariate analyses on specific subpopulations selected by different factors including the key indicators: age, sex, hospitalization.

Bayesian inference of a non-local proliferation model.

From a systems biology perspective, the majority of cancer models, although interesting and providing a qualitative explanation of some problems, have a major disadvantage in that they usually miss a genuine connection with experimental data. Having this in mind, in this paper, we aim at contributing to the improvement of many cancer models which contain a proliferation term. To this end, we propose a new non-local model of cell proliferation.

Masserstein: Linear regression of mass spectra by optimal transport.

Rationale: The linear regression of mass spectra is a computational problem defined as fitting a linear combination of reference spectra to an experimental one. It is typically used to estimate the relative quantities of selected ions. In this work, we study this problem in an abstract setting to develop new approaches applicable to a diverse range of experiments.

Jaccard/Tanimoto similarity test and estimation methods for biological presence-absence data.

Background: A survey of presences and absences of specific species across multiple biogeographic units (or bioregions) are used in a broad area of biological studies from ecology to microbiology. Using binary presence-absence data, we evaluate species co-occurrences that help elucidate relationships among organisms and environments. To summarize similarity between occurrences of species, we routinely use the Jaccard/Tanimoto coefficient, which is the ratio of their intersection to their union.

masstodon: A Tool for Assigning Peaks and Modeling Electron Transfer Reactions in Top-Down Mass Spectrometry.

Top-down mass spectrometry methods are becoming continuously more popular in the effort to describe the proteome. They rely on the fragmentation of intact protein ions inside the mass spectrometer. Among the existing fragmentation methods, electron transfer dissociation is known for its precision and wide coverage of different cleavage sites.

Estimation of Rates of Reactions Triggered by Electron Transfer in Top-Down Mass Spectrometry.

Electron transfer dissociation (ETD) is a versatile technique used in mass spectrometry for the high-throughput characterization of proteins. It consists of several concurrent reactions triggered by the transfer of an electron from its anion source to sample cations. Transferring an electron causes peptide backbone cleavage while leaving labile post-translational modifications intact.

Bayesian inference for age-structured population model of infectious disease with application to varicella in Poland.

The dynamics of the infectious disease transmission are often best understood by taking into account the structure of population with respect to specific features, for example age or immunity level. The practical utility of such models depends on the appropriate calibration with the observed data. Here, we discuss the Bayesian approach to data assimilation in the case of a two-state age-structured model.

Optimization of Mutation Pressure in Relation to Properties of Protein-Coding Sequences in Bacterial Genomes.

Most mutations are deleterious and require energetically costly repairs. Therefore, it seems that any minimization of mutation rate is beneficial. On the other hand, mutations generate genetic diversity indispensable for evolution and adaptation of organisms to changing environmental conditions.