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Most complex diseases, including cancer and non-malignant diseases like asthma, have distinct molecular subtypes that require distinct clinical approaches. However, existing computational patient stratification methods have been benchmarked almost exclusively on cancer omics data and only perform well when mutually exclusive subtypes can be characterized by many biomarkers. Here, we contribute with a massive evaluation attempt, quantitatively exploring the power of 22 unsupervised patient stratification methods using both, simulated and real transcriptome data. From this experience, we developed UnPaSt (https://apps.cosy.bio/unpast/) optimizing unsupervised patient stratification, working even with only a limited number of subtype-predictive biomarkers. We evaluated all 23 methods on real-world breast cancer and asthma transcriptomics data. Although many methods reliably detected major breast cancer subtypes, only few identified Th2-high asthma, and UnPaSt significantly outperformed its closest competitors in both test datasets. Essentially, we showed that UnPaSt can detect many biologically insightful and reproducible patterns in omic datasets., Comment: The first two authors listed are joint first authors. The last two authors listed are joint last authors

Quantitative mass spectrometry has revolutionized proteomics by enabling simultaneous quantification of thousands of proteins. Pooling patient-derived data from multiple institutions enhances statistical power but raises significant privacy concerns. Here we introduce FedProt, the first privacy-preserving tool for collaborative differential protein abundance analysis of distributed data, which utilizes federated learning and additive secret sharing. In the absence of a multicenter patient-derived dataset for evaluation, we created two, one at five centers from LFQ E.coli experiments and one at three centers from TMT human serum. Evaluations using these datasets confirm that FedProt achieves accuracy equivalent to DEqMS applied to pooled data, with completely negligible absolute differences no greater than $\text{$4 \times 10^{-12}$}$. In contrast, -log10(p-values) computed by the most accurate meta-analysis methods diverged from the centralized analysis results by up to 25-27. FedProt is available as a web tool with detailed documentation as a FeatureCloud App., Comment: 52 pages, 16 figures, 12 tables. Last two authors listed are joint last authors

In recent decades, the development of new drugs has become increasingly expensive and inefficient, and the molecular mechanisms of most pharmaceuticals remain poorly understood. In response, computational systems and network medicine tools have emerged to identify potential drug repurposing candidates. However, these tools often require complex installation and lack intuitive visual network mining capabilities. To tackle these challenges, we introduce Drugst.One, a platform that assists specialized computational medicine tools in becoming user-friendly, web-based utilities for drug repurposing. With just three lines of code, Drugst.One turns any systems biology software into an interactive web tool for modeling and analyzing complex protein-drug-disease networks. Demonstrating its broad adaptability, Drugst.One has been successfully integrated with 21 computational systems medicine tools. Available at https://drugst.one, Drugst.One has significant potential for streamlining the drug discovery process, allowing researchers to focus on essential aspects of pharmaceutical treatment research., Comment: 45 pages, 6 figures, 7 tables

Machine Learning (ML) and Artificial Intelligence (AI) have shown promising results in many areas and are driven by the increasing amount of available data. However, this data is often distributed across different institutions and cannot be shared due to privacy concerns. Privacy-preserving methods, such as Federated Learning (FL), allow for training ML models without sharing sensitive data, but their implementation is time-consuming and requires advanced programming skills. Here, we present the FeatureCloud AI Store for FL as an all-in-one platform for biomedical research and other applications. It removes large parts of this complexity for developers and end-users by providing an extensible AI Store with a collection of ready-to-use apps. We show that the federated apps produce similar results to centralized ML, scale well for a typical number of collaborators and can be combined with Secure Multiparty Computation (SMPC), thereby making FL algorithms safely and easily applicable in biomedical and clinical environments.

The article pays close attention to obtaining gender assessments in the world of work, which made it possible to characterize the effectiveness of social policy aimed at achieving gender equality., Comment: pages 20, figure 6

Aggregating transcriptomics data across hospitals can increase sensitivity and robustness of differential expression analyses, yielding deeper clinical insights. As data exchange is often restricted by privacy legislation, meta-analyses are frequently employed to pool local results. However, if class labels are inhomogeneously distributed between cohorts, their accuracy may drop. Flimma (https://exbio.wzw.tum.de/flimma/) addresses this issue by implementing the state-of-the-art workflow limma voom in a privacy-preserving manner, i.e. patient data never leaves its source site. Flimma results are identical to those generated by limma voom on combined datasets even in imbalanced scenarios where meta-analysis approaches fail., Comment: 27 pages, 7 figures

This article presents the results of a cluster analysis of the regions of the Russian Federation in terms of the main parameters of socio-economic development according to the data presented in the official data sources of the Federal State Statistics Service (Rosstat). Studied and analyzed the domestic and foreign (Eurostat) methodology for assessing the socio-economic development of territories. The aim of the study is to determine the main parameters of territorial differentiation and to identify key indicators that affect the socio-economic development of Russian regions. The authors have carried out a classification of the constituent entities of the Russian Federation not in terms of territorial location and geographical features, but in terms of the specifics and key parameters of the socio-economic situation., Comment: This research was performed in the framework of the state task in the field of scientific activity of the Ministry of Science and Higher Education of the Russian Federation, project "Development of the methodology and a software platform for the construction of digital twins, intellectual analysis and forecast of complex economic systems", grant no. FSSW-2020-0008

The article presents the results of multivariate classification of Russian regions by the indicators characterizing the population income and their concentration. The clusterization was performed upon an author approach to selecting the characteristics which determines the academic novelty in the evaluation of regional differentiation by population income and the interconnected characteristics. The performed analysis was aimed at the evaluation of the real scale of disproportions in spatial development of the country territories by the considered characteristics. The clusterization results allowed to formulate the condition of a relatively "strong" position of a group of high-income regions (the changes in the array of regions constituting it is highly unlikely in the foreseeable future). Additionally there has been revealed a group of Russian regions that the population is struggling to live on quite low income. These so-called "poor" regions, within the crisis conditions caused by Covid-19 are in need of additional public support, without which their population will impoverish., Comment: 14 pages, 2 figure