OMEN: network-based driver gene identification using mutual exclusivity.

Motivation: Network-based driver identification methods that can exploit mutual exclusivity typically fail to detect rare drivers because of their statistical rigor. Propagation-based methods in contrast allow recovering rare driver genes, but the interplay between network topology and high-scoring nodes often results in spurious predictions. The specificity of driver gene detection can be improved by taking into account both gene-specific and gene-set properties.

Symbolic Learning and Reasoning With Noisy Data for Probabilistic Anchoring.

Robotic agents should be able to learn from sub-symbolic sensor data and, at the same time, be able to reason about objects and communicate with humans on a symbolic level. This raises the question of how to overcome the gap between symbolic and sub-symbolic artificial intelligence. We propose a semantic world modeling approach based on bottom-up object anchoring using an object-centered representation of the world.

COVID-19 in people with multiple sclerosis: A global data sharing initiative.

Background: We need high-quality data to assess the determinants for COVID-19 severity in people with MS (PwMS). Several studies have recently emerged but there is great benefit in aligning data collection efforts at a global scale.

Objectives: Our mission is to scale-up COVID-19 data collection efforts and provide the MS community with data-driven insights as soon as possible.

Representing dynamic biological networks with multi-scale probabilistic models.

Dynamic models analyzing gene regulation and metabolism face challenges when adapted to modeling signal transduction networks. During signal transduction, molecular reactions and mechanisms occur in different spatial and temporal frames and involve feedbacks. This impedes the straight-forward use of methods based on Boolean networks, Bayesian approaches, and differential equations.

Simultaneous discovery of cancer subtypes and subtype features by molecular data integration.

Motivation: Subtyping cancer is key to an improved and more personalized prognosis/treatment. The increasing availability of tumor related molecular data provides the opportunity to identify molecular subtypes in a data-driven way. Molecular subtypes are defined as groups of samples that have a similar molecular mechanism at the origin of the carcinogenesis.

Network-Based Analysis of eQTL Data to Prioritize Driver Mutations.

In clonal systems, interpreting driver genes in terms of molecular networks helps understanding how these drivers elicit an adaptive phenotype. Obtaining such a network-based understanding depends on the correct identification of driver genes. In clonal systems, independent evolved lines can acquire a similar adaptive phenotype by affecting the same molecular pathways, a phenomenon referred to as parallelism at the molecular pathway level.

PheNetic: network-based interpretation of molecular profiling data.

Molecular profiling experiments have become standard in current wet-lab practices. Classically, enrichment analysis has been used to identify biological functions related to these experimental results. Combining molecular profiling results with the wealth of currently available interactomics data, however, offers the opportunity to identify the molecular mechanism behind an observed molecular phenotype.

PheNetic: network-based interpretation of unstructured gene lists in E. coli.

At the present time, omics experiments are commonly used in wet lab practice to identify leads involved in interesting phenotypes. These omics experiments often result in unstructured gene lists, the interpretation of which in terms of pathways or the mode of action is challenging. To aid in the interpretation of such gene lists, we developed PheNetic, a decision theoretic method that exploits publicly available information, captured in a comprehensive interaction network to obtain a mechanistic view of the listed genes.

SMIREP: predicting chemical activity from SMILES.

Most approaches to structure-activity-relationship (SAR) prediction proceed in two steps. In the first step, a typically large set of fingerprints, or fragments of interest, is constructed (either by hand or by some recent data mining techniques). In the second step, machine learning techniques are applied to obtain a predictive model.

Data mining and machine learning techniques for the identification of mutagenicity inducing substructures and structure activity relationships of noncongeneric compounds.

This paper explores the utility of data mining and machine learning algorithms for the induction of mutagenicity structure-activity relationships (SARs) from noncongeneric data sets. We compare (i) a newly developed algorithm (MOLFEA) for the generation of descriptors (molecular fragments) for noncongeneric compounds with traditional SAR approaches (molecular properties) and (ii) different machine learning algorithms for the induction of SARs from these descriptors. In addition we investigate the optimal parameter settings for these programs and give an exemplary interpretation of the derived models.