Representation and quantification of module activity from omics data with rROMA.

The efficiency of analyzing high-throughput data in systems biology has been demonstrated in numerous studies, where molecular data, such as transcriptomics and proteomics, offers great opportunities for understanding the complexity of biological processes. One important aspect of data analysis in systems biology is the shift from a reductionist approach that focuses on individual components to a more integrative perspective that considers the system as a whole, where the emphasis shifted from differential expression of individual genes to determining the activity of gene sets. Here, we present the rROMA software package for fast and accurate computation of the activity of gene sets with coordinated expression.

Exploring isofunctional molecules: Design of a benchmark and evaluation of prediction performance.

Identification of novel chemotypes with biological activity similar to a known active molecule is an important challenge in drug discovery called 'scaffold hopping'. Small-, medium-, and large-step scaffold hopping efforts may lead to increasing degrees of chemical structure novelty with respect to the parent compound. In the present paper, we focus on the problem of large-step scaffold hopping.

Differential CFTR-Interactome Proximity Labeling Procedures Identify Enrichment in Multiple SLC Transporters.

Proteins interacting with CFTR and its mutants have been intensively studied using different experimental approaches. These studies provided information on the cellular processes leading to proper protein folding, routing to the plasma membrane, recycling, activation and degradation. Recently, new approaches have been developed based on the proximity labeling of protein partners or proteins in close vicinity and their subsequent identification by mass spectrometry.

Recurrent Mutations in Cyclin D3 Confer Clinical Resistance to FLT3 Inhibitors in Acute Myeloid Leukemia.

Purpose: Biomarkers of response and resistance to FLT3 tyrosine kinase inhibitors (TKI) are still emerging, and optimal clinical combinations remain unclear. The purpose of this study is to identify co-occurring mutations that influence clinical response to the novel FLT3 inhibitor pexidartinib (PLX3397).

Experimental Design: We performed targeted sequencing of pretreatment blasts from 29 patients with internal tandem duplication (ITD) mutations treated on the phase I/II trial of pexidartinib in relapsed/refractory -ITD+ acute myeloid leukemia (AML).

Drug Target Identification with Machine Learning: How to Choose Negative Examples.

Identification of the protein targets of hit molecules is essential in the drug discovery process. Target prediction with machine learning algorithms can help accelerate this search, limiting the number of required experiments. However, Drug-Target Interactions databases used for training present high statistical bias, leading to a high number of false positives, thus increasing time and cost of experimental validation campaigns.

Mapping and Modeling of Discussions Related to Gastrointestinal Discomfort in French-Speaking Online Forums: Results of a 15-Year Retrospective Infodemiology Study.

Background: Gastrointestinal (GI) discomfort is prevalent and known to be associated with impaired quality of life. Real-world information on factors of GI discomfort and solutions used by people is, however, limited. Social media, including online forums, have been considered a new source of information to examine the health of populations in real-life settings.

Reconstructing Mayaro virus circulation in French Guiana shows frequent spillovers.

Characterizing the circulation of Mayaro virus (MAYV), an emerging arbovirus threat, is essential for risk assessment but challenging due to cross-reactivity with other alphaviruses such as chikungunya virus (CHIKV). Here, we develop an analytical framework to jointly assess MAYV epidemiology and the extent of cross-reactivity with CHIKV from serological data collected throughout French Guiana (N = 2697). We find strong evidence of an important sylvatic cycle for MAYV with most infections occurring near the natural reservoir in rural areas and in individuals more likely to go to the forest (i.

Wire-Active Microrheology to Differentiate Viscoelastic Liquids from Soft Solids.

Viscoelastic liquids are characterized by a finite static viscosity and a yield stress of zero, whereas soft solids have an infinite viscosity and a non-zero yield stress. The rheological nature of viscoelastic materials has long been a challenge and is still a matter of debate. Here, we provide for the first time the constitutive equations of linear viscoelasticity for magnetic wires in yield-stress materials, together with experimental measurements by using magnetic rotational spectroscopy (MRS).