Systems & Computational Biology
Unraveling ADHD: genes, co-occurring traits, and developmental dynamicsIn this study, we identify genes putatively causal for ADHD and show how their biological pathways link to co-occurring traits and biomarkers in a tissue- and time-dependent manner.
Systematic assessment of structural variant annotation tools for genomic interpretationThis study benchmarks eight structural variant prioritization tools, highlighting their comparable effectiveness in predicting pathogenicity and providing insights for improved genomic research.
Transcriptional regulators ensuring specific gene expression and decision-making at high TGFβ dosesA systems biology approach integrates measurements of TGFβ-induced signaling, gene expression, and fate decisions to reveal mechanisms of dose-dependent decoding of input signals in gene regulation.
Computing hematopoiesis plasticity in response to genetic mutations and environmental stimulationsAn integrated and single-cell-omics dataset–based computing pipeline scPlasticity is introduced to quantify cell plasticity and prioritize master regulators in normal and stress hematopoiesis.
BACH1 as a key driver in rheumatoid arthritis fibroblast-like synoviocytes identified through gene network analysisThe study identifies BACH1 as a key driver of fibroblast-like synoviocyte pathogenicity in rheumatoid arthritis, highlighting its role in regulating fatty acid metabolism and ferroptosis.
The hGIDGID4 E3 ubiquitin ligase complex targets ARHGAP11A to regulate cell migrationThis study shows that the hGIDGID4 E3 ligase controls cell migration by ubiquitinating ARHGAP11A for degradation, thereby regulating RhoA activity.
Identification of single-cell blasts in pediatric acute myeloid leukemia using an autoencoderThe authors present a novel automated approach for the identification of blasts and their developmental stage in a longitudinal pediatric acute myeloid leukemia (AML) cohort. KMT2A-rearranged AMLs show unstable immunophenotype, with most patients presenting a more differentiated phenotype at relapse.
A scalable approach to topic modelling in single-cell data by approximate pseudobulk projectionRandom projection of pseudobulk gene expression data improves the scalability and accuracy of single-cell topic modelling.
pyRBDome: a comprehensive computational platform for enhancing RNA-binding proteome dataThis study explores enhancing protein–RNA interaction prediction using machine learning.
Substrate diversity of NSUN enzymes and links of 5-methylcytosine to mRNA translation and turnoverThis study emphasises the emerging diversity of both, m5C writers and readers, affecting mRNA function and provides multiple new leads for future epitranscriptomic research.