Systems & Computational Biology
Convergent evolution and B-cell recirculation in germinal centers in a human lymph nodeThe study characterizes an ongoing immune response by sequencing B-cells from 10 germinal centers and finds diverse clonal patterns and convergent evolution, indicating re-engagement and rediversification of B-cell clones across GCs.
De novo network analysis reveals autism causal genes and developmental links to co-occurring traitsIn this study, we provide a biological argument for looking at an autistic individual’s phenotype as being related to their combined genetic risk for different clusters of traits.
Basonuclin-2 regulates extracellular matrix production and degradationBasonuclin-2 (BNC2) is identified as a novel regulator of genes associated with the extracellular matrix and cytokines in fibroblasts. BNC2 is thereby identified as a novel regulator of the tumour microenvironment where its high expression correlates with poor prognosis.
PASCAR: a multiscale framework to explore the design space of constitutive and inducible CAR T cellsAn experimentally validated protein abundance structured population dynamic model for CAR T cells (PASCAR) that integrates processes from molecules to single cells to cell populations and systematically explores the design space of constitutive and tunable CAR T cells.
A network embedding approach to identify active modules in biological interaction networksThis study proposes the AMINE method as a flexible and efficient approach to identify active modules from a data embedding combining gene expression and interaction data.
Missense variant interaction scanning reveals a critical role of the FERM domain for tumor suppressor protein NF2 conformation and functionDeep mutational interaction perturbation scanning of NF2 with conformation-dependent interaction partners KDM1A, EMILIN, and PIK3R3 revealed two regions critical for NF2 tumor suppressor function.
A new metabolic model of Drosophila melanogaster and the integrative analysis of Parkinson’s diseaseThe reconstruction of a comprehensive and literature-curated Drosophila metabolic model, iDrosophila1, provided a powerful platform for studying metabolism with systems medicine perspective.
Evaluation of genetic demultiplexing of single-cell sequencing data from model speciesThe authors demonstrate that scRNA-seq sample pooling followed by genetics-based separation of individuals is an effective means to identify individual samples in a variety of commonly studied species.
Predictive data-driven modeling of C-terminal tyrosine function in the EGFR signaling networkThe site-specific function of EGFR’s C-terminal tyrosines is interrogated by phosphotyrosine phosphoproteomics to build a data-driven model that links cell response to signaling nodes and elucidates novel associations in the EGFR signaling network.
Antibody reliability influences observed mRNA–protein correlations in tumour samplesUpadhya and Ryan show that the reliability of antibodies used for RPPA profiling influences the mRNA-protein correlations observed in tumour cohorts.