Systems & Computational Biology
- Convergent evolution and B-cell recirculation in germinal centers in a human lymph node
The 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 traits
In 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 degradation
Basonuclin-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 cells
An 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 networks
This 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 function
Deep 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 disease
The 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 species
The 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 network
The 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 samples
Upadhya and Ryan show that the reliability of antibodies used for RPPA profiling influences the mRNA-protein correlations observed in tumour cohorts.