Systems & Computational Biology
Enhancer-driven 3D chromatin domain folding modulates transcription in human mammary tumor cellsThe study shows that estrogen activates transcription within pre-established chromosomal 3D architectures, strengthening enhancer interactions through local accumulation of the estrogen receptor α.
Meta-analysis of dispensable essential genes and their interactions with bypass suppressorsThis work compiles data from several studies on dispensable essential genes in S. cerevisiae to comprehensively characterize these genes and to explore how their interactions with bypass suppressor genes reflect evolution in natural populations.
Suppressed transcript diversity and immune response in COVID-19 ICU patients: a longitudinal studyThis integrative longitudinal clinico-genomic study delves deep into the gene and transcript expression pattern dynamics in severe COVID-19 patients with ARDS admitted to the ICU.
Performance and robustness analysis reveals phenotypic trade-offs in yeastThis study combines phenotypic data from yeast cultivations with quantification of robustness over a defined perturbation space, revealing trade-offs between performance and robustness.
MICA: a multi-omics method to predict gene regulatory networks in early human embryosOur comparative analysis of gene regulatory network predictions defines a pipeline to infer transcription factor–target gene regulatory interactions in early human embryos. Mutual information refined by chromatin accessibility allowed us to construct the first network during early human development.
Pathway-driven analysis of synthetic lethal interactions in cancer using perturbation screensThis study introduces a signaling pathway-informed computational approach to identify synthetic lethal (SL) interactions in various cancer types, uncovering potential targeted therapies for specific genetic alterations.
scFseCluster: a feature selection-enhanced clustering for single-cell RNA-seq dataThis study presents a novel computational framework scFseCluster for scRNA-seq clustering analysis. Particularly, an excellent feature selection algorithm FSQSSA was encapsulated in the scFseCluster platform, which achieves optimal gene sets for clustering tasks.
KCNQ potassium channels modulate Wnt activity in gastro-oesophageal adenocarcinomasKCNQ3, a potassium channel, is frequently genetically altered in gastro-oesophageal adenocarcinomas and found to be significantly associated with WNT and MYC activity, and cellular proliferation.
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.