Systems & Computational Biology
Systemic metabolic depletion of gut microbiome undermines responsiveness to melanoma immunotherapyRelationship between gut microbiome composition and immunotherapy efficacy.
A comparative study of structural variant calling in WGS from Alzheimer’s disease familiesWe developed a flexible protocol to generate a high-quality deletion call set and a truth set of Sanger sequencing–validated deletions with precise breakpoints between 1 and 17,000 bp from whole-genome sequencing data in multiplex families with Alzheimer’s disease.
Stability of gut microbiome after COVID-19 vaccination in healthy and immuno-compromised individualsThis study highlights the resilience of the gut microbiome to host immune changes triggered by COVID-19 vaccination and suggest minimal, if any, impact on microbiome-mediated processes.
NeoMUST: an accurate and efficient multi-task learning model for neoantigen presentationNeoMUST, a multi-task learning model, efficiently predicts neoantigen presentation via MHC-I molecules, rivaling existing algorithms with significantly shorter training time. Its GitHub repository offers free access for advancing cancer immunotherapy development.
Accessory genes define species-specific routes to antibiotic resistanceIn this study, we show how decision tree models can accurately predict the AMR phenotype, and this study highlights that resistance is a result of multi-gene interactions, which are often species-specific.
Single-cell time series analysis reveals the dynamics of HSPC response to inflammationUnbiased single-cell time series analysis of gene expression response to inflammation, using novel computational approaches, links myeloid depletion to alterations in differentiation bias and pyroptosis activity.
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.
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.
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.
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.