Bioinformatics Institute

Synthetic data to explore transcriptional regulation of differentially expressed genes in ovarian cancer

In major diseases like cancer, many genes are dysregulated. While differential expression (DE) analyses help identify these genes, they do not reveal the transcriptional regulatory landscape between control and disease states. Here, we developed a process-driven model based on ge...

From Conatus to the War of Nature: Scarcity, Scientific Metaphors, and the Epistemic Rewriting of Biological Persistence

Biological persistence is both a biological and an epistemic problem: vocabularies of scarcity, struggle, competition, war, and survival make some dimensions of continuation especially easy to describe while leaving others less direct to articulate. This article reconstructs diff...

From Conatus to the War of Nature: Scarcity, Scientific Metaphors, and the Epistemic Rewriting of Biological Persistence

Biological persistence is both a biological and an epistemic problem: vocabularies of scarcity, struggle, competition, war, and survival make some dimensions of continuation especially easy to describe while leaving others less direct to articulate. This article reconstructs diff...

Microbial Ecological Damping: A Multilevel Systems-Ecology Framework for Climate–Biodiversity Resilience

Climate change and biodiversity loss alter disturbance regimes, yet resilience frameworks often underresolve the microbial infrastructure through which disturbance is attenuated, transmitted, reorganized, or amplified. This Perspective analyzes that infrastructure across three di...

Inferring tumor dependency maps from histopathology through imputed transcriptomics

Gene dependency maps from cancer cell lines define context-specific essential genes, but comparable dependencies in tumors remain largely inaccessible. This gap limits the identification of actionable therapeutic vulnerabilities. Here we present a two-stage deep learning framewor...