Understanding interaction mechanisms within cells, tissues, and organisms is crucial for
driving developments across biology and medicine. Mathematical modeling is an essential …

Implicit solvent force fields are computationally efficient but can be unsuitable for running
molecular dynamics on disordered proteins. Here I improve the a99SB-disp force field and …

The growth of omic data presents evolving challenges in data manipulation, analysis and
integration. Addressing these challenges, Bioconductor provides an extensive community …

The rapid progression of genomics and proteomics has been driven by the advent of
advanced sequencing technologies, large, diverse, and readily available omics datasets …

Clonal hematopoiesis becomes increasingly common with age, but its cause is enigmatic
because driver mutations are often absent. Serial observations infer weak selection …

Myeloid-derived suppressor cells (MDSC) play a prominent role in the tumor
microenvironment. A quantitative understanding of the tumor–MDSC interactions that …

Spatially resolved transcriptomics (SRT) has become the method of choice for characterising
the complexity of biomedical tissue samples. Until recently, scientists were restricted to SRT …

Background Effective identification of differentially expressed genes (DEGs) has been
challenging for single-cell RNA sequencing (scRNA-seq) profiles. Many existing algorithms …

Julia is a general purpose programming language that was designed for simplifying and
accelerating numerical analysis and computational science. In particular the Scientific …

BondGraphs. jl is a Julia implementation of bond graphs. Bond graphs provide a modelling
framework that describes energy flow through a physical system and by construction enforce …