Cytosplore Simian Viewer: Visual Exploration for Multi-Species Single-Cell RNA Sequencing Data

With the rapid advances in single-cell sequencing technologies, novel types of studies into the cell-type makeup of the brain have become possible. Biologists often analyze large and complex single-cell transcriptomic datasets to enhance knowledge of the intricate features of cellular and molecular tissue organization. A particular area of...

A machine learning method for the discovery of minimum marker gene combinations for cell type identification from single-cell RNA sequencing

Single-cell genomics is rapidly advancing our knowledge of the diversity of cell phenotypes, including both cell types and cell states. Driven by single-cell/-nucleus RNA sequencing (scRNA-seq), comprehensive cell atlas projects characterizing a wide range of organisms and tissues are currently underway. As a result, it is critical that the...

Comparative cellular analysis of motor cortex in human, marmoset and mouse

The primary motor cortex (M1) is essential for voluntary fine-motor control and is functionally conserved across mammals¹. Here, using high-throughput transcriptomic and epigenomic profiling of more than 450,000 single nuclei in humans, marmoset monkeys and mice, we demonstrate a broadly conserved cellular makeup of this region,...

Denitrification as an N₂O sink

The strong greenhouse gas nitrous oxide (N₂O) can be emitted from wastewater treatment systems as a byproduct of ammonium oxidation and as the last intermediate in the stepwise reduction of nitrate to N₂ by denitrifying organisms. A potential strategy to reduce N₂O emissions would be to enhance the activity of...

Metabolic modeling of denitrification in Agrobacterium tumefaciens: A tool to study inhibiting and activating compounds for the denitrification pathway

A metabolic network model for facultative denitrification was developed based on experimental data obtained with Agrobacterium tumefaciens. The model includes kinetic regulation at the enzyme level and transcription regulation at the enzyme synthesis level. The objective of this work was to study the key factors regulating the metabolic response...

Metabolic modeling of denitrification in Agrobacterium tumefaciens: A tool to study inhibiting and activating compounds for the denitrification pathway