Bacterial insertion sequences: their genomic impact and diversity

P Siguier, E Gourbeyre… - FEMS microbiology …, 2014 - academic.oup.com
Insertion sequences (ISs), arguably the smallest and most numerous autonomous
transposable elements (TEs), are important players in shaping their host genomes. This …

Advancing crop genomics from lab to field

MD Purugganan, SA Jackson - Nature genetics, 2021 - nature.com
Crop genomics remains a key element in ensuring scientific progress to secure global food
security. It has been two decades since the sequence of the first plant genome, that of …

Simulation intelligence: Towards a new generation of scientific methods

A Lavin, D Krakauer, H Zenil, J Gottschlich… - arXiv preprint arXiv …, 2021 - arxiv.org
The original" Seven Motifs" set forth a roadmap of essential methods for the field of scientific
computing, where a motif is an algorithmic method that captures a pattern of computation …

Reverse engineering and identification in systems biology: strategies, perspectives and challenges

AF Villaverde, JR Banga - Journal of the Royal Society …, 2014 - royalsocietypublishing.org
The interplay of mathematical modelling with experiments is one of the central elements in
systems biology. The aim of reverse engineering is to infer, analyse and understand …

Making ecological models adequate

WM Getz, CR Marshall, CJ Carlson, L Giuggioli… - Ecology …, 2018 - Wiley Online Library
Critical evaluation of the adequacy of ecological models is urgently needed to enhance their
utility in developing theory and enabling environmental managers and policymakers to …

Colloquium: Multiscale modeling of brain network organization

C Presigny, F De Vico Fallani - Reviews of Modern Physics, 2022 - APS
A complete understanding of the brain requires an integrated description of the numerous
scales and levels of neural organization. This means studying the interplay of genes and …

Agents. jl: a performant and feature-full agent-based modeling software of minimal code complexity

G Datseris, AR Vahdati, TC DuBois - Simulation, 2024 - journals.sagepub.com
Agent-based modeling is a simulation method in which autonomous agents interact with
their environment and one another, given a predefined set of rules. It is an integral method …

[HTML][HTML] Metabolomics and systems pharmacology: why and how to model the human metabolic network for drug discovery

DB Kell, R Goodacre - Drug Discovery Today, 2014 - Elsevier
Highlights•We now have metabolic network models; the metabolome is represented by their
nodes.•Metabolite levels are sensitive to changes in enzyme activities.•Drugs hitchhike on …

Recent applications of quantitative systems pharmacology and machine learning models across diseases

SS Aghamiri, R Amin, T Helikar - Journal of pharmacokinetics and …, 2022 - Springer
Quantitative systems pharmacology (QSP) is a quantitative and mechanistic platform
describing the phenotypic interaction between drugs, biological networks, and disease …

Can photosynthesis enable a global transition from fossil fuels to solar fuels, to mitigate climate change and fuel-supply limitations?

AK Ringsmuth, MJ Landsberg, B Hankamer - Renewable and Sustainable …, 2016 - Elsevier
This review article considers Earth as an energy-storing (photosynthetic) and energy-
consuming (metabolic) system. We evaluate whether and how photosynthetic, solar fuel …