Gene regulatory network inference in the era of single-cell multi-omics

P Badia-i-Mompel, L Wessels, S Müller-Dott… - Nature Reviews …, 2023 - nature.com
The interplay between chromatin, transcription factors and genes generates complex
regulatory circuits that can be represented as gene regulatory networks (GRNs). The study …

Metabolic engineering of Saccharomyces cerevisiae: a key cell factory platform for future biorefineries

KK Hong, J Nielsen - Cellular and Molecular Life Sciences, 2012 - Springer
Metabolic engineering is the enabling science of development of efficient cell factories for
the production of fuels, chemicals, pharmaceuticals, and food ingredients through microbial …

The developmental dynamics of the maize leaf transcriptome

P Li, L Ponnala, N Gandotra, L Wang, Y Si, SL Tausta… - Nature …, 2010 - nature.com
We have analyzed the maize leaf transcriptome using Illumina sequencing. We mapped
more than 120 million reads to define gene structure and alternative splicing events and to …

Active pharmaceutical ingredient (API) chemicals: a critical review of current biotechnological approaches

V Kumar, V Bansal, A Madhavan, M Kumar… - …, 2022 - Taylor & Francis
The aim of this article was to generate a framework of bio-based economy by an effective
utilization of biomass from the perspectives of agriculture for developing potential end bio …

[HTML][HTML] Extensive in vivo metabolite-protein interactions revealed by large-scale systematic analyses

X Li, TA Gianoulis, KY Yip, M Gerstein, M Snyder - Cell, 2010 - cell.com
Natural small compounds comprise most cellular molecules and bind proteins as substrates,
products, cofactors, and ligands. However, a large-scale investigation of in vivo protein …

Metabolic engineering for compartmentalized biosynthesis of the valuable compounds in Saccharomyces cerevisiae

MQ Yin, K Xu, T Luan, XL Kang, XY Yang, HX Li… - Microbiological …, 2024 - Elsevier
Saccharomyces cerevisiae is commonly used as a microbial cell factory to produce high-
value compounds or bulk chemicals due to its genetic operability and suitable intracellular …

[HTML][HTML] A unifying view of 21st century systems biology

M Vidal - FEBS letters, 2009 - Elsevier
The idea that multi-scale dynamic complex systems formed by interacting macromolecules
and metabolites, cells, organs and organisms underlie some of the most fundamental …

A survey of yeast genomic assays for drug and target discovery

AM Smith, R Ammar, C Nislow, G Giaever - Pharmacology & therapeutics, 2010 - Elsevier
Over the past decade, the development and application of chemical genomic assays using
the model organism Saccharomyces cerevisiae has provided powerful methods to identify …

The future of model organisms in human disease research

TJ Aitman, C Boone, GA Churchill… - Nature Reviews …, 2011 - nature.com
Abstract Model organisms have played a huge part in the history of studies of human genetic
disease, both in identifying disease genes and characterizing their normal and abnormal …

scGRN: a comprehensive single-cell gene regulatory network platform of human and mouse

X Huang, C Song, G Zhang, Y Li, Y Zhao… - Nucleic Acids …, 2024 - academic.oup.com
Gene regulatory networks (GRNs) are interpretable graph models encompassing the
regulatory interactions between transcription factors (TFs) and their downstream target …