Toward a foundation model of causal cell and tissue biology with a Perturbation Cell and Tissue Atlas

JE Rood, A Hupalowska, A Regev - Cell, 2024 - cell.com
Comprehensively charting the biologically causal circuits that govern the phenotypic space
of human cells has often been viewed as an insurmountable challenge. However, in the last …

A brief history of synthetic biology

DE Cameron, CJ Bashor, JJ Collins - Nature Reviews Microbiology, 2014 - nature.com
The ability to rationally engineer microorganisms has been a long-envisioned goal dating
back more than a half-century. With the genomics revolution and rise of systems biology in …

RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond

S Gama-Castro, H Salgado… - Nucleic acids …, 2016 - academic.oup.com
Abstract RegulonDB (http://regulondb. ccg. unam. mx) is one of the most useful and
important resources on bacterial gene regulation, as it integrates the scattered scientific …

Adaptive laboratory evolution–principles and applications for biotechnology

M Dragosits, D Mattanovich - Microbial cell factories, 2013 - Springer
Adaptive laboratory evolution is a frequent method in biological studies to gain insights into
the basic mechanisms of molecular evolution and adaptive changes that accumulate in …

Evolution of two-component signal transduction systems

EJ Capra, MT Laub - Annual review of microbiology, 2012 - annualreviews.org
To exist in a wide range of environmental niches, bacteria must sense and respond to a
variety of external signals. A primary means by which this occurs is through two-component …

A census of human transcription factors: function, expression and evolution

JM Vaquerizas, SK Kummerfeld, SA Teichmann… - Nature Reviews …, 2009 - nature.com
Transcription factors are key cellular components that control gene expression: their
activities determine how cells function and respond to the environment. Currently, there is …

A synchronized quorum of genetic clocks

T Danino, O Mondragón-Palomino, L Tsimring, J Hasty - Nature, 2010 - nature.com
The engineering of genetic circuits with predictive functionality in living cells represents a
defining focus of the expanding field of synthetic biology. This focus was elegantly set in …

Genome‐scale engineering for systems and synthetic biology

KM Esvelt, HH Wang - Molecular systems biology, 2013 - embopress.org
Genome‐modification technologies enable the rational engineering and perturbation of
biological systems. Historically, these methods have been limited to gene insertions or …

Advantages and limitations of current network inference methods

R De Smet, K Marchal - Nature Reviews Microbiology, 2010 - nature.com
Network inference, which is the reconstruction of biological networks from high-throughput
data, can provide valuable information about the regulation of gene expression in cells …

Origins of regulated cell-to-cell variability

B Snijder, L Pelkmans - Nature reviews Molecular cell biology, 2011 - nature.com
Single-cell measurements and lineage-tracing experiments are revealing that phenotypic
cell-to-cell variability is often the result of deterministic processes, despite the existence of …