Claude Lormeau's research while affiliated with Swiss Institute of Bioinformatics and other places

Publications (6)

Article
Full-text available
Cells can encode information about their environment by modulating signaling dynamics and responding accordingly. Yet, the mechanisms cells use to decode these dynamics remain unknown when cells respond exclusively to transient signals. Here, we approach design principles underlying such decoding by rationally engineering a synthetic short-pulse de...
Article
Full-text available
Background: To develop mechanistic dynamic models in systems biology, one often needs to identify all (or minimal) representations of the biological processes that are consistent with experimental data, out of a potentially large set of hypothetical mechanisms. However, a simple enumeration of all alternatives becomes quickly intractable when the...
Article
Deterministic dynamic models play a crucial role in elucidating the function of biological networks. However, the underlying biological mechanisms are often only partially known, and different biological hypotheses on the unknown molecular mechanisms lead to multiple potential network topologies for the model. Limitations in generating comprehensiv...
Article
The rational design of synthetic gene circuits has led to many successful applications over the past decade. However, increasingly complex constructs also revealed that analogies to electronics design such as modularity and ‘plug-and-play’ composition are of limited use: biology is less well characterized, more context-dependent, and overall less p...
Article
Computational methods enable the design of synthetic biological circuits demonstrating a specific dynamic behavior. Current methods are based on the assembly of parts characterized in different contexts, which often fail to operate as predicted when combined. Here we introduce a circuit design method that compensates for parts uncertainty by identi...
Article
Chronically deregulated blood-glucose concentrations in diabetes mellitus result from a loss of pancreatic insulin-producing β cells (type 1 diabetes, T1D) or from impaired insulin sensitivity of body cells and glucose-stimulated insulin release (type 2 diabetes, T2D). Here, we show that therapeutically applicable β-cell–mimetic designer cells can...

Citations

... Correlation between the pulses of NF-jB and differential gene expression patterns have been identified in the recent past (Lane et al., 2017;Zambrano et al., 2016). Subsequently, mathematical model studies revealed the topology of network motifs that are capable of generating pulses (Gao et al., 2018;Lormeau et al., 2021;Martinez-Corral et al., 2018;Zhang et al., 2016). Therefore, it is important to gain a systematic quantitative understanding of how various network motifs process pulsatile signals such that regulatory units process it as a true signal leaving out the small amplitude noisy signals. ...
... Recently TopoFilter has been made available as a MATLAB package for mechanistic model selection. 10 2.2. Control-Theoretic Approaches. ...
... Among robust circuits, the ones having simpler topologies exhibited a higher degree of robustness than those with complex topologies. 9 The results reported are for enzyme networks, and the same for TRNs are yet to be studied. Recently TopoFilter has been made available as a MATLAB package for mechanistic model selection. ...
... The realization of computational models in CRNs that use biomolecules as the substrates is primarily analogous to traditional engineering processes or systems with computational capabilities. The components in all calculation models are plug-and-play chemical reaction network calculation models in a test tube solution [3]. An important issue is abstracting the basic reaction module [4] and controlling the calculation order [5][6][7]. ...
... Engineered cell-based therapies hold great promise for the treatment of a wide range of chronic diseases. Advances in the field of synthetic biology have made it possible to engineer cells with reliable senseand-response therapeutic programs, which, upon implantation in mouse models, can treat chronic pain (1), obesity (2), gouty arthritis (3), liver disease (4), and diabetes (5)(6)(7)(8), and can reverse muscle atrophy (9). Early synthetic gene switches relied on soluble small molecules, e.g., antibiotics (10,11) or food components (1,5,12), as external input signals to control cellular behavior. ...