RNA graph partitioning for the discovery of RNA modularity: a novel application of graph partition algorithm to biology. [PDF]
PLoS ONE, 2014 Graph representations have been widely used to analyze and design various economic, social, military, political, and biological networks. In systems biology, networks of cells and organs are useful for understanding disease and medical treatments and, in
Namhee Kim +3 more
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The Evolutionary Origins of Hierarchy. [PDF]
PLoS Computational Biology, 2016 Hierarchical organization-the recursive composition of sub-modules-is ubiquitous in biological networks, including neural, metabolic, ecological, and genetic regulatory networks, and in human-made systems, such as large organizations and the Internet. To
Henok Mengistu +3 more
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On Functional Module Detection in Metabolic Networks [PDF]
Metabolites, 2013 Functional modules of metabolic networks are essential for understanding the metabolism of an organism as a whole. With the vast amount of experimental data and the construction of complex and large-scale, often genome-wide, models, the computer-aided ...
Ina Koch, Jörg Ackermann
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Modular assembly of dynamic models in systems biology. [PDF]
PLoS Computational Biology, 2021 It is widely acknowledged that the construction of large-scale dynamic models in systems biology requires complex modelling problems to be broken up into more manageable pieces.
Michael Pan +3 more
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Modularity in Biological Networks
Frontiers in Genetics, 2021 Network modeling, from the ecological to the molecular scale has become an essential tool for studying the structure, dynamics and complex behavior of living systems. Graph representations of the relationships between biological components open up a wide
Sergio Antonio Alcalá-Corona +8 more
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Engineering plasmids with synthetic origins of replication [PDF]
Nature CommunicationsPlasmids remain by far the most common medium for delivering engineered DNA to microorganisms. However, the reliance on natural plasmid replication mechanisms limits their tunability, compatibility, and modularity.
Baiyang Liu +5 more
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Evolution of networks for body plan patterning; interplay of modularity, robustness and evolvability. [PDF]
PLoS Computational Biology, 2011 A major goal of evolutionary developmental biology (evo-devo) is to understand how multicellular body plans of increasing complexity have evolved, and how the corresponding developmental programs are genetically encoded.
Kirsten H Ten Tusscher, Paulien Hogeweg
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Can life be standardized? Current challenges in biological standardization
Mètode Science Studies Journal: Annual Review, 2021 The concept of standard strongly evokes machines, industries, electric or mechanical devices, vehicles, or furniture. Indeed, our technological civilization would not be possible – at least in the terms it is structured today – without universal ...
Juli Peretó, Manuel Porcar
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Bottom-up engineering of biological systems through standard bricks: a modularity study on basic parts and devices. [PDF]
PLoS ONE, 2012 BACKGROUND: Modularity is a crucial issue in the engineering world, as it enables engineers to achieve predictable outcomes when different components are interconnected.
Lorenzo Pasotti +4 more
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Seeing Is Believing: Brain-Inspired Modular Training for Mechanistic Interpretability
Entropy, 2023 We introduce Brain-Inspired Modular Training (BIMT), a method for making neural networks more modular and interpretable. Inspired by brains, BIMT embeds neurons in a geometric space and augments the loss function with a cost proportional to the length of
Ziming Liu, Eric Gan, Max Tegmark
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