25 papers · ranked by Valyu relevance
Zachary Wu, S. B. Jennifer Kan, Russell D. Lewis, Bruce J. Wittmann + 1 more
'Frances H. Arnold'] To reduce experimental effort associated with directed protein evolution and to explore the sequence space encoded by mutating multiple positions simultaneously, we incorporate machine learning into the directed evolution workflow. Combinatorial sequence space can be quite expensive to sample…
Lara Sellés Vidal, Mark Isalan, John T. Heap, Rodrigo Ledesma-Amaro
Directed evolution is one of the most powerful tools for protein engineering and functions by harnessing natural evolution, but on a shorter timescale. It enables the rapid selection of variants of biomolecules with properties that make them more suitable for specific applications. Since the first in vitro evolution…
Pedro A.G. Tizei, Eszter Csibra, Leticia Torres, Vitor B. Pinheiro
'Vitor\xa0B. Pinheiro'] Life on Earth is incredibly diverse. Yet, underneath that diversity, there are a number of constants and highly conserved processes: all life is based on DNA and RNA; the genetic code is universal; biology is limited to a small subset of potential chemistries. A vast amount of knowledge has been…
Innocent Sibanda, Geoff Nitschke
The goal of bioengineering in synthetic biology is to redesign, reprogram, and rewire biological systems for specific applications using standardized parts such as promoters and ribosomes. For example, bioengineered micro-organisms capable of cleaning up environmental pollution or producing antibodies de novo to defend…
Douglas B. Kell
I rehearse two issues around the commentary of Whigham and colleagues. (1) There really are many more reasons than those given as to why natural evolution cannot reasonably find or select the ‘optimal’ individual. (2) A series of experimental molecular biology programmes, known generically as directed evolution, can…
Berk A. Alpay, Michael M. Desai
Directed evolution makes mutant lineages compete in climbing complicated sequence-function landscapes. Given this underlying complexity it is unclear how selection stringency, a ubiquitous parameter of directed evolution, impacts the outcome. Here we approach this question in terms of the fitnesses of the candidate…
Berk A. Alpay, Michael M. Desai
Directed evolution makes mutant lineages compete in climbing complicated sequence-function landscapes. Given this underlying complexity it is unclear how selection stringency, a ubiquitous parameter of directed evolution, impacts the outcome. Here we approach this question in terms of the fitnesses of the candidate…
Berk A. Alpay, Michael M. Desai, Arthur J. Lustig
Directed evolution makes mutant lineages compete in climbing complicated sequence-function landscapes. Given this underlying complexity it is unclear how selection stringency, a ubiquitous parameter of directed evolution, impacts the outcome. Here we approach this question in terms of the fitnesses of the candidate…
Kangbien Park
Humans have long employed directed evolution (DE) to engineer desired biological traits. In this paper, I introduce an algebraic framework that provides a quantitative representation of the general phenotypic traits of asexual populations, enabling the systematic modeling of DE processes. Within this framework, key…
Jess James, Sebastian Towers, Jakob Foerster, Harrison Steel
Directed evolution can enable engineering of biological systems with minimal knowledge of their underlying sequence-to-function relationships. A typical directed evolution process consists of iterative rounds of mutagenesis and selection that are designed to steer changes in a biological system (e.g. a protein) towards…
Sebastian Towers, Jessica James, Harrison Steel, Idris Kempf
Directed evolution is a method for engineering biological systems or components, such as proteins, wherein desired traits are optimised through iterative rounds of mutagenesis and selection of fit variants. The process of protein directed evolution can be envisaged as navigation over high-dimensional landscapes with…
Alexander Lalejini, Emily Dolson, Anya E. Vostinar, Luis Zaman
Directed microbial evolution harnesses evolutionary processes in the laboratory to construct microorganisms with enhanced or novel functional traits. Attempting to direct evolutionary processes for applied goals is fundamental to evolutionary computation, which harnesses the principles of Darwinian evolution as a…
Alexander Lalejini, Emily Dolson, Anya E Vostinar, Luis Zaman + 2 more
'C Brandon Ogbunugafor' 'Christian R Landry'] Directed microbial evolution harnesses evolutionary processes in the laboratory to construct microorganisms with enhanced or novel functional traits. Attempting to direct evolutionary processes for applied goals is fundamental to evolutionary computation, which harnesses…
Kevin Yang, Zachary Wu, Frances H. Arnold
Machine learning (ML)-guided directed evolution is a new paradigm for biological design that enables optimization of complex functions. ML methods use data to predict how sequence maps to function without requiring a detailed model of the underlying physics or biological pathways. To demonstrate ML-guided directed…
Hui Yuan, Chengzhuo Ni, Huazheng Wang, Xuezhou Zhang + 3 more
'Csaba Szepesvári' 'Mengdi Wang'] Directed Evolution (DE), a landmark wet-lab method originated in 1960s, enables discovery of novel protein designs via evolving a population of candidate sequences. Recent advances in biotechnology has made it possible to collect high-throughput data, allowing the use of machine…
Yuchi Qiu, Guo‐Wei Wei
Directed evolution is a molecular biology technique that is transforming protein engineering by creating proteins with desirable properties and functions. However, it is experimentally impossible to perform the deep mutational scanning of the entire protein library due to the enormous mutational space, which scales as…
Alexander V. Spirov, Ekaterina Myasnikova
A while ago, the ideas of evolutionary biology inspired computer scientists to develop a thriving nowadays field of evolutionary computing, in general, and genetic algorithms (GA), in particular. At the same time, the directed evolution of biological macromolecules (in vitro evolution) is reasonably interpreted as an…
Valeria A. Risso, Adrian Romero-Rivera, Luis I. Gutierrez-Rus, Mariano Ortega-Muñoz + 4 more
Directed evolution has revolutionized protein engineering. Still, enzyme optimization by random library screening remains a sluggish process, in large part due to futile probing of mutations that are catalytically neutral and/or impair stability and folding. FuncLib (funclib-weizmann.ac.il) is a novel automated…
Valeria A. Risso, Adrian Romero-Rivera, Luis I. Gutierrez-Rus, Mariano Ortega-Muñoz + 4 more
Directed evolution has revolutionized protein engineering. Still, enzyme optimization by random library screening remains a sluggish process, in large part due to futile probing of mutations that are catalytically neutral and/or impair stability and folding. FuncLib (funclib-weizmann.ac.il) is a novel automated…
Hong-Yan Shih, Harry Mickalide, David T. Fraebel, Nigel Goldenfeld + 1 more
'Seppe Kuehn'] Abstract. Phenotypes of individuals in a population of organisms are not fixed. Phenotypic fluctuations, which describe temporal variation of the phenotype of an individual or individual-to-individual variation across a population, are present in populations from microbes to higher animals. Phenotypic…
Authors not listed
Designing molecules with specific target properties remains a fundamental challenge in computational chemistry. While existing approaches show promise, most rely on simplified representations like SMILES strings or 2D graphs that lack essential three-dimensional geometric information. We present EvoDiffMol, a…
Authors not listed
A directed graph (or digraph) consists of a finite vertex set 𝑉 and a set of ordered edges 𝐸 ⊆ 𝑉 × 𝑉, each edge (𝑢, 𝑣) indicating a one-way connection from 𝑢 (source) to 𝑣 (target). A bidirected graph is a generalization of an undirected graph where each edge is assigned a direction at each of its endpoints…
Amit Kahana, Lior Segev, Doron Lancet
The origin of life must have involved an unlikely transition from chaotic chemistry to reproducing supramolecular structures. Previous quantitative analyses of reproducing mutually catalytic networks made of simple molecules have led to increasing popularity of this pre-RNA scenario for life’s origin. Here, we…
Quanjiang Ji, Hongyuan Zhang, Yifei Zhang, Wei-Xiao Wang + 4 more
New therapeutic strategies for rapid and effective treatment of tuberculosis are highly desirable, and their development can be drastically accelerated by facile genetic manipulation methods in Mycobacterium tuberculosis. CRISPR base editors allow for rapid, robust, and programmed single base substitutions and gene…
Authors not listed
Identifying synthesis routes from knowledge graphs poses challenges beyond retrosynthesis, including path–finding artifacts and data issues. We introduce “SynGPS”, a novel algorithm that overcomes these limitations by identifying viable routes even with common artifacts. SynGPS can resolve nonsensical cycles…