Recent progress in cyclic aryliodonium chemistry: syntheses and applications

X Peng, A Rahim, W Peng, F Jiang, Z Gu… - Chemical …, 2023 - ACS Publications
Hypervalent aryliodoumiums are intensively investigated as arylating agents. They are
excellent surrogates to aryl halides, and moreover they exhibit better reactivity, which allows …

Towards reproducible computational drug discovery

N Schaduangrat, S Lampa, S Simeon… - Journal of …, 2020 - Springer
The reproducibility of experiments has been a long standing impediment for further scientific
progress. Computational methods have been instrumental in drug discovery efforts owing to …

PEtab—Interoperable specification of parameter estimation problems in systems biology

L Schmiester, Y Schälte, FT Bergmann… - PLoS computational …, 2021 - journals.plos.org
Reproducibility and reusability of the results of data-based modeling studies are essential.
Yet, there has been—so far—no broadly supported format for the specification of parameter …

A microfluidic optimal experimental design platform for forward design of cell-free genetic networks

B van Sluijs, RJM Maas, AJ van der Linden… - Nature …, 2022 - nature.com
Cell-free protein synthesis has been widely used as a “breadboard” for design of synthetic
genetic networks. However, due to a severe lack of modularity, forward engineering of …

libRoadRunner 2.0: a high performance SBML simulation and analysis library

C Welsh, J Xu, L Smith, M König, K Choi… - …, 2023 - academic.oup.com
Motivation This article presents libRoadRunner 2.0, an extensible, high-performance, cross-
platform, open-source software library for the simulation and analysis of models expressed …

Modular assembly of dynamic models in systems biology

M Pan, PJ Gawthrop, J Cursons… - PLoS computational …, 2021 - journals.plos.org
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 …

Nonmodular oscillator and switch based on RNA decay drive regeneration of multimodal gene expression

B Nordick, PY Yu, G Liao, T Hong - Nucleic Acids Research, 2022 - academic.oup.com
Periodic gene expression dynamics are key to cell and organism physiology. Studies of
oscillatory expression have focused on networks with intuitive regulatory negative feedback …

Multi-layer CRISPRa/i circuits for dynamic genetic programs in cell-free and bacterial systems

BI Tickman, DA Burbano, VP Chavali, C Kiattisewee… - Cell Systems, 2022 - cell.com
CRISPR-Cas transcriptional circuits hold great promise as platforms for engineering
metabolic networks and information processing circuits. Historically, prokaryotic CRISPR …

BioUML: an integrated environment for systems biology and collaborative analysis of biomedical data

F Kolpakov, I Akberdin, T Kashapov… - Nucleic acids …, 2019 - academic.oup.com
Abstract BioUML (homepage: http://www. biouml. org, main public server: https://ict. biouml.
org) is a web-based integrated environment (platform) for systems biology and the analysis …

Engineering genetic circuits: advancements in genetic design automation tools and standards for synthetic biology

L Buecherl, CJ Myers - Current opinion in microbiology, 2022 - Elsevier
Highlights•Synthetic biology aims to apply engineering principles in biology.•Insufficient part
libraries, standards, and software are challenges to the field.•Working on the challenges will …