Best practices in designing, sequencing, and identifying random DNA barcodes

MS Johnson, S Venkataram, S Kryazhimskiy - Journal of molecular …, 2023 - Springer
Random DNA barcodes are a versatile tool for tracking cell lineages, with applications
ranging from development to cancer to evolution. Here, we review and critically evaluate …

DeLTA 2.0: A deep learning pipeline for quantifying single-cell spatial and temporal dynamics

OM O'Connor, RN Alnahhas, JB Lugagne… - PLoS computational …, 2022 - journals.plos.org
Improvements in microscopy software and hardware have dramatically increased the pace
of image acquisition, making analysis a major bottleneck in generating quantitative, single …

Genetic parts and enabling tools for biocircuit design

F Buson, Y Gao, B Wang - ACS Synthetic Biology, 2024 - ACS Publications
Synthetic biology aims to engineer biological systems for customized tasks through the
bottom-up assembly of fundamental building blocks, which requires high-quality libraries of …

A plasmid system with tunable copy number

MV Rouches, Y Xu, LBG Cortes, G Lambert - Nature communications, 2022 - nature.com
Plasmids are one of the most commonly used platforms for genetic engineering and
recombinant gene expression in bacteria. The range of available copy numbers for cloning …

Partitioning of a 2-bit hash function across 66 communicating cells

JP Padmakumar, JJ Sun, W Cho, Y Zhou… - Nature Chemical …, 2024 - nature.com
Powerful distributed computing can be achieved by communicating cells that individually
perform simple operations. Here, we report design software to divide a large genetic circuit …

Spin-split collinear antiferromagnets: A large-scale ab-initio study

Y Guo, H Liu, O Janson, IC Fulga, J van den Brink… - Materials Today …, 2023 - Elsevier
It was recently discovered that, depending on their symmetries, collinear antiferromagnets
can actually break the spin degeneracy in momentum space, even in the absence of spin …

An optogenetic toolkit for light-inducible antibiotic resistance

MB Sheets, N Tague, MJ Dunlop - Nature Communications, 2023 - nature.com
Antibiotics are a key control mechanism for synthetic biology and microbiology. Resistance
genes are used to select desired cells and regulate bacterial populations, however their use …

Genetic circuit characterization by inferring RNA polymerase movement and ribosome usage

A Espah Borujeni, J Zhang, H Doosthosseini… - Nature …, 2020 - nature.com
To perform their computational function, genetic circuits change states through a symphony
of genetic parts that turn regulator expression on and off. Debugging is frustrated by an …

Profile and resistance levels of 136 integron resistance genes

A Hipólito, L García-Pastor, E Vergara, T Jové… - npj Antimicrobials and …, 2023 - nature.com
Integrons have played a major role in the rise and spread of multidrug resistance in Gram-
negative pathogens and are nowadays commonplace among clinical isolates. These …

Redesign of an Escherichia coli Nissle treatment for phenylketonuria using insulated genomic landing pads and genetic circuits to reduce burden

AJ Triassi, BD Fields, CE Monahan, JM Means, Y Park… - Cell Systems, 2023 - cell.com
To build therapeutic strains, Escherichia coli Nissle (EcN) have been engineered to express
antibiotics, toxin-degrading enzymes, immunoregulators, and anti-cancer chemotherapies …