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 …

[HTML][HTML] Principles of digital sequencing using unique molecular identifiers

D Andersson, FT Kebede, M Escobar… - Molecular Aspects of …, 2024 - Elsevier
Massively parallel sequencing technologies have long been used in both basic research
and clinical routine. The recent introduction of digital sequencing has made previously …

A digital twin for DNA data storage based on comprehensive quantification of errors and biases

AL Gimpel, WJ Stark, R Heckel, RN Grass - Nature Communications, 2023 - nature.com
Archiving data in synthetic DNA offers unprecedented storage density and longevity.
Handling and storage introduce errors and biases into DNA-based storage systems …

Compact CRISPR genetic screens enabled by improved guide RNA library cloning

SJ Heo, LD Enriquez, S Federman, AY Chang, R Mace… - Genome Biology, 2024 - Springer
CRISPR genome editing approaches theoretically enable researchers to define the function
of each human gene in specific cell types, but challenges remain to efficiently perform …

Challenges for error-correction coding in DNA data storage: photolithographic synthesis and DNA decay

AL Gimpel, WJ Stark, R Heckel, RN Grass - Digital Discovery, 2024 - pubs.rsc.org
Efficient error-correction codes are crucial for realizing DNA's potential as a long-lasting,
high-density storage medium for digital data. At the same time, new workflows promising low …

[HTML][HTML] Purification of DNA oligonucleotides to improve hybridization chain reaction performance

M Leino, O Söderberg - New Biotechnology, 2023 - Elsevier
Abstract Hybridization Chain Reaction (HCR) is a technique to generate a linear
polymerization of oligonucleotide hairpins, used in multiple molecular biology methods. The …

In vitro generation of genetic diversity for directed evolution by error-prone artificial DNA synthesis

B Wang, Y Liu, X Bai, H Tian, L Wang, M Feng… - Communications …, 2024 - nature.com
Generating genetic diversity lies at the heart of directed evolution which has been widely
used to engineer genetic parts and gene circuits in synthetic biology. With the ever …

Highly Accurate Sequence-and Position-Independent Error Profiling of DNA Synthesis and Sequencing

H Yeom, N Kim, AC Lee, J Kim, H Kim… - ACS Synthetic …, 2023 - ACS Publications
A comprehensive error analysis of DNA-stored data during processing, such as DNA
synthesis and sequencing, is crucial for reliable DNA data storage. Both synthesis and …

[HTML][HTML] Ultrasensitive sequencing of STR markers utilizing unique molecular identifiers and the SiMSen-Seq method

M Sidstedt, AH Gynnå, KM Kiesler, L Jansson… - Forensic Science …, 2024 - Elsevier
Massively parallel sequencing (MPS) is increasingly applied in forensic short tandem repeat
(STR) analysis. The presence of stutter artefacts and other PCR or sequencing errors in the …

Optimized CRISPR guide RNA library cloning reduces skew and enables more compact genetic screens

SJ Heo, LD Enriquez, S Federman, AY Chang, R Mace… - BioRxiv, 2022 - biorxiv.org
The development of CRISPR genetic screening tools has improved functional genomics, as
these tools enable precise genomic editing, provide broad access to genomic regions …