Base editing: precision chemistry on the genome and transcriptome of living cells

HA Rees, DR Liu - Nature reviews genetics, 2018 - nature.com
RNA-guided programmable nucleases from CRISPR systems generate precise breaks in
DNA or RNA at specified positions. In cells, this activity can lead to changes in DNA …

In silico meets in vivo: towards computational CRISPR-based sgRNA design

G Chuai, QL Wang, Q Liu - Trends in biotechnology, 2017 - cell.com
CRISPR-based genome editing has been widely implemented in various cell types. In silico
single guide RNA (sgRNA) design is a key step for successful gene editing using the …

Lineage recording in human cerebral organoids

Z He, A Maynard, A Jain, T Gerber, R Petri, HC Lin… - Nature …, 2022 - nature.com
Induced pluripotent stem cell (iPSC)-derived organoids provide models to study human
organ development. Single-cell transcriptomics enable highly resolved descriptions of cell …

Inferring and perturbing cell fate regulomes in human brain organoids

JS Fleck, SMJ Jansen, D Wollny, F Zenk, M Seimiya… - Nature, 2023 - nature.com
Self-organizing neural organoids grown from pluripotent stem cells,–combined with single-
cell genomic technologies provide opportunities to examine gene regulatory networks …

CRISPResso2 provides accurate and rapid genome editing sequence analysis

K Clement, H Rees, MC Canver, JM Gehrke… - Nature …, 2019 - nature.com
To the Editor—The field of genome editing is advancing rapidly1, most recently exemplified
by the advent of base editors that enable changing single nucleotides in a predictable …

CRISPOR: intuitive guide selection for CRISPR/Cas9 genome editing experiments and screens

JP Concordet, M Haeussler - Nucleic acids research, 2018 - academic.oup.com
CRISPOR. org is a web tool for genome editing experiments with the CRISPR–Cas9 system.
It finds guide RNAs in an input sequence and ranks them according to different scores that …

[HTML][HTML] A CRISPR–Cas9 gene drive targeting doublesex causes complete population suppression in caged Anopheles gambiae mosquitoes

K Kyrou, AM Hammond, R Galizi, N Kranjc, A Burt… - Nature …, 2018 - nature.com
In the human malaria vector Anopheles gambiae, the gene doublesex (Agdsx) encodes two
alternatively spliced transcripts, dsx-female (AgdsxF) and dsx-male (AgdsxM), that control …

Efficient high-precision homology-directed repair-dependent genome editing by HDRobust

S Riesenberg, P Kanis, D Macak, D Wollny… - Nature …, 2023 - nature.com
Abstract Homology-directed repair (HDR), a method for repair of DNA double-stranded
breaks can be leveraged for the precise introduction of mutations supplied by synthetic DNA …

[HTML][HTML] Single-cell transcriptomic analysis of primary and metastatic tumor ecosystems in head and neck cancer

SV Puram, I Tirosh, AS Parikh, AP Patel, K Yizhak… - Cell, 2017 - cell.com
The diverse malignant, stromal, and immune cells in tumors affect growth, metastasis, and
response to therapy. We profiled transcriptomes of∼ 6,000 single cells from 18 head and …

Highly efficient therapeutic gene editing of human hematopoietic stem cells

Y Wu, J Zeng, BP Roscoe, P Liu, Q Yao… - Nature medicine, 2019 - nature.com
Re-expression of the paralogous γ-globin genes (HBG1/2) could be a universal strategy to
ameliorate the severe β-globin disorders sickle cell disease (SCD) and β-thalassemia by …