CRISPR in cancer biology and therapy

A Katti, BJ Diaz, CM Caragine, NE Sanjana… - Nature Reviews …, 2022 - nature.com
Over the past decade, CRISPR has become as much a verb as it is an acronym,
transforming biomedical research and providing entirely new approaches for dissecting all …

[HTML][HTML] Targeting pan-essential genes in cancer: challenges and opportunities

L Chang, P Ruiz, T Ito, WR Sellers - Cancer cell, 2021 - cell.com
Despite remarkable successes in the clinic, cancer targeted therapy development remains
challenging and the failure rate is disappointingly high. This problem is partly due to the …

Predicting transcriptional outcomes of novel multigene perturbations with GEARS

Y Roohani, K Huang, J Leskovec - Nature Biotechnology, 2024 - nature.com
Understanding cellular responses to genetic perturbation is central to numerous biomedical
applications, from identifying genetic interactions involved in cancer to develo** methods …

Engineered pegRNAs improve prime editing efficiency

JW Nelson, PB Randolph, SP Shen, KA Everette… - Nature …, 2022 - nature.com
Prime editing enables the installation of virtually any combination of point mutations, small
insertions or small deletions in the DNA of living cells. A prime editing guide RNA (pegRNA) …

[HTML][HTML] Genome-wide programmable transcriptional memory by CRISPR-based epigenome editing

JK Nuñez, J Chen, GC Pommier, JZ Cogan… - Cell, 2021 - cell.com
A general approach for heritably altering gene expression has the potential to enable many
discovery and therapeutic efforts. Here, we present CRISPRoff—a programmable epigenetic …

Prediction of on-target and off-target activity of CRISPR–Cas13d guide RNAs using deep learning

HH Wessels, A Stirn, A Méndez-Mancilla, EJ Kim… - Nature …, 2024 - nature.com
Transcriptome engineering applications in living cells with RNA-targeting CRISPR effectors
depend on accurate prediction of on-target activity and off-target avoidance. Here we design …

A survey on deep learning in medicine: Why, how and when?

F Piccialli, V Di Somma, F Giampaolo, S Cuomo… - Information …, 2021 - Elsevier
New technologies are transforming medicine, and this revolution starts with data. Health
data, clinical images, genome sequences, data on prescribed therapies and results …

Genome-wide gene expression tuning reveals diverse vulnerabilities of M. tuberculosis

B Bosch, MA DeJesus, NC Poulton, W Zhang… - Cell, 2021 - cell.com
Antibacterial agents target the products of essential genes but rarely achieve complete
target inhibition. Thus, the all-or-none definition of essentiality afforded by traditional genetic …

Microfluidics-free single-cell genomics with templated emulsification

IC Clark, KM Fontanez, RH Meltzer, Y Xue… - Nature …, 2023 - nature.com
Current single-cell RNA-sequencing approaches have limitations that stem from the
microfluidic devices or fluid handling steps required for sample processing. We develop a …

[HTML][HTML] Prediction of prime editing insertion efficiencies using sequence features and DNA repair determinants

J Koeppel, J Weller, EM Peets, A Pallaseni… - Nature …, 2023 - nature.com
Most short sequences can be precisely written into a selected genomic target using prime
editing; however, it remains unclear what factors govern insertion. We design a library of …