Design and analysis of CRISPR–Cas experiments

RE Hanna, JG Doench - Nature biotechnology, 2020 - nature.com
A large and ever-expanding set of CRISPR–Cas systems now enables the rapid and flexible
manipulation of genomes in both targeted and large-scale experiments. Numerous software …

Mechanism and regulation of centriole and cilium biogenesis

DK Breslow, AJ Holland - Annual review of biochemistry, 2019 - annualreviews.org
The centriole is an ancient microtubule-based organelle with a conserved nine-fold
symmetry. Centrioles form the core of centrosomes, which organize the interphase …

[HTML][HTML] Multimodal analysis of composition and spatial architecture in human squamous cell carcinoma

AL Ji, AJ Rubin, K Thrane, S Jiang, DL Reynolds… - cell, 2020 - cell.com
To define the cellular composition and architecture of cutaneous squamous cell carcinoma
(cSCC), we combined single-cell RNA sequencing with spatial transcriptomics and …

[HTML][HTML] Dual proteome-scale networks reveal cell-specific remodeling of the human interactome

EL Huttlin, RJ Bruckner, J Navarrete-Perea, JR Cannon… - Cell, 2021 - cell.com
Thousands of interactions assemble proteins into modules that impart spatial and functional
organization to the cellular proteome. Through affinity-purification mass spectrometry, we …

A reference map of the human binary protein interactome

K Luck, DK Kim, L Lambourne, K Spirohn, BE Begg… - Nature, 2020 - nature.com
Global insights into cellular organization and genome function require comprehensive
understanding of the interactome networks that mediate genotype–phenotype relationships …

[HTML][HTML] Quantitative proteomics of the cancer cell line encyclopedia

DP Nusinow, J Szpyt, M Ghandi, CM Rose… - Cell, 2020 - cell.com
Proteins are essential agents of biological processes. To date, large-scale profiling of cell
line collections including the Cancer Cell Line Encyclopedia (CCLE) has focused primarily …

Extracting biological insights from the project achilles genome-scale CRISPR screens in cancer cell lines

JM Dempster, J Rossen, M Kazachkova, J Pan… - BioRxiv, 2019 - biorxiv.org
One of the main goals of the Cancer Dependency Map project is to systematically identify
cancer vulnerabilities across cancer types to accelerate therapeutic discovery. Project …

FDX1 regulates cellular protein lipoylation through direct binding to LIAS

MB Dreishpoon, NR Bick, B Petrova, DM Warui… - Journal of Biological …, 2023 - jbc.org
Ferredoxins are a family of iron–sulfur (Fe-S) cluster proteins that serve as essential electron
donors in numerous cellular processes that are conserved through evolution. The …

The why, how, and when of representations for complex systems

L Torres, AS Blevins, D Bassett, T Eliassi-Rad - SIAM Review, 2021 - SIAM
Complex systems, composed at the most basic level of units and their interactions, describe
phenomena in a wide variety of domains, from neuroscience to computer science and …

A non-canonical SWI/SNF complex is a synthetic lethal target in cancers driven by BAF complex perturbation

BC Michel, AR D'Avino, SH Cassel, N Mashtalir… - Nature cell …, 2018 - nature.com
Mammalian SWI/SNF chromatin remodelling complexes exist in three distinct, final-form
assemblies: canonical BAF (cBAF), PBAF and a newly characterized non-canonical complex …