Explanipedia

Simultaneous capture of single cell RNA-seq, ATAC-seq, and CRISPR perturbation enables multiomic screens to identify gene regulatory relationships Open

Kaivalya Shevade, Yeqing Angela Yang, Kevin Feng, K. Mäder, Volkan Sevi̇m , et al. · 2025

Here, we introduce CRISPR and transcriptomics-assay for transposase-accessible chromatin (CAT-ATAC), a technique that adds CRISPR guide RNA (gRNA) capture to the existing 10× Genomics Multiome assay, generating linked transcriptome, chroma…

SAMHD1 knockout hiPSC model enables high lentiviral transduction efficiency in myeloid cell types Open

Huinan Li, Maliha Afroze, Gunisha Arora, Scot Federman, Kaivalya Shevade , et al. · 2025

Recent advances in functional genomics tools have ushered in a new era of genetic editing to identify molecular pathways relevant to developmental and disease biology. However, limited model systems are available that adequately mimic cell…

MorPhiC Consortium: towards functional characterization of all human genes Open

Mazhar Adli, Laralynne Przybyla, Tony Burdett, Paul W. Burridge, Pilar Cacheiro , et al. · 2025

Network-aware self-supervised learning enables high-content phenotypic screening for genetic modifiers of neuronal activity dynamics Open

Parker Grosjean, Kaivalya Shevade, Cuong Q. Nguyen, Sarah Ancheta, K. Mäder , et al. · 2025

High-throughput phenotypic screening has historically relied on manually selected features, limiting our ability to capture complex cellular processes, particularly neuronal activity dynamics. While recent advances in self-supervised learn…

A multiomics approach reveals RNA dynamics promote cellular sensitivity to DNA hypomethylation Open

Alex Y. Ge, Abolfazl Arab, Raymond Dai, Albertas Navickas, Lisa Fish , et al. · 2024

Variants in tubule epithelial regulatory elements mediate most heritable differences in human kidney function Open

Gabriel B. Loeb, Pooja Kathail, Richard W. Shuai, Ryan Chung, Reinier J. Grona , et al. · 2024

Kidney disease is highly heritable; however, the causal genetic variants, the cell types in which these variants function, and the molecular mechanisms underlying kidney disease remain largely unknown. To identify genetic loci affecting ki…

Rescue of a lysosomal storage disorder caused by Grn loss of function with a brain penetrant progranulin biologic Open

Todd Logan, Matthew Simon, Anil Rana, Gerald Maxwell Cherf, Ankita Srivastava , et al. · 2024

Compact CRISPR genetic screens enabled by improved guide RNA library cloning Open

Seok‐Jin Heo, Lauren D. Enriquez, Scot Federman, Amy Y. Chang, Rachel Mace , et al. · 2024

Editorial: Understanding human biology with iPSC derived cell types in the Era of CRISPR technology Open

Huinan Li, Laralynne Przybyla, Joel Blanchard · 2023

EDITORIAL article Front. Cell Dev. Biol., 22 December 2023Sec. Stem Cell Research Volume 11 - 2023 | https://doi.org/10.3389/fcell.2023.1351676

Functional genomics in stem cell models: considerations and applications Open

Kaivalya Shevade, Sailaja Peddada, K. Mäder, Laralynne Przybyla · 2023

Protocols to differentiate human pluripotent stem cells have advanced in terms of cell type specificity and tissue-level complexity over the past 2 decades, which has facilitated human disease modeling in the most relevant cell types. The …

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

Seok‐Jin Heo, Lauren D. Enriquez, Scot Federman, Amy Y. Chang, Rachel Mace , et al. · 2022

The development of CRISPR genetic screening tools has improved functional genomics, as these tools enable precise genomic editing, provide broad access to genomic regions beyond protein-coding genes, and have fewer off-target effects than …

A multiomics approach reveals RNA dynamics promote cellular sensitivity to DNA hypomethylation Open

Alex Y. Ge, Abolfazl Arab, Raymond Dai, Albertas Navickas, Lisa Fish , et al. · 2022

SUMMARY The search for new approaches in cancer therapy requires a mechanistic understanding of cancer vulnerabilities and anti-cancer drug mechanisms of action. Problematically, some effective therapeutics target cancer vulnerabilities th…

Rescue of a lysosomal storage disorder caused by Grn loss of function with a brain penetrant progranulin biologic Open

Todd Logan, Matthew Simon, Amit Kumar Rana, Gerald Maxwell Cherf, Ankita Srivastava , et al. · 2021

Understanding LRRK2 kinase activity in preclinical models and human subjects through quantitative analysis of LRRK2 and pT73 Rab10 Open

Xiang Wang, Elvira Negrou, Michael T. Maloney, Vitaliy V. Bondar, Shan V. Andrews , et al. · 2021

Understanding LRRK2 kinase activity in preclinical models and human subjects through quantitative analysis of LRRK2 and pRab10 Open

Xiang Wang, Elvira Negrou, Michael T. Maloney, Vitaliy V. Bondar, Shan V. Andrews , et al. · 2021

Variants in the leucine-rich repeat kinase 2 ( LRRK2 ) gene are associated with increased risk for familial and sporadic Parkinson’s disease (PD). Pathogenic variants in LRRK2, including the common variant G2019S, result in increased LRRK2…

TREM2 Regulates Microglial Cholesterol Metabolism upon Chronic Phagocytic Challenge Open

Alicia Nugent, Karin Lin, Bettina van Lengerich, Steve Lianoglou, Laralynne Przybyla , et al. · 2020

TREM2 Regulates Microglial Cholesterol Metabolism Upon Chronic Phagocytic Challenge Open

Alicia Nugent, Karin Lin, Bettina van Lengerich, Steve Lianoglou, Laralynne Przybyla , et al. · 2019

TMIC-43. A TENSION-MEDIATED GLYCOCALYX FEEDBACK LOOP PROMOTES A MESENCHYMAL, STEM-LIKE PHENOTYPE IN GLIOBLASTOMA Open

Shelly Kaushik, J. Matthew Barnes, Russell Bainer, K. Jason, Elliot C. Woods , et al. · 2018

Glioblastoma multiforme (GBM) is one of the deadliest central nervous system cancers, difficult to treat and largely impossible to cure. A considerable challenge in GBM therapy is treatment resistance and tumor recurrence, resulting in dis…

A tension-mediated glycocalyx–integrin feedback loop promotes mesenchymal-like glioblastoma Open

J. Matthew Barnes, Shelly Kaushik, Russell Bainer, K. Jason, Elliot C. Woods , et al. · 2018

Tissue Force Programs Cell Fate and Tumor Aggression Open

Jason J. Northey, Laralynne Przybyla, Valerie M. Weaver · 2017

Biomechanical and biochemical cues within a tissue collaborate across length scales to direct cell fate during development and are critical for the maintenance of tissue homeostasis. Loss of tensional homeostasis in a tissue not only accom…

Integrin-mediated traction force enhances paxillin molecular associations and adhesion dynamics that increase the invasiveness of tumor cells into a three-dimensional extracellular matrix Open

Armen H. Mekhdjian, FuiBoon Kai, Matthew G. Rubashkin, L. Prahl, Laralynne Przybyla , et al. · 2017

Metastasis requires tumor cells to navigate through a stiff stroma and squeeze through confined microenvironments. Whether tumors exploit unique biophysical properties to metastasize remains unclear. Data show that invading mammary tumor c…

Tissue mechanics regulate brain development, homeostasis and disease Open

J. Matthew Barnes, Laralynne Przybyla, Valerie M. Weaver · 2017

All cells sense and integrate mechanical and biochemical cues from their environment to orchestrate organismal development and maintain tissue homeostasis. Mechanotransduction is the evolutionarily conserved process whereby mechanical forc…

Mechanical Control of Epithelial-to-Mesenchymal Transitions in Development and Cancer Open

Laralynne Przybyla, Jonathon M. Muncie, Valerie M. Weaver · 2016

Mechanical force modulates development, influences tissue homeostasis, and contributes to disease. Forces sculpt tissue-level behaviors and direct cell fate by engaging mechanoreceptors and by altering organization of the cytoskeleton and …

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