A5058516038- CRISPR and Genetic Engineering
- DNA Repair Mechanisms
- Epigenetics and DNA Methylation
- RNA and protein synthesis mechanisms
- Bioinformatics and Genomic Networks
- Mitochondrial Function and Pathology
- Ubiquitin and proteasome pathways
- Gene Regulatory Network Analysis
- Fungal and yeast genetics research
- Advanced biosensing and bioanalysis techniques
- Artificial Intelligence in Games
- Advanced Breast Cancer Therapies
- Cancer-related Molecular Pathways
- Digital Games and Media
- Reinforcement Learning in Robotics
- Single-cell and spatial transcriptomics
- Gene expression and cancer classification
- Genetic Syndromes and Imprinting
- Genomics and Chromatin Dynamics
- Microbial Natural Products and Biosynthesis
- PARP inhibition in cancer therapy
- Genomics and Rare Diseases
- Gambling Behavior and Treatments
- Cell Image Analysis Techniques
- SARS-CoV-2 and COVID-19 Research
University of Minnesota
2018-2025
Twin Cities Orthopedics
2022-2025
University of Minnesota System
2020-2025
Harvard University
2018-2019
Dana-Farber Cancer Institute
2018-2019
Lawrence University
2016
The explosion of bioinformatics technologies in the form next generation sequencing (NGS) has facilitated a massive influx genomics data short reads. Short read mapping is therefore fundamental component pipelines which routinely match these reads against reference genomes for contig assembly. However, such techniques have seldom been applied to microbial marker gene studies, mostly relied on novel heuristic approaches. We propose NINJA Is Not Just Another OTU-Picking Solution (NINJA-OPS, or...
Progression through the G1 phase of cell cycle is most highly regulated step in cellular division. We employed a chemogenetic approach to discover novel networks that regulate progression. This uncovered functional clusters genes altered sensitivity cells inhibitors G1/S transition. Mutation components Polycomb Repressor Complex 2 rescued proliferation inhibition caused by CDK4/6 inhibitor palbociclib, but not S or mitosis. In addition its core catalytic subunits, mutation PRC2.1 accessory...
SARS-CoV-2 depends on host cell components for infection and replication. Identification of virus-host dependencies offers an effective way to elucidate mechanisms involved in viral If druggable, factor may present attractive strategy anti-viral therapy. In this study, we performed genome wide CRISPR knockout screens Vero E6 cells four human lines including Calu-3, UM-UC-4, HEK-293 HuH-7 identify genetic regulators infection. Our findings identified only ACE2, the cognate entry receptor, as...
Fungal pathogens such as Candida albicans pose a significant threat to human health with limited treatment options available. One strategy expand the therapeutic target space is identify genes important for pathogen growth in host-relevant environments. Here, we leverage pooled functional genomic screening fitness of C. diverse conditions. We an essential gene no known Saccharomyces cerevisiae homolog, C1_09670C, and demonstrate that it encodes subunit 3 replication factor A (Rfa3)....
DNA replication requires precise regulation achieved through post-translational modifications, including ubiquitination and SUMOylation. These modifications are linked by the SUMO-targeted E3 ubiquitin ligases (STUbLs). Ring finger protein 4 (RNF4), one of only two mammalian STUbLs, participates in double-strand break repair resolving DNA–protein cross-links. However, its role has been poorly understood. Using CRISPR/Cas9 genetic screens, we discovered an unexpected dependency RNF4 mutants...
Progression through the G1 phase of cell cycle is most highly regulated step in cellular division. We employed a chemogenetic approach to discover novel networks that regulate progression. This uncovered functional clusters genes altered sensitivity cells inhibitors G1/S transition. Mutation components Polycomb Repressor Complex 2 rescued proliferation inhibition caused by CDK4/6 inhibitor palbociclib, but not S or mitosis. In addition its core catalytic subunits, mutation PRC2.1 accessory...
CRISPR-Cas9 screens facilitate the discovery of gene functional relationships and phenotype-specific dependencies. The Cancer Dependency Map (DepMap) is largest compendium whole-genome CRISPR aimed at identifying cancer-specific genetic dependencies across human cell lines. A mitochondria-associated bias has been previously reported to mask signals for genes involved in other functions, thus, methods normalizing this dominant signal improve co-essentiality networks are interest. In study, we...
Drafting in Magic the Gathering is a sub-game within larger trading card game, where several players progressively build decks by picking cards from common pool. poses an interesting problem for game and AI research due to its large search space, mechanical complexity, multi-player nature, hidden information. Despite this, drafting remains understudied, part lack of high-quality, public datasets. To rectify this problem, we present dataset over 100,000 simulated, anonymized human drafts...
A large fraction of human and mouse autosomal genes are subject to random monoallelic expression (MAE), an epigenetic mechanism characterized by allele-specific gene that varies between clonal cell lineages. MAE is highly cell-type specific mapping it in a number tissue types can provide insight into its biological function. Its detection, however, remains challenging. We previously reported sequence-independent chromatin signature identifies, with high sensitivity specificity, multiple...
Current approaches to define chemical-genetic interactions (CGIs) in human cell lines are resource-intensive. We designed a scalable screening platform by generating DNA damage response (DDR)-focused custom sgRNA library targeting 1011 genes with 3033 sgRNAs. performed five proof-of-principle compound screens and found that the compounds' known modes-of-action (MoA) were enriched among CGIs. These recapitulated expected CGIs at comparable signal-to-noise ratio (SNR) relative genome-wide...
Abstract Progression through the G1 phase of cell cycle is most highly regulated step in cellular division. We employed a chemogenetic approach to discover novel networks that regulate progression. This uncovered functional clusters genes altered sensitivity cells inhibitors G1/S transition. Mutation components Polycomb Repressor Complex 2 rescued proliferation inhibition caused by CDK4/6 inhibitor palbociclib, but not S or mitosis. In addition its core catalytic subunits, mutation PRC2.1...
Progression through the G1 phase of cell cycle is most highly regulated step in cellular division. We employed a chemogenetic approach to discover novel networks that regulate progression. This uncovered functional clusters genes altered sensitivity cells inhibitors G1/S transition. Mutation components Polycomb Repressor Complex 2 rescued proliferation inhibition caused by CDK4/6 inhibitor palbociclib, but not S or mitosis. In addition its core catalytic subunits, mutation PRC2.1 accessory...
Progression through the G1 phase of cell cycle is most highly regulated step in cellular division. We employed a chemogenomics approach to discover novel networks that regulate progression. This uncovered functional clusters genes altered sensitivity cells inhibitors G1/S transition. Mutation components Polycomb Repressor Complex 2 rescued growth inhibition caused by CDK4/6 inhibitor palbociclib, but not S or mitosis. In addition its core catalytic subunits, mutation PRC2.1 accessory protein...
ABSTRACT CRISPR screens are used extensively to systematically interrogate the phenotype-to-genotype problem. In contrast early screens, which defined core cell fitness genes, most current efforts now aim identify context-specific phenotypes that differentiate a line, genetic background or condition of interest, such as drug treatment. While CRISPR-related technologies have shown great promise and fast pace innovation, better understanding standards methods for quality assessment screen...
We present FLEX ( F unctiona l e valuation of x perimental perturbations), a pipeline that leverages several functional annotation resources to establish reference standards for benchmarking human genome-wide CRISPR screen data and methods analyzing them. apply analyze from the diverse cell line screens generated by DepMap project. identify dominant mitochondria-associated signal, which our time-resolved analysis suggests may reflect dynamics protein stability effects rather than genetic...
CRISPR-Cas9 screens facilitate the discovery of gene functional relationships and phenotype-specific dependencies. The Cancer Dependency Map (DepMap) is largest compendium whole-genome CRISPR aimed at identifying cancer-specific genetic dependencies across human cell lines. A mitochondria-associated bias has been previously reported to mask signals for genes involved in other functions, thus, methods normalizing this dominant signal improve co-essentiality networks are interest. In study, we...