Topic 139

screens crispr cas9 genome library screening screen pooled genes essentiality guide wide fitness throughput sgrna dependencies gene dependency scale genomics systematically phenotypes identification design cancer knockout genomic genetic essential libraries targeting identify functional interference across high lines cell experimental function sgrnas guides false palindromic out rnas loss cellular enabling published therapeutic hits editing generated platform target phenotypic systems grnas single synthetic methods identifying crispri comprehensive off enables regularly pathways developed introduce streamline grna perturbation targeted previously widely coli analysis specificity integrating vemurafenib viability positives individual retron improved biology short map optimised present repeats escherichia clustered limited highly screenings greater essentials

38 items. Top items listed below.

Pooled CRISPR screening at high sensitivity with an empirically designed sgRNA library 139 33 9

Multiplex enCas12a screens show functional buffering by paralogs is systematically absent from genome-wide CRISPR/Cas9 knockout screens 139 33 9

A genome-scale CRISPR interference guide library enables comprehensive phenotypic profiling in yeast 139 33 9

Systematic genome-wide querying of coding and non-coding functional elements in E. coli using CRISPRi 139 33 9

Biases and Blind-Spots in Genome-Wide CRISPR Knockout Screens 139 9 3

CEN-tools: An integrative platform to identify the contexts of essential genes 139 112 9 4 3

GO-CRISPR: a highly controlled workflow to discover gene essentiality in loss-of-function screens 139 33 4

ACE: A Probabilistic Model for Characterizing Gene-Level Essentiality in CRISPR Screens 139 43 4

Single-cell analysis of a mutant library generated using CRISPR-guided deaminase 139 43 33 9 4

An inducible CRISPR-interference library for genetic interrogation of Saccharomyces cerevisiae biology 139 33 9 4

Improved analysis of CRISPR fitness screens and reduced off-target effects with the BAGEL2 gene essentiality classifier 139 13 4

Minimal genome-wide human CRISPR-Cas9 library 139 33 4

CRISPR-Decryptr reveals cis-regulatory elements from noncoding perturbation screens 139 33 4

Parallel CRISPR-Cas9 screens clarify impacts of p53 on screen performance 139 33 9

Integrated cross-study datasets of genetic dependencies in cancer 139 112 9 4

Computational correction of off-targeting for CRISPR-Cas9 essentiality screens 139 33 4

Discovering functional sequences with RELICS, an analysis method for tiling CRISPR screens 139 4

The impact of genetic diversity on gene essentiality within the E. coli species 139 121 12 5

High-content Imaging-based Pooled CRISPR Screens in Mammalian Cells 139 33 18 9 4

Integrating genetic dependencies and genomic alterations across pathways and cancer types 139 9

Integrative analysis of large-scale loss-of-function screens identifies robust cancer-associated genetic interactions 139 112 9

Identification of pathways modulating Vemurafenib resistance in melanoma cells via a genome-wide CRISPR/Cas9 screen 139 33 9 3

Unbiased identification of nanoparticle cell uptake mechanism via a genome-wide CRISPR/Cas9 knockout screen 139 33 18 4

Using protein interaction networks to identify cancer dependencies from tumor genome data 139 112 14 4

Drug mechanism-of-action discovery through the integration of pharmacological and CRISPR screens 139 108 14 3

Perturbing proteomes at single residue resolution using base editing 139 33 9 4

Major functional bias for mitochondrial complexes in genome-wide CRISPR screens 139 33 4

CRISPR screens in physiologic medium reveal conditionally essential genes in human cells 139 9 3

Genome-scale CRISPR screening for modifiers of cellular LDL uptake 139 9 3

Using targeted genome integration for virus-free genome-wide mammalian CRISPR screen 139 69 33 9

Insights from the reanalysis of high-throughput chemical genomics data for Escherichia coli K-12 139 4

High throughput functional variant screens via in-vivo production of single-stranded DNA 139 33 18 4

Multiplex generation, tracking, and functional screening of substitution mutants using a CRISPR/retron system 139 33 18

Bar-seq strategies for the LeishGEdit toolbox 139 33 4

Genome-wide CRISPR screens reveal multitiered mechanisms through which mTORC1 senses mitochondrial dysfunction 139 33 3

A rapid, super-selective method for detection of single nucleotide variants in C. elegans 139 33 4

CLUE: a bioinformatic and wet-lab pipeline for multiplexed cloning of custom sgRNA libraries 139 33 4

The landscape of metabolic pathway dependencies in cancer cell lines 186 9 3

Optimized RNA-targeting CRISPR/Cas13d technology outperforms shRNA in identifying essential circRNAs 139 33

A high-throughput CRISPR interference screen for dissecting functional regulators of GPCR/cAMP signaling 33 9 3

High-throughput screens of PAM-flexible Cas9 variants for gene knock-out and transcriptional modulation 33

Predicting base editing outcomes with an attention-based deep learning algorithm trained on high-throughput target library screens 7 4

Massively parallel assessment of human variants with base editor screens 33 9

Enhancing CRISPR deletion via pharmacological delay of DNA-PK 33 3

An integrative oncogene-dependency map identifies unique vulnerabilities of oncogenic EGFR, KRAS, and RIT1 in lung cancer 7 3

Image-based pooled whole genome CRISPR screening for Parkin and TFEB subcellular localization 169 7

Learning epistatic gene interactions from perturbation screens 112 4

Systematic discovery and functional interrogation of SARS-CoV-2 viral RNA-host protein interactions during infection 103 1

Functional interrogation of a SARS-CoV-2 host protein interactome identifies unique and shared coronavirus host factors 1

DIA-based systems biology approach unveils novel E3-dependent responses to a metabolic shift 45 4

Parallel genetics of regulatory sequences in vivo 134 33 9

A statistical framework for assessing pharmacological response and biomarkers using uncertainty estimates 112 4

Generation and Validation of Versatile Inducible CRISPRi Embryonic Stem Cell and Mouse Models 33 20 9 3

A non-canonical EZH2 function sensitizes solid tumors to genotoxic stress 142 108 14 3

Y2H-SCORES: A statistical framework to infer protein-protein interactions from next-generation yeast-two-hybrid sequence data 112 4

Convergent mutations in tissue-specific regulatory regions reveal novel cancer drivers 9

Conditional resampling improves calibration in single cell CRISPR screen analysis 123 4

Evaluation of CRISPR gene-editing tools in zebrafish identifies spurious mutations in 'mock control embryos 33 9 4

Genome-wide, time-sensitive interrogation of the heat shock response under diverse stressors via ReporterSeq 31 9 3

Optimized sgRNA design by deep learning to balance the off-target effects and on-target activity of CRISPR/Cas9 26 4

Large-Scale Transcriptional Profiling of Molecular Perturbations Reveals Cell Type Specific Responses and Implications for Environmental Screening 64 9

dbGuide: A database of functionally validated guide RNAs for genome editing in human and mouse cells 33 4

MPRAudit Quantifies the Fraction of Variance Described by Unknown Features in Massively Parallel Reporter Assays 4

Exploring the effects of genetic variation on gene regulation in cancer in the context of 3D genome structure 89 19 9 4

High-Throughput 5' UTR Engineering for Enhanced Protein Production in Non-Viral Gene Therapies 33 18

Analysis of chromatin organization and gene expression in T cells identifies functional genes for rheumatoid arthritis 31 9 3

HyPR-seq: Single-cell quantification of chosen RNAs via hybridization and sequencing of DNA probes 43 33 9 4

A metabolic CRISPR-Cas9 screen in Chinese hamster ovary cells identifies glutamine-sensitive genes 33

Genome-wide CRISPRi/a screens in human neurons link lysosomal failure to ferroptosis 9 3

Functional immune mapping with deep-learning enabled phenomics applied to immunomodulatory and COVID-19 drug discovery 44 1

CiBER-seq dissects genetic networks by quantitative CRISPRi profiling of expression phenotypes 33 9 3

Multiplexed conditional genome editing with Cas12a in Drosophila 33 18

Bacterial single-cell genomics enables phylogenetic analysis and reveals population structures from in vitro evolutionary studies 107 52 12 9 5 4

SLALOM: A Simple and Rapid Method for Enzymatic Synthesis of CRISPR-Cas9 sgRNA Libraries 33 18 4

Multiplex CRISPRi-Cas9 silencing of planktonic and stage-specific biofilm genes in Enterococcus faecalis 52 12

Global computational alignment of tumor and cell line transcriptional profiles 43 14 9 4

CAS-LiveFISH: Simple and versatile imaging of genomic loci in live mammalian cells and early pre-implantation embryos 33 18 8

Efficient Development of Platform Cell Lines Using CRISPR-Cas9 and Transcriptomics Analysis 33 9

Dual genome-wide CRISPR knockout and CRISPR activation screens identify common mechanisms that regulate the resistance to multiple ATR inhibitors 108 14 3

Amplification-free long read sequencing reveals unforeseen CRISPR-Cas9 off-target activity 25 4

Massively parallel quantification of CRISPR editing in cells by TRAP-seq enables better design of Cas9, ABE, CBE gRNAs of high efficiency and accuracy 33 4

Post-perturbational transcriptional signatures of cancer cell line vulnerabilities 9

GuidePro: A multi-source ensemble predictor for prioritizing sgRNAs in CRISPR/Cas9 protein knockouts 105 13 4

A functional screening platform for engineering chimeric antigen receptors with reduced on-target, off-tumour activation 33 14 10 3

Exploration of bacterial bottlenecks and Streptococcus pneumoniae pathogenesis by CRISPRi-seq 114 12

Combinatorial CRISPR screening reveals functional buffering in autophagy 33 9

Novel mosaic mice with diverse applications 33 9

Discovery of novel tumor suppressors from CRISPR screens reveals lipid-sensitive subtype of AML 142 14 9 3

Phenotypic associations among cell cycle genes in Saccharomyces cerevisiae 4

Essential gene analysis in Acinetobacter baumannii by high-density transposon mutagenesis and CRISPR interference 33 12

A simple and effective F0 knockout method for rapid screening of behaviour and other complex phenotypes 33 18 4

CRISPR-based screens uncover determinants of immunotherapy response in Multiple Myeloma 126 14 10 3

Systematic characterization and genetic interaction analysis of adhesins in Candida albicans virulence 114 79 12

Integrated genomics and comprehensive validation reveal novel drivers of genomic evolution in esophageal adenocarcinoma 14 9 3

Genome-wide maps of enhancer regulation connect risk variants to disease genes 19 9 3

CRISPR-targeted display of functional T cell receptors enables engineering of enhanced specificity and prediction of cross-reactivity 33 14 9 3

ELP-dependent expression of MCL1 promotes resistance to EGFR inhibition in triple-negative breast cancer cells 108 14 3

CRISPR Turbo Accelerated Knock Out (CRISPy TAKO) for rapid in vivo screening of gene function 33

A CRISPR/Cas9 vector system for neutrophil-specific gene disruption in zebrafish 33 3

Elucidating essential genes in plant-associated Pseudomonas protegens Pf-5 using transposon insertion sequencing 79 12 9