Publications: Lei (Stanley) Qi

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  • Affiliation: Associate Professor, Stanford University
  • Google Scholar ID: 7iV1PPYAAAAJ
  • Total Publications: 140

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Title Year Citations Score
Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression
Cell 152 (5), 1173-1183, 2013
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2013 5392 99.8%
CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes
Cell 154 (2), 442-451, 2013
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2013 4040 99.8%
Genome-scale CRISPR-mediated control of gene repression and activation
Cell 159 (3), 647-661, 2014
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2014 2630 99.6%
Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system
Cell 155 (7), 1479-1491, 2013
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2013 2127 99.4%
A protein-tagging system for signal amplification in gene expression and fluorescence imaging
Cell 159 (3), 635-646, 2014
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2014 1532 99.2%
Methods and compositions for RNA-directed target DNA modification and for RNA-directed modulation of transcription
US Patent 10,266,850, 2019
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2019 888 99.1%
CRISPR/Cas9 in genome editing and beyond
Annual review of biochemistry 85, 227-264, 2016
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2016 1186 98.9%
CRISPR interference (CRISPRi) for sequence-specific control of gene expression
Nature protocols 8 (11), 2180-2196, 2013
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2013 1309 98.9%
Engineering complex synthetic transcriptional programs with CRISPR RNA scaffolds
Cell 160 (1), 339-350, 2015
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2015 1048 98.7%
Beyond editing: repurposing CRISPR–Cas9 for precision genome regulation and interrogation
Nature reviews Molecular cell biology 17 (1), 5-15, 2016
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2016 967 98.6%
High-content CRISPR screening
Nature Reviews Methods Primers 2 (1), 8, 2022
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2022 228 98.6%
Development of CRISPR as an antiviral strategy to combat SARS-CoV-2 and influenza
Cell 181 (4), 865-876. e12, 2020
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2020 413 98.0%
A comprehensive, CRISPR-based functional analysis of essential genes in bacteria
Cell 165 (6), 1493-1506, 2016
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2016 635 97.6%
CRISPR technologies for precise epigenome editing
Nature Cell Biology 23 (1), 11-22, 2021
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2021 225 97.4%
CRISPR interference efficiently induces specific and reversible gene silencing in human iPSCs
Cell stem cell 18 (4), 541-553, 2016
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2016 509 96.9%
Engineered miniature CRISPR-Cas system for mammalian genome regulation and editing
Molecular cell 81 (20), 4333-4345. e4, 2021
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2021 188 96.6%
Small molecules enhance CRISPR genome editing in pluripotent stem cells
Cell stem cell 16 (2), 142-147, 2015
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2015 482 96.5%
Combinatorial CRISPR–Cas9 screens for de novo mapping of genetic interactions
Nature methods 14 (6), 573-576, 2017
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2017 350 95.4%
A CRISPR–dCas toolbox for genetic engineering and synthetic biology
Journal of molecular biology 431 (1), 34-47, 2019
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2019 250 95.3%
Transient non-integrative expression of nuclear reprogramming factors promotes multifaceted amelioration of aging in human cells
Nature communications 11 (1), 1545, 2020
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2020 199 95.0%
CRISPR-mediated live imaging of genome editing and transcription
Science 365 (6459), 1301-1305, 2019
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2019 217 94.5%
Complex transcriptional modulation with orthogonal and inducible dCas9 regulators
Nature methods 13 (12), 1043-1049, 2016
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2016 314 94.4%
Advances in CRISPR therapeutics
Nature Reviews Nephrology 19 (1), 9-22, 2023
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2023 45 94.0%
Optimized small guide RNAs and methods of use
US Patent 10,822,606, 2020
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2020 148 92.8%
Methods and compositions for RNA-directed target DNA modification and for RNA-directed modulation of transcription
US Patent 10,113,167, 2018
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2018 210 92.4%
The new state of the art: Cas9 for gene activation and repression
Molecular and cellular biology 35 (22), 3800-3809, 2015
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2015 258 92.3%
YAP-independent mechanotransduction drives breast cancer progression
Nature communications 10 (1), 1848, 2019
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2019 158 91.9%
CRISPR-mediated programmable 3D genome positioning and nuclear organization
Cell 175 (5), 1405-1417. e14, 2018
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2018 186 91.3%
CRISPR-based chromatin remodeling of the endogenous Oct4 or Sox2 locus enables reprogramming to pluripotency
Cell Stem Cell 22 (2), 252-261. e4, 2018
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2018 182 91.1%
Anti-CRISPR-mediated control of gene editing and synthetic circuits in eukaryotic cells
Nature communications 10 (1), 194, 2019
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2019 138 90.6%
CRISPR-ERA: a comprehensive design tool for CRISPR-mediated gene editing, repression and activation
Bioinformatics 31 (22), 3676-3678, 2015
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2015 216 90.5%
Versatile RNA-sensing transcriptional regulators for engineering genetic networks
Proceedings of the National Academy of Sciences 108 (21), 8617-8622, 2011
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2011 279 90.5%
CRISPR activation screens systematically identify factors that drive neuronal fate and reprogramming
Cell stem cell 23 (5), 758-771. e8, 2018
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2018 169 90.4%
RNA processing enables predictable programming of gene expression
Nature Biotechnology, 2012
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2012 251 90.0%
YAP induces human naive pluripotency
Cell reports 14 (10), 2301-2312, 2016
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2016 187 89.9%
Genetic interaction mapping in mammalian cells using CRISPR interference
Nature methods 14 (6), 577-580, 2017
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2017 164 89.1%
Nested epistasis enhancer networks for robust genome regulation
Science 377 (6610), 1077-1085, 2022
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2022 43 88.6%
DNMT3A and TET1 cooperate to regulate promoter epigenetic landscapes in mouse embryonic stem cells
Genome biology 19, 1-15, 2018
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2018 142 88.4%
Rationally designed families of orthogonal RNA regulators of translation
Nature chemical biology 8 (5), 447-454, 2012
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2012 199 87.0%
A single-chain photoswitchable CRISPR-Cas9 architecture for light-inducible gene editing and transcription
ACS chemical biology 13 (2), 443-448, 2018
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2018 123 86.5%
Multiplexed genome regulation in vivo with hyper-efficient Cas12a
Nature Cell Biology 24 (4), 590-600, 2022
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2022 36 86.1%
Methods and compositions for rna-directed target dna modification and for rna-directed modulation of transcription
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2016 116 83.0%
Low-frequency ultrasound-mediated cytokine transfection enhances T cell recruitment at local and distant tumor sites
Proceedings of the National Academy of Sciences 117 (23), 12674-12685, 2020
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2020 66 82.6%
Methods and compositions for RNA-directed target DNA modification and for RNA-directed modulation of transcription
US Patent 10,227,611, 2019
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2019 75 81.8%
Methods and compositions for RNA-directed target DNA modification and for RNA-directed modulation of transcription
US Patent 10,301,651, 2019
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2019 74 81.6%
Fibrinogen alpha chain knockout promotes tumor growth and metastasis through integrin–AKT signaling pathway in lung cancer
Molecular Cancer Research 18 (7), 943-954, 2020
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2020 62 81.5%
CRISPR/Cas9 for human genome engineering and disease research
Annual review of genomics and human genetics 17, 131-154, 2016
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2016 105 81.1%
Applications of CRISPR genome engineering in cell biology
Trends in cell biology 26 (11), 875-888, 2016
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2016 101 80.3%
Engineering cell sensing and responses using a GPCR-coupled CRISPR-Cas system
Nature communications 8 (1), 2212, 2017
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2017 91 80.0%
Multiple input sensing and signal integration using a split Cas12a system
Molecular cell 78 (1), 184-191. e3, 2020
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2020 57 79.9%
Methods and compositions for RNA-directed target DNA modification and for RNA-directed modulation of transcription
US Patent 10,000,772, 2018
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2018 82 79.7%
A benchmark of algorithms for the analysis of pooled CRISPR screens
Genome biology 21 (1), 1-13, 2020
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2020 56 79.5%
Engineering 3D genome organization
Nature Reviews Genetics 22 (6), 343-360, 2021
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2021 40 79.3%
Genetic and epigenetic control of gene expression by CRISPR–Cas systems
F1000Research 6, 2017
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2017 88 79.3%
Toward scalable parts families for predictable design of biological circuits
Current opinion in microbiology 11 (6), 567-573, 2008
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2008 145 79.2%
Bacterial CRISPR: accomplishments and prospects
Current opinion in microbiology 27, 121-126, 2015
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2015 103 79.1%
Single-cell transcriptome analysis of regenerating RGCs reveals potent glaucoma neural repair genes
Neuron 110 (16), 2646-2663. e6, 2022
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2022 24 78.8%
Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression
Cell 184 (3), 844, 2021
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2021 37 77.7%
Multiplexed dynamic imaging of genomic loci by combined CRISPR imaging and DNA sequential FISH
Biophysical journal 112 (9), 1773-1776, 2017
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2017 79 77.0%
Methods and compositions for controlling gene expression by RNA processing
US Patent 9,745,610, 2017
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2017 76 76.1%
A versatile framework for microbial engineering using synthetic non-coding RNAs
Nature Reviews Microbiology 12 (5), 341-354, 2014
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2014 94 75.8%
Methods and compositions for rna-directed target dna modification and for rna-directed modulation of transcription
US Patent App. 14/685,516, 2016
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2016 80 75.4%
The use of new CRISPR tools in cardiovascular research and medicine
Nature Reviews Cardiology 19 (8), 505-521, 2022
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2022 20 74.9%
Broad-spectrum CRISPR-mediated inhibition of SARS-CoV-2 variants and endemic coronaviruses in vitro
Nature communications 13 (1), 2766, 2022
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2022 20 74.9%
Double emulsion picoreactors for high-throughput single-cell encapsulation and phenotyping via FACS
Analytical chemistry 92 (19), 13262-13270, 2020
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2020 44 74.3%
Transcription factor competition allows embryonic stem cells to distinguish authentic signals from noise
Cell systems 1 (2), 117-129, 2015
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2015 80 73.5%
CRISPR-based genome editing in primary human pancreatic islet cells
Nature Communications 12 (1), 2397, 2021
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2021 30 72.9%
Engineering naturally occurring trans -acting non-coding RNAs to sense molecular signals
Nucleic acids research 40 (12), 5775-5786, 2012
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2012 93 72.8%
Reversible disruption of specific transcription factor-DNA interactions using CRISPR/Cas9
Molecular cell 74 (3), 622-633. e4, 2019
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2019 48 72.2%
Development of CRISPR as a prophylactic strategy to combat novel coronavirus and influenza
BioRxiv, 2020.03. 13.991307, 2020
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2020 39 71.5%
Targeted transcriptional repression in bacteria using CRISPR interference (CRISPRi)
CRISPR: Methods and protocols, 349-362, 2015
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2015 73 71.3%
An adaptor from translational to transcriptional control enables predictable assembly of complex regulation
Nature Methods, 2012
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2012 87 71.3%
A comprehensive analysis and resource to use CRISPR-Cas13 for broad-spectrum targeting of RNA viruses
Cell Reports Medicine 2 (4), 2021
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2021 28 71.0%
Therapeutic genome editing in cardiovascular diseases
Advanced drug delivery reviews 168, 147-157, 2021
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2021 25 68.2%
Scalable biological signal recording in mammalian cells using Cas12a base editors
Nature chemical biology 18 (7), 742-750, 2022
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2022 15 67.4%
Interrogation of the dynamic properties of higher-order heterochromatin using CRISPR-dCas9
Molecular cell 81 (20), 4287-4299. e5, 2021
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2021 23 65.9%
Specific gene repression by CRISPRi system transferred through bacterial conjugation
ACS synthetic biology 3 (12), 929-931, 2014
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2014 62 65.6%
Multi-color super-resolution imaging to study human coronavirus RNA during cellular infection
Cell reports methods 2 (2), 2022
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2022 14 65.4%
Dual CRISPR interference and activation for targeted reactivation of X-linked endogenous FOXP3 in human breast cancer cells
Molecular Cancer 21 (1), 1-8, 2022
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2022 13 63.4%
CRISPR-mediated synergistic epigenetic and transcriptional control
The CRISPR Journal 5 (2), 264-275, 2022
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2022 13 63.4%
Enhanced Cas12a multi-gene regulation using a CRISPR array separator
Elife 10, e66406, 2021
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2021 21 63.4%
CRISPhieRmix: a hierarchical mixture model for CRISPR pooled screens
Genome Biology 19, 1-13, 2018
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2018 37 60.9%
Low‐intensity extracorporeal shock wave therapy promotes myogenesis through PERK/ATF4 pathway
Neurourology and urodynamics 37 (2), 699-707, 2018
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2018 36 60.1%
Repurposing CRISPR system for transcriptional activation
RNA Activation, 147-157, 2017
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2017 40 60.0%
Durable CRISPR-based epigenetic silencing
BioDesign Research 2021, 2021
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2021 17 57.3%
CRISPR technology for genome activation and repression in mammalian cells
Cold Spring Harb Protoc 2016 (1), pdb prot090175, 2016
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2016 39 57.0%
When genome editing goes off-target
Science 364 (6437), 234-236, 2019
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2019 26 55.6%
Regulation of transcription by unnatural amino acids
Nature biotechnology 29 (2), 164-168, 2011
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2011 46 54.8%
Cas9-mediated knockout of Ndrg2 enhances the regenerative potential of dendritic cells for wound healing
Nature communications 14 (1), 4729, 2023
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2023 5 51.6%
Chimeric proteins and methods of regulating gene expression
US Patent 9,856,497, 2018
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2018 26 51.2%
Systematic genome-wide querying of coding and non-coding functional elements in E. coli using CRISPRi
Biorxiv, 2020.03. 04.975888, 2020
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2020 18 50.3%
Identification of cell context-dependent YAP-associated proteins reveals β1 and β4 integrin mediate YAP translocation independently of cell spreading
Scientific reports 9 (1), 17188, 2019
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2019 19 47.0%
Reversing the Central Dogma: RNA-guided control of DNA in epigenetics and genome editing
Molecular Cell 83 (3), 442-451, 2023
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2023 4 44.5%
CRISPRi/a screening with human iPSCs
Pluripotent Stem-Cell Derived Cardiomyocytes, 261-281, 2021
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2021 11 44.2%
Single-cell transcriptomic profiling reveals distinct mechanical responses between normal and diseased tendon progenitor cells
Cell Reports Medicine 2 (7), 2021
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2021 10 41.3%
Regenerating urethral striated muscle by CRISPRi/dCas9-KRAB-mediated myostatin silencing for obesity-associated stress urinary incontinence
The CRISPR Journal 3 (6), 562-572, 2020
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2020 13 41.3%
Lentiviral delivery of combinatorial CAR/CRISPRi circuit into human primary T cells is enhanced by TBK1/IKKɛ complex inhibitor BX795
Journal of Translational Medicine 18, 1-12, 2020
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2020 13 41.3%
Synthetic transcriptional control elements and methods of generating and using such elements
US Patent 9,593,338, 2017
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2017 18 39.4%
Methods and compositions for RNA-directed target DNA modification and for RNA-directed modulation of transcription
US Patent 10,519,467, 2019
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2019 13 37.4%
Contextual reprogramming of CAR-T cells for treatment of HER2+ cancers
Journal of Translational Medicine 19 (1), 1-18, 2021
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2021 8 35.1%
Stable expression of large transgenes via the knock-in of an integrase-deficient lentivirus
Nature Biomedical Engineering, 1-11, 2023
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2023 3 35.0%
Development of compact transcriptional effectors using high-throughput measurements in diverse contexts
bioRxiv, 2023.05. 12.540558, 2023
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2023 3 35.0%
Computational methods for analysis of large-scale CRISPR screens
Annual Review of Biomedical Data Science 3, 137-162, 2020
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2020 10 34.6%
Identification of novel regulatory genes in APAP induced hepatocyte toxicity by a genome-wide CRISPR-Cas9 screen
Scientific Reports 9 (1), 1396, 2019
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2019 11 33.6%
Methods and compositions for rna-directed target dna modification and for rna-directed modulation of transcription
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2019 11 33.6%
Transient non-integrative expression of nuclear reprogramming factors promotes multifaceted amelioration of aging in human cells. Nat Commun. 2020; 11: 1545
Nature Publishing Group 11, 1-12, 2020
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2020 7 26.6%
Biodesign research to advance the principles and applications of biosystems design
BioDesign Research, 2019
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2019 7 24.7%
Site-programmable transposition: shifting the paradigm for CRISPR-Cas systems
Molecular cell 75 (2), 206-208, 2019
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2019 7 24.7%
Scaffold rnas
US Patent App. 15/514,892, 2017
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2017 8 23.9%
Building smart CAR T cell therapies: the path to overcome current challenges
Cancer Cell 41 (10), 1689-1695, 2023
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2023 2 21.8%
Methods and compositions for RNA-directed target DNA modification and for RNA-directed modulation of transcription
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2023 2 21.8%
Nanoscale, antigen encounter-dependent, IL-12 delivery by CAR T cells plus PD-L1 blockade for cancer treatment
Journal of Translational Medicine 21 (1), 158, 2023
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2023 2 21.8%
Methods and compositions for rna-directed target dna modification and for rna-directed modulation of transcription
US Patent App. 16/136,175, 2019
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2019 5 19.1%
Methods and compositions for rna-directed target dna modification and for rna-directed modulation of transcription
US Patent App. 16/136,165, 2019
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2019 5 19.1%
Methods and compositions for rna-directed target dna modification and for rna-directed modulation of transcription
US Patent App. 16/136,168, 2019
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2019 5 19.1%
Methods and compositions for rna-directed target dna modification and for rna-directed modulation of transcription
US Patent App. 16/136,159, 2019
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2019 5 19.1%
Methods for Modulating Genome Editing
US Patent App. 15/649,304, 2018
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2018 5 17.8%
Evolution at the cutting edge: CRISPR-mediated directed evolution
Molecular Cell 72 (3), 402-403, 2018
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2018 4 14.8%
Chimeric proteins and methods of regulating gene expression
US Patent 10,457,961, 2019
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2019 3 12.2%
Methods and compositions for rna-directed target dna modification and for rna-directed modulation of transcription
US Patent App. 15/915,020, 2019
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2019 3 12.2%
Chimeric proteins and methods of immunotherapy
US Patent 10,336,807, 2019
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2019 3 12.2%
Temporal-Spatial Visualization of Endogenous Chromosome Rearrangements in Living Cells
bioRxiv, 734483, 2019
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2019 2 7.3%
Ribonucleoprotein-based imaging and detection
US Patent App. 16/619,294, 2020
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2020 2 7.3%
Lentiviral delivery of combinatorial CAR/CRISPRi circuit into human primary T cells is enhanced by TBK1/IKKÉ complex inhibitor BX795.
Journal of Translational Medicine 18 (1), NA-NA, 2020
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2020 2 7.3%
Reversible inhibition of specific transcription factor-DNA interactions using CRISPR
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2018 2 6.9%
Using CRISPR-ERA webserver for sgRNA design
Bio-protocol 7 (17), e2522-e2522, 2017
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2017 2 6.7%
a., Whitehead EH, La Russa M., Tsai JC, Weissman JS, Dueber JE, Qi LS, Lim W. a. Engineering complex synthetic transcriptional programs with CRISPR RNA scaffolds
Cell 9, 1-12, 2015
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2015 2 6.4%
Multiplex CRISPR genome regulation in mouse retina with hyper-efficient Cas12a
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2022 1 0.0%
Hormone sensitive lipase ablation promotes bone regeneration
Biochimica et Biophysica Acta (BBA)-Molecular Basis of Disease 1868 (9), 166449, 2022
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2022 1 0.0%
Computation empowers CRISPR discovery and technology
Nature Computational Science 2 (9), 533-535, 2022
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2022 1 0.0%
Programmable drug control of receptor valency modulates the potency of cell therapeutics
bioRxiv, 2023.01. 04.522664, 2023
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2023 1 0.0%
Methods and compositions for RNA-directed target DNA modification
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2016 1 0.0%
Engineering Cell Sensing and Responses Using a GPCR-Coupled CRISPR-Cas System
bioRxiv, 152496, 2017
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2017 1 0.0%
Chimeric proteins and methods of immunotherapy
US Patent 11,111,287, 2021
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2021 1 0.0%
<? span Start cssStyle=" color:# 640026"?> Genetic and Epigenetic Modulation of Gene Expression by CRISPR‐dCas Systems
CRISPR: Biology and Applications, 195-212, 2022
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2022 1 0.0%
765 Contextual secretion of nanoscale interleukin (IL)-12 by CAR T cells for the treatment of cancer
Journal for ImmunoTherapy of Cancer 8 (Suppl 3), A458-A458, 2020
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2020 1 0.0%
Chimeric proteins and methods of regulating gene expression
US Patent 11,773,411, 2023
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2023 1 0.0%
CRISPR/Cas9 Editing Of Autologous Dendritic Cells To Enhance Angiogenesis And Wound Healing
WOUND REPAIR AND REGENERATION 29 (3), A31-A32, 2021
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2021 1 0.0%
QS3: CRISPR/Cas9 editing of autologous dendritic cells to enhance angiogenesis and wound healing
Plastic and Reconstructive Surgery Global Open 9 (7 Suppl), 2021
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2021 1 0.0%
Chimeric proteins and methods of regulating gene expression
US Patent App. 16/570,827, 2020
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2020 1 0.0%