A universal deep-learning model for zinc finger design enables transcription factor reprogramming
Published 2023 View Full Article
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Title
A universal deep-learning model for zinc finger design enables transcription factor reprogramming
Authors
Keywords
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Journal
NATURE BIOTECHNOLOGY
Volume -, Issue -, Pages -
Publisher
Springer Science and Business Media LLC
Online
2023-01-27
DOI
10.1038/s41587-022-01624-4
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Note: Only part of the references are listed.- Identification and functional characterization of transcriptional activators in human cells
- (2022) Nader Alerasool et al. MOLECULAR CELL
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- (2019) David E. Paschon et al. Nature Communications
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- (2019) Carsten T. Charlesworth et al. NATURE MEDICINE
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- (2019) Jeffrey C. Miller et al. NATURE BIOTECHNOLOGY
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- (2018) Manjunatha Kogenaru et al. ACS Synthetic Biology
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- (2018) Samuel A. Lambert et al. CELL
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- (2018) Dimitrios L. Wagner et al. NATURE MEDICINE
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- (2018) Navneet Matharu et al. SCIENCE
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- (2017) Michaël Imbeault et al. NATURE
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- (2017) Binbin Chen et al. Orphanet Journal of Rare Diseases
- Krüppel-like factor 6 is a transcriptional activator of autophagy in acute liver injury
- (2017) Svenja Sydor et al. Scientific Reports
- Inheritable Silencing of Endogenous Genes by Hit-and-Run Targeted Epigenetic Editing
- (2016) Angelo Amabile et al. CELL
- Complex transcriptional modulation with orthogonal and inducible dCas9 regulators
- (2016) Yuchen Gao et al. NATURE METHODS
- Engineered CRISPR-Cas9 nucleases with altered PAM specificities
- (2015) Benjamin P. Kleinstiver et al. NATURE
- C2H2 zinc finger proteins greatly expand the human regulatory lexicon
- (2015) Hamed S Najafabadi et al. NATURE BIOTECHNOLOGY
- Highly efficient Cas9-mediated transcriptional programming
- (2015) Alejandro Chavez et al. NATURE METHODS
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- (2015) Pratiksha I Thakore et al. NATURE METHODS
- Beyond editing: repurposing CRISPR–Cas9 for precision genome regulation and interrogation
- (2015) Antonia A. Dominguez et al. NATURE REVIEWS MOLECULAR CELL BIOLOGY
- A systematic survey of the Cys2His2 zinc finger DNA-binding landscape
- (2015) Anton V. Persikov et al. NUCLEIC ACIDS RESEARCH
- A structural approach reveals how neighbouring C2H2 zinc fingers influence DNA binding specificity
- (2015) Michael Garton et al. NUCLEIC ACIDS RESEARCH
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- (2014) Hiroshi Nishimasu et al. CELL
- Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation
- (2014) Luke A. Gilbert et al. CELL
- Structural basis of PAM-dependent target DNA recognition by the Cas9 endonuclease
- (2014) Carolin Anders et al. NATURE
- Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells
- (2014) Xuebing Wu et al. NATURE BIOTECHNOLOGY
- RNA-guided gene activation by CRISPR-Cas9–based transcription factors
- (2013) Pablo Perez-Pinera et al. NATURE METHODS
- Using defined finger–finger interfaces as units of assembly for constructing zinc-finger nucleases
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- Deep sequencing of large library selections allows computational discovery of diverse sets of zinc fingers that bind common targets
- (2013) Anton V. Persikov et al. NUCLEIC ACIDS RESEARCH
- Cys2His2 zinc finger protein family: Classification, functions, and major members
- (2012) S. V. Razin et al. BIOCHEMISTRY-MOSCOW
- STAR: ultrafast universal RNA-seq aligner
- (2012) Alexander Dobin et al. BIOINFORMATICS
- A Synthetic Biology Framework for Programming Eukaryotic Transcription Functions
- (2012) Ahmad S. Khalil et al. CELL
- Highly active zinc-finger nucleases by extended modular assembly
- (2012) M. S. Bhakta et al. GENOME RESEARCH
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- (2012) Deepak Reyon et al. NATURE BIOTECHNOLOGY
- An optimized two-finger archive for ZFN-mediated gene targeting
- (2012) Ankit Gupta et al. NATURE METHODS
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- (2012) Ben Langmead et al. NATURE METHODS
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- (2012) TaeHyung Kim et al. NUCLEIC ACIDS RESEARCH
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- (2011) Eva-Maria Händel et al. HUMAN GENE THERAPY
- The Discovery of Zinc Fingers and Their Applications in Gene Regulation and Genome Manipulation
- (2010) Aaron Klug Annual Review of Biochemistry
- Adaptive Evolution in Zinc Finger Transcription Factors
- (2009) Ryan O. Emerson et al. PLoS Genetics
- Analysis of Homeodomain Specificities Allows the Family-wide Prediction of Preferred Recognition Sites
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- (2008) Marcus B. Noyes et al. NUCLEIC ACIDS RESEARCH
- Model-based Analysis of ChIP-Seq (MACS)
- (2008) Yong Zhang et al. GENOME BIOLOGY
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