Research graph
References from Computational approaches for effective CRISPR guide RNA design and evaluation. Local targets link to admitted publications; unresolved targets remain external evidence.
A machine learning approach for predicting CRISPR-Cas9 cleavage efficiencies and patterns underlying its mechanism of action
10.1371/journal.pcbi.1005807 · 2017 · External reference
10.1038/nature24049
10.1038/nature24049 · External reference
The CRISPR tool kit for genome editing and beyond
2018 · External reference
CRISPR-Cas9 off-targeting assessment with nucleic acid duplex energy parameters
10.1186/s13059-018-1534-x · 2018 · External reference
10.1038/nbt.4317
10.1038/nbt.4317 · External reference
10.1038/s41551-018-0327-6
10.1038/s41551-018-0327-6 · External reference
10.1038/nmeth.3015
10.1038/nmeth.3015 · External reference
10.1093/bioinformatics/btu048
10.1093/bioinformatics/btu048 · External reference
10.1126/science.1178811
10.1126/science.1178811 · External reference
10.1126/science.1204094
10.1126/science.1204094 · External reference
10.1038/nmeth.4284
10.1038/nmeth.4284 · External reference
CRISPR-FOCUS: a web server for designing focused CRISPR screening experiments
2017 · External reference
10.1534/genetics.111.131433
10.1534/genetics.111.131433 · External reference
10.1038/nmeth.3473
10.1038/nmeth.3473 · External reference
10.1021/acssynbio.6b00343
10.1021/acssynbio.6b00343 · External reference
10.1093/nar/gkz487
10.1093/nar/gkz487 · External reference
10.1038/cr.2013.122
10.1038/cr.2013.122 · External reference
DeepCRISPR: optimized CRISPR guide RNA design by deep learning
10.1186/s13059-018-1459-4 · 2018 · External reference
10.1016/j.tibtech.2016.06.008
10.1016/j.tibtech.2016.06.008 · External reference
10.1093/nar/gky354
10.1093/nar/gky354 · External reference
10.1126/science.1231143
10.1126/science.1231143 · External reference
10.1038/nature09886
10.1038/nature09886 · External reference
10.1038/nbt.3437
10.1038/nbt.3437 · External reference
10.1038/nbt.3026
10.1038/nbt.3026 · External reference
Efficient targeted mutagenesis of rice and tobacco genomes using Cpf1 from Francisella novicida
2016 · External reference
10.1093/nar/gkq1064
10.1093/nar/gkq1064 · External reference
10.1038/nbt.2623
10.1038/nbt.2623 · External reference
10.1038/nbt.2808
10.1038/nbt.2808 · External reference
In silico predictive modeling of CRISPR/Cas9 guide efficiency
2015 · External reference
Data imbalance in CRISPR off-target prediction
2019 · External reference
Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria
10.1073/pnas.1208507109 · 2012 · External reference
10.1038/nature24644
10.1038/nature24644 · External reference
10.1016/j.cell.2014.09.029
10.1016/j.cell.2014.09.029 · External reference
Resources for the design of CRISPR gene editing experiments
10.1186/s13059-015-0823-x · 2015 · External reference
10.1534/genetics.113.160713
10.1534/genetics.113.160713 · External reference
Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR
10.1186/s13059-016-1012-2 · 2016 · External reference
10.1126/science.aav4294
10.1126/science.aav4294 · External reference
10.1038/nmeth.2812
10.1038/nmeth.2812 · External reference
Nucleosomes impede Cas9 access to DNA in vivo and in vitro
10.7554/elife.12677 · 2016 · External reference
Identification of potential drug targets for tuberous sclerosis complex by synthetic screens combining CRISPR-based knockouts with RNAi
2015 · External reference
10.1038/nbt.2647
10.1038/nbt.2647 · External reference
Web-based design and analysis tools for CRISPR base editing
10.1186/s12859-018-2585-4 · 2018 · External reference
Crisflash: open-source software to generate CRISPR guide RNAs against genomes annotated with individual variation
10.1093/bioinformatics/btz019 · 2019 · External reference
10.1002/1873-3468.12707
10.1002/1873-3468.12707 · External reference
SeqMap: mapping massive amount of oligonucleotides to the genome
10.1093/bioinformatics/btn429 · 2008 · External reference
10.1126/science.1225829
10.1126/science.1225829 · External reference
10.1038/nbt.4061
10.1038/nbt.4061 · External reference
10.1038/nbt.3614
10.1038/nbt.3614 · External reference
10.1038/nbt.3620
10.1038/nbt.3620 · External reference
10.1126/science.aat5011
10.1126/science.aat5011 · External reference
10.1038/nbt.2800
10.1038/nbt.2800 · External reference
10.1038/nature17946
10.1038/nature17946 · External reference
A systematic evaluation of nucleotide properties for CRISPR sgRNA design
2017 · External reference
10.1128/mcb.00512-15
10.1128/mcb.00512-15 · External reference
10.1093/nar/gkx1268
10.1093/nar/gkx1268 · External reference
10.1093/nar/gkw398
10.1093/nar/gkw398 · External reference
10.1093/nar/gkz365
10.1093/nar/gkz365 · External reference
10.1038/nmeth.1923
10.1038/nmeth.1923 · External reference
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
10.1186/gb-2009-10-3-r25 · 2009 · External reference
10.1093/mp/ssu044
10.1093/mp/ssu044 · External reference
10.1093/bioinformatics/btp324
10.1093/bioinformatics/btp324 · External reference
10.1038/s41551-017-0178-6
10.1038/s41551-017-0178-6 · External reference
10.1016/j.molp.2017.01.003
10.1016/j.molp.2017.01.003 · External reference
10.1093/bioinformatics/btv423
10.1093/bioinformatics/btv423 · External reference
Sequence features associated with the cleavage efficiency of CRISPR/Cas9 system
10.1038/srep19675 · 2016 · External reference
10.1104/pp.15.00636
10.1104/pp.15.00636 · External reference
10.1016/j.molp.2017.11.010
10.1016/j.molp.2017.11.010 · External reference
A guide RNA sequence design platform for the CRISPR/Cas9 system for model organism genomes
2013 · External reference
10.1186/1745-6150-1-7 · 2006 · Admitted local publication
10.1038/nbt.2675
10.1038/nbt.2675 · External reference
Application of CRISPR-Cas12a temperature sensitivity for improved genome editing in rice, maize, and Arabidopsis
10.1186/s12915-019-0629-5 · 2019 · External reference
CRISPR/Cas9: a molecular Swiss army knife for simultaneous introduction of multiple genetic modifications in Saccharomyces cerevisiae
2015 · External reference
10.1038/nature15386
10.1038/nature15386 · External reference
FlashFry: a fast and flexible tool for large-scale CRISPR target design
10.1186/s12915-018-0545-0 · 2018 · External reference
10.1093/bioinformatics/btx564
10.1093/bioinformatics/btx564 · External reference
10.1111/pbi.13025
10.1111/pbi.13025 · External reference
10.1093/nar/gku410
10.1093/nar/gku410 · External reference
10.1038/nmeth.3543
10.1038/nmeth.3543 · External reference
10.1093/bioinformatics/btv537
10.1093/bioinformatics/btv537 · External reference
Digenome-seq web tool for profiling CRISPR specificity
10.1038/nmeth.4262 · 2017 · External reference
EuPaGDT: a web tool tailored to design CRISPR guide RNAs for eukaryotic pathogens
2015 · External reference
10.1093/bioinformatics/bty298
10.1093/bioinformatics/bty298 · External reference
10.1038/nbt.3804
10.1038/nbt.3804 · External reference
10.1038/s41580-019-0131-5
10.1038/s41580-019-0131-5 · External reference
Scalable Design of Paired CRISPR Guide RNAs for Genomic Deletion
10.1371/journal.pcbi.1005341 · 2017 · External reference
CRISPRpred: a flexible and efficient tool for sgRNAs on-target activity prediction in CRISPR/Cas9 systems
10.1371/journal.pone.0181943 · 2017 · External reference
Bidirectional promoter-based crispr-cas9 systems for plant genome editing
10.3389/fpls.2019.01173 · 2019 · External reference
10.1038/nbt.2842
10.1038/nbt.2842 · External reference
10.1093/nar/gkq319
10.1093/nar/gkq319 · External reference
10.1038/s41586-018-0686-x
10.1038/s41586-018-0686-x · External reference
Real-space and real-time dynamics of CRISPR-Cas9 visualized by high-speed atomic force microscopy
2017 · External reference
Cas9-chromatin binding information enables more accurate CRISPR off-target prediction
10.1093/nar/gkv575 · 2015 · External reference
CCTop: an intuitive, flexible and reliable crispr/cas9 target prediction tool
10.1371/journal.pone.0124633 · 2015 · External reference
Engineering of CRISPR-Cas12b for human genome editing
10.1038/s41467-018-08224-4 · 2019 · External reference
10.1073/pnas.1402597111
10.1073/pnas.1402597111 · External reference
A large-scale whole-genome sequencing analysis reveals highly specific genome editing by both Cas9 and Cpf1 (Cas12a) nucleases in rice
10.1186/s13059-018-1458-5 · 2018 · External reference
A CRISPR–Cpf1 system for efficient genome editing and transcriptional repression in plants
10.1038/nplants.2017.18 · 2017 · External reference
10.1111/pbi.13068
10.1111/pbi.13068 · External reference
A single transcript CRISPR-Cas9 system for efficient genome editing in plants
10.1016/j.molp.2016.05.001 · 2016 · External reference
10.1038/nature03556
10.1038/nature03556 · External reference
Chromatin accessibility is associated with CRISPR-Cas9 efficiency in the zebrafish (Danio rerio)
2018 · External reference
10.1016/j.molcel.2016.06.037
10.1016/j.molcel.2016.06.037 · External reference
10.1126/science.1246981
10.1126/science.1246981 · External reference
The current state and future of CRISPR-Cas9 gRNA design tools
2018 · External reference
10.1089/crispr.2017.0021
10.1089/crispr.2017.0021 · External reference
10.1186/s13059-015-0784-0
10.1186/s13059-015-0784-0 · External reference
10.1038/nbt.2889
10.1038/nbt.2889 · External reference
10.1093/bioinformatics/btt764
10.1093/bioinformatics/btt764 · External reference
10.1093/mp/ssu009
10.1093/mp/ssu009 · External reference
sgRNAcas9: a software package for designing CRISPR sgRNA and evaluating potential off-target cleavage sites
2014 · External reference
CRISPR-GE: a convenient software toolkit for CRISPR-based genome editing
10.1016/j.molp.2017.06.004 · 2017 · External reference
10.1101/gr.191452.115
10.1101/gr.191452.115 · External reference
CRISPR-Cas9 cleavage efficiency correlates strongly with target-sgRNA folding stability: from physical mechanism to off-target assessment
2017 · External reference
Benchmarking CRISPR on-target sgRNA design
10.1093/bib/bbx001 · 2018 · External reference
10.1016/j.cell.2013.08.022
10.1016/j.cell.2013.08.022 · External reference
10.1073/pnas.1810062115
10.1073/pnas.1810062115 · External reference
CRISPRMatch: an automatic calculation and visualization tool for high-throughput CRISPR genome-editing data analysis
10.7150/ijbs.24581 · 2018 · External reference
10.1016/j.cell.2015.09.038
10.1016/j.cell.2015.09.038 · External reference
10.1073/pnas.1820523116
10.1073/pnas.1820523116 · External reference
Off-target effects in CRISPR/Cas9-mediated Genome Engineering
10.1038/mtna.2015.37 · 2015 · External reference
Transcription activator-like effector nucleases enable efficient plant genome engineering
10.1104/pp.112.205179 · 2013 · External reference
10.1007/s00299-016-1967-1
10.1007/s00299-016-1967-1 · External reference
10.1016/j.molp.2019.03.011
10.1016/j.molp.2019.03.011 · External reference
Plant genome editing using FnCpf1 and LbCpf1 nucleases at redefined and altered pam sites
10.1016/j.molp.2018.03.008 · 2018 · External reference
CRISPR-Cas9 based genome editing reveals new insights into MicroRNA function and regulation in rice
10.3389/fpls.2017.01598 · 2017 · External reference
10.1007/s00299-018-2340-3
10.1007/s00299-018-2340-3 · External reference
10.1093/bioinformatics/bty1061
10.1093/bioinformatics/bty1061 · External reference
Regularization and variable selection via the elastic net
10.1111/j.1467-9868.2005.00503.x · 2005 · External reference
