E-CRISP: fast CRISPR target site identification

By Florian Heigwer, G. Kerr, Michael Boutros. Nature Methods, 2014

835 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/ad7995bbbc27a38441520238c2f21c45f12badf4

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Citations in the corpus

DeepCRISPR: optimized CRISPR guide RNA design by deep learning (2018, methodology): “…(2) hypothesis-driven, where the sgRNA knockout efficacies are scored empirically by considering the impact of genome context factors ( E-CRISP [9], CRISPR [6], CHOPCHOP [10], GuideScan [11], etc.); and (3) learning-based, where the sgRNA knockout efficacies are predicted from a training model…”
sgRNAcas9: A Software Package for Designing CRISPR sgRNA and Evaluating Potential Off-Target Cleavage Sites (2014, background): “Other online tools, such as ZiFiT (http://zifit.partners.org/ ZiFiT/ChoiceMenu.aspx) [24], ‘‘Optimized CRISPR Design’’ (http://crispr.mit.edu/) and E-CRISP (http://www.e-crisp.org/ E-CRISP/) [40] can identify all off-target sequences (preceding either NAG or NGG PAMs) across the genome.”
Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR (2016, background): “Ecrisp [10] failed to detect many off-target sites [3, 34], including off-targets with a single mismatch from the guide.”
CRISPR-P: a web tool for synthetic single-guide RNA design of CRISPR-system in plants. (2014, methodology): “Compared with other sgRNA design tools such as CRISPR DESIGN (http://crispr.mit.edu/), Cas-OFFinder (Bae et al., 2014), E-CRISPR (Heigwer et al., 2014), and Cas9 Design (Ma et al., 2013), CRISPR-P has many advantages, including (1) CRISPR-P is the first sgRNA designing tool especially for plants.”
Evaluation and Design of Genome-Wide CRISPR/SpCas9 Knockout Screens (2017, background): “Though a variety of small- and medium-scale experiments have been used to guide gRNA selection algorithms (Doench et al. 2016; Haeussler et al. 2016; Heigwer et al. 2014, 2016; Hsu et al. 2013; Liu et al. 2016; Park et al. 2016), to our knowledge our design is based on the largest available set of…”
Evaluation and Design of Genome-wide CRISPR/Cas9 Knockout Screens (2017, positive): “Though a variety of small and medium scale experiments have been used to guide gRNA selection algorithms [17-23], our design is, to our knowledge, based on the largest available set of empirical screening results.”
Cas-Designer: a web-based tool for choice of CRISPR-Cas9 target sites (2015, background): “…researchers choose appropriate target sites for Cas9 nucleases (Aach et al., 2014; Cradick et al., 2014; Doench et al., 2014; Bae et al., 2014a; Heigwer et al., 2014; Hsu et al., 2013; Lei et al., 2014; Montague et al., 2014; O'Brien and Bailey, 2014; Naito et al., 2014; Sander et al., 2010;…”
CHOPCHOP: a CRISPR/Cas9 and TALEN web tool for genome editing (2014, methodology): “CHOPCHOP has a number of features that separate it from the other CRISPR/Cas9 or TALEN tools currently available (Supplementary Table S1) (25,28-34).”
CCTop: An Intuitive, Flexible and Reliable CRISPR/Cas9 Target Prediction Tool (2015, background): “To this end, already a number of online sgRNA target finding and evaluation tools like CRISPR Design [13], E-CRISP [16] or CHOPCHOP [17] have been presented.”
GUIDE-Seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases (2014, neutral): “Bioinformatics 26, 589–595 (2010). 37. Zheng, Z. et al. Anchored multiplex PCR for targeted next-generation sequencing. Nat. Med. 20, 1479–1484 (2014). 38. Hoffmann, S. et al. A multi-split mapping algorithm for circular RNA, splicing, transsplicing and fusion detection. Genome Biol. 15, R34 (2014).”
Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9 (2016, neutral): “Importantly, we observed that the alignment tool Bowtie2 44 , used by the E-CRISP portal 45 , does not return all possible mismatched sites, especially as the number of mismatches increases ( Supplementary Fig.”
CRISPRdirect: software for designing CRISPR/Cas guide RNA with reduced off-target sites (2014, background): “Contact: y-naito@dbcls.rois.ac.jp Supplementary information: Supplementary data are available at Bioinformatics online.”
In Silico Predictive Modeling of CRISPR/Cas9 guide efficiency (2015, methodology): “Similarly, CRISPR Design 10 , E-CRISP 14 and CHOPCHOP 15 also use scoring functions with a handful of parameters determined a priori , rather than through a data-driven modeling approach based on principles of statistical estimation, such as we perform herein.”