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references.bib
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%% This BibTeX bibliography file was created using BibDesk.
%% https://bibdesk.sourceforge.io/
%% Created for Luke Hoberecht at 2022-02-10 10:55:08 -0800
%% Saved with string encoding Unicode (UTF-8)
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author={Hahne, Florian and Ivanek, Robert},
booktitle={Statistical genomics},
pages={335--351},
year={2016},
publisher={Springer}
}
@article{pollard2010detection,
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number={1},
pages={110--121},
year={2010},
publisher={Cold Spring Harbor Lab}
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@article{rtracklayer,
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author={Lawrence, Michael and Gentleman, Robert and Carey, Vincent},
journal={Bioinformatics},
volume={25},
number={14},
pages={1841--1842},
year={2009},
publisher={Oxford University Press}
}
@article{ruleset3,
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doi = {10.1038/s41467-022-33024-2},
id = {DeWeirdt2022},
isbn = {2041-1723},
journal = {Nature Communications},
number = {1},
pages = {5255},
title = {Accounting for small variations in the tracrRNA sequence improves sgRNA activity predictions for CRISPR screening},
ty = {JOUR},
url = {https://doi.org/10.1038/s41467-022-33024-2},
volume = {13},
year = {2022}
}
@article{crispro,
title={CRISPRO: identification of functional protein coding sequences based on genome editing dense mutagenesis},
author={Schoonenberg, Vivien AC and Cole, Mitchel A and Yao, Qiuming and Macias-Trevi{\~n}o, Claudio and Sher, Falak and Schupp, Patrick G and Canver, Matthew C and Maeda, Takahiro and Pinello, Luca and Bauer, Daniel E},
journal={Genome biology},
volume={19},
number={1},
pages={1--19},
year={2018},
publisher={Springer}
}
@article{ucsc,
title={The UCSC genome browser database},
author={Karolchik, Donna and Baertsch, Robert and Diekhans, Mark and Furey, Terrence S and Hinrichs, Angie and Lu, YT and Roskin, Krishna M and Schwartz, Matt and Sugnet, Charles W and Thomas, Daryl J and others},
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pages={51--54},
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publisher={Oxford University Press}
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@article{konstantakos2022crispr,
title={CRISPR--Cas9 gRNA efficiency prediction: an overview of predictive tools and the role of deep learning},
author={Konstantakos, Vasileios and Nentidis, Anastasios and Krithara, Anastasia and Paliouras, Georgios},
journal={Nucleic Acids Research},
volume={50},
number={7},
pages={3616--3637},
year={2022},
publisher={Oxford University Press}
}
@article{yusa,
title={A CRISPR dropout screen identifies genetic vulnerabilities and therapeutic targets in acute myeloid leukemia},
author={Tzelepis, Konstantinos and Koike-Yusa, Hiroko and De Braekeleer, Etienne and Li, Yilong and Metzakopian, Emmanouil and Dovey, Oliver M and Mupo, Annalisa and Grinkevich, Vera and Li, Meng and Mazan, Milena and others},
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volume={17},
number={4},
pages={1193--1205},
year={2016},
publisher={Elsevier}
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@article{sabatini,
title={Identification and characterization of essential genes in the human genome},
author={Wang, Tim and Birsoy, K{\i}van{\c{c}} and Hughes, Nicholas W and Krupczak, Kevin M and Post, Yorick and Wei, Jenny J and Lander, Eric S and Sabatini, David M},
journal={Science},
volume={350},
number={6264},
pages={1096--1101},
year={2015},
publisher={American Association for the Advancement of Science}
}
@article{toronto3,
title={Evaluation and design of genome-wide CRISPR/SpCas9 knockout screens},
author={Hart, Traver and Tong, Amy Hin Yan and Chan, Katie and Van Leeuwen, Jolanda and Seetharaman, Ashwin and Aregger, Michael and Chandrashekhar, Megha and Hustedt, Nicole and Seth, Sahil and Noonan, Avery and others},
journal={G3: Genes, Genomes, Genetics},
volume={7},
number={8},
pages={2719--2727},
year={2017},
publisher={Oxford University Press}
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@article{toronto1,
title={High-resolution CRISPR screens reveal fitness genes and genotype-specific cancer liabilities},
author={Hart, Traver and Chandrashekhar, Megha and Aregger, Michael and Steinhart, Zachary and Brown, Kevin R and MacLeod, Graham and Mis, Monika and Zimmermann, Michal and Fradet-Turcotte, Amelie and Sun, Song and others},
journal={Cell},
volume={163},
number={6},
pages={1515--1526},
year={2015},
publisher={Elsevier}
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@article{guides,
title={GUIDES: sgRNA design for loss-of-function screens},
author={Meier, Joshua A and Zhang, Feng and Sanjana, Neville E},
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volume={14},
number={9},
pages={831--832},
year={2017},
publisher={Nature Publishing Group}
}
@article{casdesigner,
title={Cas-Designer: a web-based tool for choice of CRISPR-Cas9 target sites},
author={Park, Jeongbin and Bae, Sangsu and Kim, Jin-Soo},
journal={Bioinformatics},
volume={31},
number={24},
pages={4014--4016},
year={2015},
publisher={Oxford University Press}
}
@article{crisprater,
title={Refined sgRNA efficacy prediction improves large-and small-scale CRISPR--Cas9 applications},
author={Labuhn, Maurice and Adams, Felix F and Ng, Michelle and Knoess, Sabine and Schambach, Axel and Charpentier, Emmanuelle M and Schwarzer, Adrian and Mateo, Juan L and Klusmann, Jan-Henning and Heckl, Dirk},
journal={Nucleic acids research},
volume={46},
number={3},
pages={1375--1385},
year={2018},
publisher={Oxford University Press}
}
@article{deepspcas9,
title={SpCas9 activity prediction by DeepSpCas9, a deep learning--based model with high generalization performance},
author={Kim, Hui Kwon and Kim, Younggwang and Lee, Sungtae and Min, Seonwoo and Bae, Jung Yoon and Choi, Jae Woo and Park, Jinman and Jung, Dongmin and Yoon, Sungroh and Kim, Hyongbum Henry},
journal={Science advances},
volume={5},
number={11},
pages={eaax9249},
year={2019},
publisher={American Association for the Advancement of Science}
}
@article{liu2017crispri,
title={CRISPRi-based genome-scale identification of functional long noncoding RNA loci in human cells},
author={Liu, S John and Horlbeck, Max A and Cho, Seung Woo and Birk, Harjus S and Malatesta, Martina and He, Daniel and Attenello, Frank J and Villalta, Jacqueline E and Cho, Min Y and Chen, Yuwen and others},
journal={Science},
volume={355},
number={6320},
pages={eaah7111},
year={2017},
publisher={American Association for the Advancement of Science}
}
@article{han2017synergistic,
title={Synergistic drug combinations for cancer identified in a CRISPR screen for pairwise genetic interactions},
author={Han, Kyuho and Jeng, Edwin E and Hess, Gaelen T and Morgens, David W and Li, Amy and Bassik, Michael C},
journal={Nature biotechnology},
volume={35},
number={5},
pages={463--474},
year={2017},
publisher={Nature Publishing Group}
}
@article{replogle2020combinatorial,
title={Combinatorial single-cell CRISPR screens by direct guide RNA capture and targeted sequencing},
author={Replogle, Joseph M and Norman, Thomas M and Xu, Albert and Hussmann, Jeffrey A and Chen, Jin and Cogan, J Zachery and Meer, Elliott J and Terry, Jessica M and Riordan, Daniel P and Srinivas, Niranjan and others},
journal={Nature biotechnology},
volume={38},
number={8},
pages={954--961},
year={2020},
publisher={Nature Publishing Group}
}
@Manual{granges,
title = {GenomicRanges: Representation and manipulation of genomic intervals},
author = {Aboyoun, Patrick and Pages, Herve and Lawrence, Michael},
year = {2012}
}
@article{hahne2012rbowtie,
title={Rbowtie: A r wrapper for bowtie and splicemap short read aligners},
author={Hahne, F and Lerch, A and Stadler, MB},
journal={URL http://bioconductor. org/packages/release/bioc/html/Rbowtie. html},
year={2012}
}
@article{pages2016biostrings,
title={Biostrings: String objects representing biological sequences, and matching algorithms},
author={Pages, Herv{\'e} and Aboyoun, Patrick and Gentleman, Robert and DebRoy, Saikat},
journal={R package version},
volume={2},
number={0},
pages={10--18129},
year={2016}
}
@article{abudayyeh2017rna,
title={RNA targeting with CRISPR--Cas13},
author={Abudayyeh, Omar O and Gootenberg, Jonathan S and Essletzbichler, Patrick and Han, Shuo and Joung, Julia and Belanto, Joseph J and Verdine, Vanessa and Cox, David BT and Kellner, Max J and Regev, Aviv and others},
journal={Nature},
volume={550},
number={7675},
pages={280--284},
year={2017},
publisher={Nature Publishing Group}
}
@Manual{crisprScore,
title = {crisprScore: On-Target and Off-Target Scoring Algorithms for CRISPR gRNAs},
author = {Jean-Philippe Fortin and Aaron Lun},
year = {2022},
note = {R package version 0.99.16},
url = {https://github.com/Jfortin1/crisprScore/issues},
}
@article{wang2019integrative,
title={Integrative analysis of pooled CRISPR genetic screens using MAGeCKFlute},
author={Wang, Binbin and Wang, Mei and Zhang, Wubing and Xiao, Tengfei and Chen, Chen-Hao and Wu, Alexander and Wu, Feizhen and Traugh, Nicole and Wang, Xiaoqing and Li, Ziyi and others},
journal={Nature protocols},
volume={14},
number={3},
pages={756--780},
year={2019},
publisher={Nature Publishing Group}
}
@article{imkeller2020gscreend,
title={gscreend: modelling asymmetric count ratios in CRISPR screens to decrease experiment size and improve phenotype detection},
author={Imkeller, Katharina and Ambrosi, Giulia and Boutros, Michael and Huber, Wolfgang},
journal={Genome biology},
volume={21},
number={1},
pages={1--13},
year={2020},
publisher={Springer}
}
@Manual{gcrisprtools,
title = {gCrisprTools: Suite of Functions for Pooled Crispr Screen QC and Analysis},
author = {Russell Bainer and Dariusz Ratman and Peter Haverty and Steve Lianoglou},
year = {2021},
note = {R package version 2.0.0},
}
@article{labun2019accurate,
title={Accurate analysis of genuine CRISPR editing events with ampliCan},
author={Labun, Kornel and Guo, Xiaoge and Chavez, Alejandro and Church, George and Gagnon, James A and Valen, Eivind},
journal={Genome research},
volume={29},
number={5},
pages={843--847},
year={2019},
publisher={Cold Spring Harbor Lab}
}
@article{zhu2017guideseq,
title={GUIDEseq: a bioconductor package to analyze GUIDE-Seq datasets for CRISPR-Cas nucleases},
author={Zhu, Lihua Julie and Lawrence, Michael and Gupta, Ankit and Kucukural, Alper and Garber, Manuel and Wolfe, Scot A and others},
journal={BMC genomics},
volume={18},
number={1},
pages={1--10},
year={2017},
publisher={Springer}
}
@article{lindsay2016crisprvariants,
title={CrispRVariants charts the mutation spectrum of genome engineering experiments},
author={Lindsay, Helen and Burger, Alexa and Biyong, Berthin and Felker, Anastasia and Hess, Christopher and Zaugg, Jonas and Chiavacci, Elena and Anders, Carolin and Jinek, Martin and Mosimann, Christian and others},
journal={Nature biotechnology},
volume={34},
number={7},
pages={701--702},
year={2016},
publisher={Nature Publishing Group}
}
@article{wessels2020massively,
title={Massively parallel Cas13 screens reveal principles for guide RNA design},
author={Wessels, Hans-Hermann and M{\'e}ndez-Mancilla, Alejandro and Guo, Xinyi and Legut, Mateusz and Daniloski, Zharko and Sanjana, Neville E},
journal={Nature biotechnology},
volume={38},
number={6},
pages={722--727},
year={2020},
publisher={Nature Publishing Group}
}
@article{kweon2020crispr,
title={A CRISPR-based base-editing screen for the functional assessment of BRCA1 variants},
author={Kweon, Jiyeon and Jang, An-Hee and Shin, Ha Rim and See, Ji-Eun and Lee, Woochang and Lee, Jong Won and Chang, Suhwan and Kim, Kyunggon and Kim, Yongsub},
journal={Oncogene},
volume={39},
number={1},
pages={30--35},
year={2020},
publisher={Nature Publishing Group}
}
@article{jun2020single,
title={Single-cell analysis of a mutant library generated using CRISPR-guided deaminase in human melanoma cells},
author={Jun, Soyeong and Lim, Hyeonseob and Chun, Honggu and Lee, Ji Hyun and Bang, Duhee},
journal={Communications biology},
volume={3},
number={1},
pages={1--12},
year={2020},
publisher={Nature Publishing Group}
}
@article{findlay2018accurate,
title={Accurate classification of BRCA1 variants with saturation genome editing},
author={Findlay, Gregory M and Daza, Riza M and Martin, Beth and Zhang, Melissa D and Leith, Anh P and Gasperini, Molly and Janizek, Joseph D and Huang, Xingfan and Starita, Lea M and Shendure, Jay},
journal={Nature},
volume={562},
number={7726},
pages={217--222},
year={2018},
publisher={Nature Publishing Group}
}
@article{hanna2021massively,
title={Massively parallel assessment of human variants with base editor screens},
author={Hanna, Ruth E and Hegde, Mudra and Fagre, Christian R and DeWeirdt, Peter C and Sangree, Annabel K and Szegletes, Zsofia and Griffith, Audrey and Feeley, Marissa N and Sanson, Kendall R and Baidi, Yossef and others},
journal={Cell},
volume={184},
number={4},
pages={1064--1080},
year={2021},
publisher={Elsevier}
}
@article{aho1975efficient,
title={Efficient string matching: an aid to bibliographic search},
author={Aho, Alfred V and Corasick, Margaret J},
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publisher={ACM New York, NY, USA}
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@article{koblan2018improving,
title={Improving cytidine and adenine base editors by expression optimization and ancestral reconstruction},
author={Koblan, Luke W and Doman, Jordan L and Wilson, Christopher and Levy, Jonathan M and Tay, Tristan and Newby, Gregory A and Maianti, Juan Pablo and Raguram, Aditya and Liu, David R},
journal={Nature biotechnology},
volume={36},
number={9},
pages={843--846},
year={2018},
publisher={Nature Publishing Group}
}
@article{wu2014genome,
title={Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells},
author={Wu, Xuebing and Scott, David A and Kriz, Andrea J and Chiu, Anthony C and Hsu, Patrick D and Dadon, Daniel B and Cheng, Albert W and Trevino, Alexandro E and Konermann, Silvana and Chen, Sidi and others},
journal={Nature biotechnology},
volume={32},
number={7},
pages={670--676},
year={2014},
publisher={Nature Publishing Group}
}
@article{kuscu2014genome,
title={Genome-wide analysis reveals characteristics of off-target sites bound by the Cas9 endonuclease},
author={Kuscu, Cem and Arslan, Sevki and Singh, Ritambhara and Thorpe, Jeremy and Adli, Mazhar},
journal={Nature biotechnology},
volume={32},
number={7},
pages={677--683},
year={2014},
publisher={Nature Publishing Group}
}
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title={Landscape of transcription in human cells},
author={Djebali, Sarah and Davis, Carrie A and Merkel, Angelika and Dobin, Alex and Lassmann, Timo and Mortazavi, Ali and Tanzer, Andrea and Lagarde, Julien and Lin, Wei and Schlesinger, Felix and others},
journal={Nature},
volume={489},
number={7414},
pages={101--108},
year={2012},
publisher={Nature Publishing Group}
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