@article{hahne2013package,
  title={Package ‘Rbowtie’},
  author={Hahne, Florian and Lerch, Anita and Stadler, Michael B and Stadler, Maintainer Michael and SystemRequirements, GNU},
  year={2013}
}

@article{langmead2009bowtie,
	Abstract = {Bowtie is an ultrafast, memory-efficient alignment program for aligning short DNA sequence reads to large genomes. For the human genome, Burrows-Wheeler indexing allows Bowtie to align more than 25 million reads per CPU hour with a memory footprint of approximately 1.3 gigabytes. Bowtie extends previous Burrows-Wheeler techniques with a novel quality-aware backtracking algorithm that permits mismatches. Multiple processor cores can be used simultaneously to achieve even greater alignment speeds. Bowtie is open source http://bowtie.cbcb.umd.edu.},
	Author = {Langmead, Ben and Trapnell, Cole and Pop, Mihai and Salzberg, Steven L.},
	Da = {2009/03/04},
	Doi = {10.1186/gb-2009-10-3-r25},
	Id = {Langmead2009},
	Isbn = {1474-760X},
	Journal = {Genome Biology},
	Number = {3},
	Pages = {R25},
	Title = {Ultrafast and memory-efficient alignment of short DNA sequences to the human genome},
	Ty = {JOUR},
	Url = {https://doi.org/10.1186/gb-2009-10-3-r25},
	Volume = {10},
	Year = {2009}
}


@article{lindel,
  title={Massively parallel profiling and predictive modeling of the outcomes of CRISPR/Cas9-mediated double-strand break repair},
  author={Chen, Wei and McKenna, Aaron and Schreiber, Jacob and Haeussler, Maximilian and Yin, Yi and Agarwal, Vikram and Noble, William Stafford and Shendure, Jay},
  journal={Nucleic acids research},
  volume={47},
  number={15},
  pages={7989--8003},
  year={2019},
  publisher={Oxford University Press}
}

@article{azimuth,
  title={Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9},
  author={Doench, John G and Fusi, Nicolo and Sullender, Meagan and Hegde, Mudra and Vaimberg, Emma W and Donovan, Katherine F and Smith, Ian and Tothova, Zuzana and Wilen, Craig and Orchard, Robert and others},
  journal={Nature biotechnology},
  volume={34},
  number={2},
  pages={184},
  year={2016},
  publisher={Nature Publishing Group}
}

@article{deepcas9,
  title={Optimized CRISPR guide RNA design for two high-fidelity Cas9 variants by deep learning},
  author={Wang, Daqi and Zhang, Chengdong and Wang, Bei and Li, Bin and Wang, Qiang and Liu, Dong and Wang, Hongyan and Zhou, Yan and Shi, Leming and Lan, Feng and others},
  journal={Nature communications},
  volume={10},
  number={1},
  pages={1--14},
  year={2019},
  publisher={Nature Publishing Group}
}

@article{deepcpf1,
  title={Deep learning improves prediction of CRISPR--Cpf1 guide RNA activity},
  author={Kim, Hui Kwon and Min, Seonwoo and Song, Myungjae and Jung, Soobin and Choi, Jae Woo and Kim, Younggwang and Lee, Sangeun and Yoon, Sungroh and Kim, Hyongbum Henry},
  journal={Nature biotechnology},
  volume={36},
  number={3},
  pages={239},
  year={2018},
  publisher={Nature Publishing Group}
}

@article{perturbseq,
  title={A multiplexed single-cell CRISPR screening platform enables systematic dissection of the unfolded protein response},
  author={Adamson, Britt and Norman, Thomas M and Jost, Marco and Cho, Min Y and Nu{\~n}ez, James K and Chen, Yuwen and Villalta, Jacqueline E and Gilbert, Luke A and Horlbeck, Max A and Hein, Marco Y and others},
  journal={Cell},
  volume={167},
  number={7},
  pages={1867--1882},
  year={2016},
  publisher={Elsevier}
}

@article{cropseq,
  title={Pooled CRISPR screening with single-cell transcriptome readout},
  author={Datlinger, Paul and Rendeiro, Andr{\'e} F and Schmidl, Christian and Krausgruber, Thomas and Traxler, Peter and Klughammer, Johanna and Schuster, Linda C and Kuchler, Amelie and Alpar, Donat and Bock, Christoph},
  journal={Nature methods},
  volume={14},
  number={3},
  pages={297},
  year={2017},
  publisher={Nature Publishing Group}
}

@article{crispracrisprireview,
  title={CRISPRi and CRISPRa screens in mammalian cells for precision biology and medicine},
  author={Kampmann, Martin},
  journal={ACS chemical biology},
  volume={13},
  number={2},
  pages={406--416},
  year={2018},
  publisher={ACS Publications}
}



@article{crispri,
  title={CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes},
  author={Gilbert, Luke A and Larson, Matthew H and Morsut, Leonardo and Liu, Zairan and Brar, Gloria A and Torres, Sandra E and Stern-Ginossar, Noam and Brandman, Onn and Whitehead, Evan H and Doudna, Jennifer A and others},
  journal={Cell},
  volume={154},
  number={2},
  pages={442--451},
  year={2013},
  publisher={Elsevier}
}


@article{sam,
  title={Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex},
  author={Konermann, Silvana and Brigham, Mark D and Trevino, Alexandro E and Joung, Julia and Abudayyeh, Omar O and Barcena, Clea and Hsu, Patrick D and Habib, Naomi and Gootenberg, Jonathan S and Nishimasu, Hiroshi and others},
  journal={Nature},
  volume={517},
  number={7536},
  pages={583},
  year={2015},
  publisher={Nature Publishing Group}
}

@article{fortin2019,
  title={Multiple-gene targeting and mismatch tolerance can confound analysis of genome-wide pooled CRISPR screens},
  author={Fortin, Jean-Philippe and Tan, Jenille and Gascoigne, Karen E and Haverty, Peter M and Forrest, William F and Costa, Michael R and Martin, Scott E},
  journal={Genome biology},
  volume={20},
  number={1},
  pages={21},
  year={2019},
  publisher={Springer}
}



@article{sanson2018optimized,
  title={Optimized libraries for CRISPR-Cas9 genetic screens with multiple modalities},
  author={Sanson, Kendall R and Hanna, Ruth E and Hegde, Mudra and Donovan, Katherine F and Strand, Christine and Sullender, Meagan E and Vaimberg, Emma W and Goodale, Amy and Root, David E and Piccioni, Federica and others},
  journal={Nature communications},
  volume={9},
  number={1},
  pages={1--15},
  year={2018},
  publisher={Nature Publishing Group}
}



@article{horlbeck2016compact,
  title={Compact and highly active next-generation libraries for CRISPR-mediated gene repression and activation},
  author={Horlbeck, Max A and Gilbert, Luke A and Villalta, Jacqueline E and Adamson, Britt and Pak, Ryan A and Chen, Yuwen and Fields, Alexander P and Park, Chong Yon and Corn, Jacob E and Kampmann, Martin and others},
  journal={Elife},
  volume={5},
  pages={e19760},
  year={2016},
  publisher={eLife Sciences Publications Limited}
}


@article{ceres,
  title={Computational correction of copy number effect improves specificity of CRISPR--Cas9 essentiality screens in cancer cells},
  author={Meyers, Robin M and Bryan, Jordan G and McFarland, James M and Weir, Barbara A and Sizemore, Ann E and Xu, Han and Dharia, Neekesh V and Montgomery, Phillip G and Cowley, Glenn S and Pantel, Sasha and others},
  journal={Nature genetics},
  volume={49},
  number={12},
  pages={1779--1784},
  year={2017},
  publisher={Nature Publishing Group}
}


@article{score,
  title={Prioritization of cancer therapeutic targets using CRISPR--Cas9 screens},
  author={Behan, Fiona M and Iorio, Francesco and Picco, Gabriele and Gon{\c{c}}alves, Emanuel and Beaver, Charlotte M and Migliardi, Giorgia and Santos, Rita and Rao, Yanhua and Sassi, Francesco and Pinnelli, Marika and others},
  journal={Nature},
  volume={568},
  number={7753},
  pages={511},
  year={2019},
  publisher={Nature Publishing Group}
}



@article{mit,
  title={DNA targeting specificity of RNA-guided Cas9 nucleases},
  author={Hsu, Patrick D and Scott, David A and Weinstein, Joshua A and Ran, F Ann and Konermann, Silvana and Agarwala, Vineeta and Li, Yinqing and Fine, Eli J and Wu, Xuebing and Shalem, Ophir and others},
  journal={Nature biotechnology},
  volume={31},
  number={9},
  pages={827},
  year={2013},
  publisher={Nature Publishing Group}
}



