scbs.bib

@article{kremer_scnmt,
  title={Single-cell triple-omics uncovers {DNA} methylation as key feature of stemness in the healthy and ischemic adult brain},
  author={Kremer, Lukas P. M. and Cerrizuela, Santiago and Al Shukairi, Mohammad E and Ellinger, Tobias and Straub, Jannes and Dehler, Sascha and Korkmaz, Aylin and Weichenhan, Dieter and Plass, Christoph and Anders, Simon and Martin-Villalba, Ana},
  journal={bioRxiv preprint},
  year={2022},
  publisher={Cold Spring Harbor Laboratory},
  doi={10.1101/2022.07.13.499860}
}

@article{Frommer_1992,
	doi = {10.1073/pnas.89.5.1827},
	url = {https://doi.org/10.1073/pnas.89.5.1827},
	year = 1992,
	month = {mar},
	publisher = {Proceedings of the National Academy of Sciences},
	volume = {89},
	number = {5},
	pages = {1827--1831},
	author = {M. Frommer and L. E. McDonald and D. S. Millar and C. M. Collis and F. Watt and G. W. Grigg and P. L. Molloy and C. L. Paul},
	title = {A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual {DNA} strands.},
	journal = {Proceedings of the National Academy of Sciences}
}

@article{Smallwood_2014,
	doi = {10.1038/nmeth.3035},
	url = {https://doi.org/10.1038/nmeth.3035},
	year = 2014,
	month = {jul},
	publisher = {Springer Science and Business Media {LLC}},
	volume = {11},
	number = {8},
	pages = {817--820},
	author = {S{\'{e}}bastien A Smallwood and Heather J Lee and Christof Angermueller and Felix Krueger and Heba Saadeh and Julian Peat and Simon R Andrews and Oliver Stegle and Wolf Reik and Gavin Kelsey},
	title = {Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity},
	journal = {Nature Methods}
}	

@article{Wolf_2018,
	author = {Wolf, F. Alexander and Angerer, Philipp and Theis, Fabian J.},
	year = {2018},
	title = {{SCANPY}: large-scale single-cell gene expression data analysis},
    journal = {Genome Biology},
	pages = {15},
	volume = {19},
	doi={10.1186/s13059-017-1382-0},
}

@article{luo2017single,
  title={Single-cell methylomes identify neuronal subtypes and regulatory elements in mammalian cortex},
  author={Luo, Chongyuan and Keown, Christopher L and Kurihara, Laurie and Zhou, Jingtian and He, Yupeng and Li, Junhao and Castanon, Rosa and Lucero, Jacinta and Nery, Joseph R and Sandoval, Justin P and others},
  journal={Science},
  volume={357},
  number={6351},
  pages={600--604},
  year={2017},
  publisher={American Association for the Advancement of Science},
  doi={10.1126/science.aan3351}
}

@article{methylpy,
  title={Human body epigenome maps reveal noncanonical {DNA} methylation variation},
  author={Schultz, Matthew D and He, Yupeng and Whitaker, John W and Hariharan, Manoj and Mukamel, Eran A and Leung, Danny and Rajagopal, Nisha and Nery, Joseph R and Urich, Mark A and Chen, Huaming and others},
  journal={Nature},
  volume={523},
  number={7559},
  pages={212--216},
  year={2015},
  publisher={Nature Publishing Group},
  doi={10.1038/nature14465}
}

@article{bismark,
  title={Bismark: a flexible aligner and methylation caller for {Bisulfite-Seq} applications},
  author={Krueger, Felix and Andrews, Simon R},
  journal={Bioinformatics},
  volume={27},
  number={11},
  pages={1571--1572},
  year={2011},
  publisher={Oxford University Press},
  doi={10.1093/bioinformatics/btr167}
}

@article{Kireeva_2014,
	author = {Kireeva, Natalia V. and Ovchinnikova, Svetlana I. and Tetko, Igor V. and Asiri, Abdullah M. and Balakin, Konstantin V. and Tsivadze, Aslan Yu},
	doi = {10.1002/cmdc.201400027},
	issn = {18607187},
	journal = {ChemMedChem},
	keywords = {chemography,chemoinformatics,dimensionality reduction,drug design,topographic mapping},
	mendeley-groups = {Martin_Villalba/Vorbereitung},
	number = {5},
	pages = {1047--1059},
	pmid = {24729490},
	title = {{Nonlinear dimensionality reduction for visualizing toxicity data: Distance-based versus topology-based approaches}},
	volume = {9},
	year = {2014}
}

@article{argelaguet2019gastru,
  title={Multi-omics profiling of mouse gastrulation at single-cell resolution},
  author={Argelaguet, Ricard and Clark, Stephen J and Mohammed, Hisham and Stapel, L Carine and Krueger, Christel and Kapourani, Chantriolnt-Andreas and Imaz-Rosshandler, Ivan and Lohoff, Tim and Xiang, Yunlong and Hanna, Courtney W and others},
  journal={Nature},
  volume={576},
  number={7787},
  pages={487--491},
  year={2019},
  publisher={Nature Publishing Group},
  doi={10.1038/s41586-019-1825-8}
}
 
@article{historyofmeth,
  title={{DNA} methylation: a historical perspective},
  author={Mattei, Alexandra L and Bailly, Nina and Meissner, Alexander},
  journal={Trends in Genetics},
  year={2022},
  publisher={Elsevier}
}

@article{cedar2022role,
  title={The role of {DNA} methylation in genome-wide gene regulation during development},
  author={Cedar, Howard and Sabag, Ofra and Reizel, Yitzhak},
  journal={Development},
  volume={149},
  number={2},
  pages={dev200118},
  year={2022},
  publisher={The Company of Biologists Ltd}
}

@article{bird1986cpg,
  title={{CpG-rich} islands and the function of {DNA} methylation},
  author={Bird, Adrian P},
  journal={Nature},
  volume={321},
  number={6067},
  pages={209--213},
  year={1986},
  publisher={Nature Publishing Group},
  doi={10.1038/321209a0}
}

@article{SciPy,
	author = {Virtanen, Pauli
and Gommers, Ralf and Oliphant, Travis E. and Haberland, Matt and Reddy, Tyler
and others},
	year = {2020},
	title = {{SciPy 1.0: fundamental algorithms for scientific computing in Python}},
	journal = {Nature Methods},
	pages = {261-272},
	volume = {17},
	doi = {10.1038/s41592-019-0686-2}
}

@article{Clark2018,
	doi = {10.1038/s41467-018-03149-4},
	url = {https://doi.org/10.1038/s41467-018-03149-4},
	year = {2018},
	month = feb,
	publisher = {Springer Science and Business Media {LLC}},
	volume = {9},
	number = {1},
	author = {Stephen J. Clark and Ricard Argelaguet and Chantriolnt-Andreas Kapourani and Thomas M. Stubbs and Heather J. Lee and Celia Alda-Catalinas and Felix Krueger and Guido Sanguinetti and Gavin Kelsey and John C. Marioni and Oliver Stegle and Wolf Reik},
	title = {{scNMT}-seq enables joint profiling of chromatin accessibility {DNA} methylation and transcription in single cells},
	journal = {Nature Communications}
}

@article{Baglama2005,
	doi = {10.1137/04060593x},
	url = {https://doi.org/10.1137/04060593x},
	year = {2005},
	month = jan,
	publisher = {Society for Industrial {\&} Applied Mathematics ({SIAM})},
	volume = {27},
	number = {1},
	pages = {19--42},
	author = {James Baglama and Lothar Reichel},
	title = {Augmented Implicitly Restarted {Lanczos} Bidiagonalization Methods},
	journal = {{SIAM} Journal on Scientific Computing}
}

@article{scMTseq,
  title={Simultaneous profiling of transcriptome and {DNA} methylome from a single cell},
  author={Hu, Youjin and Huang, Kevin and An, Qin and Du, Guizhen and Hu, Ganlu and Xue, Jinfeng and Zhu, Xianmin and Wang, Cun-Yu and Xue, Zhigang and Fan, Guoping},
  journal={Genome Biology},
  volume={17},
  number={1},
  pages={1--11},
  year={2016},
  publisher={BioMed Central},
  doi={10.1007/978-1-4939-9240-9_21}
}

@article{mclean2010great,
  title={{GREAT} improves functional interpretation of cis-regulatory regions},
  author={McLean, Cory Y and Bristor, Dave and Hiller, Michael and Clarke, Shoa L and Schaar, Bruce T and Lowe, Craig B and Wenger, Aaron M and Bejerano, Gill},
  journal={Nature Biotechnology},
  volume={28},
  number={5},
  pages={495--501},
  year={2010},
  publisher={Nature Publishing Group},
  doi={10.1038/nbt.1630}
}

@article{dmrseq,
  doi = {10.1093/biostatistics/kxy007},
  url = {https://doi.org/10.1093/biostatistics/kxy007},
  year = {2018},
  month = feb,
  publisher = {Oxford University Press ({OUP})},
  volume = {20},
  number = {3},
  pages = {367--383},
  author = {Keegan Korthauer and Sutirtha Chakraborty and Yuval Benjamini and Rafael A Irizarry},
  title = {Detection and accurate false discovery rate control of differentially methylated regions from whole genome bisulfite sequencing},
  journal = {Biostatistics}
}

@article{Hebestreit2013,
  doi = {10.1093/bioinformatics/btt263},
  url = {https://doi.org/10.1093/bioinformatics/btt263},
  year = {2013},
  month = may,
  publisher = {Oxford University Press ({OUP})},
  volume = {29},
  number = {13},
  pages = {1647--1653},
  author = {Katja Hebestreit and Martin Dugas and Hans-Ulrich Klein},
  title = {Detection of significantly differentially methylated regions in targeted bisulfite sequencing data},
  journal = {Bioinformatics}
}

@misc{ggpointdensity,
  title={ggpointdensity: A cross between a {2D} density plot and a scatter plot},
  author={Kremer, LPM},
  year={2019},
  publisher={R package version 0.1.0}
}

@article{mbp,
  title={Myelin basic protein: a multifunctional protein},
  author={Boggs, JM},
  journal={Cellular and Molecular Life Sciences CMLS},
  volume={63},
  pages={1945--1961},
  year={2006},
  publisher={Springer},
  doi={10.1007/s00018-006-6094-7}
}

@article{appris,
  title={{APPRIS}: annotation of principal and alternative splice isoforms},
  author={Rodriguez, Jose Manuel and Maietta, Paolo and Ezkurdia, Iakes and Pietrelli, Alessandro and Wesselink, Jan-Jaap and Lopez, Gonzalo and Valencia, Alfonso and Tress, Michael L},
  journal={Nucleic Acids Research},
  volume={41},
  number={D1},
  pages={D110--D117},
  year={2013},
  publisher={Oxford University Press},
  doi={10.1093/nar/gks1058}
}

@article{missMDA,
	title={{missMDA}: A Package for Handling Missing Values in Multivariate Data Analysis},
	volume={70},
	url={https://www.jstatsoft.org/index.php/jss/article/view/v070i01},
	doi={10.18637/jss.v070.i01},
	number={1},
	journal={Journal of Statistical Software},
	author={Josse, Julie and Husson, François},
	year={2016},
	pages={1–31}
}

@misc{biscuit,
	title={{BISCUIT} -- Understand Sequencing Data with Bisulfite Conversion },
	author={Wanding Zhou and others},
	year={2021},
	howpublished={Software, \url{https://huishenlab.github.io/biscuit}}
}
	
@article{josse2012,
  TITLE = {{Handling missing values in exploratory multivariate data analysis methods}},
  AUTHOR = {Josse, Julie and Husson, Fran{\c c}ois},
  URL = {https://hal.science/hal-00811888},
  JOURNAL = {{Journal de la Societe Fran{\c c}aise de Statistique}},
  PUBLISHER = {{Societe Fran{\c c}aise de Statistique et Societe Mathematique de France}},
  VOLUME = {153},
  NUMBER = {2},
  PAGES = {79-99},
  YEAR = {2012},
  KEYWORDS = {Missing values ; PCA ; Multiple imputation ; MCA ; EM algorithm ; Regularization ; Residual bootstrap ; Number of dimensions ; Generalized cross-validation},
  HAL_ID = {hal-00811888},
  HAL_VERSION = {v1},
}

@article{bian2018single,
	title={Single-cell multiomics sequencing and analyses of human colorectal cancer},
	author={Bian, Shuhui and Hou, Yu and Zhou, Xin and Li, Xianlong and Yong, Jun and Wang, Yicheng and Wang, Wendong and Yan, Jia and Hu, Boqiang and Guo, Hongshan and others},
	journal={Science},
	volume={362},
	number={6418},
	pages={1060--1063},
	year={2018},
	publisher={American Association for the Advancement of Science},
	doi={10.1126/science.aao3791},
}
@article{encode2020expanded,
	title={Expanded encyclopaedias of {DNA} elements in the human and mouse genomes},
	author={Moore, Jill E and Purcaro, Michael J and Pratt, Henry E and Epstein, Charles B and Shoresh, Noam and Adrian, Jessika and Kawli, Trupti and Davis, Carrie A and Dobin, Alexander and others},
	journal={Nature},
	volume={583},
	number={7818},
	pages={699--710},
	year={2020},
	publisher={Nature Publishing Group UK London},
	doi={10.1038/s41586-020-2493-4}
}
@article{argelaguet2020mofa,
	title={{MOFA+}: a statistical framework for comprehensive integration of multi-modal single-cell data},
	author={Argelaguet, Ricard and Arnol, Damien and Bredikhin, Danila and Deloro, Yonatan and Velten, Britta and Marioni, John C and Stegle, Oliver},
	journal={Genome Biology},
	volume={21},
	number={1},
	pages={1--17},
	year={2020},
	publisher={BioMed Central},
	doi = {10.1186/s13059-020-02015-1},
}
@article{liu2021dna,
	title={{DNA} methylation atlas of the mouse brain at single-cell resolution},
	author={Liu, Hanqing and Zhou, Jingtian and Tian, Wei and Luo, Chongyuan and Bartlett, Anna and Aldridge, Andrew and Lucero, Jacinta and Osteen, Julia K and Nery, Joseph R and Chen, Huaming and others},
	journal={Nature},
	volume={598},
	number={7879},
	pages={120--128},
	year={2021},
	publisher={Nature Publishing Group UK London},
	doi={10.1038/s41586-020-03182-8}
}
@article{kapourani2019melissa,
  title={Melissa: Bayesian clustering and imputation of single-cell methylomes},
  author={Kapourani, Chantriolnt-Andreas and Sanguinetti, Guido},
  journal={Genome Biology},
  volume={20},
  number={1},
  pages={61},
  year={2019},
  publisher={Springer},
  doi={10.1186/s13059-019-1665-8},
}

@article{kapourani2021scmet,
  title={{scMET}: Bayesian modeling of {DNA} methylation heterogeneity at single-cell resolution},
  author={Kapourani, Chantriolnt-Andreas and Argelaguet, Ricard and Sanguinetti, Guido and Vallejos, Catalina A},
  journal={Genome Biology},
  volume={22},
  pages={1--21},
  year={2021},
  publisher={Springer},
  doi={10.1186/s13059-021-02329-8}
}

@article{angermueller2017deepcpg,
  title={{DeepCpG}: accurate prediction of single-cell {DNA} methylation states using deep learning},
  author={Angermueller, Christof and Lee, Heather J and Reik, Wolf and Stegle, Oliver},
  journal={Genome biology},
  volume={18},
  number={1},
  pages={1--13},
  year={2017},
  publisher={BioMed Central}
}

@article{pe2020epiclomal,
  title={Epiclomal: probabilistic clustering of sparse single-cell {DNA} methylation data},
  author={de Souza, Camila PE and Andronescu, Mirela and Masud, Tehmina and Kabeer, Farhia and Biele, Justina and Laks, Emma and Lai, Daniel and Ye, Patricia and Brimhall, Jazmine and Wang, Beixi and others},
  journal={PLOS Computational Biology},
  volume={16},
  number={9},
  pages={e1008270},
  year={2020},
  publisher={Public Library of Science San Francisco, CA USA}
}

@article{welch2019single,
  title={Single-cell multi-omic integration compares and contrasts features of brain cell identity},
  author={Welch, Joshua D and Kozareva, Velina and Ferreira, Ashley and Vanderburg, Charles and Martin, Carly and Macosko, Evan Z},
  journal={Cell},
  volume={177},
  number={7},
  pages={1873--1887},
  year={2019},
  publisher={Elsevier},
  doi={10.1016/j.cell.2019.05.006}
}

@article{quinlan2010bedtools,
	title={{BEDTools}: a flexible suite of utilities for comparing genomic features},
	author={Quinlan, Aaron R and Hall, Ira M},
	journal={Bioinformatics},
	volume={26},
	number={6},
	pages={841--842},
	year={2010},
	publisher={Oxford University Press},
	doi={10.1093/bioinformatics/btq033}
}

@article{danese2021episcanpy,
	author = {Danese, Anna and Richter, Maria L. and Chaichoompu, Kridsadakorn and Fischer, David S. and Theis, Fabian J. and Colomé-Tatché, Maria},
	year = {2021},
	title = {{EpiScanpy}: integrated single-cell epigenomic analysis},
    journal = {Nature Communications},
	pages = {5228},
	volume = {12},
	issue={1},
	doi={10.1038/s41467-021-25131-3}
}

@Article{seurat5,
	author = {Yuhan Hao and Tim Stuart and Madeline H Kowalski and Saket Choudhary and Paul Hoffman and Austin Hartman and Avi Srivastava and Gesmira Molla and Shaista Madad and Carlos Fernandez-Granda and Rahul Satija},
	title = {Dictionary learning for integrative, multimodal and scalable single-cell analysis},
	journal = {Nature Biotechnology},
	year = {2023},
	doi = {10.1038/s41587-023-01767-y},
}