references.bib

## bulk rna-seq

@article{conesa2016survey,
  title={A survey of best practices for RNA-seq data analysis},
  author={Conesa, Ana and Madrigal, Pedro and Tarazona, Sonia and Gomez-Cabrero, David and Cervera, Alejandra and McPherson, Andrew and Szcze{\'s}niak, Micha{\l} Wojciech and Gaffney, Daniel J and Elo, Laura L and Zhang, Xuegong and others},
  journal={Genome biology},
  volume={17},
  number={1},
  pages={1--19},
  year={2016},
  publisher={BioMed Central},
  url={https://link.springer.com/article/10.1186/s13059-016-0881-8}
}

@article{koch2018beginner,
  title={A beginner’s guide to analysis of RNA sequencing data},
  author={Koch, Clarissa M and Chiu, Stephen F and Akbarpour, Mahzad and Bharat, Ankit and Ridge, Karen M and Bartom, Elizabeth T and Winter, Deborah R},
  journal={American journal of respiratory cell and molecular biology},
  volume={59},
  number={2},
  pages={145--157},
  year={2018},
  publisher={American Thoracic Society},
  url={https://www.atsjournals.org/doi/full/10.1165/rcmb.2017-0430TR}
}

@article{marioni2008rna,
  title={RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays},
  author={Marioni, John C and Mason, Christopher E and Mane, Shrikant M and Stephens, Matthew and Gilad, Yoav},
  journal={Genome research},
  volume={18},
  number={9},
  pages={1509--1517},
  year={2008},
  publisher={Cold Spring Harbor Lab},
  url={https://genome.cshlp.org/content/18/9/1509}
}

@article{schurch2016many,
  title={How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use?},
  author={Schurch, Nicholas J and Schofield, Piet{\'a} and Gierli{\'n}ski, Marek and Cole, Christian and Sherstnev, Alexander and Singh, Vijender and Wrobel, Nicola and Gharbi, Karim and Simpson, Gordon G and Owen-Hughes, Tom and others},
  journal={Rna},
  volume={22},
  number={6},
  pages={839--851},
  year={2016},
  publisher={Cold Spring Harbor Lab}
}

@article{zhao2018rnaseqsamplesize,
  title={RnaSeqSampleSize: real data based sample size estimation for RNA sequencing},
  author={Zhao, Shilin and Li, Chung-I and Guo, Yan and Sheng, Quanhu and Shyr, Yu},
  journal={BMC bioinformatics},
  volume={19},
  number={1},
  pages={1--8},
  year={2018},
  publisher={BioMed Central}
}

@article{hart2013calculating,
  title={Calculating sample size estimates for RNA sequencing data},
  author={Hart, Steven N and Therneau, Terry M and Zhang, Yuji and Poland, Gregory A and Kocher, Jean-Pierre},
  journal={Journal of computational biology},
  volume={20},
  number={12},
  pages={970--978},
  year={2013},
  publisher={Mary Ann Liebert, Inc. 140 Huguenot Street, 3rd Floor New Rochelle, NY 10801 USA}
}

@article{liu2014rna,
  title={RNA-seq differential expression studies: more sequence or more replication?},
  author={Liu, Yuwen and Zhou, Jie and White, Kevin P},
  journal={Bioinformatics},
  volume={30},
  number={3},
  pages={301--304},
  year={2014},
  publisher={Oxford University Press}
}

@article{gallego2014rna,
  title={RNA-seq: impact of RNA degradation on transcript quantification},
  author={Gallego Romero, Irene and Pai, Athma A and Tung, Jenny and Gilad, Yoav},
  journal={BMC biology},
  volume={12},
  number={1},
  pages={1--13},
  year={2014},
  publisher={BioMed Central}
}

@article{kim2012short,
  title={Short structured RNAs with low GC content are selectively lost during extraction from a small number of cells},
  author={Kim, Young-Kook and Yeo, Jinah and Kim, Boseon and Ha, Minju and Kim, V Narry},
  journal={Molecular cell},
  volume={46},
  number={6},
  pages={893--895},
  year={2012},
  publisher={Elsevier}
}

@article{zhao2015comparison,
  title={Comparison of stranded and non-stranded RNA-seq transcriptome profiling and investigation of gene overlap},
  author={Zhao, Shanrong and Zhang, Ying and Gordon, William and Quan, Jie and Xi, Hualin and Du, Sarah and von Schack, David and Zhang, Baohong},
  journal={BMC genomics},
  volume={16},
  number={1},
  pages={1--14},
  year={2015},
  publisher={BioMed Central}
}

@article{levin2010comprehensive,
  title={Comprehensive comparative analysis of strand-specific RNA sequencing methods},
  author={Levin, Joshua Z and Yassour, Moran and Adiconis, Xian and Nusbaum, Chad and Thompson, Dawn Anne and Friedman, Nir and Gnirke, Andreas and Regev, Aviv},
  journal={Nature methods},
  volume={7},
  number={9},
  pages={709--715},
  year={2010},
  publisher={Nature Publishing Group US New York}
}

@article{chhangawala2015impact,
  title={The impact of read length on quantification of differentially expressed genes and splice junction detection},
  author={Chhangawala, Sagar and Rudy, Gabe and Mason, Christopher E and Rosenfeld, Jeffrey A},
  journal={Genome biology},
  volume={16},
  number={1},
  pages={1--10},
  year={2015},
  publisher={BioMed Central}
}

@article{corley2017differentially,
  title={Differentially expressed genes from RNA-Seq and functional enrichment results are affected by the choice of single-end versus paired-end reads and stranded versus non-stranded protocols},
  author={Corley, Susan M and MacKenzie, Karen L and Beverdam, Annemiek and Roddam, Louise F and Wilkins, Marc R},
  journal={BMC genomics},
  volume={18},
  number={1},
  pages={1--13},
  year={2017},
  publisher={BioMed Central}
}

@article{hsieh2019effect,
  title={Effect of de novo transcriptome assembly on transcript quantification},
  author={Hsieh, Ping-Han and Oyang, Yen-Jen and Chen, Chien-Yu},
  journal={Scientific reports},
  volume={9},
  number={1},
  pages={8304},
  year={2019},
  publisher={Nature Publishing Group UK London}
}

@article{wang2017comprehensive,
  title={Comprehensive evaluation of de novo transcriptome assembly programs and their effects on differential gene expression analysis},
  author={Wang, Sufang and Gribskov, Michael},
  journal={Bioinformatics},
  volume={33},
  number={3},
  pages={327--333},
  year={2017},
  publisher={Oxford University Press}
}

@article{fu2018elimination,
  title={Elimination of PCR duplicates in RNA-seq and small RNA-seq using unique molecular identifiers},
  author={Fu, Yu and Wu, Pei-Hsuan and Beane, Timothy and Zamore, Phillip D and Weng, Zhiping},
  journal={Bmc Genomics},
  volume={19},
  pages={1--14},
  year={2018},
  publisher={Springer}
}

@article{parekh2016impact,
  title={The impact of amplification on differential expression analyses by RNA-seq},
  author={Parekh, Swati and Ziegenhain, Christoph and Vieth, Beate and Enard, Wolfgang and Hellmann, Ines},
  journal={Scientific reports},
  volume={6},
  number={1},
  pages={25533},
  year={2016},
  publisher={Nature Publishing Group UK London}
}

@article{klepikova2017effect,
  title={Effect of method of deduplication on estimation of differential gene expression using RNA-seq},
  author={Klepikova, Anna V and Kasianov, Artem S and Chesnokov, Mikhail S and Lazarevich, Natalia L and Penin, Aleksey A and Logacheva, Maria},
  journal={PeerJ},
  volume={5},
  pages={e3091},
  year={2017},
  publisher={PeerJ Inc.}
}

@article{baruzzo2017simulation,
  title={Simulation-based comprehensive benchmarking of RNA-seq aligners},
  author={Baruzzo, Giacomo and Hayer, Katharina E and Kim, Eun Ji and Di Camillo, Barbara and FitzGerald, Garret A and Grant, Gregory R},
  journal={Nature methods},
  volume={14},
  number={2},
  pages={135--139},
  year={2017},
  publisher={Nature Publishing Group US New York}
}

@article{dillies2013comprehensive,
  title={A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis},
  author={Dillies, Marie-Agn{\`e}s and Rau, Andrea and Aubert, Julie and Hennequet-Antier, Christelle and Jeanmougin, Marine and Servant, Nicolas and Keime, C{\'e}line and Marot, Guillemette and Castel, David and Estelle, Jordi and others},
  journal={Briefings in bioinformatics},
  volume={14},
  number={6},
  pages={671--683},
  year={2013},
  publisher={Oxford University Press}
}

@article{evans2018selecting,
  title={Selecting between-sample RNA-Seq normalization methods from the perspective of their assumptions},
  author={Evans, Ciaran and Hardin, Johanna and Stoebel, Daniel M},
  journal={Briefings in bioinformatics},
  volume={19},
  number={5},
  pages={776--792},
  year={2018},
  publisher={Oxford University Press}
}

@article{wagner2012measurement,
  title={Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples},
  author={Wagner, G{\"u}nter P and Kin, Koryu and Lynch, Vincent J},
  journal={Theory in biosciences},
  volume={131},
  pages={281--285},
  year={2012},
  publisher={Springer}
}

@article{zhao2020misuse,
  title={Misuse of RPKM or TPM normalization when comparing across samples and sequencing protocols},
  author={Zhao, Shanrong and Ye, Zhan and Stanton, Robert},
  journal={Rna},
  volume={26},
  number={8},
  pages={903--909},
  year={2020},
  publisher={Cold Spring Harbor Lab}
}

@article{liu2016evaluation,
  title={Evaluation of methods in removing batch effects on RNA-seq data},
  author={Liu, Q and Markatou, M},
  journal={Infect Dis Transl Med},
  volume={2},
  number={1},
  pages={3--9},
  year={2016},
  publisher={Page 2}
}

@article{manimaran2016batchqc,
  title={BatchQC: interactive software for evaluating sample and batch effects in genomic data},
  author={Manimaran, Solaiappan and Selby, Heather Marie and Okrah, Kwame and Ruberman, Claire and Leek, Jeffrey T and Quackenbush, John and Haibe-Kains, Benjamin and Bravo, Hector Corrada and Johnson, W Evan},
  journal={Bioinformatics},
  volume={32},
  number={24},
  pages={3836--3838},
  year={2016},
  publisher={Oxford University Press}
}

@article{seyednasrollah2015comparison,
  title={Comparison of software packages for detecting differential expression in RNA-seq studies},
  author={Seyednasrollah, Fatemeh and Laiho, Asta and Elo, Laura L},
  journal={Briefings in bioinformatics},
  volume={16},
  number={1},
  pages={59--70},
  year={2015},
  publisher={Oxford University Press}
}

@article{law2020guide,
  title={A guide to creating design matrices for gene expression experiments},
  author={Law, Charity W and Zeglinski, Kathleen and Dong, Xueyi and Alhamdoosh, Monther and Smyth, Gordon K and Ritchie, Matthew E},
  journal={F1000Research},
  volume={9},
  year={2020},
  publisher={Faculty of 1000 Ltd}
}

@article{soneson2020exploremodelmatrix,
  title={ExploreModelMatrix: interactive exploration for improved understanding of design matrices and linear models in R},
  author={Soneson, Charlotte and Marini, Federico and Geier, Florian and Love, Michael I and Stadler, Michael B},
  journal={F1000Research},
  volume={9},
  number={512},
  pages={512},
  year={2020},
  publisher={F1000 Research Limited}
}

@article{law2016rna,
  title={RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR},
  author={Law, Charity W and Alhamdoosh, Monther and Su, Shian and Smyth, Gordon K and Ritchie, Matthew E},
  journal={F1000Research},
  volume={5},
  year={2016},
  publisher={Faculty of 1000 Ltd}
}

@article{teng2016benchmark,
  title={A benchmark for RNA-seq quantification pipelines},
  author={Teng, Mingxiang and Love, Michael I and Davis, Carrie A and Djebali, Sarah and Dobin, Alexander and Graveley, Brenton R and Li, Sheng and Mason, Christopher E and Olson, Sara and Pervouchine, Dmitri and others},
  journal={Genome biology},
  volume={17},
  number={1},
  pages={1--12},
  year={2016},
  publisher={BioMed Central}
}

@online{elixirbelgium2022,
    title        = {Data Volume},
    author       = {Elixir},
    year         = {2022},
    url          = {https://rdm.elixir-belgium.org/data_volume.html},
    urldate      = {01-05-2023}
}

## sc gene expression ----------------------------------------------------------------------------

@article{luecken2019current,
  title={Current best practices in single-cell RNA-seq analysis: a tutorial},
  author={Luecken, Malte D and Theis, Fabian J},
  journal={Molecular systems biology},
  volume={15},
  number={6},
  pages={e8746},
  year={2019}
}

@article{heumos2023best,
  title={Best practices for single-cell analysis across modalities},
  author={Heumos, Lukas and Schaar, Anna C and Lance, Christopher and Litinetskaya, Anastasia and Drost, Felix and Zappia, Luke and L{\"u}cken, Malte D and Strobl, Daniel C and Henao, Juan and Curion, Fabiola and others},
  journal={Nature Reviews Genetics},
  pages={1--23},
  year={2023},
  publisher={Nature Publishing Group UK London}
}

@article{fullgrabe2020guidelines,
  title={Guidelines for reporting single-cell RNA-seq experiments},
  author={F{\"u}llgrabe, Anja and George, Nancy and Green, Matthew and Nejad, Parisa and Aronow, Bruce and Fexova, Silvie Korena and Fischer, Clay and Freeberg, Mallory Ann and Huerta, Laura and Morrison, Norman and others},
  journal={Nature biotechnology},
  volume={38},
  number={12},
  pages={1384--1386},
  year={2020},
  publisher={Nature Publishing Group US New York}
}

@article{nguyen2018experimental,
  title={Experimental considerations for single-cell RNA sequencing approaches},
  author={Nguyen, Quy H and Pervolarakis, Nicholas and Nee, Kevin and Kessenbrock, Kai},
  journal={Frontiers in cell and developmental biology},
  volume={6},
  pages={108},
  year={2018},
  publisher={Frontiers Media SA}
}

@article{zhang2020determining,
  title={Determining sequencing depth in a single-cell RNA-seq experiment},
  author={Zhang, Martin Jinye and Ntranos, Vasilis and Tse, David},
  journal={Nature communications},
  volume={11},
  number={1},
  pages={774},
  year={2020},
  publisher={Nature Publishing Group UK London}
}

@article{baran2018experimental,
  title={Experimental design for single-cell RNA sequencing},
  author={Baran-Gale, Jeanette and Chandra, Tamir and Kirschner, Kristina},
  journal={Briefings in functional genomics},
  volume={17},
  number={4},
  pages={233--239},
  year={2018},
  publisher={Oxford University Press}
}

@article{svensson2017power,
  title={Power analysis of single-cell RNA-sequencing experiments},
  author={Svensson, Valentine and Natarajan, Kedar Nath and Ly, Lam-Ha and Miragaia, Ricardo J and Labalette, Charlotte and Macaulay, Iain C and Cvejic, Ana and Teichmann, Sarah A},
  journal={Nature methods},
  volume={14},
  number={4},
  pages={381--387},
  year={2017},
  publisher={Nature Publishing Group US New York}
}

@article{melsted2019modular,
  title={Modular and efficient pre-processing of single-cell RNA-seq},
  author={Melsted, P{\'a}ll and Booeshaghi, A Sina and Gao, Fan and Beltrame, Eduardo and Lu, Lambda and Hjorleifsson, Kristj{\'a}n Eldj{\'a}rn and Gehring, Jase and Pachter, Lior},
  journal={BioRxiv},
  pages={673285},
  year={2019},
  publisher={Cold Spring Harbor Laboratory}
}

@article{xi2021benchmarking,
  title={Benchmarking computational doublet-detection methods for single-cell RNA sequencing data},
  author={Xi, Nan Miles and Li, Jingyi Jessica},
  journal={Cell systems},
  volume={12},
  number={2},
  pages={176--194},
  year={2021},
  publisher={Elsevier}
}

@article{xie2021automatic,
  title={Automatic cell type identification methods for single-cell RNA sequencing},
  author={Xie, Bingbing and Jiang, Qin and Mora, Antonio and Li, Xuri},
  journal={Computational and Structural Biotechnology Journal},
  volume={19},
  pages={5874--5887},
  year={2021},
  publisher={Elsevier}
}

@article{sun2022comprehensive,
  title={A comprehensive comparison of supervised and unsupervised methods for cell type identification in single-cell RNA-seq},
  author={Sun, Xiaobo and Lin, Xiaochu and Li, Ziyi and Wu, Hao},
  journal={Briefings in bioinformatics},
  volume={23},
  number={2},
  pages={bbab567},
  year={2022},
  publisher={Oxford University Press}
}

@article{wang2019comparative,
  title={Comparative analysis of differential gene expression analysis tools for single-cell RNA sequencing data},
  author={Wang, Tianyu and Li, Boyang and Nelson, Craig E and Nabavi, Sheida},
  journal={BMC bioinformatics},
  volume={20},
  number={1},
  pages={1--16},
  year={2019},
  publisher={BioMed Central}
}

@article{argelaguet2021computational,
  title={Computational principles and challenges in single-cell data integration},
  author={Argelaguet, Ricard and Cuomo, Anna SE and Stegle, Oliver and Marioni, John C},
  journal={Nature biotechnology},
  volume={39},
  number={10},
  pages={1202--1215},
  year={2021},
  publisher={Nature Publishing Group US New York}
}

@article{luecken2022benchmarking,
  title={Benchmarking atlas-level data integration in single-cell genomics},
  author={Luecken, Malte D and B{\"u}ttner, Maren and Chaichoompu, Kridsadakorn and Danese, Anna and Interlandi, Marta and M{\"u}ller, Michaela F and Strobl, Daniel C and Zappia, Luke and Dugas, Martin and Colom{\'e}-Tatch{\'e}, Maria and others},
  journal={Nature methods},
  volume={19},
  number={1},
  pages={41--50},
  year={2022},
  publisher={Nature Publishing Group US New York}
}

@article{ouyang2021shinycell,
  title={ShinyCell: simple and sharable visualization of single-cell gene expression data},
  author={Ouyang, John F and Kamaraj, Uma S and Cao, Elaine Y and Rackham, Owen JL},
  journal={Bioinformatics},
  volume={37},
  number={19},
  pages={3374--3376},
  year={2021},
  publisher={Oxford Academic}
}

@article{cakir2020comparison,
  title={Comparison of visualization tools for single-cell RNAseq data},
  author={Cakir, Batuhan and Prete, Martin and Huang, Ni and Van Dongen, Stijn and Pir, Pinar and Kiselev, Vladimir Yu},
  journal={NAR Genomics and Bioinformatics},
  volume={2},
  number={3},
  pages={lqaa052},
  year={2020},
  publisher={Oxford University Press}
}

@article{tran2020benchmark,
  title={A benchmark of batch-effect correction methods for single-cell RNA sequencing data},
  author={Tran, Hoa Thi Nhu and Ang, Kok Siong and Chevrier, Marion and Zhang, Xiaomeng and Lee, Nicole Yee Shin and Goh, Michelle and Chen, Jinmiao},
  journal={Genome biology},
  volume={21},
  pages={1--32},
  year={2020},
  publisher={Springer},
  url={https://link.springer.com/article/10.1186/s13059-019-1850-9}
}

@article{saelens2019comparison,
  title={A comparison of single-cell trajectory inference methods},
  author={Saelens, Wouter and Cannoodt, Robrecht and Todorov, Helena and Saeys, Yvan},
  journal={Nature biotechnology},
  volume={37},
  number={5},
  pages={547--554},
  year={2019},
  publisher={Nature Publishing Group US New York},
  url={https://www.nature.com/articles/s42003-022-03175-5}
}

@article{abdelaal2019comparison,
  title={A comparison of automatic cell identification methods for single-cell RNA sequencing data},
  author={Abdelaal, Tamim and Michielsen, Lieke and Cats, Davy and Hoogduin, Dylan and Mei, Hailiang and Reinders, Marcel JT and Mahfouz, Ahmed},
  journal={Genome biology},
  volume={20},
  pages={1--19},
  year={2019},
  publisher={Springer},
  url={https://link.springer.com/article/10.1186/s13059-019-1795-z}
}

@article{andreatta2024semi,
  title={Semi-supervised integration of single-cell transcriptomics data},
  author={Andreatta, Massimo and H{\'e}rault, L{\'e}onard and Gueguen, Paul and Gfeller, David and Berenstein, Ariel J and Carmona, Santiago J},
  journal={Nature Communications},
  volume={15},
  number={1},
  pages={872},
  year={2024},
  publisher={Nature Publishing Group UK London},
  url={https://www.nature.com/articles/s41467-024-45240-z}
}

@article{almet2021landscape,
  title={The landscape of cell--cell communication through single-cell transcriptomics},
  author={Almet, Axel A and Cang, Zixuan and Jin, Suoqin and Nie, Qing},
  journal={Current opinion in systems biology},
  volume={26},
  pages={12--23},
  year={2021},
  publisher={Elsevier},
  url={https://www.sciencedirect.com/science/article/pii/S2452310021000081}
}

@article{bilous2024building,
  title={Building and analyzing metacells in single-cell genomics data},
  author={Bilous, Mariia and H{\'e}rault, L{\'e}onard and Gabriel, Aur{\'e}lie AG and Teleman, Matei and Gfeller, David},
  journal={Molecular Systems Biology},
  pages={1--23},
  year={2024},
  publisher={Nature Publishing Group UK London},
  url={https://doi.org/10.1038/s44320-024-00045-6}
}

## sc spatial -------------------------------------------------------------------------------

@article{walker2022deciphering,
  title={Deciphering tissue structure and function using spatial transcriptomics},
  author={Walker, Benjamin L and Cang, Zixuan and Ren, Honglei and Bourgain-Chang, Eric and Nie, Qing},
  journal={Communications biology},
  volume={5},
  number={1},
  pages={220},
  year={2022},
  publisher={Nature Publishing Group UK London}
}

@article{yue2023guidebook,
  title={A guidebook of spatial transcriptomic technologies, data resources and analysis approaches},
  author={Yue, Liangchen and Liu, Feng and Hu, Jiongsong and Yang, Pin and Wang, Yuxiang and Dong, Junguo and Shu, Wenjie and Huang, Xingxu and Wang, Shengqi},
  journal={Computational and Structural Biotechnology Journal},
  year={2023},
  publisher={Elsevier},
  url={https://www.sciencedirect.com/science/article/pii/S2001037023000156}
}

@article{moses2022museum,
  title={Museum of spatial transcriptomics},
  author={Moses, Lambda and Pachter, Lior},
  journal={Nature Methods},
  volume={19},
  number={5},
  pages={534--546},
  year={2022},
  publisher={Nature Publishing Group US New York},
  url={https://www.nature.com/articles/s41592-022-01409-2}
}

## atacseq --------------------------------------------------------------------------------------

@article{stuart2021single,
  title={Single-cell chromatin state analysis with Signac},
  author={Stuart, Tim and Srivastava, Avi and Madad, Shaista and Lareau, Caleb A and Satija, Rahul},
  journal={Nature methods},
  volume={18},
  number={11},
  pages={1333--1341},
  year={2021},
  publisher={Nature Publishing Group US New York},
  url={https://www.nature.com/articles/s41592-021-01282-5}
}

@article{grandi2022chromatin,
  title={Chromatin accessibility profiling by ATAC-seq},
  author={Grandi, Fiorella C and Modi, Hailey and Kampman, Lucas and Corces, M Ryan},
  journal={Nature Protocols},
  volume={17},
  number={6},
  pages={1518--1552},
  year={2022},
  publisher={Nature Publishing Group UK London},
  url={https://www.nature.com/articles/s41596-022-00692-9}
}

@article{yan2020reads,
  title={From reads to insight: a hitchhiker’s guide to ATAC-seq data analysis},
  author={Yan, Feng and Powell, David R and Curtis, David J and Wong, Nicholas C},
  journal={Genome biology},
  volume={21},
  pages={1--16},
  year={2020},
  publisher={Springer},
  url={https://link.springer.com/article/10.1186/s13059-020-1929-3}
}

@article{chen2019assessment,
  title={Assessment of computational methods for the analysis of single-cell ATAC-seq data},
  author={Chen, Huidong and Lareau, Caleb and Andreani, Tommaso and Vinyard, Michael E and Garcia, Sara P and Clement, Kendell and Andrade-Navarro, Miguel A and Buenrostro, Jason D and Pinello, Luca},
  journal={Genome biology},
  volume={20},
  number={1},
  pages={1--25},
  year={2019},
  publisher={BioMed Central},
  url={https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1854-5}
}

@article{wang2022benchmarking,
  title={Benchmarking automated cell type annotation tools for single-cell ATAC-seq data},
  author={Wang, Yuge and Sun, Xingzhi and Zhao, Hongyu},
  journal={Frontiers in Genetics},
  volume={13},
  pages={1063233},
  year={2022},
  publisher={Frontiers Media SA},
  url={https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2022.1063233/full}
}

@article{de2024systematic,
  title={Systematic benchmarking of single-cell ATAC-sequencing protocols},
  author={De Rop, Florian V and Hulselmans, Gert and Flerin, Chris and Soler-Vila, Paula and Rafels, Albert and Christiaens, Valerie and Gonz{\'a}lez-Blas, Carmen Bravo and Marchese, Domenica and Caratu, Ginevra and Poovathingal, Suresh and others},
  journal={Nature biotechnology},
  volume={42},
  number={6},
  pages={916--926},
  year={2024},
  publisher={Nature Publishing Group US New York},
  url={https://genomebiology.biomedcentral.com/articles/10.1186/s13059-024-03356-x}
}

@article{luo2024benchmarking,
  title={Benchmarking computational methods for single-cell chromatin data analysis},
  author={Luo, Siyuan and Germain, Pierre-Luc and Robinson, Mark D and von Meyenn, Ferdinand},
  journal={Genome Biology},
  volume={25},
  number={1},
  pages={225},
  year={2024},
  publisher={Springer},
  url={https://link.springer.com/article/10.1186/s13059-024-03356-x}
}

@article{granja2021archr,
  title={ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis},
  author={Granja, Jeffrey M and Corces, M Ryan and Pierce, Sarah E and Bagdatli, S Tansu and Choudhry, Hani and Chang, Howard Y and Greenleaf, William J},
  journal={Nature genetics},
  volume={53},
  number={3},
  pages={403--411},
  year={2021},
  publisher={Nature Publishing Group US New York},
  url={https://www.nature.com/articles/s41588-021-00790-6}
}

@article{fang2021comprehensive,
  title={Comprehensive analysis of single cell ATAC-seq data with SnapATAC},
  author={Fang, Rongxin and Preissl, Sebastian and Li, Yang and Hou, Xiaomeng and Lucero, Jacinta and Wang, Xinxin and Motamedi, Amir and Shiau, Andrew K and Zhou, Xinzhu and Xie, Fangming and others},
  journal={Nature communications},
  volume={12},
  number={1},
  pages={1337},
  year={2021},
  publisher={Nature Publishing Group UK London},
  url={https://www.nature.com/articles/s41467-021-21583-9}
}

@article{shi2022fundamental,
  title={Fundamental and practical approaches for single-cell ATAC-seq analysis},
  author={Shi, Peiyu and Nie, Yage and Yang, Jiawen and Zhang, Weixing and Tang, Zhongjie and Xu, Jin},
  journal={Abiotech},
  volume={3},
  number={3},
  pages={212--223},
  year={2022},
  publisher={Springer},
  url={https://link.springer.com/article/10.1007/s42994-022-00082-5}
}

@article{baek2020single,
  title={Single-cell ATAC sequencing analysis: from data preprocessing to hypothesis generation},
  author={Baek, Seungbyn and Lee, Insuk},
  journal={Computational and structural biotechnology journal},
  volume={18},
  pages={1429--1439},
  year={2020},
  publisher={Elsevier},
  url={https://www.sciencedirect.com/science/article/pii/S2001037020303019}
}

## airr ----------------------------------------------------------------------------------------

@article{irac2024single,
  title={Single-cell immune repertoire analysis},
  author={Irac, Sergio E and Soon, Megan Sioe Fei and Borcherding, Nicholas and Tuong, Zewen Kelvin},
  journal={Nature Methods},
  pages={1--16},
  year={2024},
  publisher={Nature Publishing Group US New York},
  url={https://www.nature.com/articles/s41592-024-02243-4}
}

@article{breden2017reproducibility,
  title={Reproducibility and reuse of adaptive immune receptor repertoire data},
  author={Breden, Felix and Luning Prak, Eline T and Peters, Bjoern and Rubelt, Florian and Schramm, Chaim A and Busse, Christian E and Vander Heiden, Jason A and Christley, Scott and Bukhari, Syed Ahmad Chan and Thorogood, Adrian and others},
  journal={Frontiers in immunology},
  volume={8},
  pages={1418},
  year={2017},
  publisher={Frontiers Media SA},
  url={https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2017.01418/full}
}

@article{vander2018airr,
  title={AIRR community standardized representations for annotated immune repertoires},
  author={Vander Heiden, Jason Anthony and Marquez, Susanna and Marthandan, Nishanth and Bukhari, Syed Ahmad Chan and Busse, Christian E and Corrie, Brian and Hershberg, Uri and Kleinstein, Steven H and Matsen IV, Frederick A and Ralph, Duncan K and others},
  journal={Frontiers in immunology},
  volume={9},
  pages={2206},
  year={2018},
  publisher={Frontiers Media SA},
  url={https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2018.02206/full}
}

@article{eugster2022airr,
  title={AIRR Community Guide to Planning and Performing AIRR-Seq Experiments},
  author={Eugster, Anne and Bostick, Magnolia L and Gupta, Nidhi and Mariotti-Ferrandiz, Encarnita and Kraus, Gloria and Meng, Wenzhao and Soto, Cinque and Tr{\"u}ck, Johannes and Stervbo, Ulrik and Prak, Eline T Luning and others},
  journal={Methods and Protocols},
  pages={261},
  year={2022},
  url={https://library.oapen.org/bitstream/handle/20.500.12657/57008/1/978-1-0716-2115-8.pdf}
}

@article{georgiou2014promise,
  title={The promise and challenge of high-throughput sequencing of the antibody repertoire},
  author={Georgiou, George and Ippolito, Gregory C and Beausang, John and Busse, Christian E and Wardemann, Hedda and Quake, Stephen R},
  journal={Nature biotechnology},
  volume={32},
  number={2},
  pages={158--168},
  year={2014},
  publisher={Nature Publishing Group US New York},
  url={https://www.nature.com/articles/nbt.2782}
}

@article{barennes2021benchmarking,
  title={Benchmarking of T cell receptor repertoire profiling methods reveals large systematic biases},
  author={Barennes, Pierre and Quiniou, Valentin and Shugay, Mikhail and Egorov, Evgeniy S and Davydov, Alexey N and Chudakov, Dmitriy M and Uddin, Imran and Ismail, Mazlina and Oakes, Theres and Chain, Benny and others},
  journal={Nature biotechnology},
  volume={39},
  number={2},
  pages={236--245},
  year={2021},
  publisher={Nature Publishing Group US New York},
  url={https://www.nature.com/articles/s41587-020-0656-3}
}

@book{janeway-1994,
	author = {Janeway, Charles and Travers, Paul},
	month = {1},
	publisher = {Taylor & Francis},
	title = {{Immunobiology}},
	year = {1994}
}

@article{andreani2022benchmarking,
  title={Benchmarking computational methods for B-cell receptor reconstruction from single-cell RNA-seq data},
  author={Andreani, Tommaso and Slot, Linda M and Gabillard, Samuel and Struebing, Carsten and Reimertz, Claus and Yaligara, Veeranagouda and Bakker, Aleida M and Olfati-Saber, Reza and Toes, Ren{\'e} EM and Scherer, Hans U and others},
  journal={NAR Genomics and Bioinformatics},
  volume={4},
  number={3},
  pages={lqac049},
  year={2022},
  publisher={Oxford University Press},
  url={https://academic.oup.com/nargab/article/4/3/lqac049/6643029}
}

@article{smakaj2020benchmarking,
  title={Benchmarking immunoinformatic tools for the analysis of antibody repertoire sequences},
  author={Smakaj, Erand and Babrak, Lmar and Ohlin, Mats and Shugay, Mikhail and Briney, Bryan and Tosoni, Deniz and Galli, Christopher and Grobelsek, Vendi and D’Angelo, Igor and Olson, Branden and others},
  journal={Bioinformatics},
  volume={36},
  number={6},
  pages={1731--1739},
  year={2020},
  publisher={Oxford University Press},
  url={https://academic.oup.com/bioinformatics/article/36/6/1731/5686386}
}

@article{rosati2017overview,
  title={Overview of methodologies for T-cell receptor repertoire analysis},
  author={Rosati, Elisa and Dowds, C Marie and Liaskou, Evaggelia and Henriksen, Eva Kristine Klemsdal and Karlsen, Tom H and Franke, Andre},
  journal={BMC biotechnology},
  volume={17},
  number={1},
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  year={2017},
  publisher={BioMed Central},
  url={https://bmcbiotechnol.biomedcentral.com/articles/10.1186/s12896-017-0379-9}
}

@article{greiff2015bioinformatic,
  title={Bioinformatic and statistical analysis of adaptive immune repertoires},
  author={Greiff, Victor and Miho, Enkelejda and Menzel, Ulrike and Reddy, Sai T},
  journal={Trends in immunology},
  volume={36},
  number={11},
  pages={738--749},
  year={2015},
  publisher={Elsevier},
  url={https://www.cell.com/trends/immunology/fulltext/S1471-4906(15)00223-9}
}

@article{yermanos2018tracing,
  title={Tracing antibody repertoire evolution by systems phylogeny},
  author={Yermanos, Alexander Dimitri and Dounas, Andreas Kevin and Stadler, Tanja and Oxenius, Annette and Reddy, Sai T},
  journal={Frontiers in immunology},
  volume={9},
  pages={2149},
  year={2018},
  publisher={Frontiers Media SA},
  url = {https://www.frontiersin.org/articles/10.3389/fimmu.2018.02149/full},
}

@article{ralph2020using,
  title={Using B cell receptor lineage structures to predict affinity},
  author={Ralph, Duncan K and Matsen IV, Frederick A},
  journal={PLOS Computational Biology},
  volume={16},
  number={11},
  pages={e1008391},
  year={2020},
  publisher={Public Library of Science San Francisco, CA USA},
  url={https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008391}
}

@article{hoehn2022phylogenetic,
  title={Phylogenetic analysis of migration, differentiation, and class switching in B cells},
  author={Hoehn, Kenneth B and Pybus, Oliver G and Kleinstein, Steven H},
  journal={PLoS computational biology},
  volume={18},
  number={4},
  pages={e1009885},
  year={2022},
  publisher={Public Library of Science San Francisco, CA USA},
  url={https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1009885}
}

@article{pavlovic2021immuneml,
  title={The immuneML ecosystem for machine learning analysis of adaptive immune receptor repertoires},
  author={Pavlovi{\'c}, Milena and Scheffer, Lonneke and Motwani, Keshav and Kanduri, Chakravarthi and Kompova, Radmila and Vazov, Nikolay and Waagan, Knut and Bernal, Fabian LM and Costa, Alexandre Almeida and Corrie, Brian and others},
  journal={Nature Machine Intelligence},
  volume={3},
  number={11},
  pages={936--944},
  year={2021},
  publisher={Nature Publishing Group UK London},
  url={https://www.nature.com/articles/s42256-021-00413-z}
}

@article{collins2024airr,
  title={AIRR-C IG Reference Sets: curated sets of immunoglobulin heavy and light chain germline genes},
  author={Collins, Andrew M and Ohlin, Mats and Corcoran, Martin and Heather, James M and Ralph, Duncan and Law, Mansun and Mart{\'\i}nez-Barnetche, Jesus and Ye, Jian and Richardson, Eve and Gibson, William S and others},
  journal={Frontiers in Immunology},
  volume={14},
  pages={1330153},
  year={2024},
  publisher={Frontiers},
  url={https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2023.1330153/full}
}

@article{yaari2015practical,
  title={Practical guidelines for B-cell receptor repertoire sequencing analysis},
  author={Yaari, Gur and Kleinstein, Steven H},
  journal={Genome medicine},
  volume={7},
  pages={1--14},
  year={2015},
  publisher={Springer},
  url={https://link.springer.com/article/10.1186/s13073-015-0243-2}
}


@article{primorac2022adaptive,
  title={Adaptive immune responses and immunity to SARS-CoV-2},
  author={Primorac, Dragan and Vrdoljak, Kristijan and Brlek, Petar and Paveli{\'c}, Eduard and Molnar, Vilim and Mati{\v{s}}i{\'c}, Vid and Erceg Ivko{\v{s}}i{\'c}, Ivana and Par{\v{c}}ina, Marijo},
  journal={Frontiers in Immunology},
  volume={13},
  pages={2035},
  year={2022},
  publisher={Frontiers},
  url={https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2022.848582/full}
}

@article{de2018single,
  title={Single cell T cell receptor sequencing: techniques and future challenges},
  author={De Simone, Marco and Rossetti, Grazisa and Pagani, Massimiliano},
  journal={Frontiers in Immunology},
  volume={9},
  pages={1638},
  year={2018},
  publisher={Frontiers Media SA},
  url={https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2018.01638/full}
}

@Inbook{Kavathas2019,
author="Kavathas, Paula B.
and Krause, Peter J.
and Ruddle, Nancy H.",
editor="Krause, Peter J.
and Kavathas, Paula B.
and Ruddle, Nancy H.",
title="Organization and Cells of the Immune System",
bookTitle="Immunoepidemiology",
year="2019",
publisher="Springer International Publishing",
address="Cham",
pages="21--38",
abstract="The human immune system is designed for protection against invading pathogens. The areas of the body exposed to microbes are the skin and mucosal surfaces of the intestinal, respiratory, reproductive, and urinary tracts. The immune system associated with these surfaces is called barrier immunity. Once a pathogen has entered the body, cells of the innate and adaptive immune system can be activated to fight the infection. Macrophages, dendritic cells, granulocytes, innate lymphoid cells, and invariant and conventional T and B cells function to protect the host. Characteristics of different immune cell types and some of their functions such as phagocytosis (eating) and NETosis (trapping) are presented in this chapter. In order to mount a coordinated and appropriate response, there is cross-talk between the different immune cells. Soluble mediators called cytokines and chemokines are important mechanisms for cell--cell communication. Cytokines and chemokines also provide communication between immune cells and other organs of the body. The adult lymphoid system is composed of primary (bone marrow and thymus) and secondary (lymph node, spleen, Peyer's patches, tonsils, adenoids, lymphoid tissue associated with mucosal surfaces) lymphoid organs that are connected through blood and lymphatic vessels. The lymphatic vessels transport immune cells, fluid, antigen, and fat throughout the body. Tertiary lymphoid organs can form in the context of chronic inflammation. This chapter provides a broad overview of the components of the immune system with greater detail provided in later chapters.",
isbn="978-3-030-25553-4",
doi="10.1007/978-3-030-25553-4_2",
url="https://doi.org/10.1007/978-3-030-25553-4_2"
}

@incollection{LEWIS201919,
title = {2 - Organization of the Immune System},
editor = {Robert R. Rich and Thomas A. Fleisher and William T. Shearer and Harry W. Schroeder and Anthony J. Frew and Cornelia M. Weyand},
booktitle = {Clinical Immunology (Fifth Edition)},
publisher = {Elsevier},
edition = {Fifth Edition},
address = {London},
pages = {19-38.e1},
year = {2019},
isbn = {978-0-7020-6896-6},
doi = {10.1016/B978-0-7020-6896-6.00002-8},
url = {https://www.sciencedirect.com/science/article/pii/B9780702068966000028},
author = {Dorothy E. Lewis and Sarah E. Blutt},
keywords = {Hematopoetic stem cells, Lymphopoiesis, Cluster of differentiation markers, Cytokines, Primary lymphoid organ, Secondary lymphoid organ, Systemic immune system, Mucosal immune system},
abstract = {The human immune system has sites of production, i.e., bone marrow and the thymus; and sites of differentiation and proliferation, i.e., lymph nodes and the spleen. Immune organization also occurs in the lung, gastrointestinal tract, skin, and adipose tissue. Cells can be tissue bound or move to sites during infection via blood or lymphatics. Pluripotent stem cells in bone marrow give rise to progenitors, which differentiate into lymphoid and myeloid cells as well as red blood cells and platelets. Myeloid cells include neutrophils, basophils, and eosinophils with functions in innate immune responses, as well as monocytes, macrophages, and dendritic cells, which are phagocytic and act as an interface with cells of the acquired immune system. Lymphocytes include antigen-specific cells with DNA-rearranged receptors, T cells and B cells, as well as cells termed innate lymphoid cells, which can be cytotoxic (natural killer cells) or noncytotoxic, with functions that mirror classic T-cell functions.}
}

@article{MORGAN2022210,
title = {Unraveling B cell trajectories at single cell resolution},
journal = {Trends in Immunology},
volume = {43},
number = {3},
pages = {210-229},
year = {2022},
issn = {1471-4906},
doi = {10.1016/j.it.2022.01.003},
url = {https://www.sciencedirect.com/science/article/pii/S1471490622000035},
author = {Dhakshayini Morgan and Vinay Tergaonkar},
abstract = {During adaptive immunity, B cells differentiate either into memory B cells or plasma cells and produce antibodies against foreign antigens to fight infection. Additionally, they behave as antigen-presenting cells and participate in T cell activation during cellular immune responses. However, their functional dysregulation can result in various autoimmune diseases and cancers. With significant breakthroughs in single cell technologies, assessing individual B cell genomics, transcriptomics, and proteomics can give deeper insights into mammalian B cell development, differentiation, antibody repertoire, and responses under conditions of homeostasis, infection, and aberrations during disease. In this review, we discuss the adoption of single cell approaches to identify different B cell gene signatures and biomarkers in normal and diseased tissues, and subsequent benefits for future therapeutic discoveries.}
}

## meta transcriptomics ------------------------------------------------------------------------

@article{mehta2021asaim,
  title={ASaiM-MT: a validated and optimized ASaiM workflow for metatranscriptomics analysis within Galaxy framework},
  author={Mehta, Subina and Crane, Marie and Leith, Emma and Batut, B{\'e}r{\'e}nice and Hiltemann, Saskia and Arntzen, Magnus {\O} and Kunath, Benoit J and Pope, Phillip B and Delogu, Francesco and Sajulga, Ray and others},
  journal={F1000Research},
  volume={10},
  pages={103},
  year={2021},
  publisher={F1000 Research Limited London, UK}
}