@article{scverse,
	doi = {10.1038/s41587-023-01733-8},
	url = {https://doi.org/10.1038%2Fs41587-023-01733-8},
	year = 2023,
	month = {apr},
	publisher = {Springer Science and Business Media {LLC}},
	author = {Isaac Virshup and Danila Bredikhin and Lukas Heumos and Giovanni Palla and Gregor Sturm and Adam Gayoso and Ilia Kats and Mikaela Koutrouli and Philipp Angerer and Volker Bergen and Pierre Boyeau and Maren Büttner and Gokcen Eraslan and David Fischer and Max Frank and Justin Hong and Michal Klein and Marius Lange and Romain Lopez and Mohammad Lotfollahi and Malte D. Luecken and Fidel Ramirez and Jeffrey Regier and Sergei Rybakov and Anna C. Schaar and Valeh Valiollah Pour Amiri and Philipp Weiler and Galen Xing and Bonnie Berger and Dana Pe'er and Aviv Regev and Sarah A. Teichmann and Francesca Finotello and F. Alexander Wolf and Nir Yosef and Oliver Stegle and Fabian J. Theis and},
	title = {The scverse project provides a computational ecosystem for single-cell omics data analysis},
	journal = {Nature Biotechnology}
}

@article{hsc_tgfb,
  title = {GIPC-Regulated IGFBP-3 Promotes HSC Migration In Vitro and Portal Hypertension In Vivo Through a β1-Integrin Pathway},
  volume = {10},
  ISSN = {2352-345X},
  url = {http://dx.doi.org/10.1016/j.jcmgh.2020.05.005},
  DOI = {10.1016/j.jcmgh.2020.05.005},
  number = {3},
  journal = {Cellular and Molecular Gastroenterology and Hepatology},
  publisher = {Elsevier BV},
  author = {Yaqoob,  Usman and Luo,  Fanghong and Greuter,  Thomas and Jalan Sakrikar,  Nidhi and Sehrawat,  Tejasav S. and Lu,  Jianwen and Hu,  Xiao and Gao,  Jinhang and Kostallari,  Enis and Chen,  Jingbiao and Arab,  Juan Pablo and Martin-Mateos,  Rosa and Cao,  Sheng and Shah,  Vijay H.},
  year = {2020},
  pages = {545–559}
}

@article{pydeseq,
  title = {PyDESeq2: a python package for bulk RNA-seq differential expression analysis},
  volume = {39},
  ISSN = {1367-4811},
  url = {http://dx.doi.org/10.1093/bioinformatics/btad547},
  DOI = {10.1093/bioinformatics/btad547},
  number = {9},
  journal = {Bioinformatics},
  publisher = {Oxford University Press (OUP)},
  author = {Muzellec,  Boris and Teleńczuk,  Maria and Cabeli,  Vincent and Andreux,  Mathieu},
  editor = {Ponty,  Yann},
  year = {2023},
  month = sep 
}

@article{limma,
  title = {limma powers differential expression analyses for RNA-sequencing and microarray studies},
  volume = {43},
  ISSN = {0305-1048},
  url = {http://dx.doi.org/10.1093/nar/gkv007},
  DOI = {10.1093/nar/gkv007},
  number = {7},
  journal = {Nucleic Acids Research},
  publisher = {Oxford University Press (OUP)},
  author = {Ritchie,  Matthew E. and Phipson,  Belinda and Wu,  Di and Hu,  Yifang and Law,  Charity W. and Shi,  Wei and Smyth,  Gordon K.},
  year = {2015},
  month = jan,
  pages = {e47–e47}
}

@article{edger,
  title = {<tt>edgeR</tt>: a Bioconductor package for differential expression analysis of digital gene expression data},
  volume = {26},
  ISSN = {1367-4803},
  url = {http://dx.doi.org/10.1093/bioinformatics/btp616},
  DOI = {10.1093/bioinformatics/btp616},
  number = {1},
  journal = {Bioinformatics},
  publisher = {Oxford University Press (OUP)},
  author = {Robinson,  Mark D. and McCarthy,  Davis J. and Smyth,  Gordon K.},
  year = {2009},
  month = nov,
  pages = {139–140}
}

@article{decoupler,
  title = {decoupleR: ensemble of computational methods to infer biological activities from omics data},
  volume = {2},
  ISSN = {2635-0041},
  url = {http://dx.doi.org/10.1093/bioadv/vbac016},
  DOI = {10.1093/bioadv/vbac016},
  number = {1},
  journal = {Bioinformatics Advances},
  publisher = {Oxford University Press (OUP)},
  author = {Badia-i-Mompel,  Pau and Vélez Santiago,  Jesús and Braunger,  Jana and Geiss,  Celina and Dimitrov,  Daniel and M\"{u}ller-Dott,  Sophia and Taus,  Petr and Dugourd,  Aurelien and Holland,  Christian H and Ramirez Flores,  Ricardo O and Saez-Rodriguez,  Julio},
  editor = {Kuijjer,  Marieke Lydia},
  year = {2022},
  month = jan 
}

@article{grn_review,
  title = {Gene regulatory network inference in the era of single-cell multi-omics},
  volume = {24},
  ISSN = {1471-0064},
  url = {http://dx.doi.org/10.1038/s41576-023-00618-5},
  DOI = {10.1038/s41576-023-00618-5},
  number = {11},
  journal = {Nature Reviews Genetics},
  publisher = {Springer Science and Business Media LLC},
  author = {Badia-i-Mompel,  Pau and Wessels,  Lorna and M\"{u}ller-Dott,  Sophia and Trimbour,  Rémi and Ramirez Flores,  Ricardo O. and Argelaguet,  Ricard and Saez-Rodriguez,  Julio},
  year = {2023},
  month = jun,
  pages = {739–754}
}

@article{collectri,
  title = {Expanding the coverage of regulons from high-confidence prior knowledge for accurate estimation of transcription factor activities},
  volume = {51},
  ISSN = {1362-4962},
  url = {http://dx.doi.org/10.1093/nar/gkad841},
  DOI = {10.1093/nar/gkad841},
  number = {20},
  journal = {Nucleic Acids Research},
  publisher = {Oxford University Press (OUP)},
  author = {M\"{u}ller-Dott,  Sophia and Tsirvouli,  Eirini and Vazquez,  Miguel and Ramirez Flores,  Ricardo O and Badia-i-Mompel,  Pau and Fallegger,  Robin and T\"{u}rei,  Dénes and Lægreid,  Astrid and Saez-Rodriguez,  Julio},
  year = {2023},
  month = oct,
  pages = {10934–10949}
}

@article{dorothea,
  title = {Benchmark and integration of resources for the estimation of human transcription factor activities},
  volume = {29},
  ISSN = {1549-5469},
  url = {http://dx.doi.org/10.1101/gr.240663.118},
  DOI = {10.1101/gr.240663.118},
  number = {8},
  journal = {Genome Research},
  publisher = {Cold Spring Harbor Laboratory},
  author = {Garcia-Alonso,  Luz and Holland,  Christian H. and Ibrahim,  Mahmoud M. and Turei,  Denes and Saez-Rodriguez,  Julio},
  year = {2019},
  month = jul,
  pages = {1363–1375}
}

@article{msigdb,
  title = {Molecular signatures database ({MSigDB}) 3.0},
  author = {Liberzon, Arthur and Subramanian, Aravind and Pinchback, Reid
           and Thorvaldsd{\'o}ttir, Helga and Tamayo, Pablo and Mesirov,
           Jill P},
  journal = {Bioinformatics},
  publisher = {Oxford University Press (OUP)},
  volume = {27},
  number = {12},
  pages = {1739--1740},
  month = jun,
  year = {2011}
}

@article{progeny,
  title={Perturbation-response genes reveal signaling footprints in cancer gene expression},
  volume={9},
  ISSN={2041-1723},
  url={http://dx.doi.org/10.1038/s41467-017-02391-6},
  DOI={10.1038/s41467-017-02391-6},
  number={1},
  journal={Nature Communications},
  publisher={Springer Science and Business Media LLC},
  author={Schubert, Michael and Klinger, Bertram and Klünemann, Martina and Sieber, Anja and Uhlitz,
          Florian and Sauer, Sascha and Garnett, Mathew J. and Blüthgen, Nils and Saez-Rodriguez, Julio},
  year={2018},
  month=jan
}

@article{psbulk,
  title={Confronting false discoveries in single-cell differential expression},
  volume={12},
  ISSN={2041-1723},
  url={http://dx.doi.org/10.1038/s41467-021-25960-2},
  DOI={10.1038/s41467-021-25960-2},
  number={1},
  journal={Nature Communications},
  publisher={Springer Science and Business Media LLC},
  author={Squair, Jordan W. and Gautier, Matthieu and Kathe, Claudia and Anderson, Mark A. and James,
          Nicholas D. and Hutson, Thomas H. and Hudelle, Rémi and Qaiser, Taha and Matson,
          Kaya J. E. and Barraud, Quentin and Levine, Ariel J. and La Manno, Gioele and Skinnider,
          Michael A. and Courtine, Grégoire},
  year={2021},
  month=sep
}

@article{covid5k,
  title={Elevated Calprotectin and Abnormal Myeloid Cell Subsets Discriminate Severe from Mild COVID-19},
  volume={182},
  ISSN={0092-8674},
  url={http://dx.doi.org/10.1016/j.cell.2020.08.002},
  DOI={10.1016/j.cell.2020.08.002},
  number={6},
  journal={Cell},
  publisher={Elsevier BV},
  author={Silvin, Aymeric and Chapuis, Nicolas and Dunsmore, Garett and Goubet,
          Anne-Gaëlle and Dubuisson, Agathe and Derosa, Lisa and Almire, Carole and Hénon,
          Clémence and Kosmider, Olivier and Droin, Nathalie and Rameau, Philippe and Catelain,
          Cyril and Alfaro, Alexia and Dussiau, Charles and Friedrich, Chloé and Sourdeau,
          Elise and Marin, Nathalie and Szwebel, Tali-Anne and Cantin, Delphine and Mouthon,
          Luc and Borderie, Didier and Deloger, Marc and Bredel, Delphine and Mouraud,
          Severine and Drubay, Damien and Andrieu, Muriel and Lhonneur, Anne-Sophie and Saada,
          Véronique and Stoclin, Annabelle and Willekens, Christophe and Pommeret,
          Fanny and Griscelli, Frank and Ng, Lai Guan and Zhang, Zheng and Bost,
          Pierre and Amit, Ido and Barlesi, Fabrice and Marabelle, Aurélien and Pène,
          Frédéric and Gachot, Bertrand and André, Fabrice and Zitvogel, Laurence and Ginhoux,
          Florent and Fontenay, Michaela and Solary, Eric},
  year={2020},
  month=sep,
  pages={1401-1418.e18}
}

@article{panglaodb,
  title = {PanglaoDB: a web server for exploration of mouse and human single-cell RNA sequencing data},
  volume = {2019},
  ISSN = {1758-0463},
  url = {http://dx.doi.org/10.1093/database/baz046},
  DOI = {10.1093/database/baz046},
  journal = {Database},
  publisher = {Oxford University Press (OUP)},
  author = {Franzén,  Oscar and Gan,  Li-Ming and Bj\"{o}rkegren,  Johan L M},
  year = {2019},
  month = jan 
}

@article{msvisium,
  title = {Cell type mapping reveals tissue niches and interactions in subcortical multiple sclerosis lesions},
  volume = {27},
  ISSN = {1546-1726},
  url = {http://dx.doi.org/10.1038/s41593-024-01796-z},
  DOI = {10.1038/s41593-024-01796-z},
  number = {12},
  journal = {Nature Neuroscience},
  publisher = {Springer Science and Business Media LLC},
  author = {Lerma-Martin,  Celia and Badia-i-Mompel,  Pau and Ramirez Flores,  Ricardo O. and Sekol,  Patricia and Sch\"{a}fer,  Philipp S. L. and Riedl,  Christian J. and Hofmann,  Annika and Th\"{a}wel,  Thomas and W\"{u}nnemann,  Florian and Ibarra-Arellano,  Miguel A. and Trobisch,  Tim and Eisele,  Philipp and Schapiro,  Denis and Haeussler,  Maximilian and Hametner,  Simon and Saez-Rodriguez,  Julio and Schirmer,  Lucas},
  year = {2024},
  month = nov,
  pages = {2354–2365}
}

@article{liana,
  title = {LIANA+ provides an all-in-one framework for cell–cell communication inference},
  volume = {26},
  ISSN = {1476-4679},
  url = {http://dx.doi.org/10.1038/s41556-024-01469-w},
  DOI = {10.1038/s41556-024-01469-w},
  number = {9},
  journal = {Nature Cell Biology},
  publisher = {Springer Science and Business Media LLC},
  author = {Dimitrov,  Daniel and Sch\"{a}fer,  Philipp Sven Lars and Farr,  Elias and Rodriguez-Mier,  Pablo and Lobentanzer,  Sebastian and Badia-i-Mompel,  Pau and Dugourd,  Aurelien and Tanevski,  Jovan and Ramirez Flores,  Ricardo Omar and Saez-Rodriguez,  Julio},
  year = {2024},
  month = sep,
  pages = {1613–1622}
}

@article{hcop,
  title = {Updates to HCOP: the HGNC comparison of orthology predictions tool},
  volume = {22},
  ISSN = {1477-4054},
  url = {http://dx.doi.org/10.1093/bib/bbab155},
  DOI = {10.1093/bib/bbab155},
  number = {6},
  journal = {Briefings in Bioinformatics},
  publisher = {Oxford University Press (OUP)},
  author = {Yates,  Bethan and Gray,  Kristian A and Jones,  Tamsin E M and Bruford,  Elspeth A},
  year = {2021},
  month = may 
}

@article{omnipath,
  title = {OmniPath: guidelines and gateway for literature-curated signaling pathway resources},
  volume = {13},
  ISSN = {1548-7105},
  url = {http://dx.doi.org/10.1038/nmeth.4077},
  DOI = {10.1038/nmeth.4077},
  number = {12},
  journal = {Nature Methods},
  publisher = {Springer Science and Business Media LLC},
  author = {T\"{u}rei,  Dénes and Korcsmáros,  Tamás and Saez-Rodriguez,  Julio},
  year = {2016},
  month = nov,
  pages = {966–967}
}

@article{knocktf,
  title = {KnockTF: a comprehensive human gene expression profile database with knockdown/knockout of transcription factors},
  volume = {48},
  ISSN = {1362-4962},
  url = {http://dx.doi.org/10.1093/nar/gkz881},
  DOI = {10.1093/nar/gkz881},
  number = {D1},
  journal = {Nucleic Acids Research},
  publisher = {Oxford University Press (OUP)},
  author = {Feng,  Chenchen and Song,  Chao and Liu,  Yuejuan and Qian,  Fengcui and Gao,  Yu and Ning,  Ziyu and Wang,  Qiuyu and Jiang,  Yong and Li,  Yanyu and Li,  Meng and Chen,  Jiaxin and Zhang,  Jian and Li,  Chunquan},
  year = {2019},
  month = oct,
  pages = {D93–D100}
}

@inbook{bauprc,
  title = {Master Your Metrics with Calibration},
  ISBN = {9783030445843},
  ISSN = {1611-3349},
  url = {http://dx.doi.org/10.1007/978-3-030-44584-3_36},
  DOI = {10.1007/978-3-030-44584-3_36},
  booktitle = {Advances in Intelligent Data Analysis XVIII},
  publisher = {Springer International Publishing},
  author = {Siblini,  Wissam and Fréry,  Jordan and He-Guelton,  Liyun and Oblé,  Frédéric and Wang,  Yi-Qing},
  year = {2020},
  pages = {457–469}
}

@article{erygast,
  title={A single-cell molecular map of mouse gastrulation and early organogenesis},
  volume={566},
  ISSN={1476-4687},
  url={http://dx.doi.org/10.1038/s41586-019-0933-9},
  DOI={10.1038/s41586-019-0933-9},
  number={7745},
  journal={Nature},
  publisher={Springer Science and Business Media LLC},
  author={Pijuan-Sala, Blanca and Griffiths, Jonathan A. and Guibentif, Carolina and Hiscock, Tom W. and Jawaid, Wajid and Calero-Nieto, Fernando J. and Mulas, Carla and Ibarra-Soria, Ximena and Tyser, Richard C. V. and Ho, Debbie Lee Lian and Reik, Wolf and Srinivas, Shankar and Simons, Benjamin D. and Nichols, Jennifer and Marioni, John C. and Göttgens, Berthold},
  year={2019},
  month=feb,
  pages={490–495}
}

@article{mofacell,
  title = {Multicellular factor analysis of single-cell data for a tissue-centric understanding of disease},
  volume = {12},
  ISSN = {2050-084X},
  url = {http://dx.doi.org/10.7554/eLife.93161},
  DOI = {10.7554/elife.93161},
  journal = {eLife},
  publisher = {eLife Sciences Publications,  Ltd},
  author = {Ramirez Flores,  Ricardo Omar and Lanzer,  Jan David and Dimitrov,  Daniel and Velten,  Britta and Saez-Rodriguez,  Julio},
  year = {2023},
  month = nov 
}

@article{scanpy,
  title = {SCANPY: large-scale single-cell gene expression data analysis},
  volume = {19},
  ISSN = {1474-760X},
  url = {http://dx.doi.org/10.1186/s13059-017-1382-0},
  DOI = {10.1186/s13059-017-1382-0},
  number = {1},
  journal = {Genome Biology},
  publisher = {Springer Science and Business Media LLC},
  author = {Wolf,  F. Alexander and Angerer,  Philipp and Theis,  Fabian J.},
  year = {2018},
  month = feb 
}

@article{paga,
  title = {PAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells},
  volume = {20},
  ISSN = {1474-760X},
  url = {http://dx.doi.org/10.1186/s13059-019-1663-x},
  DOI = {10.1186/s13059-019-1663-x},
  number = {1},
  journal = {Genome Biology},
  publisher = {Springer Science and Business Media LLC},
  author = {Wolf,  F. Alexander and Hamey,  Fiona K. and Plass,  Mireya and Solana,  Jordi and Dahlin,  Joakim S. and G\"{o}ttgens,  Berthold and Rajewsky,  Nikolaus and Simon,  Lukas and Theis,  Fabian J.},
  year = {2019},
  month = mar 
}

@article{pax5,
  title = {Pax5: the guardian of B cell identity and function},
  volume = {8},
  ISSN = {1529-2916},
  url = {http://dx.doi.org/10.1038/ni1454},
  DOI = {10.1038/ni1454},
  number = {5},
  journal = {Nature Immunology},
  publisher = {Springer Science and Business Media LLC},
  author = {Cobaleda,  César and Schebesta,  Alexandra and Delogu,  Alessio and Busslinger,  Meinrad},
  year = {2007},
  month = apr,
  pages = {463–470}
}

@article{aucell,
  title = {SCENIC: single-cell regulatory network inference and clustering},
  volume = {14},
  ISSN = {1548-7105},
  url = {http://dx.doi.org/10.1038/nmeth.4463},
  DOI = {10.1038/nmeth.4463},
  number = {11},
  journal = {Nature Methods},
  publisher = {Springer Science and Business Media LLC},
  author = {Aibar,  Sara and González-Blas,  Carmen Bravo and Moerman,  Thomas and Huynh-Thu,  V\^an Anh and Imrichova,  Hana and Hulselmans,  Gert and Rambow,  Florian and Marine,  Jean-Christophe and Geurts,  Pierre and Aerts,  Jan and van den Oord,  Joost and Atak,  Zeynep Kalender and Wouters,  Jasper and Aerts,  Stein},
  year = {2017},
  month = oct,
  pages = {1083–1086}
}

@article{gsea,
  title = {Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles},
  volume = {102},
  ISSN = {1091-6490},
  url = {http://dx.doi.org/10.1073/pnas.0506580102},
  DOI = {10.1073/pnas.0506580102},
  number = {43},
  journal = {Proceedings of the National Academy of Sciences},
  publisher = {Proceedings of the National Academy of Sciences},
  author = {Subramanian,  Aravind and Tamayo,  Pablo and Mootha,  Vamsi K. and Mukherjee,  Sayan and Ebert,  Benjamin L. and Gillette,  Michael A. and Paulovich,  Amanda and Pomeroy,  Scott L. and Golub,  Todd R. and Lander,  Eric S. and Mesirov,  Jill P.},
  year = {2005},
  month = sep,
  pages = {15545–15550}
}

@article{gsva,
  title = {GSVA: gene set variation analysis for microarray and RNA-Seq data},
  volume = {14},
  ISSN = {1471-2105},
  url = {http://dx.doi.org/10.1186/1471-2105-14-7},
  DOI = {10.1186/1471-2105-14-7},
  number = {1},
  journal = {BMC Bioinformatics},
  publisher = {Springer Science and Business Media LLC},
  author = {H\"{a}nzelmann,  Sonja and Castelo,  Robert and Guinney,  Justin},
  year = {2013},
  month = jan 
}

@inproceedings{xgboost,
  series = {KDD ’16},
  title = {XGBoost: A Scalable Tree Boosting System},
  url = {http://dx.doi.org/10.1145/2939672.2939785},
  DOI = {10.1145/2939672.2939785},
  booktitle = {Proceedings of the 22nd ACM SIGKDD International Conference on Knowledge Discovery and Data Mining},
  publisher = {ACM},
  author = {Chen,  Tianqi and Guestrin,  Carlos},
  year = {2016},
  month = aug,
  pages = {785–794},
  collection = {KDD ’16}
}

@article{ora,
  title = {On the Interpretation of χ 2 from Contingency Tables,  and the Calculation of P},
  volume = {85},
  ISSN = {0952-8385},
  url = {http://dx.doi.org/10.2307/2340521},
  DOI = {10.2307/2340521},
  number = {1},
  journal = {Journal of the Royal Statistical Society},
  publisher = {JSTOR},
  author = {Fisher,  R. A.},
  year = {1922},
  month = jan,
  pages = {87}
}

@article{viper,
  title = {Functional characterization of somatic mutations in cancer using network-based inference of protein activity},
  volume = {48},
  ISSN = {1546-1718},
  url = {http://dx.doi.org/10.1038/ng.3593},
  DOI = {10.1038/ng.3593},
  number = {8},
  journal = {Nature Genetics},
  publisher = {Springer Science and Business Media LLC},
  author = {Alvarez,  Mariano J and Shen,  Yao and Giorgi,  Federico M and Lachmann,  Alexander and Ding,  B Belinda and Ye,  B Hilda and Califano,  Andrea},
  year = {2016},
  month = jun,
  pages = {838–847}
}

@article{zscore,
  title = {Robust inference of kinase activity using functional networks},
  volume = {12},
  ISSN = {2041-1723},
  url = {http://dx.doi.org/10.1038/s41467-021-21211-6},
  DOI = {10.1038/s41467-021-21211-6},
  number = {1},
  journal = {Nature Communications},
  publisher = {Springer Science and Business Media LLC},
  author = {Yılmaz,  Serhan and Ayati,  Marzieh and Schlatzer,  Daniela and undefinedi\c{c}ek,  A. Erc\"{u}ment and Chance,  Mark R. and Koyut\"{u}rk,  Mehmet},
  year = {2021},
  month = feb 
}
