References

References#

[AGBM+17]

Sara Aibar, Carmen Bravo González-Blas, Thomas Moerman, Vân Anh Huynh-Thu, Hana Imrichova, Gert Hulselmans, Florian Rambow, Jean-Christophe Marine, Pierre Geurts, Jan Aerts, Joost van den Oord, Zeynep Kalender Atak, Jasper Wouters, and Stein Aerts. Scenic: single-cell regulatory network inference and clustering. Nature Methods, 14(11):1083–1086, October 2017. URL: http://dx.doi.org/10.1038/nmeth.4463, doi:10.1038/nmeth.4463.

[ASG+16]

Mariano J Alvarez, Yao Shen, Federico M Giorgi, Alexander Lachmann, B Belinda Ding, B Hilda Ye, and Andrea Califano. Functional characterization of somatic mutations in cancer using network-based inference of protein activity. Nature Genetics, 48(8):838–847, June 2016. URL: http://dx.doi.org/10.1038/ng.3593, doi:10.1038/ng.3593.

[BiMVSB+22]

Pau Badia-i-Mompel, Jesús Vélez Santiago, Jana Braunger, Celina Geiss, Daniel Dimitrov, Sophia Müller-Dott, Petr Taus, Aurelien Dugourd, Christian H Holland, Ricardo O Ramirez Flores, and Julio Saez-Rodriguez. Decoupler: ensemble of computational methods to infer biological activities from omics data. Bioinformatics Advances, January 2022. URL: http://dx.doi.org/10.1093/bioadv/vbac016, doi:10.1093/bioadv/vbac016.

[BiMWMullerD+23]

Pau Badia-i-Mompel, Lorna Wessels, Sophia Müller-Dott, Rémi Trimbour, Ricardo O. Ramirez Flores, Ricard Argelaguet, and Julio Saez-Rodriguez. Gene regulatory network inference in the era of single-cell multi-omics. Nature Reviews Genetics, 24(11):739–754, June 2023. URL: http://dx.doi.org/10.1038/s41576-023-00618-5, doi:10.1038/s41576-023-00618-5.

[CG16]

Tianqi Chen and Carlos Guestrin. Xgboost: a scalable tree boosting system. In Proceedings of the 22nd ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, KDD ’16, 785–794. ACM, August 2016. URL: http://dx.doi.org/10.1145/2939672.2939785, doi:10.1145/2939672.2939785.

[CSDB07]

César Cobaleda, Alexandra Schebesta, Alessio Delogu, and Meinrad Busslinger. Pax5: the guardian of b cell identity and function. Nature Immunology, 8(5):463–470, April 2007. URL: http://dx.doi.org/10.1038/ni1454, doi:10.1038/ni1454.

[DSchaferF+24]

Daniel Dimitrov, Philipp Sven Lars Schäfer, Elias Farr, Pablo Rodriguez-Mier, Sebastian Lobentanzer, Pau Badia-i-Mompel, Aurelien Dugourd, Jovan Tanevski, Ricardo Omar Ramirez Flores, and Julio Saez-Rodriguez. Liana+ provides an all-in-one framework for cell–cell communication inference. Nature Cell Biology, 26(9):1613–1622, September 2024. URL: http://dx.doi.org/10.1038/s41556-024-01469-w, doi:10.1038/s41556-024-01469-w.

[FSL+19]

Chenchen Feng, Chao Song, Yuejuan Liu, Fengcui Qian, Yu Gao, Ziyu Ning, Qiuyu Wang, Yong Jiang, Yanyu Li, Meng Li, Jiaxin Chen, Jian Zhang, and Chunquan Li. Knocktf: a comprehensive human gene expression profile database with knockdown/knockout of transcription factors. Nucleic Acids Research, 48(D1):D93–D100, October 2019. URL: http://dx.doi.org/10.1093/nar/gkz881, doi:10.1093/nar/gkz881.

[Fis22]

R. A. Fisher. On the interpretation of χ 2 from contingency tables, and the calculation of p. Journal of the Royal Statistical Society, 85(1):87, January 1922. URL: http://dx.doi.org/10.2307/2340521, doi:10.2307/2340521.

[FGBjorkegren19]

Oscar Franzén, Li-Ming Gan, and Johan L M Björkegren. Panglaodb: a web server for exploration of mouse and human single-cell rna sequencing data. Database, January 2019. URL: http://dx.doi.org/10.1093/database/baz046, doi:10.1093/database/baz046.

[GAHI+19]

Luz Garcia-Alonso, Christian H. Holland, Mahmoud M. Ibrahim, Denes Turei, and Julio Saez-Rodriguez. Benchmark and integration of resources for the estimation of human transcription factor activities. Genome Research, 29(8):1363–1375, July 2019. URL: http://dx.doi.org/10.1101/gr.240663.118, doi:10.1101/gr.240663.118.

[HanzelmannCG13]

Sonja Hänzelmann, Robert Castelo, and Justin Guinney. Gsva: gene set variation analysis for microarray and rna-seq data. BMC Bioinformatics, January 2013. URL: http://dx.doi.org/10.1186/1471-2105-14-7, doi:10.1186/1471-2105-14-7.

[LMBiMRF+24]

Celia Lerma-Martin, Pau Badia-i-Mompel, Ricardo O. Ramirez Flores, Patricia Sekol, Philipp S. L. Schäfer, Christian J. Riedl, Annika Hofmann, Thomas Thäwel, Florian Wünnemann, Miguel A. Ibarra-Arellano, Tim Trobisch, Philipp Eisele, Denis Schapiro, Maximilian Haeussler, Simon Hametner, Julio Saez-Rodriguez, and Lucas Schirmer. Cell type mapping reveals tissue niches and interactions in subcortical multiple sclerosis lesions. Nature Neuroscience, 27(12):2354–2365, November 2024. URL: http://dx.doi.org/10.1038/s41593-024-01796-z, doi:10.1038/s41593-024-01796-z.

[LSP+11]

Arthur Liberzon, Aravind Subramanian, Reid Pinchback, Helga Thorvaldsdóttir, Pablo Tamayo, and Jill P Mesirov. Molecular signatures database (MSigDB) 3.0. Bioinformatics, 27(12):1739–1740, June 2011.

[MullerDTV+23]

Sophia Müller-Dott, Eirini Tsirvouli, Miguel Vazquez, Ricardo O Ramirez Flores, Pau Badia-i-Mompel, Robin Fallegger, Dénes Türei, Astrid Lægreid, and Julio Saez-Rodriguez. Expanding the coverage of regulons from high-confidence prior knowledge for accurate estimation of transcription factor activities. Nucleic Acids Research, 51(20):10934–10949, October 2023. URL: http://dx.doi.org/10.1093/nar/gkad841, doi:10.1093/nar/gkad841.

[MTCA23]

Boris Muzellec, Maria Teleńczuk, Vincent Cabeli, and Mathieu Andreux. Pydeseq2: a python package for bulk rna-seq differential expression analysis. Bioinformatics, September 2023. URL: http://dx.doi.org/10.1093/bioinformatics/btad547, doi:10.1093/bioinformatics/btad547.

[PSGG+19]

Blanca Pijuan-Sala, Jonathan A. Griffiths, Carolina Guibentif, Tom W. Hiscock, Wajid Jawaid, Fernando J. Calero-Nieto, Carla Mulas, Ximena Ibarra-Soria, Richard C. V. Tyser, Debbie Lee Lian Ho, Wolf Reik, Shankar Srinivas, Benjamin D. Simons, Jennifer Nichols, John C. Marioni, and Berthold Göttgens. A single-cell molecular map of mouse gastrulation and early organogenesis. Nature, 566(7745):490–495, February 2019. URL: http://dx.doi.org/10.1038/s41586-019-0933-9, doi:10.1038/s41586-019-0933-9.

[RFLD+23]

Ricardo Omar Ramirez Flores, Jan David Lanzer, Daniel Dimitrov, Britta Velten, and Julio Saez-Rodriguez. Multicellular factor analysis of single-cell data for a tissue-centric understanding of disease. eLife, November 2023. URL: http://dx.doi.org/10.7554/eLife.93161, doi:10.7554/elife.93161.

[RPW+15]

Matthew E. Ritchie, Belinda Phipson, Di Wu, Yifang Hu, Charity W. Law, Wei Shi, and Gordon K. Smyth. Limma powers differential expression analyses for rna-sequencing and microarray studies. Nucleic Acids Research, 43(7):e47–e47, January 2015. URL: http://dx.doi.org/10.1093/nar/gkv007, doi:10.1093/nar/gkv007.

[RMS09]

Mark D. Robinson, Davis J. McCarthy, and Gordon K. Smyth. <tt>edger</tt>: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics, 26(1):139–140, November 2009. URL: http://dx.doi.org/10.1093/bioinformatics/btp616, doi:10.1093/bioinformatics/btp616.

[SKK+18]

Michael Schubert, Bertram Klinger, Martina Klünemann, Anja Sieber, Florian Uhlitz, Sascha Sauer, Mathew J. Garnett, Nils Blüthgen, and Julio Saez-Rodriguez. Perturbation-response genes reveal signaling footprints in cancer gene expression. Nature Communications, January 2018. URL: http://dx.doi.org/10.1038/s41467-017-02391-6, doi:10.1038/s41467-017-02391-6.

[SFHG+20]

Wissam Siblini, Jordan Fréry, Liyun He-Guelton, Frédéric Oblé, and Yi-Qing Wang. Master Your Metrics with Calibration, pages 457–469. Springer International Publishing, 2020. URL: http://dx.doi.org/10.1007/978-3-030-44584-3_36, doi:10.1007/978-3-030-44584-3_36.

[SCD+20]

Aymeric Silvin, Nicolas Chapuis, Garett Dunsmore, Anne-Gaëlle Goubet, Agathe Dubuisson, Lisa Derosa, Carole Almire, Clémence Hénon, Olivier Kosmider, Nathalie Droin, Philippe Rameau, Cyril Catelain, Alexia Alfaro, Charles Dussiau, Chloé Friedrich, Elise Sourdeau, Nathalie Marin, Tali-Anne Szwebel, Delphine Cantin, Luc Mouthon, Didier Borderie, Marc Deloger, Delphine Bredel, Severine Mouraud, Damien Drubay, Muriel Andrieu, Anne-Sophie Lhonneur, Véronique Saada, Annabelle Stoclin, Christophe Willekens, Fanny Pommeret, Frank Griscelli, Lai Guan Ng, Zheng Zhang, Pierre Bost, Ido Amit, Fabrice Barlesi, Aurélien Marabelle, Frédéric Pène, Bertrand Gachot, Fabrice André, Laurence Zitvogel, Florent Ginhoux, Michaela Fontenay, and Eric Solary. Elevated calprotectin and abnormal myeloid cell subsets discriminate severe from mild covid-19. Cell, 182(6):1401–1418.e18, September 2020. URL: http://dx.doi.org/10.1016/j.cell.2020.08.002, doi:10.1016/j.cell.2020.08.002.

[SGK+21]

Jordan W. Squair, Matthieu Gautier, Claudia Kathe, Mark A. Anderson, Nicholas D. James, Thomas H. Hutson, Rémi Hudelle, Taha Qaiser, Kaya J. E. Matson, Quentin Barraud, Ariel J. Levine, Gioele La Manno, Michael A. Skinnider, and Grégoire Courtine. Confronting false discoveries in single-cell differential expression. Nature Communications, September 2021. URL: http://dx.doi.org/10.1038/s41467-021-25960-2, doi:10.1038/s41467-021-25960-2.

[STM+05]

Aravind Subramanian, Pablo Tamayo, Vamsi K. Mootha, Sayan Mukherjee, Benjamin L. Ebert, Michael A. Gillette, Amanda Paulovich, Scott L. Pomeroy, Todd R. Golub, Eric S. Lander, and Jill P. Mesirov. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proceedings of the National Academy of Sciences, 102(43):15545–15550, September 2005. URL: http://dx.doi.org/10.1073/pnas.0506580102, doi:10.1073/pnas.0506580102.

[TureiKSR16]

Dénes Türei, Tamás Korcsmáros, and Julio Saez-Rodriguez. Omnipath: guidelines and gateway for literature-curated signaling pathway resources. Nature Methods, 13(12):966–967, November 2016. URL: http://dx.doi.org/10.1038/nmeth.4077, doi:10.1038/nmeth.4077.

[VBH+23]

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

[WAT18]

F. Alexander Wolf, Philipp Angerer, and Fabian J. Theis. Scanpy: large-scale single-cell gene expression data analysis. Genome Biology, February 2018. URL: http://dx.doi.org/10.1186/s13059-017-1382-0, doi:10.1186/s13059-017-1382-0.

[WHP+19]

F. Alexander Wolf, Fiona K. Hamey, Mireya Plass, Jordi Solana, Joakim S. Dahlin, Berthold Göttgens, Nikolaus Rajewsky, Lukas Simon, and Fabian J. Theis. Paga: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells. Genome Biology, March 2019. URL: http://dx.doi.org/10.1186/s13059-019-1663-x, doi:10.1186/s13059-019-1663-x.

[YLG+20]

Usman Yaqoob, Fanghong Luo, Thomas Greuter, Nidhi Jalan Sakrikar, Tejasav S. Sehrawat, Jianwen Lu, Xiao Hu, Jinhang Gao, Enis Kostallari, Jingbiao Chen, Juan Pablo Arab, Rosa Martin-Mateos, Sheng Cao, and Vijay H. Shah. Gipc-regulated igfbp-3 promotes hsc migration in vitro and portal hypertension in vivo through a β1-integrin pathway. Cellular and Molecular Gastroenterology and Hepatology, 10(3):545–559, 2020. URL: http://dx.doi.org/10.1016/j.jcmgh.2020.05.005, doi:10.1016/j.jcmgh.2020.05.005.

[YGJB21]

Bethan Yates, Kristian A Gray, Tamsin E M Jones, and Elspeth A Bruford. Updates to hcop: the hgnc comparison of orthology predictions tool. Briefings in Bioinformatics, May 2021. URL: http://dx.doi.org/10.1093/bib/bbab155, doi:10.1093/bib/bbab155.

[YAS+21]

Serhan Yılmaz, Marzieh Ayati, Daniela Schlatzer, A. Ercüment undefinediçek, Mark R. Chance, and Mehmet Koyutürk. Robust inference of kinase activity using functional networks. Nature Communications, February 2021. URL: http://dx.doi.org/10.1038/s41467-021-21211-6, doi:10.1038/s41467-021-21211-6.