Improve enrichment analysis chapter

jupyter-book/conditions/gsea_pathway.bib

@@ -96,6 +96,140 @@ @article{schubert2018perturbation
   publisher={Nature Publishing Group}
 }
 
+@Article{jiang2021cytocig,
+  title={Systematic investigation of cytokine signaling activity at the tissue and single-cell levels},
+  author={Jiang, Peng and Zhang, Yu and Ru, Beibei and Yang, Yuan and Vu, Trang and Paul, Rohit and Mirza, Amer and Altan-Bonnet, Gr{\'e}goire and Liu, Lingrui and Ruppin, Eytan and Wakefield, Lalage and Wucherpfennig, Kai W.},
+  journal={Nature Methods},
+  volume={18},
+  number={10},
+  pages={1181-1191},
+  year={2021},
+  publisher={Nature Publishing Group}
+}
+
+@Article{mathur2018gsetcomp,
+  title={Gene set analysis methods: a systematic comparison},
+  author={Mathur, Ravi and Rotroff, Daniel and Ma, Jun and Shojaie, Ali and Motsinger-Reif, Alison},
+  journal={BioData Mining},
+  volume={11},
+  number={1},
+  pages={8},
+  year={2018},
+  publisher={Springer}
+}
+
+@Article{squair2021psbulk,
+  title={Confronting false discoveries in single-cell differential expression},
+  author={Squair, Jordan W. and Gautier, Matthieu and Kathe, Claudia and Anderson, Mark A. and James, Nicholas D. and Hutson, Thomas H. and Hudelle, R{\'e}mi 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, Gr{\'e}goire},
+  journal={Nature Communications},
+  volume={12},
+  number={1},
+  pages={5692},
+  year={2021},
+  publisher={Nature Publishing Group}
+}
+
+@article{dugourd2019footprint,
+  title={Footprint-based functional analysis of multiomic data},
+  author={Aurelien Dugourd and Julio Saez-Rodriguez},
+  journal={Current Opinion in Systems Biology},
+  volume={15},
+  pages={82-90},
+  year={2019},
+  publisher={Elsevier}
+}
+
+@Article{alvarez2016viper,
+  title={Functional characterization of somatic mutations in cancer using network-based inference of protein activity},
+  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}, 
+  journal={Nature Genetics},
+  volume={48},
+  number={8},
+  pages={838-847},
+  year={2016},
+  publisher={Nature Publishing Group}
+}
+
+@article{qoku2022muvi,
+  title={Encoding Domain Knowledge in Multi-view Latent Variable Models: A Bayesian Approach with Structured Sparsity},
+  author={Arber Qoku and Florian Buettner},
+  journal={arXiv},
+  year={2022}
+}
+
+@article{kunes2022spectra,
+  title={Supervised discovery of interpretable gene programs from single-cell data},
+  author={Kunes, Russell Z. and Walle, Thomas and Nawy, Tal and Pe{\textquoteright}er, Dana},
+  journal={bioRxiv},
+  year={2022}
+}
+
+@article{geistlinger2020gsetbench,
+  title={Toward a gold standard for benchmarking gene set enrichment analysis},
+  author={Geistlinger, Ludwig and Csaba, Gergely and Santarelli, Mara and Ramos, Marcel and Schiffer, Lucas and Turaga, Nitesh and Law, Charity and Davis, Sean and Carey, Vincent and Morgan, Martin and Zimmer, Ralf and Waldron, Levi},
+  journal={Briefings in Bioinformatics},
+  volume={22},
+  number={1},
+  pages={545-556},
+  year={2020},
+  publisher={Oxford University Press}
+}
+
+@article{szalai2020pwmethods,
+  title={Why do pathway methods work better than they should?},
+  author={Szalai, Bence and Saez-Rodriguez, Julio},
+  journal={FEBS Letters},
+  volume={594},
+  number={24},
+  pages={4189-4200},
+  year={2020},
+  publisher={John Wiley & Sons}
+}
+
+@article{crowell2020muscat,
+  title={muscat detects subpopulation-specific state transitions from multi-sample multi-condition single-cell transcriptomics data},
+  author={Crowell, Helena L. and Soneson, Charlotte and Germain, Pierre-Luc and Calini, Daniela and Collin, Ludovic and Raposo, Catarina and Malhotra, Dheeraj and Robinson, Mark D.},
+  journal={Nature Communications},
+  volume={11},
+  number={1},
+  pages={6077},
+  year={2020},
+  publisher={Nature Publishing Group}
+}
+
+@article{varemo2013piano,
+  title={Enriching the gene set analysis of genome-wide data by incorporating directionality of gene expression and combining statistical hypotheses and methods},
+  author={Väremo, Leif and Nielsen, Jens and Nookaew, Intawat},
+  journal={Nucleic Acids Research},
+  volume={41},
+  number={8},
+  pages={4378-4391},
+  year={2013},
+  publisher={Oxford University Press}
+}
+
+@article{alhamdoosh2016egsea,
+  title={Combining multiple tools outperforms individual methods in gene set enrichment analyses},
+  author={Alhamdoosh, Monther and Ng, Milica and Wilson, Nicholas J and Sheridan, Julie M and Huynh, Huy and Wilson, Michael J and Ritchie, Matthew E},
+    journal={Bioinformatics},
+    volume={33},
+    number={3},
+    pages={414-424},
+    year={2016},
+    publisher={Oxford University Press}
+}
+
+@article{turei2021omnipath,
+  title = {Integrated intra- and intercellular signaling knowledge for multicellular omics analysis},
+  author = {Türei, Dénes and Valdeolivas, Alberto and Gul, Lejla and Palacio-Escat, Nicolàs and Klein, Michal and Ivanova, Olga and Ölbei, Márton and Gábor, Attila and Theis, Fabian and Módos, Dezső and Korcsmáros, Tamás and Saez-Rodriguez, Julio},
+  journal = {Molecular Systems Biology},
+  volume = {17},
+  number = {3},
+  pages = {e9923},
+  year = {2021},
+  publisher={EMBO Press}
+}
+
 @article{garcia2019benchmark,
   title={Benchmark and integration of resources for the estimation of human transcription factor activities},
   author={Garcia-Alonso, Luz and Holland, Christian H and Ibrahim, Mahmoud M and Turei, Denes and Saez-Rodriguez, Julio},