RISSO, DAVIDE
RISSO, DAVIDE
Dipartimento di Scienze Statistiche
Differential detection workflows for multi-sample single-cell RNA-seq data
2025 Gilis, Jeroen; Perin, Laura; Malfait, Milan; L Crowell, Helena; Van Den Berge, Koen; Takele Assefa, Alemu; Verbist, Bie; Risso, Davide; Clement, Lieven
Guided structure learning of DAGs for count data
2025 Nguyen, Thi Kim Hue; Chiogna, Monica; Risso, Davide; Banzato, Erika
Pan-cancer immune and stromal deconvolution predicts clinical outcomes and mutation profiles
2025 Bhinder, Bhavneet; Friedl, Verena; Sethuraman, Sunantha; Risso, Davide; Chiotti, Kami E; Mashl, R Jay; Ellrott, Kyle P; Lee, Jordan A; Wong, Christopher K; Gyan, Kofi; Deshpande, Aditya; Imielinski, Marcin; Bareja, Rohan; Stuart, Josh; Peto, Myron; Hoadley, Katherine A; Lazar, Alexander J; Cherniack, Andrew D; Zhu, Jingchun; Cao, Shaolong; Rubin, Mark; Wang, Wenyi; Bathe, Oliver F; Robine, Nicolas; Ding, Li; Laird, Peter W; Zhou, Wanding; Shen, Hui; Thorsson, Vésteinn; Yeh, Jen Jen; Bailey, Matthew H; Zhou, Daniel Cui; Peng, Xianlu L; Goldman, Mary; Li, Yongsheng; Korkut, Anil; Sahni, Nidhi; Hayes, D Neil; Mensah, Michael K A; Felau, Ina; Kemal, Anab; Caesar-Johnson, Samantha; Demchok, John A; Yang, Liming; Ferguson, Martin L; Tarnuzzer, Roy; Wang, Zhining; Zenklusen, Jean C; Spellman, Paul; Elemento, Olivier
Spatially Informed Nonnegative Matrix Trifactorization for Coclustering Mass Spectrometry Data
2025 Sottosanti, Andrea; Denti, Francesco; Galimberti, Stefania; Risso, Davide; Capitoli, Giulia
A global transcriptional atlas of the effect of acute sleep deprivation in the mouse frontal cortex
2024 Ford, Kaitlyn; Zuin, Elena; Righelli, Dario; Medina, Elizabeth; Schoch, Hannah; Singletary, Kristan; Muheim, Christine; Frank, Marcos G.; Hicks, Stephanie C.; Risso, Davide; Peixoto, Lucia
Exploring public cancer gene expression signatures across bulk, single-cell and spatial transcriptomics data with signifinder Bioconductor package
2024 Pirrotta, Stefania; Masatti, Laura; Bortolato, Anna; Corrà, Anna; Pedrini, Fabiola; Aere, Martina; Esposito, Giovanni; Martini, Paolo; Risso, Davide; Romualdi, Chiara; Calura, Enrica
Improving replicability in single-cell RNA-Seq cell type discovery with Dune
2024 Roux de Bézieux, Hector; Street, Kelly; Fischer, Stephan; Van den Berge, Koen; Chance, Rebecca; Risso, Davide; Gillis, Jesse; Ngai, John; Purdom, Elizabeth; Dudoit, Sandrine
A Bartlett-type correction for likelihood ratio tests with application to testing equality of Gaussian graphical models
2023 Banzato, Erika; Chiogna, Monica; Djordjilović, Vera; Risso, Davide
benchdamic: benchmarking of differential abundance methods for microbiome data
2023 Calgaro, Matteo; Romualdi, Chiara; Risso, Davide; Vitulo, Nicola
Co-clustering of Spatially Resolved Transcriptomic Data
2023 Sottosanti, Andrea; Risso, Davide
Curated single cell multimodal landmark datasets for R/Bioconductor
2023 Eckenrode, Kelly B; Righelli, Dario; Ramos, Marcel; Argelaguet, Ricard; Vanderaa, Christophe; Geistlinger, Ludwig; Culhane, Aedin C; Gatto, Laurent; Carey, Vincent; Morgan, Martin; Risso, Davide; Waldron, Levi
Designing spatial transcriptomic experiments
2023 Righelli, Dario; Sottosanti, Andrea; Risso, Davide
Structure learning for zero-inflated counts with an application to single-cell RNA sequencing data
2023 Nguyen, THI KIM HUE; Van den Berge, Koen; Chiogna, Monica; Risso, Davide
Contributed discussion to "Bayesian Nonstationary and Nonparametric Covariance Estimation for Large Spatial Data"
2022 Sottosanti, Andrea; Risso, Davide; Castiglione, Cristian
NewWave: a scalable R/Bioconductor package for the dimensionality reduction and batch effect removal of single-cell RNA-seq data
2022 Agostinis, Federico; Romualdi, Chiara; Sales, Gabriele; Risso, Davide
Normalization benchmark of ATAC-seq datasets shows the importance of accounting for GC-content effects
2022 Van den Berge, Koen; Chou, Hsin-Jung; Roux de Bézieux, Hector; Street, Kelly; Risso, Davide; Ngai, John; Dudoit, Sandrine
PsiNorm: a scalable normalization for single-cell RNA-seq data
2022 Borella, Matteo; Martello, Graziano; Risso, Davide; Romualdi, Chiara
Receiver operating characteristic estimation and threshold selection criteria in three-class classification problems for clustered data
2022 To, DUC KHANH; Adimari, Gianfranco; Chiogna, Monica; Risso, Davide
SpatialExperiment: infrastructure for spatially resolved transcriptomics data in R using Bioconductor
2022 Righelli, Dario; Weber, Lukas M; Crowell, Helena L; Pardo, Brenda; Collado-Torres, Leonardo; Ghazanfar, Shila; Lun, Aaron T L; Hicks, Stephanie C; Risso, Davide
A mouse-specific retrotransposon drives a conserved Cdk2ap1 isoform essential for development
2021 Modzelewski, Andrew J.; Shao, Wanqing; Chen, Jingqi; Lee, Angus; Qi, Xin; Noon, Mackenzie; Tjokro, Kristy; Sales, Gabriele; Biton, Anne; Anand, Aparna; Speed, Terence P.; Xuan, Zhenyu; Wang, Ting; Risso, Davide; He, Lin