RISSO, DAVIDE
RISSO, DAVIDE
Dipartimento di Scienze Statistiche
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
Guided structure learning of DAGs for count data
2024 Nguyen, Thi Kim Hue; Chiogna, Monica; Risso, Davide; Banzato, Erika
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
A multimodal cell census and atlas of the mammalian primary motor cortex
2021 Callaway, Edward M.; Dong, Hong-Wei; Ecker, Joseph R.; Hawrylycz, Michael J.; Huang, Z. Josh; Lein, Ed S.; Ngai, John; Osten, Pavel; Ren, Bing; Tolias, Andreas Savas; White, Owen; Zeng, Hongkui; Zhuang, Xiaowei; Ascoli, Giorgio A.; Behrens, M. Margarita; Chun, Jerold; Feng, Guoping; Gee, James C.; Ghosh, Satrajit S.; Halchenko, Yaroslav O.; Hertzano, Ronna; Lim, Byung Kook; Martone, Maryann E.; Ng, Lydia; Pachter, Lior; Ropelewski, Alexander J.; Tickle, Timothy L.; Yang, X. William; Zhang, Kun; Bakken, Trygve E.; Berens, Philipp; Daigle, Tanya L.; Harris, Julie A.; Jorstad, Nikolas L.; Kalmbach, Brian E.; Kobak, Dmitry; Li, Yang Eric; Liu, Hanqing; Matho, Katherine S.; Mukamel, Eran A.; Naeemi, Maitham; Scala, Federico; Tan, Pengcheng; Ting, Jonathan T.; Xie, Fangming; Zhang, Meng; Zhang, Zhuzhu; Zhou, Jingtian; Zingg, Brian; Armand, Ethan; Yao, Zizhen; Bertagnolli, Darren; Casper, Tamara; Crichton, Kirsten; Dee, Nick; Diep, Dinh; Ding, Song-Lin; Dong, Weixiu; Dougherty, Elizabeth L.; Fong, Olivia; Goldman, Melissa; Goldy, Jeff; Hodge, Rebecca D.; Hu, Lijuan; Keene, C. Dirk; Krienen, Fenna M.; Kroll, Matthew; Lake, Blue B.; Lathia, Kanan; Linnarsson, Sten; Liu, Christine S.; Macosko, Evan Z.; Mccarroll, Steven A.; Mcmillen, Delissa; Nadaf, Naeem M.; Nguyen, Thuc Nghi; Palmer, Carter R.; Pham, Thanh; Plongthongkum, Nongluk; Reed, Nora M.; Regev, Aviv; Rimorin, Christine; Romanow, William J.; Savoia, Steven; Siletti, Kimberly; Smith, Kimberly; Sulc, Josef; Tasic, Bosiljka; Tieu, Michael; Torkelson, Amy; Tung, Herman; van Velthoven, Cindy T. J.; Vanderburg, Charles R.; Yanny, Anna Marie; Fang, Rongxin; Hou, Xiaomeng; Lucero, Jacinta D.; Osteen, Julia K.; Pinto-Duarte, Antonio; Poirion, Olivier; Preissl, Sebastian; Wang, Xinxin; Aldridge, Andrew I.; Bartlett, Anna; Boggeman, Lara; O’Connor, Carolyn; Castanon, Rosa G.; Chen, Huaming; Fitzpatrick, Conor; Luo, Chongyuan; Nery, Joseph R.; Nunn, Michael; Rivkin, Angeline C.; Tian, Wei; Dominguez, Bertha; Ito-Cole, Tony; Jacobs, Matthew; Jin, Xin; Lee, Cheng-Ta; Lee, Kuo-Fen; Miyazaki, Paula Assakura; Pang, Yan; Rashid, Mohammad; Smith, Jared B.; Vu, Minh; Williams, Elora; Biancalani, Tommaso; Booeshaghi, A. Sina; Crow, Megan; Dudoit, Sandrine; Fischer, Stephan; Gillis, Jesse; Hu, Qiwen; Kharchenko, Peter V.; Niu, Sheng-Yong; Ntranos, Vasilis; Purdom, Elizabeth; Risso, Davide; de Bézieux, Hector Roux; Somasundaram, Saroja; Street, Kelly; Svensson, Valentine; Vaishnav, Eeshit Dhaval; Van den Berge, Koen; Welch, Joshua D.; An, Xu; Bateup, Helen S.; Bowman, Ian; Chance, Rebecca K.; Foster, Nicholas N.; Galbavy, William; Gong, Hui; Gou, Lin; Hatfield, Joshua T.; Hintiryan, Houri; Hirokawa, Karla E.; Kim, Gukhan; Kramer, Daniel J.; Li, Anan; Li, Xiangning; Luo, Qingming; Muñoz-Castañeda, Rodrigo; Stafford, David A.; Feng, Zhao; Jia, Xueyan; Jiang, Shengdian; Jiang, Tao; Kuang, Xiuli; Larsen, Rachael; Lesnar, Phil; Li, Yaoyao; Li, Yuanyuan; Liu, Lijuan; Peng, Hanchuan; Qu, Lei; Ren, Miao; Ruan, Zongcai; Shen, Elise; Song, Yuanyuan; Wakeman, Wayne; Wang, Peng; Wang, Yimin; Wang, Yun; Yin, Lulu; Yuan, Jing; Zhao, Sujun; Zhao, Xuan; Narasimhan, Arun; Palaniswamy, Ramesh; Banerjee, Samik; Ding, Liya; Huilgol, Dhananjay; Huo, Bingxing; Kuo, Hsien-Chi; Laturnus, Sophie; Li, Xu; Mitra, Partha P.; Mizrachi, Judith; Wang, Quanxin; Xie, Peng; Xiong, Feng; Yu, Yang; Eichhorn, Stephen W.; Berg, Jim; Bernabucci, Matteo; Bernaerts, Yves; Cadwell, Cathryn René; Castro, Jesus Ramon; Dalley, Rachel; Hartmanis, Leonard; Horwitz, Gregory D.; Jiang, Xiaolong; Ko, Andrew L.; Miranda, Elanine; Mulherkar, Shalaka; Nicovich, Philip R.; Owen, Scott F.; Sandberg, Rickard; Sorensen, Staci A.; Tan, Zheng Huan; Allen, Shona; Hockemeyer, Dirk; Lee, Angus Y.; Veldman, Matthew B.; Adkins, Ricky S.; Ament, Seth A.; Bravo, Héctor Corrada; Carter, Robert; Chatterjee, Apaala; Colantuoni, Carlo; Crabtree, Jonathan; Creasy, Heather; Felix, Victor; Giglio, Michelle; Herb, Brian R.; Kancherla, Jayaram; Mahurkar, Anup; Mccracken, Carrie; Nickel, Lance; Olley, Dustin; Orvis, Joshua; Schor, Michael; Hood, Greg; Dichter, Benjamin; Grauer, Michael; Helba, Brian; Bandrowski, Anita; Barkas, Nikolaos; Carlin, Benjamin; D’Orazi, Florence D.; Degatano, Kylee; Gillespie, Thomas H.; Khajouei, Farzaneh; Konwar, Kishori; Thompson, Carol; Kelly, Kathleen; Mok, Stephanie; Sunkin, Susan
A spatially resolved brain region- and cell type-specific isoform atlas of the postnatal mouse brain
2021 Joglekar, A.; Prjibelski, A.; Mahfouz, A.; Collier, P.; Lin, S.; Schlusche, A. K.; Marrocco, J.; Williams, S. R.; Haase, B.; Hayes, A.; Chew, J. G.; Weisenfeld, N. I.; Wong, M. Y.; Stein, A. N.; Hardwick, S. A.; Hunt, T.; Wang, Q.; Dieterich, C.; Bent, Z.; Fedrigo, O.; Sloan, S. A.; Risso, D.; Jarvis, E. D.; Flicek, P.; Luo, W.; Pitt, G. S.; Frankish, A.; Smit, A. B.; Ross, M. E.; Tilgner, H. U.