T. K. H. Nguyen, K. Van den Berge, M. Chiogna, D. Risso (2020). Structure learning for zero-inflated counts, with an application to single-cell RNA sequencing data. arXiv.
F. Agostinis, C. Romualdi, G. Sales, D. Risso (2021) NewWave: a scalable R/Bioconductor package for the dimensionality reduction and batch effect removal of single-cell RNA-seq data bioRxiv.
M. Borella, G. Martello, D. Risso, C. Romualdi (2021) PsiNorm: a scalable normalization for single-cell RNA-seq data. bioRxiv.
D. Righelli, L. M. Weber, H. L. Crowell, B. Pardo, L. Collado-Torres, S. Ghazanfar, A. T. L. Lun, S. C. Hicks, D. Risso (2021) SpatialExperiment: infrastructure for spatially resolved transcriptomics data in R using Bioconductor. bioRxiv.
H. Roux de Bezieux, K. Street, S. Fischer, K. Van den Berge, R. Chance, D. Risso, J. Gillis, J. Ngai, E. Purdom, S. Dudoit (2020) Improving replicability in single-cell RNA-Seq cell type discovery with Dune. bioRxiv.
Z. Yao, …, D. Risso, …, BRAIN Initiative Cell Census Network (BICCN), H. Zeng, E. A. Mukamel (2020). An integrated transcriptomic and epigenomic atlas of mouse primary motor cortex cell types. bioRxiv.
BRAIN Initiative Cell Census Network (BICCN), …, D. Risso, … (2020). A multimodal cell census and atlas of the mammalian primary motor cortex. bioRxiv.
D. Risso, S. M. Pagnotta (2021) Per-sample standardization and asymmetric winsorization lead to accurate clustering of RNA-seq expression profiles. Bioinformatics 37(16):2356-2364.
S. Hicks, R. Liu, Y. Ni, E. Purdom, D. Risso (2021) mbkmeans: fast clustering for single cell data using mini-batch k-means. PLOS Computational Biology 17(1):e1008625.
A. Joglekar, A. Prjibelski, A. Mahfouz, P. Collier, S. Lin, A. K. Schlusche, J. Marrocco, S. R. Williams, B. Haase, A. Hayes, J. G. Chew, N. I. Weisenfeld, M. Y. Wong, A. N. Stein, S. Hardwick, T. Hunt, Q. Wang, C. Dieterich, Z. Bent, O. Fedrigo, S. A. Sloan, D. Risso, E. D. Jarvis, P. Flicek, W. Luo, G. S. Pitt, A. Frankish, A. B. Smit, M. E. Ross, H. U. Tilgner (2021) A spatially resolved brain region- and cell type-specific isoform atlas of the postnatal mouse brain. Nature Communications 12:463.
M. Calgaro, C. Romualdi, L. Waldron, D. Risso, N. Vitulo (2020). Assessment of statistical methods from single cell, bulk RNA-seq and metagenomics applied to microbiome data. Genome Biology 21:191.
D. H. Brann, T. Tsukahara, C. Weinreb, M. Lipovsek, K. Van den Berge, B. Gong, R. Chance, I. C. Macaulay, H. Chou, R. Fletcher, D. Das, K. Street, H. Roux de Bezieux, Y. Choi, D. Risso, S. Dudoit, E. Purdom, J. S. Mill, R. Abi Hachem, H. Matsunami, D. W. Logan, B. J. Goldstein, M. S. Grubb, J. Ngai, S. R. Datta (2020) Non-neuronal expression of SARS-CoV-2 entry genes in the olfactory system suggests mechanisms underlying COVID-19-associated anosmia. Science Advances 6:eabc5801.
J. Y. Xue, Y. Zhao, J. Aronowitz, T. T. Mai, A. Vides, B. Qeriqi, D. Kim, C. Li, E. de Stanchina, L. Mazutis, D. Risso, P. Lito (2020). Rapid non-uniform adaptation to conformation-specific KRAS-G12C inhibition. Nature 577:421-425.
R. A. Amezquita, A. T. L. Lun, E. Becht, V. J. Carey, L. N. Carpp, L. Geistlinger, F. Marini, K. Rue-Albrecht, D. Risso, C. Soneson, L. Waldron, H. Pag`es, M. Smith, W. Huber, M. Morgan, R. Gottardo, S. C. Hicks (2020). Orchestrating Single-Cell Analysis with Bioconductor. Nature Methods 17:137-145.
M. Furnari, L. H. Eusebi, E. Savarino, C. Petruzzellis, G. Esposito, M. Maida, L. Ricciardiello, S. Pecere, A. Buda, M. De Bona, C. Spada, E. Di Giulio, G. Costamagna, I. Boskoski, E. G. Giannini, S. Angeletti, F. Barbaro, M. Brunacci, M. Cazzato, V. D. Corleto, M. G. Demarzo, E. Giambruno, G. Morreale, A. Moscatelli, M. Pesenti, L. Polese, D. Risso, G. Tamanini, F. Zingone (2020). Effects of SARS-CoV-2 emergency measures on highrisk lesions detection: a multicentre crosssectional study. Gut [Online first].
M. B. Cole∗, D. Risso∗, A. Wagner, D. DeTomaso, J. Ngai, E. Purdom, S. Dudoit, N. Yosef (2019). Performance Assessment and Selection of Normalization Procedures for Single-Cell RNA-Seq. Cell Systems 8(4) 315-328 (∗=joint first authorship.)
D. Risso, L. Purvis, R. Fletcher, D. Das, J. Ngai, S. Dudoit, E. Purdom (2018). clusterExperiment and RSEC: A Bioconductor package and framework for clustering of single-cell and other large gene expression datasets. PLoS Computational Biology. 14(9):e1006378.
K. Street, D. Risso, R. B. Fletcher, D. Das, J. Ngai, N. Yosef, E. Purdom, S. Dudoit (2018). Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics. BMC Genomics. 19:477.
D. Risso, F. Perraudeau, S. Gribkova, S. Dudoit, JP. Vert (2018). A general and flexible method for signal extraction from single-cell RNA-seq data. Nature Communications 9:284.
C. Vallejos∗, D.Risso∗, A. Scialdone∗, S. Dudoit, J. Marioni (2017). Challenges in the normalization of single-cell RNA sequencing datasets. Nature Methods 14 565–571.
Y J Choi*, C Lin*, D Risso*, S Chen, T A Kim, M H Tan, J B Li, Y Wu, C Chen, Z Xuan, T Macfarlan, W Peng, KC Lloyd, S Y Kim, T P Speed, L He (2017). Deficiency of microRNA miR-34a expands cell fate potential in pluripotent stem cells. Science.
L. Peixoto, D. Risso, S. G. Poplawski, M. E. Wimmer, T. P. Speed, M. A. Wood, T. Abel (2015). How data analysis affects power, reproducibility and biological insight of RNA-seq studies in complex datasets. Nucleic Acids Research, 43 (16), 7664-7674.
D. Risso, J. Ngai, T.P. Speed and S. Dudoit (2014). Normalization of RNA-seq data using factor analysis of control genes or samples. Nature Biotechnology, 32, 896-902.
D. Risso, K. Schwartz, G. Sherlock, S. Dudoit (2011). GC-content normalization for RNA-Seq data. BMC Bioinformatics, 12, 480.
D. Risso, M.S. Massa, M. Chiogna, C. Romualdi (2009). A modified LOESS normalization applied to microRNA arrays: a comparative evaluation. Bioinformatics, 25(20), 2685-2691.