SMGen: A Generator of Synthetic Models of Biochemical Reaction Networks
Riva, Simone G., Cazzaniga, Paolo, Nobile, Marco S., Spolaor, Simone, Rundo, Leonardo, Besozzi, Daniela, Tangherloni, Andrea
Published in Symmetry (Basel) (01.01.2022)
Published in Symmetry (Basel) (01.01.2022)
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Journal Article
MAGNETO: Cell type marker panel generator from single-cell transcriptomic data
Tangherloni, Andrea, Riva, Simone G., Myers, Brynelle, Buffa, Francesca M., Cazzaniga, Paolo
Published in Journal of biomedical informatics (01.11.2023)
Published in Journal of biomedical informatics (01.11.2023)
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Journal Article
GTAC enables parallel genotyping of multiple genomic loci with chromatin accessibility profiling in single cells
Turkalj, Sven, Jakobsen, Niels Asger, Groom, Angus, Metzner, Marlen, Riva, Simone G., Gür, E. Ravza, Usukhbayar, Batchimeg, Salazar, Mirian Angulo, Hentges, Lance D., Mickute, Gerda, Clark, Kevin, Sopp, Paul, Davies, James O.J., Hughes, Jim R., Vyas, Paresh
Published in Cell stem cell (04.05.2023)
Published in Cell stem cell (04.05.2023)
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Journal Article
CATCH-UP: A High-Throughput Upstream-Pipeline for Bulk ATAC-Seq and ChIP-Seq Data
Riva, Simone G, Georgiades, Emily, Gur, E Ravza, Baxter, Matthew, Hughes, Jim R
Published in Journal of visualized experiments (22.09.2023)
Published in Journal of visualized experiments (22.09.2023)
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Journal Article
Consensus Clustering Strategy for Cell Type Assignments of scRNA-seq Data
Riva, Simone G., Myers, Brynelle, Cazzaniga, Paolo, Buffa, Francesca M., Tangherloni, Andrea
Published in 2023 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB) (29.08.2023)
Published in 2023 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB) (29.08.2023)
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Conference Proceeding
A Deep Learning Pipeline for the Automatic cell type Assignment of scRNA-seq Data
Riva, Simone G., Myers, Brynelle, Cazzaniga, Paolo, Tangherloni, Andrea
Published in 2022 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB) (15.08.2022)
Published in 2022 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB) (15.08.2022)
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Conference Proceeding
Multi-objective Optimization for Marker Panel Identification in Single-cell Data
Tangherloni, Andrea, Riva, Simone G., Myers, Brynelle, Cazzaniga, Paolo
Published in 2022 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB) (15.08.2022)
Published in 2022 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB) (15.08.2022)
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Conference Proceeding
The Impact of Representation on the Optimization of Marker Panels for Single-cell RNA Data
Tangherloni, Andrea, Riva, Simone G., Spolaor, Simone, Besozzi, Daniela, Nobile, Marco S., Cazzaniga, Paolo
Published in 2021 IEEE Congress on Evolutionary Computation (CEC) (28.06.2021)
Published in 2021 IEEE Congress on Evolutionary Computation (CEC) (28.06.2021)
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Conference Proceeding
Predicting and Characterizing Legal Claims of Hospitals with Computational Intelligence: the Legal and Ethical Implications
Gallese, Chiara, Fuchs, Caro, Riva, Simone G., Foglia, Emanuela, Schettini, Fabrizio, Ferrario, Lucrezia, Falletti, Elena, Nobile, Marco S.
Published in 2022 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB) (15.08.2022)
Published in 2022 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB) (15.08.2022)
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Conference Proceeding
Structural and non-coding variants increase the diagnostic yield of clinical whole genome sequencing for rare diseases
Pagnamenta, Alistair T, Camps, Carme, Giacopuzzi, Edoardo, Taylor, John M, Hashim, Mona, Calpena, Eduardo, Kaisaki, Pamela J, Hashimoto, Akiko, Yu, Jing, Sanders, Edward, Schwessinger, Ron, Hughes, Jim R, Lunter, Gerton, Dreau, Helene, Ferla, Matteo, Lange, Lukas, Kesim, Yesim, Ragoussis, Vassilis, Vavoulis, Dimitrios V, Allroggen, Holger, Ansorge, Olaf, Babbs, Christian, Banka, Siddharth, Baños-Piñero, Benito, Beeson, David, Ben-Ami, Tal, Bennett, David L, Bento, Celeste, Blair, Edward, Brasch-Andersen, Charlotte, Bull, Katherine R, Cario, Holger, Cilliers, Deirdre, Conti, Valerio, Davies, E Graham, Dhalla, Fatima, Dacal, Beatriz Diez, Dong, Yin, Dunford, James E, Guerrini, Renzo, Harris, Adrian L, Hartley, Jane, Hollander, Georg, Javaid, Kassim, Kane, Maureen, Kelly, Deirdre, Kelly, Dominic, Knight, Samantha J L, Kreins, Alexandra Y, Kvikstad, Erika M, Langman, Craig B, Lester, Tracy, Lines, Kate E, Lord, Simon R, Lu, Xin, Mansour, Sahar, Manzur, Adnan, Maroofian, Reza, Marsden, Brian, Mason, Joanne, McGowan, Simon J, Mei, Davide, Mlcochova, Hana, Murakami, Yoshiko, Németh, Andrea H, Okoli, Steven, Ormondroyd, Elizabeth, Ousager, Lilian Bomme, Palace, Jacqueline, Patel, Smita Y, Pentony, Melissa M, Pugh, Chris, Rad, Aboulfazl, Ramesh, Archana, Riva, Simone G, Roberts, Irene, Roy, Noémi, Salminen, Outi, Schilling, Kyleen D, Scott, Caroline, Sen, Arjune, Smith, Conrad, Stevenson, Mark, Thakker, Rajesh V, Twigg, Stephen R F, Uhlig, Holm H, van Wijk, Richard, Vona, Barbara, Wall, Steven, Wang, Jing, Watkins, Hugh, Zak, Jaroslav, Schuh, Anna H, Kini, Usha, Wilkie, Andrew O M, Popitsch, Niko, Taylor, Jenny C
Published in Genome medicine (09.11.2023)
Published in Genome medicine (09.11.2023)
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Journal Article
Integration of Multiple scRNA-Seq Datasets on the Autoencoder Latent Space
Riva, Simone G., Cazzaniga, Paolo, Tangherloni, Andrea
Published in 2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) (09.12.2021)
Published in 2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) (09.12.2021)
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Conference Proceeding