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Mihaljevic, Ante; Rubin, Philip D; Chouvardas, Panagiotis; Esposito, Roberta (2024). Cell type specific long non-coding RNA targets identified by integrative analysis of single-cell and bulk colorectal cancer transcriptomes. Scientific Reports, 14(10939) Nature Publishing Group 10.1038/s41598-024-61430-7
Ovchinnikova, Katja; Born, Jannis; Chouvardas, Panagiotis; Rapsomaniki, Marianna; Kruithof-de Julio, Marianna (2024). Overcoming limitations in current measures of drug response may enable AI-driven precision oncology. NPJ precision oncology, 8(95) Springer Nature 10.1038/s41698-024-00583-0
Dhaka, Bhavya; Zimmerli, Marc; Hanhart, Daniel; Moser, Mario B; Guillen-Ramirez, Hugo; Mishra, Sanat; Esposito, Roberta; Polidori, Taisia; Widmer, Maro; García-Pérez, Raquel; Kruithof-de Julio, Marianna; Pervouchine, Dmitri; Melé, Marta; Chouvardas, Panagiotis; Johnson, Rory (2024). Functional identification of cis-regulatory long noncoding RNAs at controlled false discovery rates. Nucleic acids research, 52(6), pp. 2821-2835. Oxford University Press 10.1093/nar/gkae075
Hanhart, Daniel; Gossi, Federico; Rapsomaniki, Maria Anna; Kruithof-de Julio, Marianna; Chouvardas, Panagiotis (2024). ScLinear predicts protein abundance at single-cell resolution. Communications biology, 7(267) Springer Nature 10.1038/s42003-024-05958-4
Aghagolzadeh, Parisa; Plaisance, Isabelle; Bernasconi, Riccardo; Treibel, Thomas A; Pulido Quetglas, Carlos; Wyss, Tania; Wigger, Leonore; Nemir, Mohamed; Sarre, Alexandre; Chouvardas, Panagiotis; Johnson, Rory; González, Arantxa; Pedrazzini, Thierry (2023). Assessment of the Cardiac Noncoding Transcriptome by Single-Cell RNA Sequencing Identifies FIXER, a Conserved Profibrogenic Long Noncoding RNA. Circulation, 148(9), pp. 778-797. American Heart Association 10.1161/CIRCULATIONAHA.122.062601
La Manna, Federico; Hanhart, Daniel; Kloen, Peter; van Wijnen, Andre J; Thalmann, George; Kruithof-de Julio, Marianna; Chouvardas, Panagiotis (2023). Molecular profiling of osteoprogenitor cells reveals FOS as a master regulator of bone non-union. Gene, 874(147481), p. 147481. Elsevier 10.1016/j.gene.2023.147481
Plaisance, Isabelle; Chouvardas, Panagiotis; Sun, Yuliangzi; Nemir, Mohamed; Aghagolzadeh, Parisa; Aminfar, Farhang; Shen, Sophie; Shim, Woo Jun; Rochais, Francesca; Johnson, Rory; Palpant, Nathan; Pedrazzini, Thierry (2023). A transposable element into the human long noncoding RNA CARMEN is a switch for cardiac precursor cell specification. Cardiovascular research, 119(6), pp. 1361-1376. Oxford University Press 10.1093/cvr/cvac191
Gossi, Federico; Pati, Pushpak; Chouvardas, Panagiotis; Martinelli, Adriano Luca; Kruithof-de Julio, Marianna; Rapsomaniki, Maria Anna (2023). Matching single cells across modalities with contrastive learning and optimal transport. Briefings in bioinformatics, 24(3) Oxford University Press 10.1093/bib/bbad130
Minoli, Martina; Cantore, Thomas; Hanhart, Daniel; Kiener, Mirjam; Fedrizzi, Tarcisio; La Manna, Federico; Karkampouna, Sofia; Chouvardas, Panagiotis; Genitsch, Vera; Rodriguez-Calero, Antonio; Compérat, Eva; Klima, Irena; Gasperini, Paola; Kiss, Bernhard; Seiler, Roland; Demichelis, Francesca; Thalmann, George N; Kruithof-de Julio, Marianna (2023). Bladder cancer organoids as a functional system to model different disease stages and therapy response. Nature Communications, 14(1), p. 2214. Springer Nature 10.1038/s41467-023-37696-2
Botos, Marius Alexandru; Arora, Prateek; Chouvardas, Panagiotis; Mercader, Nadia (2023). Transcriptomic data meta-analysis reveals common and injury model specific gene expression changes in the regenerating zebrafish heart. Scientific Reports, 13(1), p. 5418. Nature Publishing Group 10.1038/s41598-023-32272-6
Esposito, Roberta; Polidori, Taisia; Meise, Dominik F; Pulido-Quetglas, Carlos; Chouvardas, Panagiotis; Forster, Stefan; Schaerer, Paulina; Kobel, Andrea; Schlatter, Juliette; Kerkhof, Erik; Roemmele, Michaela; Rice, Emily S.; Zhu, Lina; Lanzós, Andrés; Guillen-Ramirez, Hugo A; Basile, Giulia; Carrozzo, Irene; Vancura, Adrienne; Ullrich, Sebastian; Andrades, Alvaro; ... (2022). Multi-hallmark long noncoding RNA maps reveal non-small cell lung cancer vulnerabilities. Cell genomics, 2(9), p. 100171. Elsevier 10.1016/j.xgen.2022.100171
Ntari, Lydia; Nikolaou, Christoforos; Kranidioti, Ksanthi; Papadopoulou, Dimitra; Christodoulou-Vafeiadou, Eleni; Chouvardas, Panagiotis; Meier, Florian; Geka, Christina; Denis, Maria C; Karagianni, Niki; Kollias, George (2021). Combination of subtherapeutic anti-TNF dose with dasatinib restores clinical and molecular arthritogenic profiles better than standard anti-TNF treatment. Journal of translational medicine, 19(1), p. 165. BioMed Central 10.1186/s12967-021-02764-y
Carlevaro-Fita, Joana; Liu, Leibo; Zhou, Yuan; Zhang, Shan; Chouvardas, Panagiotis; Johnson, Rory; Li, Jianwei (2019). LnCompare: gene set feature analysis for human long non-coding RNAs. Nucleic acids research, 47(W1), W523-W529. Oxford University Press 10.1093/nar/gkz410
