TimeDelay-ARACNE: Reverse engineering of gene networks from time-course data by an information theoretic approach von Zoppoli, Pietro, Morganella, Sandro, Ceccarelli, Michele

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Deep learning predicts short non-coding RNA functions from only raw sequence data von Noviello, Teresa Maria Rosaria, Ceccarelli, Francesco, Ceccarelli, Michele, Cerulo, Luigi

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Machine learning prediction of oncology drug targets based on protein and network properties von Dezső, Zoltán, Ceccarelli, Michele

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RNA-Seq Signatures Normalized by mRNA Abundance Allow Absolute Deconvolution of Human Immune Cell Types von Monaco, Gianni, Lee, Bernett, Xu, Weili, Mustafah, Seri, Hwang, You Yi, Carré, Christophe, Burdin, Nicolas, Visan, Lucian, Ceccarelli, Michele, Poidinger, Michael, Zippelius, Alfred, Pedro de Magalhães, João, Larbi, Anis

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TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data von Colaprico, Antonio, Silva, Tiago C, Olsen, Catharina, Garofano, Luciano, Cava, Claudia, Garolini, Davide, Sabedot, Thais S, Malta, Tathiane M, Pagnotta, Stefano M, Castiglioni, Isabella, Ceccarelli, Michele, Bontempi, Gianluca, Noushmehr, Houtan

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Pan-cancer onco-signatures reveal a novel mitochondrial subtype of luminal breast cancer with specific regulators von Simeone, Ines, Ceccarelli, Michele

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A variational algorithm to detect the clonal copy number substructure of tumors from scRNA-seq data von De Falco, Antonio, Caruso, Francesca, Su, Xiao-Dong, Iavarone, Antonio, Ceccarelli, Michele

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Evolution of Metastases in Space and Time under Immune Selection von Angelova, Mihaela, Mlecnik, Bernhard, Vasaturo, Angela, Bindea, Gabriela, Fredriksen, Tessa, Lafontaine, Lucie, Buttard, Bénédicte, Morgand, Erwan, Bruni, Daniela, Jouret-Mourin, Anne, Hubert, Catherine, Kartheuser, Alex, Humblet, Yves, Ceccarelli, Michele, Syed, Najeeb, Marincola, Francesco M., Bedognetti, Davide, Van den Eynde, Marc, Galon, Jérôme

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Learning gene regulatory networks from only positive and unlabeled data von Cerulo, Luigi, Elkan, Charles, Ceccarelli, Michele

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Differential methylation of circulating free DNA assessed through cfMeDiP as a new tool for breast cancer diagnosis and detection of BRCA1/2 mutation von Grisolia, Piera, Tufano, Rossella, Iannarone, Clara, De Falco, Antonio, Carlino, Francesca, Graziano, Cinzia, Addeo, Raffaele, Scrima, Marianna, Caraglia, Francesco, Ceccarelli, Anna, Nuzzo, Pier Vitale, Cossu, Alessia Maria, Forte, Stefano, Giuffrida, Raffaella, Orditura, Michele, Caraglia, Michele, Ceccarelli, Michele

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TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages [version 2; peer review: 1 approved, 2 approved with reservations] von Silva, Tiago C, Colaprico, Antonio, Olsen, Catharina, D'Angelo, Fulvio, Bontempi, Gianluca, Ceccarelli, Michele, Noushmehr, Houtan

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A metabolic function of FGFR3-TACC3 gene fusions in cancer von Frattini, Véronique, Pagnotta, Stefano M., Tala, Fan, Jerry J., Russo, Marco V., Lee, Sang Bae, Garofano, Luciano, Zhang, Jing, Shi, Peiguo, Lewis, Genevieve, Sanson, Heloise, Frederick, Vanessa, Castano, Angelica M., Cerulo, Luigi, Rolland, Delphine C. M., Mall, Raghvendra, Mokhtari, Karima, Elenitoba-Johnson, Kojo S. J., Sanson, Marc, Huang, Xi, Ceccarelli, Michele, Lasorella, Anna, Iavarone, Antonio

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Single-cell transcriptome analysis of lineage diversity in high-grade glioma von Yuan, Jinzhou, Levitin, Hanna Mendes, Frattini, Veronique, Bush, Erin C, Boyett, Deborah M, Samanamud, Jorge, Ceccarelli, Michele, Dovas, Athanassios, Zanazzi, George, Canoll, Peter, Bruce, Jeffrey N, Lasorella, Anna, Iavarone, Antonio, Sims, Peter A

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Pancancer network analysis reveals key master regulators for cancer invasiveness von Jethalia, Mahesh, Jani, Siddhi P, Ceccarelli, Michele, Mall, Raghvendra

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Transcriptional regulatory networks of tumor-associated macrophages that drive malignancy in mesenchymal glioblastoma von Sa, Jason K, Chang, Nakho, Lee, Hye Won, Cho, Hee Jin, Ceccarelli, Michele, Cerulo, Luigi, Yin, Jinlong, Kim, Sung Soo, Caruso, Francesca P, Lee, Mijeong, Kim, Donggeon, Oh, Young Taek, Lee, Yeri, Her, Nam-Gu, Min, Byeongkwi, Kim, Hye-Jin, Jeong, Da Eun, Kim, Hye-Mi, Kim, Hyunho, Chung, Seok, Woo, Hyun Goo, Lee, Jeongwu, Kong, Doo-Sik, Seol, Ho Jun, Lee, Jung-Il, Kim, Jinho, Park, Woong-Yang, Wang, Qianghu, Sulman, Erik P, Heimberger, Amy B, Lim, Michael, Park, Jong Bae, Iavarone, Antonio, Verhaak, Roel G W, Nam, Do-Hyun

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Identification of therapeutic targets in osteoarthritis by combining heterogeneous transcriptional datasets, drug-induced expression profiles, and known drug-target interactions von Costa, Maria Claudia, Angelini, Claudia, Franzese, Monica, Iside, Concetta, Salvatore, Marco, Laezza, Luigi, Napolitano, Francesco, Ceccarelli, Michele

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Guadecitabine plus ipilimumab in unresectable melanoma: five-year follow-up and integrated multi-omic analysis in the phase 1b NIBIT-M4 trial von Noviello, Teresa Maria Rosaria, Di Giacomo, Anna Maria, Caruso, Francesca Pia, Covre, Alessia, Mortarini, Roberta, Scala, Giovanni, Costa, Maria Claudia, Coral, Sandra, Fridman, Wolf H., Sautès-Fridman, Catherine, Brich, Silvia, Pruneri, Giancarlo, Simonetti, Elena, Lofiego, Maria Fortunata, Tufano, Rossella, Bedognetti, Davide, Anichini, Andrea, Maio, Michele, Ceccarelli, Michele

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The epitranscriptome of high-grade gliomas: a promising therapeutic target with implications from the tumor microenvironment to endogenous retroviruses von Ramsoomair, Christian K, Ceccarelli, Michele, Heiss, John D, Shah, Ashish H

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Dysregulation of Principal Cell miRNAs Facilitates Epigenetic Regulation of AQP2 and Results in Nephrogenic Diabetes Insipidus von Petrillo, Federica, Iervolino, Anna, Angrisano, Tiziana, Jelen, Sabina, Costanzo, Vincenzo, D'Acierno, Mariavittoria, Cheng, Lei, Wu, Qi, Guerriero, Ilaria, Mazzarella, Maria Cristina, De Falco, Alfonso, D'Angelo, Fulvio, Ceccarelli, Michele, Caraglia, Michele, Capasso, Giovambattista, Fenton, Robert A, Trepiccione, Francesco

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Specific gene expression signatures induced by the multiple oncogenic alterations that occur within the PTEN/PI3K/AKT pathway in lung cancer von De Marco, Carmela, Laudanna, Carmelo, Rinaldo, Nicola, Oliveira, Duarte Mendes, Ravo, Maria, Weisz, Alessandro, Ceccarelli, Michele, Caira, Elvira, Rizzuto, Antonia, Zoppoli, Pietro, Malanga, Donatella, Viglietto, Giuseppe

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