Tools for mapping high-throughput sequencing data
FONSECA, Nuno A, RUNG, Johan, BRAZMA, Alvis, MARIONI, John C
Published in Bioinformatics (01.12.2012)
Published in Bioinformatics (01.12.2012)
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Expression Atlas update: from tissues to single cells
Papatheodorou, Irene, Moreno, Pablo, Manning, Jonathan, Fuentes, Alfonso Muñoz-Pomer, George, Nancy, Fexova, Silvie, Fonseca, Nuno A, Füllgrabe, Anja, Green, Matthew, Huang, Ni, Huerta, Laura, Iqbal, Haider, Jianu, Monica, Mohammed, Suhaib, Zhao, Lingyun, Jarnuczak, Andrew F, Jupp, Simon, Marioni, John, Meyer, Kerstin, Petryszak, Robert, Prada Medina, Cesar Augusto, Talavera-López, Carlos, Teichmann, Sarah, Vizcaino, Juan Antonio, Brazma, Alvis
Published in Nucleic acids research (08.01.2020)
Published in Nucleic acids research (08.01.2020)
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A Pan-cancer Transcriptome Analysis Reveals Pervasive Regulation through Alternative Promoters
Demircioğlu, Deniz, Cukuroglu, Engin, Kindermans, Martin, Nandi, Tannistha, Calabrese, Claudia, Fonseca, Nuno A., Kahles, André, Lehmann, Kjong-Van, Stegle, Oliver, Brazma, Alvis, Brooks, Angela N., Rätsch, Gunnar, Tan, Patrick, Göke, Jonathan
Published in Cell (05.09.2019)
Published in Cell (05.09.2019)
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Journal Article
Expression Atlas: gene and protein expression across multiple studies and organisms
Papatheodorou, Irene, Fonseca, Nuno A, Keays, Maria, Tang, Y Amy, Barrera, Elisabet, Bazant, Wojciech, Burke, Melissa, Füllgrabe, Anja, Fuentes, Alfonso Muñoz-Pomer, George, Nancy, Huerta, Laura, Koskinen, Satu, Mohammed, Suhaib, Geniza, Matthew, Preece, Justin, Jaiswal, Pankaj, Jarnuczak, Andrew F, Huber, Wolfgang, Stegle, Oliver, Vizcaino, Juan Antonio, Brazma, Alvis, Petryszak, Robert
Published in Nucleic acids research (04.01.2018)
Published in Nucleic acids research (04.01.2018)
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Journal Article
Expression Atlas update--a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments
Petryszak, Robert, Burdett, Tony, Fiorelli, Benedetto, Fonseca, Nuno A, Gonzalez-Porta, Mar, Hastings, Emma, Huber, Wolfgang, Jupp, Simon, Keays, Maria, Kryvych, Nataliya, McMurry, Julie, Marioni, John C, Malone, James, Megy, Karine, Rustici, Gabriella, Tang, Amy Y, Taubert, Jan, Williams, Eleanor, Mannion, Oliver, Parkinson, Helen E, Brazma, Alvis
Published in Nucleic acids research (01.01.2014)
Published in Nucleic acids research (01.01.2014)
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Tumors induce de novo steroid biosynthesis in T cells to evade immunity
Mahata, Bidesh, Pramanik, Jhuma, van der Weyden, Louise, Polanski, Krzysztof, Kar, Gozde, Riedel, Angela, Chen, Xi, Fonseca, Nuno A, Kundu, Kousik, Campos, Lia S, Ryder, Edward, Duddy, Graham, Walczak, Izabela, Okkenhaug, Klaus, Adams, David J, Shields, Jacqueline D, Teichmann, Sarah A
Published in Nature communications (17.07.2020)
Published in Nature communications (17.07.2020)
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Journal Article
Convergent evolution at the gametophytic self-incompatibility system in Malus and Prunus
Aguiar, Bruno, Vieira, Jorge, Cunha, Ana E, Fonseca, Nuno A, Iezzoni, Amy, van Nocker, Steve, Vieira, Cristina P
Published in PloS one (19.05.2015)
Published in PloS one (19.05.2015)
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Journal Article
Tumour gene expression signature in primary melanoma predicts long-term outcomes
Garg, Manik, Couturier, Dominique-Laurent, Nsengimana, Jérémie, Fonseca, Nuno A, Wongchenko, Matthew, Yan, Yibing, Lauss, Martin, Jönsson, Göran B, Newton-Bishop, Julia, Parkinson, Christine, Middleton, Mark R, Bishop, D Timothy, McDonald, Sarah, Stefanos, Nikki, Tadross, John, Vergara, Ismael A, Lo, Serigne, Newell, Felicity, Wilmott, James S, Thompson, John F, Long, Georgina V, Scolyer, Richard A, Corrie, Pippa, Adams, David J, Brazma, Alvis, Rabbie, Roy
Published in Nature communications (18.02.2021)
Published in Nature communications (18.02.2021)
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Journal Article
Gramene 2016: comparative plant genomics and pathway resources
Tello-Ruiz, Marcela K, Stein, Joshua, Wei, Sharon, Preece, Justin, Olson, Andrew, Naithani, Sushma, Amarasinghe, Vindhya, Dharmawardhana, Palitha, Jiao, Yinping, Mulvaney, Joseph, Kumari, Sunita, Chougule, Kapeel, Elser, Justin, Wang, Bo, Thomason, James, Bolser, Daniel M, Kerhornou, Arnaud, Walts, Brandon, Fonseca, Nuno A, Huerta, Laura, Keays, Maria, Tang, Y Amy, Parkinson, Helen, Fabregat, Antonio, McKay, Sheldon, Weiser, Joel, D'Eustachio, Peter, Stein, Lincoln, Petryszak, Robert, Kersey, Paul J, Jaiswal, Pankaj, Ware, Doreen
Published in Nucleic acids research (04.01.2016)
Published in Nucleic acids research (04.01.2016)
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Journal Article
Instructive Nanofibrous Scaffold Comprising Runt-Related Transcription Factor 2 Gene Delivery for Bone Tissue Engineering
Monteiro, Nelson, Ribeiro, Diana, Martins, Albino, Faria, Susana, Fonseca, Nuno A, Moreira, João N, Reis, Rui L, Neves, Nuno M
Published in ACS nano (26.08.2014)
Published in ACS nano (26.08.2014)
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Journal Article
Targeted liposomal doxorubicin/ceramides combinations: The importance to assess the nature of drug interaction beyond bulk tumor cells
Cruz, Ana Filipa, Fonseca, Nuno A., Malheiro, Ana Rita, B. Melo, Joana, Gaspar, Maria Manuela, Fernandes, Rui, Moura, Vera, Simões, Sérgio, Moreira, João Nuno
Published in European journal of pharmaceutics and biopharmaceutics (01.03.2022)
Published in European journal of pharmaceutics and biopharmaceutics (01.03.2022)
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Journal Article
High-resolution mapping of transcriptional dynamics across tissue development reveals a stable mRNA-tRNA interface
Schmitt, Bianca M, Rudolph, Konrad L M, Karagianni, Panagiota, Fonseca, Nuno A, White, Robert J, Talianidis, Iannis, Odom, Duncan T, Marioni, John C, Kutter, Claudia
Published in Genome research (01.11.2014)
Published in Genome research (01.11.2014)
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Journal Article
A user guide for the online exploration and visualization of PCAWG data
Goldman, Mary J., Zhang, Junjun, Fonseca, Nuno A., Cortés-Ciriano, Isidro, Xiang, Qian, Craft, Brian, Piñeiro-Yáñez, Elena, O’Connor, Brian D., Bazant, Wojciech, Barrera, Elisabet, Muñoz-Pomer, Alfonso, Petryszak, Robert, Füllgrabe, Anja, Al-Shahrour, Fatima, Keays, Maria, Haussler, David, Weinstein, John N., Huber, Wolfgang, Valencia, Alfonso, Park, Peter J., Papatheodorou, Irene, Zhu, Jingchun, Ferretti, Vincent, Vazquez, Miguel
Published in Nature communications (07.07.2020)
Published in Nature communications (07.07.2020)
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Journal Article
Inoculated Cell Density as a Determinant Factor of the Growth Dynamics and Metastatic Efficiency of a Breast Cancer Murine Model
Gregório, Ana C, Fonseca, Nuno A, Moura, Vera, Lacerda, Manuela, Figueiredo, Paulo, Simões, Sérgio, Dias, Sérgio, Moreira, João Nuno
Published in PloS one (07.11.2016)
Published in PloS one (07.11.2016)
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Journal Article
Cell surface Nucleolin represents a novel cellular target for neuroblastoma therapy
Brignole, Chiara, Bensa, Veronica, Fonseca, Nuno A, Del Zotto, Genny, Bruno, Silvia, Cruz, Ana F, Malaguti, Fabiana, Carlini, Barbara, Morandi, Fabio, Calarco, Enzo, Perri, Patrizia, Moura, Vera, Emionite, Laura, Cilli, Michele, De Leonardis, Francesco, Tondo, Annalisa, Amoroso, Loredana, Conte, Massimo, Garaventa, Alberto, Sementa, Angela R, Corrias, Maria V, Ponzoni, Mirco, Moreira, Joao N, Pastorino, Fabio
Published in Journal of experimental & clinical cancer research (02.06.2021)
Published in Journal of experimental & clinical cancer research (02.06.2021)
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