Search Results - "Fonseca, Nuno A"

Tools for mapping high-throughput sequencing data by FONSECA, Nuno A, RUNG, Johan, BRAZMA, Alvis, MARIONI, John C

“…A ubiquitous and fundamental step in high-throughput sequencing analysis is the alignment (mapping) of the generated reads to a reference sequence. To…”
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Expression Atlas update: from tissues to single cells by 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

“…Abstract Expression Atlas is EMBL-EBI’s resource for gene and protein expression. It sources and compiles data on the abundance and localisation of RNA and…”
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A Pan-cancer Transcriptome Analysis Reveals Pervasive Regulation through Alternative Promoters by 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

“…Most human protein-coding genes are regulated by multiple, distinct promoters, suggesting that the choice of promoter is as important as its level of…”
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Expression Atlas: gene and protein expression across multiple studies and organisms by 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

“…Abstract Expression Atlas (http://www.ebi.ac.uk/gxa) is an added value database that provides information about gene and protein expression in different…”
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RNA-Seq gene profiling--a systematic empirical comparison by Fonseca, Nuno A, Marioni, John, Brazma, Alvis

“…Accurately quantifying gene expression levels is a key goal of experiments using RNA-sequencing to assay the transcriptome. This typically requires aligning…”
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Expression Atlas update--a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments by 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

“…Expression Atlas (http://www.ebi.ac.uk/gxa) is a value-added database providing information about gene, protein and splice variant expression in different cell…”
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Tumors induce de novo steroid biosynthesis in T cells to evade immunity by 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.

“…Tumors subvert immune cell function to evade immune responses, yet the complex mechanisms driving immune evasion remain poorly understood. Here we show that…”
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Long-range enhancers regulating Myc expression are required for normal facial morphogenesis by Uslu, Veli Vural, Petretich, Massimo, Ruf, Sandra, Langenfeld, Katja, Fonseca, Nuno A, Marioni, John C, Spitz, François

“…François Spitz and colleagues identify cis -acting enhancers of Myc in a region orthologous to human 8q24 that are required for normal development of the face…”
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Convergent evolution at the gametophytic self-incompatibility system in Malus and Prunus by Aguiar, Bruno, Vieira, Jorge, Cunha, Ana E, Fonseca, Nuno A, Iezzoni, Amy, van Nocker, Steve, Vieira, Cristina P

“…S-RNase-based gametophytic self-incompatibility (GSI) has evolved once before the split of the Asteridae and Rosidae. This conclusion is based on the…”
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Tumour gene expression signature in primary melanoma predicts long-term outcomes by 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

“…Adjuvant systemic therapies are now routinely used following resection of stage III melanoma, however accurate prognostic information is needed to better…”
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Lipid-Based Nanoparticles for siRNA Delivery in Cancer Therapy: Paradigms and Challenges by Gomes-da-Silva, Lígia C, Fonseca, Nuno A, Moura, Vera, Pedroso de Lima, Maria C, Simões, Sérgio, Moreira, João N

“…RNA interference (RNAi) is a specific gene-silencing mechanism that can be mediated by the delivery of chemical synthesized small-interfering RNA (siRNA). RNAi…”
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Gramene 2016: comparative plant genomics and pathway resources by 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

“…Gramene (http://www.gramene.org) is an online resource for comparative functional genomics in crops and model plant species. Its two main frameworks are…”
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Instructive Nanofibrous Scaffold Comprising Runt-Related Transcription Factor 2 Gene Delivery for Bone Tissue Engineering by Monteiro, Nelson, Ribeiro, Diana, Martins, Albino, Faria, Susana, Fonseca, Nuno A, Moreira, João N, Reis, Rui L, Neves, Nuno M

“…Inducer molecules capable of regulating mesenchymal stem cell differentiation into specific lineages have proven effective in basic science and in preclinical…”
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The RNASeq-er API-a gateway to systematically updated analysis of public RNA-seq data by Petryszak, Robert, Fonseca, Nuno A, Füllgrabe, Anja, Huerta, Laura, Keays, Maria, Tang, Y Amy, Brazma, Alvis

“…The exponential growth of publicly available RNA-sequencing (RNA-Seq) data poses an increasing challenge to researchers wishing to discover, analyse and store…”
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In Vitro and In Vivo Tumor Models for the Evaluation of Anticancer Nanoparticles by Abreu, Teresa R, Biscaia, Mariana, Gonçalves, Nélio, Fonseca, Nuno A, Moreira, João Nuno

“…Multiple studies about tumor biology have revealed the determinant role of the tumor microenvironment in cancer progression, resulting from the dynamic…”
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High-resolution mapping of transcriptional dynamics across tissue development reveals a stable mRNA-tRNA interface by 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

“…The genetic code is an abstraction of how mRNA codons and tRNA anticodons molecularly interact during protein synthesis; the stability and regulation of this…”
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A user guide for the online exploration and visualization of PCAWG data by 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

“…The Pan-Cancer Analysis of Whole Genomes (PCAWG) project generated a vast amount of whole-genome cancer sequencing resource data. Here, as part of the…”
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Targeted liposomal doxorubicin/ceramides combinations: The importance to assess the nature of drug interaction beyond bulk tumor cells by Cruz, Ana Filipa, Fonseca, Nuno A., Malheiro, Ana Rita, B. Melo, Joana, Gaspar, Maria Manuela, Fernandes, Rui, Moura, Vera, Simões, Sérgio, Moreira, João Nuno

“…[Display omitted] One of the major assets of anticancer nanomedicine is the ability to co-deliver drug combinations, as it enables targeting of different…”
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MIMt: a curated 16S rRNA reference database with less redundancy and higher accuracy at species-level identification by Cabezas, M. Pilar, Fonseca, Nuno A, Muéoz-Mérida, Antonio

“…Motivation Accurate determination and quantification of the taxonomic composition of microbial communities, especially at the species level, is one of the…”
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Inoculated cell density as a determinant factor of the growth dynamics and metastatic efficiency of a breast cancer murine model by Gregório, Ana C., Fonseca, Nuno A., Moura, Vera, Lacerda, Manuela, Figueiredo, Paulo, Simões, Sérgio, Dias, Sérgio, Moreira, João Nuno

“…Copyright: © 2016 Gregório et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits…”
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