Search Results - "de Almeida, Bernardo P"

Roadmap of DNA methylation in breast cancer identifies novel prognostic biomarkers by Almeida, Bernardo, Apolónio, Joana Dias, Binnie, Alexandra, Castelo Branco, Pedro

“…© The Author(s). 2019. Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License…”
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Developmental and housekeeping transcriptional programs display distinct modes of enhancer-enhancer cooperativity in Drosophila by Loubiere, Vincent, de Almeida, Bernardo P., Pagani, Michaela, Stark, Alexander

“…Genomic enhancers are key transcriptional regulators which, upon the binding of sequence-specific transcription factors, activate their cognate target…”
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Over-elongation of centrioles in cancer promotes centriole amplification and chromosome missegregation by Marteil, Gaëlle, Guerrero, Adan, Vieira, André F., de Almeida, Bernardo P., Machado, Pedro, Mendonça, Susana, Mesquita, Marta, Villarreal, Beth, Fonseca, Irina, Francia, Maria E., Dores, Katharina, Martins, Nuno P., Jana, Swadhin C., Tranfield, Erin M., Barbosa-Morais, Nuno L., Paredes, Joana, Pellman, David, Godinho, Susana A., Bettencourt-Dias, Mónica

“…Centrosomes are the major microtubule organising centres of animal cells. Deregulation in their number occurs in cancer and was shown to trigger tumorigenesis…”
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Pan-cancer association of a centrosome amplification gene expression signature with genomic alterations and clinical outcome by Almeida, Bernardo, Vieira, André F., Paredes, Joana, Bettencourt-Dias, Mónica, BARBOSA MORAIS, NUNO LUÍS

“…Copyright: © 2019 de Almeida et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits…”
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Decoding a cancer-relevant splicing decision in the RON proto-oncogene using high-throughput mutagenesis by Braun, Simon, Enculescu, Mihaela, Setty, Samarth T., Cortés-López, Mariela, de Almeida, Bernardo P., Sutandy, F. X.  Reymond, Schulz, Laura, Busch, Anke, Seiler, Markus, Ebersberger, Stefanie, Barbosa-Morais, Nuno L., Legewie, Stefan, König, Julian, Zarnack, Kathi

“…Mutations causing aberrant splicing are frequently implicated in human diseases including cancer. Here, we establish a high-throughput screen of randomly…”
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Identification of candidate causal variants and target genes at 41 breast cancer risk loci through differential allelic expression analysis by Xavier, Joana M., Magno, Ramiro, Russell, Roslin, de Almeida, Bernardo P., Jacinta-Fernandes, Ana, Besouro-Duarte, André, Dunning, Mark, Samarajiwa, Shamith, O’Reilly, Martin, Maia, António M., Rocha, Cátia L., Rosli, Nordiana, Ponder, Bruce A. J., Maia, Ana-Teresa

“…Understanding breast cancer genetic risk relies on identifying causal variants and candidate target genes in risk loci identified by genome-wide association…”
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DeepSTARR predicts enhancer activity from DNA sequence and enables the de novo design of synthetic enhancers by de Almeida, Bernardo P., Reiter, Franziska, Pagani, Michaela, Stark, Alexander

“…Enhancer sequences control gene expression and comprise binding sites (motifs) for different transcription factors (TFs). Despite extensive genetic and…”
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Allosteric Antagonist Modulation of TRPV2 by Piperlongumine Impairs Glioblastoma Progression by Conde, João, Pumroy, Ruth A, Baker, Charlotte, Rodrigues, Tiago, Guerreiro, Ana, Sousa, Bárbara B, Marques, Marta C, de Almeida, Bernardo P, Lee, Sohyon, Leites, Elvira P, Picard, Daniel, Samanta, Amrita, Vaz, Sandra H, Sieglitz, Florian, Langini, Maike, Remke, Marc, Roque, Rafael, Weiss, Tobias, Weller, Michael, Liu, Yuhang, Han, Seungil, Corzana, Francisco, Morais, Vanessa A, Faria, Cláudia C, Carvalho, Tânia, Filippakopoulos, Panagis, Snijder, Berend, Barbosa-Morais, Nuno L, Moiseenkova-Bell, Vera Y, Bernardes, Gonçalo J. L

“…The use of computational tools to identify biological targets of natural products with anticancer properties and unknown modes of action is gaining momentum…”
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A foundational large language model for edible plant genomes by Mendoza-Revilla, Javier, Trop, Evan, Gonzalez, Liam, Roller, Maša, Dalla-Torre, Hugo, de Almeida, Bernardo P., Richard, Guillaume, Caton, Jonathan, Lopez Carranza, Nicolas, Skwark, Marcin, Laterre, Alex, Beguir, Karim, Pierrot, Thomas, Lopez, Marie

“…Significant progress has been made in the field of plant genomics, as demonstrated by the increased use of high-throughput methodologies that enable the…”
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Allelic expression imbalance of PIK3CA mutations is frequent in breast cancer and prognostically significant by Correia, Lizelle, Magno, Ramiro, Xavier, Joana M., de Almeida, Bernardo P., Duarte, Isabel, Esteves, Filipa, Ghezzo, Marinella, Eldridge, Matthew, Sun, Chong, Bosma, Astrid, Mittempergher, Lorenza, Marreiros, Ana, Bernards, Rene, Caldas, Carlos, Chin, Suet-Feung, Maia, Ana-Teresa

“…PIK3CA mutations are the most common in breast cancer, particularly in the estrogen receptor-positive cohort, but the benefit of PI3K inhibitors has had…”
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Are genomic language models all you need? Exploring genomic language models on protein downstream tasks by Boshar, Sam, Trop, Evan, de Almeida, Bernardo P, Copoiu, Liviu, Pierrot, Thomas

“…Large language models, trained on enormous corpora of biological sequences, are state-of-the-art for downstream genomic and proteomic tasks. Since the genome…”
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Enhancers display constrained sequence flexibility and context-specific modulation of motif function by Reiter, Franziska, de Almeida, Bernardo P, Stark, Alexander

“…The information about when and where each gene is to be expressed is mainly encoded in the DNA sequence of enhancers, sequence elements that comprise binding…”
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Targeted design of synthetic enhancers for selected tissues in the Drosophila embryo by de Almeida, Bernardo P., Schaub, Christoph, Pagani, Michaela, Secchia, Stefano, Furlong, Eileen E. M., Stark, Alexander

“…Enhancers control gene expression and have crucial roles in development and homeostasis 1 – 3 . However, the targeted de novo design of enhancers with…”
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Systematic identification and characterization of repressive domains in Drosophila transcription factors by Klaus, Loni, de Almeida, Bernardo P, Vlasova, Anna, Nemčko, Filip, Schleiffer, Alexander, Bergauer, Katharina, Hofbauer, Lorena, Rath, Martina, Stark, Alexander

“…All multicellular life relies on differential gene expression, determined by regulatory DNA elements and DNA‐binding transcription factors that mediate…”
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Dissecting celastrol with machine learning to unveil dark pharmacology by Rodrigues, Tiago, de Almeida, Bernardo P, Barbosa-Morais, Nuno L, Bernardes, Gonçalo J L

“…By coalescing bespoke machine learning and bioinformatics analyses with cell-based assays, we unveil the pharmacology of celastrol. Celastrol is a direct…”
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Natural product–drug conjugates for modulation of TRPV1-expressing tumors by Baker, Charlotte, Rodrigues, Tiago, de Almeida, Bernardo P., Barbosa-Morais, Nuno L., Bernardes, Gonçalo J.L.

“…[Display omitted] We report the design, synthesis and biological evaluation of natural product–drug conjugates for treatment of prostate cancers…”
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Expression of receptor activator of NFkB (RANK) drives stemness and resistance to therapy in ER+HER2- breast cancer by Fernandes Gomes, Inês, Almeida, Bernardo, Dâmaso, Sara, Mansinho, André, Correia, Inês, Henriques, Sara, Duarte, Raquel, Vilhais, Guilherme, Félix, Pedro, Borges Alves, Patrícia, Martins Corredeira, Patrícia Isabel, BARBOSA MORAIS, NUNO LUÍS, Costa, Luis, Cara de Anjo Casimiro, Sandra Cristina

“…© Gomes et al. Copyright: Gomes et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License 3.0 (CC BY 3.0),…”
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Multi-modal Transfer Learning between Biological Foundation Models by Garau-Luis, Juan Jose, Bordes, Patrick, Gonzalez, Liam, Roller, Masa, de Almeida, Bernardo P, Hexemer, Lorenz, Blum, Christopher, Laurent, Stefan, Grzegorzewski, Jan, Lang, Maren, Pierrot, Thomas, Richard, Guillaume

“…Biological sequences encode fundamental instructions for the building blocks of life, in the form of DNA, RNA, and proteins. Modeling these sequences is key to…”
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