PAULO DE PAIVA ROSA AMARAL

PAULO DE PAIVA ROSA AMARAL

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The status of the human gene catalogue
(2023) PAULO DE PAIVA ROSA AMARAL; Carbonell-Sala, Silvia; De La Vega, Francisco M.; Faial, Tiago; Frankish, Adam; Gingeras, Thomas; Guigo, Roderic; Harrow, Jennifer L.; Hatzigeorgiou, Artemis G.; Johnson, Rory; Murphy, Terence D.; Pertea, Mihaela; Pruitt, Kim D.; Pujar, Shashikant; Takahashi, Hazuki; Ulitsky, Igor; Varabyou, Ales; Wells, Christine A.; Yandell, Mark; Carninci, Piero; Salzberg, Steven L.
Scientists have been trying to identify every gene in the human genome since the initial draft was published in 2001. In the years since, much progress has been made in identifying protein-coding genes, currently estimated to number fewer than 20,000, with an ever-expanding number of distinct protein-coding isoforms. Here we review the status of the human gene catalogue and the efforts to complete it in recent years. Beside the ongoing annotation of protein-coding genes, their isoforms and pseudogenes, the invention of high-throughput RNA sequencing and other technological breakthroughs have led to a rapid growth in the number of reported non-coding RNA genes. For most of these non-coding RNAs, the functional relevance is currently unclear; we look at recent advances that offer paths forward to identifying their functions and towards eventually completing the human gene catalogue. Finally, we examine the need for a universal annotation standard that includes all medically significant genes and maintains their relationships with different reference genomes for the use of the human gene catalogue in clinical settings.
Long non-coding RNAs associated with infection and vaccine-induced immunity
(2021) Lüscher-Dias, Thomaz; Conceição, Izabela Mamede; Schuch, Viviane; Maracaja-Coutinho, Vinicius; PAULO DE PAIVA ROSA AMARAL
RNA modifications detection by comparative Nanopore direct RNA sequencing
(2021) Leger, Adrien; PAULO DE PAIVA ROSA AMARAL; Pandolfini, Luca; Capitanchik, Charlotte; Capraro, Federica; Miano, Valentina; Migliori, Valentina; Toolan-Kerr, Patrick; Sideri, Theodora; Enright, Anton J.; Tzelepis, Konstantinos; Werven, Folkert J. van; Luscombe, Nicholas M.; Barbieri, Isaia; Ule, Jernej; Fitzgerald, Tomas; Birney, Ewan; Leonardi, Tommaso; Kouzarides, Tony
RNA, the Epicenter of Genetic Information
(2023) Mattick, John; PAULO DE PAIVA ROSA AMARAL
The origin story and emergence of molecular biology is muddled. The early triumphs in bacterial genetics and the complexity of animal and plant genomes complicate an intricate history. This book documents the many advances, as well as the prejudices and founder fallacies. It highlights the premature relegation of RNA to simply an intermediate between gene and protein, the underestimation of the amount of information required to program the development of multicellular organisms, and the dawning realization that RNA is the cornerstone of cell biology, development, brain function and probably evolution itself. Key personalities, their hubris as well as prescient predictions are richly illustrated with quotes, archival material, photographs, diagrams and references to bring the people, ideas and discoveries to life, from the conceptual cradles of molecular biology to the current revolution in the understanding of genetic information. FONTE: https://www.taylorfrancis.com/books/oa-mono/10.1201/9781003109242/rna-epicenter-genetic-information-john-mattick-paulo-amaral
The evolution of knowledge on genes associated with human diseases
(2022) Lüscher-Dias, Thomaz; Dalmolin, Rodrigo Juliani Siqueira; PAULO DE PAIVA ROSA AMARAL; Alves, Tiago Lubiana; Schuch, Viviane; Franco, Glória Regina; Nakaya, Helder I.