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Details

  • Name

    Pedro Gabriel Ferreira
  • Cluster

    Computer Science
  • Role

    External Research Collaborator
  • Since

    20th September 2018
Publications

2018

The effects of death and post-mortem cold ischemia on human tissue transcriptomes

Authors
Ferreira, PG; Munoz Aguirre, M; Reverter, F; Sa Godinho, CPS; Sousa, A; Amadoz, A; Sodaei, R; Hidalgo, MR; Pervouchine, D; Carbonell Caballero, J; Nurtdinov, R; Breschi, A; Amador, R; Oliveira, P; Cubuk, C; Curado, J; Aguet, F; Oliveira, C; Dopazo, J; Sammeth, M; Ardlie, KG; Guigo, R;

Publication
NATURE COMMUNICATIONS

Abstract
Post-mortem tissues samples are a key resource for investigating patterns of gene expression. However, the processes triggered by death and the post-mortem interval (PMI) can significantly alter physiologically normal RNA levels. We investigate the impact of PMI on gene expression using data from multiple tissues of post-mortem donors obtained from the GTEx project. We find that many genes change expression over relatively short PMIs in a tissue-specific manner, but this potentially confounding effect in a biological analysis can be minimized by taking into account appropriate covariates. By comparing ante-and postmortem blood samples, we identify the cascade of transcriptional events triggered by death of the organism. These events do not appear to simply reflect stochastic variation resulting from mRNA degradation, but active and ongoing regulation of transcription. Finally, we develop a model to predict the time since death from the analysis of the transcriptome of a few readily accessible tissues.

2018

Cosmology and fundamental physics with the Euclid satellite

Authors
Amendola, L; Appleby, S; Avgoustidis, A; Bacon, D; Baker, T; Baldi, M; Bartolo, N; Blanchard, A; Bonvin, C; Borgani, S; Branchini, E; Burrage, C; Camera, S; Carbone, C; Casarini, L; Cropper, M; de Rham, C; Dietrich, JP; Di Porto, C; Durrer, R; Ealet, A; Ferreira, PG; Finelli, F; Garcia Bellido, J; Giannantonio, T; Guzzo, L; Heavens, A; Heisenberg, L; Heymans, C; Hoekstra, H; Hollenstein, L; Holmes, R; Hwang, ZQ; Jahnke, K; Kitching, TD; Koivisto, T; Kunz, M; La Vacca, G; Linder, E; March, M; Marra, V; Martins, C; Majerotto, E; Markovic, D; Marsh, D; Marulli, F; Massey, R; Mellier, Y; Montanari, F; Mota, DF; Nunes, NJ; Percival, W; Pettorino, V; Porciani, C; Quercellini, C; Read, J; Rinaldi, M; Sapone, D; Sawicki, I; Scaramella, R; Skordis, C; Simpson, F; Taylor, A; Thomas, S; Trotta, R; Verde, L; Vernizzi, F; Vollmer, A; Wang, Y; Weller, J; Zlosnik, T;

Publication
LIVING REVIEWS IN RELATIVITY

Abstract
Euclid is a European Space Agency medium-class mission selected for launch in 2020 within the cosmic vision 2015-2025 program. The main goal of Euclid is to understand the origin of the accelerated expansion of the universe. Euclid will explore the expansion history of the universe and the evolution of cosmic structures by measuring shapes and red-shifts of galaxies as well as the distribution of clusters of galaxies over a large fraction of the sky. Although the main driver for Euclid is the nature of dark energy, Euclid science covers a vast range of topics, from cosmology to galaxy evolution to planetary research. In this review we focus on cosmology and fundamental physics, with a strong emphasis on science beyond the current standard models. We discuss five broad topics: dark energy and modified gravity, dark matter, initial conditions, basic assumptions and questions of methodology in the data analysis. This review has been planned and carried out within Euclid's Theory Working Group and is meant to provide a guide to the scientific themes that will underlie the activity of the group during the preparation of the Euclid mission.