Professor Pedro Ferreira

Abstract:

Chronic lymphocytic leukemia (CLL) has heterogeneous clinical and biological behavior. Whole-genome and -exome sequencing has contributed to the characterization of the mutational spectrum of the disease, but the underlying transcriptional profile is still poorly understood. We have performed deep RNA sequencing in different subpopulations of normal B-lymphocytes and CLL cells from a cohort of 98 patients, and characterized the CLL transcriptional landscape with unprecedented resolution. We detected thousands of transcriptional elements differentially expressed between the CLL and normal B cells, including protein-coding genes, noncoding RNAs, and pseudogenes. Transposable elements are globally derepressed in CLL cells. In addition, two thousand genes-most of which are not differentially expressed-exhibit CLL-specific splicing patterns. Genes involved in metabolic pathways showed higher expression in CLL, while genes related to spliceosome, proteasome, and ribosome were among the most down-regulated in CLL. Clustering of the CLL samples according to RNA-seq derived gene expression levels unveiled two robust molecular subgroups, C1 and C2. C1/C2 subgroups and the mutational status of the immunoglobulin heavy variable (IGHV) region were the only independent variables in predicting time to treatment in a multivariate analysis with main clinico-biological features. This subdivision was validated in an independent cohort of patients monitored through DNA microarrays. Further analysis shows that B-cell receptor (BCR) activation in the microenvironment of the lymph node may be at the origin of the C1/C2 differences.

Abstract:

HI intensity mapping (IM) is a novel technique capable of mapping the large-scale structure of the Universe in three dimensions and delivering exquisite constraints on cosmology, by using HI as a biased tracer of the dark matter density field. This is achieved by measuring the intensity of the redshifted 21cm line over the sky in a range of redshifts without the requirement to resolve individual galaxies. In this chapter, we investigate the potential of SKA1 to deliver HI intensity maps over a broad range of frequencies and a substantial fraction of the sky. By pinning down the baryon acoustic oscillation and redshift space distortion features in the matter power spectrum - Thus determining the expansion and growth history of the Universe - These surveys can provide powerful tests of dark energy models and modifications to General Relativity. They can also be used to probe physics on extremely large scales, where precise measurements of spatial curvature and primordial non-Gaussianity can be used to test inflation; on small scales, by measuring the sum of neutrino masses; and at high redshifts where non-standard evolution models can be probed. We discuss the impact of foregrounds as well as various instrumental and survey design parameters on the achievable constraints. In particular we analyse the feasibility of using the SKA1 autocorrelations to probe the large-scale signal.

Abstract:

21 cm intensity mapping experiments aim to observe the diffuse neutral hydrogen (HI) distribution on large scales which traces the Cosmic structure. The Square Kilometre Array (SKA) will have the capacity to measure the 21 cm signal over a large fraction of the sky. However, the redshifted 21 cm signal in the respective frequencies is faint compared to the Galactic foregrounds produced by synchrotron and free-free electron emission. In this article, we review selected foreground subtraction methods suggested to effectively separate the 21 cm signal from the foregrounds with intensity mapping simulations or data. We simulate an intensity mapping experiment feasible with SKA phase 1 including extragalactic and Galactic foregrounds. We give an example of the residuals of the foreground subtraction with a independent component analysis and show that the angular power spectrum is recovered within the statistical errors on most scales. Additionally, the scale of the Baryon Acoustic Oscillations is shown to be unaffected by foreground subtraction.

Abstract:

The imprint of baryon acoustic oscillations (BAO) in large-scale structure can be used as a standard ruler for mapping out the cosmic expansion history, and hence for testing cosmological models. In this chapter we briefly describe the scientific background to the BAO technique, and forecast the potential of the Phase 1 and 2 SKA telescopes to perform BAO surveys using both galaxy catalogues and intensity mapping, assessing their competitiveness with current and future optical galaxy surveys. We find that a 25,000 deg2 intensity mapping survey on a Phase 1 array will preferentially constrain the radial BAO, providing a highly competitive 2% constraint on the expansion rate at z ≃ 2. A 30,000 deg2 galaxy redshift survey on SKA2 will outperform all other planned experiments for z < ∼ 1:4.

Abstract:

The peculiar motion of galaxies can be a particularly sensitive probe of gravitational collapse. As such, it can be used to measure the dynamics of dark matter and dark energy as well the nature of the gravitational laws at play on cosmological scales. Peculiar motions manifest themselves as an overall anisotropy in the measured clustering signal as a function of the angle to the line-ofsight, known as redshift-space distortion (RSD). Limiting factors in this measurement include our ability to model non-linear galaxy motions on small scales and the complexities of galaxy bias. The anisotropy in the measured clustering pattern in redshift-space is also driven by the unknown distance factors at the redshift in question, the Alcock-Paczynski distortion. This weakens growth rate measurements, but permits an extra geometric probe of the Hubble expansion rate. In this short chapter we will briefly describe the scientific background to the RSD technique, and forecast the potential of the SKA phase 1 and the SKA2 to measure the growth rate using both galaxy catalogues and intensity mapping, assessing their competitiveness with current and future optical galaxy surveys.