User profiles for Nuno Fonseca

Nuno A Fonseca

BIOPOLIS-CIBIO/InBIO, University of Porto, Portugal
Verified email at cibio.up.pt
Cited by 11264

Two independent modes of chromatin organization revealed by cohesin removal

…, A Pekowska, G Fudenberg, Y Loe-Mie, NA Fonseca… - Nature, 2017 - nature.com
Imaging and chromosome conformation capture studies have revealed several layers of
chromosome organization, including segregation into megabase-sized active and inactive …

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

…, D Earl, S Emrich, P Fedotov, NA Fonseca… - …, 2013 - academic.oup.com
Background The process of generating raw genome sequence data continues to become
cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished …

Expression Atlas update—an integrated database of gene and protein expression in humans, animals and plants

…, M Keays, YA Tang, NA Fonseca… - Nucleic acids …, 2016 - academic.oup.com
Expression Atlas ( http://www.ebi.ac.uk/gxa ) provides information about gene and protein
expression in animal and plant samples of different cell types, organism parts, developmental …

Assemblathon 1: a competitive assessment of de novo short read assembly methods

…, Z Ning, M Haimel, JT Simpson, NA Fonseca… - Genome …, 2011 - genome.cshlp.org
Low-cost short read sequencing technology has revolutionized genomics, though it is only
just becoming practical for the high-quality de novo assembly of a novel large genome. We …

ArrayExpress update–from bulk to single-cell expression data

…, L Huerta, A Ali, C Snow, NA Fonseca… - Nucleic acids …, 2019 - academic.oup.com
ArrayExpress ( https://www.ebi.ac.uk/arrayexpress ) is an archive of functional genomics data
from a variety of technologies assaying functional modalities of a genome, such as gene …

[HTML][HTML] Analyses of non-coding somatic drivers in 2,658 cancer whole genomes

…, D Craft, P Dhingra, K Diamanti, NA Fonseca… - Nature, 2020 - nature.com
The discovery of drivers of cancer has traditionally focused on protein-coding genes 1 , 2 , 3
– 4 . Here we present analyses of driver point mutations and structural variants in non-…

Expression Atlas update: from tissues to single cells

…, N George, S Fexova, NA Fonseca… - Nucleic acids …, 2020 - academic.oup.com
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 proteins in various biological …

[HTML][HTML] Genomic basis for RNA alterations in cancer

… 3 4 5 6 7 Demircioğlu Deniz 8 9 Fonseca Nuno A. 2 He … - Nature, 2020 - nature.com
Transcript alterations often result from somatic changes in cancer genomes 1 . Various forms
of RNA alterations have been described in cancer, including overexpression 2 , altered …

Expression Atlas: gene and protein expression across multiple studies and organisms

I Papatheodorou, NA Fonseca, M Keays… - Nucleic acids …, 2018 - academic.oup.com
Expression Atlas ( http://www.ebi.ac.uk/gxa ) is an added value database that provides
information about gene and protein expression in different species and contexts, such as tissue, …

Expression Atlas update—a database of gene and transcript expression from microarray-and sequencing-based functional genomics experiments

…, T Burdett, B Fiorelli, NA Fonseca… - Nucleic acids …, 2014 - academic.oup.com
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 types, organism parts, …