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Details

  • Name

    Nuno Fonseca
  • Cluster

    Computer Science
  • Role

    External Research Collaborator
  • Since

    01st June 2009
Publications

2018

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

Authors
Papatheodorou, I; Fonseca, NA; Keays, M; Tang, YA; Barrera, E; Bazant, W; Burke, M; Füllgrabe, A; Pomer Fuentes, AM; George, N; Huerta, L; Koskinen, S; Mohammed, S; Geniza, MJ; Preece, J; Jaiswal, P; Jarnuczak, A; Huber, W; Stegle, O; Vizcaíno, JA; Brazma, A; Petryszak, R;

Publication
Nucleic Acids Research

Abstract

2018

Gramene 2018: unifying comparative genomics and pathway resources for plant research

Authors
Tello Ruiz, MK; Naithani, S; Stein, JC; Gupta, P; Campbell, M; Olson, A; Wei, S; Preece, J; Geniza, MJ; Jiao, Y; Lee, YK; Wang, B; Mulvaney, J; Chougule, K; Elser, J; Bader, NA; Kumari, S; Thomason, J; Kumar, V; Bolser, DM; Naamati, G; Tapanari, E; Fonseca, NA; Huerta, L; Iqbal, H; Keays, M; Pomer Fuentes, AM; Tang, YA; Fabregat, A; D'Eustachio, P; Weiser, J; Stein, LD; Petryszak, R; Papatheodorou, I; Kersey, PJ; Lockhart, P; Taylor, C; Jaiswal, P; Ware, D;

Publication
Nucleic Acids Research

Abstract

2018

Inferences on specificity recognition at the Malusxdomestica gametophytic self-incompatibility system

Authors
Pratas, MI; Aguiar, B; Vieira, J; Nunes, V; Teixeira, V; Fonseca, NA; Iezzoni, A; van Nocker, S; Vieira, CP;

Publication
SCIENTIFIC REPORTS

Abstract
In Malus x domestica (Rosaceae) the product of each SFBB gene (the pollen component of the gametophytic self-incompatibility (GSI) system) of a S-haplotype (the combination of pistil and pollen genes that are linked) interacts with a sub-set of non-self S-RNases (the pistil component), but not with the self S-RNase. To understand how the Malus GSI system works, we identified 24 SFBB genes expressed in anthers, and determined their gene sequence in nine M. domestica cultivars. Expression of these SFBBs was not detected in the petal, sepal, filament, receptacle, style, stigma, ovary or young leaf. For all SFBBs (except SFBB15), identical sequences were obtained only in cultivars having the same S-RNase. Linkage with a particular S-RNase was further established using the progeny of three crosses. Such data is needed to understand how other genes not involved in GSI are affected by the S-locus region. To classify SFBBs specificity, the amino acids under positive selection obtained when performing intra-haplotypic analyses were used. Using this information and the previously identified S-RNase positively selected amino acid sites, inferences are made on the S-RNase amino acid properties (hydrophobicity, aromatic, aliphatic, polarity, and size), at these positions, that are critical features for GSI specificity determination.

2018

ArrayExpress update – from bulk to single-cell expression data

Authors
Athar, A; Füllgrabe, A; George, N; Iqbal, H; Huerta, L; Ali, A; Snow, C; Fonseca, NA; Petryszak, R; Papatheodorou, I; Sarkans, U; Brazma, A;

Publication
Nucleic Acids Research

Abstract

2017

QmihR: Pipeline for Quantification of Microbiome in Human RNA-seq

Authors
Cavadas, B; Ferreira, J; Camacho, R; Fonseca, NA; Pereira, L;

Publication
11th International Conference on Practical Applications of Computational Biology & Bioinformatics, PACBB 2017, Porto, Portugal, 21-23 June, 2017

Abstract