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Details

  • Name

    Nuno Fonseca
  • Cluster

    Computer Science
  • Role

    External Research Collaborator
  • Since

    01st June 2009
Publications

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

2017

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; Fuentes, AM; George, N; Huerta, L; Koskinen, S; Mohammed, S; Geniza, M; Preece, J; Jaiswal, P; Jarnuczak, AF; Huber, W; Stegle, O; Vizcaino, JA; Brazma, A; Petryszak, R;

Publication
Nucleic Acids Research

Abstract

2017

The RNASeq-er API - a gateway to systematically updated analysis of public RNA-seq data

Authors
Petryszak, R; Fonseca, NA; Füllgrabe, A; Huerta, L; Keays, M; Tang, YA; Brazma, A;

Publication
Bioinformatics

Abstract

2017

Transcription factor activities enhance markers of drug sensitivity in cancer

Authors
Garcia-Alonso, LM; Iorio, F; Matchan, A; Fonseca, NA; Jaaks, P; Peat, G; Pignatelli, M; Falcone, F; Benes, CH; Dunham, I; Bignell, GR; McDade, S; Garnett, MJ; Saez-Rodriguez, J;

Publication
Cancer Research

Abstract

2017

Two independent modes of chromatin organization revealed by cohesin removal

Authors
Schwarzer, W; Abdennur, N; Goloborodko, A; Pekowska, A; Fudenberg, G; Loe Mie, Y; Fonseca, NA; Huber, W; Haering, CH; Mirny, L; Spitz, F;

Publication
Nature

Abstract
Imaging and chromosome conformation capture studies have revealed several layers of chromosome organization, including segregation into megabase-sized active and inactive compartments, and partitioning into sub-megabase domains (TADs). It remains unclear, however, how these layers of organization form, interact with one another and influence genome function. Here we show that deletion of the cohesin-loading factor Nipbl in mouse liver leads to a marked reorganization of chromosomal folding. TADs and associated Hi-C peaks vanish globally, even in the absence of transcriptional changes. By contrast, compartmental segregation is preserved and even reinforced. Strikingly, the disappearance of TADs unmasks a finer compartment structure that accurately reflects the underlying epigenetic landscape. These observations demonstrate that the three-dimensional organization of the genome results from the interplay of two independent mechanisms: cohesin-independent segregation of the genome into fine-scale compartments, defined by chromatin state; and cohesin-dependent formation of TADs, possibly by loop extrusion, which helps to guide distant enhancers to their target genes.