Dr Angela Goncalves | Postdoctoral Fellow

Goncalves, Angela

Welcome to my research page. I am a computational biologist interested in uncovering genetic (and non-genetic) bases for the molecular and functional variability observed in human pluripotent stem cells.

Currently, I am one of the analysts of the Human Induced Pluripotent Stem Cell Initiative - HipSci - a consortium generating a large collection of human iPSCs from healthy donors. Using computational and statistical methods, I am trying to identify the relative contribution of various biological and technical predictors to variation in transcription, epigenetic marking and differentiation potential of stem cell lines. I am also interested in the origin and clonal evolution of DNA lesions in normal tissues which can lead to the development of cancer and I am a member of the Early Detection Programme of the Cambridge Cancer Centre.

Before joining Sanger, I trained with Alvis Brazma for a PhD in Molecular Biology at the European Bioinformatics Institute (EBI-EMBL) and the University of Cambridge. There I worked on computational methods for the analysis of RNA sequencing data and applied them to study the divergence of gene expression and isoform usage in mammals. Earlier still, I have spent a year at the Centre for Earth Observation of the European Space Agency (ESA), working on a toolbox for analysing remote sensing satellite data and did my undergraduate at the University of Coimbra, Portugal, where I studied Computer Science.

Publications

  • Fgf and Esrrb integrate epigenetic and transcriptional networks that regulate self-renewal of trophoblast stem cells.

    Latos PA, Goncalves A, Oxley D, Mohammed H, Turro E and Hemberger M

    Nature communications 2015;6;7776

  • Regulatory Divergence of Transcript Isoforms in a Mammalian Model System.

    Leigh-Brown S, Goncalves A, Thybert D, Stefflova K, Watt S et al.

    PloS one 2015;10;9;e0137367

  • Extensive compensatory cis-trans regulation in the evolution of mouse gene expression.

    Goncalves A, Leigh-Brown S, Thybert D, Stefflova K, Turro E et al.

    Genome research 2012;22;12;2376-84

  • Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads.

    Turro E, Su SY, Gonçalves Â, Coin LJ, Richardson S and Lewin A

    Genome biology 2011;12;2;R13

  • A pipeline for RNA-seq data processing and quality assessment.

    Goncalves A, Tikhonov A, Brazma A and Kapushesky M

    Bioinformatics (Oxford, England) 2011;27;6;867-9

  • A global map of human gene expression.

    Lukk M, Kapushesky M, Nikkilä J, Parkinson H, Goncalves A et al.

    Nature biotechnology 2010;28;4;322-4

  • Fgf and Esrrb integrate epigenetic and transcriptional networks that regulate self-renewal of trophoblast stem cells.

    Latos PA, Goncalves A, Oxley D, Mohammed H, Turro E and Hemberger M

    Nature communications 2015;6;7776

  • Regulatory Divergence of Transcript Isoforms in a Mammalian Model System.

    Leigh-Brown S, Goncalves A, Thybert D, Stefflova K, Watt S et al.

    PloS one 2015;10;9;e0137367

  • Extensive compensatory cis-trans regulation in the evolution of mouse gene expression.

    Goncalves A, Leigh-Brown S, Thybert D, Stefflova K, Turro E et al.

    Genome research 2012;22;12;2376-84

  • Waves of retrotransposon expansion remodel genome organization and CTCF binding in multiple mammalian lineages.

    Schmidt D, Schwalie PC, Wilson MD, Ballester B, Gonçalves A et al.

    Cell 2012;148;1-2;335-48

  • Rapid turnover of long noncoding RNAs and the evolution of gene expression.

    Kutter C, Watt S, Stefflova K, Wilson MD, Goncalves A et al.

    PLoS genetics 2012;8;7;e1002841

  • Pol III binding in six mammals shows conservation among amino acid isotypes despite divergence among tRNA genes.

    Kutter C, Brown GD, Gonçalves A, Wilson MD, Watt S et al.

    Nature genetics 2011;43;10;948-55

  • A pipeline for RNA-seq data processing and quality assessment.

    Goncalves A, Tikhonov A, Brazma A and Kapushesky M

    Bioinformatics (Oxford, England) 2011;27;6;867-9

  • Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads.

    Turro E, Su SY, Gonçalves Â, Coin LJ, Richardson S and Lewin A

    Genome biology 2011;12;2;R13

  • A global map of human gene expression.

    Lukk M, Kapushesky M, Nikkilä J, Parkinson H, Goncalves A et al.

    Nature biotechnology 2010;28;4;322-4

Career/Research Highlights

Goncalves, Angela
Angela's Timeline
2013

Joined Darwin College as a Postdoctoral Affiliate

Joined Sanger

2012

6 month bridging postdoc at EBI

2009

EMBL (EBI) predoctoral fellowship

2007

Joined European Space Agency

M.Sc. in Computer Science