Dr Cei Abreu-Goodger

Reader in Bioinformatics

Institute of Ecology and Evolution
School of Biological Sciences

Abreu RNAlab

Street: Rm 117, Ashworth Building
City
Post code

Biography

Background

2021- Reader in Bioinformatics at the Institute of Evolutionary Biology, University of Edinburgh

2010-2021 Group leader at the National Laboratory of Genomics for Biodiversity (Langebio Cinvestav), Irapuato, Mexico

2008-2010 Postdoctoral research fellow at the EMBL-European Bioinformatics Institute (EBI), Cambridge, UK

2006-2008 Postdoctoral research fellow at the Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK

2005-2006 Postdoctoral research fellow at the Centre for Genomic Sciences, National Autonomous University of Mexico

2000-2005 Ph.D. Biochemical Sciences (Bioinformatics), Institute of Biotechnology (IBT), National Autonomous University of Mexico

1995-2000 B.Sc. Basic Biomedical Research, Institute of Biomedical Research (IIB), National Autonomous University of Mexico

Teaching & PhD supervision

Undergraduate teaching

Genomes and Genomics 3 (BILG09005) (Lecturer)

Postgraduate teaching

Statistics and Data Analysis (PGBI11003) (Lecturer and Course Organiser)
Next Generation Genomics (BILG11004) (Lecturer)

Open to PhD supervision enquiries?

Yes

Areas of interest for supervision

Bioinformatic projects related to small non-coding RNA, gene expression and regulation, transposable elements, genome evolution.

Current PhD students supervised

Current students (2023)

Isaac Martinez-Ugalde (3rd year Evolutionary Biology)
Yenetzi Villagrana-Pacheco (2nd year Evolutionary Biology)
Adriana Orrego-Durañona (1st year Cell and Molecular Biology), co-supervised with Dr Elizabeth Bayne
Logan Wang (MSc Bioinfomatics dissertation project)
Yao Tong (MSc Bioinformatics dissertation project)
Thomas Cattanach (Honours thesis project, Cell Biology)

Past PhD students supervised

Recently graduated students (2000-2022)

Xiaoqi Luo. MSc dissertation: “Predicting regulatory motifs from large scale transcriptome resources”. Master of Science in Bioinformatics. August 2022.
Guanke Bao. MSc dissertation: “Predicting regulatory motifs from large scale transcriptome resources”. Master of Science in Bioinformatics. August 2022.
Ruoci Chen. MSc dissertation: “Dissecting RNA interference mechanisms and functions in the human pathogen Cryptococcus neoformans”. Master of Science in Bioinformatics. August 2022. Co-supervised with Dr Elizabeth Bayne.
Tantely Delaine. BSc thesis: “Genomic drivers of gene regulation by small RNA in the parasitic nematode, Heligmosomoides bakeri”. BSc (Hons) Biological Sciences (Evolutionary Biology). May 2022.
Panachai Punnatin. MSc dissertation: “Traversing networks of transcriptomes to predict regulatory motifs”. Master of Science in Bioinformatics. August 2021.
Zulia Fernandina Nieves López. MSc thesis: “Origin and function of phytopathogen small RNAs produced during infection”. Plant Biotechnology Master’s program (Mexico). August 2021.
Yenetzi Villagrana Pacheco. MSc thesis: “Predicting microRNA functions from individual cell transcriptomes”. Plant Biotechnology Master’s program (Mexico). August 2021.
José Roberto Bermúdez Barrientos. PhD thesis: “Species interactions mediated by small RNAs”. Integrative Biology PhD program (Mexico). August 2020.
Gonzalo Córdova López. MSc thesis: “Function and horizontal transfer of the RmNV-20S and RmNV-23S Narnavirus that reside within Rhizopus microsporus”. Integrative Biology Master’s program (Mexico). August 2020. Co-supervised with Dr Laila Pamela Partida-Martínez.
Carlos Daniel Luna Gómez. MSc thesis: “Genome-wide prediction of tissue-specific enhancers during Drosophila melanogaster development”. Integrative Biology Master’s program (Mexico). August 2020. Co-supervised with Dr Katarzyna Oktaba-Sosin.
Daniel Lepe Soltero. PhD thesis: “Effects of hybridization on paternal genome activation in Arabidopsis embryogenesis”. Plant Biotechnology PhD program (Mexico). July 2020. Co-supervised with Dr Charles Stewart Gillmor III.
Isaac Martínez Ugalde. MSc thesis: “Characterization of the biogénesis of secreted transposable element derived small RNAs by Heligmosomoides bakeri”. Integrative Biology Master’s program (Mexico). February 2020.
Michelle Crisely Munguía Figueroa. MSc thesis: “The cellular mechanisms of lifespan extension by metformin in budding yeast”. Integrative Biology Master’s program (Mexico). February 2020. Co-supervised with Dr Alexander de Luna-Fors.

I am currently a Reader in Bioinformatics at the Institute of Ecology and Evolution (University of Edinburgh). My research interests are focused on gene regulation, small RNAs and transposable elements, using computational analyses and a variety of host-pathogen models. I did my PhD in Mexico, studying the evolution of regulatory RNA in bacteria, a postdoc in Cambridge UK working on the function of microRNAs in vertebrates, and was a group leader in Mexico for ten years before moving to the University of Edinburgh.

Publications

Gene expression differentiation in the reproductive tissues of Drosophila willistoni subspecies and their hybrids 31 Mar 2023 In: Molecular Ecology
DOI: https://doi.org/10.1111/mec.16941
Research output: Contribution to Journal › Article (E-pub ahead of print)
Translation comes first: Ancient and convergent selection of codon usage bias across prokaryotic genomes (14 pages) 1 Dec 2022 In: Journal of molecular evolution, vol. 90, pp. 438-451
DOI: https://doi.org/10.1007/s00239-022-10074-0
Research output: Contribution to Journal › Article (Published)
Hybridization alters maternal and paternal genome contributions to early plant embryogenesis 31 Oct 2022 In: Development
DOI: https://doi.org/10.1242/dev.201025
Research output: Contribution to Journal › Article (Published)
Triploid-induced complete sterility in the scallop Nodipecten subnodosus might be triggered by an early and sustained DNA damage response 15 Oct 2022 In: Aquaculture, vol. 559
DOI: https://doi.org/10.1016/j.aquaculture.2022.738422
Research output: Contribution to Journal › Article (Published)
Multiscale analysis of the randomization limits of the chromosomal gene organization between Lepidoptera and Diptera (9 pages) 26 Jan 2022 In: Proceedings of the Royal Society B-Biological Sciences, vol. 289
DOI: https://doi.org/10.1098/rspb.2021.2183
Research output: Contribution to Journal › Article (Published)
A de novo transcriptional atlas in Danaus plexippus reveals variability in dosage compensation across tissues (13 pages) 25 Jun 2021 In: Communications biology, vol. 4
DOI: https://doi.org/10.1038/s42003-021-02335-3
Research output: Contribution to Journal › Article (Published)
Differential gene expression reflects larval development and survival of monarch butterflies on different milkweed hosts 6 Sep 2020
DOI: https://doi.org/10.1101/2020.09.05.284489
Research output: › Working paper (Published)
Narnaviruses: Novel players in fungal–bacterial symbioses (12 pages) 1 Jul 2020 In: The ISME Journal: Multidisciplinary Journal of Microbial Ecology, vol. 14, pp. 1743–1754
DOI: https://doi.org/10.1038/s41396-020-0638-y
Research output: Contribution to Journal › Article (Published)
Maternal genome dominance in early plant embryogenesis 15 Jan 2020
DOI: https://doi.org/10.1101/2020.01.14.905992
Research output: › Working paper (Published)
Disentangling sRNA-Seq data to study RNA communication between species 27 Dec 2019 In: Nucleic Acids Research
DOI: https://doi.org/10.1093/nar/gkz1198
Research output: Contribution to Journal › Article (Published)
Highlights of the mini-symposium on extracellular vesicles in inter-organismal communication, held in Munich, Germany, August 2018 (8 pages) 1 Dec 2019 In: Journal of Extracellular Vesicles, vol. 8
DOI: https://doi.org/10.1080/20013078.2019.1590116
Research output: Contribution to Journal › Article (Published)
Secretion of an Argonaute protein by a parasitic nematode and the evolution of its siRNA guides (13 pages) 1 Mar 2019 In: Nucleic Acids Research
DOI: https://doi.org/10.1093/nar/gkz142
Research output: Contribution to Journal › Article (E-pub ahead of print)
Danger signals activate a putative innate immune system during regeneration in a filamentous fungus (21 pages) 30 Nov 2018 In: PLoS Genetics
DOI: https://doi.org/10.1371/journal.pgen.1007390
Research output: Contribution to Journal › Article (Published)
Precursor miRNAs are trafficked along axons associated with vesicles and locally processed to regulate growth cone steering (42 pages) 14 Nov 2018
DOI: https://doi.org/10.1101/470393
Research output: › Working paper (Published)
Identification of miR-708-5p in peripheral blood monocytes: Potential marker for postmenopausal osteoporosis in Mexican-Mestizo population (10 pages) 15 Oct 2018 In: Experimental Biology and Medicine, vol. 243, pp. 1027–1036
DOI: https://doi.org/10.1177/1535370218806828
Research output: Contribution to Journal › Article (Published)
Sex determination and differentiation genes in a functional hermaphrodite scallop, Nodipecten subnodosus (14 pages) 1 Jan 2018 In: Marine Genomics, vol. 37, pp. 161-175
DOI: https://doi.org/10.1016/j.margen.2017.11.004
Research output: Contribution to Journal › Article (Published)
Arabidopsis thaliana miRNAs promote embryo pattern formation beginning in the zygote (11 pages) 15 Nov 2017 In: Developmental Biology, vol. 431, pp. 141-151
DOI: https://doi.org/10.1016/j.ydbio.2017.09.009
Research output: Contribution to Journal › Article (Published)
Annotating and quantifying pri-miRNA transcripts using RNA-Seq data of wild type and serrate-1 globular stage embryos of Arabidopsis thaliana (6 pages) 12 Oct 2017 In: Data in brief, vol. 15, pp. 642-647
DOI: https://doi.org/10.1016/j.dib.2017.10.019
Research output: Contribution to Journal › Article (E-pub ahead of print)
Transcriptional responses of ecologically diverse drosophila species to larval diets differing in relative sugar and protein ratios (17 pages) 23 Aug 2017 In: PLoS ONE, vol. 12
DOI: https://doi.org/10.1371/journal.pone.0183007
Research output: Contribution to Journal › Article (Published)
RNA-mediated communication between helminths and their hosts: The missing links (6 pages) 2 Feb 2017 In: Rna biology, vol. 14, pp. 436-441
DOI: https://doi.org/10.1080/15476286.2016.1274852
Research output: Contribution to Journal › Article (E-pub ahead of print)

View all 33 publications on Research Explorer

This article was published on 25 Sep, 2023