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Ana Raquel Soares is an Assistant Researcher (CEECIND/00284/2018) and PI of the tRNA epitranscriptome and disease Group (tRED) at iBiMED-UAveiro. She holds a major in Pharmaceutical Sciences, obtained in 2005 at the Faculty of Pharmacy, UCoimbra and completed her PhD in Pharmaceutical Sciences - Molecular and Cellular Biology in 2011 by the same institution. Currently, she leads a team of 6, including 2 Master students, 3 PhD students, and 1 Post-doc. Past members include 1 Post-doctoral researcher, 1 PhD student, 7 Technicians, 13 Master students and 1 Project Manager. Throughout her scientific path, she published 31 papers in SCI indexed journals and 2 book chapters. During her PhD, she was one of the first to apply next generation sequencing (NGS) technologies to uncover novel miRNAs and miRNA expression patterns during vertebrate development, generated miRNA profiles for different stages of cervical cancer and used siRNA technologies to uncover miRNA targets in zebrafish. During that period, she was a visiting researcher at CESAM, UAveiro, IGC - Gulbenkian Science Institute Lisbon, and the GIGA Interdisciplinary Biomedical Sciences Research Center, ULiege, Belgium. After obtaining the PhD, Ana was awarded a FCT post-doctoral grant at UAveiro to study small non-coding RNAs derived from tRNAs and found that those molecules were able to enter the RNAi pathway and were differentially expressed in infection and in cancer, an indicator of biomarker potential. Ana was also involved in the development of an animal model (zebrafish) of translation errors and found that tRNA mutations that affected translation have a potent impact on proteostasis, promoting gradual cellular degeneration, in animal and cellular models. In 2015, she moved to iBiMED, and focused her research on tRNA epitranscriptome dynamics and how it impacts translation and proteostasis maintenance in physiology and pathology. She is particularly interested in understanding the molecular mechanisms governing tRNA modifications, their relevance for translation control and what drives tRNA modification disruption, and consequently, translation dysfunction and its relevance in the context of aging, age-related diseases and disease susceptibility. The main goal is to uncover if epitranscriptome signatures can constitute disease biomarkers and if epitranscriptome modulation can be used as a therapeutic strategy in diseases where translation dysfunction is a hallmark. In the last years she obtained funding as PI for 5 projects on the topic from different sources, namely FCT, H2020 and Alzheimer's Association, in a total of 1,5M euros. Her team has also found that tRNA modifications regulate tsRNA generation in response to stress. Furthermore, she was involved in studies that show that tRNA anticodon hypomodification induces codon-specific mistranslation and protein aggregation and that tRNA pool changes occur in lung cancer and correlate with malignant behavior, indicating that targeting tRNAs in cancer cells may render cells susceptible to therapy. Her group has also evidence that specific tRNA modifying enzymes can represent sensors of protein aggregation burden in Alzheimer's, and that specific tRNA modifications are essential for protein translation and replication of codon-biased viral genomes (in prep). The tRED group has active collaborations with different groups from national and international institutions, namely Goethe University Frankfurt, Centre dImmunologie Marseille-Luminy, Stark Neurosciences Research Institute, iMED - ULisbon, and UAveiro. Ana is also actively engaged in outreach activities: she coordinates the participation of iBiMED in dissemination activities such as Xperimenta UA, and formed the UAVR-RNA Club, supported by the RNA Society. She represents iBiMED in the PT-OPENScreen consortium, and is currently the Coordinator of the Molecular Medicine laboratory/OpenSpace Facility at iBiMED.
Identification

Personal identification

Full name
Ana Raquel Santos Calhôa Mano Soares

Citation names

  • Soares, Ana Raquel

Author identifiers

Ciência ID
A812-9698-9321
ORCID iD
0000-0003-4000-7461

Email addresses

  • anarsoares@gmail.com (Personal)

Knowledge fields

  • Natural sciences - Biological Sciences - Other Biological Topics
  • Medical and Health Sciences - Medical Biotechnology - Technologies Involving the Manipulation of Cells, Tissues, Organs or the Whole Organism
  • Medical and Health Sciences - Medical Biotechnology - Gene-based Diagnostics and Therapeutic Interventions
  • Natural sciences - Biological Sciences - Other Biological Topics
  • Natural sciences - Biological Sciences - Cell Biology
  • Natural sciences - Biological Sciences - Molecular Biology
  • Medical and Health Sciences - Basic Medicine - Human Genetics
  • Medical and Health Sciences - Basic Medicine - Neurosciences
  • Natural sciences - Biological Sciences - Biochemistry
  • Natural sciences - Biological Sciences - Developmental Biology

Languages

Language Speaking Reading Writing Listening Peer-review
English Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1)
French Intermediate (B1) Intermediate (B1) Intermediate (B1) Intermediate (B1)
German Beginner (A1) Beginner (A1) Beginner (A1) Beginner (A1)
Portuguese (Mother tongue)
Education
Degree Classification
2022/06/22 - 2022/06/24
Concluded
EMBO Project Management Course (Outros)
EMBO Solutions GmbH, Germany
2022/04 - 2022/04
Concluded
EMBO Laboratory Leadership for Group Leaders (Outros)
EMBO Solutions GmbH, Germany

Leadership Sculptor GmbH, Germany
2021/10 - 2022/01
Concluded
International Professional Development Program for University Professors and Researchers (iPDP) (Outros)
IMFAHE - International Mentoring Foundation for the Advancement of Higher Education, Spain
2018 - 2018
Concluded
HiTech – Technology commercialization and entrepreneurship for researchers (Outros)
Universidade do Porto Porto Business School, Portugal

HiSeedTech - Porto Business School, Portugal

Brown University, United States

Rutgers University New Brunswick, United States
2014
Concluded
Introductory Bioinformatics (IB14S) (Outros)
Instituto Gulbenkian de Ciência, Portugal
2012
Concluded
Coordinator Researcher (Animal Laboratory Science) – Category C FELASA (Título de especialista)
Direcção-Geral de Alimentação e Veterinária, Portugal
2011/09
Concluded
PhD in Pharmaceutical Sciences - Molecular and cellular biology branch (Doutoramento)
Universidade de Coimbra Faculdade de Farmácia, Portugal
"Zebrafish small RNAs: unraveling the expression and functions of novel microRNAs and tRNAfragments in a vertebrate model" (THESIS/DISSERTATION)
Approved with distinction and honor by unanimity
2005
Concluded
Pharmaceutical Sciences degree (Licenciatura)
Major in Pharmaceutical Sciences
Universidade de Coimbra Faculdade de Farmácia, Portugal
"Lipoplexes with NLS to increase transfection efficiency" (THESIS/DISSERTATION)
15
Affiliation

Science

Category
Host institution
Employer
2020/07/01 - Current Auxiliary Researcher (Research) Universidade de Aveiro, Portugal
Universidade de Aveiro Instituto de Biomedicina, Portugal
2019/01/01 - 2020/06/30 Contracted Researcher (Research) Universidade de Aveiro Instituto de Biomedicina, Portugal
2018/08/01 - 2018/12/31 Postdoc (Research) Universidade de Aveiro Instituto de Biomedicina, Portugal
2018/02/01 - 2018/07/31 Invited Auxiliary Researcher (Research) Universidade de Aveiro Departamento de Ciências Médicas, Portugal
2015/02/01 - 2018/01/31 Postdoc (Research) Universidade de Aveiro Instituto de Biomedicina, Portugal
2012/02/01 - 2015/01/31 Postdoc (Research) Universidade de Aveiro Centro de Estudos do Ambiente e do Mar, Portugal
2011/01/15 - 2012/01/14 Researcher (Research) Universidade de Aveiro Centro de Estudos do Ambiente e do Mar, Portugal
2007/06 - 2011/09 Researcher (Research) Universidade de Coimbra Faculdade de Farmácia, Portugal
2010/03 - 2010/06 Visiting Researcher (Research) Centre hospitalier universitaire de Liège, Belgium
2007 - 2010 Visiting Researcher (Research) Universidade de Aveiro Centro de Estudos do Ambiente e do Mar, Portugal
2007/09 - 2007/10 Visiting Researcher (Research) Instituto Gulbenkian de Ciência, Portugal
2005/12/01 - 2006/09/30 Researcher (Research) CNC.IBILI, Portugal
2004/10/01 - 2005/04/01 Research Trainee (Research) Universiteit Utrecht, Netherlands

Others

Category
Host institution
Employer
2006/09 - 2007/05 PhD fellow - BEB PhD program CNC.IBILI, Portugal
Projects

Contract

Designation Funders
2024/04/01 - Current Role of transfer RNAs modifications during plasmacytoid dendritic cell activation
2023.09709.CBM
Principal investigator
Universidade de Aveiro Instituto de Biomedicina, Portugal

Centre d'Immunologie de Marseille-Luminy, France
Fundação para a Ciência e a Tecnologia
Ongoing
2023/11/01 - Current AD-EpiMark: Exploring the tRNA epitranscriptome as a novel AD modifier
1149641
Principal investigator
Universidade de Aveiro Instituto de Biomedicina, Portugal
Alzheimer's Association
Ongoing
2023/03 - Current COST ACTION - Translational control in Cancer European Network (TRANSLACORE)
Researcher
Ongoing
2022 - Current Alzheimer's multi target teranostics
2022.06064.PTDC
Researcher
Universidade de Aveiro, Portugal
Ongoing
2021/01/01 - Current EpiViral - Viruses and Epitranscriptomics: seeking novel targets for antiviral therapy
952373
Principal investigator
Universidade de Aveiro Instituto de Biomedicina, Portugal

Goethe-Universität Frankfurt am Main, Germany

Leids Universitair Medisch Centrum, Netherlands
EU Framework Programme for Research and Innovation Spreading Excellence and Widening Participation
Ongoing
2020/07 - Current CEECIND/00284/2018 - tRNA-modifying enzymes and tRNA modifications as novel regulators of proteostasis in health and disease
CEECIND/00284/2018
Principal investigator
Universidade de Aveiro Instituto de Biomedicina, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
2018/06/01 - Current WISDOM - Impact of widespread protein aggregation through mammal lifespan and implications for age-related disease development
PTDC/BTM-TEC/29843/2017
Principal investigator
Universidade de Aveiro Instituto de Biomedicina, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
2017 - 2021/09 Protein aggregation through aging - pAGE
CENTRO-01-0145-FEDER-000003
Researcher
Comissão de Coordenação e Desenvolvimento Regional do Centro
2016/06/01 - 2019/12/31 Understanding the role of tRNA modifying enzymes in proteostasis in human health and disease.
PTDC/BIM-MEC/1719/2014
Principal investigator
Universidade de Aveiro Instituto de Biomedicina, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2016/06 - 2018/05 Role of ER-stress associated molecules IRE1 and GADD34 on innate activation by nucleic acids
PTDC/IMI-IMU/3615/2014
Researcher
Universidade de Aveiro Instituto de Biomedicina, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2010/05 - 2013/10 Functional genomics of ribosome infidelity phenotypes associated to human diseases.
PhD Student Fellow
Fundação para a Ciência e a Tecnologia
Concluded
2011 - 2012 Finding biomarkers of anti-microbial drug resistance - biology analysis of fungal pathogen interactions with the human immune system
SYBARIS – FP7-HEALTH
Integration into Research Grant Fellow
Concluded
2005 - 2006 Development of syntetic viral vectors for gene transfer: angiogenic factor expression for the therapy of vascular diseases
POCTI/BIO/48735/2002
Integration into Research Grant Fellow
Concluded
Outputs

Publications

Book chapter
  1. Soares, A.R.; Pereira, P.M.; Santos, M.A.S.. "Next-generation sequencing of miRNAs with Roche 454 GS-FLX technology: Steps for a successful application". 2012.
    10.1007/978-1-61779-427-8_13
  2. S. Santos, Manuel A.; Raquel, Ana. "Computational Tools for Identification of microRNAs in Deep Sequencing Data Sets". In Computational Biology and Applied Bioinformatics. InTech, 2011.
    10.5772/21173
Conference abstract
  1. Soares, Ana Raquel. "m5U54 tRNA hypomodification induces the generation of tRNA-derived small RNAs". Paper presented in RNA 2021, Virtual, 2021.
  2. Soares, Ana Raquel. "Influenza A Virus Disturbs the Host Cell Protein Homeostasis by Inducing the Accumulation of Insoluble Proteins". Paper presented in Viruses 2020—Novel Concepts in Virology, Barcelona, 2020.
    Published
Conference poster
  1. Mariana Marques; Bruno Ramos; Albuquerque, Hélio; Sarabando, Jéssica; Nunes, Alexandre; Ana Rita Ferreira; Artur M. S. Silva; et al. "Influenza A virus-induced formation of insoluble protein aggregates during infection as a potential target for novel host-directed antiviral strategies". Paper presented in European Congress of Virology, 2023.
  2. Diana Roberta Ribeiro; Nunes, Alexandre; Stefanie Kaiser; Daniela Ribeiro; Soares, Ana Raquel. "Impact of host cell tRNA modifications on Influenza A virus infection". Paper presented in European Congress of Virology, 2023.
  3. Marisa Pereira; Diana Barbosa; Stefanie Kaiser; Miguel Moutinho; Soares, Ana Raquel. "tRNA epitranscriptome altered dynamics in Alzheimer’s disease - a novel disease biomarker". Paper presented in RNA in disease - IX ptRNA meeting, 2023.
  4. Diana Roberta Ribeiro; Rafaela Salvador; Alexandre Nunes; Stefanie Kaiser; Daniela Ribeiro; Soares, Ana Raquel. "tRNA wobble uridine modifications are important for pathogenicity of influenza a virus". Paper presented in RNA in Disease - IX ptRNA, 2023.
  5. Marisa Pereira; Soares, Ana Raquel. "Amyloid pathology disrupts the tRNA epitranscriptome leading to impaired proteostasis in Alzheimer’s disease models". Paper presented in Workshop on “Novel Diagnostic Tools for Alzheimer’s Disease", 2023.
  6. Nunes, Alexandre; Daniela Ribeiro; Soares, Ana Raquel. "Unfolding the interplay between viruses and cellular proteostasis". Paper presented in Measuring translational dynamics by ribosome profiling course 2023, EMBO, 2023.
  7. Mariana Marques; Bruno Ramos; Albuquerque, Hélio; Artur M. S. Silva; Maria João Amorim; Soares, Ana Raquel; Daniela Ribeiro. "Targeting virus-induced accumulation of insoluble protein aggregates as an antiviral strategy against influenza A virus infection". Paper presented in XLVIII SPI Annual Meeting 2023, 2023.
  8. Ribeiro, Diana Roberta; Rafaela Salvador; Stefanie Kaiser; Daniela Ribeiro; Soares, Ana Raquel. Corresponding author: Soares, Ana Raquel. "tRNA wobble uridine modifications are important for pathogenicity and host responses upon influenza a virus infection". Paper presented in EMBO - The complex life of RNA, 2022.
  9. Marisa Pereira; Diana Barbosa; Stefanie Kaiser; Miguel Moutinho; Soares, Ana Raquel. Corresponding author: Soares, Ana Raquel. "ELP3 expression and tRNA modification levels are predictors of protein aggregation burden in Alzheimer disease models". Paper presented in EMBO - The complex life of RNA, 2022.
  10. Mariana Marques; Soares, Ana Raquel; Daniela Ribeiro. "Influenza A virus induces IRE1 activation and the accumulation of protein aggregates to ensure efficient viral propagation". Paper presented in ASV 2022, 2022.
  11. Bruno Ramos; Mariana Marques; Soares, Ana Raquel; Daniela Ribeiro. "Influenza A virus regulates the IRE1-dependent unfolded protein response to ensure efficient viral propagation". Paper presented in ASV 2021, 2021.
  12. Mariana Marques; Hélio Albuquerque; Soares, Ana Raquel; Daniela Ribeiro. "Exploring the interplay between influenza A virus and the host cell proteostasis". Paper presented in ASV 2021, 2021.
  13. Soares, Ana Raquel. "Lack of m5U modification in tRNAs induces the formation of tRNA-derived fragments". Paper presented in Keystone Virtual meeting on RNA Editing and Modifications: From Biology to Therap, 2020.
  14. Soares, Ana Raquel. "Influenza A virus disturbs the host-cell protein homeostasis by inducing the accumulation of insoluble proteins". Paper presented in Viruses2020 - Novel Concepts in Virology, 2020.
  15. Soares, Ana Raquel. "Proteomic analysis of tissue-specific protein aggregation signatures throughout mammalian aging". Paper presented in Protein Homeostasis in Health and Disease. November 11 - 14, 2020, Virtual, 2020.
  16. Soares, Ana Raquel. "From transcriptomics to proteomics: An integrated characterization of age-related protein aggregation throughout the mammalian lifespan.". Paper presented in EMBL Conference: From Functional Genomics to Systems Biology, 2020.
  17. Soares, Ana Raquel. "Characterization of wide-spread proteome aggregation through aging in mammals". Paper presented in EMBO Proteostasis, 2019.
  18. Soares, Ana Raquel. "Investigating the role of tRNA modifying enzymes in human proteostasis". Paper presented in RNA 2019, 2019.
  19. Soares, Ana Raquel. "Discovery of tRNA modifying enzymes that affect proteostasis by high content screenings". Paper presented in ptRNA 2019, 2019.
  20. Soares, Ana Raquel. "Influenza A virus induces alterations on the pool of host-cell tRNAmodifying". Paper presented in V Post-Graduate Symposium in Biomedicine, 2019.
  21. Soares, Ana Raquel. "Using CRISPR-Cas9 system to knockout ELP3 in human cells". Paper presented in V Post-Graduate Symposium in Biomedicine, 2019.
  22. Soares, Ana Raquel. "Identification of tRNA modifying enzymes as novel proteostasis players in human cells". Paper presented in tRNA 2018, 2018.
  23. Soares, Ana Raquel. "Identifying novel proteostasis players in health and disease". Paper presented in Cold Spring Harbor meeting - Protein Homeostasis in Health and Disease, 2018.
  24. Soares, Ana Raquel. "A reporter assay to monitor protein aggregation in vivo in mammalian cells". Paper presented in EMBO Conference - Protein Quality Control: Success and failure in health and disease, 2017, 2017.
  25. Soares, Ana Raquel. "Human cells cope with tRNA misexpression by activating protein quality control mechanisms". Paper presented in EMBO Conference - Protein Quality Control: Success and failure in health and disease, 2017, 2017.
  26. Marisa Pereira; Soares, Ana Raquel. "tRNA modifying enzymes - novel players in proteostasis regulation in mammals". Paper presented in III iBiMED Symposium, University of Aveiro, 2017.
  27. "De-regulation of specific tRNA modifying enzymes lead to accumulation of misfolded proteins in human cells". Paper presented in XLI Jornadas Portuguesas de Genética, 2017.
  28. Soares, Ana Raquel. "Study of proteome imbalances during aging in mice". Paper presented in Unfolded Proteins: from basic to bedside, 2016.
  29. "Study of proteome imbalances during aging in mice". Paper presented in UnfoldedProteins: from basic to bedside, 2016.
  30. "A new class of zebrafish tissue-specific non-coding RNAs derived from tRNAs with miRNA-like features". Paper presented in Young EMBO Scientists’ forum, 2013.
  31. "Genome mistranslation leads to proteome instability through protein aggregation and accumulation of oxidative stress in zebrafish". Paper presented in Barcelona BioMed conferences – Gene translation: fidelity and quality control, 2013.
  32. "Ribosome mistranslations produce reactive oxygen species and increase protein aggregation in zebrafish". Paper presented in FEBS International workshop: New developments in RNA biology, 2012.
  33. "Identification of dicer-dependent tRNA derived fragments in zebrafish". Paper presented in FEBS International workshop: New developments in RNA biology, 2012.
  34. "Proteome instability induced by tRNA misreading leads to protein aggregation and produces oxidative stress in zebrafish embryos". Paper presented in EMBO|EMBL Symposium Quality Control from molecules to organelles, 2012.
  35. "Impact of RNA mistranslation on zebrafish development". Paper presented in XXXVI Jornadas Portuguesas de Genética, 2011.
  36. "Induced serine mistranslation in zebrafish". Paper presented in 23rd international tRNA workshop: from the origin of life to biomedicine, 2010.
  37. "Parallel DNA pyrosequencing unveils a novel class of small non-coding RNAs derived from tRNAs in zebrafish". Paper presented in 23rd international tRNA workshop: from the origin of life to biomedicine, 2010.
  38. "A new class of zebrafish tissue-specific non-coding RNAs originated from Dicer processing of transfer RNAs". Paper presented in EMBO-EMBL Symposium The non-coding genome, 2010.
  39. "Identification of novel zebrafish microRNAs using parallel DNA pyrosequencing". Paper presented in Keystone Symposia -The Biology of RNA silencing, 2009.
  40. "Identification of novel zebrafish microRNAs by highthroughput sequencing and target validation of novel dre-miR-2188". Paper presented in VI Congresso Nacional de RNA, 2009.
  41. "microRNA expression deregulation in Human Cervical Cancer". Paper presented in Miami 2008 WinterSymposium “Regulatory RNA in Biology and Human Health, 2008.
  42. "MicroRNA expressionprofiling in cervical cancer". Paper presented in EMBO Protein Synthesis and Translational Control Meeting, 2007.
  43. "Diversity of miRNAS in zebrafish using massive parallel sequencing". Paper presented in MicroRNAs Europe 2007 Meeting on MicroRNAs: Biology to Development and Disease (Cambridge, UK), 2007.
  44. "Global microRNA profiles in cervical cancer". Paper presented in MicroRNAs Europe 2007 Meeting on MicroRNAs: Biology to Development and Disease (Cambridge,UK)., 2007.
  45. "Highthroughput sequencing of zebrafish miRNAS". Paper presented in IV Congresso Nacional de RNA, 2007.
Journal article
  1. Marques, Mariana; Ramos, Bruno; Albuquerque, Hélio; Pereira, Marisa; Ribeiro, Diana Roberta; Nunes, Alexandre; Sarabando, Jéssica; et al. "Influenza A virus propagation requires the activation of the unfolded protein response and the accumulation of insoluble protein aggregates". iScience 27 3 (2024): 109100. http://dx.doi.org/10.1016/j.isci.2024.109100.
    10.1016/j.isci.2024.109100
  2. Silva, Ana Rita R.; Silva, Patrícia V.; Soares, Ana Raquel; González-Alcaraz, M. Nazaret; van Gestel, Cornelis A. M.; Roelofs, Dick; Moura, Gabriela; Soares, Amadeu M. V. M.; Loureiro, Susana. "Daphnia magna Multigeneration Exposure to Carbendazim: Gene Transcription Responses". Toxics 11 11 (2023): 918. http://dx.doi.org/10.3390/toxics11110918.
    Published • 10.3390/toxics11110918
  3. Pereira, Marisa; Ribeiro, Diana R.; Berg, Maximilian; Tsai, Andy P.; Dong, Chuanpeng; Nho, Kwangsik; Kaiser, Stefanie; Moutinho, Miguel; Soares, Ana R.. "Amyloid pathology reduces ELP3 expression and tRNA modifications leading to impaired proteostasis". Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease (2023): 166857. http://dx.doi.org/10.1016/j.bbadis.2023.166857.
    Published • 10.1016/j.bbadis.2023.166857
  4. Diana Roberta Ribeiro; Alexandre Nunes; Daniela Ribeiro; Soares, Ana Raquel. Corresponding author: Soares, Ana Raquel. "The hidden RNA code: implications of the RNA epitranscriptome in the context of viral infections". Frontiers in genetics (2023): https://doi.org/10.3389/fgene.2023.1245683.
    Published • https://doi.org/10.3389/fgene.2023.1245683
  5. Gonçalves, Bruna; Barbosa, Ana; Soares, Ana Raquel; Henriques, Mariana; Silva, Sónia. "Sfl1 is required for Candida albicans biofilm formation under acidic conditions". Biochimie (2023): http://dx.doi.org/10.1016/j.biochi.2023.01.011.
    Published • 10.1016/j.biochi.2023.01.011
  6. Marisa Pereira; Diana R. Ribeiro; Maximilian Berg; Andy P Tsai; Kwangsik Nho; Stefanie Kaiser; Miguel Moutinho; Soares, Ana Raquel. Corresponding author: Soares, Ana Raquel. "Amyloid pathology reduces ELP3 expression and tRNA modifications leading to impaired proteostasis". BBA - Molecular Basis of Disease (2023):
    Under revision
  7. Diana Roberta Ribeiro; Alexandre Nunes; Daniela Ribeiro; Soares, Ana Raquel. Corresponding author: Soares, Ana Raquel. "The hidden RNA code: implications of the RNA epitranscriptome in the context of viral infections". Frontiers in Genetics - RNA (2023):
    Under revision
  8. Mariana Marques; Soares, Ana Raquel; Daniela Ribeiro. "Influenza A virus activates the unfolded protein response and induces the accumulation of insoluble protein aggregates that are essential for efficient viral propagation". Molecular Cell (2023):
    Submitted
  9. Sara B Salazar; Maria Joana F Pinheiro; Danielle Sotti-Novais; Ana R Soares; Maria M Lopes; Teresa Ferreira; Vitória Rodrigues; et al. "Disclosing azole resistance mechanisms in resistant Candida glabrata strains encoding wild-type or gain-of-function CgPDR1 alleles through comparative genomics and transcriptomics". G3 Genes|Genomes|Genetics (2022): https://doi.org/10.1093/g3journal/jkac110.
    10.1093/g3journal/jkac110
  10. "Steroid Quinoline Hybrids for Disruption and Reversion of Protein Aggregation Processes". ACS Med. Chem. Lett. (2022): https://pubs.acs.org/doi/abs/10.1021/acsmedchemlett.1c00604.
    Published
  11. "The role of microRNAs on proteostasis decline and protein aggregation during brain and skeletal muscle aging". IJMS (2022): https://www.mdpi.com/1422-0067/23/6/3232.
    Published • https://doi.org/10.3390/ijms23063232
  12. Mafalda Santos; Ana Fidalgo; Ana Sofia Varanda; Ana Raquel Soares; Gabriela M. Almeida; Diana Martins; Nuno Mendes; Carla Oliveira; Manuel A.S. Santos. Corresponding author: Manuel A.S. Santos. "Upregulation of tRNA-Ser-AGA-2-1 promotes malignant behavior in normal bronchial cells". Frontiers Molecular Biosciences - Cellular Biochemistry (2022):
    Accepted • DOI: 10.3389/fmolb.2022.809985
  13. Soares, Ana Raquel; Marjolein kikkert; Stefanie Kellner-Kaiser; Daniela Ribeiro. "Editorial: Viruses and Epitranscriptomes: Regulation of Infection and Antiviral Response". Front Cell Dev Biol. (2022): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9125315/.
    Published
  14. Sandra Magalhães; Idália Almeida; Filipa Martins; Fátima Camões; Ana R. Soares; Brian J. Goodfellow; Sandra Rebelo; Alexandra Nunes. "FTIR Spectroscopy as a Tool to Study Age-Related Changes in Cardiac and Skeletal Muscle of Female C57BL/6J Mice". Molecules (2021): https://doi.org/10.3390/molecules26216410.
    10.3390/molecules26216410
  15. Margarida Ferreira; Stephany Franscisco; Soares, Ana Raquel; Ana Nobre; Miguel Pinheiro; Andreia Reis; Sonya Neto; et al. "Integration of differential gene expression with weighted gene correlation network analysis identifies genes whose expression is remodeled throughout physiological aging in mouse tissues". Aging (2021): https://www.aging-us.com/article/203379.
    Published • https://doi.org/10.18632/aging
  16. Marisa Pereira; Diana Roberta Ribeiro; Miguel M. Pinheiro; Margarida Ferreira; Stefanie Kellner; Soares, Ana Raquel. "m5U54 tRNA Hypomodification by lack of TRMT2A Drives the Generation of tRNA-Derived Small RNAs". IJMS (2021): https://www.mdpi.com/1422-0067/22/6/2941.
    Open access • Published • 10.3390/ijms22062941
  17. Joana F Tavares; Nick K. Davis; Ana Poim; Andreia Reis; Stefanie Kellner; Inês Sousa; Ana R. Soares; et al. "tRNA-modifying enzyme mutations induce codon-specific mistranslation and protein aggregation in yeast". RNA Biology (2020): https://doi.org/10.1080/15476286.2020.1819671.
    10.1080/15476286.2020.1819671
  18. Nunes, Alexandre; Ribeiro, Diana Roberta; Marques, Mariana; Santos, Manuel A.S.; Ribeiro, Daniela; Soares, Ana Raquel. "Emerging Roles of tRNAs in RNA Virus Infections". Trends in Biochemical Sciences (2020): http://dx.doi.org/10.1016/j.tibs.2020.05.007.
    10.1016/j.tibs.2020.05.007
  19. Soares, Ana Raquel. "Does proteostasis get lost in translation? Implications for protein aggregation across the lifespan.". Ageing Research Reviews (2020): https://doi.org/10.1016/j.arr.2020.101119.
    Published • doi.org/10.1016/j.arr.2020.101119
  20. Ana Sofia Varanda; Mafalda Santos; Ana R. Soares; Rui Vitorino; Patrícia Oliveira; Carla Oliveira; Manuel A. S. Santos. "Human cells adapt to translational errors by modulating protein synthesis rate and protein turnover". RNA Biology (2019): https://doi.org/10.1080/15476286.2019.1670039.
    10.1080/15476286.2019.1670039
  21. Marques, Mariana; Ramos, Bruno; Soares, Ana; Ribeiro, Daniela. "Cellular Proteostasis During Influenza A Virus Infection—Friend or Foe?". Cells 8 3 (2019): 228. http://dx.doi.org/10.3390/cells8030228.
    Open access • Published • 10.3390/cells8030228
  22. Pereira, Marisa; Francisco, Stephany; Varanda, Ana Sofia; Santos, Mafalda; Santos, Manuel A. S.; Soares, Ana Raquel. "Impact of tRNA Modifications and tRNA-Modifying Enzymes on Proteostasis and Human Disease". IJMS (2018): https://www.mdpi.com/1422-0067/19/12/3738.
    Published • 10.3390/ijms19123738
  23. Pereira, M.; Tomé, D.; Domingues, A.S.; Varanda, A.S.; Paulo, C.; Santos, M.A.S.; Soares, A.R.. "A Fluorescence-Based Sensor Assay that Monitors General Protein Aggregation in Human Cells". Biotechnology Journal 13 4 (2018): http://www.scopus.com/inward/record.url?eid=2-s2.0-85043346932&partnerID=MN8TOARS.
    10.1002/biot.201700676
  24. Soares, A.R.; Santos, M.. "Discovery and function of transfer RNA-derived fragments and their role in disease". Wiley Interdisciplinary Reviews: RNA 8 5 (2017): http://www.scopus.com/inward/record.url?eid=2-s2.0-85020414744&partnerID=MN8TOARS.
    10.1002/wrna.1423
  25. Matos, J.C.; Soares, A.R.; Domingues, I.; Monteiro, G.A.; Gonçalves, M.C.. "ORMOPLEXEs for gene therapy: In vitro and in vivo assays". Materials Science and Engineering C 63 (2016): 546-553. http://www.scopus.com/inward/record.url?eid=2-s2.0-84960932733&partnerID=MN8TOARS.
    10.1016/j.msec.2016.03.006
  26. Ferreira, C.; Soares, A.R.; Lamosa, P.; Santos, M.A.; da Costa, M.S.. "Comparison of the compatible solute pool of two slightly halophilic planctomycetes species, Gimesia maris and Rubinisphaera brasiliensis". Extremophiles 20 6 (2016): 811-820. http://www.scopus.com/inward/record.url?eid=2-s2.0-84981267587&partnerID=MN8TOARS.
    10.1007/s00792-016-0868-0
  27. Moura, G.R.; Pinheiro, M.; Freitas, A.; Oliveira, J.L.; Frommlet, J.C.; Carreto, L.; Soares, A.R.; Bezerra, A.R.; Santos, M.A.S.. "Erratum: Species-Specific Codon Context Rules Unveil Non-Neutrality Effects of Synonymous Mutations (PLoS ONE (2011) 6:10 (e26817))". PLoS ONE 10 12 (2015): http://www.scopus.com/inward/record.url?eid=2-s2.0-84956899012&partnerID=MN8TOARS.
    10.1371/journal.pone.0145593
  28. Soares, A.R.; Fernandes, N.; Reverendo, M.; Araújo, H.R.; Oliveira, J.L.; Moura, G.M.R.; Santos, M.A.S.. "Conserved and highly expressed tRNA derived fragments in zebrafish". BMC Molecular Biology 16 1 (2015): http://www.scopus.com/inward/record.url?eid=2-s2.0-84951822589&partnerID=MN8TOARS.
    10.1186/s12867-015-0050-8
  29. Terawaki, S.; Camosseto, V.; Prete, F.; Wenger, T.; Papadopoulos, A.; Rondeau, C.; Combes, A.; et al. "RUN and FYVE domain-containing protein 4 enhances autophagy and lysosome tethering in response to Interleukin-4". Journal of Cell Biology 210 7 (2015): 1133-1152. http://www.scopus.com/inward/record.url?eid=2-s2.0-84962467120&partnerID=MN8TOARS.
    10.1083/jcb.201501059
  30. Reverendo, M.; Soares, A.R.; Pereira, P.M.; Carreto, L.; Ferreira, V.; Gatti, E.; Pierre, P.; Moura, G.R.; Santos, M.A.. "TRNA mutations that affect decoding fidelity deregulate development and the proteostasis network in zebrafish". RNA Biology 11 9 (2014): 1199-1213. http://www.scopus.com/inward/record.url?eid=2-s2.0-84921709623&partnerID=MN8TOARS.
    10.4161/rna.32199
  31. Soares, A.R.; Reverendo, M.; Pereira, P.M.; Nivelles, O.; Pendeville, H.; Bezerra, A.R.; Moura, G.R.; Struman, I.; Santos, M.A.S.. "Dre-miR-2188 targets Nrp2a and mediates proper intersegmental vessel development in zebrafish embryos". PLoS ONE 7 6 (2012): http://www.scopus.com/inward/record.url?eid=2-s2.0-84862690378&partnerID=MN8TOARS.
    10.1371/journal.pone.0039417
  32. Soares, A.R.; Pereira, P.M.; Ferreira, V.; Reverendo, M.; Simóes, J.; Bezerra, A.R.; Moura, G.R.; Santos, M.A.S.. "Ethanol exposure induces upregulation of specific microRNAs in zebrafish embryos". Toxicological Sciences 127 1 (2012): 18-28. http://www.scopus.com/inward/record.url?eid=2-s2.0-84860179523&partnerID=MN8TOARS.
    10.1093/toxsci/kfs068
  33. Moura, G.R.; Pinheiro, M.; Freitas, A.; Oliveira, J.L.; Frommlet, J.C.; Carreto, L.; Soares, A.R.; Bezerra, A.R.; Santos, M.A.S.. "Species-specific codon context rules unveil non-neutrality effects of synonymous mutations". PLoS ONE 6 10 (2011): http://www.scopus.com/inward/record.url?eid=2-s2.0-80055031054&partnerID=MN8TOARS.
    10.1371/journal.pone.0026817
  34. Pereira, P.M.; Marques, J.P.; Soares, A.R.; Carreto, L.; Santos, M.A.S.. "Microrna expression variability in human cervical tissues". PLoS ONE 5 7 (2010): http://www.scopus.com/inward/record.url?eid=2-s2.0-77955615260&partnerID=MN8TOARS.
    10.1371/journal.pone.0011780
  35. Soares, A.R.; Pereira, P.M.; Santos, B.; Egas, C.; Gomes, A.C.; Arrais, J.; Oliveira, J.L.; Moura, G.R.; Santos, M.A.S.. "Parallel DNA pyrosequencing unveils new zebrafish microRNAs". BMC Genomics 10 (2009): http://www.scopus.com/inward/record.url?eid=2-s2.0-65949098165&partnerID=MN8TOARS.
    10.1186/1471-2164-10-195
Journal issue
  1. Soares, Ana Raquel; Marjolein kikkert; Stefanie Kellner-Kaiser; Daniela Ribeiro. "Editorial: Viruses and Epitranscriptomes: Regulation of Infection and Antiviral Response". Front Cell Dev Biol. (2022): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9125315/.
    Published • doi: 10.3389/fcell.2022.917894
Magazine article
  1. Soares, Ana Raquel. "Understanding the role of tRNA modifying enzymes in proteostasis in human health and disease", Impact, 2017, https://www.ingentaconnect.com/content/sil/impact/2017/00002017/00000008/art00034.
    https://doi.org/10.21820/23987073.2017.8.95
Preprint
  1. Marisa Pereira; Diana R. Ribeiro; Maximilian Berg; Andy P. Tsai; Kwangsik Nho; Stefanie Kaiser; Miguel Moutinho; Soares, Ana Raquel. Corresponding author: Soares, Ana Raquel. "Amyloid pathology reduces ELP3 expression and tRNA modifications leading to impaired proteostasis in Alzheimer’s disease models". 2023. https://doi.org/10.1101/2023.05.02.538928.
  2. Mariana Marques; Bruno Ramos; Albuquerque, Hélio; Marisa Pereira; Diana Roberta Ribeiro; Alexandre Nunes; Sarabando, Jéssica; et al. Corresponding author: Soares, Ana Raquel. "Influenza A virus activates the unfolded protein response and induces the accumulation of insoluble protein aggregates that are essential for efficient viral propagation". 2023. https://doi.org/10.1101/2023.09.11.557148.
    https://doi.org/10.1101/2023.09.11.557148
Thesis / Dissertation
  1. Soares, Ana Raquel. "Zebrafish small RNAs: Unravelling expression and functions of novel microRNAs and tRNA fragments in a vertebrate model". PhD, Universidade de Coimbra Faculdade de Farmácia, 2011.

Other

Other output
  1. Integration of differential gene expression with weighted gene correlation network analysis identifies genes whose expression is remodeled throughout physiological aging in mouse tissues. 2021. Margarida Ferreira; Stephany Francisco; Ana Raquel Soares; Ana Nobre; Miguel Pinheiro; Andreia Reis; Sonya Neto; et al. https://doi.org/10.1101/2021.02.18.431793.
    10.1101/2021.02.18.431793
  2. m5U54 tRNA Hypomodification by lack of TRMT2A Drives the Generation of tRNA-Derived Small RNAs. 2021. Marisa Pereira; Diana R. Ribeiro; Miguel M. Pinheiro; Margarida Ferreira; Stefanie Kellner; Ana R. Soares. https://doi.org/10.20944/preprints202101.0227.v1.
    10.20944/preprints202101.0227.v1
  3. Heat Shock Protein Reports on Proteome Stress. Commentary by the Biotechnology Journal Editors on the publication A Fluorescence-Based Sensor Assay that Monitors General Protein Aggregation in Human Cells, co-authored by me.. 2018. Yu Liu; Xin Zhang. https://onlinelibrary.wiley.com/doi/10.1002/biot.201800039.
    https://doi.org/10.1002/biot.201800039
Activities

Oral presentation

Presentation title Event name
Host (Event location)
2024/02 Wobble uridine transfer RNA modifications shape influenza A virus infection in a codon-dependent manner Viruses 2024 - A World of Viruses
(Barcelona, Spain)
2023/12 Experimental evolution and dynamics of adaptation of yeast lacking tRNA-modifying enzymes Keystone symposium: RNA Modifications in Health and Disease
Keystone Symposia (Banff, Canada)
2023/07/07 RNA modification and Function - relevance for disease onset and progression SPG Hot Topics
Sociedade Portuguesa de Genética (Virtual, Portugal)
2023/06 Design and synthesis of steroid-quinoline hybrid compounds targeting protein aggregation processes Workshop on “Novel Diagnostic Tools for Alzheimer’s Disease"
Department of Medical Sciences, University of Aveiro (Aveiro, Portugal)
2023/02 tRNA modification levels in Alzheimer’s disease correlate with protein aggregation burden 2023 Gordon Conference Translation in Health and Disease
Gordon Conference (Galveston, United States)
2022/11/23 Cracking the tRNA epitranscriptome - in the quest for novel disease biomarkers and therapeutic targets Brainload - Power Up Your Knowledge
Scientific Junior Value (Aveiro, Portugal)
2022/11/17 tRNA epitranscriptome reprograming in Alzheimer’s disease correlates with protein aggregation burden 26th Annual meeting of the Portuguese Society of Human Genetics
Sociedade Portuguesa Genética Humana (Coimbra, Portugal)
2022/01 TIPS for a successful assistant researcher application @ CEEC 5th edition 2022 TIPS for applying to CEEC 5th edition 2022
Lyris - advanced health education (Online)
2022 Applying for a CEEC Individual funding and being successful - what did I learn? GAI Info session on the 5th edition of the CEEC Individual - online event
University of Aveiro (Aveiro, Portugal)
2022 tRNA wobble uridine modifications are important for pathogenicity and host responses upon influenza a virus infection EMBO - The complex life of RNA
EMBO (Heidelberg, Germany)
2021 Lack of TRMT2A, a tRNA methyltransferase, leads to m5U54 tRNA hypomodification and generation of tRNA-derived small RNAs ncRNA2021
MDPI
2021 Influenza A virus disturbs the host-cell protein homeostasis by inducing the accumulation of insoluble proteins pAGE Final Workshop
iBiMED - University of Aveiro (Portugal)
2020 Identification of novel therapeutic targets to modulate proteostasis in humans Research Summit
University of Aveiro (Aveiro, Portugal)
2020 Lack of m5U modification in tRNAs induces the formation of tRNA-derived fragments Virtual live Keystone eSymposia meeting|RNA Editing and Modifications: From Biology to Therapy
Keystone (United States)
2019 tRNA modifying enzymes: novel proteostasis players in human cells VII National RNA meeting: ptRNA2019
I3S - Porto (Porto, Portugal)
2019 tRNA modifying enzymes and tRNA modifications – novel therapeutic targets for age-related diseases CBMinaRs Cycle on Biomedical Sciences
CBMR, University of Algarve (Faro, Portugal)
2019 Investigating the role of tRNA-modifying enzymes in human proteostasis 24th Annual Meeting of the RNA Society
RNA Society (Kraków, Poland)
2018 Protein aggregation across the mouse lifespan Research Summit UA
Universidade de Aveiro (Aveiro, Portugal)
2018 Identification of tRNA modifying enzymes as novel proteostasis players in human cells 27th tRNA conference
IUBMB (Strasbourg, France)
2018 "Development of a protein aggregation sensor" - Distinguished with the Best Pitch Award UA Research Summit
University of Aveiro (Aveiro, Portugal)
2017 Development of a protein aggregation reporter for the identification of aging biomarkers Meeting with Science and Technology
Fundação para a Ciência e Tecnologia (Lisbon, Portugal)
2017 Identification of novel protein aggregation regulators in health and disease UA research day
University of Aveiro (Aveiro, Portugal)
2016 Identification of conserved tRNA derived fragments in zebrafish reveals their potential as gene expression modulators and disease biomarkers 8th HARC workshop: perspectives for new diagnostic and therapeutic tools
Medical University of Lodz (Lodz, Poland)
2013 A highly expressed zebrafish tRNA derived fragment with microRNA-like features 8th European Zebrafish Meeting
(Barcelona, Spain)
2012 Next generation sequencing technologies applied to microRNA discovery and profiling Next Generation Sequencing Meeting: applications in genetic and infectious diseases
Instituto Nacional de Saúde Dr. Ricardo Jorge (Lisbon, Portugal)
2011 A novel class of zebrafish small RNAs derived from transfer RNAs XXXVI Jornadas Portuguesas de Genética
(Coimbra, Portugal)
2009 Target validation of dre-miR-2188, a novel Zebrafish miRNA identified by high throughput sequencing CNC annual Meeting
Center for neuroscience and Cell Biology (Cantanhede, Portugal)
2008 Identification of novel zebrafish microRNAs using massively parallel DNA sequencing”, Advanced Molecular Genomics Course, Biocant Park, Cantanhede, Portugal Advanced Molecular Genomics Course
Biocant Park - Advanced service unit (Cantanhede, Portugal)
2008 Identification of novel zebrafish microRNAs using next generation sequencing MicroRNAs Europe 2008 meeting
University of Cambridge (Cambridge, United Kingdom)
2008 Diversity of miRNAS in zebrafish using massive parallel sequencing Post graduation symposium (Biology Department, University of Aveiro)
(Aveiro, Portugal)

Supervision

Thesis Title
Role
Degree Subject (Type)
Institution / Organization
2023/09 - Current Reprograming tRNA modifications as a novel therapeutic strategy for neurodegenerative disorders
Supervisor
BSc in Biology (Degree)
Universidade de Aveiro Departamento de Biologia, Portugal

Universidade de Aveiro Departamento de Ciências Médicas, Portugal
2023 - Current MSc Thesis: Transcriptome analysis as a complimentary genetic tool to investigate aberrant splicing in complex diseases
Co-supervisor
MSc in Clinical Bioinformatics (Master)
Universidade de Aveiro Departamento de Ciências Médicas, Portugal

Biocant Associação de Transferência de Tecnologia, Portugal
2022/10 - Current MSc thesis: Runs of homozygosity analysis in over 8,000 exomes: validation of a new bioinformatics model for variant prioritization and discovery of disease-causing genes
Co-supervisor
MSc in Clinical Bioinformatics (Master)
Universidade de Aveiro Instituto de Biomedicina, Portugal

Universidade de Aveiro Departamento de Ciências Médicas, Portugal
2022/09 - Current MSc thesis: Developing novel analysis pipelines to explore small non-coding RNA sequencing data
Supervisor
Clinical Bioinformatics (Master)
Universidade de Aveiro Departamento de Ciências Médicas, Portugal
2022/09 - Current MSc thesis: Exploring the interplay between viruses and host proteostasis
Co-supervisor
Molecular Biomedicine (Master)
Universidade de Aveiro Departamento de Ciências Médicas, Portugal
2021/10/01 - Current Research fellow supervision under the scope of the project WISDOM - PTDC/BTM-TEC/29843/2017
Supervisor
Universidade de Aveiro Instituto de Biomedicina, Portugal
2021/03/01 - Current PhD thesis: Unfolding the interplay between viruses and cellular proteostasis
Co-supervisor of Alexandre Nunes
PhD in Biomedical Sciences (PhD)
Universidade de Aveiro Departamento de Ciências Médicas, Portugal

Universidade de Aveiro Instituto de Biomedicina, Portugal
2021 - Current MSc Thesis: The crosstalk between miRNAs and tRNA modifying enzymes– an alternative pathway to regulate the tRNA epitranscriptome
Supervisor of Diana Bastos
Mestrado em Biomedicina Molecular (Master)
Universidade de Aveiro Departamento de Ciências Médicas, Portugal
2021 - Current MSc thesis: Small non-coding RNAs as determinants of viral replication
Supervisor of Rafaela Salvador
Mestrado em Biomedicina Molecular (Master)
Universidade de Aveiro Departamento de Ciências Médicas, Portugal
2019/08/02 - Current PhD Thesis: Impact of tRNA modifications and translation control for pathogenicity and host responses upon influenza A virus infection
Supervisor of Diana Ribeiro
PhD in Biomedical Sciences (PhD)
Universidade de Aveiro Instituto de Biomedicina, Portugal

Universidade de Aveiro Departamento de Ciências Médicas, Portugal
2019/08/02 - Current PhD Thesis: Unraveling the contribution of protein synthesis accuracy to healthy aging in the mouse
Co-supervisor of Stephany Francisco
PhD in Biomedical Sciences (PhD)
Universidade de Aveiro Instituto de Biomedicina, Portugal

Universidade de Aveiro Departamento de Ciências Médicas, Portugal
2018/12 - 2023/11 PhD Thesis: Identification of novel therapeutic targets to modulate proteostasis in humans
Supervisor of Marisa Pereira
PhD in Biomedical Sciences (PhD)
Universidade de Aveiro Instituto de Biomedicina, Portugal

Universidade de Aveiro Departamento de Ciências Médicas, Portugal
2020/09/01 - 2021/12 MSc Thesis: Unraveling the profile and role of the tRFs in influenza A virus infection
Co-supervisor of Daniel Monteiro
Master in Molecular Biomedicine (Master)
Universidade de Aveiro Departamento de Ciências Médicas, Portugal

Universidade de Aveiro Instituto de Biomedicina, Portugal
2018/12 - 2019/06 Research fellow supervision under the scope of the project "Understanding the role of tRNA modifying enzymes in proteostasis in human health and disease" - PTDC/BIM-MEC/1719/2014
Supervisor of Diana Roberta Ribeiro
Universidade de Aveiro Departamento de Ciências Médicas, Portugal

Universidade de Aveiro Instituto de Biomedicina, Portugal
2018 - 2019 MSc Thesis: Influence of tRNA modifying enzymes during Influenza Virus infection
Co-supervisor of Alexandre Nunes
Master in Molecular Biomedicine (Master)
Universidade de Aveiro Instituto de Biomedicina, Portugal

Universidade de Aveiro Departamento de Ciências Médicas, Portugal
2017 - 2018 MSc thesis: Contribution of novel proteostasis related genes for proteotoxic stress
Supervisor of Cristiana Paulo
Master in Molecular Biomedicine (Master)
Universidade de Aveiro Departamento de Ciências Médicas, Portugal

Universidade de Aveiro Instituto de Biomedicina, Portugal
2017 - 2018 Research fellow supervision under the scope of the project "Understanding the role of tRNA modifying enzymes in proteostasis in human health and disease" - PTDC/BIM-MEC/1719/2014
Supervisor of Marisa Pereira
Universidade de Aveiro Instituto de Biomedicina, Portugal

Universidade de Aveiro Departamento de Ciências Médicas, Portugal
2017 - 2018 Research fellow supervision under the scope of the project UID/BIM/04501/2013 to work on iBiMED strategic program, in the sub-topic "Proteostasis imbalances upon viral infections
Co-supervisor of Mariana Marques
Universidade de Aveiro Instituto de Biomedicina, Portugal

Universidade de Aveiro Departamento de Ciências Médicas, Portugal
2016 - 2017 MSc Thesis: Identification of tRNA modifying enzymes involved in protein aggregation
Supervisor of Marisa Pereira
Master in Molecular Biomedicine (Master)
Universidade de Aveiro Departamento de Ciências Médicas, Portugal

Universidade de Aveiro Instituto de Biomedicina, Portugal
2016 - 2017 Research fellow supervision under the scope of the project UID/BIM/04501/2013 to work on iBiMED strategic program, in the sub-topic "Construction of mouse models of age related proteome aggregation"
Supervisor of Stephany Francisco
Universidade de Aveiro Departamento de Ciências Médicas, Portugal

Universidade de Aveiro Instituto de Biomedicina, Portugal
2016 - 2017 Research fellow supervision under the scope of the project "Understanding the role of tRNA modifying enzymes in proteostasis in human health and disease" - PTDC/BIM-MEC/1719/2014
Supervisor of Sofia Varanda
Universidade de Aveiro Departamento de Ciências Médicas, Portugal

Universidade de Aveiro Instituto de Biomedicina, Portugal
2015 - 2016 MSc Thesis: Protein aggregation and proteostasis in aging mice
Supervisor of Stephany Francisco
Master in Molecular biomedicine (Master)
Universidade de Aveiro Departamento de Ciências Médicas, Portugal

Universidade de Aveiro Instituto de Biomedicina, Portugal
2015 - 2016 MSc Thesis: A reporter system to study the role of tRNA modifying enzymes in human proteostasis
Supervisor of Ana Sofia Domingues
Master in Molecular Biomedicine (Master)
Universidade de Aveiro Departamento de Ciências Médicas, Portugal

Universidade de Aveiro Instituto de Biomedicina, Portugal
2015 - 2016 Research Fellow supervision under the scope of the project UID/BIM/04501/2013 to work on iBiMED strategic program, in the sub-topic "Construction of mouse models of age related proteome aggregation"
Supervisor of Diogo Tomé
Universidade de Aveiro Departamento de Ciências Médicas, Portugal

Universidade de Aveiro Instituto de Biomedicina, Portugal
2015 - 2015 MSc Thesis: The contribution of tRNA pool deregulation in the acquisition of a malignant phenotype
Supervisor of ANA PATRÍCIA FIGUEIREDO FIDALGO
Biologia Molecular e Celular (Master)
Universidade de Aveiro, Portugal
2015 - 2015 MSc Thesis: Study of tRNA modifying enzymes and codon usage bias in cancer
Supervisor of CARLOS ANTÓNIO PASCOAL MARQUES
Biologia Molecular e Celular (Master)
Universidade de Aveiro, Portugal
2014 - 2014 MSc Thesis: Effects of translational errors in zebrafish
Supervisor of ANA CATARINA REIS VELA NEVES
Biologia Molecular e Celular (Master)
Universidade de Aveiro, Portugal
2013 - 2013 MSc Thesis: Assessing silencing ability of tRNA derived fragments in zebrafish
Supervisor of NOÉMIA RITA ALVES FERNANDES
Biologia Molecular e Celular (Master)
Universidade de Aveiro, Portugal
2010 - 2011 MSc Thesis: The role of amino acids nutricional imbalance in zebrafish development
Co-supervisor of Pedro Vieira
Master in Molecular and Cellular Biology (Master)
Universidade de Aveiro Centro de Estudos do Ambiente e do Mar, Portugal

Universidade de Aveiro Departamento de Biologia, Portugal

Event organisation

Event name
Type of event (Role)
Institution / Organization
2022/10 - Current UAVR-RNA Club: organization of RNA-related seminars and workshops open to all the University of Aveiro community interested in learning and establish collaborations within the RNA field (2022)
Seminar (President of the Organising Committee)
Universidade de Aveiro Instituto de Biomedicina, Portugal
2019 - Current Coordinator of the participation of iBiMED's researchers at TechDays, promoted by Aveiro's city Hall. Techdays is a technology fair that promotes the best innovation initiatives centered in the promotion of better life quality. iBiMED's participation allowed the dissemination of several health-related projects, with special focus on the use of state-of-the-art technologies, such as genome sequencing and genetic screenings. (2019 - 2019)
Exhibition (Other)
2024/06/04 - 2024/06/07 RNA Biology in Host-Pathogen Interactions Conference (2024/06/04 - 2024/06/07)
Conference (Co-organisor)
Universidade de Aveiro Departamento de Ciências Médicas, Portugal

Universidade de Aveiro Instituto de Biomedicina, Portugal
2024/03/13 - 2024/03/15 Soft Transferable Skills Training Program 2024 (2024/03/13 - 2024/03/15)
Workshop (Member of the Organising Committee)
Universidade de Aveiro, Portugal
2023/09/04 - 2023/09/06 EpiViral Summer School 2023: Deciphering the Epitranscriptome - analysis of tRNA and mRNA modifications (2023/09/04 - 2023/09/06)
Workshop (Member of the Scientific Committee)
Universidade de Aveiro Instituto de Biomedicina, Portugal
2023/03/22 - 2023/03/24 1st Joint Twinning Soft Transferable Skills Workshop (2023/03/22 - 2023/03/24)
Workshop (Co-organisor)
Universidade de Aveiro Associação para a Formação Profissional e Investigação, Portugal
2022/09 - 2022/09 EpiViral Summer School 2022: RNA viruses: interactions with hosts, vectors and cells (2022/09)
Workshop (Member of the Organising Committee)
Universidade de Aveiro, Portugal
2022/04/28 - 2022/04/29 Coordination of the participation of DCM and iBiMED's researchers in the Xperimenta UA event, University of Aveiro. A science dissemination activity to show the research performed at the university for prospective students. (2022/04/28 - 2022/04/29)
Exhibition (Co-organisor)
Universidade de Aveiro, Portugal

Universidade de Aveiro Departamento de Ciências Médicas, Portugal

Universidade de Aveiro Instituto de Biomedicina, Portugal
2022/01/10 - 2022/01/10 1st EpiViral Symposium (2022/01/10 - 2022/01/10)
Symposium (Co-organisor)
Universidade de Aveiro Instituto de Biomedicina, Portugal
2021/06 - 2021/06 EpiViral Spring seminars 2021 (2021/06 - 2021/06)
Seminar (Co-organisor)
Universidade de Aveiro Instituto de Biomedicina, Portugal
2021 - 2021 UACOOPERA at the service of the community (2021)
Workshop (Member of the Organising Committee)
Universidade de Aveiro, Portugal
2021 - 2021 R&D results and entrepreneurship workshop (2021)
Workshop (Member of the Organising Committee)
Universidade de Aveiro, Portugal
2021 - 2021 R&D results: how to protect workshop (2021)
Workshop (Member of the Organising Committee)
Universidade de Aveiro, Portugal
2019/04 - 2019/04 Coordination of the participation of DCM and iBiMED's researchers in the Xperimenta UA event, University of Aveiro. A science dissemination activity to show the research performed at the university for prospective students. (2019)
Exhibition (Other)
Universidade de Aveiro, Portugal
2016 - 2016 Organizer of the II post-graduate symposia in Biomedicine held at iBiMED, University of Aveiro, Aveiro, Portugal (2016)
Symposium (President of the Organising Committee)
Universidade de Aveiro Instituto de Biomedicina, Portugal
2010 - 2010 Organizer of the international 23rd tRNA Workshop - from the origin of life to biomedicine, held at Centro Cultural de Congressos, Aveiro, Portugal. (2010)
Congress (Member of the Organising Committee)
Universidade de Aveiro, Portugal
2008 - 2008 Organizer of the microRNA expression profilling course at CESAM, University of Aveiro, Aveiro, Portugal. (2008)
Workshop (Member of the Organising Committee)
Universidade de Aveiro Centro de Estudos do Ambiente e do Mar, Portugal

Event participation

Activity description
Type of event
Event name
Institution / Organization
2021 - Current StudySmart - advanced study strategies to improve students learning abilities
Workshop
StudySmart
Maastricht University - Education and Innovation Lab (EDLAB), Netherlands
2013 - Current Scientific monitor for the University of Aveiro Summer Academy, an activity directed to high school students, where they have the opportunity, during the course of 1 week, to engage in the research activities developed at our laboratories and understand its scientific relevance. I have participated in this yearly activity every year since 2013.
Other
Summer Academy
Universidade de Aveiro, Portugal
2023/06/16 - 2023/06/17 Chair of the Session 2 of the Workshop on novel diagnostic tools for Alzheimers disease
Workshop
Workshop on novel diagnostic tools for Alzheimers disease
Universidade de Aveiro Departamento de Ciências Médicas, Portugal
2022/04/02 - 2022/04/02 GLOBAL Minisymposium on science communication
Symposium
COMMUNICATION IN SCIENCE, GLOBAL MINISYMPOSIUM
IMFAHE - International Mentoring Foundation for the Advancement of Higher Education, Spain

Universidad de Valladolid, Spain
2022/02/23 - 2022/02/23 Chair of the morning session of the Medisis Open Day 2022
Conference
Medisis Open Day 2022
Universidade de Aveiro Instituto de Biomedicina, Portugal
2021/04 - 2021/04 Speaker at the national initiative Talk with a scientist - decades of science for vaccine days
Workshop
Conversas com cientistas: décadas de Ciência para dias de vacinas
Ciência Viva, Portugal
2021/03/19 - 2021/03/20 TRAINING on Proposal Writing and Project Management for EU Horizon Europe Program (19-20 March 2021)
Workshop
TRAINING | Proposal Writing and Project Management for EU Horizon Europe Program
2018 - 2018 Presenter of the technological exhibition on the subject “Keeping Proteostasis is essential to maintain health” at UA Open Campus, University of Aveiro. A science dissemination activity to show the research performed at the university for prospective students.
Exhibition
UA Open Campus
Universidade de Aveiro, Portugal

Jury of academic degree

Topic
Role
Candidate name (Type of degree)
Institution / Organization
2024/12 Developing novel analysis pipelines to explore small non-coding RNA sequencing data
Supervisor
Gonçalo Costa (Master)
Universidade de Aveiro Departamento de Ciências Médicas, Portugal
2023/11/06 Identification of novel therapeutic targets to modulate proteostasis in humans
Supervisor
Marisa Pereira (PhD)
Universidade de Aveiro, Portugal
2022/12/07 m6A modification in gastric cancer: the function of the YTH family of proteins
(Thesis) Main arguer
Maria Beatriz Almeida (Master)
Universidade do Porto, Portugal
2022/12 Functional characterization of putative miRNA-like sequences encoded in the HIV genome
(Thesis) Main arguer
Carolina dos Santos Ruivinho (Master)
Universidade de Lisboa, Portugal
2021/12 Thesis title: tRNA-Ser-AGA: a new player in NSCLC cisplatin resistance
(Thesis) Main arguer
Sérgio Manuel Pires Marinho (Master)
Universidade do Porto Faculdade de Medicina, Portugal
2018/12 Thesis title: Unravelling the role of ACOX3 and MCT2 in prostate cancer
(Thesis) Main arguer
Rui Pedro Duarte Oliveira (Master)
Universidade de Aveiro Departamento de Biologia, Portugal
2018/10 Thesis title: Contribution of novel proteostasis related genes for proteotoxic stress
Supervisor
Cristiana Paulo (Master)
Universidade de Aveiro Departamento de Ciências Médicas, Portugal
2018 Thesis title: Peroxisomes and viral infections: beyond antiviral defense
(Thesis) Arguer
Ana Rita Filgueiras Ferreira (PhD)
Universidade de Aveiro Departamento de Ciências Médicas, Portugal
2017 Thesis title: Identification of tRNA modifying enzymes involved in protein aggregation
Supervisor
Marisa Pereira (Master)
Universidade de Aveiro Departamento de Ciências Médicas, Portugal
2016 Thesis title: Protein aggregation and proteostasis in aging mice
Supervisor
Stephany Francisco (Master)
Universidade de Aveiro Departamento de Ciências Médicas, Portugal
2016 Thesis title: A reporter system to study the role of tRNA modifying enzymes in human proteostasis
Supervisor
Ana Sofia Domingues (Master)
Universidade de Aveiro Departamento de Biologia, Portugal
2015 Thesis title: The contribution of tRNA pool deregulation in the acquisition of a malignant phenotype
Supervisor
Ana Fidalgo (Master)
Universidade de Aveiro Departamento de Biologia, Portugal
2015 Thesis title: Study of tRNA modifying enzymes and codon usage bias in cancer
Supervisor
Carlos Marques (Master)
Universidade de Aveiro Departamento de Biologia, Portugal
2014 Thesis title: Effects of translation errors in zebrafish
Supervisor
Ana Neves (Master)
Universidade de Aveiro Departamento de Biologia, Portugal
2013 Thesis title: Deciphering the role of tRNA derived fragments in vertebrates
Supervisor
Noémia Fernandes (Master)
Universidade de Aveiro Departamento de Biologia, Portugal
2011 Thesis title: The role of amino acids nutricional imbalance in zebrafish development
Supervisor
Pedro Vieira (Master)
Universidade de Aveiro Departamento de Biologia, Portugal

Ad Hoc journal article review

Journal title (ISSN) Publisher
2023 - Current ACS Central Science ACS
2019/06/01 - Current Acta Physiologica (1748-1716) Wiley (Blackwell Publishing)
2019 - Current International Journal of Molecular Sciences (1422-0067) MDPI AG
2019 - Current Molecules (1420-3049) MDPI AG
2019 - Current Genes MDPI AG
2019 - Current Cells (2073-4409) MDPI AG
2018 - Current RNA Biology (1555-8584) Landes Bioscience
2017 - Current Current Biotechnology (2211-5501) Bentham Science
2015 - Current PLoS ONE (1932-6203) Public Library of Science
2013 - Current RNA (1469-9001) Cold Spring Harbor Laboratory
2012 - Current BMC Genomics (1471-2164) Springer (Biomed Central Ltd.)

Association member

Society Organization name Role
2023/05 - Current Biochemistry Portuguese Society Member
2023/02 - Current Portuguese Society of Medical Genetics Associate
2021 - Current ANICT
2019 - Current The RNA Society

Committee member

Activity description
Role
Institution / Organization
2022/03/19 - Current Elected member of the University of Aveiro Scientific Council
Member
Universidade de Aveiro, Portugal
2022 - Current Election Committee Member - iBiMED Director elections 2022
Member
Universidade de Aveiro Instituto de Biomedicina, Portugal
2022 - Current Elected member of the Medical Sciences Department Scientific Council
Member
Universidade de Aveiro Departamento de Ciências Médicas, Portugal
2021 - Current Member of the Department of Medical Sciences Biosafety Committee
Member
Universidade de Aveiro Departamento de Ciências Médicas, Portugal
2020 - Current Coordinator of the Molecular Medicine/OpeSpace Facility from the Institute of Biomedicine (iBiMED)
Coordinator
Universidade de Aveiro, Portugal
2019 - Current Local coordinator (iBiMED) of the PT-OpenScreen infrastructure
Coordinator
Universidade de Aveiro Instituto de Biomedicina, Portugal
2016 - Current Member of the iBiMED scientific council.
Member
Universidade de Aveiro Instituto de Biomedicina, Portugal

Conference scientific committee

Conference name Conference host
2023/05 - 2023/05 VI iBiMED Symposium iBiMED - University of Aveiro

Consulting

Activity description Institution / Organization
2020/07/01 - Current Consulting activities under the scope of SARS-CoV-2 testing in the area of data analysis (qPCR) for the iBiMED Covid Task-force, responsible for SARS-CoV-2 testing for elderly homes and regional hospitals (Aveiro and Santa Maria da Feira). Universidade de Aveiro Instituto de Biomedicina, Portugal
2020/03/20 - 2020/07 iBiMED's SARS-CoV-2 Task Force - coordination of the analysis team. Universidade de Aveiro Instituto de Biomedicina, Portugal

Course / Discipline taught

Academic session Degree Subject (Type) Institution / Organization
2023 - Current Research in Biomedicine Biomedical Sciences (Bacharelato)
2022/09 - Current Genetics and epigenetics - Master discipline in Clinical Bioinformatics Clinical Bioinformatics (Mestrado) Universidade de Aveiro Departamento de Ciências Médicas, Portugal
2022/05 - Current RNA Biology in Health and Disease PhD in Biomedicine (Curso de doutoramento (conclusão de unidades curriculares)) Universidade de Aveiro, Portugal

Universidade Nova de Lisboa, Portugal
2021/09 - Current Program based learning - Functional and Organic Systems I - Biomedicine degree, Department of Health Sciences, University of Aveiro (Licenciatura) Universidade de Aveiro, Portugal
2020/02 - Current Program based learning – Functional and Organic Systems IV - Biomedicine degree, Department of Health Sciences, University of Aveiro Ciências Biomédicas (Licenciatura) Universidade de Aveiro, Portugal
2020 - Current Program based learning - Functional and Organic Systems II- Biomedicine degree, Department of Health Sciences, University of Aveiro Biomedicine Degree (Licenciatura) Universidade de Aveiro Departamento de Ciências Médicas, Portugal
2019 - Current Program based learning – Functional and Organic Systems II and From the Molecule to the Man - Biomedicine degree, Department of Health Sciences, University of Aveiro Program based learning – Functional and Organic Systems II and From the Molecule to the Man (Licenciatura) Universidade de Aveiro Departamento de Ciências Médicas, Portugal
2017 - 2021 RNA Biology in aging - Aging advanced course, Biomedical Sciences PhD program, Department f Health Sciences, University of Aveiro (Curso de doutoramento (conclusão de unidades curriculares)) Universidade de Aveiro Departamento de Ciências Médicas, Portugal
2018 - 2018 Biotechnology - Biomedicine degree, Department of Health Sciences, University of Aveiro, Aveiro, Portugal Biotechnology (Licenciatura) Universidade de Aveiro Departamento de Ciências Médicas, Portugal
2017 - 2017 Laboratory Techniques in Biomedicine - Biomedicine degree, Department of Health Sciences, University of Aveiro, Aveiro, Portugal Laboratory Techniques in Biomedicine (Licenciatura) Universidade de Aveiro Departamento de Ciências Médicas, Portugal
2016 - 2017 Program based learning – Functional and Organic Systems III and Biopathology - Biomedicine degree, Department of Health Sciences, University of Aveiro Program based learning – Functional and Organic Systems III and Biopathology (Licenciatura) Universidade de Aveiro Departamento de Ciências Médicas, Portugal
2016 - 2016 Exploring gene expression analysis: hands on using microarray data – Omics: linking genes to metabolites Course – iBiMED International Advanced Training Schools, iBiMED, Department of Health Sciences, University of Aveiro, Aveiro, Portugal (Outros) Universidade de Aveiro, Portugal
2015 - 2015 "Zebrafish microinjection techniques” - 8th edition of CAL-AQUA (Animal Laboratory Science - aquatic organisms) – Ciimar, University of Porto, Porto, Portugal (Especialização pós-licenciatura) Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal
2013 - 2015 Medical genetics – Biomedicine degree, Department of Health Sciences, University of Aveiro, Aveiro, Portugal Medical genetics (Licenciatura) Universidade de Aveiro Departamento de Ciências Médicas, Portugal
2014 - 2014 “Zebrafish microinjection techniques” - 7th edition of CAL-AQUA (Animal Laboratory Science - aquatic organisms) – Ciimar, University of Porto, Porto, Portugal (Especialização pós-licenciatura) Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal

Evaluation committee

Activity description
Role
Institution / Organization Funding entity
2023/09 - Current Reviewer of grant proposals for the National Science Centre Poland
Evaluator
Narodowe Centrum Nauki, Poland Narodowe Centrum Nauki
2023 - Current Alzheimer's Association Research Grant Review Committee member
Evaluator
Alzheimer's Association, United States Alzheimer's Association
2023 - Current Czech Science Foundation Standard Research Project Grant Evaluator Grantová agentura Ceské republiky, Czech Republic Grantová agentura Ceské republiky
2021 - Current Evaluation of posters at the RNA Conference 2021, organized by the RNA Society
Evaluator
2018 - Current Remote reviewer for ERC consolidator grants
Evaluator
European Research Council, Belgium European Research Council
2022/05 - 2022/09 Evaluation member of the 2022 Call for PhD Research Studentships
Evaluator
Fundação para a Ciência e a Tecnologia, Portugal Fundação para a Ciência e a Tecnologia
2022/05/29 - 2022/05/29 JURY of the oral Presentations of the IMFAHE Conference
Evaluator
IMFAHE - International Mentoring Foundation for the Advancement of Higher Education, Spain IMFAHE - International Mentoring Foundation for the Advancement of Higher Education

Interview (newspaper / magazine)

Activity description Newspaper / Forum
2021/06/19 Description of the strategic project EpiViral – Viruses and Epitranscriptomics: seeking novel targets for antiviral therapy Research@UA Volume 11
2020/06/03 Research highlight Research@UA Volume 10
2020/03/30 Press release concerning EpiViral Twinning award News@UA
2017/10 Interview for the science dissemination magazine "Impact" from Science Impact Lda publisher, focusing on my current research and financed project ThiMES. Impact

Interview (tv / radio show)

Program Topic
2024/01/11 - Current 90'' with Science (90'' com Ciência)
2021/12 - Current "UAU - ciência sem limites" - a science and technology tv show aiming to disseminate the research that takes place at UA. I participated and showcased my research in episode 5, dedicated to health research. Health related Research at the University of Aveiro

Journal scientific committee

Journal title (ISSN) Publisher
2023 - Current Frontiers in Genetics - Epigenomics and Epigenetics Frontiers
2021/12 - Current Biomedicines MDPI
2020/11 - Current Frontiers in Cell and Developmental Biology Frontiers

Other jury / evaluation

Activity description Institution / Organization
2012 - Current Jury member of research grant fellowships under the scope of financed research projects Universidade de Aveiro, Portugal
Distinctions

Award

2024 Programa Pessoa - Bilateral Cooperation Portugal-France 2023
Fundação para a Ciência e a Tecnologia, Portugal
2018 Invited Researcher fellowship
Fundação para a Ciência e a Tecnologia, Portugal
2018 IC&DT Project grant
Fundação para a Ciência e a Tecnologia, Portugal
2017 Best Poster award
Universidade de Aveiro Instituto de Biomedicina, Portugal
2015 Post-doctoral fellowship
Fundação para a Ciência e a Tecnologia, Portugal
2015 IC&DT Project Grant
Fundação para a Ciência e a Tecnologia, Portugal
2012 Post-doctoral fellowship
Fundação para a Ciência e a Tecnologia, Portugal
2011 Award Prof. Doutor Amândio Sampaio Tavares - best oral communication
2010 Fee waiver
2007 Outstanding poster award in microRNA field
2006 PhD Fellowship
CNC.IBILI, Portugal

Universidade de Coimbra, Portugal

Fundação para a Ciência e a Tecnologia, Portugal

Title

2023 Review Editor
Frontiers Media SA, Switzerland
2019 Auxiliary researcher position - CEECIND/00284/2018
Fundação para a Ciência e a Tecnologia, Portugal

Other distinction

2020 Guest Associate Editor - Frontiers in Cell and Developmental Biology
2018 Selected for the HiTec scientific entrepreneurship program
HiSeedTech - Porto Business School, Portugal