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Ricardo F. dos Santos is an ERC funded Postdoc between Instituto de Biologia Experimental e Tecnológica and NOVA Medical School-CEDOC, Universidade NOVA de Lisboa (UNL) at the Proliferation and Fate Regulation of Stem Cells laboratory headed by Dr. Catarina Homem. Ricardo produced significant scientific discoveries resulting in 5 first-author (e.g. EMBO J, mBio, Current Genetics) and 5 co-authored publications (5-year h-index of 7). Notably, he had an article highlighted in the News & Views of EMBO Journal. He has demonstrated science communication skills as verified by a best oral presentation award and by the initiation of he's teaching activities within the Molecular Biosciences PhD program and the Medical Microbiology MSc courses of UNL. Ricardo has mentored various BSc students during summer science initiatives, supervised a BSc student's project and 2 MSc research fellows. In addition, he has co-coordinated project development and international collaborations with researchers from RNA biology and bioinformatics fields. Ricardo F. dos Santos completed his PhD by the Institute of Chemical and Biological Technologies (ITQB) of UNL in early 2019. His doctoral work was centered on the study of non-coding RNAs and RNA-binding proteins (RBPs), which included several RNA-based applications. Notably, he attended the Advance Course in NGS Bioinformatics at the Wellcome Genome Campus - housing the Wellcome Sanger Institute and EMBL-EBI - and employed various sequencing approaches throughout his research. He performed and analyzed Ribosome sequencing and RNA-seq data that led to relevant publications (Andrade, dos Santos et al, EMBO J., 2018; dos Santos et al, Current Genetics, 2019; dos Santos et al, RNA Chaperones, 2020). In addition, he collaborated in the analysis of different kinds of NGS datasets of multiple organisms generated within the scope of various projects. These included RNA-seq of human pathogenic bacteria Salmonella enterica and Listeria monocytogenes, CLIP-seq of RNA-binding proteins and whole genome sequencing of a new bacterial Vibrio strain isolated from Cold Spring Harbor. Currently Ricardo is developing his postdoctoral work in the field of neural stem cells, with an interest in how neural cell fate establishment is regulated. Ricardo's 10-year experience in RNA biology and high technical knowledge in bioinformatic data generation and analysis of whole genomic and transcriptomic datasets will allow him to successfully apply this knowledge to disclose new molecular mechanisms governing neural cell differentiation.
Identification

Personal identification

Full name
Ricardo Filipe da Cruz Duarte dos Santos

Citation names

  • dos Santos, Ricardo F.

Author identifiers

Ciência ID
EA1E-5AA7-9932
ORCID iD
0000-0002-0244-2596
Google Scholar ID
0G_d1PcAAAAJ
Researcher Id
I-5747-2012
Scopus Author Id
56094688000

Email addresses

  • ricardo.santos@nms.unl.pt (Professional)

Knowledge fields

  • Natural sciences - Biological Sciences - Molecular Biology
  • Medical and Health Sciences - Basic Medicine - Neurosciences
  • Exact Sciences - Computer and Information Sciences - Bioinformatics

Languages

Language Speaking Reading Writing Listening Peer-review
Portuguese (Mother tongue)
English Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1)
Spanish; Castilian Intermediate (B1) Upper intermediate (B2) Elementary (A2) Upper intermediate (B2) Intermediate (B1)
French Beginner (A1) Intermediate (B1) Beginner (A1) Beginner (A1) Beginner (A1)
Education
Degree Classification
2015/01/01 - 2019/02/08
Concluded
Biociências Moleculares (Doutoramento)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
"More than an RNA matchmaker: Expanding the roles of Hfq into ribosome biogenesis" (THESIS/DISSERTATION)
2013
Concluded
Microbiologia Médica (Mestrado)
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
"New insights on ribosome biogenesis: The critical role of Hfq and RNase R on rRNA quality control" (THESIS/DISSERTATION)
2011
Concluded
Ciências e Tecnologia Forense (Pós-Graduação)
Instituto Politécnico de Lisboa Escola Superior de Tecnologia da Saúde de Lisboa, Portugal
2011
Concluded
Biologia Celular e Molecular (Licenciatura)
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
"n/a" (THESIS/DISSERTATION)
Affiliation

Others

Category
Host institution
Employer
2020/10 - Current Postdoc (ERC funded, ID-759853) Instituto de Biologia Experimental e Tecnológica, Portugal
Universidade Nova de Lisboa Centro de Estudos de Doenças Crónicas, Portugal
2019/04 - 2020/09 Postdoc (FCT funded, 32525-12-2019) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2019/01 - 2019/04 Research Fellow (Horizon2020 funded, ID-635536) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2015/01/01 - 2018/12/31 PhD Student (FCT funded, PD/BD/105733/2014) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2014/04/01 - 2014/10/31 Research Fellow (FP7 funded, ID-289326) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2013/10/01 - 2014/03/31 Research Fellow (FCT funded, PTDC/BIA-MIC/4142/2012) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
Projects

Grant

Designation Funders
2022/01/01 - 2024/12/31 ZeroToNeuron: Neuronal maturation, the early steps of a nascent neuron
PTDC/BIA-BID/0681/2021
Principal investigator
Universidade Nova de Lisboa Centro de Estudos de Doenças Crónicas, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
2019/01 - 2019/04 EmPowerPutida: Exploiting native endowments by re-factoring, reprogramming and implementing novel control loops in Pseudomonas putida for bespoke biocatalysis
635536
Research Fellow
Horizon 2020
Ongoing
2015/01 - 2019/02 An RNA-based approach to bacterial infection: The function of PNPase and regulatory noncoding RNAs in Listeria virulence
PTDC/IMI-MIC/4463/2014
PhD Student Fellow
Fundação para a Ciência e a Tecnologia
Concluded
2015/01 - 2019/02 Determination of the architecture and the RNA degradation strategy of Ribonuclease R: implications for pathogen control
PTDC/BIA-MIC/1399/2014
PhD Student Fellow
Fundação para a Ciência e a Tecnologia
Concluded
2014/04 - 2014/10 ST-Flow Standardization and orthogonalization of the gene expression flow for robust engineering of NTN (new-to-nature) biological properties
FP7-KBBE-2011-1 - 289326
Research Fellow
European Commission Seventh Framework Programme for Research and Technological Development
Concluded
2013/10 - 2014/03 The role of RNases and small functional RNAs in Salmonella persistence inside eukaryotic cells, Acronym: PARNAs - Persistence Attributing RNAs
PTDC/BIA-MIC/4142/2012
Research Fellow
Fundação para a Ciência e a Tecnologia
Concluded

Contract

Designation Funders
2020/10 - Current Metabolic and Timed Control of Stem Cell Fate in the Developing Animal
759853
Post-doc
Instituto de Biologia Experimental e Tecnológica, Portugal
European Research Council
2019/07 - 2020/09 The RNA-binding protein Hfq interactome in the human pathogen Listeria monocytogenes
32525-12-2019
Post-doc
Fundação para a Ciência e a Tecnologia
Outputs

Publications

Book
  1. dos Santos, R.F.; Quendera, A.P.; Boavida, S.; Seixas, A.F.; Arraiano, C.M.; Andrade, J.M.. Major 3'–5' Exoribonucleases in the Metabolism of Coding and Non-coding RNA. 2018.
    10.1016/bs.pmbts.2018.07.005
Conference poster
  1. Quendera, A.P.; Seixas, A.F.; Boavida, S.; dos Santos, R.F.; Arraiano, C.M.; Andrade, J.M.. "Inactivation of PNPase as a genetic tool to identify non-coding RNAs". Paper presented in VIII National RNA Meeting: ptRNA2019, 2019.
  2. Boavida, S.; dos Santos, R.F.; Quendera, A.P.; Arraiano, C.M.; Andrade, J.M.. "Characterization of new stress response genes in Listeria monocytogenes". Paper presented in 19th Biennial Meeting SFRRI, 2018.
  3. dos Santos, R.F.; Andrade, J.M.; Chelysheva, I.; Ignatova, Z.; Arraiano, C.M.. "The RNA-binding protein Hfq is a novel assembly factor in ribosome biogenesis". Paper presented in 5th Meeting of Regulating with RNA in Bacteria & Archaea, 2018.
  4. Boavida, S.; dos Santos, R.F.; Garcia, S.; Arraiano, C.M.; Andrade, J.M.. "A new toxin-antitoxin system identified in the pathogen Listeria monocytogenes". Paper presented in XLI Jornadas Portuguesas de Genética, 2017.
  5. dos Santos, R.F.; Andrade, J.M.; Arraiano, C.M.. "The RNA chaperone Hfq is involved in ribosome biogenesis". Paper presented in 7th ITQB NOVA PhD Meeting, 2016.
  6. Saramago, M.; Apura, P.; Barahona, S.; dos Santos, R.F.; Bravo, A.M.; Casinhas, J.; Matos, R.G.; et al. "The role of RNases in the regulation of small RNAs". Paper presented in Regulating with RNA in Bacteria and Archaea Conference, 2015.
  7. Pobre, V.; Andrade, J.M.; dos Santos, Ricardo F.; Arraiano, C.M.. "The role of Hfq and RNA determinants in the degradation pathways of small non-coding RNAs". Paper presented in FEBS – ASM workshop on: Biology of RNA in host-pathogen interactions, 2014.
Journal article
  1. Ricardo F. dos Santos; José M. Andrade; Joana Pissarra; Murray P. Deutscher; Cecília M. Arraiano. "Hfq and RNase R Mediate rRNA Processing and Degradation in a Novel RNA Quality Control Process". mBio 11 5 (2020): https://doi.org/10.1128%2Fmbio.02398-20.
    10.1128/mbio.02398-20
  2. Quendera, Ana P.; Seixas, André F.; dos Santos, Ricardo F.; Santos, Inês; Silva, João P. N.; Arraiano, Cecília M.; Andrade, José M.. "RNA-Binding Proteins Driving the Regulatory Activity of Small Non-coding RNAs in Bacteria.". Frontiers in molecular biosciences (2020): https://europepmc.org/articles/PMC7237705.
    10.3389/fmolb.2020.00078
  3. Dos Santos RF; Bárria C; Arraiano CM; Andrade JM. "Isolation and Analysis of Bacterial Ribosomes Through Sucrose Gradient Ultracentrifugation.". Methods in molecular biology (Clifton, N.J.) (2020): http://europepmc.org/abstract/med/31889266.
    10.1007/978-1-0716-0231-7_19
  4. Andrade JM; Dos Santos RF; Arraiano CM. "RNA Structure Analysis by Chemical Probing with DMS and CMCT.". Methods in molecular biology (Clifton, N.J.) (2020): http://europepmc.org/abstract/med/31889260.
    10.1007/978-1-0716-0231-7_13
  5. dos Santos, R.F.; Arraiano, C.M.; Andrade, J.M.. "New molecular interactions broaden the functions of the RNA chaperone Hfq". Current Genetics (2019): http://www.scopus.com/inward/record.url?eid=2-s2.0-85066097576&partnerID=MN8TOARS.
    10.1007/s00294-019-00990-y
  6. Andrade, J.M.; dos Santos, R.F.; Chelysheva, I.; Ignatova, Z.; Arraiano, C.M.. "The RNA-binding protein Hfq is important for ribosome biogenesis and affects translation fidelity". EMBO Journal 37 11 (2018): http://www.scopus.com/inward/record.url?eid=2-s2.0-85045724786&partnerID=MN8TOARS.
    10.15252/embj.201797631
  7. Matos, R.G.; Casinhas, J.; Bárria, C.; Dos Santos, R.F.; Silva, I.J.; Arraiano, C.M.. "The role of ribonucleases and sRNAs in the virulence of foodborne pathogens". Frontiers in Microbiology 8 MAY (2017): http://www.scopus.com/inward/record.url?eid=2-s2.0-85019756774&partnerID=MN8TOARS.
    10.3389/fmicb.2017.00910
  8. Susana Domingues; Ricardo N. Moreira; José M. Andrade; Ricardo F. dos Santos; Cátia Bárria; Sandra C. Viegas; Cecília M. Arraiano. "The role of RNase R in trans-translation and ribosomal quality control". Biochimie 114 (2015): 113-118. http://dx.doi.org/10.1016/j.biochi.2014.12.012.
    10.1016/j.biochi.2014.12.012
  9. Saramago, M.; Bárria, C.; dos Santos, R.F.; Silva, I.J.; Pobre, V.; Domingues, S.; Andrade, J.M.; Viegas, S.C.; Arraiano, C.M.. "The role of RNases in the regulation of small RNAs". Current Opinion in Microbiology 18 1 (2014): 105-115. http://www.scopus.com/inward/record.url?eid=2-s2.0-84897370826&partnerID=MN8TOARS.
    10.1016/j.mib.2014.02.009
Activities

Oral presentation

Presentation title Event name
Host (Event location)
2019/07/06 The RNA-binding protein Hfq is important for ribosome biogenesis and affects translation fidelity The 44th FEBS Congress
Federation of European Biochemical Societies (Krakow, Poland)
2018/11/07 Making translation right: Hfq is a novel ribosome biogenesis factor 9th ITQB NOVA PhD students’ meeting
(Oeiras, Portugal)
2018/07/02 Dis3L2 and other RNase II-like proteins in Health and Disease Encontro Ciência 2018
(Lisboa, Portugal)
2017/06/08 An RNA chaperone controlling ribosome biogenesis and translation fidelity XLI Jornadas Portuguesas de Genética
(Aveiro, Portugal)
2016/12/08 The Sm-like protein Hfq is important for ribosome biogenesis and affects translational fidelity XIX National Congress of Biochemistry
(Guimarães, Portugal)
2016/07/10 The Sm-like protein Hfq is important for ribosome biogenesis and affects translational fidelity Post-Transcriptional Control of Gene Expression: mRNA Decay
Federation of American Societies for Experimental Biology (Lisboa, Portugal)
2015/05/25 A novel protein complex involved in ribosome biogenesis and rRNA quality control XXXIX Jornadas Portuguesas da Genética
(Braga, Portugal)
2013/07/03 Guard and protect versus Seek and destroy the antisense: contrasting roles of Hfq and PNPase in the regulation of non-coding RNAs Young Scientists' Forum (YSF) 2013/FEBS
(St. Petersburg, Russia)

Event organisation

Event name
Type of event (Role)
Institution / Organization
2016/11/23 - 2016/11/25 Member of the organizing committee of the 7th ITQB NOVA PhD students¿ meeting (2018/11/07 - 2018/11/09)
Meeting (Co-organisor)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal

Event participation

Activity description
Type of event
Event name
Institution / Organization
2019 - 2019 (Course) Wellcome Genome Campus Advance Course: NGS Bioinformatics (Course) Wellcome Genome Campus Advance Course: NGS Bioinformatics
Wellcome Genome Campus, United Kingdom
2019 - 2019 (Course) Biostatistics using R
Workshop
(Course) Biostatistics using R
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2016 - 2016 (Course) EMBO Advance Course: Non-coding RNA in infection (Course) EMBO Advance Course: Non-coding RNA in infection
Julius-Maximilians-Universität Würzburg, Germany
2015 - 2015 (Course) Research Skills Development (15th Edition) (Course) Research Skills Development (15th Edition)
Universidade Nova de Lisboa, Portugal
2014 - 2014 (Course) Introduction to High Throughput Sequencing (using R) (Course) Introduction to High Throughput Sequencing (using R)
Instituto Gulbenkian de Ciência, Portugal
2014 - 2014 (Course) SUMMER SCHOOL - Erasmus Intensive Program: Research in Biomedicine and Biotechnology (Course) SUMMER SCHOOL - Erasmus Intensive Program: Research in Biomedicine and Biotechnology
Universidad de Granada, Spain
2011 - 2011 (Course) Real-time PCR (Course) Real-time PCR
Instituto Politécnico de Lisboa Escola Superior de Tecnologia da Saúde de Lisboa, Portugal

Mentoring / Tutoring

Topic Student name
2019/08 - 2020/02 Inês Santos
2019/08 - 2020/02 João Silva