HUGO ALEXANDRE MENDES DE OLIVEIRA (D91A-2590-A70C)

Curriculum Vitae

HUGO ALEXANDRE MENDES DE OLIVEIRA

Since 2010, Hugo has worked within the Bacteriophage & Biofilm group of the Centre of Biological Engineering at Uminho, where he got several competitive FCT grants for research positions (PhD 2010-2014, Post-Doc 2015-2021 and Assistant Researcher (currently)). He also took 2 Assistant Professor positions (2014, 2017) and was involved in 6 different courses in 2 MSc courses/1 PhD programme. During his PhD in Chemical and Biological Engineering (2010-2014), he developed antibacterial agents to control bacterial pathogens, by exploiting bacteriophages (phages) and its encoded proteins called endolysins as therapeutic agents. He rotated >1 year in 3 international labs at Institute of Environmental Science and Research (New Zealand), Catholic University of Leuven (Belgium) and Iberian Nanotechnology Laboratory (Portugal) to learn Protein Engineering, NGS and Spectroscopy to identify/characterize these proteins that degrade the cell wall and cause subsequent lysis of bacterial pathogens, resulting in high impact and highly cited papers, 1 international granted patent and 1 license agreement with Lysando AG (Liechtenstein). During his Post-Doc, he focused on the development of antivirulence strategies to control drug-resistant bacterial pathogens, by applying other phage-derived proteins called tailpikes or depolymerases. During this period, he trained in 3 different research centers (CNR - Italy, KU Leuven - Belgium, IST - Portugal), for protein functional analysis, NGS and invertible models to assess bacterial virulence. In parallel, he developed advance genomic screening methods in collaboration with national and international scientists based on python scripts/machine learning techniques, to characterize phage genomes and proteins, building fast scheme tools to identify novel phage proteins with biotechnological potential interest. Moreover, 1 licensing agreement is currently been made with Nemis Technologies (Switzerland). Currently (since 2021) he became an Assistant Researcher at CEB-Uminho. Among other activities, I have been focused on pursuing his new research objectives i.e. “Addressing Antimicrobial Resistance through New Phage-inspired Strategies”, with particular focus in Genetic Engineering, Molecular Biology and Bioinformatics scientific domains. He participated in several national/international scientific projects (11 between 2017-2022 that totalize >3 M€ of competitive funds). As Coordinator, he managed 4 competitive projects: 2 national (FCT - POCI-01-0145-FEDER-029628 - 234 k€; PRR - PRR-C05-i03-I-000179 - 638 K€) and 2 internationals (ESCMID - 20 k€ - approval rate of 20% and Instruct-ERIC - 14 k€ - approval rate of 14%). He was also involved in the preparation of Marie Curie applications (2020) and applied to the ERC Starting grant (2021) where he got a final panel score of B. He is/was involved in the supervision of 1 post-doc fellow, 2 master fellows, 4 PhD students and 10 master students. He has 19 oral presentations in national/international scientific meetings. He co-organized international courses/meetings: Hands-on phage biotechnology in 2015, 2017, 2019, 2023 (25 participants); iVOM Webinars in 2020, 2023 (~1000 unique participants) and co-organized the biggest conference in virology - Viruses of Microbes 2022 (700 participants, ~250 k€ income; link). His current bibliometrics includes 45 peer-reviewed research articles (20 as first and 11 as corresponding/senior author) mostly in Q1 and in Top5 journals (e.g. Env Micr 2017; Jour Virol 2019; App Env Micr 2019; Bionif 2019; Trends Micro 2022) in SJR index, an h-index of 26 and +3000 citations (Google Scholar). He also has 10 scientific distinctions, 1 international granted patent, and 1 license agreement with an international biotechnological company.

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Identification

Personal identification

Full name: HUGO ALEXANDRE MENDES DE OLIVEIRA

Citation names

Oliveira, H.

Author identifiers

Ciência ID: D91A-2590-A70C
ORCID iD: 0000-0001-9564-5714
Google Scholar ID: DDvpyzMAAAAJ
Scopus Author Id: 52464172600

Email addresses

hugooliveira@deb.uminho.pt (Professional)

Websites

https://www.ceb.uminho.pt/People/Profile/hugooliveira (Professional)

Knowledge fields

Agrarian Sciences - Agrarian and Food Biotechnology - Agricultural Biotechnology and Food Biotechnology
Medical and Health Sciences - Health Sciences - Infectious Diseases

Languages

Language	Speaking	Reading	Writing	Listening	Peer-review
Portuguese (Mother tongue)
English	Proficiency (C2)	Proficiency (C2)	Proficiency (C2)	Proficiency (C2)	Proficiency (C2)

Education

	Degree	Classification
2010/04 - 2014/03 Concluded	Chemical and Biological Engineering (Doutoramento) Universidade do Minho Centro de Engenharia Biológica, Portugal "Molecular studies on bacteriophage endolysins and their potential to control Gram-negative bacteria" (THESIS/DISSERTATION)	Approved unanimously
2002/09 - 2008/09 Concluded	Biological Engineering (Mestrado integrado) Universidade do Minho Escola de Engenharia, Portugal "Characterization of bitter beer compounds in different process of beer production and optimization of their laboratory analyses" (THESIS/DISSERTATION)	15 (ECTS Grading scale, Class A)

Affiliation

Science

	Category Host institution	Employer
2021 - Current	Research Assistant (Research)	Universidade do Minho, Portugal
	Universidade do Minho Centro de Engenharia Biológica, Portugal
2018/12 - Current	Contracted Researcher (Research)	Universidade do Minho, Portugal
	Universidade do Minho Centro de Engenharia Biológica, Portugal
2014/05 - 2018/11	Postdoc (Research)	Universidade do Minho, Portugal
	Universidade do Minho, Portugal

Teaching in Higher Education

	Category Host institution	Employer
2017 - 2017	Invited Associate Professor (University Teacher)	Universidade do Minho, Portugal
	Universidade do Minho Departamento de Engenharia Biológica, Portugal
2014 - 2015	Invited Associate Professor (University Teacher)	Universidade do Minho, Portugal
	Universidade do Minho Departamento de Engenharia Biológica, Portugal

Others

	Category Host institution	Employer
2010/04 - 2014/03	PhD student	Universidade do Minho Centro de Engenharia Biológica, Portugal
	Universidade do Minho Centro de Engenharia Biológica, Portugal
2014 - 2014	Visiting PhD student	International Iberian Nanotechnology Laboratory, Portugal
	Universidade do Minho, Portugal
2012 - 2012	Visiting PhD student	Katholieke Universiteit Leuven - Campus Kulak Kortrijk, Belgium
	Universidade do Minho Centro de Engenharia Biológica, Portugal
2010 - 2011	Visiting PhD student	Institute of Environmental Science and Research (ESR), New Zealand
	Universidade do Minho Centro de Engenharia Biológica, Portugal
2009/09 - 2010/03	Quality Engineer	Grupo PRIMOR, Portugal

2009/09 - 2009/12	Professional Internship	Brauwelt brewery , Germany

2007/02 - 2008/09	Erasmus Student Internship	Šariš Brewery, Slovakia

Projects

Grant

	Designation	Funders
2010 - 2014	Molecular studies on bacteriophage endolysins and their potential to control Gram-negative bacteria SFRH/BD/63734/2009 PhD Student Fellow Universidade do Minho, Portugal	Fundação para a Ciência e a Tecnologia

Contract

	Designation	Funders
2023 - 2025	BioFago - New strategies in the control of Fire Blight PRR-C05-i03-I-000179 Principal investigator Universidade do Minho Centro de Engenharia Biológica, Portugal	IFAP - Instituto de Financiamento de Agricultura e Pescas, IP
2022 - 2024	FITTED - A flexible platform for generating synthetic virus to control infectious diseases LCF/PR/HP21/52310017 Researcher Universidade do Minho, Portugal	”la Caixa” Foundation Ongoing
2021 - 2024	DeathTrigger - Activating Dormant Bacteria with phage-derived proteins to enhance antibiotic efficacy PTDC/BIA-MIC/2312/2020 Post-doc Universidade do Minho, Portugal	Fundação para a Ciência e a Tecnologia Ongoing
2021 - 2024	FITTED - A flexible platform for generating synthetic virus to control infectious diseases HR21-00533 Other	Fundação "la Caixa"
2021 - 2022	Reprograming bacteriophage tailspikes through structure-guided design ID:112 Principal investigator Universidade do Minho, Portugal	European Research - Instruct-ERIC Ongoing
2020/04/01 - 2021/09/30	ViBBiP - Viral-Based Bioconjugation Platform for vaccines development against bacterial pathogens ViBBiP Principal investigator Universidade do Minho Centro de Engenharia Biológica, Portugal	European Society of Clinical Microbiology and Infectious Diseases Ongoing
2018/09/17 - 2021/09/16	SUSPHAGE - Development of a phage-based product to control Escherichia coli associated post-weaning diarrhoea in piglets POCI-01-0247-FEDER-033679 Researcher Universidade do Minho Centro de Engenharia Biológica, Portugal	Fundação para a Ciência e a Tecnologia Ongoing
2018/07/26 - 2021/07/25	PhageSTEC - Development of a formulation of encapsulated bacteriophages to reduce enterotoxigenic E. coli in ruminants POCI-01-0145-FEDER-029628 Principal investigator Universidade do Minho Centro de Engenharia Biológica, Portugal	Fundação para a Ciência e a Tecnologia Ongoing
2018/07/16 - 2021/07/15	PACKTERIOPHAGE - Bacteriophage-releasing nanostructured smart packaging materials for the control of food-borne campylobacter POCI-01-0145-FEDER-032594 Researcher Universidade do Minho Centro de Engenharia Biológica, Portugal	Fundação para a Ciência e a Tecnologia Ongoing
2018/07/16 - 2021/07/15	Phages-on-chip - An integrated phage-based microdevice for multiplex detection of bloodstream infections POCI-01-0145-FEDER-032442 Researcher Universidade do Minho Centro de Engenharia Biológica, Portugal	Fundação para a Ciência e a Tecnologia Ongoing
2012/05 - 2015/08	True-Lyse - Lysin properties adapted to cold temperatures PTDC/AGR-ALI/121057/2010 Researcher Universidade do Minho Centro de Engenharia Biológica, Portugal	Fundação para a Ciência e a Tecnologia
2013/05 - 2014/12	Lysins G-Force - Development of strategies for the application of phage endolysins to control Gram-negative bacteria EXPL/BBB-BIO/0907/2012 Researcher Universidade do Minho Centro de Engenharia Biológica, Portugal	Fundação para a ciência e tecnologia Concluded
2010/02 - 2013/02	PhageFoodSafe - Development of a phage-based product to control Salmonella and Campylobacter in foodstuffs and food processing surfaces PTDC/AGR-ALI/100492/2008 Researcher Universidade do Minho Centro de Engenharia Biológica, Portugal	Fundação para a ciência e tecnologia

Outputs

Publications

Book chapter	Santos, Sílvio B.; Melo, Luís D.R.; Oliveira, Hugo. "Phage Structural Antimicrobial Proteins". In Bacterial Viruses: Exploitation for Biocontrol and Therapeutics. Ireland: Caister Academic Press, 2020. Published • 10.21775/9781913652517.12 Oliveira, H; Melo, L.D.R.; Santos, Sílvio B.. "Bacteriophage Proteins as Antimicrobials to Combat Antibiotic Resistance". In Antibiotic Drug Resistance, edited by Muthyala, R.; Martinez, JLC.; Igrejas, G.; Sham, Y.. John Wiley & Sons, Inc., 2019. Published Sampaio, Marta; Rocha, Miguel; Oliveira, Hugo; Dias, Oscar. "Predicting Promoters in Phage Genomes Using Machine Learning Models". In Practical Applications of Computational Biology and Bioinformatics, 13th International Conference, 105-112. Springer International Publishing, 2019. Published • 10.1007/978-3-030-23873-5_13 Melo, L.D.R.; Oliveira, H.; Santos, Sílvio B.; Sillankorva, S.; Azeredo, J.. "Phages Against Infectious Diseases". In Bioprospecting - Success, Potential and Constraints, edited by Paterson, Russell; Lima, Nelson, 269-294. Springer International Publishing, 2017. Published
Conference poster	Domingues R; Oliveira H; Azeredo J. "Engineering therapeutic bacteriophages against A. baumannii by adjusting phage specificity to cover a large range of capsular types". Paper presented in 33rd European Congress of Clinical Microbiology & Infectious Disease (ECCMID), 2023. Vieira M; Duarte J; Dias O; Rocha M; Azeredo J; Oliveira, H. "Development of comprehensive methodologies for bacteriophage-host studies". Paper presented in Bioinformatics Open Days 2023, 2023. Oliveira, H. "Development of comprehensive methodologies for bacteriophage-host studies". Paper presented in Bioinformatics Open Days 2023, 2023. Oliveira, H. "Characterization of Acinetobacter baumannii phage vB_Ab-P-7". Paper presented in Virus of Microbes, 2023. Oliveira, H. "Advances in the diversity of Acinetobacter phage-encoded capsular depolymerases". Paper presented in Virus of Microbes, 2023. "Studies on the interaction of T4-like phages and diarrheagenic Escherichia coli strains". Paper presented in FEMS22, 2022. "PhageDPO: Phage Depolymerase Finder". Paper presented in XI Bioinformatics Open Days, 2022. Monteiro R; Melo R; Domingues R; Oliveira, H; Maarten J; Azeredo J. "The Acinetobacter baumannii SOS gene ddrR is crucial for prophage maintenance and induction". Paper presented in Virus of Microbes 2022, 2022. Domingues R; Oliveira R; Almeida C; Cho GS; Franz C; Resch G; Azeredo J; Oliveira, H. "Building a collection of phage-derived capsular depolymerases to tackle relevant A. baumannii capsular types". Paper presented in Virus of Microbes 2022, 2022. Oliveira, H.. "Adaptation of a lytic mutant phage for the generation of an antibiofilm phage cocktail with potential use in phage therapy". Paper presented in ECCMID 2021, 2021. "Bacteriophages to tackle swine colibacillosis: assessing the potential of this alternative therapy". Paper presented in World Microbe Forum, 2021. Oliveira, H.. "Safety assessment of the biocontrol of Shiga toxin-producing Escherichia coli using bacteriophages". Paper presented in Phage Futures Congress, 2021. Pacio, O.; Blasco, L.; Bleriot, I.; Fernandez-Garcia, L.; Bardanca1, M.G.; Ambroa, A.; López, M.; et al. "Activity of an engineered-phage in combination with natural lytic phages against clinical strains of A. baumannii". Paper presented in American Society of Microbiology (ASM) Microbe 2020, 2020. Oliveira, H; Balem, A.; Gonçalves, S.; Garcia-Meniño, I; Flament-Simon, S.C.; Blanco, J.E.; Pinto, J.; et al. "Prevalence and Genetic Characterization of Shiga Toxin-Producing Escherichia coli (STEC) Isolates from cattle in Portugal". Paper presented in 30th European Congress of Clinical Microbiology and Infectious Diseases (ECCMID), 2020. Ballem A.; Gonçalves, S.; Ferreira A. I.; Fernandes C.; Saavedra M. J.; Pinto C.; Oliveira, H; Almeida G.; Almeida, C.. "Prevalence of shigatoxigenic escherichia coli in bovine cattle: a survey in the north region of portugal". Paper presented in SAlimentar 2019 - 1º Simpósio INIAV para a Segurança Alimentar (Rumo à Alimentação do Futuro), 2019. Gonçalves, Soraia; Ferreira, Isabel; Guedes, Hugo; Oliveira, H; Almeida, Carina; Afonso, Isabel; Almeida, Gonçalo. "Perfil de resistência a antibióticos de escherichia coli produtoras e não produtoras da toxina shiga". Paper presented in SAlimentar 2019 - 1º Simpósio INIAV para a Segurança Alimentar (Rumo à Alimentação do Futuro), 2019. Ribeiro, Henrique G; Melo, Luís D. R.; Oliveira, H.; Boon, Maarten; Lavigne, Rob; Azeredo, Joana; Oliveira, A.. "API480: features towards therapy in honeybee hives". Paper presented in 23rd Biennial Evergreen International Phage Meeting, 2019. Sampaio, M.; Rocha, M.; Oliveira, H; Dias, O.. "Predicting promoters in phage genomes using PhagePromoter". Paper presented in Bioinformatics Open Days, 2019. Akturk, E.; Oliveira, H.; Sílvio B. Santos; Melo, L.D.R.; Azeredo, J.. "Interaction of Phage and Gentamicin Combinations in Pseudomonas aeruginosa and Staphylococcus aureus Polymicrobial Biofilms23rd Biennial Evergreen International Phage Meeting". Paper presented in 23rd Biennial Evergreen International Phage Meeting, 2019. Oliveira, H; Costa, A.R.; Ferreira, A.; Mil-Homens, D.; Fialho, A.M.; Azeredo, J.. "Anti-virulent properties of a phage-encoded depolymerase against A. baumannii K2 capsular type". Paper presented in Viruses of Microbes, 2018. Oliveira, H; Akturk, E.; Melo, L.D.R.; Azeredo, J.. "Synergetic efect between phage and antibiotics as an alternative strategy to control Pseudomonas aeruginosa biofilm associated infections". Paper presented in Viruses of Microbes 2018, 2018. Oliveira, H; Akturk, E.; Melo, L.D.R.; Azeredo, J.. "Combined treatment with bacteriophages and antibiotics as a strategy to control biofilm associated infections". Paper presented in Microbiotec'17 - Congress of Microbiology and Biotechnology 2017, 2017. Buttimer, C.; Oliveira, H; Hendrix, H.; Lavigne, R.; Neve, H.; McAuliffe, O.; Hill, C.; O’Mahony, J.; Coffey, A.. "Characterization of the Enterobacteria 'jumbo' bacteriophage vb_Pcam_CBB". Paper presented in International Union of Microbiological Societes, 2017. Buttimer, C; Hendrix, H; Oliveira, H; Lavigne, R; Neves, R.; McAuliffe, O; Hill, C; O’Mahony, J; Coffey, A. "Characterization of the Enterobacteria 'jumbo' bacteriophage VB_Pcam_CBB". Paper presented in IMUS 2017 - 15th International Congress of Bacteriology and Applied Microbiology, 15th International Congress of Mycology and Eukaryotic Microbiology and 17th International Congress of Virology, 2017. Santos, Sílvio B.; Brandão, A.; Oliveira, A.; Melo, L.D.R.; Pinto, G.; Oliveira, H; Ferreira, E.; Azeredo, J.. "New Bacterial Biorecognition Elements from Phage Origin". Paper presented in CEB Scientific Annual Meeting, 2017. 10.29173/ikc3217 Graça, P.; Oliveira, H; Oliveira, A.; Azeredo, J.. "Characterization of novel broad-spectra Citrobacter freundii infecting bacteriophage". Paper presented in Evergreen International Phage Biology Meeting, 2017. Buttimer, C.; Oliveira, H; Hendrix, H.; Lavigne, R.; Neve, H.; McAuliffe, O.; Hill, C.; O’Mahony, J.; Coffey, A.. "Analysis of the atypical ‘hairy’ Enterobacteriacea phage vB_PcaM_CBB". Paper presented in Viruses of Microbes, 2016. Oliveira, H; Pires, D.; Melo, L.D.R.; Kluskens, L.D.; Sillankorva, S.; Azeredo, J.. "Bacteriophage depolymerases: novel polysaccharide degrading enzymes". Paper presented in Biofilms, 2016. Briers, Y.; Walmagh, M.; Puyenbroeck, V.V.; Cornelissen, A.; Cenens, W.; Aertsen, A.; Oliveira, H; et al. "Polycationic, endolysin-based ´Artlysins´ to combact multidrug resistant Gram-negative pathogens". Paper presented in Viruses of Microbes, 2014. Oliveira, H; Thiagarajan, V.; Walmagh, M.; Sillankorva, S.; Secundo, F.; Lavigne, R.; Neves-Petersen, M.T.; Kluskens, L.D.; Azeredo, J.. "Biochemical characterization of highly stable endolysins with a powerful and broad anti-Gram-negative lytic activity in the presence of weak acids". Paper presented in Viruses of Microbes, 2014. Trigo, G.; Martins, T.G.; Oliveira, H; Fraga, A.G.; Castro A.G.; Azeredo, J.; Pedrosa, J.. "Innovative anti-microbial strategies against Buruli ulcer: Bacteriophage Therapy". Paper presented in MicroBiotec - Congress of Microbiology and Biotechnology, 2013. Nóbrega, F.L.; Oliveira, H.; Melo, L.D.R.; Santos, Sílvio B.; Cerca, N.; Ferreira, E.C.; Azeredo, J.. "Insights into phage endolysins". Paper presented in Bioinformatics Open Days, 2013. Oliveira, H; Melo, L.D.R.; Nóbrega, F.L.; Santos, Sílvio B.; Cerca, N.; Ferreira, E.C.; Azeredo, J.. "Unraveling the insights into phage endolysin association". Paper presented in Viruses of Microbes, 2012. Oliveira, H; Carvalho, CM; Santos, SB; Kluskens, LD; Azeredo, J. "Exploiting the biotechnological potential of bacteriophages towards food safety". Paper presented in 3rd Meeting of the Institute for Biotechnology and Bioengineering, 2012. Oliveira, H; Walmagh, M.; Kluskens, L.D.; Sillankorva, S.; Lavigne, R.; Azeredo, J.. "Antibacterial activity on opportunistic Pseudomonas aeruginosa pathogen by a novel Salmonella phage endolysin". Paper presented in MicroBiotec - Congress of Microbiology and Biotechnology, 2011. Oliveira, H; Walmagh, M.; Kluskens, L.D.; Sillankorva, S.; Lavigne, Rob; Azeredo, J.. "Biochemical and antibacterial characterization of a novel phage endolysin against the Gram-negative pathogen Pseudomonas aeruginosa". Paper presented in Evergreen International Phage Biology Meeting, 2011. Kluskens, Leon; Santos, Sílvio B.; Fernandes, Elisabete Ramos; Oliveira, H.; Melo, Luís D. R.; Cerca, Nuno; Sillankorva, Sanna; Azeredo, Joana. "The use of bacteriophage endolysins as antibacterial compounds". Paper presented in CEB anual meeting, 2010.
Journal article	Castro, Joana; Oliveira, Ricardo; Fernandes, Liliana; Carvalho, Isabel; Oliveira, H.; Brinks, Erik; Cho, Gyu-Sung; et al. "Molecular characterization and virulence profile of Klebsiella pneumoniae and Klebsiella oxytoca isolated from ill cats and dogs in Portugal". Veterinary Microbiology 292 (2024): 110056. http://dx.doi.org/10.1016/j.vetmic.2024.110056. Published • 10.1016/j.vetmic.2024.110056 Gabriel Abreu; Edgar Garcia; Ana Oliveira; Hugo Oliveira; Kenneth M. Stedman. "Genome sequence of Erwinia amylovora bacteriophage Omen". Microbiology Resource Announcements (2024): https://doi.org/10.1128/mra.00122-24. 10.1128/mra.00122-24 Akturk, Ergun; Melo, Luís D.R.; Oliveira, Hugo; Crabbé, Aurélie; Coenye, Tom; Azeredo, Joana. "Combining phages and antibiotic to enhance antibiofilm efficacy against an in vitro dual species wound biofilm". Biofilm 6 (2023): 100147. http://dx.doi.org/10.1016/j.bioflm.2023.100147. Published • 10.1016/j.bioflm.2023.100147 Neto, Sofia; Vieira, Ana; Oliveira, Hugo; Espiña, Begoña. "Assessing Acinetobacter baumannii virulence and treatment with a bacteriophage using zebrafish embryos". The FASEB Journal 37 7 (2023): http://dx.doi.org/10.1096/fj.202300385r. Published • 10.1096/fj.202300385r Oliveira, Hugo; Santos, Sílvio; Pires, Diana P.; Boeckaerts, Dimitri; Pinto, Graça; Domingues, Rita; Otero, Jennifer; et al. "CkP1 bacteriophage, a S16-like myovirus that recognizes Citrobacter koseri lipopolysaccharide through its long tail fibers". Applied Microbiology and Biotechnology 107 11 (2023): 3621-3636. http://dx.doi.org/10.1007/s00253-023-12547-8. Published • 10.1007/s00253-023-12547-8 Gomes, Marta; Domingues, Rita; Turner, Dann; Oliveira, Hugo. "Genomic Analysis of Two Novel Bacteriophages Infecting Acinetobacter beijerinckii and halotolerans Species". Viruses 15 3 (2023): 643. http://dx.doi.org/10.3390/v15030643. Published • 10.3390/v15030643 Oliveira, Ana; Dias, Carla; Oliveira, Ricardo; Almeida, Carina; Fuciños, Pablo; Sillankorva, Sanna; Oliveira, Hugo. "Paving the way forward: Escherichia coli bacteriophages in a One Health approach". Critical Reviews in Microbiology 50 1 (2023): 87-104. http://dx.doi.org/10.1080/1040841x.2022.2161869. Published • 10.1080/1040841x.2022.2161869 Ricardo Oliveira; Joana Castro; Sónia Silva; Hugo Oliveira; Maria José Saavedra; Nuno Filipe Azevedo; Carina Almeida. "Exploring the Antibiotic Resistance Profile of Clinical Klebsiella pneumoniae Isolates in Portugal". Antibiotics (2022): https://doi.org/10.3390/antibiotics11111613. 10.3390/antibiotics11111613 Hanna Fokt; Sara Cleto; Hugo Oliveira; Daniela Araújo; Joana Castro; Nuno Cerca; Maria João Vieira; Carina Almeida. "Bacteriocin Production by Escherichia coli during Biofilm Development". Foods (2022): https://doi.org/10.3390/foods11172652. 10.3390/foods11172652 Hugo Oliveira; Zuzanna Drulis-Kawa; Joana Azeredo. "Exploiting phage-derived carbohydrate depolymerases for combating infectious diseases". Trends in Microbiology 30 8 (2022): 707-709. https://doi.org/10.1016/j.tim.2022.05.002. 10.1016/j.tim.2022.05.002 Hugo Oliveira; Rita Domingues; Benjamin Evans; J. Mark Sutton; Evelien M. Adriaenssens; Dann Turner. "Genomic Diversity of Bacteriophages Infecting the Genus Acinetobacter". Viruses (2022): https://doi.org/10.3390/v14020181. 10.3390/v14020181 L. Blasco; I. Bleriot; M. González de Aledo; L. Fernández-García; O. Pacios; H. Oliveira; M. López; et al. "«Development of an anti- Acinetobacter baumannii biofilm phage cocktail: Genomic Adaptation to the Host»". Antimicrobial Agents and Chemotherapy (2022): https://doi.org/10.1128/AAC.01923-21. 10.1128/AAC.01923-21 Oliveira, Hugo; Azeredo, Joana. "Treating Bacterial Infections With a Protein From a Virus". Frontiers for Young Minds 9 (2021): http://dx.doi.org/10.3389/frym.2021.648764. Published • 10.3389/frym.2021.648764 Rita Domingues; Ana Barbosa; Sílvio B. Santos; Diana Priscila Pires; Jonathan Save; Grégory Resch; Joana Azeredo; Hugo Oliveira. "Unpuzzling Friunavirus-Host Interactions One Piece at a Time: Phage Recognizes Acinetobacter pittii via a New K38 Capsule Depolymerase". Antibiotics 10 11 (2021): 1304-1304. https://doi.org/10.3390/antibiotics10111304. 10.3390/antibiotics10111304 Pinto, Graça; Minnich, Scott A; Hovde, Carolyn J; Oliveira, Hugo; Smidt, Hauke; Almeida, Carina; Azeredo, Joana. "The interactions of bacteriophage Ace and Shiga toxin-producing Escherichia coli during biocontrol". FEMS Microbiology Ecology 97 8 (2021): http://dx.doi.org/10.1093/femsec/fiab105. Published • 10.1093/femsec/fiab105 Pinto, Graça; Sampaio, Marta; Dias, Oscar; Almeida, Carina; Azeredo, Joana; Oliveira, Hugo. "Insights into the genome architecture and evolution of Shiga toxin encoding bacteriophages of Escherichia coli". BMC Genomics 22 1 (2021): http://dx.doi.org/10.1186/s12864-021-07685-0. Published • 10.1186/s12864-021-07685-0 Ballem, Andressa; Gonçalves, Soraia; Garcia-Meniño, Isidro; Flament-Simon, Saskia C.; Blanco, Jesús E.; Fernandes, Conceição; Saavedra, Maria José; et al. "Prevalence and serotypes of Shiga toxin-producing Escherichia coli (STEC) in dairy cattle from Northern Portugal". PLOS ONE 15 12 (2020): e0244713. http://dx.doi.org/10.1371/journal.pone.0244713. Published • 10.1371/journal.pone.0244713 Silva, Maria Daniela; Oliveira, Hugo; Faustino, Alberta; Sillankorva, Sanna. "Characterization of MSlys, the endolysin of Streptococcus pneumoniae phage MS1". Biotechnology Reports (2020): e00547. http://dx.doi.org/10.1016/j.btre.2020.e00547. Published • 10.1016/j.btre.2020.e00547 Fiedler, Gregor; Ballem, Andressa; Brinks, Erik; Almeida, Carina; Franz, Charles M. A. P.; Oliveira, Hugo. "Draft Genome Sequences of 12 Shiga Toxin-Producing Escherichia coli Strains Isolated from Dairy Cattle in Portugal". Microbiology Resource Announcements 9 38 (2020): http://dx.doi.org/10.1128/mra.00790-20. 10.1128/mra.00790-20 Ferreira, Alice; Oliveira, Hugo; Silva, Daniela; Almeida, Carina; Burgan, Julia; Azeredo, Joana; Oliveira, Ana. "Complete Genome Sequences of Eight Phages Infecting Enterotoxigenic Escherichia coli in Swine". Microbiology Resource Announcements 9 36 (2020): http://dx.doi.org/10.1128/mra.00858-20. Published • 10.1128/mra.00858-20 Dias, Carla; Almeida, Carina; Lobocka, Malgorzata; Oliveira, Hugo. "Genome Sequences of Four Potentially Therapeutic Bacteriophages Infecting Shiga Toxin-Producing Escherichia coli". Microbiology Resource Announcements 9 36 (2020): http://dx.doi.org/10.1128/mra.00749-20. Published • 10.1128/mra.00749-20 Oliveira, Hugo; Pinto, Graça; Mendes, Bruna; Dias, Oscar; Hendrix, Hanne; Akturk, Ergun; Noben, Jean-Paul; et al. "Tailspike with EPS-depolymerase activity, encoded by a phage belonging to a new genus, makes Providencia stuartii susceptible to serum-mediated killing". Applied and Environmental Microbiology (2020): http://dx.doi.org/10.1128/aem.00073-20. Accepted • 10.1128/aem.00073-20 Oliveira, Hugo; Melo, Luís D. R.; Pires, Diana P.; Dabrowska, Krystyna; Azeredo, Joana. "Phage therapy efficacy: a review of the last 10 years of preclinical studies". Critical Reviews in Microbiology (2020): 1-22. http://dx.doi.org/10.1080/1040841x.2020.1729695. Published • 10.1080/1040841x.2020.1729695 Hugo Oliveira; Marta Sampaio; Luís D. R. Melo; Oscar Dias; Welkin H. Pope; Graham F. Hatfull; Joana Azeredo. "Staphylococci phages display vast genomic diversity and evolutionary relationships". BMC Genomics 20 1 (2019): https://doi.org/10.1186/s12864-019-5647-8. Published • 10.1186/s12864-019-5647-8 Ribeiro, Henrique G.; Melo, Luís D. R.; Oliveira, Hugo; Boon, Maarten; Lavigne, Rob; Noben, Jean-Paul; Azeredo, Joana; Oliveira, Ana. "Characterization of a new podovirus infecting Paenibacillus larvae". Scientific Reports 9 1 (2019): http://dx.doi.org/10.1038/s41598-019-56699-y. Published • 10.1038/s41598-019-56699-y Luís D. R. Melo; R. Ferreira; Ana R. Costa; H. Oliveira; J. Azeredo. "Efficacy and safety assessment of two enterococci phages in an in vitro biofilm wound model". Scientific Reports 9 1 (2019): https://doi.org/10.1038/s41598-019-43115-8. Published • 10.1038/s41598-019-43115-8 Milho, Catarina; Silva, Maria Daniela; Alves, Diana; Oliveira, Hugo; Sousa, Clara; Pastrana, Lorenzo M.; Azeredo, Joana; Sillankorva, Sanna. "Escherichia coli and Salmonella Enteritidis dual-species biofilms: interspecies interactions and antibiofilm efficacy of phages". Scientific Reports 9 1 (2019): http://dx.doi.org/10.1038/s41598-019-54847-y. Published • 10.1038/s41598-019-54847-y Fraga, Alexandra G.; Trigo, Gabriela; Murthy, Ramya K.; Akhtar, Shamim; Hebbur, Madhavi; Pacheco, Ana Rita; Dominguez, Juan; et al. "Antimicrobial activity of Mycobacteriophage D29 Lysin B during Mycobacterium ulcerans infection". PLOS Neglected Tropical Diseases 13 8 (2019): e0007113. http://dx.doi.org/10.1371/journal.pntd.0007113. Published • 10.1371/journal.pntd.0007113 Sampaio, Marta; Rocha, Miguel; Oliveira, Hugo; Dias, Oscar. "Predicting promoters in phage genomes using PhagePromoter". Bioinformatics 35 24 (2019): 5301-5302. http://dx.doi.org/10.1093/bioinformatics/btz580. Published • 10.1093/bioinformatics/btz580 Akturk, Ergun; Oliveira, Hugo; Santos, Sílvio B.; Costa, Susana; Kuyumcu, Suleyman; Melo, Luís D. R.; Azeredo, Joana. "Synergistic Action of Phage and Antibiotics: Parameters to Enhance the Killing Efficacy Against Mono and Dual-Species Biofilms". Antibiotics 8 3 (2019): 103. http://dx.doi.org/10.3390/antibiotics8030103. Published • 10.3390/antibiotics8030103 Oliveira, H.; Mendes, A.; Fraga, A.G.; Ferreira, A.; Pimenta, A.I.; Mil-Homens, D.; Fialho, A.M.; Pedrosa, J.; Azeredo, J.. "K2 Capsule Depolymerase Is Highly Stable, Is Refractory to Resistance, and Protects Larvae and Mice from Acinetobacter baumannii Sepsis". Applied and environmental microbiology 85 17 (2019): http://www.scopus.com/inward/record.url?eid=2-s2.0-85071352666&partnerID=MN8TOARS. Published • 10.1128/AEM.00934-19 Oliveira, H.; Costa, A.R.; Ferreira, A.; Konstantinides, N.; Santos, S.B.; Boon, M.; Noben, J.-P.; Lavigne, R.; Azeredo, J.. "Functional analysis and antivirulence properties of a new depolymerase from a myovirus that infects acinetobacter baumannii capsule K45". Journal of Virology 93 4 (2019): http://www.scopus.com/inward/record.url?eid=2-s2.0-85061125005&partnerID=MN8TOARS. Published • 10.1128/JVI.01163-18 Oliveira, Hugo; São-José, Carlos; Azeredo, Joana. "Phage-Derived Peptidoglycan Degrading Enzymes: Challenges and Future Prospects for In Vivo Therapy". Viruses 10 6 (2018): 292. http://dx.doi.org/10.3390/v10060292. Published • 10.3390/v10060292 Oliveira, Hugo; Costa, Ana R.; Konstantinides, Nico; Ferreira, Alice; Akturk, Ergun; Sillankorva, Sanna; Nemec, Alexandr; et al. "Ability of phages to infectAcinetobacter calcoaceticus-Acinetobacter baumanniicomplex species through acquisition of different pectate lyase depolymerase domains". Environmental Microbiology 19 12 (2017): 5060-5077. http://dx.doi.org/10.1111/1462-2920.13970. Published • 10.1111/1462-2920.13970 Endersen, Lorraine; Buttimer, Colin; Nevin, Eoghan; Coffey, Aidan; Neve, Horst; Oliveira, Hugo; Lavigne, Rob; O'Mahony, Jim. "Investigating the biocontrol and anti-biofilm potential of a three phage cocktail against Cronobacter sakazakii in different brands of infant formula". International Journal of Food Microbiology 253 (2017): 1-11. http://dx.doi.org/10.1016/j.ijfoodmicro.2017.04.009. Published • 10.1016/j.ijfoodmicro.2017.04.009 Oliveira, Hugo; Pinto, Graça; Oliveira, Ana; Noben, Jean-Paul; Hendrix, Hanne; Lavigne, Rob; Lobocka, Malgorzata; Kropinski, Andrew M.; Azeredo, Joana. "Characterization and genomic analyses of two newly isolated Morganella phages define distant members among Tevenvirinae and Autographivirinae subfamilies". Scientific Reports 7 1 (2017): http://dx.doi.org/10.1038/srep46157. Published • 10.1038/srep46157 Oliveira, H.; Pinto, G.; Hendrix, H.; Noben, J.-P.; Gawor, J.; Kropinski, A.M.; Lobocka, M.; Lavigne, R.; Azeredo, J.. "A lytic Providencia rettgeri virus of potential therapeutic value is a deepbranching member of the T5virus genus". Applied and Environmental Microbiology 83 23 (2017): http://www.scopus.com/inward/record.url?eid=2-s2.0-85034062121&partnerID=MN8TOARS. Published • 10.1128/AEM.01567-17 Buttimer, C.; Hendrix, H.; Oliveira, H.; Casey, A.; Neve, H.; McAuliffe, O.; Paul Ross, R.; et al. "Things are getting hairy: Enterobacteria bacteriophage vB_PcaM_CBB". Frontiers in Microbiology 8 JAN (2017): http://www.scopus.com/inward/record.url?eid=2-s2.0-85011961519&partnerID=MN8TOARS. Published • 10.3389/fmicb.2017.00044 Ferreira, Carina; Gonçalves, Bruna; Vilas Boas, Diana; Oliveira, Hugo; Henriques, Mariana; Azeredo, Joana; Silva, Sónia. "Candida tropicalisbiofilm and human epithelium invasion is highly influenced by environmental pH". Pathogens and Disease 74 8 (2016): ftw101. http://dx.doi.org/10.1093/femspd/ftw101. Published • 10.1093/femspd/ftw101 Oliveira, H.; Pinto, G.; Oliveira, A.; Oliveira, C.; Faustino, M.A.; Briers, Y.; Domingues, L.; Azeredo, J.. "Characterization and genome sequencing of a Citrobacter freundii phage CfP1 harboring a lysin active against multidrug-resistant isolates". Applied Microbiology and Biotechnology 100 24 (2016): 10543-10553. http://www.scopus.com/inward/record.url?eid=2-s2.0-84988927829&partnerID=MN8TOARS. Published • 10.1007/s00253-016-7858-0 Oliveira, H.; Boas, D.V.; Mesnage, S.; Kluskens, L.D.; Lavigne, R.; Sillankorva, S.; Secundo, F.; Azeredo, J.. "Structural and enzymatic characterization of ABgp46, a novel phage endolysin with broad anti-gram-negative bacterial activity". Frontiers in Microbiology 7 FEB (2016): http://www.scopus.com/inward/record.url?eid=2-s2.0-84962129551&partnerID=MN8TOARS. Published • 10.3389/fmicb.2016.00208 Pires, D.P.; Oliveira, H.; Melo, L.D.R.; Sillankorva, S.; Azeredo, J.. "Bacteriophage-encoded depolymerases: their diversity and biotechnological applications". Applied Microbiology and Biotechnology 100 5 (2016): 2141-2151. http://www.scopus.com/inward/record.url?eid=2-s2.0-84954421775&partnerID=MN8TOARS. Published • 10.1007/s00253-015-7247-0 Oliveira, Hugo; Sillankorva, Sanna; Merabishvili, Maia; Kluskens, Leon D.; Azeredo, Joana. "Unexploited opportunities for phage therapy". Frontiers in Pharmacology 6 (2015): http://dx.doi.org/10.3389/fphar.2015.00180. Published • 10.3389/fphar.2015.00180 Oliveira, Hugo; Thiagarajan, Viruthachalam; Walmagh, Maarten; Sillankorva, Sanna; Lavigne, Rob; Neves-Petersen, Maria Teresa; Kluskens, Leon D.; Azeredo, Joana. "A Thermostable Salmonella Phage Endolysin, Lys68, with Broad Bactericidal Properties against Gram-Negative Pathogens in Presence of Weak Acids". PLoS ONE 9 10 (2014): e108376. http://dx.doi.org/10.1371/journal.pone.0108376. Published • 10.1371/journal.pone.0108376 Briers, Yves; Walmagh, Maarten; Van Puyenbroeck, Victor; Cornelissen, Anneleen; Cenens, William; Aertsen, Abram; Oliveira, Hugo; et al. "Engineered Endolysin-Based “Artilysins” To Combat Multidrug-Resistant Gram-Negative Pathogens". mBio 5 4 (2014): http://dx.doi.org/10.1128/mbio.01379-14. Published • 10.1128/mbio.01379-14 Oliveira, H.; Melo, L. D. R.; Santos, S. B.; Nobrega, F. L.; Ferreira, E. C.; Cerca, N.; Azeredo, J.; Kluskens, L. D.. "Molecular Aspects and Comparative Genomics of Bacteriophage Endolysins". Journal of Virology 87 8 (2013): 4558-4570. http://dx.doi.org/10.1128/jvi.03277-12. Published • 10.1128/jvi.03277-12 Oliveira, Hugo; Azeredo, Joana; Lavigne, Rob; Kluskens, Leon. D.. "Bacteriophage endolysins as a response to emerging foodborne pathogens". Trends in Food Science & Technology 28 2 (2012): 103-115. http://dx.doi.org/10.1016/j.tifs.2012.06.016. Published • 10.1016/j.tifs.2012.06.016 Oliveira, Hugo; Sillankorva, Sanna M.; Azeredo, Joana. "Bacteriophages and Their Role in Food Safety". International Journal of Microbiology 2012 (2012): 1-13. http://dx.doi.org/10.1155/2012/863945. Published • 10.1155/2012/863945 Sillankorva, Sanna; Pires, Diana; Oliveira, Hugo; Neubauer, Peter; Azeredo, Joana. "The Influence of P. fluorescens Cell Morphology on the Lytic Performance and Production of Phage ¿IBB-PF7A". Current Microbiology 63 4 (2011): 347-353. http://dx.doi.org/10.1007/s00284-011-9987-0. Published • 10.1007/s00284-011-9987-0
Magazine article	"Bacteriófagos: Novos agentes antibacterianos para controlo alimentar", TecnoAlimentar, 2021, http://www.tecnoalimentar.pt/noticias/bacteriofagos-novos-agentes-antibacterianos-para-controlo-alimentar/.
Preprint	Vieira, Maria; Duarte, José; Domingues, Rita; Oliveira, H; Dias, Oscar. "PhageDPO: Phage Depolymerase Finder". 2023. http://dx.doi.org/10.1101/2023.02.24.529883. 10.1101/2023.02.24.529883
Report	Oliveira, H.. 2018. Create one new genus, Priunavirus, containing one new species, in the family Siphoviridae, order Caudovirales 2018. https://talk.ictvonline.org/ictv/proposals/2018.128B.A.v1.Priunasvirus.zip.
Website	Oliveira, H. Microsummit. 2022. www.microsummit-2022.com.

Artistic / Performance

Artistic performance	2023. Podcast “Os Microbiólogos” creation.
Video recording	Oliveira, H; TecMinho (Producer). 2018. Novel antimicrobial therapy with phage derived depolymerases. Oliveira, H; Centre of Biological Enginnering (Producer). 2017. Explorando o potencial dos vírus para o tratamento de infeções bacterianas. Oliveira, H; Tecminho (Producer). 2013. MAGniPHI combate infeções.

Intellectual property

Patent

Oliveira, H.; Azeredo, J.. 2018. "Novel endolysin (international patent)".
Granted/Issued

Other

Other output

Special issue. Oliveira, Ana. 2019. Special issue: Bacteriophage Ecology and Evolution. Guest Editor of Virology Journal.. 2019. Oliveira, H. https://www.biomedcentral.com/collections/bacteriophageecoevo.
Online tool. PhagePromoter detects promoters in phage genomes.. 2019. Oliveira, H. https://bit.ly/2Dfebfv..

Activities

Oral presentation

	Presentation title	Event name Host (Event location)
2024	Advancements in bacteriophage-based therapies to control multidrug resistant infections	13th Congress of the Serbian Society for Microbiology (Belgrade , Serbia)
2023	Genetic manipulation of A. baumannii-infecting bacteriophages to tackle a larger range of capsular types	13th International Symposium on the Biology of Acinetobacter (Coimbra, Portugal)
2023	Engineering Phages to Target Different Bacterial Capsule Serotypes	IV Encontro Internacional da Sociedade Portuguesa de Genética (Braga, Portugal)
2023	Machine Learning in the Service of Phage Analysis: Advancements, Applications, Future Prospects	Phages Hands on International Course
2023	The use of bacteriophages to reduce antibiotic-resistant pathogens	2th Egas Moniz One Health Symposium (Lisbon, Portugal)
2022	Disclosing the full diversity of A. baumannii bacteriophage capsular depolymerases	AcinetoVibes
2022	Understanding the complete reservoir of bacteriophage depolymerases against A. baumannii capsules	Viruses of Microbes (Guimarães, Portugal)
2022	Proteínas imunogénicas contra A. baumannii: recurso para combater multirresistência
2021/11/23	Prevalence and control of Shiga toxin-producing E. coli: from diversity in dairy cattle to phage therapy	Microbiotec 2021 (Portugal)
2021/08/04	CkP1 is a novel S16-like broad-host-range myovirus that recognizes Citrobacter koseri lipopolysaccharide through its long tail fibres	24th Biennial Evergreen Phage Meeting Evergreen State College (Evergreen, Seattle, United States)
2021/06	Reprograming bacteriophage tailspikes through structure-guided design	Portuguese Centre for Integrated Structural Biology webinar Universidade NOVA de Lisboa (Lisbon, Portugal)
2021/06	Phage Capsular Depolymerases	World Microbe Forum American Society of Microbiology (ASM) and the Federation of European Microbiological Societies (FEMS)
2021	Encapsulated bacteriophages for pre-slaughter interventions to reduce Shiga toxin-producing E. coli (STEC) in ruminants	VIII jornadas Internacionais de Bovinicultura
2021	Phage Capsular Depolymerases, from exploration to exploitation	Word Microbe Forum
2021	Bacteriophage tailspikes through structure-guided design	Instruct-Eric webinar
2020/09/10	Long tail fibers of CkP1, a S16-like phage, exhibit broad binding spectrum against Citrobacter koseri	Oxford Bacteriophage Conference – Phages 2020 Oxford University (Oxford, United Kingdom)
2020/02/05	Bacteriophage depolymerases: evolutionary insights and antivirulence strategies against bacterial pathogens	Viruses 2020 - Novel Concepts in Virology (Barcelona, Spain)
2019/12/06	Novel capsular depolymerases-based strategy to kill multidrug-resistant pathogenic bacteria	Microbiotec'19 - Congress of Microbiology and Biotechnology 2019 University of Coimbra (Coimbra, Portugal)
2019/09/11	Bacteriophage-depolymerases: their diversity and therapeutic properties	Oxford Bacteriophage Conference – Phages University of Leicester (Oxford, United Kingdom)
2018/11/08	Endolysin binding domain is highly conserved in staphylococcal phage genomes	International symposoium on Antimicrobial hydrolytic enzymes Rockefeller university (New york, United States)
2018/11/08	Bacteriophages lysins to detect and control pathogens: two case studies	The 2nd International Symposium on Antimicrobial Hydrolytic Enzymes Rockefeller University (New York, United States)
2018/07/09	Novel antimicrobial therapy with phage derived depolymerases	iTeams PhD MIT program (Lisbon, Portugal)
2018/07/03	Bacteriophage polysaccharide depolymerases, their role and biotechnological applications	Viruses of Microbes 2018 University of Wroclaw (Wroclaw, Poland)
2017/11/23	Explorando o potencial dos vírus para o tratamento de infeções bacterianas	CEB Talk Startup Braga (Braga, Portugal)
2017/07/06	Bacteriophage-derived enzymes: from exploration to exploitation	CEB Scientific Annual Meeting University of Minho (Braga, Portugal)
2016/10/13	Capsule depolymerase activity of phages infecting the Acinetobacter baumannii-calcoaceticus complex	International Scientific Conference. Bacteriophages: Theoretical and Practical Aspects of Their Application in Medicine Marins Park Hotel (Moscow, Russia)
2014/07/05	Development of Bacteriophage Endolysins to Control Gram-negative Pathogens	Symposium Istituto di Chimica del Riconoscimento Molecolare (Milan, Italy)
2013/10/02	Molecular and functional aspects of bacteriophage endolysins	BioMicroWorld – International Conference on Environmental, Industrial and Applied Microbiology Faculty of Medicine - Complutense University (Madrid, Spain)
2012/03/01	Insights into phage endolysins	Bioinformatics Open Days University of Minho (Braga, Portugal)
2010/10/27	The use of bacteriophage endolysins as antibacterial compounds	2nd Meeting of the Institute for Biotechnology and Bioengineering Uniservidade do Minho (Braga, Portugal)

Supervision

	Thesis Title Role	Degree Subject (Type) Institution / Organization
2024 - 2034	Isolation of broad-host range phages targeting Acinetobacter/Klebsiella Supervisor	Biological Engineering (Master) Universidade do Minho, Portugal
2023 - 2024	Isolation of bacteriophages targeting E. amylovora phytopathogen isolates Supervisor	Applied Biochemistry (Master) Universidade do Minho, Portugal
2023 - 2024	ErwiniaTyping - Genotyping tool for Erwinia amylovora capsules Supervisor	Bioinformatics (Master) Universidade do Minho, Portugal
2021/01/01 - 2023/12/31	A flexible platform for generating Acinetobacter synthetic phages to control infectious diseases Co-supervisor	Chemical and Biologiocal Enginnering (Other)
2022 - 2023	PhageAnnotate: Viral Genome Classifier Supervisor	Bioinformatics (Master) Universidade do Minho, Portugal
2022 - 2023	New Vector for Controlled Gene Expression in Acinetobacter baumannii Supervisor	Biotechnology (Master) Universidade do Minho, Portugal
2021/09 - 2022/07	Assessing a novel anti-virulence therapy against drug-resistant bacterial infections using the Zebrafish in vivo model Supervisor	Biomedical Engineering (Master) Universidade do Minho, Portugal
2021/09 - 2022/07	Isolation of novel immunogenic protein carriers for vaccine development Supervisor	Biotechnology (Master) Universidade do Minho, Portugal
2021 - 2022	Characterization of novel Acinetobacter baumannii phage-derived depolymerases with anti-virulence properties Supervisor	Biotechnology (Master) Universidade do Minho Centro de Engenharia Biológica, Portugal
2021 - 2022	PhageDPO: Phage Depolymerase Finder Supervisor	Computer science (Master) Universidade do Minho Centro de Engenharia Biológica, Portugal
2021 - 2021	Instruct project Supervisor	Master researcher (Other) Universidade do Minho Centro de Engenharia Biológica, Portugal
2018 - 2021	PhageSTEC project Supervisor	Postdoctoral Reseracher (Other) Universidade do Minho Centro de Engenharia Biológica, Portugal
2019 - 2020	Bacteriophage-host determinants: identification of bacteriophage receptors through machine learning techniques Co-supervisor of Pedro Henrique Matela Aidos Manso de Araújo	Bioinformatics (Master) Universidade do Minho Centro de Engenharia Biológica, Portugal
2019 - 2020	Microencapsulation of bacteriophages against food pathogens for oral administration to ruminants Supervisor	Biotechnology (Master) Universidade do Minho Centro de Engenharia Biológica, Portugal
2019 - 2019	Phage-based depolymerases as antibiotics Supervisor	Applied Biology (Degree) Universidade do Minho Centro de Engenharia Biológica, Portugal
2017 - 2018	PhagePromoter: Phage Promoters Online Analysis Tool Co-supervisor of Marta Sofia Costa Sampaio	Bioinformatics (Master) Universidade do Minho Centro de Engenharia Biológica, Portugal
2017 - 2018	Otopathogens: characterization and alternative treatments Supervisor	Biomedical Engineering (Master) Universidade do Minho, Portugal
2016 - 2017	Targeting acinetobacter baumannii infectious biofilms with a multivalent phage and bacteria based enzyme cocktail Supervisor of Alice Maria Fernandes Ferreira	Biotechnology (Master) Universidade do Minho Centro de Engenharia Biológica, Portugal
2016 - 2017	Genomic comparisons of novel Providencia infecting bacteriophages Supervisor	Computer science (Master) Universidade do Minho Centro de Engenharia Biológica, Portugal

Event organisation

	Event name Type of event (Role)	Institution / Organization
2023 - 2024	iVoM2023 (iVOM3) webinar (2023 - 2024) Meeting (Co-organisor)	Universidade do Minho, Portugal
2020/09 - 2021/03	iVoM2020 and the title Viruses of Microbes 2020 webinar series: take a walk on the VoM side (2020/09 - 2021/03) Seminar (Co-organisor)	Universidade do Minho Centro de Engenharia Biológica, Portugal
2020/07/13 - 2020/07/17	Organizer of Virus of Microbes 2020 (2020/07/13 - 2020/07/17) Conference (Co-organisor)	Universidade do Minho, Portugal
2017/06/19 - 2017/06/23	Organiser of the 3rd International hands-on phage biotechnology course (HOP III) (2017/06/19 - 2017/06/23) Workshop (Co-organisor)	Universidade do Minho, Portugal
2015/06/15 - 2015/06/19	Organiser of the 2nd International hands-on phage biotechnology course (HOP II) (2015/06/15 - 2015/06/19) Workshop (Co-organisor)	Universidade do Minho, Portugal
2013/07/01 - 2013/07/04	Organiser of the 1st International hands-on phage biotechnology course (HOP I) (2013/07/01 - 2013/07/04) Workshop (Member of the Organising Committee)	Universidade do Minho, Portugal
2009/05/09 - 2009/05/13	3rd International Practical Course on Biofilm Sciences (2009/05/09 - 2009/05/13) Workshop (Co-organisor)	Universidade do Minho, Portugal

Event participation

	Activity description Type of event	Event name Institution / Organization
2022/05/18 - 2022/05/20	Participant Conference	London Calling 2022 Oxford Nanopore Technologies Plc, United Kingdom
2022 - 2022	Microsummit 2022 Conference	Universidade do Minho, Portugal
2021/11/26 - 2021/11/26	Speaker at t secondary school of Barcelos, Portugal about phage biotechonolgy Seminar	CEB AT SCHOOL Universidade do Minho, Portugal
2021/09/24 - 2021/09/24	Increase awareness of research and innovation activities to the general public Exhibition	European Researchers' Night 2021 Universidade do Minho, Portugal
2018/11/24 - 2018/11/24	Instructor Workshop	CEB open day (outreach activity) Universidade do Minho Centro de Engenharia Biológica, Portugal
2018/07/26 - 2018/07/26	Instructor Workshop	Verão no Campus (outreach activity) Universidade do Minho Centro de Engenharia Biológica, Portugal
2016/02 - 2016/02	Participant Workshop	Course in Laboratory Animal Science - FELASA, category C Universidade do Minho Escola de Medicina, Portugal
2013/09 - 2013/12	Participant Workshop	Training program in technology commercialization (COHiTEC) Universidade Católica Portuguesa Católica Porto Business School, Portugal
2010/05 - 2010/05	Participant Workshop	Methods of DNA analyses: state of the art Universidade do Minho Escola de Medicina, Portugal

Jury of academic degree

	Topic Role	Candidate name (Type of degree) Institution / Organization
2023	Insights on the mechanisms underlying the development of heteroresistance to colistin in Acinetobacter baumannii (Thesis) Main arguer	Sarah Viegas (Master) Universidade Nova de Lisboa Instituto de Higiene e Medicina Tropical, Portugal
2022	PhageDPO: Phage Depolymerase Finder Supervisor	José Duarte (Master) Universidade do Minho, Portugal
2022	Isolation of novel immunogenic protein carriers for vaccine development Supervisor	Marta Gomes (Master) Universidade do Minho, Portugal
2021/07	Aptamers for Staphylococcal Enterotoxin A: Effect of nucleic acid mimics (Thesis) Arguer	Roberto Pinto (Other) Instituto Politécnico do Porto, Portugal
2021	PhagePro: Prophage ¿nding tool (Thesis) Arguer	João Dias (Master) Universidade do Minho, Portugal
2021	Characterization of novel Acinetobacter baumannii phage-derived depolymerases with anti-virulence properties Supervisor	Rita Domingues (Master) Universidade do Minho, Portugal
2017	Genomic comparisons of novel Providencia infecting bacteriophages Supervisor	Bruna Silva (Master) Universidade do Minho, Portugal
2017	Targeting Acinetobacter species with bacteriophage derived proteins Supervisor	Alice Ferreira (Master) Universidade do Minho, Portugal

Ad Hoc journal article review

	Journal title (ISSN)	Publisher
2022 - Current	Nature comunications	Nature Publishing Group
2022 - Current	Frontiers in Cellular and Infection Microbiology	Frontiers Media SA
2021 - Current	Current Opinion in Microbiology	Elsevier
2021 - Current	Current Opinion in Biotechnology	Elsevier
2021 - Current	ACS Infectious Diseases	ACS publications
2020 - Current	Journal of Virology	ASM
2019 - Current	Frontiers in Microbiology	Frontiers Media SA
2019 - Current	Environmental Microbiology	Wiley
2019 - Current	International Journal of Molecular Sciences	MDPI
2019 - Current	Viruses	MPDI
2018 - Current	Applied and Environmental Microbiology	ASM
2018 - Current	Open Life Sciences	Walter de Gruyter GmbH
2017 - Current	Journal of General Virology	Microbiology Society
2017 - Current	Microbial Drug Resistance	Mary Ann Liebert
2016 - Current	Applied Microbiology and Biotechnology	Springer-Verlag
2015 - Current	Scientific Reports	Springer Nature
2015 - Current	Journal of Infection and Chemotherapy	Elsevier
2015 - Current	PLoS ONE	Public Library of Science
2014 - Current	Virology Journal	Springer (Biomed Central Ltd.)
2013 - Current	Antimicrobial Agents and Chemotherapy	ASM

Association member

	Society Organization name	Role
2021 - Current	SPM - Sociedade Portuguesa de Microbiologia	Member
2019 - Current	ANICT - National Association of Researchers in Science and Technology	Member
2018 - Current	ICTV - International Committee on Taxonomy of Viruses, United States	Evaluator
2018 - Current	ESCMID - European Society of Clinical Microbiology and Infectious Diseases	Member
2015 - Current	CEB - Integrated member of the Scientific Committee of the Centre of Biological Engineering, University of Minho	Member

Committee member

	Activity description Role	Institution / Organization
2018 - Current	Editor Member	Virology Journal, United Kingdom

Conference scientific committee

	Conference name	Conference host
2022 - Current	Microbiologia 2022	Online conference
2022 - Current	Microsummit 2022
2021 - Current	World Microbe Forum	Online conference
2024 - 2024	13th Congress of the Serbian Society for Microbiology
2022/03 - 2022/03	Viruses of Microbes 2022

Course / Discipline taught

	Academic session	Degree Subject (Type)	Institution / Organization
2020 - Current	Laboratório de Bioprocessos em Bioprocessos	Biotecnologia (Mestrado integrado)	Universidade do Minho, Portugal
2019 - Current	Transferência de Calor e Massa	Engenharia Biomédica (Mestrado integrado)	Universidade do Minho, Portugal
2015 - Current	Técnicas Avançadas em Bioengenharia	Biotecnologia (Mestrado integrado)	Universidade do Minho, Portugal
2014 - Current	Tópicos Avançados em Engenharia Química e Biológica II	Engenharia Química e Biológica (Doutoramento)	Universidade do Minho, Portugal
2024 - 2024	Virologia Aplicada	Licenciatura em Biologia Aplicada (Ensino básico 2º ciclo)	Universidade do Minho, Portugal
2016 - 2019	Projeto de Biotecnologia	Biotecnologia (Mestrado integrado)	Universidade do Minho, Portugal
2016 - 2018	Projeto de Bioinformatica	Bioinformática (Mestrado integrado)	Universidade do Minho, Portugal
2014 - 2018	Laboratórios Integrados de Bioengenharia	Biotecnologia (Mestrado integrado)	Universidade do Minho, Portugal
2016 - 2017	Fenómenos Interfaciais	Engenharia Biomédica (Mestrado integrado)	Universidade do Minho, Portugal
2014 - 2017	Laboratórios Integrados I	Engenharia Biomédica (Mestrado integrado)	Universidade do Minho, Portugal

Evaluation committee

	Activity description Role	Institution / Organization	Funding entity
2021 - Current	Expert evaluator of grant research proposals Evaluator	Poland National Science Centre, Poland	Poland National Science Centre
2021 - Current	Evaluator of Marie Sklodowska-Curie Individual Fellowships (HE-MSCA-PF 2021) from the European Commission Evaluator	European Commission, Belgium	European Commission
2024 - 2026	Expert evaluator of grant research proposals Evaluator		ESF College of Expert Reviewers
2023 - 2023	Expert evaluator of grant research proposals Evaluator		Belgian Public Research Programme (BPRP)
2023 - 2023	Expert evaluator of grant research proposals Evaluator		Swiss National Science Foundation (SNSF)
2023 - 2023	Expert evaluator of grant research proposals Evaluator		University of Ljubljana for new, expanded and start-up research programmes (ICUL)
2022/02 - 2022/02	Expert evaluator of FCT PhD studenships Evaluator	Universidade do Minho, Portugal	Associação para a Inovação e Desenvolvimento da FCT
2022 - 2022	Expert evaluator of grant research proposals Evaluator
2021/07/26 - 2021/09/07	Expert evaluator of grant research proposals in response to the call entitled: Resistance Pathogens. Evaluator	Ministry of science and technology of Israel, Israel	Ministry of science and technology of Israel
2020/09 - 2020/11	Expert evaluator of Individual Marie Sklodowska-Curie Fellowships (H2020-MSCA-IF-2020) Evaluator	European Commission, Belgium	European Commission

Mentoring / Tutoring

	Topic	Student name
2019 - 2020	Phage-based depolymerases as antibiotics	Rita Alexandra Carpinteiro Domingues
2018 - 2019	Biotechnology of bacteriophages	Seila Agún García
2017 - 2018	Biotechnology of bacteriophages	Jennifer Otero Carrera
2016 - 2017	Control of bacterial infectious with phage endolysins	Mafalda Almeida

Distinctions

Award

2020	Science comunication for non-specialists Portuguese Society of Microbiology, Portugal
2015	Post-Doc fellowship (SFRH/BPD/ 111653/2015) Fundação para a Ciência e a Tecnologia, Portugal
2013	Best poster award at MicroBiotec'13 - Congress of Microbiology and Biotechnology Universidade de Aveiro, Portugal
2011	Best poster award at the MicroBiotec'11 - Congress of Microbiology and Biotechnology Universidade do Minho, Portugal
2010	PhD fellowship (SFRH/BD/63734/2009) Fundação para a Ciência e a Tecnologia, Portugal

Other distinction

2020	Spotlight recognition - Oliveira H et al. AEM journal. doi: 10.1128/AEM.00073-20 Applied and Environmental journal (AEM), United States
2019	Spotlight recognition - Oliveira H et al. AEM journal. doi: 10.1128/AEM.00934-19 Applied and Environmental journal (AEM), United States
2013	Highly cited - Oliveira H et al. JV journal. doi: 10.1128/JVI.03277-12 Journal of Virology (JV), United States