Vânia Pobre (881D-F4FE-7097)

Curriculum Vitae

Vânia Pobre

Vânia Pobre has a PhD in Molecular Biology. She Is currently a senior researcher at ITQB NOVA in the Control of Gene Expression Group. During her postdoctoral work she has dedicated most of her efforts to the field of RNA bioinformatics with a strong focus on transcriptomics and Big Data analysis. She has applied the advantage of her dual knowledge of being both an experimental and a computational biologist to study the roles of exoribonucleases and small non-coding RNAs in the control of gene expression. She has published 12 research papers, 6 reviews and 4 book chapters on this field. In some of the publications she performed practically all the work alone (e.g., Pobre and Arraiano- where Arraiano is the lab coordinator), and in others she is already the corresponding author. She has published as first and main author in BMC Genomics and in 2019 in Scientific Reports (as first and corresponding author). In two of her recent publications, she has predicted novel sRNAs for biotechnological relevant bacteria and connected basic science with biotechnology. To expand her bioinformatic knowledge she has attended courses to learn Python and R statistical programming languages. To develop her work, she has attended with success national and international courses on transcriptomics and regulatory networks. She has supervised the work of Master and PhD students as well as other internships in the lab. She also taught classes in the MolBioS PhD program and in the Medical Microbiology Master programs at ITQB NOVA since 2012. She has also participated in teaching in ERASMUS programs abroad. She has transmitted her knowledge by teaching bioinformatics to students who came in lab rotations, and she has organized Transcriptomic workshops for PhD students. As a scientist she also participated and co-organized several science dissemination and communication activities both for other scientists as well as for the general public (e.g., ITQB open day, and in town activities during the Day of the Microorganism). She attended several conferences and presented over 30 posters and gave 15 oral communications including some as invited speaker at the Universidade Federal do Paraná, Brazil. She also established several national and international collaborations that allowed her to expand her field of knowledge. In 2021 she was also elected the representative of the ITQB NOVA biology division for the ITQB/iBET postdoctoral association (PDA) and she is the guest editor for the Antibiotics special Issue Bacterial Biofilms: From Regulation to Strategies to Study and Fight Them. Since 2022 she also is part of the Bioda.pt (Portuguese ELIXIR node).

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Identification

Personal identification

Full name: Vânia Pobre

Citation names

Pobre, Vânia

Author identifiers

Ciência ID: 881D-F4FE-7097
ORCID iD: 0000-0002-4339-8472
Researcher Id: M-4115-2013
Scopus Author Id: 26027101400

Email addresses

vaniapobre@itqb.unl.pt (Professional)

Addresses

ITQB Nova - Avenida da República, 2780-157, Oeiras, Oeiras, Portugal (Professional)

Websites

pt.linkedin.com/in/VaniaPobre (Professional)

Knowledge fields

Exact Sciences - Computer and Information Sciences - Bioinformatics
Natural sciences - Biological Sciences - Molecular Biology
Natural sciences - Biological Sciences - Microbiology

Languages

Language	Speaking	Reading	Writing	Listening
Portuguese (Mother tongue)
English	Upper intermediate (B2)	Proficiency (C2)	Upper intermediate (B2)	Proficiency (C2)
Spanish; Castilian	Beginner (A1)	Intermediate (B1)	Beginner (A1)	Beginner (A1)

Education

	Degree	Classification
2009/01/01 - 2012/12/17 Concluded	PhD in Biological Sciences (Doutoramento) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal "Interplay of exoribonucleases, Hfq and small RNAs structural determinants in the control of gene expression" (THESIS/DISSERTATION)	n/a
2006 Concluded	Biochemistry (Licenciatura) Universidade da Beira Interior, Portugal "Study of the Expression of Androgen and Estrogen Receptors and Localization of AndrogePron Receptor in Testis, Prostate, Seminal Vesicles and Epididymis of Rats at Different Postnatal Ages" (THESIS/DISSERTATION)	15

Affiliation

Science

	Category Host institution	Employer
2018/11/01 - Current	Researcher (Research)	Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal

2013/01/01 - 2018/10/31	Postdoc (Research)	Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal

Projects

Grant

	Designation	Funders
2022/03/01 - 2025/02/28	Understanding the mechanisms of inactivation of ultraviolet light emitting diodes to develop effective water disinfection systems PTDC/EAM-AMB/1561/2021 Researcher Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal	Ongoing
2022/01/01 - 2023/06/30	RNase R, a new virulence determinant with pleitropic effects in Streptococcus pneumoniae infections EXPL/BIA-MOL/1244/2021 Researcher Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal	Ongoing
2018/10/03 - 2021/10/02	The RNA-binding protein Hfq interactome in the human pathogen Listeria monocytogenes: piecing together the elusive role of a virulence regulator PTDC/BIA-MIC/32525/2017 Researcher Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal	Fundação para a Ciência e a Tecnologia Ongoing
2018/09 - 2020	EmPower Putida: Re-programming the lifestyles of Pseudomonas putida for bespoke catalysis 635536 Researcher	Horizon 2020 Concluded
2015 - 2020	Desvendando redes de regulação de sRNAs regulatórios em genomas bacteriano FCT/13262/4/8/2015/S Researcher	Fundação para a Ciência e a Tecnologia Coordenação de Aperfeiçoamento de Pessoal de Nível Superior Concluded
2017/01/01 - 2019/12/31	An Omics Network to Prevent and Control Infectious Diseases and Antimicrobial Resistance. SAICTPAC/0015/2015 Researcher	Ongoing
2016/01 - 2018/12	An RNA-based approach to bacterial infection: The function of PNPase and regulatory noncoding RNAs in Listeria virulence Provided by PTCRIS: 143095 Researcher	Fundação para a Ciência e a Tecnologia Concluded
2015/12 - 2018/11	Determination of the architecture and the RNA degradation strategy of Ribonuclease R: implications for pathogen control. Provided by PTCRIS: 142677 Provided by PTCRIS: 140024 Researcher	Fundação para a Ciência e a Tecnologia
2015/01 - 2017/12	Molecular, Structural and Cellular Microbiology Provided by PTCRIS: 147361 Researcher	Fundação para a Ciência e a Tecnologia
2013/05 - 2015/07	Salmonella Persistence in eukaryotic cells: Examining the Role of RNases and Small Functional RNAs. Acronym: PARNAs - Persistence Attributing RNAs grant.Provided by PTCRIS: 130846 Researcher	Fundação para a Ciência e a Tecnologia
2011/04 - 2014/09	Biochemical and Functional studies of exoribonucleases focusing on their determinant role in the control of gene expression. grant.Provided by PTCRIS: 111757 PhD Student Fellow	Fundação para a Ciência e a Tecnologia
2010/01 - 2013/04	Innovative Strategies to Combat Foodborne Pathogens: Examining the Role of RNases and Small RNAs grant.Provided by PTCRIS: 102293 PhD Student Fellow	Fundação para a Ciência e a Tecnologia
2010/01 - 2013/04	Examining a Multifunctional RNA Degrading Machine: the Arabidopsis Catalytic subunit of the Exosome grant.Provided by PTCRIS: 100509 grant.Provided by PTCRIS: 55106 PhD Student Fellow	Fundação para a Ciência e a Tecnologia
2010/01 - 2013/03	Lost in Septation: Characterization of a novel regulatory pathway of cell division and morphology centered on the bolA gene. grant.Provided by PTCRIS: 100507 PhD Student Fellow	Fundação para a Ciência e a Tecnologia

Other

	Designation	Funders
2019/01/01 - 2019/12/01	Molecular, Structural and Cellular Microbiology UID/CBQ/04612/2019 Researcher	Ongoing

Outputs

Publications

Book chapter	Pobre, Vânia; Arraiano, Cecília M.. "Characterizing the Role of Exoribonucleases in the Control of Microbial Gene Expression: Differential RNA-Seq". In High-Density Sequencing Applications in Microbial Molecular Genetics, 1-24. 2018. 10.1016/bs.mie.2018.08.010 Bárria, C.; Pobre, Vânia; Bravo, Afonso M.; Arraiano, Cecília M.. "Ribonucleases as Modulators of Bacterial Stress Response". In Stress and Environmental Regulation of Gene Expression and Adaptation in Bacteria, 174-184. John Wiley & Sons, Inc., 2016. 10.1002/9781119004813.ch14 Matos, Rute G; Pobre, Vânia; Reis, Filipa P.; Malecki, Michal; Andrade, José; Arraiano, Cecília M.. "Structure and Degradation Mechanisms of 3' to 5' Exoribonucleases". In Nucleic Acids and Molecular Biology, 193-222. Springer Berlin Heidelberg, 2011. 10.1007/978-3-642-21078-5_8 Andrade, José; Pobre, Vânia; Silva, Inês Jesus; Domingues, Susana; Arraiano, Cecília M.. "The Role of 3'–5' Exoribonucleases in RNA Degradation". In Molecular Biology of RNA Processing and Decay in Prokaryotes, 187-229. Elsevier, 2009. 10.1016/s0079-6603(08)00805-2
Conference abstract	Pobre, Vânia; Andrade, José Marques; Arraiano, C.M.. "Characterization of the non-coding MicA RNA in Escherichia coli: mutational analysis shows that 3 ' end controls stability of this sRNA". Paper presented in 34th FEBS Congress, Prague, 2009. Published
Conference poster	Silva, J; Arraiano, C.M; Pobre, Vânia. "Prediction of novel small non-coding RNAs from Pseudomonas aeruginosa RNA-Seq data". Paper presented in Microbiotec23, 2023. Condinho, M.; Pinto, S.N.; Arraiano C.M.; Pobre, Vânia. "The role of PNPase in the biofilm formation of Escherichia coli". Paper presented in Microbiotec23, 2023. Silva, J; Arraiano, C.M.; Pobre, Vânia. "Discovering novel Pseudomonas aeruginosa small non-coding RNAs involved in biofilm and antibiotic resistance mechanisms". Paper presented in IV International meeting of the portuguese society of genetics, 2023. Condinho, M.; Pinto, S.N.; Arraiano C.M.; Pobre, Vânia. "The role of PNPase in the biofilm formation of Escherichia coli". Paper presented in IV International meeting of the portuguese society of genetics, 2023. Alípio, AF; Bárria, Cátia; Pobre, Vânia; Matos, R; Amblar, Mónica; Arraiano, Cecília Maria; Domingues, Susana. "RNase R Controls Membrane Fatty Acid Composition in Streptococcus pneumoniae.". Paper presented in 7th Meeting on Regulating with RNA in Bacteria and Archaea, 2023. Condinho, Manuel; Pinto, Sandra N.; Arraiano, Cecília M.; Pobre, Vânia. "PNPase, a conserved exoribonuclease fundamental for biofilm formation of Escherichia coli". Paper presented in FEMS2023 \| Congress of European Microbiologists, 2023. Condinho, Manuel; Pinto, S.N; Arraiano, C.M.; Pobre, Vânia. "The importance of PNPase for biofilm formation". Paper presented in EMBO\|EMBL Symposium: New approaches and concepts in microbiology, 2023. Arraiano CM; Andrade JM; Bárria C; Costa S; Costa VG; Cunha MV; Domingues S; et al. "RNAs, RNA-binding Proteins and RNases: A World still Full of Surprises!". Paper presented in LS4Future 1st General Meeting, 2023. Pobre, Vânia; Carvalho, Beatriz; Arraiano, Cecília Maria. "Detection of novel small non-coding RNAs involved in Pseudomonas aeruginosa biofilm and antibiotic resistance". Paper presented in EMBO Workshop Bacterial networks, 2022. Condinho, Manuel; Arraiano, Cecília Maria; Pobre, Vânia. "Identification of the mechanisms by which exoribonucleases affect biofilm formation and acidic stress response". Paper presented in IUBMB–FEBS–PABMB Congress, 2022. Quendera, Ana Patrícia; Pinto, Sandra N.; Antunes, Wilson; Pobre, Vânia; Arraiano, Cecília Maria; Andrade, José Marques. "The RNA-binding protein PNPase regulates biofilm formation and virulence in Listeria monocytogenes". Paper presented in IUBMB-FEBS-PABMB Congress, 2022. Condinho, Manuel; Arraiano, Cecília Maria; Pobre, Vânia. "Identification of the mechanisms by which exoribonucleases affect biofilm formation and acidic stress response". Paper presented in IUBMB–FEBS–PABMB Young Scientists’ Forum, 2022. Condinho, Manuel; Arraiano, Cecília Maria; Pobre, Vânia. "The role of exoribonucleases in biofilm formation and acidic stress response". Paper presented in 12th ITQB NOVA PhD Students' Meeting, 2022. Condinho, Manuel; dos Santos, Fábio; Arraiano, Cecília M.; Pobre, Vânia. "Investigating how exoribonucleases and small RNAs influence bacterial adaption to stress". Paper presented in Microbiotec´21, 2021. Viegas, Sandra C.; Pobre, Vânia; Graça-Lopes, Gil; Apura, Patrícia; Domingues, Susana; Saramago, Margarida; Ankenbauer, Andreas; Takors, Ralf; Arraiano, Cecília M.. "Novel non-coding RNAs whose expression is relevant for the growth of Pseudomonas putida in a bioreactor". Paper presented in SPB 2020 – XXI National Congress of Biochemistry “Tunning Biochemistry with Life and Society, 2021. Pobre, Vânia; Condinho, Manuel; dos Santos, Fábio; Arraiano, Cecília M.. "Investigating how exoribonucleases and small RNAs influence bacterial adaptation to stress". Paper presented in RNA2021, 26th Annual Meeting of the RNA Society, 2021. Carvalho, Beatriz; Arraiano, Cecília M.; Pobre, Vânia. "Identification of novel Pseudomonas aeruginosa small non-coding RNAs and their role in biofilm and antibiotic resistance mechanisms". Paper presented in Microbiology Annual Conference Online, 2021. Ankenbauer, A.; Schäfer, R.A.; Viegas, Sandra Cristina; Pobre, Vânia; Voß, B.; Arraiano, Cecília M.; Takors, R.. "Deciphering Persistence Strategies of Pseudomonas putida KT2440". Paper presented in BioProScale Symposium, 2020. Graça-Lopes, G.; Pobre, Vânia; Saramago, Margarida; Ankenbauer, A.; Takors, R.; Arraiano, C.M.; Viegas, Sandra C.. "Prediction of novel non-coding RNAs relevant to the adaptation of Pseudomonas putida grown in a bioreactor". Paper presented in International meeting of the Portuguese society of genetics, 2020. Pobre, Vânia; Graça-Lopes, G.; Saramago, M.; Ankenbauer, A.; Takors, R.; Arraiano, C.M.; Viegas, Sandra C.. "Prediction of novel non-coding RNAs relevant for the growth of Pseudomonas putida in a bioreactor". Paper presented in Microbiotec’19 Congress, 2019. Graça-Lopes, G.; Pobre, Vânia; Saramago, Margarida; Ankenbauer, A.; Takors, R.; Arraiano, C.M.; Viegas, Sandra C.. "Prediction of novel non-coding RNAs relevant to the adaptation of Pseudomonas putida grown in a bioreactor". Paper presented in 8th Congress of European Microbiologists: FEMS 2019, 2019. Pobre, Vânia; Dobrzanski, Tatiane; Steffens, Maria Berenice Reynaud; Arraiano, C.M.. "Lost in transition: Defining the role of exoribonucleases in the shift between exponential and stationary phases". Paper presented in The 44th FEBS congress, 2019. Pobre, Vânia; Dobrzanski, Tatiane; Steffens, Maria Berenice Reynaud; Arraiano, C.M.. "Lost in transition: Defining the role of exoribonucleases in the shift between exponential and stationary phases". Paper presented in VIII National RNA Meeting: ptRNA2019, 2019. Pobre, Vânia; Dobrzanski, Tatiane; Paschoal, A.R.; Lopes, F.M.; Steffens, Maria Berenice Reynaud; Arraiano, C.M.. "Exploring small RNAs functions using RNA-Seq data and target prediction programs to construct regulatory networks". Paper presented in Bacterial networks (BacNet17), 2017. Dobrzanski, Tatiane; Garcia, A.C.; Lopes, F.M.; Pobre, Vânia; Arraiano, C.M.; Steffens, Maria Berenice Reynaud. "Identification of non-coding RNAs and their targets in Herbaspirillum seropedicae SmR1 using interaction network". Paper presented in Bacterial networks (BacNet17), 2017. Pobre, Vânia; Dobrzanski, Tatiane; Paschoal, A.R.; Lopes, F.M.; Steffens, Maria Berenice Reynaud; Arraiano, C.M.. "Bioinformatics and NGS as tools to study regulation of gene expression". Paper presented in 4º Encontro de Jovens Investigadores de Biologia Computacional Estrutural (EJIBCE), 2016. Dobrzanski, Tatiane; Garcia, A.C.; Lopes, F.M.; Pobre, Vânia; Arraiano, C.M.; Steffens, Maria Berenice Reynaud. "Prediction ncRNA-mRNA interactions network from Herbaspirillum seropedicae SmR1". Paper presented in 4º Encontro de Jovens Investigadores de Biologia Computacional Estrutural (EJIBCE), 2016. Pobre, Vânia. "NGS as a tool to study the role of exoribonucleases and small RNAs in the control of gene expression". Paper presented in 3rd Inter-institutional postdoc retreat, 2016. Pobre, Vânia; Bravo, A.M.; Arraiano, C.M.. "Comparative Global Analysis of the roles of exoribonucleases in E. Coli". Paper presented in Post-Transcriptional Control of Gene Expression: mRNA Decay. FASEB, 2016. Pobre, Vânia; Bravo, A.M.; Arraiano, C.M.. "The influence of exoribonucleases in the regulation of stress related small RNAs". Paper presented in Workshop de Genética, 2016. Pobre, Vânia; Bravo, A.M.; Arraiano, C.M.. "The influence of exoribonucleases in the regulation of stress related small RNAs". Paper presented in Microbiotec15, 2015. Pobre, Vânia; Andrade, José Marques; dos Santos, Ricardo; 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. Pobre, Vânia; Dressaire, Clémentine; Laguerre, Sandrine; Girbal, Laurence; Cocaign-Bousquet, Muriel; Arraiano, C.M.. "Identification of RNase R and PNPase targets in Escherichia coli during stationary phase". Paper presented in FEBS – ASM workshop on: Biology of RNA in host-pathogen interactions, 2014. Andrade, José Marques; Pobre, Vânia; Matos, A. M.; Arraiano, C.M.. "Important factors in small RNA degradation: contrasting roles of PNPase and Hfq in the regulation of non-coding RNAs". Paper presented in 4th EMBO meeting, 2012. Pobre, Vânia; Andrade, José Marques; Arraiano, C.M.. "Small RNA modules confer different stabilities and selectively choose among different targets". Paper presented in 2012 FEBS RNA Satellite Meeting, 2012. Dressaire, Clémentine; Laguerre, Sandrine; Pobre, Vânia; Girbal, Laurence; Cocaign-Bousquet, Muriel; Arraiano, C.M.. "Identification of RNase R and PNPase targets in Escherichia coli during stationary phase". Paper presented in 2012 FEBS RNA Satellite Meeting, 2012. Pobre, Vânia; Andrade, José Marques; Arraiano, C.M.. "The role of Hfq and RNA determinants in the degradation pathways of small non-coding RNAs". Paper presented in MicroBiotec11 – The Portuguese Society for Microbiology and the Portuguese Society for Biotechnology, 2011. Pobre, Vânia; Andrade, José Marques; Arraiano, C.M.. "Stability determinants of the regulatory small non-coding MicA RNA". Paper presented in 1st ITQB PhD Students’ Meeting, 2010. Andrade, José Marques; Pobre, Vânia; Arraiano, C.M.. "Stability determinants of a small non-coding RNA". Paper presented in FASEB Post-transcriptional control of gene expression: Mechanisms of mRNA decay, 2010. Pobre, Vânia; Andrade, José Marques; Arraiano, C.M.. "Characterization of the non-coding MicA RNA in Escherichia coli: mutational analysis shows that 3' end controls stability of this sRNA". Paper presented in EMBO Computational RNA Biology, 2010. Pobre, Vânia; Andrade, José; Arraiano, Cecília M.. "Characterization of the non-coding MicA RNA in Escherichia coli: mutational analysis shows that 3 ' end controls stability of this sRNA". Paper presented in 34th FEBS Congress, 2009. Pobre, Vânia; Andrade, José Marques; Arraiano, C.M.. "Characterization of the non-coding MicA RNA in Escherichia coli: mutational analysis shows that 3' end controls stability of this sRNA". Paper presented in V Meeting on RNA research in Portugal, 2009. Andrade, José Marques; Pobre, Vânia; Matos, A.M.; Arraiano, C.M.. "PNPase is a key player in the regulation of small RNAs that control the expression of outer membrane proteins". Paper presented in Post-Transcriptional Control of Gene Expression: Mechanism of mRNA Decay, 2008. Matos, A.M.; Andrade, José Marques; Pobre, Vânia; Arraiano, C.M.. "The RNA Chaperone Hfq controls the stability of the small non-coding MicA". Paper presented in IV Encontro Nacional de RNA, 2007. Andrade, José Marques; Matos, A.M.; Pobre, Vânia; Arraiano, C.M.. "PNPase is a key player in the regulation of small non-coding RNAs". Paper presented in IV Encontro Nacional de RNA, 2007. Pobre, Vânia; Andrade, José Marques; Barbas, A.; Arraiano, C.M.. "RNA Helicases and non-coding RNA metabolism". Paper presented in IV Encontro Nacional de RNA, 2007.
Journal article	Quendera, Ana Patrícia; Pinto, Sandra Nunes; Pobre, Vânia; Antunes, Wilson; Bonifácio, Vasco D. B.; Arraiano, Cecília Maria; Andrade, José Marques. "The ribonuclease PNPase is a key regulator of biofilm formation in Listeria monocytogenes and affects invasion of host cells". npj Biofilms and Microbiomes 9 1 (2023): http://dx.doi.org/10.1038/s41522-023-00397-1. 10.1038/s41522-023-00397-1 Raimundo, Ana F.; Ferreira, Sofia; Pobre, Vânia; Lopes-da-Silva, Mafalda; Brito, José A.; dos Santos, Daniel J. V. A.; Saraiva, Nuno; dos Santos, Cláudia N.; Menezes, Regina. "Urolithin B: Two-way attack on IAPP proteotoxicity with implications for diabetes". Frontiers in Endocrinology 13 (2022): http://dx.doi.org/10.3389/fendo.2022.1008418. Published • 10.3389/fendo.2022.1008418 Gaspar-Cordeiro, Ana; Amaral, Catarina; Pobre, Vânia; Antunes, Wilson; Petronilho, Ana; Paixão, Paulo; Matos, António P.; Pimentel, Catarina. "Copper Acts Synergistically With Fluconazole in Candida glabrata by Compromising Drug Efflux, Sterol Metabolism, and Zinc Homeostasis". Frontiers in Microbiology 13 (2022): http://dx.doi.org/10.3389/fmicb.2022.920574. 10.3389/fmicb.2022.920574 Condinho, Manuel; Carvalho, Beatriz; Cruz, Adriana; Pinto, Sandra N.; Arraiano, Cecília M.; Pobre, Vânia. "The role of RNA regulators, quorum sensing and c-di-GMP in bacterial biofilm formation". FEBS Open Bio (2022): http://dx.doi.org/10.1002/2211-5463.13389. Open access • 10.1002/2211-5463.13389 Cruz, Adriana; Condinho, Manuel; Carvalho, Beatriz; Arraiano, Cecília M.; Pobre, Vânia; Pinto, Sandra N.. "The Two Weapons against Bacterial Biofilms: Detection and Treatment". Antibiotics 10 12 (2021): 1482. http://dx.doi.org/10.3390/antibiotics10121482. 10.3390/antibiotics10121482 Ankenbauer, Andreas; Schäfer, Richard A.; Viegas, Sandra C.; Pobre, Vânia; Voß, Björn; Arraiano, Cecília M.; Takors, Ralf. "Pseudomonas putida KT2440 is naturally endowed to withstand industrial-scale stress conditions". Microbial Biotechnology (2020): http://dx.doi.org/10.1111/1751-7915.13571. 10.1111/1751-7915.13571 Dobrzanski, Tatiane; Pobre, Vânia; Moreno, Leandro Ferreira; Barbosa, Helba Cirino de Souza; Monteiro, Rose Adele; de Oliveira Pedrosa, Fábio; de Souza, Emanuel Maltempi; Arraiano, Cecília Maria; Steffens, Maria Berenice Reynaud. "In silico prediction and expression profile analysis of small non-coding RNAs in Herbaspirillum seropedicae SmR1". BMC Genomics 21 1 (2020): http://dx.doi.org/10.1186/s12864-019-6402-x. Open access • 10.1186/s12864-019-6402-x Pobre, Vânia; Graça-Lopes, Gil; Saramago, Margarida; Ankenbauer, Andreas; Takors, Ralf; Arraiano, Cecília M.; Viegas, Sandra C.. "Prediction of novel non-coding RNAs relevant for the growth of Pseudomonas putida in a bioreactor". Microbiology 166 2 (2020): 149-156. http://dx.doi.org/10.1099/mic.0.000875. 10.1099/mic.0.000875 Pobre, Vânia; Barahona, Susana; Dobrzanski, Tatiane; Maria Berenice Reynaud Steffens; Arraiano, Cecília M.. "Defining the impact of exoribonucleases in the shift between exponential and stationary phases". Scientific Reports 9 1 (2019): https://doi.org/10.1038/s41598-019-52453-6. 10.1038/s41598-019-52453-6 Dressaire, Clémentine; Pobre, Vânia; Laguerre, Sandrine; Girbal, Laurence; Arraiano, Cecília M.; Cocaign-Bousquet, Muriel. "PNPase is involved in the coordination of mRNA degradation and expression in stationary phase cells of Escherichia coli". BMC Genomics 19 1 (2018): http://dx.doi.org/10.1186/s12864-018-5259-8. 10.1186/s12864-018-5259-8 Pobre, Vânia; Arraiano, Cecília M.. "Next generation sequencing analysis reveals that the ribonucleases RNase II, RNase R and PNPase affect bacterial motility and biofilm formation in E. coli". BMC Genomics 16 1 (2015): http://dx.doi.org/10.1186/s12864-015-1237-6. 10.1186/s12864-015-1237-6 Saramago, Margarida; Bárria, Cátia; dos Santos, Ricardo F; Silva, Inês Jesus; Pobre, Vânia; Domingues, Susana; Andrade, José; Viegas, Sandra C.; Arraiano, Cecília M.. "The role of RNases in the regulation of small RNAs". Current Opinion in Microbiology 18 (2014): 105-115. http://dx.doi.org/10.1016/j.mib.2014.02.009. 10.1016/j.mib.2014.02.009 Reis, Filipa P.; Pobre, Vânia; Silva, Inês Jesus; Malecki, Michal; Arraiano, Cecília M.. "The RNase II/RNB family of exoribonucleases: putting the ‘Dis’ in disease". Wiley Interdisciplinary Reviews: RNA 4 5 (2013): 607-615. http://dx.doi.org/10.1002/wrna.1180. 10.1002/wrna.1180 Andrade, José; Pobre, Vânia; Arraiano, Cecília Maria. "Small RNA Modules Confer Different Stabilities and Interact Differently with Multiple Targets". PLoS ONE 8 1 (2013): e52866. http://dx.doi.org/10.1371/journal.pone.0052866. 10.1371/journal.pone.0052866 Andrade, José; Pobre, Vânia; Matos, A. M.; Arraiano, C. M.. "The crucial role of PNPase in the degradation of small RNAs that are not associated with Hfq". RNA 18 4 (2012): 844-855. http://dx.doi.org/10.1261/rna.029413.111. 10.1261/rna.029413.111 Matos, Rute G; Bárria, Cátia; Pobre, Vânia; Andrade, José; Arraiano, Cecília M.. "Exoribonucleases as Modulators of Virulence in Pathogenic Bacteria". Frontiers in Cellular and Infection Microbiology 2 (2012): http://dx.doi.org/10.3389/fcimb.2012.00065. 10.3389/fcimb.2012.00065 Arraiano, Cecília M.; Andrade, José; Domingues, Susana; Guinote, Inês B.; Malecki, Michal; Matos, Rute G; Moreira, Ricardo N.; et al. "The critical role of RNA processing and degradation in the control of gene expression". FEMS Microbiology Reviews 34 5 (2010): 883-923. http://dx.doi.org/10.1111/j.1574-6976.2010.00242.x. 10.1111/j.1574-6976.2010.00242.x
Preprint	Filipe Alípio, André; Bárria, Cátia; Pobre, Vânia; Matos, Rita; Amblar, Mónica; Maria Arraiano, Cecília; Domingues, Susana. "RNase R Controls Membrane Fatty Acid Composition in Streptococcus pneumoniae". 2023. http://dx.doi.org/10.1101/2023.03.21.533657. 10.1101/2023.03.21.533657
Thesis / Dissertation	Pobre, Vânia Sofia Fidalgo. "Interplay of Exoribonucleases, Hfq and Small RNAs Structural Determinants in the Control of Gene Expression". PhD, 2012. http://hdl.handle.net/10362/10590.

Activities

Oral presentation

	Presentation title	Event name Host (Event location)
2023/10/18	The role of RNA degradation mechanisms in biofilm formation and acidic stress response	13th ITQB NOVA PhD Student’s Meeting ITQB-NOVA (Oeiras, Portugal)
2023/01/16	RNAs, RNA-binding Proteins and RNases: A World still Full of Surprises!	RNA in Disease - RiboMed, IX ptRNA IMM (Lisbon, Portugal)
2022/09/04	Detection of novel small non-coding RNAs involved in Pseudomonas aeruginosa biofilm and antibiotic resistance	Bacterial networks EMBO (Sant Feliu de Guixols, Spain)
2022/06/19	RNAs and RNases: A World still full of surprises	FASEB Science Conference on “The Post-transcriptional Control of Gene Expression Conference: Mechanisms of RNA Decay FASEB (Jupiter, United States)
2022/04/23	Identification of novel small non-coding RNAs involved in biofilm and antibiotic resistance	32nd European Congress of Clinical Microbiology and Infectious Diseases ESCMID (Lisbon, Portugal)
2022/04/20	The RNA-binding protein PNPase regulates biofilm formation and virulence in Listeria monocytogenes	12th ITQB NOVA PhD Students' Meeting ITQB-NOVA (Oeiras, Portugal)
2021/07/01	Influence of exoribonucleases on small RNAs expression and bacterial stress response	II International Meeting of the Portuguese society of genetics Portuguese Society of Genetics
2020/11/04	Exploring bacterial transcriptomes to unravel RNA regulation and discover new RNAs	Science Conferences at Noon -SCAN ITQB NOVA (Oeiras, Portugal)
2019/12/05	Lost in transition: Defining the role of exoribonucleases in the shift between exponential and stationary phases.	Microbiotec’19 Congress Universidade de Coimbra (Coimbra, Portugal)
2018/11/20	Seminar for work progress presentation (in frame of WP4 of EmPowerPutida European project)	7th General Assembly of EmPowerPutida (Wageningen, Netherlands)
2018/10/19	The differential role of exoribonucleases during bacterial growth	Seminar for the Department of Biochemistry in Universidade Federal do Paraná Universidade Federal do Paraná (Curitiba, Brazil)
2018/07/02	Dis3L2 and other RNase II-like proteins in Health and Disease	Encontro Ciência (Lisboa, Portugal)
2016/10/03	The role of exoribonucleases and small RNAs in the control of gene expression	Seminar for the Department of Biochemistry in Universidade Federal do Paraná Universidade Federal do Paraná (Curitiba, Brazil)
2016/06/02	The influence of exoribonucleases in the regulation of stress related small RNAs	XL Jornadas Portuguesas de Genética Universidade de Coimbra (Coimbra, Portugal)
2015/12/10	Next generation sequencing analysis reveals that exoribonucleases affect bacterial motility and biofilm formation	Microbiotec15 (Évora, Portugal)
2014/06/01	Next Generation Sequencing and RNA Bioinformatics	Erasmus Intensive Programme. Towards a Scientific Career: an Introductory Course for Research in Biomedicine and Biotechnology University of Granada (Granada, Spain)
2014/05/30	Modulation of small RNA stabilities and target interaction	KBBE Synthetic Biology - ST Flow Instituto de Tecnologia Química e Biológica António Xavier (O, Portugal)
2012/10/10	High throughput technologies and detailed analysis reveal the importance of exoribonucleases and RNA sequence and structure in the control gene expression	3rd ITQB phD Meeting (Oeiras, Portugal)
2012/01/26	The crucial role of PNPase in the degradation of small RNAs that are not associated with Hfq	Portuguese RNA meeting 2012 (Lisboa, Portugal)
2011/05/09	Stability determinants of a small non-coding RNA: from computer to bench	The Gulbenkian Training Programme in Bioinformatics Instituto Gulbenkian de Ciência (Oeiras, Portugal)
2010/07/05	Stability determinants of the regulatory small non-coding MicA RNA	The Gulbenkian Training Programme in Bioinformatics Instituto Gulbenkian de Ciência (Oeiras, Portugal)
2010/06	Stability determinants of the regulatory small non-coding MicA RNA	XXXV Jornadas Portuguesas de Genética 2010 (Braga, Portugal)
2007/11	PNPase is a key player in the regulation of small non-coding RNAs	MICRO’07 BIOTEC’07-XXXIII JPG congress (Lisboa, Portugal)

Supervision

	Thesis Title Role	Degree Subject (Type) Institution / Organization
2020/01/01 - 2024/12/31	Exploring RNA Degradation Mechanisms Co-supervisor of Manuel Carvalho	Applied and Environmental Microbiology (PhD) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2022/09/01 - 2023/10/31	Discovering novel Pseudomonas aeruginosa small non-coding RNAs involved in biofilm and antibiotic resistance mechanisms Supervisor of Joana Silva	Mestrado Microbiologia Médica (Master) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2023/03/13 - 2023/07/15	Estudo dos Pequenos RNAs e do c-di-GMP como reguladores de biofilmes bacterianos Supervisor of Gonçalo Alves	estágio (Degree) Instituto Politécnico de Setúbal Escola Superior de Tecnologia do Barreiro, Portugal
2023/03 - 2023/07	Optimization of RNA extraction methods from biofilm samples of Staphylococcus aureus Co-supervisor of Beatriz Branco	estágio (Degree) Associação do Instituto Superior Técnico para a Investigação e Desenvolvimento, Portugal
2020/09/01 - 2021/07/31	Identification of novel Pseudomonas aeruginosa small non-coding RNAs and their involvement in biofilm and antibiotic resistance mechanisms Supervisor of Beatriz Carvalho	Mestrado em bioengenheria (Master) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal Associação do Instituto Superior Técnico para a Investigação e Desenvolvimento, Portugal
2020/09/01 - 2021/06/30	Procura por mecanismos complementares, induzidos pela deleção de exoribonucleases hidrolíticas em Escherichia coli Supervisor of Fábio Santos	Projecto final de Licenciatura (Degree) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal Universidade Lusófona de Humanidades e Tecnologias Escola de Psicologia e Ciências da Vida, Portugal
2016 - 2019/04/29	VALIDAÇÃO DE sRNAS E REDES DE INTERAÇÃO sRNA/mRNA EM Herbaspirillum seropedicae SmR1 Co-supervisor of Tatiane Dobrzanski	Bioquímica (PhD) Universidade Federal do Paraná, Brazil
2015 - 2015	The influence of exoribonucleases in the regulation of stress related small RNAs. Co-supervisor of Afonso Martins Bravo	Microbiologia Médica (Master) Universidade Nova de Lisboa Instituto de Higiene e Medicina Tropical, Portugal

Event organisation

	Event name Type of event (Role)	Institution / Organization
2022/12 - 2023/01/26	Local organization of the Day2Day Data Management Course (2023/01/26 - 2023/01/26) Workshop (Co-organisor)	Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal BioData.pt, Portugal
2022/03/01 - 2022/11/30	COLife Postdoc Day (2022/11/18 - 2022/11/18) Meeting (Co-organisor)	Instituto Gulbenkian de Ciência, Portugal
2019/09/17 - 2019/09/17	Member of the local organizing committee of the International Microorganism Day (2019/09/17 - 2019/09/17) Exhibition (Other)	Associação para o Desenvolvimento do Instituto Superior Técnico, Portugal
2012/09/01 - 2012/09/04	Member of the organizing committee of the FEBS 2012 RNA Satellite Meeting. (2012/09/01 - 2012/09/04) Meeting (Member of the Organising Committee)
2007/11/08 - 2007/11/10	Member of the organizing committee of the 2007 RNA congress (2007/11/08 - 2007/11/10) Congress (Member of the Organising Committee)

Event participation

	Activity description Type of event	Event name Institution / Organization
2022/07/18 - 2022/07/22	Summer Science @ ITQB NOVA Other	Summer Science @ ITQB NOVA Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2020/07/20 - 2020/07/23	The Summer Science @ ITQB NOVA provides undergraduate students (2nd or 3rd year undergraduates) the opportunity to experience science in a cutting-edge research institute. Exhibition	Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2020/02/13 - 2020/02/14	Grant Writing Course Workshop	Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2020/01/29 - 2020/01/29	Advanced Data Management Plans Workshop	BioData Course
2020/01/10 - 2020/01/10	Introduction to Data Management Plans Workshop	BioData Course
2018/09/18 - 2018/09/19	DD-DeCaF 2nd Workshop: data-driven cell factory design Workshop
2017/04/18 - 2017/04/19	Workshop on Data Management and Stewardship using FAIRDOMHub Workshop
2016/11/14 - 2016/11/18	Introductory Biostatistics for Biologists Workshop	Instituto Gulbenkian de Ciência, Portugal
2014/03/26 - 2014/03/26	CLC Genomics Workshop Workshop
2013/10/15 - 2013/10/17	Pathways, Networks and Systems Workshop	Instituto Gulbenkian de Ciência, Portugal
2012/06/18 - 2012/06/20	Bioinformatics and Functional Genomics using R Workshop	Instituto Gulbenkian de Ciência, Portugal
2012/02/27 - 2012/03/01	Transcriptome Assembly, Automatic Functional Annotation and Data Mining Workshop	Instituto Gulbenkian de Ciência, Portugal
2011/09 - 2011/10	Nova Forum – Bioentrepreneurship Workshop	Universidade Nova de Lisboa, Portugal
2011/05/21 - 2011/05/27	MicroRNA-profiling: From in-situ hybridization to next-gen sequencing Workshop	EMBO Course
2011/05/02 - 2011/05/07	Bioinformatics using Python for Biologists Workshop	Instituto Gulbenkian de Ciência, Portugal
2010/10/06 - 2010/10/07	Scientific writing course Workshop	Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2010/07/05 - 2010/07/07	RNA Bioinformatics Workshop	Instituto Gulbenkian de Ciência, Portugal
2010/04/26 - 2010/05/01	Computational RNA Biology Workshop	EMBO course
2009/06/13 - 2009/06/25	Molecular Genetics with fission yeast Schizosaccharomyces pombe Workshop	EMBO course

Committee member

	Activity description Role	Institution / Organization
2021/09/01 - Current	Elected ITQB-NOVA Biology Division representative in the ITQB/iBET Postdoctoral Association (PdA). The PdA exists to promote a sense of community among the postdoctoral researchers, to organise activities that enhance professional and personal development, to organise networking and career development events and, more generally, to promote ITQB NOVA and iBET’s postdoctoral researchers and to support their interests within the scientific community. https://www.itqb.unl.pt/education/postdocs/itqb-post-doctoral-association Member	Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal

Course / Discipline taught

	Academic session	Degree Subject (Type)	Institution / Organization
2015 - Current	Introduction to Bioinformatics	(Outros)
2024/01/11 - 2024/01/11	DNA and RNA Biology	Biociências Moleculares (Doutoramento)	Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2023/04/11 - 2023/05/02	Módulo do RNA	Microbiologia Médica (Mestrado)	Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2023/01/10 - 2023/01/10	DNA and RNA Biology	Biociências Moleculares (Doutoramento)	Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2022/10/04 - 2022/10/04	Introdução á Microbiologia, Genética Microbiana e Tecnologia de DNA Recombinante	Microbiologia Médica (Mestrado)	Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2022/07/04 - 2022/07/08	RNA-Seq data analysis Course	(Outros)	Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2022/04/05 - 2022/04/28	Módulo do RNA	Microbiologia Médica (Mestrado)	Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2022/01/12 - 2022/01/12	DNA and RNA Biology	Biociências Moleculares (Doutoramento)	Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2021/10 - 2021/10	Introdução á Microbiologia, Genética Microbiana e Tecnologia de DNA Recombinante	Microbiologia Médica (Mestrado)	Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2021/07/12 - 2021/07/16	RNA-Seq data analysis Course	(Outros)	Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2021/04/19 - 2021/05/04	Módulo do RNA	Microbiologia Médica (Mestrado)	Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2021/01/14 - 2021/01/14	DNA and RNA Biology	Biociências Moleculares (Doutoramento)	Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2020/10/08 - 2020/10/08	Introdução á Microbiologia, Genética Microbiana e Tecnologia de DNA Recombinante	Microbiologia Médica (Mestrado)	Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2020/04/27 - 2020/05/12	Módulo do RNA	Microbiologia Médica (Mestrado)	Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2019/10/03 - 2019/10/03	DNA and RNA Biology	Biociências Moleculares (Doutoramento)	Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2019/10 - 2019/10	Introdução á Microbiologia, Genética Microbiana e Tecnologia de DNA Recombinante	Microbiologia Médica (Mestrado)	Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2019/04 - 2019/04	Módulo do RNA	Microbiologia Médica (Mestrado)	Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2018/10 - 2018/10	Introdução á Microbiologia, Genética Microbiana e Tecnologia de DNA Recombinante	Microbiologia Médica (Mestrado)	Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2018/04/12 - 2018/04/19	Módulo do RNA	Microbiologia Médica (Mestrado)	Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2018/01/11 - 2018/01/11	DNA and RNA Biology	Biociências Moleculares (Doutoramento)	Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2017/10/18 - 2017/10/18	Introdução á Microbiologia, Genética Microbiana e Tecnologia de DNA Recombinante	Microbiologia Médica (Mestrado)	Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2017/01/11 - 2017/01/12	DNA and RNA Biology	Biociências Moleculares (Doutoramento)	Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2016/04/14 - 2016/04/20	Módulo do RNA	Microbiologia Médica (Mestrado)	Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2016/01/14 - 2016/01/14	DNA and RNA Biology	Biociências Moleculares (Doutoramento)	Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2015/10/24 - 2015/10/24	Introdução á Microbiologia, Genética Microbiana e Tecnologia de DNA Recombinante	Microbiologia Médica (Mestrado)	Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2015/01/15 - 2015/01/15	DNA and RNA Biology	Biociências Moleculares (Doutoramento)	Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2014/04/03 - 2014/04/28	Módulo do RNA	Microbiologia Médica (Mestrado)	Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2014/01/15 - 2014/01/15	DNA and RNA Biology	Biociências Moleculares (Doutoramento)	Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2013/10/24 - 2013/10/24	Introdução á Microbiologia, Genética Microbiana e Tecnologia de DNA Recombinante	Microbiologia Médica (Mestrado)	Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2012/05/07 - 2012/05/07	Módulo do RNA	Microbiologia Médica (Mestrado)	Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal

Interview (newspaper / magazine)

	Activity description	Newspaper / Forum
2022/04/23	Interview for NewsFarma during ECCMID22	NewsFarma

Journal scientific committee

	Journal title (ISSN)	Publisher
2023/01 - Current	Frontiers in Cellular and Infection Microbiology - Review Editor	Frontiers
2021/09/01 - 2022/08/31	Antibiotics - guest Editor (2079-6382)	MDPI

Distinctions

Award

2007	Andrade J.M., Matos A.M., POBRE V. and Arraiano C.M. - "PNPase is a key player in the regulation of small non-coding RNAs". de 2007. The oral communication received the 1st Prize in the session "Cell Physiology, Biochemistry and Molecular Biology"
2006	Pobre, V. Award for Best Oral Presentation performed by a student Universidade da Beira Interior Centro de Investigação em Ciências da Saúde, Portugal

Other distinction

2010	EMBO bursary for participation at the EMBO Practical course – “Computational RNA Biology”, Cargèse, Corsica, April 26 – May 1, 2010. Gesellschaft zur Förderung der Lebenswissenschaften Heidelberg GmbH, Germany
2009	FEBS bursary for participation at the 34th FEBS Conference - Life’s Molecular Interaction
2009	EMBO bursary for participation at the EMBO Practical course – “Molecular Genetics with fission yeast Schizosaccharomyces pombe”, Manchester, UK, 13-25 June, 2009. Gesellschaft zur Förderung der Lebenswissenschaften Heidelberg GmbH, Germany