Paulo Caldas (0F15-BC17-2F60)

Curriculum Vitae

Paulo has BSc and a MSc degree in Biochemistry from the University of Lisbon - Faculdade de Ciências (FCUL) completed in 2014. Then, he moved to Austria to start his PhD in the field of "Biochemistry, Biophysics and Molecular Biology" with Professor Martin Loose at Institute of Science and Technology Austria (IST Austria). His PhD project was focused on exploring the dynamics of several proteins involved in the mechanism of bacterial cytokinesis, where he gained a multi-disciplinary skill between wet lab experiments and computational work. These included a wide variety of in vitro biochemistry and molecular biology experiments, high-resolution microscopy, and quantitative image analysis. Towards the end of graduate school, his focus shifted entirely to the computational side of his work and he became a full-time computational biologist, dedicating most of his time building tools for quantitative image analysis, which required mathematical modeling and automated analysis protocols. Paulo was awarded with a Boehringer Ingelheim Fonds (BIF) PhD fellowship during his PhD, published two peer-reviewed articles and a book chapter. After finishing his PhD in September 2020, he went for a short internship at Roche Diagnostics (Vienna, AT) and then joined the Computational Multi-Omics Lab (Prof. Ana Rita Grosso Group at FCT-NOVA, Lisbon, PT) for his first postdoc in Bioinformatics (January 2021). Since then, he has been using a variety of computational multi-omics approaches to decipher transcriptomic and epigenomic alterations underlying a wide range of cellular processes. He has enrolled in multiple collaborative projects - Michael Potente, BIH Berlin (GE); Ana Pombo, MDC Berlin (GE); Claudio Franco, iMM Lisbon (PT); Sergio Almeida, iMM Lisbon (PT); Martin Loose, IST Austria (AT); Simão Rocha, IBB-IST Lisbon (PT) where he contributed mostly with multi-omics data analyses (e.g. analyzing RNA-seq, ChIP-seq, Exome-Seq and Allele-specific data), but also leveraging some of his expertise in image analysis and high-resolution microscopy. In this context, he was awarded with a Marie Curie Postdoctoral Fellowship to explore the mechanisms involved in FOXO-dependent transcription dysregulation occurring in aging cells.

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Identification

Personal identification

Full name: Paulo Caldas

Citation names

Caldas, Paulo

Author identifiers

Ciência ID: 0F15-BC17-2F60
ORCID iD: 0000-0001-6730-4461

Email addresses

p.caldas@fct.unl.pt (Professional)

Telephones

Mobile phone

928123332 (Personal)

Websites

https://www.linkedin.com/in/paulo-caldas-25982a78/ (Professional)

Knowledge fields

Exact Sciences - Computer and Information Sciences - Bioinformatics
Natural sciences - Biological Sciences - Biology
Natural sciences - Biological Sciences - Molecular Biology
Natural sciences - Biological Sciences - Biochemistry
Natural sciences - Biological Sciences - Biophysics
Medical and Health Sciences - Basic Medicine - Human Genetics

Languages

Language	Speaking	Reading	Writing	Listening	Peer-review
English	Advanced (C1)	Advanced (C1)	Advanced (C1)	Advanced (C1)	Advanced (C1)

Education

	Degree	Classification
2015/09/15 - 2020/09/15 Concluded	Molecular Biology, Biochemistry and Biophysics (Doctor of Philosophy) Institute of Science and Technology Austria, Austria "Organization and dynamics of cytoskeletal networks of FtsZ and its crosslinkers" (THESIS/DISSERTATION)
2012/09/01 - 2014/09/01 Concluded	Bioquímica (Mestrado) Major in Biomédica Universidade de Lisboa Faculdade de Ciências, Portugal "Modulation of calcitonin amyloid formation by lipid membranes and extracellular matrix: implications for the mechanism of cytotoxicity of amyloidogenic polypeptides" (THESIS/DISSERTATION)	18/20
2009/09/01 - 2012/06/01 Concluded	Bioquímica (Licenciatura) Universidade de Lisboa Faculdade de Ciências, Portugal	17/20

Affiliation

Science

	Category Host institution	Employer
2021/01/01 - Current	Postdoc (Research)	Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
	Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2015/09/15 - 2020/09/15	Researcher (Research)	Institute of Science and Technology Austria, Austria

2014/10/01 - 2015/06/01	Researcher (Research)	Fundação para a Ciência e a Tecnologia, Portugal
	Universidade de Lisboa Instituto Superior Técnico, Portugal

Others

	Category Host institution	Employer
2020/09/01 - 2020/12/01	Product Manager Intern	Roche Austria GmbH, Austria

Projects

Grant

	Designation	Funders
2022/06/01 - 2024/06/30	Dissecting FOXO-mediated Transcription Noise to Stall Cellular Dysfunction in Ageing HORIZON-MSCA-2021-PF-01/101066912 Co-Principal Investigator (Co-PI) Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal	European Commission Marie Sklodowska-Curie Actions Ongoing
2021/01/01 - 2022/03/31	Inibição da heterogeneidade intra-tumoral como uma estratégia promissora no tratamento do cancro PTDC/MED-ONC/28660/2017 Post-doc Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal	Fundação para a Ciência e a Tecnologia Concluded
2016/09/15 - 2020/09/15	Self-Organization of the Bacterial Cell ERC-2015-StG-679239 PhD Student Fellow Institute of Science and Technology Austria, Austria	European Research Council Concluded
2017/09/01 - 2019/09/01	Rebuilding the Bacterial Cell Division Machinery - PhD Student Fellow Institute of Science and Technology Austria, Austria	Boehringer Ingelheim Fonds Concluded

Outputs

Publications

Book chapter	Caldas, Paulo; Radler, Philipp; Sommer, Christoph; Loose, Martin. "Computational analysis of filament polymerization dynamics in cytoskeletal networks". In Methods in Cell Biology, 145-161. Elsevier, 2020. Published • 10.1016/bs.mcb.2020.01.006
Conference poster	Caldas, Paulo; Luz, Mariana; Simone Baseggio; Rita Andrade; Grosso, Ana Rita. Corresponding author: Caldas, Paulo. "Transcription readthrough is prevalent in healthy human tissues and determined by inherent genomic features". Paper presented in RNA in Disease - RiboMed and IX ptRNA joint meeting, 2023. Caldas, Paulo; Grosso, Ana Rita; Luz, Mariana; Sobral, Daniel. Corresponding author: Grosso, Ana Rita. "RNA in Disease - IX PT RNA Meeting". Paper presented in Transcription Readthrough is prevalent in healthy human tissues and determined by inherent genomic features, 2023. Caldas, Paulo; Loose, Martin; Sommer, Christoph. "Computational analysis of filament polymerization dynamics in cytoskeletal networks". Paper presented in Quantitative BioImaging Conferenc, 2020. Caldas, Paulo; Loose, Martin. "ZapA cooperatively stabilizes FtsZ filament bundles without slowing down treadmilling dynamics". Paper presented in Cell Biology of Prokaryotes, 2019. Caldas, Paulo; Loose, Martin. "ZapA cooperatively stabilizes FtsZ filament bundles without slowing down treadmilling dynamics". Paper presented in Gordon Research Conference on Plant and Microbial Cytoskeleton, 2018.
Journal article	Silvia Carvalho; Luna Zea-Redondo; Tsz Ching Chloe Tang; Philipp Stachel-Braum; Duncan Miller; Paulo Caldas; Alexander Kukalev; et al. "SRRM2 splicing factor modulates cell fate in early development". Biology Open (2024): https://doi.org/10.1242/bio.060415. 10.1242/bio.060415 Paulo Caldas; Mariana Luz; Simone Baseggio; Rita Andrade; Daniel Sobral; Ana Rita Grosso. "Transcription readthrough is prevalent in healthy human tissues and associated with inherent genomic features". Communications Biology (2024): https://doi.org/10.1038/s42003-024-05779-5. 10.1038/s42003-024-05779-5 Marta F Fidalgo; Catarina G Fonseca; Paulo Caldas; Alexandre ASF Raposo; Tania Balboni; Lenka Henao-Mišíková; Ana R Grosso; Francisca F Vasconcelos; Cláudio A Franco. "Aerocyte specification and lung adaptation to breathing is dependent on alternative splicing changes". Life Science Alliance (2022): https://doi.org/10.26508/lsa.202201554. 10.26508/lsa.202201554 Philipp Radler; Natalia Baranova; Paulo Caldas; Christoph Sommer; Mar López-Pelegrín; David Michalik; Martin Loose. "In vitro reconstitution of Escherichia coli divisome activation". Nature Communications 13 1 (2022): http://dx.doi.org/10.1038/s41467-022-30301-y. 10.1038/s41467-022-30301-y Sabino, João C; de Almeida, Madalena R; Abreu, Patrícia L; Ferreira, Ana M; Caldas, Paulo; Domingues, Marco M; Santos, Nuno C; et al. "Epigenetic reprogramming by TET enzymes impacts co-transcriptional R-loops". eLife 11 (2022): http://dx.doi.org/10.7554/elife.69476. 10.7554/elife.69476 Ishihara, Keisuke; Decker, Franziska; Caldas, Paulo; Pelletier, James F.; Loose, Martin; Brugués, Jan; Mitchison, Timothy J.. "Spatial variation of microtubule depolymerization in large asters". Molecular Biology of the Cell 32 9 (2021): 869-879. http://dx.doi.org/10.1091/mbc.e20-11-0723. Published • 10.1091/mbc.e20-11-0723 Caldas, Paulo; López-Pelegrín, Mar; Pearce, Daniel J. G.; Budanur, Nazmi Burak; Brugués, Jan; Loose, Martin. "Cooperative ordering of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinker ZapA". Nature Communications 10 1 (2019): http://dx.doi.org/10.1038/s41467-019-13702-4. Published • 10.1038/s41467-019-13702-4
Preprint	Ana Cláudia Raposo; Paulo Caldas; Maria Arez; Joana Jeremias; Pedro Barbosa; Rui Sousa-Luís; Frederico Água; et al. "Erosion of X-Chromosome Inactivation in female hiPSCs is heterogeneous and persists during differentiation". 2024. https://doi.org/10.1101/2024.03.15.585169. 10.1101/2024.03.15.585169 Silvia Carvalho; Luna Zea-Redondo; Tsz Ching Chloe Tang; Philipp Stachel-Braum; Duncan Miller; Paulo Caldas; Alexander Kukalev; et al. "SRRM2 splicing factor modulates cell fate in early development". 2023. https://doi.org/10.1101/2023.12.15.571825. 10.1101/2023.12.15.571825 Marta F. Fidalgo; Catarina G. Fonseca; Paulo Caldas; Alexandre A. S. F. Raposo; Tania Balboni; Ana R. Grosso; Francisca F. Vasconcelos; Cláudio A. Franco. "Alternative splicing changes are associated with pre-birth adaptation during lung development". 2022. https://doi.org/10.1101/2022.01.19.476886. 10.1101/2022.01.19.476886
Thesis / Dissertation	Caldas, Paulo. "Organization and dynamics of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinkers". PhD, Institute of Science and Technology Austria, 2020. https://research-explorer.app.ist.ac.at/record/8358.

Activities

Supervision

	Thesis Title Role	Degree Subject (Type) Institution / Organization
2023/02/01 - 2023/09/30	Explore how FOXO1 dysregulation promotes functional decline of the vascular endothelium Supervisor	Ciências de Engenharia - Engenharia Biológica (Master) Universidade de Lisboa Instituto Superior Técnico, Portugal
2021/10/01 - 2022/09/30	Assessing the Prevalence of Transcription Readthrough in Healthy Tissues Through Computational Approaches Co-supervisor	Genética Molecular e Biomedicina (Master) Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2021/08/01 - 2022/08/01	Assessing the prevalence of transcription readthrough in healthy tissues through computational approaches Co-supervisor	Genética Molecular e Biomedicina (Master) Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2022/02/01 - 2022/03/01	Dissecting transcription readthrough in ageing tissues through computational approaches Co-supervisor	Biologia Celular e Molecular (Degree) Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2022/02/01 - 2022/03/01	Explore the association between splicing defects and transcription readthrough in human healthy tissues Co-supervisor	Bioquímica (Degree) Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2020/01/01 - 2020/07/31	The effect of ZapE on FtsZ filament organization and dynamics Co-supervisor	Medical and Pharmaceutical Biotechnology (Master) IMC Fachhochschule Krems, Austria Institute of Science and Technology Austria, Austria
2018/07/01 - 2018/09/30	Modulation of the bacterial Z-ring by the crosslinker protein ZapC Co-supervisor	Biotechnology (Scientific initiation) Institute of Science and Technology Austria, Austria

Event participation

	Activity description Type of event	Event name Institution / Organization
2024/03/07 - 2024/03/08	Conference: Applied Bioinformatics in Life Sciences - Aimed to address the evolving landscape of bioinformatics in medical and basic research, showcasing recent scientific findings and fostering collaboration among participants. https://www.vibconferences.be/events/applied-bioinformatics-in-life-sciences-5th-edition Conference	Applied Bioinformatics in Life Sciences
2024/02/27 - 2024/03/01	EMBL Course: Integrative analysis of multi-omics data - Hands-on training in the mathematical and practical skills needed to analyze multi-omics data through integrated statistical analysis and computational modeling techniques. https://www.embl.org/about/info/course-and-conference-office/events/mmd24-01/ Workshop	Integrative analysis of multi-omics data EMBL Heidelberg Genome Biology, Germany
2023/06/19 - 2023/06/22	EMBO Workshop On X-chromosome inactivation: New insights on its 60th anniversary - This EMBO Workshop will bring together a diverse range of experts across the world working on different aspects of the X-inactivation process to share their ongoing and unpublished work, contributing to building a more integrated overview of this epigenetic and developmental phenomenon, 60+ years after the seminal paper by geneticist Mary Lyon in 1961 proposing the X-inactivation hypothesis. Conference	EMBO Workshop On X-chromosome inactivation Gesellschaft zur Förderung der Lebenswissenschaften Heidelberg GmbH, Germany
2023/04/27 - 2023/04/27	Workshop on Decoding the genome with deep learning - In this course, we will provide an overview of how deep learning can be used to learn the regulatory code of the genome, discuss specific models and applications, and get hands-on experience implementing them. Workshop	Decoding the Genome with Deep Learning Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
2023/01/26 - 2023/01/27	RNA in Disease - IX PT RNA Meeting - A broad event covering several aspects of RNA biology, from RNA structure and function to RNA-associated dysfunctions and implications in human health. Conference	RNA in Disease - IX PT RNA Meeting Universidade de Lisboa Instituto de Medicina Molecular João Lobo Antunes, Portugal
2022/07/22 - 2022/07/22	RiboMed Satellite Conference on RNA in Disease - several talks by distinguished researchers on RNA in biomedical contexts. Session was extended to a poster session and two short talks selected from submitted abstracts. Conference	RiboMed Satellite Conference on RNA in Disease Universidade de Lisboa Instituto de Medicina Molecular João Lobo Antunes, Portugal
2021/07/05 - 2021/07/10	RiboMed Summer School on Single-cell RNA-seq and spatial transcriptomics - A practical hands-on course that required basic experience in bioinformatics. Workshop	RiboMed Summer School on Single-cell RNA-seq and spatial transcriptomics Universidade de Lisboa Instituto de Medicina Molecular João Lobo Antunes, Portugal
2020/01/06 - 2020/01/09	Quantitative BioImaging Conference - International and Interdisciplinary conference on the Analysis of Bioimaging data - https://www.quantitativebioimaging.com/qbi2020/ Conference	Quantitative BioImaging Conference (QBI 2020) University of Oxford, United Kingdom University of Oxford Mathematical Institute, United Kingdom
2019/04/07 - 2019/04/11	Cell Biology of Prokaryotes Conference - International conference focused on the molecular mechanisms that underlie the spatiotemporal organization of fundamental cellular processes in prokaryotes - https://www.eventbrite.de/e/cell-biology-of-prokaryotes-registration-49977814990 Conference	Cell Biology of Prokaryotes Conference Transregional Collaborative Research Center TRR 174, Germany
2018/08/12 - 2018/08/17	Gordon Research Conference on Plant and Microbial Cytoskeleton - Quantitative approaches to investigate the underlying molecular mechanisms controlling the organization, dynamics and function of the cytoskeleton in model plant, fungal and bacterial cell systems - https://www.grc.org/plant-and-microbial-cytoskeleton-conference/2018/ Conference	Gordon Research Conference - Plant and Microbial Cytoskeleton Gordon Research Conferences, United States

Association member

	Society Organization name	Role
2017/03/01 - 2018/03/01	Graduate Student Association (GSA)	Graduate Student Representative

Course / Discipline taught

	Academic session	Degree Subject (Type)	Institution / Organization
2019/09/01 - 2019/10/31	Introduction to Programming with Python	IST Austria Graduate School (Doktor (PhD))	Institute of Science and Technology Austria, Austria
2019/01/01 - 2019/03/31	Biology Core Course	IST Austria Graduate School (Doktor (PhD))	Institute of Science and Technology Austria, Austria
2018/01/01 - 2018/03/01	Biology Core Course	IST Austria Graduate School (Doktor (PhD))	Institute of Science and Technology Austria, Austria

Distinctions

Award

2022	Marie Sklodowska-Curie Postdoctoral Fellowship Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2020	Best Poster Prize at Cell Biology of Prokaryotes Conference Ludwig-Maximilians-Universität München Fakultät für Biologie, Germany
2017	Boehringer Ingelheim Fonds (BIF) PhD Fellowship Boehringer Ingelheim Fonds, Germany
2014	Best Poster Prize at the XVIII Congress of the Portuguese Biochemical Society Sociedade Portuguesa de Bioquímica, Portugal

Other distinction

2021	Research Fellowship Fundação para a Ciência e a Tecnologia, Portugal
2020	Expert Internship Grant - Intersecting Science & Business Ludwig Boltzmann Gesellschaft, Austria
2014	Research Fellowship Fundação para a Ciência e a Tecnologia, Portugal
2013	Research Fellowship Fundação para a Ciência e a Tecnologia, Portugal