# 2024

## International articles with referee 
1. Melnik, T., Sinval, J., Pinho, V. D. de, Junior, J. A. S. H., Oliveira, M. da S., & Lopes, F. M. (2025). Knowledge and use of evidence-based practice in psychology in the clinical practice of Brazilian psychologists: A cross-sectional study. Healthcare, 13(4), 1–18. https://doi.org/10.3390/healthcare13040431
1. Nevado B, Atchison GW, Bridges EL, Orzell S, Filatov D, Hughes CE. Pleistocene diversification of unifoliolate-leaved Lupinus (Leguminosae: Paplionoideae) in Florida. Molecular Ecology (accepted). 
1. Andrade, R., Laranjeiro, N., & Vieira, M. (2024). BugHub: A Large Scale Issue Report Dataset. In 19th European Dependable Computing Conference - EDCC, accepted for publication. Leuven.
1. Sinval, J., Oliveira, P., Novais, F., Almeida, C. M., & Telles-Correia, D. (2024). Correlates of burnout and dropout intentions in medical students: A cross-sectional study. Journal of Affective Disorders. https://doi.org/10.1016/j.jad.2024.08.003
1. "Leveraging LLMs for On-the-fly Instruction Guided Image Editing" dos autores Rodrigo Santos, João Silva e António Branco EPIA 2024, International Conference on Artificial Intelligence (https://doi.org/10.48550/arXiv.2403.08004)
1. Morais, I., Carneiro, F. A., Sinval, J., Costa, P. A., & Leal, I. (2024). The Walsh Family Resilience Questionnaire: Validity evidence from Portugal. Family Relations. https://doi.org/10.1111/fare.13078
1. Sinval, J., Oliveira, P., Novais, F., Almeida, C. M., & Telles-Correia, D. (2024). Exploring the impact of depression, anxiety, stress, academic engagement, and dropout intention on medical students’ academic performance: A prospective study. Journal of Affective Disorders. https://doi.org/10.1016/j.jad.2024.09.116
1. Melo, L. E. A. de, Sinval, J., & Isler, C. A. (2025). Prospective avenues in travel behavior research supported by the cognitive dissonance theory: A scoping review. Transportation Research Part F: Traffic Psychology and Behaviour, 109, 501–519. https://doi.org/10.1016/j.trf.2024.12.022
1. Galamba, N., Sickle Cell Hemoglobin “Drugged” with Cyclic Peptides is Aggregation Incompetent, J. Phys. Chem. B, 128, 36, 8662, 2024 
URL: https://doi.org/10.1021/acs.jpcb.4c03805
1. Martins, G., Galamba, N., Wild Type α-Synuclein Structure and Aggregation: A Comprehensive Coarse-Grained and All-Atom Molecular Dynamics Study, J. Chem. Inf. Model., 64, 15, 6115, 2024  URL: https://doi.org/10.1021/acs.jcim.4c00965 
1. Gomes I., Martins, G., Galamba N., Essential Dynamics of Ubiquitin in Water and in a Natural Deep Eutectic Solvent, Phys. Chem. Chem. Phys., 26, 18244, 2024 
URL: htps://pubs.rsc.org/en/Content/ArticleLanding/2024/CP/D4CP01773K
1. Iana Lychko; Cátia Lopes Soares; Barbosa, A.J.M.; Tomás Rosa Calmeiro; Rodrigo Ferrão de Paiva Martins; Ana Margarida Gonçalves Carvalho Dias; Ana Cecília Afonso Roque. "Kinetics of charge-dependent reversible condensation of reflectin nanostructures". Materials Advances (2024): https://doi.org/10.1039/D4MA00788C.
1. In silico identification of novel PqsD inhibitors: promising molecules for quorum sensing interference in Pseudomonas aeruginosa – Tatiana F. Vieira; Nuno M. F. S. A. Cerqueira; Manuel Simões; Sérgio F. Sousa – Molecular Systems Design & Engineering – 2024 – 10.1039/D3ME00107E
1. The fungicide cymoxanil impairs respiration in Saccharomyces cerevisiae via cytochrome oxidase inhibition – Filipa Mendes; Cátia Santos-Pereira; Tatiana F. Vieira; Mélanie Martins Pinto; Bruno B. Castro; Sérgio F. Sousa; Maria João Sousa; Anne Devin; Susana Chaves – FEBS Letters – 2024 – 10.1002/1873-3468.14907
1. Dual action of benzaldehydes: Inhibiting quorum sensing and enhancing antibiotic efficacy for controlling Pseudomonas aeruginosa biofilms – Miguel M. Leitão; Tatiana F. Vieira; Sérgio F. Sousa; Fernanda Borges; Manuel Simões; Anabela Borges – Microbial Pathogenesis – 2024 – 10.1016/j.micpath.2024.106663
1. Montelukast and cefoperazone act as antiquorum sensing and antibiofilm agents against Pseudomonas
aeruginosa – Tatiana F Vieira; Miguel M Leitão; Nuno M F S A Cerqueira; Sérgio F Sousa; Anabela Borges; Manuel Simões – Journal of Applied Microbiology – 2024 – 10.1093/jambio/lxae088
1. In silico-guided discovery and in vitro validation of novel sugar-tethered lysinated carbon nanotubes for targeted drug delivery of doxorubicin – Fábio G. Martins; Chanchal Kiran Thakur; Chandrabose Karthikeyan; Subhasmita Bhal; Chanakya Nath Kundu; N. S. Hari Narayana Moorthy; Sérgio F. Sousa – Journal of Molecular Modeling – 2024 https://doi.org/10.1007/s00894-024-06061-5
1. Protocol for in silico characterization of natural-based molecules as quorum-sensing inhibitors – Susana Fernandes; Mariana Sousa; Fábio G. Martins; Manuel Simões; Sérgio F. Sousa – STAR Protocols – 2024 – http://dx.doi.org/10.1016/j.xpro.2024.103367
1. Protocolo de Bioinformática para ensino de estrutura e função de proteínas. Roggero, A., Nicodemo, I.,
Annunciato, I., da Silva Fernandes, P. H., Mota, V., & Toyama, M. H. (2024). Revista de Ensino de Bioquímica, 22(2), 119-136. https://doi.org/10.16923/reb.v22i2.1088
1. Structural insights of an LCP protein–LytR–from Streptococcus dysgalactiae subs. dysgalactiae through
biophysical and in silico methods - J Paquete-Ferreira, F Freire, HS Fernandes, J Muthukumaran, J Ramos, et al. Frontiers in Chemistry 12, 1379914, 2024 https://doi.org/10.3389/fchem.2024.1379914
Evaluation of the impact of two C5 genetic variants on C5-eculizumab complex stability at the molecular level - VP Peixoto, C Prudêncio, M Vieira, SF Sousa, Journal of Biomolecular Structure and Dynamics, 1-10, 2024, https://doi.org/10.1080/07391102.2024.2331091
1. Exploiting Locusta migratoria as a source of bioactive peptides with anti-fibrosis properties using an in silico approach (vol 15, pg 493, 2024) CSS Teixeira, R Biltes, C Villa, SF Sousa, J Costa, IM Ferreira, I Mafra - FOOD & FUNCTION 15 (5), 2773-2773, https://doi.org/10.1039/D3FO04246D
1. Glucocorticoid receptor-dependent therapeutic efficacy of tauroursodeoxycholic acid in preclinical models of spinocerebellar ataxia type 3 - S Duarte-Silva, JD Da Silva, D Monteiro-Fernandes, MD Costa, SF Sousa et al. The Journal of clinical investigation 134 (5) (2024) 10.1172/JCI162246
1. Substitution models of protein evolution with selection on enzymatic activity D Ferreiro, R Khalil, SF Sousa, M Arenas, Molecular Biology and Evolution 41 (2), 2024 msae026 https://doi.org/10.1093/molbev/msae026
1. Machine Learning-Driven Discovery and Database of Cyanobacteria Bioactive Compounds: A Resource for
Therapeutics and Bioremediation - R Soares, L Azevedo, V Vasconcelos, D Pratas, SF Sousa, J Carneiro - Journal of Chemical Information and Modeling 64 (24), 9576-9593 https://doi.org/10.1021/acs.jcim.4c00995
1. Advances in structure-based drug design targeting membrane protein markers in prostate cancer - Batista- Silva J.P., Gomes D., Sousa S.F., Sousa Â., Passarinha L.A. - Drug Discovery Today, 2024, 29(9): 104130 https://doi.org/10.1016/j.drudis.2024.104130
1. Structural insights and photophysical properties of mononuclear and pentanuclear Zn(II) acetate complexes with pyridyl-based thiazolyl-hydrazones - Araškov J.B., Garcia-Sosa A.T., Višnjevac A., Sousa S.F., Holló B.B., Uğuz Ö., Koca A., Monge M., Rodríguez-Castillo M., López-de-Luzuriaga J.M., Todorović T.R., Filipović N.R. - Polyhedron, 2024, 262: 117162 https://doi.org/10.1016/j.poly.2024.117162
1. In silico analysis of aptamer-RNA conjugate interactions with human transferrin receptor Vasconcelos D., Pina A., Habib N., Sousa S.F. - Biophysical Chemistry, 2024, 314: 107308 https://doi.org/10.1016/j.bpc.2024.107308
1. LC-ESI-UHR-QqTOF-MS/MS profiling and anti-inflammatory potential of the cultivated Opuntia ficus-indica (L.) Mill. and the wild Opuntia stricta (Haw.) Haw. fruits from the Algerian region - Zeghbib W., Boudjouan F., Carneiro J., Oliveira A.L.S., Sousa S.F., Pintado M.E., Ourabah A., Vasconcelos V., Lopes G. - Food Chemistry, 2024, 460: 140414 https://doi.org/10.1016/j.foodchem.2024.140414
1. Design, synthesis, and pharmacological evaluation of heteroaryl thiol-linked kojic acid derivatives as a novel class of acetylcholinesterase inhibitors for Alzheimer’s disease therapy - Singh M., Karthikeyan C., Waiker D.K., Tiwari A., Shrivastava S.K., Sousa S.F., Kiriwan D., Martins F.G., Moorthy N.S.H.N. - 3 Biotech, 2025, 15(5): 134 https://doi.org/10.1007/s13205-025-04295-5
1. A comprehensive update of genotype–phenotype correlations in PMM2-CDG: insights from molecular and structural analyses - Oliveira T., Ferraz R., Azevedo L., Quelhas D., Carneiro J., Jaeken J., Sousa S.F. - Orphanet Journal of Rare Diseases, 2025, 20(1): 207 https://doi.org/10.1186/s13023-025-03669-5
1. Design and biological evaluation of 2-phenylquinoxaline carbonyl piperazine derivatives as novel FASN inhibitors with anticancer activity - S Singh, S Paul, FG Martins, SF Sousa, CN Kundu, C Karthikeyan, - Bioorganic Chemistry, 2025, 10869 https://doi.org/10.1016/j.bioorg.2025.108697
1. Two cinnamic acid derivatives as inhibitors of Pseudomonas aeruginosa las and pqs quorum-sensing
systems: Impact on biofilm formation and virulence factors - MM Leitão, ASC Gonçalves, SF Sousa, F Borges, M Simões, A Borges, Biomedicine & Pharmacotherapy 2025, 187, 118090 https://doi.org/10.1016/j.biopha.2025.118090
1. Gonçalves, C., Moutinho Cabral, I., Alves de Matos, A.P., Grosso, A.R. and Costa, P.M. (2024). Transcriptome profiling of the posterior salivary glands of the cuttlefish Sepia officinalis from the Portuguese West coast. Front. Mar. Sci. 11, 1362824. doi:10.3389/fmars.2024.1362824
1. Martins, C., Carvalho, L.M., Moutinho Cabral, I., Saúde, L., Dreij, K. and Costa, P.M. (2024). A mechanistic study on the interaction effects between legacy and pollutants of emerging concern: A case study with B[a]P and diclofenac. Environ Pollut. 363, 125189. doi:10.1016/j.envpol.2024.125189
1. Rodrigo, A.P., Moutinho Cabral, I., Alexandre, A. and Costa, P.M. (2024). Exploration of toxins from a marine annelid: An analysis of phyllotoxins and accompanying bioactives. Animals (Basel). 14, 635. doi:10.3390/ani14040635

1.	Feature Selection Techniques for CR Isotope Identification with the AMS-02 Experiment in Space	Marta Borchiellini, Leandro Mano, Fernando Barão e Manuels Vecchi	Particles 2024, 7(2), 417-434	2024-04-11	https://doi.org/10.3390/particles7020024
1.	Properties of Cosmic Deuterons Measured by the Alpha Magnetic Spectrometer	AMS Collaboration (248 authors)	Phys. Rev. Lett. 132 (2024) 261001		10.1103/PhysRevLett.132.261001
1.	Probing the 𝐶𝑃 nature of the top–Higgs Yukawa coupling in 𝑡 ̄ 𝑡𝐻 and 𝑡𝐻 events with 𝐻 → 𝑏 ̄ 𝑏 decays using the ATLAS detector at the LHC	ATLAS Collaboration (A. L. Carvalho, E. Gouveia, R. Gonçalo, A. Onofre, et al)	Phys. Lett. B 849 (2024) 138469		10.1016/j.physletb.2024.138469
1.	Simulation-based inference in the search for CP violation in leptonic WH production	R.  Barrué, P. Conde Muíño, V. Dao, R. Santos	J. High Energ. Phys. 2024, 14	2024-03-13	https://doi.org/10.1007/JHEP04%282024%29014
1.	Combination of searches for heavy spin-1 resonances using 139 fb−1 of proton-proton collision data at  \sqrt{s}=13 TeV with the ATLAS detector	ATLAS Collaboration (Inês Ochoa et al)	J. High Energy Phys. 4 (2024) 118		10.1007/JHEP04(2024)118
1.	The ATLAS Experiment at the CERN Large Hadron Collider: A Description of the Detector Configuration for Run 3	ATLAS Collaboration (R. Pedro et al.)	J. Instrum. 19 (2024) P05063	2023-05-26	10.1088/1748-0221/19/05/P05063
1.	Search for invisible particles produced in association with single top quarks in proton-proton collisions at s√=13 TeV with the ATLAS detector	ATLAS Collaboration (M. Barros, N. Castro, R. Pedro et al. )	JHEP 05 (2024) 263		10.1007/JHEP05%282024%29263
1.	Search for singly produced vector-like top partners in multilepton final states with 139 $mathrm{fb}^{-1}$ of $pp$ collision data at $sqrt{s} = 13$ TeV with the ATLAS detector	ATLAS Collaboration (N. Castro, T. Vale)	Phys. Rev. D 109 (2024) 112012	2024-06-11	10.1103/PhysRevD.109.112012
1.	The ATLAS trigger system for LHC Run 3 and trigger performance in 2022	ATLAS Collaboration (R. Barrué, P. Conde Muíño, I. Ochoa et al. )	2024 JINST 19 P06029	2024-05-28	10.1088/1748-0221/19/06/P06029
1.	Asymmetries in invisible dark matter mediator production associated with tt final states	Esteban Chalbaud, Rui Miguel Silva, António Onofre, Ricardo Gonçalo, Miguel C. N. Fiolhais	Phys. Rev. D 110, 076016		10.1103/PhysRevD.110.076016
1.	Operation and performance of the ATLAS tile calorimeter in LHC Run 2	ATLAS Collaboration (TileCal/LIP group et al.)	Eur. Phys. J. C 84 (2024) 1313	2024-09-01	10.1140/epjc/s10052-024-13151-4
1.	The Pierre Auger Observatory Open Data	The Pierre Auger Collaboration	Eur. Phys C.	2024-09-30	
1.	Ground observations of a space laser for the assessment of its in-orbit performance	The Pierre Auger Collaboration	Optica 11 (2024) 263-272	2023-12-05	doi.org/10.1364/OPTICA.507619
1.	Proton-air interactions at ultra-high energies in muon-depleted air showers with different depths	L.Cazon, R.Conceição, M.A.Martins, F.Riehn	Phys. Lett. B 859 (2024) 139115	2024-11-01	https://doi.org/10.1016/j.physletb.2024.139115
1.	Study of central exclusive production processes by proton-proton collisions at 13 TeV with the CMS experiment	Matteo Pisano (for the CMS Collaboration)	Nuovo Cim. C 47 (2024) 81	2024-03-18	10.1393/ncc/i2024-24081-4
1.	Development of the CMS detector for the CERN LHC Run 3	CMS Collaboration (2535 authors)	JINST 19 (2024) 05, P05064	2023-11-06	10.1088/1748-0221/19/05/P05064
1.	Search for central exclusive production of top quark pairs in proton-proton collisions at 13 TeV with tagged protons	CMS and TOTEM collaborations	JHEP 06 (2024) 187	2024-05-20	
1.	A Novel Diamond-like Carbon based photocathode for PICOSEC Micromegas detectors	X.Wang, M.Gallinaro et al.	J. Instrum. 19 (2024) P08010	2024-08-01	10.1088/1748-0221/19/08/P08010
1.	Measurement of the polarizations of prompt and non-prompt J/psi and psi(2S) mesons produced in pp collisions at 13 TeV	CMS collaboration	Phys. Lett. B 858 (2024) 139044	2024-10-07	
1.	Optimization of LYSO crystals and SiPM parameters for the CMS MIP timing detector	A.Boletti, M.Gallinaro, J.Varela et al.	JINST 19 (2024) 12, P12020	2024-10-11	
1.	PICOSEC-Micromegas Detector, an innovative solution for Lepton Time Tagging	A. Kallitsopoulou, M.Gallinaro et al.	Nucl.Instrum.Meth.A 1069 (2024) 169920	2024-10-16	
1.	TOFHIR2: the readout ASIC of the CMS barrel MIP Timing Detector	E. Albuquerque et al.	JINST 19 (2024) 05, P05048	2024-10-31	10.1088/1748-0221/19/05/P05048
1.	Constraints On Covariant WIMP-Nucleon Effective Field Theory Interactions from the First Science Run of the LUX-ZEPLIN Experiment	J. Aalbers et al. (LZ Collaboration)	Phys. Rev. Lett. 133, 221801 (2024)		https://doi.org/10.1103/PhysRevLett.133.221801
1.	Two-neutrino double electron capture of 124Xe in the first LUX-ZEPLIN exposure	J. Aalbers et al.	Journal of Physics G: Nuclear and Particle Physics, Volume 52, Number 1 (2024)	2024-11-08	10.1088/1361-6471/ad9039
1.	A next-generation liquid xenon observatory for dark matter and neutrino physics	J. Aalbers et al.	Journal of Physics G- Nuclear and particle Physics 50, 013001 (2023)	2024-07-26	10.1088/1361-6471/ac841a
1.	Event generators for high-energy physics experiments	J.M. Campbell, et. al.	SciPost Phys. 16 (2024) 5, 130		10.21468/SciPostPhys.16.5.130
1.	Software Quality Assurance as a Service: Encompassing the Quality Assessment of Software and Services	Samuel Bernardo, Pablo Orviz, Mario David, Jorge Gomes, David Arce, Diana Naranjo, Ignacio Blanquer, Isabel Campos, Germán Moltó, Joao Pina	Future Generation Computer Systems, 2024, ISSN 0167-739X	2024-03-12	10.1016/j.future.2024.03.024
1.	Event-by-Event Direction Reconstruction of Solar Neutrinos in a High Light-Yield Liquid Scintillator	A. Allega et al., The SNO+ Collaboration	Phys. Rev. D 109, 072002		https://journals.aps.org/prd/abstract/10.1103/PhysRevD.109.072002
1.	Measurement of the 8B Solar Neutrino Flux Using the Full SNO+ Water Phase	A. Allega et al. (SNO+ Collaboration)	Phys. Rev. D 110, 122003	2024-08-28	10.1103/PhysRevD.110.122003
1.	Initial measurement of reactor antineutrino oscillation at SNO+	A. Allega et al (SNO+ Collaboration)	Eur. Phys. J. C 85, 17 (2025)	2024-12-05	https://doi.org/10.1140/epjc/s10052-024-13687-5
1.	Electromagnetic Transition Form Factors of Baryon Resonances	G. Ramalho, M.T Peña	Prog.Part.Nucl.Phys. 136 (2024) 104097		https://doi.org/10.1016/j.ppnp.2024.104097
1.	Simple high-accuracy method for solving bound-state equations with the Cornell potential in momentum space	A. Stadler, E. P. Biernat, and V. Valverde	Phys. Rev. D 110, 114039 (2024).	2024-12-31	
1.	Electromagnetic |GE/GM| ratios of hyperons at large timelike q2	G. Ramalho, M.T. Peña, K. Tsushima, Myung-Ki Cheoun	Phys.Lett.B 858 (2024) 139060	2024-12-31	https://doi.org/10.1016/j.physletb.2024.139060
1.	Natural linewidths of Cu K1,2 spectra obtained with an antiparallel double-crystal x-ray spectrometer	Y. Ito, T. Tochio, M. Yamashita, S. Fukushima, Ł. Syrocki, K. Słabkowska, M. Polasik, J. P. Marques, and F. Parente	Y. Ito, T. Tochio, M. Yamashita, S. Fukushima, Ł. Syrocki, K. Słabkowska, M. Polasik, J. P. Marques, and F. Parente, “Natural linewidths of Cu K1,2 spectra obtained with an antiparallel double-crystal x-ray spectrometer”. J. Anal. At. Spectrom. 39, 1094 (2024).	2024-02-23	https://doi.org/10.1039/d3ja00367a
1.	Databases of L-shell X-ray intensity ratios for various elements after photon excitation	A. Zidi, A. Kahoul, J. P. Marques, S. Daoudi, J. M. Sampaio, F. Parente, A. Hamidani, S. Croft, A. Favalli, Y. Kasri, K. Amari, B. Berkani	7. A. Zidi, A. Kahoul, J. P. Marques, S. Daoudi, J. M. Sampaio, F. Parente, A. Hamidani, S. Croft, A. Favalli, Y. Kasri, K. Amari, B. Berkani, “Databases of L-shell X-ray intensity ratios for various elements after photon excitation”. At. Nucl. Data Tables 157, 101645 (2024)	2024-02-02	https://doi.org/10.1016/j.adt.2024.101645
1.	Semi-Empirical and Theoretical calculation of L1, L2, and L3  Subshell Fluorescence Yields	K. Meddouh, A. Kahoul, J. M. Sampaio, S. Daoudi, J. P. Marques, F. Parente, N.Kup Aylikci, V. Aylikci, Y. Kasri, A. Hamidani	K. Meddouh, A. Kahoul, J. M. Sampaio, S. Daoudi, J. P. Marques, F. Parente, N.Kup Aylikci, V. Aylikci, Y. Kasri, A. Hamidani, “Semi-Empirical and Theoretical calculation of L1, L2, and L3  Subshell Fluorescence Yields”. J.Quant. Sprctr. & Rad. Transf. 322, 109013 (2024).	2024-04-16	https://doi.org/10.1016/j.jqsrt.2024.109013
1.	Measurement of nuclear interaction cross sections towards neutron-skin thickness determination	L. Ponnath, T. Aumann, C. A. Bertulani, et al.	Phys. Lett. B855, 138780 (2024)		10.1016/j.physletb.2024.138780
1.	Experimental K-shell fluorescence cross sections for elements in the atomic number range 16 ≤ Z ≤ 92 by photon impact at various energies	K. Amari, A. Kahoul, J.P. Marques, S. Daoudi, J.M. Sampaio, F. Parente, A. Hamidani, S. Croft, A.Favalli, Y. Kasri, A. Zidi, B. Berkani.	K. Amari, A. Kahoul, J.P. Marques, S. Daoudi, J.M. Sampaio, F. Parente, A. Hamidani, S. Croft, A.Favalli, Y. Kasri, A. Zidi, B. Berkani. “Experimental K-shell fluorescence cross sections for elements in the atomic number range 16 ≤ Z ≤ 92 by photon impact at various energies”. Atomic Data and Nuclear Data Tables 159, (2024) 101662.	2024-05-22	https://doi.org/10.1016/j.adt.2024.101662
1.	Strong coupling effects on near-barrier 15C + 208Pb elastic scattering	V.G. Távora, J.D. Ovejas, I. Martel, et al.	Phys. Lett. B 855 (2024) 138770		10.1016/j.physletb.2024.138770
1.	Vacancy transfer probability parameters: database and a new empirical value for elements in the atomic number range 16 ≤ Z ≤ 92	B. Berkani, A. Kahoul, J.P. Marques, S. Daoudi, J.M. Sampaio, F. Parente, A. Hamidani, S. Croft, A.Favalli, Y. Kasri, A. Zidi, K. Amari.	3. B. Berkani, A. Kahoul, J.P. Marques, S. Daoudi, J.M. Sampaio, F. Parente, A. Hamidani, S. Croft, A.Favalli, Y. Kasri, A. Zidi, K. Amari. “Vacancy transfer probability parameters: database and a new empirical value for elements in the atomic number range 16 ≤ Z ≤ 92”. Radiation Physics and Chemistry 225, (2024) 112106.	2024-12-04	https://doi.org/10.1016/j.radphyschem.2024.112106
1.	Investigating Empirical and Theoretical Calculations for Intensity Ratios of L-Shell X-ray transitions in atoms with 39 ≤ Z ≤ 94	A. Zidi, A. Kahoul, J.P. Marques, S. Daoudi, J.M. Sampaio, F. Parente, A. Hamidani, S. Croft, A.Favalli, Y. Kasri, K. Amari, B. Berkani	A. Zidi, A. Kahoul, J.P. Marques, S. Daoudi, J.M. Sampaio, F. Parente, A. Hamidani, S. Croft, A.Favalli, Y. Kasri, K. Amari, B. Berkani. «Investigating Empirical and Theoretical Calculations for Intensity Ratios of L-Shell X-ray transitions in atoms with 39 ≤ Z ≤ 94”. Journal of Electron Spectroscopy and Related Phenomena 275, (2024) 147473.	2024-07-10	https://doi.org/10.1016/j.elspec.2024.147473
1.	Empirical calculation of K-shell fluorescence cross sections for elements in the atomic range 16≤Z≤92 by photon effects ranging from 5.46 to 123.6 keV (Three-dimensional formulae)	K. Amari, A. Kahoul, J.M. Sampaio, Y. Kasri, J.P. Marques, F. Parente, A. Hamidani, S. Croft, A. Favalli, S. Daoudi, A. Zidi, B. Berkani	K. Amari, A. Kahoul, J.M. Sampaio, Y. Kasri, J.P. Marques, F. Parente, A. Hamidani, S. Croft, A. Favalli, S. Daoudi, A. Zidi, B. Berkani, “Empirical calculation of K-shell fluorescence cross sections for elements in the atomic range 16≤Z≤92 by photon effects ranging from 5.46 to 123.6 keV (Three-dimensional formulae)”. Physica Scripta 99, (2024) 105402.	2024-08-21	https://doi.org/10.1088/1402-4896/ad720e
1.	Measurement of differential collisional excitation cross sections for the Kα emission of He-like oxygen	Filipe Grilo, Chintan Shah, José Marques, José Paulo Santos, José R. Crespo López-Urrutia, and Pedro Amaro.	Filipe Grilo, Chintan Shah, José Marques, José Paulo Santos, José R. Crespo López-Urrutia, and Pedro Amaro.  « Measurement of differential collisional excitation cross sections for the Kα emission of He-like oxygen”. Physical Review A110, 042827(2025).	2024-09-30	10.1103/PhysRevA.110.042827
1.	Relativistic and semi-theoretical calculations of K-shell to L-shell/subshell vacancy transfer probabilities	. Berkani, A. Kahoul, J.P. Marques, S. Daoudi, J.M. Sampaio, F. Parente, A. Hamidani, S. Croft, A.Favalli, Y. Kasri, A. Zidi, K. Amari	B. Berkani, A. Kahoul, J.P. Marques, S. Daoudi, J.M. Sampaio, F. Parente, A. Hamidani, S. Croft, A.Favalli, Y. Kasri, A. Zidi, K. Amari. “Relativistic and semi-theoretical calculations of K-shell to L-shell/subshell vacancy transfer probabilities”. Spectrochimica Acta Part B: Atomic Spectroscopy 224, (2025) 107089.  https://doi.org/10.1016/j.sab.2024.107089	2024-11-26	https://doi.org/10.1016/j.sab.2024.107089
1.	Multislit gamma camera for external beam radiotherapy assistance: Experimental proof of concept	H Simões, L Lopes,  PJBM Rachinhas, P Crespo	ARNM 2024, 2(3), 4099	2024-08-23	10.36922/arnm.4099
1.	Final COMPASS results on the transverse-spin-dependent azimuthal asymmetries in the pion-induced Drell-Yan process	G.D. Alexeev et al. (COMPASS Coll.)	Phys. Rev. Lett. 133, 071902 (2024)	2024-05-14	10.1103/PhysRevLett.133.071902
1.	Jet quenching in anisotropic flowing matter	Matvey V. Kuzmin, Xoán Mayo López, Andrey V. Sadofyev	Phys.Rev.D 109 (2024) 1, 014036		https://doi.org/10.1103/PhysRevD.109.014036
1.	Jet substructure observables for jet quenching in Quark Gluon Plasma: a Machine Learning driven analysis	Miguel Crispim Romão, José Guilherme Milhano, Marco van Leeuwen	SciPost Phys. 16, 015 (2024)	2023-12-21	
1.	Picturing QCD jets in anisotropic matter: from jet shapes to Energy Energy Correlators	João Barata, José Guilherme Milhano, Andrey V. Sadofyev	Eur. Phys. J. C (2024) 84:174		10.1140/epjc/s10052-024-12514-1
1.	Von Neumann entropy and Lindblad decoherence in the high energy limit of strong interactions	G. Chachamis, A. Sabio Vera			10.1103/PhysRevD.109.054015
1.	Axions and superfluidity in Weyl semimetals	Emil Mottola, Andrey V. Sadofyev, Andreas Stergiou	Phys.Rev.B 109 (2024) 13, 134512		https://doi.org/10.1103/PhysRevB.109.134512
1.	Exploring the time axis within medium-modified jets	Liliana Apolinário, Pablo Guerrero-Rodríguez, Korinna Zapp	Eur.Phys.J.C 84 (2024) 7, 672		10.1140/epjc/s10052-024-13048-2
1.	Jet substructure	Liliána Apolinário, Yang-Ting Chien, Leticia Cunqueiro Mendez	Int.J.Mod.Phys.E 33 (2024) 07, 2430003		10.1142/S0218301324300030
1.	Dynamics of particle-particle correlations and the ridge effect in proton-proton collisions	G. Calé, G. Chachamis, A. Sabio Vera			https://doi.org/10.1103/PhysRevD.110.074009
1.	Jet quenching in the glasma phase: Medium-induced radiation	João Barata, Sigtryggur Hauksson, Xoán Mayo López, Andrey V. Sadofyev	Phys.Rev.D 110 (2024) 9, 094055		https://doi.org/10.1103/PhysRevD.110.094055
1.	In-medium gluon radiation spectrum with all-order resummation of multiple scatterings in longitudinally evolving media	Carlota Andres, Liliana Apolinário, Fabio Dominguez, Marcos Gonzalez Martinez	JHEP 11 (2024) 025		10.1007/JHEP11(2024)025
1.	Multijet event shape variables for Mueller Navelet jet topologies	C. Baldenegro, G. Chachamis, M. Kampshoff, M. Klasen, J. G. Milhano, C. Royon, A. Sabio Vera	Phys.Rev.D 110 (2024) 11, 114027	2024-11-23	https://doi.org/10.1103/PhysRevD.110.114027
1.	Systematic Study on the Quality of Flux-grown Al2O3 Single Crystals for Dosimetry Applications	Rodrigues, C., Saraiva, J. G. M., Gonçalves, A. P., Peralta L	SSS160_107835	2024-12-10	10.1016/j.solidstatesciences.2025.107835
1.	Utility of realistic microscopy-based cell models in simulation studies of nanoparticle-enhanced photon radiotherapy	Joana Antunes, Catarina I G Pinto, Maria Paula Cabral Campello, Pedro Santos, Filipa Mendes, António Paulo and Jorge M Sampaio	Biomedical Physics & Engineering Express 10 (2024): 025015	2024-01-18	10.1088/2057-1976/ad2020
1.	Development of a plastic scintillating optical fibers array dosimeter for radiobiology	D.R. Guerreiro ,J.G. Saraiva , M.J. Borges, J.M. Sampaio and L. Peralta	J. Inst. 19 P05006	2024-03-25	10.1088/1748-0221/19/05/P05006
1.	A primary simulation study of scintillating fibre dosimetry for a proton minibeam	D.R. Guerreiro, B.C. Alves, C. Rodrigues, J.G. Saraiva, L. Peralta, J.M. Sampaio	Radiation Physics and Chemistry Volume 224  (2024), 112102		10.1016/j.radphyschem.2024.112102
1.	Novel Bragg peak characterization method using proton flux measurements on plastic scintillators	D R Guerreiro, J G Saraiva, L Peralta, C Rodrigues, M Rovituso, E van der Wal, Dennis R Schaart, P Crespo, H Simões and J M Sampaio	Phys. Med. Biol. 69 (2024) 225005		https://doi.org/10.1088/1361-6560/ad8da0
1.	Developing competencies through flow, gamification and cultural integration: an analysis of the potential of games in teaching/learning	L. Lopes, S. Schreurs, C. Licour, S. Soares	Radiat. Eff. Defects Solids 179 (2024) 3-13	2024-01-02	10.1080/10420150.2024.2318700
1.	Thickness and Uniformity of Commercial Aluminum Foils	L. Peralta, A. I. Campos and M. S. Rodrigues	Journal of Materials Engineering and Performance	2024-12-22	https://doi.org/10.1007/s11665-025-10722-8
1.	New readout scheme for large area timing & position RPCs	Joao Saraiva, Alberto Blanco	Nucl. Instrum. Methods Phys. Res. Sect. A-Accel. Spectrom. Dect. Assoc. Equip. 1068 (2024) 169803	2024-11-01	10.1016/j.nima.2024.169803
1.	SND@LHC: The Scattering and Neutrino Detector at the LHC	SND@LHC Collaboration (202 authors)	JINST 19 (2024) P05067	2024-05-23	10.1088/1748-0221/19/05/P05067
1.	Results and Perspectives from the First Two Years of Neutrino Physics at the LHC by the SND@LHC Experiment	SND@LHC Collaboration	Symmetry 16 (2024) 6, 702	2024-06-06	
1.	Observation of collider neutrinos without final state muons with the SND@LHC experiment	SND@LHC Collaboration	CERN-EP-2024-316	2024-11-25	
1.	Differentiable Vertex Fitting for Jet Flavour Tagging	Rachel E. C. Smith, Inês Ochoa, Rúben Inácio, Jonathan Shoemaker, Michael Kagan	PHYSICAL REVIEW D 110, 052010 (2024)		10.1103/PhysRevD.110.052010
1.	Spatial Analysis of Determinants of COVID-19 Vaccine Hesitancy in Portugal	Constança Pinto de Carvalho, Manuel Ribeiro, Diogo Godinho Simões, Patrícia Pita Ferreira, Leonardo Azevedo, Joana Gonçalves-Sá, Sara Mesquita, Licínio Gonçalves, Pedro Pinto Leite, André Peralta-Santos	Vaccines 2024, 12(2), 119		10.3390/vaccines12020119
1.	Correction to: Fundamental parameters for 45 open clusters with Gaia DR2, an improved extinction correction and a metallicity gradient prior	H Monteiro, W S Dias, A Moitinho, T Cantat-Gaudin, J R D Lépine, G Carraro, E Paunzen	Monthly Notices of the Royal Astronomical Society, Volume 528, Issue 4, March 2024, Page 6129		https://doi.org/10.1093/mnras/stae363
1.	Gaia Focused Product Release: A catalogue of sources around quasars to search for strongly lensed quasars	Andre Moitinho et al.		2023-10-09	https://doi.org/10.1051/0004-6361/202347273
1.	Discovery of a dormant 33 solar-mass black hole in pre-release Gaia astrometry	Andre Moitinho et al.	A&A, 686, L2 (2024)	2024-03-30	https://doi.org/10.1051/0004-6361/202449763
1.	Programmable Optical Synaptic Linking of Neuromorphic Photonic-Electronic RTD Spiking Circuits	Matěj Hejda, Weikang Zhang, Qusay Raghib Ali Al-Taai, Ekaterina Malysheva, Dafydd Owen-Newns, José M. L. Figueiredo, Bruno Romeira, Joshua Robertson, Victor Dolores-Calzadilla, Edward Wasige, Antonio Hurtado	ACS Photonics 2024, 11, 4279−4287	2024-09-18	https://doi.org/10.1021/acsphotonics.4c01199
1.	ELEPHANT: ExtragaLactic alErt Pipeline for Hostless AstroNomical Transients	A. Moitinho et al.		2024-09-09	https://doi.org/10.1051/0004-6361/202450535
1.	Photonic-electronic spiking neuron with multi-modal and multiwavelength excitatory and inhibitory operation for high-speed neuromorphic sensing and computing	Weikang Zhang, Matěj Hejda, Qusay Raghib Ali Al-Taai, Dafydd Owen-Newns , Bruno Romeira , José M. L. Figueiredo , Joshua Robertson, Edward Wasige, Antonio Hurtado	Neuromorph. Comput. Eng. 4 044006	2024-11-01	DOI 10.1088/2634-4386/ad8df8
1.	Spiking flip-flop memory in Resonant Tunnelling Diode neurons	Giovanni Donati, Dafydd Owen-Newns, Joshua Robertson, Ekaterina Malysheva, Andrew Adair, José Figueiredo, Bruno Romeira, Victor Dolores-Calzadilla, Antonio Hurtado	PHYSICAL REVIEW LETTERS 133, 267301 (2024)	2024-11-18	10.1103/PhysRevLett.133.267301
1.	A Large Jet Narrow-line Seyfert 1 Galaxy: Observations from Parsec to 100 kpc Scales	Sina Chen, Preeti Kharb, Silpa Sasikumar, Sumana Nandi, Marco Berton, Emilia Järvelä, Ari Laor, Ehud Behar, Luigi Foschini, Amelia Vietri, Minfeng Gu, Giovanni La Mura, Luca Crepaldi, and Minhua Zhou	Astrophysical Journal, Volume 963, Number 1		10.3847/1538-4357/ad182a
1.	Potential of water-Cherenkov air shower arrays for detecting transient sources of high-energy astrophysical neutrinos	J. Alvarez-Muñiz, R. Conceição, P. J. Costa, B. S. González, M. Pimenta, and B. Tomé	Phys. Rev. D 110, 023032	2024-06-13	10.1103/PhysRevD.110.023032
1.	High resolution gamma/hadron and composition discriminant variable for water-Cherenkov detector cosmic-ray observatories	Ruben Conceição, Pedro J. Costa, Lucio Gibilisco, Mário Pimenta and Bernardo Tomé	Phys. Rev. D 110, 023033	2024-06-24	https://doi.org/10.1103/PhysRevD.110.023033
1. Oliveira, F.S.B.F., A.B. Fortunato, P. Freire (2024). Beach Nourishment Protection against Storms for Contrasting Backshore Typologies, Journal of Marine Science and Engineering, 12/9: 1465. 
1. Muralha, A.; Melo, J.F.; Ramos, H.M. Validation of Computational Methods for Free-Water Jet Diffusion and Pressure Dynamics in a Plunge Pool. Appl. Sci. 2025, 15, 1963. https://doi.org/10.3390/app15041963
1. Muralha, A.; Melo, J.F.; Ramos, H.M. Numerical simulation of a plunging jet. Performance comparison between volume-of fluid and two-phase Euler solvers, Proceedings of the 8th IAHR Europe Congress "Water across boundaries", Lisboa, Portugal, 4 - 7 junho.
1. Garzon, J.L.; Ferreira, Ó.; Plomaritis, T.A.; A.C. Zózimo, A.C.; Fortes, C.J.E.M.; Pinheiro, L.V. (2024). "Development of a Bayesian network-based early warning system for storm-driven coastal erosion", in Coastal Engineering, Vol. 189 (2024), 104460, ISSN 0378-3839, https://doi.org/10.1016/j.coastaleng.2024.104460
1. Pinheiro, L.V.; Zózimo, A.C.; Fortes, C.J.E.M. (2024). "New developments in the Praia da Vitória Coastal Bay and Harbor Early Warning System", in Coastal and Offshore Science and Engineering, Year II - Vol.4 - 2023, pp. 6-18, DOI: 10.53256/COSE_230201.

## Oral Presentations
1. LFcin Refinery: A machine learning approach to improve antimicrobial peptides’ efficacy against
nontuberculous mycobacteria Gabriel S. Oliveira, Maria Salomé Gomes, Sérgio F. Sousa, Tânia Silva - IMAP 2024 11th International Meeting on Antimicrobial Peptides 2024/09/02-04 (London, United Kingdom)
1- Tackling biofilm formation using an in silico approach Tatiana F. Vieira - LAQV Webinar
2024/04/17 (Porto, Portugal) (online)
1. Exploring pH-dependent Dynamics Of Doxorubicin Delivery Using Functionalized Multi-walled Carbon
Nanotubes: Insights From Molecular Dynamics Simulations Fábio G. Martins, Sérgio F. Sousa – Biophysics Festival - 4th Meeting of Young Biophysics 9-10.05.2024 (Covilhã, Portugal)
1. Development of a Computational Protocol for the Rational Design of Nanomedicines Aimed at Cardiovascular Diseases Fábio G. Martins, Sérgio F. Sousa – XXII National Congress of Biochemistry 24-26.10.2024 (Aveiro, Portugal)
1. Use of HPC Computing for Accelerating Drug Discovery Targeting the SARS-CoV-2 S-RDB/ACE2 Interaction
Fábio G. Martins, Sérgio F. Sousa IBERGRID 2024 – 28-30.10.2024 (Porto, Portugal)
1. A Computational Strategy for the Design of Targeted Nanomedicines in Cardiovascular Diseases
Fábio G. Martins, Sérgio F. Sousa – XXVIII Encontro Galego-Português de Química 13-15.11.2024 (Vigo, Spain)
1. Molecular Insights into HIV-1 Integration: A Computational Study of Intasome-Nucleosome Interactions
Fábio G. Martins, Sérgio F. Sousa – LAQV WEBINAR 21.05.2025 (Online)
1. Development and Application of a Multi-Level Computational and In Vitro Approach for Identifying MAPK3
Inhibitors in Leishmania martiniquensis and Leishmania orientalis – Duangnapa Kiriwan, Tatiana F. Vieira,
Nutnaree Kumsiri, Kiattawee Choowongkomon, Sergio F. Sousa - BIOPHYSICS FESTIVAL – 4 th Meeting of Young
Biophysicists - 9-10.05.2024
1. Tripeptide-Based Inhibition of EGFR Tyrosine Kinase in Lung Cancer: Findings from Computational and
Experimental Studies - Duangnapa Kiriwan, Supaphorn Seetaha, Nattanan Jiwacharoenchai, Lueacha Tabtimmai,
Napat Songtawee, Kiattawee Choowongkomon, Sérgio F. Sousa - XXII SPB National Congress of Biochemistry - 24- 26.10.2024 
1. From plants to anti-snakebite mechanisms. Airam Roggero, Isabelly Annunciato, Fabio G. Martins, Igor Nicodemo, Marcos H.Toyama, Sergio F. Sousa. 6th Meeting on Medicinal Biotechnology 2024
1. Effects of Morin on Cell Membrane Fluidity: An Analysis of the Anti-inflammatory Efficacy of Flavonoids. Airam Roggero, Caroline Ramos da Cruz, Marcos H. Toyama, Sergio F. Sousa. - XXIX National Meeting of the Portuguese Chemical Society, Coimbra, Portugal, 2025.
1. Enzyme Modulation and Inflammation: A New Therapeutic Target. Airam Roggero, Marcos H. Toyama, Sergio F. Sousa - 7th Symposium on Medicinal Chemistry of University of Minho, Braga, Portugal, 2025.
1. Aspartame and Inflammation: An In Silico Evaluation of Interference in the Land’s Cycle and Cell Membrane Integrity. Isabelly Annunciato; Michelle Rafael; Igor Nicodemo; Airam Roggero; Caroline R. da Cruz; Mariana N. Belchor; Adeilso B. S. Junior; Gustavo A. Fernandes; Marcos A. de Oliveira; Sérgio F. Sousa; Marcos Hikari Toyama – XXVII Encontro Luso Galego de Química 22/11/2023 to 24/11/ 2023 (Porto, Portugal)
1. Use of HPC Resources to Find New Drugs Against Biofilm Formation Tatiana F. Vieira, Sérgio F. Sousa - IBERGRID 2024 2024/10/28-30 (Porto, Portugal)
1. Engineering aptamers for Biomedical Application using Biomolecular Simulations Sérgio F. Sousa - 26th Congress of the International Union of Biochemistry and Molecular Biology (IUBMB) 2024/09/25 (Melbourne, Australia)
1. Development of Computational Methods For Aptamer Engineering For Targeted-Drug Delivery Sérgio F. Sousa - XXVIII EFMC International Symposium on Medicinal Chemistry 2024/09/03 (Rome, Italy) (Flash talk/poster)
1. Application of QM/MM Methods in Enzyme Bioengineering Efforts: Understanding PET Degrading Activity of
PETases Sérgio F. Sousa - XLVII International Congress of Theoretical Chemists of Latin Expression (Chitel2024) 2024/07/03 (Namur, Belgium)
1. Application of QM/MM Methods in the Study of the Enzyme Efficiency by PET Degrading Enzymes
Sérgio F. Sousa - ESPA2024 Meeting (Electronic Structure Principles and Applications Conference)
2024/06/06 (Tarragona, Spain)
1. Probing the Role Played by Different Amino Acid Residues in the Catalytic Mechanism of Plastic PET
Degrading Enzymes by QM/MM Methods Sérgio F. Sousa - International Society of Quantum Biology and Pharmacology (ISQBP) 2024 President’s Meeting 2024/05/21 (Athens, Greece)
1. Towards One Health: Combining Biomolecular Simulations, Artificial Intelligence and Scientific Databases Sérgio F. Sousa - 1-day Course for the PhD Program in Integrated Health (One Health) at FMUP (Invited Lecture) 2024/11/15 – (Porto, Portugal)
1. Development of Multi-Level Biomolecular Simulation Protocols for Aptamer Engineering for Biomedical
Applications Sérgio F. Sousa - 13th Iberian Grid Conference – IBERGRID 2024 (Plenary Lecture) 2024/10/30 – (Porto, Portugal)
1. Application of QM/MM Methods in Enzyme Bioengineering Efforts: Understanding PET Degrading Activity of
PETases Sérgio F. Sousa - International Symposium on Future in Enzyme Modeling (FEM2024) (Invited lecture) 2024/10/25 – (Tianjin, China)
1. Combining Biomolecular Simulations with Medicinal Chemistry: Expanding Horizons Sérgio F. Sousa - Global Health Horizons: Empowering Pharmacists Through Research and Development Conference - World Pharmacists Day 2024 - Indira Gandhi National Tribal University (Plenary Lecture) 2024/09/24 – (Amarkantak, Madhya Pradesh, India) (online)
1. Combining Different In Silico Methods for Drug Design and Development: Challenges and Opportunities
Sérgio F. Sousa - Virus-Host-AI Meeting (Invited Lecture) 2024/07/29 – (Figueira da Foz, Portugal)
1. Multiscale Modelling of DNA/RNA Aptamers for Molecular Recognition Sérgio F. Sousa - XLVIII International Congress of Theoretical Chemists of Latin Expression (Chitel2025) 2025/07/17 (Cartagena-das-Indias, Colombia)
1. Exploring the interaction between nitrosamines with PAF-AH enzyme: in silico prospection for new therapeutic strategies Isabelly Annunciato - International Conference on Integrative Bioinformatics and Computer Systems Biology (ICIBCSB - 23) - 05/10/2023 - (Milan, Italy)
1. Understanding the mechanism of action of multi-target anti-diabetic natural compounds using Virtual
Screening Carlos S. H. Shiraishi; Fábio G. Martins, Sérgio F. Sousa, Miguel A. Prieto, Sandrina A. Heleno and Rui M. V. Abreu. Academy Branch of the Conference,4th Insure Hub Conference “Innovation, Sustainability and Regeneration, October 29-30, 2024, in Porto.
1. Madeira C (presenter), Lohmann D, Kirner A, Gaspar J, Bornhäuser J, Martins C, D’Ambrosio M, António C, Maricato R, Araújo E, Rodrigues AM, Costa PM, Diniz MS (2025). Climate change in the Eastern Tropical Pacific: Adaptive responses of the commercial fish spotted rose snapper – Implications for Conservation. Global Coral Reef Monitoring Network Meeting – Eastern Tropical Pacific Node, 15-04-2025, online.
1. Madeira C (presenter), Missionário M, Cabral IM, Fernandes JF, António C, Rodrigues AM, D’Ambrosio M, Menconça V, Grosso AR, Costa PM, Madeira D (2024). Iberian goby populations from colder sites display low phenotypic variation despite high molecular plasticity in response to heat. SEB Society for Experimental Biology Congress, 2nd-5th July, Prague, Czech Republic.
1. Madeira C, Costa PM (2024) Marine molecular networks for a healthy ocean and a sustainable blue economy. Scientific Conference Series, Institute Maurice Lamontagne – Department of Fisheries and Oceans Canada, 16-05-2024, Mont-Joli, Québec, Canada. Invited by Dr. Kathleen McGregor.
1. Madeira C, António C, Rodrigues AM, Lohmann D, Martins C, Kirner A, Bornhäuser J, Gaspar J, D’Ambrosio M, Estcourt T, Schwerdt S, von Hammerstein H, Vince J, Calvo-Elizondo E, Esquivel E, Chacon-Guzman J, Diaz-Pulido G, Doo S, Clarke T, di Falco C, Bejarano S, Costa PM, Diniz MS (2024) Tropical fish on the move: climate change impacts in species physiology and potential biodiversity redistributions. University of Québec at Rimouski, 08-05-2024, Rimouski, Québec, Canada. Invited by Prof. Piero Calosi.
1. Madeira C, Costa PM, Madeira D, Vinagre C (2024) From molecules to ecosystems: thermal biology of marine fish, Reef Systems WG Workshop EU-Colombia, Leibniz Centre for Tropical Marine Research, 25-01-2024, Bremen, Germany. Invited by Dr. Sonia Bejarano.
1. Madeira C, Costa PM, Madeira D, Vinagre C (2024) Multilayer networks in benthic fish responses to environmental stressors in intertidal environments, AG Voolstra Lab Networking Seminar, Department of Biology, Universität Konstanz, 18-01-2024, Konstanz, Germany. Invited by Prof. Christian Voolstra.
1. Madeira C, Costa PM, Madeira D, Vinagre C (2024) Molecular networks in small benthic fish adaptation to labile environments, Institute of Evolution and Ecology Seminars, Faculty of Science, University of Tübingen, 17-01-2024, Tübingen, Germany. Invited by Prof. Nico Michiels.
1. Madeira C, Costa PM, Madeira D, Vinagre C (2024) Stress response mechanisms of small benthic fish in fluctuating environments, Institute of Marine Ecosystem and Fishery Science Seminars, Universität Hamburg, Faculty of Mathematics, Informatics and Natural Science, 15-01-2024, Hamburg, Germany. Invited by Prof. Flemming Dahlke.
1. Missionário M (presenter), Madeira D, Vinagre C, Costa PM, Madeira C (2022). Marine shallow waters as climate change hotspots – multi-omics approaches unravel fish response patterns across latitudes, seasons and climate scenarios. BioSeminars@UCIBIO. UCIBIO-NOVA & UCIBIO-Porto, 21-12-2022, Online.
1. Cabral IM (presenter), Costa PM, Grosso AR, Madeira C (2023) A transcriptomic approach to unravel molecular mechanisms contributing to heat acclimatization of a non-conventional model marine organism. InSilicoClub@UCIBIO, UCIBIO-NOVA & UCIBIO-Porto, 26-03-2023, Online.
1. E. Faustino, S.L. Mendes, J. Carvalho, C. Sousa-Santos; V.C. Sousa. Hybridization between currently allopatric species at the root of speciation? The case of Iberian chubs (Genus Squalius) XX ENBE Annual Meeting of the Portuguese Association for Evolutionary Biology in BIOPOLIS – CIBIO, Research Centre in Biodiversity and Genetic Resources, Vila do Conde, Portugal. 19-20 December 2024.
1. A. Blanckaert, V.C. Sousa. Interactions between mechanisms of reproductive isolation, 3rd Joint Congress of Evolutionary Biology, Montreal, Canada. 30th July 2024. 
1. S.L. Mendes, E. Faustino, C. Bernardo, S. Perea, I. Doadrio, C. Sousa-Santos, P.G. Feulner, V.C. Sousa. “Hybridization is prevalent but outcomes are distinct across Iberian chubs”. 3rd Joint Congress on Evolutionary Biology. Montreal, Canada. 30th July 2024
1. "The octocoral microbiome: exploring pathogens, probiotics and climate change impacts" at Biological Sciences Research Group, Instituto Superior Técnico, University of Lisbon, Portugal
1. Institute Seminar entitled "Designing probiotics to promote octocoral health under climate change" at Department of Bioengineering, Instituto Superior Técnico, University of Lisbon, Portugal
1. Martins,R; Fortunato, A B; Oliveira, A, Jesus, G; Mani, S; Meyers, E; Moghimi, S (2024). OPENMeshS: an online, open, unstructured mesh generator for OPENCoastS, 8th IAHR Congress Full papers, 177-182. DOI: 10.34638/3zcb-9082
1. Fortunato, A B; Freire, P; Ana, R; Viseu, T; Rodrigues, M (2024). Mapping inundation of estuarine margins driven by ocean and fluvial forcings, 8th IAHR Congress Full papers, 229-235. DOI: 10.34638/3zcb-9082
1. Rodrigues, M; Fortunato, A B; Martins, R J; Jesus, G; Brito, A C; Oliveira, A; Nahon, A; Costa, J L.; Alves, E; Korani, Z M; Azevedo, A (2024). CONNECT – Local coastal monitoring service for Portugal, 8th IAHR Congress Full papers, 237-246. DOI: 10.34638/3zcb-9082 
1. SASSETTI MENDES, L.; MURALHA, A.; MELO, J.F.; VISEU, T. (2024). _Why Computational Fluid Dynamics is Mandatory in Physical Modelling Of Large Hydraulic Structures_: A Six-Step Methodology Of Integration. 8th IAHR Europe Congress. LNEC, Lisboa, 4 a 7 de Junho de 2024.
1. SASSETTI MENDES, L., ALVES, E. (2024). _Volume-Of-Fluid vs Euler-Euler - CFD Of Pisão Dam’s Stilling Basin_. 6th Foam@Iberia. Ferrol, Espanha. 3 a 4 de outubro de 2024. 
## Proceeding in international conferences
1. Arias, D., Gadelho, J. and Guedes Soares, C., 2024. Numerical simulations evaluating the influence of different geometric features in the pneumatic efficiency of OWC devices. In Innovations in Renewable Energies Offshore (pp. 249-256). CRC Press. DOI: 10.1201/9781003558859-28
1. Li, H.S., Wang, S. and Guedes Soares, C., 2024. Uncertainty assessment of the scale effects on a submerged cylinder. In Advances in Maritime Technology and Engineering (pp. 139-148). CRC Press. DOI: 10.1201/9781003508779-15 
1. Fortes, C.J.E.M.; Pinheiro, L.V.; Zózimo, A.C.; Lima, L.; Serrazina, V. (2024). "HIDRALERTA: Emergency Response Module for Coastal Wave Overtopping and Flooding at Praia da Vitória bay", in proceedings of the 8th IAHR Congress, LNEC, Lisbon, 4-7 June, 2p.
1. Garzon, J.L.; Ferreira, Ó.; Zózimo, A.C.; Fortes, C.J.E.M.; Pinheiro, L.V., (2024). "Development of an efficient early warning system for wave-induced flooding", 38th ICCE, Rome, 8-14 September, 2p, comunicação feita, a aguardar publicação das atas (versão digital obtida através da Conftool do congresso).
1. Zózimo, A.C.; Pinheiro, L.V.; Chenneveau, L.; Manz, A.; Garzon, J.L.; Fortes, C. (2024). "Deep learning framework to use complex models in operational forecast systems", 38th ICCE, Rome, 8-14 September, 2p, comunicação feita, a aguardar publicação das atas (versão digital obtida através da Conftool do congresso).

## Posters (internation meetings)
1. Galamba, N. Cyclic Peptides as Protein Aggregation Inhibitors for Globular and Intrinsically Disordered Disease-Related Proteins, The Leuven Protein Aggregation Meeting (2nd edition), September 11-13, 2024, Leuven, Belgium – poster
1. Jéssica Rodrigues; Carlos Costa; Carolina Mota Natal; Ana Margarida Gonçalves Carvalho Dias; Roque, ACA; Moura Barbosa, Arménio J.. Autor correspondente: Moura Barbosa, Arménio J.. "Molecular Modeling in Biotechnology: Design and Discovery of small molecule adsorbents". Trabalho apresentado em EuroQSAR 2024, 2024. 
1. Jéssica Rodrigues; Carlos Costa; Carolina Mota Natal; Ana Margarida Dias; Roque, ACA; Moura Barbosa, Arménio J.. Autor correspondente: Moura Barbosa, Arménio J.. "In silico Affinity Ligands: Design and Discovery of small molecule adsorbents". Trabalho apresentado em Bpi Europe 2024, 2024.
1. Moura Barbosa, Arménio J.; Soares, Cátia Lopes; Esteves, Carina; Nurrito, Ariana; Lychko, Iana; Ana Margarida Dias; Pina, Ana Sofia; Roque, Ana Cecília Afonso. "From code to structure: molecular modeling in biomaterials assembly". Trabalho apresentado em SUPRAlife Second School – “Bioinspired Supramolecular Self-Assemblies, 2024.  
1. Using QSAR models to refine antimicrobial peptides against Mycobacterium abscessus Gabriel S. Oliveira, Maria Salomé Gomes, Sérgio F. Sousa, Tânia Silva - ESCMID Global 2025 2025/04/11-15 (Wien, Austria)
1. Metodologia in silico para identificação de novos compostos para inibição da formação de biofilme em P. aeruginosa Tatiana F. Vieira, Manuel Simões, Nuno M. F. S. A. Cerqueira, Sérgio F. Sousa – Ciência 2024: Encontro com a Ciência e Tecnologia em Portugal, Porto 2024/07/3-5 (Porto, Portugal)
1. Molecular Dynamics Simulations of Lysinated Multiwalled Carbon Nanotubes for Enhanced Delivery of
Doxorubicin in Cancer Therapy Fábio G. Martins; Sérgio F. Sousa – 6th Meeting on Medicinal Biotechnology
17.05.2024 (Porto, Portugal)
1. Optimizing Doxorubicin Delivery in Cancer Treatment with Lysinated Multiwalled Carbon Nanotubes: A
Molecular Dynamics Study Fábio G. Martins, Sérgio F. Sousa – Encontro Ciência 2024 03.07.2024 (Porto, Portugal)
1. Modeling HIV-1 Intasome-Nucleosome Interactions: A Molecular Perspective Fábio G. Martins, Sérgio F. Sousa – 7th Meeting on Medicinal Biotechnology 30.05.2025 (Porto, Portugal)
1. Multi-level Computational and In Vitro Approach for Identifying MAPK3 Inhibitors in Leishmania martiniquensis and Leishmania orientalis (E-poster) - Duangnapa Kiriwan, Tatiana F. Vieira, Nutnaree Kumsiri, Kiattawee Choowongkomon, Sergio F. Sousa – Portuguese Science Summit 2024 – 03-05.07.2024
1. Computational Identification of Dual Protein Targets for Anti-leishmanial Drug Development - Duangnapa Kiriwan, Sergio F. Sousa – 7th Meeting on Medicinal Biotechnology - 30.05.2025 (Porto, Portugal)
1. Creation of a 3D-Molecular Database of Voltage-Gate Sodium Channels - João Boazinha, João Carneiro, Nuno M.F.S.A Cerqueira, Sérgio F. Sousa - 6th Meeting on Medicinal Biotechnology 2024/05/17 (Porto,  Portugal)
1. Development of a 3D-Molecular Database of Voltage-Gate Sodium Channels (E-Poster) - João Boazinha, João Carneiro, Nuno M.F.S.A Cerqueira, Sérgio F. Sousa - Encontro Ciência 2024 2024/07/03 to 2024/07/05 (Porto, Portugal)
1. Influence of Nonsteroidal Anti-inflammatory Drugs on Membrane Repair. Airam Roggero, Igor Nicodemo, Fabio G. Martins, Marcos H. Toyama, Sergio F. Sousa.. Encontro Ciência 2024. Porto, Portugal 2024.
1. Impact of NSAIDs on the Enzymatic Alteration of the Lands Cycle and Their Long-Term Hepatic Effects - Aiam Roggero, Fabio G. Martins, Marcos H. Toyama, Sergio F. Sousa..3ª edição do Congresso de Ciências. Faculdade de Ciências da Universidade do Porto, Porto, Portugal 2024.
1. From Sustainability Until Green Engineering A Puzzle to Classes - Airam Roggero; Pedro H. S. Fernandes; Marcos H.Toyama; Sergio F. Sousa.. XXII National Congress of Biochemistry. University of Aveiro, Aveiro, Portugal 2024.
1. Exploring The Sites of Interaction Of Non-Steroidal Antiinflammatory Drugs With Enzymes In The Landis Cycle. Biophysics Festival - Airam Roggero, Isabelly Annunciato, Igor Nicodemo, Fabio G. Martins, Marcos Hikari Toyama, Sergio F. Sousa. – 4th Meeting of Young Biophysicists. Faculty of Sciences of University of Beira Interior, Covilhã, Portugal
1. NSAIDs from antiinflammatory to PAF AH potential inhibitor, far beyond inhibition of COX to potential anti- tumor agent - Roggero , I. Annunciato, I. Nicodemo, C.R. Costa, G.A. Fernandes, A.B. Junior, M. Rafae, M.A. de Oliveira, S.F. Sousa, M.H. Toyama..48th FEBS Congress, Milan, Italy, 2024.
1. Gallic Acid as a Supportive Agent in the Immunotherapy of Cancer. Airam Roggero, Caroline Ramos da Cruz, Igor Nicodemo, Pedro Loyola, Marcos H. Toyama, Sergio F. Sousa. - 7th Meeting on Medicinal Biotechnology & 3rd Iberian Congress on Medicinal Biotechnology. Escola Superior de Saúde, Porto, Portugal, 2025.
1. Lands cycle is a new therapeutic target for antitumor drugs. Airam Roggero, Igor Nicodemo, Pedro Loyola, Carol R. Cruz, Marcos H. Toyama, Sergio F. Sousa - Encontro Ciência 2025. Lisboa, Portugal, 2025.
1. Activating Factor Regulation: A Computational Prospection for Therapeutic Insights - . Annunciato, I. ; Toyama, Marcos Hikari ; Santos Junior, A. B. ; Roggero, A. ; Cruz. C, R, C. ; Sousa, S. F. ; Oliveira, M. A. ; Rafael, M. ; Nicodemo, I. ; Fernandes, Gustavo Antônio . Exploring Nitrosamines' Impact on Patelet. - Brazilian Society of Biochemistry and Molecular Biology (SBBq), 2024, Águas de Lindóia. 53rd Annual Meeting of the Brazilian Society of Biochemistry and Molecular Biology (SBBq), 2024.
1. NSAIDs from anti-inflammatory to PAF AH potential inhibitor, far beyond inhibition of COX to potential anti- tumor agent. Roggero, A., Annunciato, I., Nicodemo, I., Costa, C.R.C., Junior, A.B.S., Rafael, M., Oliveira, M.A., Souza, S.F., Toyama M.H.1, Toyama, M.Η.. Brazilian Society of Biochemistry and Molecular Biology (SBBq), 2024, Águas de Lindóia. 53rd Annual Meeting of the Brazilian Society of Biochemistry and Molecular Biology (SBBq), 2024.
1. Development of Combined Multi-scaled In Silico Tools For Aptamer Design Sérgio F. Sousa - 15th European Biophysics Congress (EBSA2025) 2025/07/03 (Rome, Italy)
1. Computational Chemistry Driven Development of DNA/RNA Aptamers Sérgio F. Sousa - 49th FEBS Congress (FEBS2025) 2025/07/06 (Istanbul, Turkey)
1. Innovative method to identify plants with antidiabetic ingredients using high performance computing
Carlos S. H. Shiraishi; Fábio A. Martins ; Sérgio F. Sousa ; Miguel Prieto Sandrina Heleno and Rui Abreu. International Conference on Sutainable Foods - Achieving the Sustainable Development Goals (ICSF), School of Technology and Management (ESTiG) of the Polytechnic Institute of Bragança on July 24th and 25th of 2024.
1. Triagem Virtual de Potenciais Inibidores Naturais Antidiabético do Cotransportador de Glicose de Sódio Tipo 2 (SGLT2) Carlos S. H. Shiraishi; Fábio A. Martins ; Sérgio F. Sousa ; Miguel Prieto
Sandrina Heleno and Rui Abreu. IPO Porto Summit held on May 9-11, 2024 at the Portuguese Oncology Institute of Porto.
1. Identification of dual-target antidiabetic mushrooms natural compounds using virtual screening
Carlos S. H. Shiraishi; Fábio A. Martins ; Sérgio F. Sousa ; Miguel Prieto Sandrina Heleno and Rui Abreu. 2nd Conference of the Doctoral Program in Metabolism – Clinical and Experimental, within the topic of “METAINFLAMMATION: A HOT TOPIC IN METABOLIC DYSFUNCTION”, held at the Faculty of Medicine of the
University of Porto, Portugal on the 25th of October 2024.
1. An In silico prospection for new therapeutic strategies: the impact of nitrosamines in PAF regulation
Isabelly Annunciato; Igor Nicodemo; Michelle Rafael; Airam Roggero; Caroline C. Ramos; Mariana N. Belchor; Adeilso B. S. Júnior; Gustavo A. Fernandes; Marcos A. Oliveira; Sérgio F. Sousa; Marcos H. Toyama – 3D-Bioinfo-PT Annual Meeting – Faculdade de Ciências e Tecnologia da Universidade de Coimbra – 18.12.2023
1. C5 Genetic Variants Affect the Stability of the C5-Eculizumab Complex Vanda P. Peixoto, Cristina Prudêncio, Mónica Vieira, Sérgio F. Sousa – 7th Meeting on Medicinal Biotechnology & 3rd
Iberian Congress on Medicinal Biotechnology 30.05.2025 (Porto, Portugal)
1. KDM4C epigenetic therapy for triple-negative breast cancer Sofia M. Sousa; Fernanda Proença; Marta Costa; Sérgio F. Sousa - Encontro Ciência 2024 - Science and Technology Summit 2024/07/3-5 (Porto, Portugal)
1. Design of new epigenetic inhibitors for the treatment of triple negative breast cancer Sofia M. Sousa; Fernanda Proença; Marta Costa; Sérgio F. Sousa - 6th Meeting of Medicinal Biotechnology
2024/05/17 (Porto, Portugal)
1. Therapeutic epigenetic KDM4C remodeling for the treatment of triple negative breast cancer
Sofia M. Sousa; Fernanda Proença; Marta Costa; Sérgio F. Sousa - 30th Porto Cancer Meeting
2024/05/9-10 (Porto, Portugal)
1. Ferri, A., Moutinho Cabral, I., Sabia, C., Iseppi, R., Costa, P.M., Simonini, R. (2024) "Unveiling the biotechnological potential of marine polychaete Halla parthenopeia: Insights into hallachrome antimicrobial properties and toxin identification". 57th European Marine Biology Symposium.
1. Madeira, C., António, C., Rodrigues, A.M., Lohmann, D., Martins, C.A., Kirner, A., Bornhäuser J., et al. (2024) "Marine molecular networks underpinning stress tolerance to warming and acidification in the spotted rose snapper Lutjanus guttatus from the Eastern Tropical Pacific". Society for Experimental Biology Congress.
1. Madeira C, António C, Rodrigues AM, Lohmann D, Martins C, Kirner A, Bornhäuser J, Estcourt T, Schwerdt S, von Hammerstein H, Vince J, Calvo E, Esquivel E, Chacon-Guzman J, Diaz-Pulido G, Doo S, Diniz MS, Costa PM, Bejarano S (2024) Marine molecular networks underpinning stress tolerance to warming and acidification in the spotted rose snapper Lutjanus guttatus from the Eastern Tropical Pacific. Society for Experimental Biology (SEB) Congress, 2nd-5th July, Prague, Czech Republic.
## Posters (national meetings)

## Thesis / Dissertation

### PhD Thesis

#### Finished
Innovative approach to fight tuberculosis and malaria targeting the extraordinary PLP synthase
macromolecular complex Student: André Pina (Supervisor Principal: Nuno Cerqueira; Co-Supervisor: Sérgio Sousa) Doutoramento: Programa Doutoral em Biomedicina (PhD) Universidade do Porto Faculdade de Medicina, Portugal Janeiro de 2024
1. Development of biocidal formulations for effective biofouling control Student: Susana Maria da Fonseca Fernandes (Supervisor Principal: Manuel Simões; Outros Supervisores: Sérgio Sousa e Fernanda Borges ) Doutoramento: Programa Doutoral em Engenharia Química e Biológica (PhD) Universidade do Porto Faculdade de Engenharia, Portugal Fevereiro de 2024
1. Paroxysmal Nocturnal Hemoglobinuria: Unraveling Epidemiological Patterns, Molecular Mechanisms, And
Biotechnological Advances Student: Vanda Patrícia Pinto Peixoto (Supervisor Principal: Mónica Vieira, ESS; Co-supervisor: Sérgio F. Sousa) Doutoramento: PhD Program in Advanced Biotechnology (PhD) Universidade de Vigo, Spain Junho 2024
1. New Drugs Against Biofilm Formation and Development: a Computational and Experimental Approach
Student: Cláudia Tatiana Vieira (Supervisor Principal: Sérgio F. Sousa; Outros Supervisores: Manuel Simões e Sérgio F. Sousa ) Doutoramento: Programa Doutoral em Biomedicina (PhD) Universidade do Porto Faculdade de Medicina, Portugal Julho de 2024

#### Ongoing
1. Sofia Mendes, Biology PhD programme, Host: CE3C-Ciências (12.2019-07.2025) Co-supervisors: Dr. Carla Sousa-Santos (ISPA), Dr. Philine Feulner (EAWAG). Thesis: The role of hybridization in speciation and adaptation: insights from Iberian freshwater fish species. Funding: FCT scholarship SFRH/BD/145153/2019 to SM.
1. João Carvalho, BIODIV PhD programme, Host: CE3C-Ciências (03.2018-02.2024) Co-supervisors: Prof. Roger Butlin (Sheffield U.), Dr. Rui Faria (CIBIO, U. Porto). Thesis: Genomics of ecotype formation: interplay between demographic processes and natural selection. Funding: FCT scholarship PD/BD/128350/2017 to JC.
1. Hydrodynamic Analysis of Oscillating Water Column Wave Energy Converters using OPENFOAM, Jorge Filipe Marques Gadelho, Instituto Superior Técnico, 14/03/2025
1. Matilde MArques, "Insights into the octocoral microbiome in health and disease: from climate change impacts to probiotic prospects" at Instituto Superior Técnico, University of Lisbon, Portugal
1.	Study by simulation and reconstruction of a brain-dedicated positron emission tomograph based on resistive plate chambers		Ana Luísa Lopes	UC
1.	Quarkonium production studies at LHC energies: towards the understanding of bound-state formation by the strong force		Mariana Araújo	IST
1.	Tomografia de Muões com RPCs na Mina do Lousal		Pedro Teixeira	UÉvora
1.	Study of the Spin/CP properties of the Higgs coupling to W-bosons with ATLAS at the LHC		Ricardo Barrué	IST
1.	Using online behaviour to track global outbreaks and pandemics		Sara Mesquita	UNL-NOVA
1.	Searching for dark matter with the ATLAS detector using unconventional signatures		Maura Teixeira	UMinho
1.	Modeling the radiobiological effects of gold nanoparticles in proton therapy of glioblastomas		Joana Antunes	FCUL
1.	Evaluating the Effectiveness of Mini-Beam Radiation in Cancer Therapy		Miguel Molina-Hernández	IST
1.	Bragg Peak monitoring through prompt-gamma: detection and instrumentation		José Patuleia Venâncio	IST
1.	Search for new physics in exclusive processes at the Large Hadron Collider		Matteo Pisano	IST
1.	A next-generation gamma-ray observatory powered by Machine Learning techniques		Borja González	IST
1.	Pentaquark spectroscopy for the LHC		Raúl Torres	IST
1.	Phase-II Tracking in ATLAS and search for ttHH production using Run-2 and Run-3 LHC Data		Luis Coelho	UC
1.	The substructure of in-medium jets		João Martins da Silva	IST
1.	Radiation Damage of Optical Components in Scintillator Detectors: from the ATLAS/LHC Tile Calorimeter to Future Experiments		Beatriz Pinheiro Pereira	IST
1.	Radiation Damage of the TileCal Optics components at the High Luminosity LHC phase		Rudnei Machado	IST
1.	Raios Cósmicos: desenvolvimento de módulos de divulgação através de design participativo		Luís Afonso	UP
1.	Accelerating the ATLAS Trigger system with Graphical Processing Units		Nuno Fernandes	IST
1.	Study of lepton universality in top quarks pairs events		Giacomo Da Molin	IST
1.	Measurement of Collider Neutrinos with the SND@LHC Experiment		Guilherme Soares	IST
1.	Disentangling and Quantifying Jet-Quenching With Generative Deep Learning		João Arruda Gonçalves	IST
1.	Probing CP couplings in ttX production at the Run3 of the LHC		Esteban Chalbaud	UC
1.	Measurements of Short Range Correlations on Exotic Nuclei at R3B using TRPCs		Manuel Xarepe	FCUL
1.	The effects of proton therapy on protein self-organization: potential benefits for neurodegenerative disorders		Carina Coelho	FCUL
1.	Development of microdosimetric detectors for radiobiology in hadron therapy facilities		Cristiana Rodrigues	FCUL
1.	Reaching for PeVatrons with the future Southern Wide-field Gamma-ray Observatory		Lucio Gibilisco	IST
1.	Developing Multi-Beam FLASH with Proton Beams		Joana Leitão	IST
1.	Adaptive dose reconstruction with online in-vivo range verification in particle therapy		Mariana Brás	IST
1.	Transporte de carga por iões negativos em gases nobres com dopantes eletronegativos		Afonso Paixão Marques	UC
1.	Timing Detectors and Measurements of Higgs Boson Properties		Johan Wulff	IST
1.	AutoBSM: Validating Beyond the Standard Model Physics with Machine Learning		Fernando Souza	UMinho
1.	Multi-messenger physics with the Pierre Auger Observatory and SWGO		Pedro Costa	IST
1.	The Partonic Structure of Hadrons		Eduardo Ferreira	UniGraz
1.	Enhanced Searches with the Pierre Auger Observatory in the Era of Multi-messenger Astrophysics		Alexandra Fernandes	UMinho
1.	Formal and phenomenological studies in the high energy limit of QCD 		Dario Vaccaro	IST
1.	Characterization of liquid argon detectors for next generation neutrino physics		Wallison Campanelli 	FCUL
1.	Search for New Physics in gauge boson scattering with the CMS experiment at the Large Hadron Collider		Giovanni Marozzo	IST
1.	Studying the origin of the elements with radioactive ions at ISOLDE/CERN		Francisco Barba	FCUL
1.	Study of hadronic interactions through the muon component of inclined extensive air showers with the Pierre Auger 		Miguel Martins	IGFAE/USC
1.	Jetography in Heavy Ion Collisions		André Cordeiro	IST
1.	Atomic inputs for probing the r-process in kilonovae		Ricardo Silva	FCUL
1.	Differential tracking on disinformation websites and its impact on search engine results		Íris Damião	IST
1.	Heavy baryon excitations with functional calculatiosn: Confirming CERN discoveries and predicting new states		André Torcato	IST
1.	Probing the nature of the neutrino with large scale dark matter detectors		Kai Jenkins	UC
1.	Search for New Physics Phenomena at the ATLAS/LHC experiment with Anomaly Detection techniques based on Machine Learning		Annalisa Berti	UMinho
1.	Space Radiation in Low Earth Orbit and Space Weather on board the Space Rider		Cristiana Francisco	UC
1.	Optimization of the sensitivity of the LZ and XLZD detectors for Xe-136 0𝝂𝛽𝛽 decay and low mass WIMP searches		Sandro Saltão	UC
1.	The Social Bayesian Brain: The roles of identity complexity and informational environment in belief updating		Angela Rijo	ISCTE
1.	Neutrinoless double-beta decay search with SNO+: Enhancing sensitivity through improved event reconstruction using Machine Learning		Beymar Surco	UC
1.	Study of the influence of natural elevated background radiation on the growth of mint in the region of Covilhã		Lígia Lopes	UBI
1.	Charting QCD jet evolution in extreme conditions		Nuno Olavo	IST
1.	Advanced Methods for Solar Energetic Particle Events Characterization in the Inner Solar System		António Pessanha Gomes	IST
1.	Search for anomalous couplings in the HWW vertex with the ATLAS detector at the LHC		Marina Kholodenko	IST
1.	Probing the primordial quark gluon plasma with heavy flavour		Henrique Legoinha	IST
1.	Are radiocesium and natural radioisotopes ( 238U and progeny, 232Th and progeny, 40K, 7Be) good tracers to understand the erosion processes and dispersion of contaminants in Serra da Estrela? Radioprotection concern?		Caroline Licour	UBI
1.	Cancer weapons against neurodegeneration		Francisca Afonso	FCUL
1.	PicoMonitoring: sub-ns FLASH beam monitoring with Si devices		Rui Fernandez	IST
1.	Thermal and Optomechanical Design Improvement of Hera Mission LIDAR for Near-Earth Object Observation		Pedro Conceição	UBI
1.	Structural Health Monitoring System (SHM) for Reusable Spacecrafts		Geraldo Rodrigues	IST
1.	Space Debris algorithms on satellite constellation pictures for debris characterisation and orbit determination		Joel Filho	UC
1.	PhysiVerse - Leveraging Virtual Reality for Enhanced Physics Education		José Graça	FCUL
1.	Jet physics in the precision era of heavy-ion collision		Marco Leitão	IST
1.	Characterization of the energy spectrum of extensive air showers with the Pierre Auger Observatory data.		Milton Freitas	IST
1.	Measurements of Higgs boson properties and search for BSM physics		Raphaël Guitton	IST
1.	Cosmic-ray isotopic composition measurements with the Alpha Magnetic Spectrometer on the International Space Station		João Carlos Antunes	IST
1.	Development of a timing RPC-based neutron detector		Giorgio Canezin	UC
1.	SpaceRAD &#821.1.; An Integrated Framework for the Radiation Environment in Space, on Mars and on the Moon and its Implications for Human Space Flight		Bruna Lima	IST
1.	Development of a cubesat constelation payload detector demonstrator with polarimetric capabilities		José Sousa	UC
1.	Satellite avionics for navigation and space awareness applications		Beltrán Arribas	UBI
### Master Thesis
#### Finished
1. Vasco Neto – MSc, “Probing the Anti-Sickling Power of Distinct Drugs in Sickle Cell Disease”, scientific advisor, Biochemistry and Biomedicine MSc, FCUL
1. Inês Gomes – MSc, “Probing the Stability of Biomolecules in Deep Eutectic Solvents”, scientific advisor, Biochemistry and Biomedicine MSc, FCUL
1. Catarina Nascimento – MSc, “Molecular Mechanisms of Amyloid Aggregation in Neurodegenerative Diseases”, scientific advisor, Biochemistry and Biomedicine MSc, FCUL
1. 11/2024, Computational Modeling of Biopharmaceuticals Purification Systems, Jéssica Rodrigues, Master in Computational Biology and Bioinformatics, FCT UNL.
1. Designing Optimal 3D Enzyme Computational Models for Efficient Plastic Degradation
Student: Mariana Gomes Fernandes (Supervisor Principal: João Carneiro; Co-Supervisor: Sérgio F. Sousa e Diogo Pratas) Mestrado: Bioinformatics and Computational Biology Faculdade de Ciências da Universidade do Porto, Portugal Dezembro de 2024
1. Machine Learning Enhanced Optimization of Plastic-Degrading Enzymes for Sustainable Ocean Cleanup
Student: Ana Clara Cerqueira (Supervisor Principal: João Carneiro; Co-Supervisor: Sérgio F. Sousa e Diogo Pratas) Mestrado: Bioinformatics and Computational Biology Faculdade de Ciências da Universidade do Porto, Portugal Dezembro de 2024
1. Discovery of New Molecules for the Treatment of Machado-Joseph Disease Student: Filipe Rocha
Mestrado: Medicinal Chemistry (Supervisor Principal: Sérgio F. Sousa; Co-Supervisor: Fernanda Proença)
Universidade do Minho, Portugal Dezembro de 2024
1. Designing In-Silico Aptamers for Potential Use in Marine Bioremediation Student: Rafael Vieira
Mestrado: Bioinformatics and Computational Biology (Supervisor Principal: Sérgio F. Sousa; Co-Supervisor: João Carneiro e Diogo Pratas) Faculdade de Ciências da Universidade do Porto, Portugal
Novembro 2024
1. Desenvolvimento de nanomateriais hidrofílicos de carbono com propriedades biomiméticas de enzimas
antioxidantes Student: Andreia Daniela Rosa Veloso (Supervisor Principal: Maria C. Oliveira; Co-Supervisors: Nuno Cerqueira e Romeu Videira) Doutoramento: Doutoramento em Ciências Químicas e Biológicas (PhD) Universidade de Trás-os-Montes e Alto Douro, Portugal Novembro de 2024
1. Evaluation of acute hepatic toxicity and inflammation induced by nitrosamines in Mus musculus and Danio rerio Student: Isabelly Annunciato (Supervisor Principal: Marcos Hikari Toyama; Co-Supervisor: Sérgio Sousa) Mestrado: Biodiversity in Coastal Environments Institute of Biosciences, Paulista State University, Brazil Agosto de 2024
1. Lohmann D (2023-2024, main supervisor). Multi-omics approach to unravel phenotypic responses of tropical fish from the Eastern Tropical Pacific to ocean warming and acidification scenarios. MSc in Computational Biology and Bioinformatics thesis. NOVA School of Science and Technology, NOVA University of Lisbon, Portugal. 91 pp. Supervisor team Dr. Carolina Madeira and Pedro M. Costa. Funded by project EASMO BiodivClim/0001/2019. Defended 17-12-2024. http://hdl.handle.net/10362/182661
1. Lopes J (2023-2024, co-supervisor). Multilayer molecular networks shaping goby fish physiological responses to marine heatwaves in intertidal habitats. MSc in Computational Biology and Bioinformatics. NOVA School of Science and Technology, NOVA University of Lisbon, Portugal. 116 pp. Supervisor team Pedro M. Costa and Dr. Carolina Madeira. Funded by project ExtremeOceans PTDC/BIA-BMA/1494/2020. Defended 05-12-2024. http://hdl.handle.net/10362/181947
1. Catarina Bernardo, MSc in Evolutionary and Developmental Biology, Ciências (09.2023-02.2024) Thesis: Signatures of adaptation at the mitochondrial level in endemic freshwater fish species from contrasting environments.
1. Optimization of an Oscillating Water Column (OWC) pneumatic efficiency testing different geometries using CFD, Diana Arias, Instituto Superior Técnico, 2024
1.	Reconstrução de Eventos de Neutrinos Solares com Técnicas de Aprendizagem de Máquina Usando Dados da Experiência SNO+		Joan Kladnik	Orientador:	Nuno Barros	2024-12-06	UMinho
1.	Estudo da dispersão de partículas alfa em filmes finos		Ana Campos	Orientador:	Luis Peralta	2024-01-05	FCUL
1.	Launching the Radiation Hard Electron Monitor aboard the ESA JUICE mission		Francisca Santos	Orientador:	Patrícia Gonçalves	2024-07-01	IST
1.	search for dark matter (spin 1)		João Lopes Carreira	Orientador:	António Onofre	2024-12-31	FCUL
1.	Cálculo de espetro de emissão de Auger para simulações de radioterapia sensibilizada com nanopartículas de ouro    		Fábio do Carmo	Orientador:	Jorge Sampaio	2024-01-29	FCUL
1.	Next-generation Neutrino Physics: Development of the DUNE laser-based Calibrations		Joana Vences	Orientador:	José Maneira	2024-12-27	FCUL
1.	Construção de um protótipo para o estudo da exalação de radão por materiais de construção		Nuno Taborda	Orientador:	Luis Peralta	2024-01-11	FCUL
1.	Particle-Particle and Jet-Jet Angular Correlations at the Parton Level	http://hdl.handle.net/10451/65219	Guilherme Calé	Orientador:	Grigorios Chachamis	2024-06-30	FCUL
1.	Integration of the HiRezBrainPET with a clinical PET/CT system – Image performance evaluation of a prototype for next-generation brain tomography 		Miguel Lopes	Orientador:	Patrícia Gonçalves	2024-07-01	IST
1.	Interlock electronics for the high Granularity Timing Detector od the ATLAS		Maria Miguel	Orientador:	Ricardo Gonçalo	2024-02-28	UC
1.	Implementation of quark mass effects in QCD three-jet production observables produced by hadronic decays of the Z-boson at FCC-ee collider	https://hdl.handle.net/10400.5/95506	Joana Reis	Orientador:	João Nuno Pires	2024-07-25	FCUL
1.	Pre-equilibrium of the Quark-Gluon Plasma		Guilherme Crispim	Orientador:	Liliana Apolinário	2024-07-02	IST
1.	The deuteron as a six-quark state in QCD		André Nunes	Orientador:	Ana Arriaga	2024-01-12	FCUL
1.	Searching for beyond Standard Model particles decaying to muon pairs in SND@LHC		Henrique Santos	Orientador:	Nuno Leonardo	2024-11-28	IST
1.	Design and benchmark of an innovative concept to measure light charged particles in the R3B/FAIR using RPCs		Diogo Miguel	Orientador:	Daniel Galaviz	2024-12-19	FCUL
1.	Planing for muon tomography campaigns in urban settings		Francisco Manuel Ferreira	Orientador:	Sofia Andringa	2024-12-03	IST
1.	3D imaging from underground with muon tomography		Isabel Alexandre	Orientador:	Sofia Andringa	2024-12-03	IST
1.	Event Selection and Angular Reconstruction for W Boson Events at Future e+e− Colliders		André Silva	Orientador:	Ricardo Gonçalo	2024-09-27	UC
1.	Thermal Analysis and Effects on Resolution of CZT Detectors exposed to LEO Conditions on board the International Space Station	https://hdl.handle.net/10316/117946	Alexandra Roque	Orientador:	Rui Curado Silva	2024-09-30	UC
1.	Proton range verification for irradiation of anthropomorphic phantoms implemented in Geant4 Monte Carlo simulations		Francisco Miguéis	Orientador:	Paulo Crespo	2024-09-23	UC
1.	New Physics searches at the LHC using Anomaly Detection		Inês Moreira	Orientador:	Rute Pedro	2024-11-28	IST
1.	Quantum computing applications to quantum chromodynamics: Jet evolution in a quantum computer		Gabriela Oliveira	Orientador:	Nuno Castro	2024-07-25	UMinho
1.	Anomaly detection as a quality control tool in an industrial context		Miguel Peixoto	Orientador:	Nuno Castro	2024-12-11	UMinho
1.	Biophysical modelling and simulation of BFE/Au multifunctional nanoplatforms for proton therapy		Bianca Alves	Orientador:	Jorge Sampaio	2024-12-19	FCUL
1.	Robust Anomaly Detection in Independent Searches for New Physics with the ATLAS/LHC Experiment		Inês Pinto	Orientador:	Rute Pedro	2024-11-28	IST
1.	Improving the vacuum baseline for in-medium jet physics studies		Diogo Costa	Orientador:	Liliana Apolinário	2024-11-27	IST
1.	Development of digital techniques for data processing and instrument control		Gil Ramos Madeira	Orientador:	Nuno Barros	2024-09-30	UC
1.	Procura de acoplamentos anómalos do bosão de Higgs com o detetor ATLAS		Marta Silva	Orientador:	Inês Ochoa	2024-12-03	IST
1.	Assembly and beam commissioning of the high rate TOF/SCI detector SAFARI		Beatriz Amorim	Orientador:	Daniel Galaviz	2024-10-25	FCUL
1.	O Radão e a Radioatividade: presente no quotidiano e ausente no currículo escolar		Carolina Rosa	Orientador:	Sandra Soares	2024-07-15	UBI
1.	Study of the hadronic interaction in the fixed-target experiment AMBER (CERN)		Ema Fadiga	Orientador:	Carlos Azevedo	2024-12-02	UA
1.	In-medium Gluon Radiation in General Kinematics		Afonso Guerreiro	Orientador:	Guilherme Milhano	2024-12-03	IST
1.	Multichannel study of cosmic ray variability over different temporal scales	http://fisgeo.unipg.it/pacetti/3-LM-Margherita-Fioroni.pdf	Margherita Fioroni	Orientador:	Nicola Tomassetti	2024-04-18	UniPerugia
1.	Using embeddings to infer diagnostics from medical prescriptions	https://fenix.tecnico.ulisboa.pt/cursos/mecd/dissertacao/1972678479056342	Tiago Miranda	Orientador:	Joana Gonçalves-Sá	2024-11-18	IST
1.	Higgs boson properties and tau lepton identification at the 3 TeV Muon Collider	http://cds.cern.ch/record/2913377	Lorenzo Valla	Orientador:	Michele Gallinaro	2024-09-30	LIPL
1.	Investigation of the Operation Modes of Optoelectronic Oscillators based on Resonant Tunnelling Diodes	https://repositorio.ulisboa.pt/handle/10400.5/97384	Tiago Ferro	Orientador:	José Figueiredo	2024-07-01	FCUL
1.	Modelling the Evolution of the Galactic Disk Scale Height Traced by Open Clusters	https://repositorio.ulisboa.pt/handle/10451/64671	Sandro Moreira	Orientador:	André Moitinho	2024-04-01	FCUL
1.	E(xtraterrestris). Coli : adapting genome-scale metabolic models to non-standard thermodynamical constraints	http://hdl.handle.net/10451/64476	Lucas Monteiro	Orientador:	André Moitinho	2024-03-01	FCUL
1.	Galactic and Extragalactic Insights: A Visualisation Approach to Gaia Data Exploitation	http://hdl.handle.net/10400.5/97170	Maria Eduarda Pimentel	Orientador:	André Moitinho	2024-04-01	FCUL
1. Assessment of wave overtopping at Praia da Vitória, Terceira, Azores, with SWASH model, by DINUSH SHAYAMAN PRIYANKER BADDAVIDANA, Master’s in Coastal Hazards, Risks, Climate Change Impacts and Adaptation, UAlg, Delft. Submitted for defence.
#### Ongoing
1. Duque A (2024 to present, main supervisor). Computational tools to assess adaptation and resilience to thermal stress in intertidal fish: a functional genomics approach. MSc in Computational Biology and Bioinformatics. NOVA School of Science and Technology, Portugal. Supervisor team Dr. Carolina Madeira and Prof. Pedro M. Costa. Funded by project ExtremeOceans PTDC/BIA-BMA/1494/2020. (status – ongoing).
1. Estêvão Faustino, MSc in Evolutionary and Developmental Biology, Ciências (09.2023-03.2025) Thesis: Unravelling hybridization dynamics of Iberian chubs through demographic modelling.
1.	searck for dark matter with top quarks		Gonçalo Freitas	Orientador:	António Onofre	FCUL
1.	Study of neutrino interactions in the LZ Dark Matter detector		Natalija Novak	Orientador:	Alexandre Lindote	UniGraz
1.	Life prospection on Mars - Studing the Martian Subsurface Radiation Environment		Igor Miguel Gago	Orientador:	Patrícia Gonçalves	IST
1.	The soft-hard antenna spectrum in presence of a QGP		Tomás Cabrito	Orientador:	Guilherme Milhano	IST
1.	Gamma-ray Polarization in BL Lac Objects with AMEGO		André Neves	Orientador:	Rui Curado Silva	FCTUC
1.	Simulations and benchmark of a fast neutron detector for nuclear astrophysics 		Carolina Felgueiras	Orientador:	Daniel Galaviz	FCUL
1.	Isotope Studies with the Alpha Magnetic Spectrometer (AMS)		Guilherme Gaspar	Orientador:	Fernando Barão	IST
1.	Configuration of the Interlock-FPGA for the HGTD Detector 		Rui Vieira	Orientador:	Helena Santos	IST
1.	Configuration of the Monitoring FPGA for the HGTD Interlock		Alexandre Parreira	Orientador:	Helena Santos	IST
1.	Heavy Quarks Formation time		Inês Alexandre Serra	Orientador:	Liliana Apolinário	IST
1.	THOR Project Scientific Payload Environmental Tests Validation 		Mário Cainé	Orientador:	Rui Curado Silva	UC
1.	Polarimetry with THOR-SR Mission CdTe Gamma-Ray Tracker Development Models		Mariana Letra	Orientador:	Rui Curado Silva	UC
1.	Associated production of Dark Matter with heavy fermions at the RUN3 of the LHC	https://hdl.handle.net/1822/92171	Rui Miguel Silva	Orientador:	António Onofre	UMinho
1.	Space Rider maiden flight orbital particles identification using machine learning techniques		Joana da Orada	Orientador:	Rui Curado Silva	UC
1.	Acceleration of the ATLAS Calorimeter Calibration Algorithms using GPUs		Bruno Semião	Orientador:	Patricia Conde	IST
1.	Search for central exclusive production of tau+ tau- pairs in proton-proton collisions at the LHC		Madalena Ferreira	Orientador:	Jonathan Hollar	UA
1.	116Sn(p,g)117Sb reaction cross-section determination at energies relevant for the astrophysical p-process using gamma- and X-rays emission yields		Ricardo Pires	Orientador:	Daniel Galaviz	FCUL
1.	Charmonium production in hadron collisions at the COMPASS experiment		Bárbara Pereira	Orientador:	Catarina Quintans	FCUL
1.	Antiproton production in proton on helium collisions at the AMBER Experiment		Guilherme Almeida	Orientador:	Catarina Quintans	FCUL
1.	AMEGO science potential and impact on aviation safety of TGF analysis		Filipa Bessa Almeida	Orientador:	Rui Curado Silva	UC
1.	Towards the neutrinoless double-beta decay study with SNO+: radioactive background characterisation with SNO+ scintillator data		Manuel Abreu	Orientador:	Valentina Lozza	IST
1.	Characterization of anomalous air shower events in SWGO		Inês Martins	Orientador:	Ruben Conceição	IST
1.	THOR OBC Scientific Operations		Pedro Carmo	Orientador:	Rui Curado Silva	UC
1.	Imagiologia por raios gama espontâneos para verificação de alcance de feixes de hélio		Gegimma José	Orientador:	Paulo Crespo	UC
1.	Future collider calorimeter optimisation with machine learning		Bruno Rodrigues	Orientador:	Inês Ochoa	FCUL
1.	Celestial Objects Position Compton Reconstrunction with THOR		Duarte Rodrigues	Orientador:	Rui Curado Silva	UC
1.	Graphical Neural Learning applied to jets produced in heavy-ion collisions		Pedro Esperanço	Orientador:	Helena Santos	IST
1.	Deteção de Flashes de Raios-gama Terrestres para a Segurança Aérea		Bruna Filipa Frade Jorge	Orientador:	Rui Curado Silva	UC
1.	TBC		Carolina Miranda	Orientador:	Gonçalo Ribeiro	IST
1.	Análise dos registos de TGFs no espaço e a sua implicação no processo de emissão nas nuvens comulonimbus		Henrique Gaspar	Orientador:	Rui Curado Silva	UC
1.	Desenvolvimento de algoritmos de trigger com GPUs		Gabriela Sereniski	Orientador:	José Rufino	IPB
1.	Identification of UHE neutrino events in vertical air showers		David Dias	Orientador:	Ruben Conceição	IST
1.	Using Machine Learning algorithms to discriminate 0𝝂𝛽𝛽 decay and background events in xenon time projection chambers		João António Rodrigues	Orientador:	Alexandre Lindote	UC
1.	Pile-up event identification and rejection in SNO+: enhancing the signal to noise ratio		Tomás Baltazar	Orientador:	Valentina Lozza	IST
1.	Electronics for the High Granularity Timing Detector of the ATLAS Experiment		Carlos Brito	Orientador:	Ricardo Gonçalo	UC
1.	Impacto de atmosferas ricas em radão no crescimento e desenvolvimento da Mentha spicata		Mariana Vicente	Orientador:	Sandra Soares	UBI
1.	Aplicação de AI no steering de um Sistema de Secagem Industrial		Leonor Martins	Orientador:	Francisco Neves	UC
1.	Calorimetry studies at the Future Circular Collider		Ariana Queda	Orientador:	Ricardo Gonçalo	UC
1.	Design optimization for a flat-panel PET scanner with DoI capability		Marta Simões	Orientador:	Patrícia Gonçalves	IST
1.	Conceito de um detector baseado em nRPCs para neutrões epitérmicos e rápidos		Jesús Villoria	Orientador:	Luís Margato	UC
1.	Avaliação da taxa de exalação de radão de materiais de construção		Thais Alves	Orientador:	Sandra Soares	UBI
1.	Optimization of the local reconstruction in a high granular calorimeter using a heterogenous computing model		Daniela Cardoso	Orientador:	Pedro Ferreira da Silva	IST
1.	Search for new physics with forward protons at the LHC		Pedro Batista	Orientador:	Jonathan Hollar	FCUL
1.	Measurement of  muon flux at the LHC		Alexandre Mendonça	Orientador:	Nuno Leonardo	IST

## Patents



## Datasets
1. SeaTox toxin database [Version 12.2024.001]. Zenodo. doi:10.5281/zenodo.14355541).
## Courses 
1. Course for Biochemistry BSc Degree: Introduction to Biomolecular Simulation, at FCT UNL. The course aims to introduce students to the field of biomolecular simulation. HPC computing time for students.