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\begin{itemize}
\section*{Papers}

\subsection*{International Journals}

\item[1] ``E-cadherin variants associated with oral facial clefts trigger aberrant cell motility in a REG1A-dependent manner'', J. Pereira, S. Melo, R.\,M. Ferreira, P. Carneiro, V.\,T. Yang, A.\,F. Maia, J. Carvalho, C. Figueiredo, J.\,C. Machado, E. Morais-de-Sá, R. Seruca, J. Figueiredo, Cell Commun. Signal. {\bf 22 (1)}, 152 (2024).

\item[2] ``A mathematical model of fibrinogen-mediated erythrocyte-erythrocyte adhesion'', CS Lopes, J Curty, FA Carvalho, A Hernandez-Machado, K Kinoshita, NC Santos, RDM Travasso, Commun. Biol. {\bf 6(1)}, 192 (2023).

\item[3] ``The ECM and tissue architecture are major determinants of early invasion mediated by E-cadherin dysfunction'', S Melo, P Guerrero, MM Soares, JR Bordin, F Carneiro, P Carneiro, MB Dias, J Carvalho, J Figueiredo, R Seruca, RDM Travasso, Commun. Biol. {\bf 6 (1)}, 1132 (2023).

\item[4] ``A computational model of organism development and carcinogenesis resulting from cells bioelectric properties and communication'', Carvalho, J, Sci. Rep. {\bf 12(1)} (2022).

\item[5] ``A multiscale cell-based model of tumor growth for chemotherapy assessment and tumor-targeted therapy through a 3D computational approach'', SJ Nivlouei, M Soltani, E Shirani, MR Salimpour, R Travasso, J Carvalho, Cell Prolif. {\bf 55(3)}, e13187 (2022).

\item[6] ``A bioelectric model of carcinogenesis, including propagation of cell membrane depolarization and reversal therapies'', Carvalho, J, Sci Rep {\bf 11, 13607} (2021).

\item[7] ``A three dimensional computer model of urothelium and bladder cancer initiation, progress and collective invasion'', J. Carvalho, V. Lopes, R. Travasso, Inform. Med. Unlocked {\bf 26}, 100750 (2021).

\item[8] ``Tumor cell invasiveness in the initial stages of bladder cancer development - A computational study'', J. Carvalho, V. Lopes, R. Travasso, Int J Numer Method Biomed Eng. {\bf 37(1)}, e3417 (2021).

\item[9] ``Cell Reversal From a Differentiated to a Stem-Like State at Cancer Initiation'', Carvalho, J, Front. Oncol. {\bf 10}, 541 (2020).

\item[10] ``Tumor cell invasiveness in the initial stages of bladder cancer development - A computational study'', J Carvalho, V Lopes, R Travasso, Int J Numer Method Biomed Eng, e3417 (2020).

\item[11] ``Cofilin-1 Is a Mechanosensitive Regulator of Transcription'', C Domingues, AM Geraldo, SI Anjo, A Matos, C Almeida, I Caramelo, JA Lopes-da-Silva, A Paiva, J Carvalho, RP das Neves, B Manadas, M Graos, Front. Cell Dev. Biol. {\bf 8}, 678 (2020).

\item[12] ``Soft culture substrates favor stem-like cellular phenotype and facilitate reprogramming of human mesenchymal stem/stromal cells (hMSCs) through mechanotransduction'', H Gerardo, A Lima, J Carvalho, JRD Ramos, S Couceiro, RDM Travasso, RP das Neves, M Graos, Sci. Rep. {\bf 9}, 9086 (2019).

\item[13] ``Capillary network formation from dispersed endothelial cells: Influence of cell traction, cell adhesion, and extracellular matrix rigidity'', João R. D. Ramos, Rui Travasso, João Carvalho, , Phys. Rev. E {\bf 97}, 012408 (2018).

\item[14] ``Angiogenic Factors produced by Hypoxic Cells are a leading driver of Anastomoses in Sprouting Angiogenesis – a computational study'', Maurício Moreira-Soares, Rita Coimbra, Luís Rebelo, João Carvalho, Rui D. M. Travasso, , Scientific Reports {\bf 8}, 8726 (2018).

\item[15] ``A local uPAR-plasmin-TGFβ1 positive feedback loop in a qualitative computational model of angiogenic sprouting explains the in vitro effect of fibrinogen variants'', Sonja E. M. Boas,  Joao Carvalho, Marloes van den Broek, Ester M. Weijers, Marie-José Goumans, Pieter Koolwijk, Roeland M. H. Merks, PLoS Comput Biol {\bf 14}, e1006239 (2018).

\item[16] ``Stationarity of the inter-event power-law distributions'', Yerali Gandica , João Carvalho , Fernando Sampaio dos Aidos , Renaud Lambiotte , Timoteo Carletti, PLOS One {\bf 12(3): e0174509} (2017).

\item[17] ``Wikipedia editing dynamics'', Y. Gandica, J. Carvalho, F. Sampaio dos Aidos, PHYSICAL REVIEW E {\bf 91}, 012824 (2015).

\item[18] ``The dynamic nature of conflict in Wikipedia'', Y. Gandica, F. Sampaio dos Aidos, J. Carvalho, Eur. Phys. Lett. {\bf 108}, 18003 (2014).

\item[19] ``Observation of a new particle in the search for the Standard Model Higgs boson with the ATLAS detector at the LHC'', ATLAS Collaboration, J. Carvalho, Physics Letters B {\bf 716}, 1-29 (2012).

\item[20] ``The ATLAS Experiment at the CERN Large Hadron Collider'', ATLAS Collaboration, J. Carvalho, Journal of Instrumentation {\bf 3} (2008).

\item[21] ``Probing anomalous Wtb couplings in top pair decays'', J. A. Aguilar-Saavedra, J. Carvalho, N. Castro, A. Onofre, F. Veloso, European Physical Journal C {\bf 50}, 519-533 (2007).

\item[22] ``Limits for the central production of Theta(+) and Xi(--) pentaquarks in 920-GeV pA collisions'', ATLAS Collaboration, J. Carvalho, Physical Review Letters {\bf 93}, 212003 (2004).

\item[23] ``Tests of CPT symmetry and quantum mechanics with experimental data from CPLEAR'', CPLEAR Collaboration, J. Carvalho, Physics Letters B {\bf 364}, 239-245 (1995).

\section*{Proceedings}

\subsection*{International Conferences}

\item[24] ``A cellular Potts model describing wound healing assays in diverse cell motility and cell adhesion conditions'', J Carvalho, S Jafari, G Martins, Eur. J. Clin. Invest. {\bf 52(1)} (2022).

\item[25] ``Three dimensional computer model of urothelium, bladder cancer development and collective tumor invasion'', J Carvalho, V Lopes, R Travasso, Eur. J. Clin. Investig. {\bf 51}, 104-104 (2021).

\item[26] ``Circadian Patterns on Wikipedia Edits'', Y. Gandica, R. Lambiotte, T. Carletti, F. Sampaio dos Aidos, J. Carvalho, Complex Networks VII {\bf 644}, 293-300 (2016).

\section*{Communications}

\subsection*{Invited}

\item[27] ``Angiogenic Factors Produced by Hypoxic Cells drive Anastomoses in Sprouting Angiogenesis'', Rui DM Travasso, Mauricio Soares, Rita Coimbra Luís Rebelo , João Carvalho, University of Castilla la Mancha, Ciudad Real, Spain, 29th Jun (2017).

\item[28] ``Mechanically-driven pattern formation in cell cultures'', João R. D. Ramos, Rui Travasso, João Carvalho, mini-symposium Angiogenesis and cell motility, in Mathematics of Complex Systems: from precision medicine to smart cities, Coimbra, Portugal, 5th-6th Dec (2016).

\item[29] ``Angiogenic factors produced by hypoxic cells drive anastomosis in sprouting angiogenesis'', M. M. Soares, L. Rebelo, R. Coimbra, J. Carvalho, R. D. M. Travasso, , mini-symposium Angiogenesis and cell motility, in Mathematics of Complex Systems: from precision medicine to smart cities, Coimbra, Portugal, 5th-6th Dec (2016).

\subsection*{Oral}

\item[30] ``Influence of the Underlining Duct Structure in Prostate Adenocarcinoma 
Progression'', F. Paiva, J. Carvalho, G. Lorenzo, R. Travasso, Encontro Novos Talentos em Física, Coimbra, Portugal, 23rd–24th Jul (2022).

\item[31] ``Influence of the Underlining Duct Structure in Prostate Adenocarcinoma 
Progression'', F. Paiva, J. Carvalho, G. Lorenzo, R. Travasso, Research School and Workshop on Mathematical Modeling of Self Organization in Medicine, Biology and Ecology, Palermo, Italy, 30th May – 3rd Jun (2022).

\item[32] ``Role of prostate gland network structure in early stage prostate cancer growth'', António Sérgio Morais, Guillermo Lorenzo, Rui DM Travasso, João Carvalho, 55th Annual Scientific Meeting of ESCI, 9th - 11th Jun (2021).

\item[33] ``Role of prostate gland network structure in early stage prostate cancer growth'', António Sérgio Morais, Guillermo Lorenzo, Rui DM Travasso, João Carvalho, Virtual SMB 2021 Annual Meeting, 13th - 17th June (2021).

\item[34] ``Three dimensional computer model of urothelium, bladder cancer development and collective tumor invasion'', João Carvalho, Valéria Lopes, Rui Travasso, 55th Annual Scientific Meeting of ESCI, 9th - 11th Jun (2021).

\item[35] ``3D Multiscale Modeling of Chemotherapeutic Drug Delivery to Malignant Tumors'', Sahar Jafari Nivlouei, M Soltani, João Carvalho, Rui DM Travasso, Mohammad Reza Salimpour, Ebrahim Shirani, 55th Annual Scientific Meeting of ESCI, 9th - 11th Jun (2021).

\item[36] ``3D Multiscale Modeling of Chemotherapeutic Drug Delivery to Malignant Tumors'', Sahar Jafari Nivlouei, M Soltani, João Carvalho, Rui DM Travasso, Mohammad Reza Salimpour, Ebrahim Shirani, Virtual SMB 2021 Annual Meeting, 13th - 17th June (2021).

\item[37] ``Tumor angiogenesis: a mathematical model in three dimensions'', M. M. Soares, L. Rebelo, R. A. Coimbra, J. Carvalho, R. D. M. Travasso, , Physical Biology of Tissue Morphogenesis - Mechanics, Metabolism and Signaling, Dresden, Germany, 17th-21st Oct (2016).

\item[38] ``Vascular Growth in Tumor Angiogenesis: a Mathematical Model in Three Dimensions'', Rita Coimbra, Maurício Moreira-Soares , João Carvalho, Rui DM Travasso, Física 2016, Braga, Portugal, 8th-10th Sep (2016).

\item[39] ``Reconstrução Automática da Rede Capilar da Retina de um Paciente'', Rute Marto, Luís Cruz, Rui DM Travasso, João Carvalho, Presentation of Projects in Biomedical Engineering, Coimbra, Portugal, 30th May (2016).

\item[40] ``Regulation of Blood Vessel Growth'', Patrícia Oliveira, Rui DM Travasso, João Carvalho, Orlando Oliveira, Presentation of Projects in Biomedical Engineering, Coimbra, Portugal, 30th May (2014).

\subsection*{Poster}

\item[41] ``Modelling the growth of glioblastomas'', Marina Oliveira, João Carvalho, Rui DM Travasso, Presentation of Projects in Biomedical Engineering, Coimbra, Portugal, 9th Feb (2018).

\item[42] ``Modelling the growth of glioblastomas'', Marina Oliveira, João Carvalho, Rui DM Travasso, Presentation of Projects in Biomedical Engineering, Coimbra, Portugal, 1st Jun (2018).

\item[43] ``Tumor Angiogenesis: a Mathematical Model in Three Dimensions'', Maurício Moreira-Soares , Rita Coimbra, João Carvalho, Rui DM Travasso, Ciência 2016, Lisbon, Portugal, 4th-6th Jul (2016).

\item[44] ``Vascular Growth in Tumor Angiogenesis: a Mathematical Model in Three Dimensions'', Rita Coimbra, Maurício Moreira-Soares, João Carvalho, Rui DM Travasso, Porto Meetings in Mathematics and Biology, Porto, Portugal, 15th-17th Jun (2016).

\item[45] ``Reconstrução Automática da Rede Capilar da Retina de um Paciente'', Rute Marto, Luís Cruz, Rui DM Travasso, João Carvalho, Presentation of Projects in Biomedical Engineering, Coimbra, Portugal, 10th Feb (2016).

\item[46] ``Regulation of Blood Vessel Growth'', Patrícia Oliveira, Rui DM Travasso, João Carvalho, Orlando Oliveira, Presentation of Projects in Biomedical Engineering, Coimbra, Portugal, 12th-14th Feb (2014).

\end{itemize}
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