André Amado

scientist | developer

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Peer-reviewed publications (18)

Molecular Biology and Evolution (2024)

Journal of Physics A (2024)

In this paper, Claudia and I explore an ecological fitness landscape model in which fitness depends dynamically on the frequencies of the different genotypes through competition for existing resources. The resource competition introduces ecology in the fitness landscape, leading to an eco-evolutionary fitness landscape. We show that this fitness landscape yields more diverse populations than the corresponding "traditional" non-ecological fitness landscape.

Bioinformatics Advances (2023)

This paper introduces a software package that Li Juan, Claudia, and I initially developed for our internal usage and that grew to be its own independent software! It allows the user to run simulations of adaptive trajectories of populations over arbitrary fitness landscapes, with or without recombination. The program is open-source, comes with a detailed manual, and the code is fully documented. I wrote it in Rust, a really cool language!

Molecular Ecology (2023)

Philosophical Transactions of the Royal Society B (2022)

The European Physical Journal C (2020)

In this work, Azadeh and I explore a new ϕ6 soliton with a long-range tail. We find the solitonic solution and its oscillation modes. Then we study the interaction of this soliton with scalar fields (considering two possible couplings) and a fermion field. Excitingly, we were able to obtain most results analytically!
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Evolutionary Ecology (2019)

Organisms are expected to face trade-offs when trying to extract the most energy of a resource as swiftly as possible. While this is well-known, the effects that it has at the community level are not very well explored. We suppose a system with several resources whose rates of acquisition and processing are subject to this type of restrictions. Then, we study the consequences it implies to the diversity and dynamics of the microbial communities that depend on those resources. To parametrize these complex trade-offs, we draw inspiration from computer graphics and make use of the flexible Bézier surfaces!

The European Physical Journal Plus (2019)

We study a stochastic model in which agents acquire resources from their environment. The resource influx and death rate are subject to random fluctuations. We derive equilibrium distributions analytically for a single species. Later, we generalize the model to include an arbitrary number of species and resources and study the coexistence of species in this setting.

Physics of Life Reviews (2019)

Ecological Modelling (2018)

Evolution (2018)

Physica A (2017)

Physics Letters B (2017)

Journal of Statistical Mechanics (2017)

Trade-offs represent constraints that limit the capacity of organisms to optimize different traits simultaneously. Since trade-offs are widespread in nature, life has developed crafty ways to circumvent these restrictions. One of these ways is the division of labor, with different organisms, or different units within the same organism, performing distinct functions and then sharing the benefits of them all. This probably constitutes one of the leading forces behind the evolution of multicellularity and cell specialization. In most models, trade-offs are treated individually, though, while it is more realistic to consider them in complex networks of interacting functions. In this work, we propose a model where trade-offs are naturally incorporated in networks and study the consequences this has on the evolution of cell differentiation.

The European Physical Journal C (2017)

Royal Society Open Science (2016)

Physical Review E (2016)

Physica A (2015)



Other publications (2)

(2013)

Acta Physica Polonica B (2012)



Conference participations and seminars (10)

Congress of the European Society for Evolutionary Biology (Prague, Czech Republic)

2022

Talk: Dynamic eco-evolutionary fitness landscapes display complex trajectories and sustained diversity

Bern Data Science Day (Bern, Switzerland)

2022

Poster: Dynamic eco-evolutionary fitness landscapes display complex evolutionary trajectories and sustained diversity

PREPARE meeting (Gulbenkian Science, Portugal)

2019

Talk: Modelling fitness landscapes across environments

Young Scientists Retreat 2019 (Gulbenkian Science and Institut Curie, Portugal)

2019

Poster: Modeling fitness landscapes across environments

Postdoc Seminar (Gulbenkian Science, Portugal)

2019

Talk: Fitness costs of antimicrobial resistance in E. coli

From Molecular Basis to Predictability and Control of Evolution (Nordita, Stockholm, Sweden)

2019

Participation

IX Brazilian Meeting on Simulational Physics (International Institute of Physics, Natal, Brazil)

2019

Poster: Evolution of multicellularity: a mechanistic model

Encontro de Física 2016 (Sociedade Brasileira de Física, Natal, Brazil)

2016

Poster: Tradeoffs and the evolution of complexity

Models in Population Dynamics and Ecology 15 (Universidade Federal Fluminense, Nitéroi, Brazil)

2015

Poster: Predictability in populations evolving under imitation

Excited QCD (Peniche, Portugal)

2012

Talk: Study of compact U(1) flux tubes in 3+1 dimensions in lattice gauge theory using GPU's



Student supervisions (2)

The combination of a Rough Mt. Fuji fitness landscape and a consumer resource model leads to more coexisting genotypes than resources available (Msc project and thesis)

University of Bern, Switzerland

2023

Jérôme Stäheli (supervisor: Claudia Bank, co-supervisor: André Amado)

Avaliação da qualidade de um modelo de fitness landscapes em múltiplos ambientes (BSc project and thesis)

Universidade Nova de Lisboa, Portugal

2020

Inês Borges (supervisor: André Amado, co-supervisor: Claudia Bank)



Peer review for scientific journals

Evolution

(Oxford University Press)

Evolutionary Applications

(Wiley)

Journal of Molecular Evolution

(Springer)

Journal of Physics A: Mathematical and Theoretical

(IOP Publishing)

PLOS ONE

(PLOS)

Proceeding of the Royal Society B

(Royal Society)

Scientific Reports

(Nature)


Schools and other courses (5)

Ready for BioData Management, BioData.pt

2019

Gulbenkian Science, Portugal

Física Biológica (10 hours)

2015

Federal University of Pernambuco, Brazil

Contour Dynamics and Integrable Systems (10 hours)

2015

Federal University of Pernambuco, Brazil

Escola de Astrofísica e Gravitação

2012

Instituto Superior Técnico, Portugal

Summer School on Particle Physics

2011

The Abdus Salam International Centre for Theoretical Physics (ICTP), Italy