André Amado

Multidisciplinary scientist

Main skills

Python Rust C++ SQL git data analysis model development software development statistics mathematics physics scientific communication scientific writing collaboration skills MacOS Linux Windows

I am a multidisciplinary scientist and developer. I have a M.Sc. in Engineering Physics (Técnico, Portugal) and a Ph.D. in Physics (UFPE, Brazil). After the Ph.D., I completed three postdocs (UFPE; Gulbenkian Science; University of Bern). My research career started in physics, and I have since worked on different subjects, with a focus on biological problems.

My background in physics and research experience gives me the flexibility to learn and approach different problems. It also provides me with a solid mathematical and statistics background. Science and academics allowed me to work in a collaborative and international environment and develop my scientific writing and communication skills. From a technical side, my career has had a robust modeling and simulation component, reinforcing my development skills and ability to write efficient code. I have programmed in various languages, particularly Python, Rust, and C++. I have frequently used Python data analysis and visualization libraries, such as NumPy, SciPy, pandas, Matplotlib, and sklearn.

Besides modeling, I analyzed experimental biological data, especially microbial fitness data, during my last two postdocs. These experimental data were sourced from collaborators or data available from different groups. My function was to characterize various statistics from those data and extract as much information as possible with the ultimate goal of predicting microbial fitness in different environments or situations. I worked especially with prediction of antibiotic resistance in different environments. To achieve this, I applied a combination of approaches, especially examining correlations within the data or fitting biological models to generalize the information contained in the data.

Professional experience

University of Bern (Theoretical Ecology and Evolution)

02/2021 - 03/2023

Postdoctoral researcher

Modeled biological systems; analyzed experimental data; supervised junior researchers; developed computational tools for modeling.

Main skills Python Rust LaTeX data analysis model development software development model fitting biology evolution theory scientific writing collaboration skills MacOS

Instituto Gulbenkian de Ciência (Evolutionary Dynamics lab)

05/2019 - 01/2021

Postdoctoral researcher

Modeled biological systems; analyzed experimental data; supervised junior researchers; developed computational tools for modeling.

Main skills Python Rust Wolfram Mathematica LaTeX data analysis model fitting model development software development biology evolution theory scientific writing collaboration skills MacOS

Universidade Federal de Pernambuco (Physics Department/Laboratório de Física Teórica e Computacional)

04/2018 - 03/2019

Postdoctoral researcher

Modeled biological systems; developed computational tools for modeling; taught physics courses to engineering students.

Main skills Python C++ Wolfram Mathematica LaTeX data analysis model fitting model development software development evolution theory physics scientific writing collaboration skills Linux

Instituto Superior Técnico (Centro de Física Teórica de Partículas)

04/2011 - 10/2011

Research fellow

Developed a CUDA C++ code for high-energy physics simulations.

Main skills C++ CUDA C++ software development high-performance computing physics Linux

Instituto Superior Técnico

01/2008 - 09/2008

Developer

Maintained a Java application to access remote controlled scientific experiments.

Main skills Java software development Linux

Education

Universidade Federal de Pernambuco

2018

Ph.D. in Physics (thesis)

Main skills mathematics statistics physics evolution theory model development software development Python C++ LaTeX Wolfram Mathematica scientific writing collaboration skills Linux

Instituto Superior Técnico

2012

M.Sc. in Engineering Physics (thesis)

Main skills mathematics statistics physics software development C++ LaTeX Wolfram Mathematica scientific writing collaboration skills Linux

Peer-reviewed publications (17)

(2023)

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!

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 (3)

(2023)

(2013)

Acta Physica Polonica B (2012)

Conference participations and seminars (10)

Congress of the European Society for Evolutionary Biology

Prague, Czech Republic

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

2022

Bern Data Science Day

Bern, Switzerland

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

2022

PREPARE meeting

Gulbenkian Science, Portugal

Talk: Modelling fitness landscapes across environments

2019

Young Scientists Retreat 2019

Gulbenkian Science and Institut Curie, Portugal

Poster: Modeling fitness landscapes across environments

2019

Postdoc Seminar

Gulbenkian Science, Portugal

Talk: Fitness costs of antimicrobial resistance in E. coli

2019

From Molecular Basis to Predictability and Control of Evolution

Nordita, Stockholm, Sweden

Participation

2019

IX Brazilian Meeting on Simulational Physics

International Institute of Physics, Natal, Brazil

Poster: Evolution of multicellularity: a mechanistic model

2019

Encontro de Física 2016

Sociedade Brasileira de Física, Natal, Brazil

Poster: Tradeoffs and the evolution of complexity

2016

Models in Population Dynamics and Ecology 15

Universidade Federal Fluminense, Nitéroi, Brazil

Poster: Predictability in populations evolving under imitation

2015

Excited QCD

Peniche, Portugal

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

2012

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

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

2023

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

Universidade Nova de Lisboa, Portugal

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

2020

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

(Public Library of Science)

Proceeding of the Royal Society B

(Royal Society)

Scientific Reports

(Nature)

Schools and other courses (5)

Ready for BioData Management, BioData.pt

Gulbenkian Science, Portugal

2019

Física Biológica (10 hours)

Federal University of Pernambuco, Brazil

2015

Contour Dynamics and Integrable Systems (10 hours)

Federal University of Pernambuco, Brazil

2015

Escola de Astrofísica e Gravitação

Instituto Superior Técnico, Portugal

2012

Summer School on Particle Physics

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

2011

Online courses (5)

SQL for Data Science

Coursera/University of California, Davis

2023

Django 4 and Python Full-Stack Developer Masterclass

Udemy

2023

Research Integrity: Concise (core course)

Epigeum Online Course System, Oxford University Press

2020

Programming Languages

Coursera/University of Washington

2013

Heterogeneous Parallel Programming

Coursera/University of Illinois at Urbana-Champaign

2013

Contact me!

Name

Message

André Amado

Ecological tradeoffs lead to complex evolutionary trajectories and sustained diversity on dynamic fitness landscapes (accepted) (A Amado, C Bank)

STUN: forward-time Simulation on TUnable fitNess landscapes in recombining populations (A Amado, Li Juan, C Bank)

Rapid adaptation of recombining populations on tunable fitness landscapes (Li Juan, A Amado, C Bank)

Epistasis decreases with increasing antibiotic pressure but not temperature (AH Ghenu, A Amado, I Gordo, C Bank)

A ϕ6 soliton with a long-range tail (A Amado, A Mohammadi)

Ecological specialization under multidimensional trade-offs (A Amado, PRA Campos)

Interplay of sources of stochastic noise in a resource-based model (A Amado, JV Santana-Filho, PRA Campos, EP Raposo)

Agent-based models of collective intelligence (SM Reia, A Amado, JF Fontanari)

The interplay of tradeoffs within the framework of a resource-based modelling (VM Oliveira, A Amado, PRA Campos)

A theoretical approach to the size‐complexity rule (A Amado, C Batista, PRA Campos)

A mechanistic model for the evolution of multicellularity (A Amado, C Batista, PRA Campos)

Quantum corrections to the generalized Proca theory via a matter field (A Amado, Z Haghani, A Mohammadi, S Shahidi)

The influence of the composition of tradeoffs on the generation of differentiated cells (A Amado, PRA Campos)

Coupled fermion–kink system in Jackiw–Rebbi model (A Amado, A Mohammadi)

Competing metabolic strategies in a multilevel selection model (A Amado, L Fernández, W Huang, FF Ferreira, PRA Campos)

Coexistence of competing metabolic pathways in well-mixed populations (L Fernández, A Amado, PRA Campos, FF Ferreira)

Learning process in public goods games (A Amado, W Huang, PRA Campos, FF Ferreira)

Unpredictability of the fitness effects of antimicrobial resistance mutations across environments in Escherichia coli (submitted) (A Hinz, A Amado, R Kassen, C Bank, A Wong)

Flux tube widening in compact U(1) lattice gauge theory computed at T < Tc with the multilevel method and GPUs (A Amado, N Cardoso, P Bicudo)

Study of compact U(1) flux tubes in 3+1 dimensions in lattice gauge theory using GPU's (A Amado, N Cardoso, N Cardoso, P Bicudo)