The Serrapilheira/ICTP-SAIFR Training Program in Quantitative Biology and Ecology will train young Brazilian and other Latin American scientists for world-class research on biology and ecology using the quantitative methods of mathematics, physics, and computer science. It strategically makes use of the country’s well-established excellence in mathematics and physics to tap into Brazil’s tremendous potential in life sciences.

Brazil’s ecosystems are among the richest in the world, and it is becoming increasingly clear that their inherent complexity poses enormous scientific challenges to find solutions that allow them to survive and flourish. The goal is to build an interconnected network of highly skilled scientists who can make significant contributions to advance the field in Brazil and Latin America.

To reach its goal, the training program will be highly selective and involve students who have already developed quantitative skills and are interested in applying these skills in solving cutting-edge problems in biology and ecology. Lectures in all areas of biology and ecology will be presented by international experts, and no previous knowledge of biology is required.

After a one-month online version of the program in 2021, the program in 2022 will involve a five-month in-person version divided into a two-month introductory module from July 4 – Sept. 3, 2022 and a three-month advanced module from Sept. 12 – Dec. 2, 2022. Students selected to the program will receive accommodations in São Paulo and a monthly stipend of 1500 reais for food and transportation, as well as airfare from their home city.

Students with quantitative skills who are either enrolled in an undergraduate program or have finished their undergraduate studies at a Latin-American institution and have not yet begun their doctoral degree can apply to participate in the five-month training program by reading the application instructions and submitting the online application form before April 13, 2022 at 17:00 BRT.. Approximately 30 students will be accepted into the program, and priority will be given to the first 500 applications received. Confirmed lecturers in the 2022 program will be listed on this webpage, and any questions should be sent to qbioprogram@ictp-saifr.org

Click here for Application Instructions in English.

Click here for Application Instructions in Portuguese.

Click here for Frequently Asked Questions in English and Portuguese.

Please send any questions to qbioprogram@ictp-saifr.org

Quantitative foundations of biological concepts

• Joshua Weitz – Georgia Institute of Technology, USA
Weitz and his team study how viruses transform human health and the fate of our planet at multiple scales including the molecular, populational and evolutionary. Weitz works on the structure and dynamics of complex biological systems, theoretical ecology and evolutionary biology, and disease dynamics and epidemiology.

• Adriana Lucia Sanz Garcia – Georgia Institute of Technology, USA
Lucia-Sanz’s research broadly focuses on describing qualitatively and quantitatively the behavior of biological systems. They investigate how biological systems can be described from the ground level, and to what extent a model captures the phenomenology observed in nature.

• Jeremy Harris – Georgia Institute of Technology, USA
Harris works on modeling asymptomatic transmission in COVID-19. His long-term project is to develop models of eco-evolutionary dynamics of viruses and their microbial hosts that incorporate phenotypic responses to cellular MOI.

• Jacopo Marchi – Georgia Institute of Technology, USA
Marchi is interested in studying biological systems using theoretical models that capture the key features leading to the observed experimental behavior, borrowing tools from nonlinear dynamics and statistical mechanics. Marchi works on bacteriophage therapy research. He is addressing how to steer the co-evolution between phages and bacteria to devise successful therapy strategies.

Hypothesis-driven research

• Glauco Machado – University of São Paulo, Brazil
Machado’s work focuses on the following topics: evolution of sexually selected traits, interrelationship between parental care and sexual selection, and defense mechanisms against predation. To answer these questions, Machado uses empirical—including comparative methods and field and laboratory experiments—and theoretical approaches—including the development of computational models.

• Ricard Alert-Zenón – Max Planck Inst. for Complex Systems, Germany
Alert´s main research topic is theoretical biophysics and soft matter, using and developing the physics of active matter to understand collective behaviors in cells and tissues. Among other topics, Alert´s lab studies how groups of bacteria migrate collectively and also the stability of propagating fronts of chemotactic bacteria.

Data-driven research

• C. Daniela Robles-Espinoza – Universidad Nacional Autónoma de México
Robles-Espinoza studies the genetic factors that influence cancer development, especially melanoma, in high-risk families, particularly in noncoding DNA, using bioinformatics and computational methods. Her expertise comprises the technical and functional analyses of next generation sequencing data.

• Mariana Gómez-Schiavon – Universidad Nacional Autónoma de México
Gómez-Schiavon’s research combines evolutionary theory, population genetics, computational biology, and biophysical models of gene regulatory circuits. At the International Laboratory for Human Genome Research (LIIGH), she aims to understand how the dynamic properties of gene regulatory circuits emerge, proliferate, and persist through natural selection.

Computational Methods

• Sara Mortara – Re. Green/U. of São Paulo
Mortara has academic experience in Statistical Modeling in Ecology, Biodiversity Informatics, and teaching computational skills and programming in R. She is an enthusiast of reproducibility in Science, co-founder of ¡liibre! (Independent Laboratory for Biodiversity and Reproducibility in Ecology Informatics) and a member of R-Ladies Rio.

• Andrea Sánchez-Tapia – Rio de Janeiro Botanical Garden Research Institute, Brazil
Sánchez-Tapia’s main interests are biodiversity informatics and plant ecology. She is a quantitative ecologist with a strong background in ecological niche modelling, biodiversity informatics, and data analysis in R. She develops reproducible biodiversity informatics workflows for ecological niche models, occurrence data cleaning, standardization to DwC (Darwin Core Standard), taxonomical and geographical validation, and data processing for IUCN (International Union for Conservation of Nature) extinction risk analysis.

• Ricardo Cerri – Federal University of São Carlos, Brazil
Cerri works with neural networks and genetic algorithms for hierarchical and multi-label problems. He has experience working mainly with Bioinformatics and Machine Learning, focusing on advanced methods for data classification, such as multi-output and structured learning (multi-label and hierarchical).

Conservation science and decision-making

• Michael Bode – Queensland University of Technology, Australia
Bode is interested in the behavior and control of uncertain and complex dynamical systems, and in spatial aspects of ecology and conservation—particularly when multiple conservation actors operate in a landscape.

• Paul Armsworth – University of Tennessee, USA
Armsworth’s research examines conservation efforts intended to protect biodiversity and enhance ecosystem services. His approach is highly interdisciplinary, and he combines techniques from ecology and economics such as mathematical modelling, statistical analyses, GIS, ecological field surveys, socioeconomic data, and other approaches. Armsworth also collaborates closely with a range of public agencies and conservation nonprofits.

Mathematical modelling in biology

• Ricardo Martínez-García – ICTP-SAIFR, Brazil
Martínez-García’s research investigates how individuals can create large natural structures and how these structures affect ecological and evolutionary dynamics through a multidisciplinary approach that combines mathematical modelling and data analysis. His research topics include collective foraging and self-organized group formation; long-range competition and vegetation patterns; and persistence and stability of ecological communities.

• Roberto Kraenkel – Institute of Theoretical Physics at UNESP, Brazil
Kraenkel works on mathematical biology and complex systems, with applications to ecology and epidemiology (infectious disease dynamics); and research on nonlinear dynamics of water-waves, population biology, water-reservoirs, and early warning signals of critical transitions.

Genetics and epigenetics

• Deborah Toiber – Ben-Gurion University of the Negev, Israel
Toiber works on DNA repair mechanisms and defects in DNA integrity associated with tumorigenesis, immunodeficiencies and aging. Toiber’s research focuses on understanding the role played by chromatin modifications and chromatin modifying enzymes in DNA repair mechanisms, and the consequences of the malfunction of these pathways causing disease, particularly in neurodegeneration and aging.

• Sean H. Rice – Texas Tech University, USA
Rice works on evolutionary biology, including developmental modeling, morphological evolution in invertebrates (ammonites and snails) and vertebrates (human), population and quantitative genetics, macroevolution, and the philosophical and conceptual basis of evolutionary theory.

Evolution

• Thomas Flatt – University of Fribourg, Switzerland
Flatt works on the genomics of adaptation, using the fruit fly Drosophila melanogaster as an experimentally tractable model. His work focuses on the genetic basis of variation and evolutionary changes in fitness-related traits such as fecundity, lifespan, survival, growth, and size. Other research topics of his lab include: the evolution of life histories and aging, and population genetics.

• Hanna Kokko – University of Zurich, Switzerland
Kokko works on the evolutionary ecology of sexual and asexual reproduction, analysis and management of animal populations, evolution of reproductive and social strategies, and sustainability science.

Developmental biology

• Moisés Mallo – Instituto Gulbenkian de Ciência, Portugal
Mallo and his team intend to understand the regulatory networks controlling each body area and the genetic regulations and controls on axial progenitors (group of cells that progressively make head, trunk, and tail structures), using rats as a model. Mallo also works on mutation genes combining transgenic and genome edition approaches with genome-wide analyses and advanced imaging techniques.

• Ross Sozzani – North Carolina State University, USA
Sozzani’s research leverages techniques derived from molecular, developmental and cell biology, mathematics, physics, chemistry, computer science and engineering. The Sozzani Lab’s team aims to reveal a specific molecular pathway of plant stem cells in its organization and maintenance, providing broader insights into the fundamental properties of stem cells across the plant and animal kingdoms.

Neurobiology

• Joe Paton – Champalimaud Foundation, Portugal
Paton’s research topics include animal behavioral learning, sensory cues, and neural mechanisms. Paton’s lab focuses on unraveling how animals in their context of being exposed to a myriad of sensory stimuli perform tasks that lead them to estimate intervals.

• Mauro Copelli – Federal University of Pernambuco, Brazil
Copelli’s research combines concepts and tools from statistical physics and information theory to understand neural dynamics. Some of Copelli’s most recent projects have focused on seeking signatures of criticality across cortical states, studying topological properties in functional brain networks as well as in quantifying neural signatures of psychotic disorders. In his research he confronts theoretical descriptions of these phenomena with experimental data.

Molecular and structural biology

• José Onuchic – Rice University, USA
Onuchic works on a variety of model biochemical and biological systems, on multiple scales including molecular-level interactions and multi-cellular structures. His research topics include medical applications on cancer, protein and chromatin folding, and stochastic effects in gene networks.

• Paul Whitford – Northeastern University, USA
Whitford’s research probes the energetic properties of biomolecular dynamics through a combination of theoretical modeling and high-performance computing (HPC). His investigations of biomolecular order-disorder transitions and energy transduction processes span from protein and ribonucleic acid folding to large-scale conformational rearrangements in molecular machines.

Systems biology

• Jorge Carneiro – Instituto Gulbenkian de Ciência, Portugal
Carneiro studies how cells within a multicellular organism interact with each other to ensure the development and maintenance of the body throughout life. Assessing the properties of the whole organism, Carneiro and his team search for general principles of biological organization and eventually the design of artificial systems.

Immunology

• Daniel Mucida – The Rockefeller University, USA
Mucida studies how the immune system associated with intestinal mucosae maintains a careful balance by generating efficient protective responses without jeopardizing its tolerance to innocuous foreign substances.

• Carolina Lucas – Yale University School of Medicine, USA
Lucas’ fields of research are microbiology and immunology. Lucas’ study focuses on identifying early immunology biomarkers levels across a whole spectrum of immune profile patients and clinical manifestations. Techniques in molecular genetics and virology are used as molecular signature and finally, as a diagnostic tool to prevent the development of diseases.

• Carmen Molina-Paris – Leeds University, UK
Molina-Paris is an applied mathematician working immunology and, more specifically, on understanding the molecular mechanisms of immune response (focusing mainly on T and B cells). Carmen’s research topics include T cell receptor-ligand binding and T cell receptor signaling, size and receptor diversity of the different T cell populations, interactions between dendritic cells and T cells, in vivo and in real-time.

Biophysics

• Vijay Balasubramanian – University of Pennsylvania, USA
In his biophysics research, Balasubramanian seeks to uncover the principles that underlie the organization of neural circuits across scales from cells to the whole brain, with applied lessons like adaptive molecular sensing from the olfactory system and adaptive immune system in vertebrates and bacteria (CRISPR).

• Curtis Callan – Princeton University, USA
Callan focused for most of his career on understanding the workings of quantum field theories, but over the last decade, his interest has shifted to theoretical problems in cellular biology using DNA sequence data modelling, and statistical inference approaches. He has been developing concrete examples of how this might work in problems ranging from gene regulation in bacteria to the functioning of the immune system in humans.

Community ecology and biodiversity

• Paulo Guimarães – University of São Paulo, Brazil
Guimarães’ work focuses on understanding the origin, maintenance, and fragility of large-scale patterns in ecological networks, in terms of ecological and evolutionary processes that operate at different scales. Guimarães achieves this by combining empirical data from ecological interactions, information on the natural history of interacting species, mathematical modelling, and network science.

• Miguel Lurgi – Swansea University, UK
Lurgi is a computational ecologist focusing on the development of ecological theory and the analysis of large datasets to gain a better understanding of community assembly and ecological patterns of species distributions and interactions in complex natural communities. His main research focus is on the mechanisms behind the emergence of complexity in ecological networks and the development of theoretical models of community and network dynamics to better understand these mechanisms and the patterns they give rise to.

Climate change impact on biodiversity

• Malin Pinsky – Rutgers University, USA
Pinsky’s research focuses on the ecological and evolutionary mechanisms driving global biodiversity change across scales of biological organization, from genomes to communities. His work integrates ecological theory with big data from global observing networks and temporal genomics to understand the dynamics of ecological systems in a changing world.

• Morgan Tingley – University of California, Los Angeles, USA
Tingley’s research addresses both fundamental and applied ecological questions of how species respond to large-scale, and predominantly anthropogenic changes to their environments, particularly the effects of climate change—including fire—on bird communities.

Behavioral ecology

• Iain Couzin – Max Planck Institute of Animal Behaviour, Germany
Couzin’s work aims to reveal the fundamental principles that underlie evolved collective behavior. His research includes the study of a wide range of biological systems, from insect swarms to fish schools and primate groups.

Microbial ecology

• Jacopo Grilli – ICTP-Trieste, Italy
Grilli studies how diversity is generated, organized, and maintained in ecological communities, mainly on microbial communities with a deep and sincere synergy between theory-driven and data-driven approaches.

• Martina dal Bello – Massachusetts Institute of Technology, USA
dal Bello’s research includes a wide variety of topics: microbial diversity, environmental drivers of microbial community composition and pheromone learning and optimal foraging in C. elegans.

Disease ecology and epidemiology

• Cara Haney – The University of British Columbia, Canada
Haney works on the genetic and environmental factors that regulate plant-microbiome associations, using as models plant Arabidopsis and its associated bacteria, such as Pseudomonas fluorescens. One of Haney’s research projects investigates how microbes, including P. fluorescens, can colonize a host despite the presence of an intact immune system.

• Zayda Morales Moreira – The University of British Columbia, Canada
Moreira’s research fields are Applied Microbiology, Biotechnology Engineering and Plant-Microbe interactions. She investigates microbiomes in different crops and plant colonization by endophytic bacteria, addressing and developing soil management based on the biocontrol potential of individual isolates.

• Jessica Metcalf – Princeton Univ., USA
Metcalf’s lab develops new methods to model host dynamics with the aim of providing insights to the fundamental drivers of immune function. Specifically, the lab focuses on characterizing the landscape of immunity in support of public health and developing a framework for understanding the evolution of immune function. To address these questions, Metcalf uses data-streams such as mobile phone call data records and also climatic drivers to understand how seasonal human aggregation/movement affects the transmission of pathogens.

Click HERE to access Timetable of Lectures and Discussion Sessions

 Confirmed Lecturers (in order of lectures) presently include:

Participants

Organizers

Advisory Board

Jordi Bascompte
Professor of Ecology at the University of Zurich, Switzerland, and director of the master’s Program in Environmental Sciences at the same university.

William Bialek
John Archibald Wheeler/Battelle Professor in Physics at Princeton University, USA, Visiting Professor of Physics at The Graduate Center at CUNY,USA, co-director of the Center for the Physics of Biological Function (The Graduate Center at CUNY and Princeton University).

Thiago Carvalho
Graduate Program Coordinator at the Champalimaud Foundation, Portugal.

António Coutinho
Former director of the Doctoral Program of the Gulbenkian Institute of Science (IGC), in Portugal.

Akiko Iwasaki
Professor at Yale University and principal investigator at the Howard Hughes Medical Institute (HHMI), USA.

Maria Leptin
Director of the European Research Council (ERC).

Simon Levin
James S. McDonnell Distinguished University Professor in the Department of Ecology and Evolutionary Biology at Princeton University (USA) and Director of the Center for BioComplexity at the Environmental Institute, also at Princeton.

Gabriel Mindlin
Professor of Physics at the University of Buenos Aires.

Stevens Rehen
Director of Research at Instituto D’Or de Pesquisa e Ensino (IDOR) and Full Professor at the Federal University of Rio de Janeiro (UFRJ).

• Deterministic Mathematical Modeling
Speaker: Roberto Kraenkel – Institute of Theoretical Physics at UNESP, Brazil
VIDEO PLAYLIST (classes from 04 of July to 29 of July, 2022)

• Computational Methods
Speakers: Sara Mortara – Re. Green/U. of São Paulo
Andrea Sánchez Tapia – Rio de Janeiro Botanical Garden
VIDEO PLAYLIST (classes from 04 of July to 11 of August, 2022)

• Hypothesis-driven research
Speaker: Glauco Machado – University of São Paulo
VIDEO PLAYLIST (classes from 1 of August to 2 of August, 2022)

• Data-Driven Research
Speakers: Daniela Robles-Espinoza – Universidad Nacional Autónoma de México
Mariana Gomez-Schiavon – Universidad Nacional Autónoma de México
VIDEO PLAYLIST (classes from 15 of August to 26 of August, 2022)

• Computational Methods / Machine Learning
Speaker: Ricardo Cerri – Federal University of São Carlos
VIDEO PLAYLIST (classes from 23 of August to 25 of August, 2022)

• Genetics and Epigenetics
Speakers: Deborah Toiber – Ben-Gurion University of the Negev
Sean H. Rice – Texas Tech University
VIDEO PLAYLIST (classes from 12 of September to 23 of September, 2022)

• Community ecology and biodiversity
Speakers: Paulo Guimarães – University of São Paulo
Caroline Dracxler – University of São Paulo
Erika M. Santana – University of São Paulo
Miguel Lurgi – Swansea University
VIDEO PLAYLIST (classes from 12 of September to 23 of September, 2022)

• Biophysics
Speakers: Vijay Balasubramanian – University of Pennsylvania
Curtis Callan – Princeton University
VIDEO PLAYLIST (classes from 26 of September to 14 of October, 2022)

• Genetics and Epigenetics
Speakers: Jessica Metcalf – Princeton University
Benjamin Rice – Princeton University
VIDEO PLAYLIST (classes from 03 of October to 07 of October, 2022)

• Molecular and structural biology
Speaker: José Onuchic – Rice University
VIDEO PLAYLIST (classes from 03 of October to 07 of October, 2022)

• Microbial Ecology
Speakers: Martina Dal Bello – Massachusetts Institute of Technology
Jacopo Grilli – ICTP Trieste
VIDEO PLAYLIST (classes from 10 of October to 17 of October, 2022)

• QBIO PROGRAM – Seminars
VIDEO PLAYLIST