Serrapilheira/ICTP-SAIFR

Research Training Program in Quantitative Biology

July 2021

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List of speakers

1. Oded Rechavi (Tel Aviv U.) – Genetics, epigenetics and large datasets

Oded Rechavi works on the transgenerational inheritance through epigenetic mechanism involving small RNAs.

Recent publications:
Three Rules Explain Transgenerational Small RNA Inheritance in C. elegans. Houri-Zeevi L et al. Cell. 2020;
Illuminating Genetic Mysteries of the Dead Sea Scrolls. Anava S et al. Cell. 2020; 
Neuronal Small RNAs Control Behavior Transgenerationally. Posner R et al. Cell. 2019.

 

2. Eva Nogales (HHMI/U. California at Berkeley) – Molecular, structural and cell biology

Eva Nogales studies macromolecular assemblies and molecular function by direct visualization of the architecture of macro molecular complexes, their functional states, and their regulatory interactions using state-of-the-art cryo-electron microscopy and image analysis, as well as biochemical and biophysical assays.

Recent publications:
Structure of human TFIID and mechanism of TBP loading onto promoter DNA. Patel AB et al. Science. 2018;
Near-atomic model of microtubule-tau interactions. Kellogg EH et al. Science. 2018;
How Cryo-EM Became so Hot. Cheng Y et al. Cell. 2017.

 

3. Daniel Mucida (Rockefeller U.) – Host-pathogen interactions and disease ecology and epidemiology

Daniel 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.

Recent publications:
Microbiota-modulated CART+ enteric neurons autonomously regulate blood glucose. Muller PA et al. Science. 2020;
Microbiota modulate sympathetic neurons via a gut-brain circuit. Muller PA et al. Nature. 2020
Adrenergic Signaling in Muscularis Macrophages Limits Infection-Induced Neuronal Loss. Matheis F et al. Cell. 2020.

 

4. William Bialek (Princeton U.) – Biophysics

William Bialek uses physics to tackle complex biological questions such as the dynamics of individual biological molecules, developmental decisions in the embryo, and the brain.

Recent publications:
Coarse Graining, Fixed Points, and Scaling in a Large Population of Neurons. Meshulam L et al. Phys Rev Lett. 2019;
Collective Behavior of Place and Non-place Neurons in the Hippocampal Network. Meshulam L et al. Neuron. 2017;
Thermodynamics and signatures of criticality in a network of neurons. Tkačik G et al. Proc Natl Acad Sci U S A. 2015.

 

5. Hanna Kokko (U. Zurich) – Evolutionary biology

Hanna Kokko works on evolutionary ecology of sexual and asexual reproduction, analysis and management of animal populations, evolution of reproductive and social strategies, and sustainability science.

Recent publications:
Optimal germination timing in unpredictable environments: the importance of dormancy for both among- and within-season variation. Ten Brink H et al. Ecol Lett. 2020
When sex differences lead to extinction. Kokko H. Nature. 2018
The rate of facultative sex governs the number of expected mating types in isogamous species. Constable GWA et al. Nat Ecol Evol. 2018.

 

6. Jordi Bascompte (U. Zurich) – Community ecology and biodiversity, and ecological networks

Jordi Bascompte combines mathematical models, simulations, and data set analyses to address fundamental and applied questions in ecology. His current major research interest focuses on the structure and dynamics of ecological networks.

Recent publications:
Indigenous knowledge networks in the face of global change. Cámara-Leret R et al. Proc Natl Acad Sci U S A. 2019;
Ecological networks. On the structural stability of mutualistic systems. Rohr RP et al. Science. 2014;
The sudden collapse of pollinator communities. Lever JJ et al. Ecol Lett. 2014.

 

7. Silvia de Monte (ENS Paris/Max Planck Inst. for Evolutionary Biology) – Microbial ecology

By combining mathematical models, experiments in controlled conditions and environmental data analysis, Silvia de Monte and her team explore the interplay of cellular-level properties and collective function on the ecological and evolutionary time scales.

Recent publications:
Ubiquitous abundance distribution of non-dominant plankton across the global ocean. Ser-Giacomi E et al. Nat Ecol Evol. 2018;
The evolution of adhesiveness as a social adaptation. Garcia T et al. Elife. 2015;
Can we detect oceanic biodiversity hotspots from space? De Monte S et al. ISME J. 2013.

 

8. Ingrid Lohmann (U. Heidelberg) – Developmental biology

Ingrid Lohmann is a developmental biologist and her team works on the fundamental role of Hox proteins in the process of development of the fruit fly. More specifically, their interest goes from the control of stem cell proliferation to neurogenesis and metabolism during the process of development

Recent publications:
ATF4-Induced Warburg Metabolism Drives Over-Proliferation in Drosophila. Sorge S et al. Cell Rep. 2020;
Multi-level and lineage-specific interactomes of the Hox transcription factor Ubx contribute to its functional specificity. Carnesecchi H. Nature Commun. 2020;
The Hox transcription factor Ubx stabilizes lineage commitment by suppressing cellular plasticity in Drosophila. Domsch K. et al. Elife 2019.

 

9. Corina E. Tarnita (Princeton University) – Game Theory in Ecology and Evolution.

Corina E. Tarnita’s research examines the organization and emergent properties of complex adaptive systems at multiple scales, from single cells to entire ecosystems. Her approach is mainly theoretical and combines evolutionary dynamics, evolutionary game theory and elements of network theory but her lab works in collaboration with experimental and field ecologists, molecular biologists and evolutionary biologists to integrate modeling and empirical work.

Recent publications:
Eco-evolutionary significance of ‘loners’. Rossine, Fernando, et al. PLoS Biology (2020);
Emergence of diverse life cycles and life histories at the origin of multicellularity. Staps, Merlijn, Jordi van Gestel, and Corina E. Tarnita. Nature Ecology & Evolution (2019);
Fitness benefits and emergent division of labour at the onset of group living. Ulrich, Yuko, et al. Nature 560 (2018): , 560, 635-638.

 

10. Iain Couzin (Max Planck Institute of Animal Behavior) – Behavioral Ecology

Iain Couzin’s work aims to reveal the fundamental principles that underlie evolved collective behavior, and consequently his research includes the study of a wide range of biological systems, from insect swarms to fish schools and primate groups.

Recent publications:
Vortex phase matching as a strategy for schooling in robots and in fish. L Li et al., Nature communications 11 (1), 1-9 2020.
Individual and collective encoding of risk in animal groups. MMG Sosna et al., Proceedings of the National Academy of Sciences 116 (41), 20556-20561; 2019.
Shared decision-making drives collective movement in wild baboons. A Strandburg-Peshkin, et al., Science 348 (6241), 1358-1361 2015.

 

11. Max Rietkerk (Utrecht University) – Spatial Ecology

Recent publications:
The effect of climate change on the resilience of ecosystems with adaptive spatial pattern formation. R Bastiaansen, et al., Ecology Letters 23 (3), 414-429 (2020).
Multistability of model and real dryland ecosystems through spatial self-organization. R Bastiaansen, et al., Proceedings of the National Academy of Sciences 115 (44), 11256-11261 2018.
Phase separation driven by density-dependent movement: a novel mechanism for ecological patterns. QX Liu et al.,  Physics of life reviews 19, 107-121(2016).

 

12. Malin Pinsky (Rutgers University) – Climate change impacts of biodiversity + Conservation, management and decision-making

 Recent publications:

 

13. Carla Staver (Yale University) – Ecology & Introduction to ecological theory. 

Recent publications:

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