CES-Funded Projects
2025
Long Cai (BBE)
"Understanding the Emergence of Germ Cells and Somatic Cells in Animal Multicellularity"
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Bil Clemons, Matt Thomson, Yan Zhang, & Zachary Martinez (BBE)
"Deciphering the Evolution of Protein Cages with Deep Learning: From Nature to Engineered Designs"
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Michael Dickinson (BBE)
"The Evolution of Gyroscopes and the Adaptive Radiation of Flies"
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Woodward Fischer & Forest McCann (GPS)
"The Evolutionary Mechanics of Lichen Symbioses: Comparative Genomic Analyses of Lichen-Associated Bacteria"
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Woodward Fischer, Victoria Orphan, & Calvin Rusley (GPS)
"PEAPOD: A New Approach for Detecting Deep Evolutionary Relationships Between Proteins in the Twilight Zone"
Bruce Hay & Thomas Adamo-Schmidt (BBE)
"Intraspecific Plasmid Competition as an Evolutionary Solution to the Plasmid Paradox"
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Diane Newman & Jarek Kwiecinski (BBE)
"Evolution of Terrestrial Bacteria: Lessons from the Biophysics of Desiccation Tolerance"
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Trevor Nolan (BBE)
"Leveraging Cross-Species Single-Cell Genomics to Illuminate Evolutionary Innovations in Root Development"
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Joe Parker & Hayley Smihula (BBE)
"Rove Beetle Chemosensation and the Evolution of Symbiotic Lifestyles"
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Angelike Stathopoulos (BBE)
"Investigating Dual-Function FGFs through an Evolutionary Lens"
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Paul Sternberg, Hillel Schwartz, & James Chieh-Hsiang Tan (BBE)
"Evolutionary Origin of Nematode-Bacteria Symbiosis"
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Julia Tejada & Andres Rodriguez (GPS)
"Testing the Inverse Kinetic Isotope Effect of Threonine Deaminase"
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Yuk Yung, Woodward Fischer, Stuart Bartlett & Josh Goldford (GPS)
"Investigating the Emergence of Ancient Enzyme Functionality with Primitive Amino Acid Libraries"
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Magdalena Zernicka-Goetz, & Sergio de la Rosa Garcia (BBE)
"The Role of Transposable Element Proteins in Early Embryo Development"
2023-2024​​
David Anderson & Youcef Ouadah (BBE)
Evolution of a curious male social behavior in Drosophila
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Zhen Chen (BBE)
Biomechanical adaptations of microtubule structures in mammalian sperm
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Bruce Hay (BBE)
Cleave, Rescue and Ratchet: Can a diploid population be driven to extinction using an engineered version of Muller's ratchet?
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Carlos Lois (BBE)
How does bird domestication regulate the suppression of intrinsic intracellular immunity to retroviruses?
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Sarkis Mazmanian & Joseph Boktor (BBE)
A discovery platform for mediators of host-microbe interactions
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Lior Pachter (BBE)
Phylogenetic analysis of gene expression based on a biophysical model
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Rob Phillips & Kian Faizi (BBE)
Charting the influence of human activity on marine phosphorus cycling
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Julia Tejada (GPS)
Deep-time ecology and evolution of dietary adaptations through fingerprints in dental enamel
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Alex Varshavsky (BBE)
Analyzing evolution of the Arg/N-degron pathway by discovering C. elegans N-terminal amidase
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Rebecca Vorhees (BBE)
Evolution of metabolic regulation of mitochondria protein integration
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Yuk Yung, Stuart Bartlett, Elle Chimiak, Josh Goldford & Jiani Yang (GPS)
Using Machine Learning to Uncover the First Proteins
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2022-2023
Claire Bucholz & Francois Tissot (GPS)
Uranium in ophiolites as a record of deep ocean oxygenation
Yuki Oka (BBE)
Jerboaized mouse brain for studying fluid regulation
Daniel Wagenaar and Frank Lanfranchi (BBE)
From early mammals to modern machines: Tracing the evolution of visual cortex and neural networks
Margaret McFall-Ngai and Vera Beilinson (BBE/Carnegie)
Evolution of Strain Variation Symbiosis in the Squid-Vibrio Model
Jerry Wang, Abdullah Farooq, Matt Thomson (BBE)
The emergence of associations: dissecting learning behavior in ancient unicellular organisms
Alexei Aravin (BBE)
Intragenomic conflicts as drivers of evolution
Michael Dickinson (BBE)
Molecular specializations of the Dipteran wing motor
Bil Clemons (CCE)
An evolutionary foundation for the role of Get3d in photosynthesis
David Glover (BBE)
Evolution of the BBSome complex in the Diverse Visual Systems of Insects and Vertebrates
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2021-2022
Victoria Orphan (GPS)
Comparative analysis of molecular adaptation mechanisms in Archaea
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Mary Kennedy (BBE)
Evolution of the synaptic protein synGAP and its potential relationship to emergence of the vertebrate postsynaptic density
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Elizabeth Hong (BBE)
Evolutionary diversification of antennal form and function in phorid flies
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Thanos Siapas (BBE)
Comparative analysis of hippocampal activity in mice and Octodon degus
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Pamela Bjorkman (BBE)
Exploration of evolutionary relationships of sarbecoviruses with mosaic nanoparticle immunization
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Jared Leadbetter (GPS/EAS)
Comparative Genomic and Ultrastructural Analyses of Surface Features in Distinct Lineages of Manganese Chemolithoautotrophs
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Marianne Bronner (BBE)
Building bridges: Comparative analysis of spinal cord regenerative ability from basal vertebrates to amniotes
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Woody Fischer (GPS)
Directed evolution of ‘ancient’ Cyanobacteria to study the past, present, and future of biological carbon fixation
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2020-2021
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Alex Sessions (GPS)
Adaptations of algae to the increasing oxygen levels during the Earth history
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Paul Sternberg (BBE)
Molecular genetics of Steinernema hermaphroditum
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Matilde Marcolli (PMA/EAS)
New geometric methods for the study of language evolution
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Carlos Lois & Michael Dickinson (BBE)
The Molecular Origins of Brain Laterality
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Christian Frankenberg (GPS)
Evolution of sustainable living in modern times
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Lea Goentoro (BBE)
Making Drosophila regenerate limb
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Shuki Bruck (EAS)
Predicting Evolution – The SARS-Cov-2 Story
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Alexei Aravin (BBE)
Chasing the Red Queen: co-evolution of piRNAs and their target genes
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Michael Elowitz (BBE)
Evolutionary expansion of ligand-receptor computation in the BMP pathway
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Francois Tissot (GPS)
U isotopes in shark teeth: A sharper picture of ancient marine anoxia?
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Victoria Orphan (GPS)
Co-evolution of genome organization and its hijacking at the Archaea-eukaryote boundary
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Bruce Hay (BBE)
Engineered gene drive in plants
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2019-2020
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Michael Dickinson (BBE)
Evolution of the Dipteran Flight Motor
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Elliot Meyerowitz (BBE)
Evolution of an alternative form of life
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Rob Phillips & Victoria Orphan (BBE/GPS)
Evolution of the Regulatory Genome
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Yuki Oka (BBE)
Evolutional Adaptation of Ingestive Behaviors
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Carlos Lois (BBE)
Syntax as an exaptation of neuronal redundancy
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Marianne Bronner (BBE)
Acquisition of enteric glia during the course of vertebrate evolution
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Francois Tissot (GPS)
Did the extinction of the G. newtonii and other megafauna coincide with human arrival into Australia >65 to 45 ka?
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David Anderson (BBE)
Immediate early gene responses and neuronal subtype evolution in a jellyfish
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Bil Clemons (CCE)
The evolution of tail-anchored membrane protein targeting
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Joe Kirschvink (GPS)
Evolutionary divergence in the use of geomagnetic cues by native speakers of English vs. Gurindji
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Lior Pachter (BBE)
Comparative genomics infrastructure for evolutionary studies
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Matt Thomson (BBE)
Reconstituting the evolution of the eukaryotic cytoskeleton in active matter
José Andrade (EAS)
Unearthing the Ant Tunnel Algorithm
Frances Arnold (CCE)
Experimental evolution of tryptophan synthase: mapping and learning from fitness landscapes
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Kaihang Wang (BBE)
Escherichia coli Genome Minimization
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Woody Fischer (GPS)
Energetic tradeoffs and the accumulation of taxonomic and ecological diversity: Budgeting the bivalve shell
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