Projects | Evolution
top of page
CES-Funded Projects
2025
Long Cai (BBE)
"Understanding the Emergence of Germ Cells and Somatic Cells in Animal Multicellularity"
Bil Clemons, Matt Thomson, Yan Zhang, & Zachary Martinez (BBE)
"Deciphering the Evolution of Protein Cages with Deep Learning: From Nature to Engineered Designs"
Michael Dickinson (BBE)
"The Evolution of Gyroscopes and the Adaptive Radiation of Flies"
Woodward Fischer & Forest McCann (GPS)
"The Evolutionary Mechanics of Lichen Symbioses: Comparative Genomic Analyses of Lichen-Associated Bacteria"
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"
Diane Newman & Jarek Kwiecinski (BBE)
"Evolution of Terrestrial Bacteria: Lessons from the Biophysics of Desiccation Tolerance"
Trevor Nolan (BBE)
"Leveraging Cross-Species Single-Cell Genomics to Illuminate Evolutionary Innovations in Root Development"
Joe Parker & Hayley Smihula (BBE)
"Rove Beetle Chemosensation and the Evolution of Symbiotic Lifestyles"
Angelike Stathopoulos (BBE)
"Investigating Dual-Function FGFs through an Evolutionary Lens"
Paul Sternberg, Hillel Schwartz, & James Chieh-Hsiang Tan (BBE)
"Evolutionary Origin of Nematode-Bacteria Symbiosis"
Julia Tejada & Andres Rodriguez (GPS)
"Testing the Inverse Kinetic Isotope Effect of Threonine Deaminase"
Yuk Yung, Woodward Fischer, Stuart Bartlett & Josh Goldford (GPS)
"Investigating the Emergence of Ancient Enzyme Functionality with Primitive Amino Acid Libraries"
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
Zhen Chen (BBE)
Biomechanical adaptations of microtubule structures in mammalian sperm
Bruce Hay (BBE)
Cleave, Rescue and Ratchet: Can a diploid population be driven to extinction using an engineered version of Muller's ratchet?
Carlos Lois (BBE)
How does bird domestication regulate the suppression of intrinsic intracellular immunity to retroviruses?
Sarkis Mazmanian
& Joseph Boktor
(BBE)
A discovery platform for mediators of host-microbe interactions
Lior Pachter (BBE)
Phylogenetic analysis of gene expression based on a biophysical model
Rob Phillips & Kian Faizi (BBE)
Charting the influence of human activity on marine phosphorus cycling
Julia Tejada (GPS)
Deep-time ecology and evolution of dietary adaptations through fingerprints in dental enamel
Alex Varshavsky (BBE)
Analyzing evolution of the Arg/N-degron pathway by discovering
C. elegans N-terminal amidase
Rebecca Vorhees (BBE)
Evolution of metabolic regulation of mitochondria protein integration
Yuk Yung, Stuart Bartlett, Elle Chimiak, Josh Goldford & Jiani Yang (GPS)
Using Machine Learning to Uncover the First Proteins
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 reg
ulation
Daniel Wagenaar and Frank Lanfranchi (BBE)
From early mam
mals to modern machines: Tracing the evolution of visual cortex and neural netw
orks
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
2021-2022
Victoria Orphan
(GPS)
Comparative analysis of molecular adaptation mechanisms in A
rchaea
Mary Kennedy
(BBE)
Evolution of the synaptic protein synGAP and its potential relationship to emergence of the vertebrate postsynaptic density
Elizabeth Hong
(BBE)
Evolutionary diversification of antennal form and function in phorid flies
Thanos Siapas
(BBE)
Comparative analysis of hippocampal activity in mice and
Octodon degus
Pamela Bjorkman
(BBE)
Exploration of evolutionary relationships of sarbecoviruses with mosaic nanoparticle immunization
ared Leadbetter
(GPS/EAS)
Comparative Genomic and Ultrastructural Analyses of Surface Features in Distinct Lineages of Manganese Chemolithoautotrophs
Marianne Bronner
(BBE)
Building bridges: Comparative analysis of spinal cord regenerative ability from basal vertebrates to amniotes
Woody Fischer
(GPS)
Directed evolution of ‘ancient’ Cyanobacteria to study the past, present, and future of biological carbon fixation
2020-2021
Alex Sessions
(GPS)
Adaptations of algae to the increasing oxygen levels during the Earth history
Paul Sternberg
(BBE)
Molecular genetics of
Steinernema hermaphroditum
Matilde Marcolli (PMA/EAS)
New geometric methods for the study of language evolution
Carlos Lois & Michael Dickinson
(BBE)
The Molecular Origins of Brain Laterality
Christian Frankenbe
rg
(GPS)
Evolution of sustainable living in modern times
Lea Goentoro (BBE)
Making
Drosophila
regenerate limb
Shuki Bruck
(EAS)
Predicting Evolution – The SARS-Cov-2 Story
Alexei Aravin
(BBE)
Chasing the Red Queen: co-evolution of piRNAs and their target genes
Michael Elowitz
(BBE)
Evolutionary expansion of ligand-receptor computation in the BMP pathway
Francois Tissot
(GPS)
U isotopes in shark teeth: A sharper picture of ancient marine anoxia?
Victoria Orphan
(GPS)
Co-evolution of genome organization and its hijacking at the Archaea-
eukaryote boundary
Bruce Hay
(BBE)
Engineered gene drive in plants
2019-2020
Michael Dickinson
(BBE)
Evolution of the Dipteran Flight Motor
Elliot Meyerowitz
(BBE)
Evolution of an alternative form of life
Rob Phillips & Victoria Orphan
(BBE/GPS)
Evolution of the Regulatory Genome
Yuki Oka
(BBE)
Evolutional Adaptation of Ingestive Behaviors
Carlos Lois
(BBE)
Syntax as an exaptation of neuronal redundancy
Marianne Bronner
(BBE)
Acquisition of enteric glia during the course of vertebrate evolution
Francois Tissot
(GPS)
Did the extinction of the
G. newtonii
and other megafauna coincide with human arrival into Australia >65 to 45 ka?
David Anderson (BBE)
Immediate early gene responses and neuronal subtype evolution in a jellyfish
Bil Clemons
(CCE)
The evolution of tail-anchored membrane protein targeting
Joe Kirschvink
(GPS)
Evolutionary divergence in the use of geomagnetic cues by native speakers of English vs. Gurindji
Lior Pachter
(BBE)
Comparative genomics infrastructure for evolutionary studies
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
Kaihang Wang
(BBE)
Escherichia coli
Genome Minimization
Woody Fischer
(GPS)
Energetic tradeoffs and the accumulation of taxonomic and ecological diversity: Budgeting the bivalve shell
bottom of page