Current Lab Members

Joe Thornton, Ph.D
Professor,
University of Chicago
joet1 (at) uchicago.edu
773-834-3423
Joe is is a Professor at the University of Chicago (Department of Human Genetics and Department of Ecology and Evolution).  He was previously on the faculty of the Institute for Ecology and Evolution and Department of Biology at the University of Oregon.   He has been working on nuclear receptor evolution since his thesis work at the American Museum of Natural History and his postdoctoral work at Columbia University. Before that he was the research coordinator for Greenpeace’s U.S. and international toxics campaigns; he became interested in receptor evolution while working on endocrine disruption by pesticides and other synthetic chemicals. Joe was an undergraduate English major and didn’t take a biology course until he was 30, because he was too busy playing the bass and helping people reform the chemical and waste disposal industries. He spends an inordinate amount of time on his bicycle(s).  You can read a profile that Nature recently did on our work here.
Tyler Starr
Graduate Student
University of Chicago
Department of Molecular Biology and Biochemistry
Tyler, an NSF graduate research fellow, is studying how the topology of protein sequence-function space shaped the evolution of ancient proteins.  Originally from Minnesoooota, Tyler spent four years in Oregon as an undergraduate at Willamette University and spent a summer as an undergraduate researcher in the Thornton lab at UO before his triumphant return to the Midwest.
Aarti Venkat
Graduate Student
University of Chicago
Dept. of Human Genetics
Aarti is currently studying the molecular mechanisms for the evolution of specificity and  cooperativity in DNA-binding transcription factors.  She did her undergraduate work in biochemistry at St. Xavier’s College in Mumbai, and then completed a master’s degree in bioinformatics at the University of Illinois, where she worked with Gene Robinson.  Aarti then worked with Molly Przeworski at the University of Chicago before beginning the PhD program in human genetics and joining the Thornton lab.
Mo Siddiq
Graduate Student
University of Chicago
Dept. of Ecology and Evolution
Mo is studying the molecular mechanisms of functional evolution in alcohol dehydrogenase of those Drosophila.  Mo did his undergraduate degree at the University of Indiana, where he worked with Kristi Montooth on evolutionary genetics in Drosophila.  Mo so thoroughly enjoyed having tiny flies buzzing around his head that he refuses to consider working with any other kind of organism.  He is a devastatingly effective pitcher for our slow-pitch softball team, the Cremasters.
Arvind S. Pillai
Graduate student
Department of Ecology and Evolution
Arvind studies the evolution of molecular complexity using ancestral protein reconstruction and biochemical experiments.  His work focuses on the evolution of hemoglobins —  a heterotetramer in a larger family of monomers homodimers — as a tractable model for the evolution of a complex molecular machine with multiple intersubunit interfaces.  Arvind was a neurobiology major at the University of Texas, where he studied the evolution of gene families involved in neural transmission.  In his spare time, Arvind is the reincarnation of Jorge Luis Borges.
Brian Metzger, Ph.D.
Postdoc
Brian, an NRSA-funded postdoc, is interested in whether the historical mechanisms by which new functions evolved represent the most functionally effective or mutationally accessible trajectories or, alternatively, whether there were many alternative routes that evolution could have taken. To address this question, Brian is applying techniques from protein engineering — experimental evolution and deep mutational scanning — to trace pathways from reconstructed ancient proteins to towards their modern functions. Brian did his graduate work with Trisha Wittkopp at the University of Michigan and received his undergraduate degree from the University of Wisconsin. His website, which is here, cannot describe how terrifying an opponent he is at board games.
Georg Hochberg, Ph.D.  Georg is a biophysicist by training who is interested in the evolution of protein complexes and protein-protein interactions. He studies how the oligomeric architecture of proteins changes over evolutionary time and how oligomeric proteins evolve a high degree of specificity in their assemblies. Socially Georg claims to be quiet and withdrawn, offering as evidence the photo of him at left from Mo’s wedding.

Lab Alumni

Jamie Bridgham, Ph.D
In the lab: Research scientist, University of Oregon
And then: Assistant (Research) Professor, University of Oregon
Now: Happily retired!

Jamie served as the anchor of the Eugene lab. A former NIH/NRSA fellow, Jamie has worked extensively on the evolution of steroid receptor specificity for ligands and DNA binding sites, but she has had a hand in most of the lab’s molecular projects. Jamie completed her Ph.D. at Notre Dame, working with Alan Johnson on the function and evolution of death receptors involved in apoptosis.
Geeta Eick, Ph.D
In the lab: Postdoctoral research scientist, University of Oregon
Now: Research scientist and laboratory manager, University of Oregon
beick (at) uoregon.edu
  Geeta is resurrecting ancestral steroid receptors to understand the evolution of androgen, progestagen, and corticosteroid sensitivity in early receptor lineages. She is also the master of the lab’s steroid receptor sequence database and leads much of our work in phylogenetic analysis. She studied biochemistry, phylogenetics, and evolution at the University of Stellenbosch and the University of Cape Town and then was trained in molecular biology at the Yale School of Medicine before coming to the UO in early 2007.  Geeta once hiked 57 miles with 17,000 feet of elevation gain in a single day, while carrying a 95-pound pack.
Mike Harms, Ph.D
In the lab: Postdoc till 9/2013
Now: Assistant Prof., Univ. of Oregon
harms (at) uoregon.edu
website
  Mike is a biophysicist who will begin an appointment as an Assistant Professor in the Chemistry Department and Institute of Molecular Biology at the University of Oregon in September, 2013. did his graduate work at Johns Hopkins with Bertrand Garcia-Moreno. Mike’s postdoctoral work in the Thornton lab addressed how the biophysical properties of proteins affect evolutionary processes and to reveal why proteins have the properties they do. Mike is currently studying the biophysics of permissive mutations.

Lora Picton, Ph.D
In the lab: Research scientist and lab manager until 2016
Now: Research scientist at Stanford University
University of Chicago
  Early in her scientific career, Lora developed a real desire to connect biochemical characterization with biological consequences. After undergraduate training in biochemistry, Lora did her doctoral thesis at Johns Hopkins with Blake Hill, studying the biochemistry and structure of mitochondrial fission proteins. Along with managing the UChicago branch of the Thornton Lab, she is eager to study how proteins take on new challenges through evolution. When not at the bench, Lora is a voracious reader, an aspiring chef, and a lover of hiking and biking outdoors.
Carrie Olson-Manning, Ph.D
In the lab: Postdoctoral research scientist until 2016
Now: Assistant Professor, Augustana University
colsonmanning (at) uchicago.edu
  Carrie is interested in the evolution of enzyme activity and metabolic pathways. She is studying how the corticosteroid synthesis pathway evolved in vertebrates. She completed her PhD at Duke University working with Tom Mitchell-Olds, where she studied the biochemical evolution of herbivore resistance in the charismatic relatives of broccoli.  Carrie up in North Dakota and did her undergraduate research with Tony Dean in Minnesota, so she loves the balmy winters of Chicago.
Qinwen Liu, Ph.D
In the lab: Postdoctoral research scientist, until 2015
Now: Staff Scientist, Grail Inc.
qinwen (at) uchicago.edu
  Qinwen is interested in the evolution of DNA specificity and other functions in developmentally important transcription factors in Drosophila.  She did her PhD in the evolutionary developmental biology in Caenorrhabditis species with Eric Haag at the University of Maryland.  When she is not seeking a deep and systematic understanding of the evolutionary factors that have generated phenotypic diversity, Qinwen is enjoying the diverse cultures and nature of Chicago and the rest of the U.S.
Paul Cziko, Ph.D.
In the lab: Graduate student, University of Oregon
Now: Research Scientist, University of Oregon
Paul is a multidisciplinary polar biologist. In the lab, he studied nuclear receptor evolution and functional diversity in invertebrates. Paul was an undergraduate and then a research assistant at the University of Illinois, where he studied antifreeze proteins in Antarctic notothenoid fishes. He was an NSF Graduate Research Fellow and continued to make research voyages to Antarctica during his dissertation work. He is now an NSF-funded antarctic research scientist. In his spare time, he enjoys scuba diving in ocean water under a 20-foot thick layer of surface ice.
Dave Anderson, Ph.D.
In the lab: Graduate student, University of Oregon
Now: NSERC postdoctoral scientist, University of British Columbia
Dave studied the evolution of DNA specificity in steroid receptors.  He received his undergraduate degree in theoretical astronomy from the Arts and Science Program at McMaster University.  Trading star-dust for nucleotides, Dave cannonballed into the world of evolutionary biology with a master’s degree in evolutionary genetics with Ben Evans, also at McMaster.  While at the UO, Dave was supported by a predoctoral Fellowship from the American Heart Association and a Doctoral Scholarship from Canada’s National Sciences and Engineering Research Council.  He is now a postdoc with Nobu Tokuriki in the Chemistry Department at UBC. Dave also enjoys collecting stray dogs, occasionally producing extraordinarily cute babies, and inspiring mass resistance to the adaptationist paradigm. He has 37″ biceps.
Alesia McKeown, Ph.D.
In the lab: Graduate student, University of Oregon
Now: Damon Runyon postdoc, University of Utah
Alesia studied the mechanisms for the evolution of specificity in steroid receptor DNA-binding domains. She helped pioneer the biochemistry side of the Thornton lab, revealing the mechanisms for the evolution of novel DNA-binding in the steroid receptors. Alesia was educated in the wholesome embrace of her native North Carolina, where she worked with Paulo Almeida on the mechanisms of cytolytic peptides. Alesia is now a postdoc in Nels Elde’s lab at the University of Utah. When she is not hiking in the mountains, Alesia can be found walking her ravenous beagle Sir Gustav the Great and blackmailing her former PI with her photo collection.
Bryan Kolaczkowski, Ph.D
In the lab: postdoc and grad student
Now: Assistant Professor, University of Florida
webpage
Bryan is a computer scientist and phylogeneticist. He was a graduate student in the lab and stayed on as a postdoc to complete several projects. Bryan studied the effect of evolutionary heterogeneity on current phylogenetic methods and developing new mixed-model techniques that are more accurate when the evolutionary process varies among lineages and sites. He has also done some beautiful work on the behavior of Bayesian phylogenetic methods. A former member of UO’s IGERT training program in Evolution, Development, and Genomics, Bryan is now an Assistant Professor at the University of Florida.

 

Jennifer Fox, Ph.D.
In the lab: our first postdoc
Now: Executive Director,
Oregon Translational Research and Development Institute
Jennifer was an NIH/NRSA fellow in the lab from 2004 to 2007. She was chief cell biologist and is now executive director at the Oregon Translational Research and Development Institute. When she was in the lab, Jennifer established an experimental evolution system in yeast to study how receptors evolve affinity for new ligands. Before joining us, Jennifer did her Ph.D. with John McLachlan at Tulane, where she discovered that endocrine disrupters in the environment can interfere with the symbiosis of plants and nitrogen-fixing rhizobacteria and was a postdoc with Craig Jordan at Northwestern, where she worked on ligand- and tissue-specific coactivators for the estrogen receptor.

 

Victor Hanson-Smith, Ph.D.
In the lab Grad student
Then: Postdoc, Sandy Johnson Lab, UCSF
Now: Genomics scientist, Verge Genomicswebpage
Victor was a graduate student in the Computer and Information Sciences Department at the University of Oregon and an NSF IGERT fellow. Victor studied the performance and accuracy of algorithms for phylogenetic inference and ancestral sequence reconstruction and played a lead role in our collaborative project reconstructing ancestral VTPases with Greg Finnigan and Tom Stevens. In addition to being an impressive computational biologist, Victor also happens to be a conservatory-trained classical pianist and world-class hiker.

 

Sean Carroll, Ph.D.
In the lab: Graduate student
Then: Postdoc, Chris Marx lab, HarvardNow: Staff scientist, Axcella Corp.
Sean was a graduate student in the Biology Department and an NSF IGERT fellow. Sean studied early glucocorticoid receptor evolution. He graduated in August 2009 and is now a postdoc with Chris Marx at Harvard, where he is using experimental evolutionary approaches in bacteria to study molecular adaptation. Sean is a very good frisbee player who occasionally has life-threatening bike accidents.

 

June Keay, Ph.D., D. Pharm
In the lab: Former grad student
Then: Oregon State University School of Pharmacy
June was a graduate student at UO and an NSF graduate research fellow. June studied the functional diversity of estrogen receptors in invertebrates and was the lead researcher for the lab’s publications on ERs in mollusks and annelids, as well as ERRs in nemerteans. June is now completing her training at OSU’s School of Pharmacy.
Justine Brown, Ph.D.
Former undergrad researcher
Then: PhD student, University of WashingtonNow: Program manager, Colorado Foundation for Public Health and the Environment
Justine Brown was an undergraduate research assistant in the lab from 2006-2008. Justine studied the evolution of steroid hormone receptors in cephalochordates following a crucial gene duplication. While in the lab, Justine won the UO Undergraduate Research Fellowship, and her Biology honors thesis work was published in PLOS Genetics. Justine’s goal is to apply evolutionary, molecular, and epidemiological approaches to address the AIDS pandemic in sub-Saharan Africa. She is now a doctoral student in the Pathobiology Program at the University of Washington.
Jackson Wong
In the lab: Undergrad researcher
Now: medical student, Oregon Health Sciences University
Jackson was an undergraduate in the lab from 2010-2012. He cloned and functionally characterized several ancestral estrogen-related receptors to define the genetic basis for the evolution of a new function in this family. Jackson is currently a research technician in Kirsten Lampi’s lab at Oregon Health & Science University, and will be applying for medical school in the fall. He likes to longboard, garden, and make his own kombucha (which, he assures us, is entirely legal).
Luke Webb
In the lab: undergrad researcher
Now: medical student, OHSU
Luke was an undergraduate researcher in the lab from 2009-2010. He worked on the development of a yeast system for directed evolution of ancestral steroid receptors and the expression and purification of resurrected glucocorticoid receptors. Luke is now a medical student at OHSU and remains, we believe, an awesome surfer and guitar player.
John St. John, Ph.D.
In the lab: Undergrad researcher
Then: PhD student, UC Santa Cruz Bioengineering DepartmentNow: Founder and chief scientist, Driver Group
John St. John was an undergraduate research assistant in the lab from 2007-2009. John used his programming abilities to study the accuracy of methods for selecting models for phylogenetic analysis. John completed an honors thesis in computer science and is now a doctoral student the Bioengineering Program at UC Santa Cruz.
Jesse Zaneveld, Ph.D
In the lab: Undergrad researcher
Then: Ph.D. student at University of Colorado, postdoc at Oregon State University
Now: Assistant Professor, University of Washington, Bothell
Jesse’s Biology Honors thesis was a phylogenetic and structural analysis of the evolution of ligand-binding in the entire nuclear receptor superfamily. Jesse found that, contrary to current wisdom, the ancestral receptor was almost certainly liganded, and so-called “orphan receptors,” which are not regulated by hormones and other ligands, are evolutionary novelties. Jesse completed his Ph.D in the MCB program at U. Colorado and is now a postdoc in microbiology at Oregon State.

 

Molly Klein-McDowell
In the lab: Undergrad researcher
Then: Graduate student,
San Francisco State UniversityNow: Genentech, Inc.
As a UO undergraduate, Molly isolated, cloned, and sequenced steroid receptors from basal chordates, including skate and lancelet. Molly is now a Master’s student in biology with Sarah Cohen at SFSU, where she is working on the evolutionary response of fish populations to chemical contamination.
Elle Need, MD
In the lab: our first research assistant
Now: Physician and Research Fellow,
University of Adelaide,
Australia
Elle was the first member of the Oregon lab, having arrived in Eugene 2 days before Joe did.  She was a research assistant in the lab for two years, during which time she characterized the functions of the Aplysia estrogen receptor — the first invertebrate steroid receptor discovered — and of the resurrected ancestral steroid receptor, which existed > 600 million years ago. She returned to Australia, completed an MD/PhD, and is now a physician-scientist focused on the role of the androgen receptor in reproductive cancers.
Anne Belusko, DDS
In the lab: undergrad researcher
Then: Oregon Health Sciences University
Anne was an undergraduate at the UO. She came to the lab because she was interested in endocrine disruption and public health. Anne worked on isolating steroid receptors from invertebrates. She completed dental school at Oregon Health Sciences University and is now a practicing dentist.