People

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), and he continues to run his lab at the University of Oregon (Institute for Ecology and Evolution and Department of Biology).   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 recently led the Lane County Adult Hockey league in penalty minutes, but that’s not mentioned in the profile that Nature recently did on our work, which you can read here.
Jamie Bridgham, Ph.D
Research scientist
University of Oregon
jamieb (at) uoregon.edu
541-346-1537

Jamie serves 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
Postdoctoral research scientist
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
Postdoc till 9/2013, then
Assistant Prof., Univ. of Oregon
harms (at) uoregon.edu
website
541-346-1537
  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
Research manager at the
University of Chicago
lpicton (at) uchicago.edu
  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
Postdoctoral research scientist
University of Chicago
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
Postdoctoral research scientist
University of Chicago
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. candidate
University of Oregon
Institute for Ecology and Evolution
Paul is studying 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. Paul is an NSF Graduate Research Fellow and continues to make research voyages to Antarctica. In his spare time, he enjoys scuba diving in ocean water under a 20-foot thick layer of surface ice.
Dave Anderson
Ph.D. candidate
University of Oregon
Institute for Ecology and Evolution
Dave is studying the evolution of global 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.  Since coming to the UO, Dave has garnered a predoctoral Fellowship from the American Heart Association and a Doctoral Scholarship from Canada’s National Sciences and Engineering Research Council.  Dave also enjoys repeatedly watching films based on the timeless novels of Nicholas Sparks, collecting stray dogs, and inspiring mass resistance to the adaptationist paradigm.  He has 37″ biceps.
Alesia McKeown
Ph.D. candidate
University of Oregon
Institute of Molecular Biology
Alesia was educated in the wholesome embrace of her native North Carolina, where she worked with Paulo Almeida on the mechanisms of cytolytic peptides. Since beginning grad school at the University of Oregon, Alesia has helped pioneer the biochemistry side of the Thornton lab, revealing the mechanisms for the evolution of novel DNA-binding in the steroid receptors. When she is not in the lab or hiking in the mountains, Alesia can be found petting brontosaurus skeletons, walking her ravenous beagle Sir Gustav the Great, or rounding out her portfolio of embarrassing photos of her PI.
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 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.
Hussein Al-Asadi
Graduate student
University of Chicago
Committee on Evolutionary Biology
  Hussein is working on the performance of phylogenetic methods for inferring adaptive evolution in gene sequences.  He is generally interested in quantitative methods in phylogenetics and evolutionary biology, including the evolution of complexity. Hussein was an undergraduate at the University of Michigan where he majored in mathematics and did research with Tricia Wittkopp.  Hussein is an NSF Graduate Research Fellow. In his spare time, he likes to fish and tell jokes which are even worse than he thinks.

Lab Alumni

Bryan Kolaczkowski, Ph.D
Former 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
Former 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
Former Grad student
Now: Postdoc, Sandy Johnson Lab, UCSF
webpage

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
Former grad student
Now: Postdoc, Chris Marx lab, Harvard

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
Former grad student
Now: student, OSU 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
Former undergrad researcher
Now: PhD candidate, University of Washington
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
Undergrad researcher
Now: research assistant, OHSU
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
Former 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
Undergrad researcher
Now: PhD student, UC Santa Cruz
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
Undergrad researcher
Now: postdoc at Oregon State University

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
Undergrad researcher
Now: Graduate student,
San Francisco State University
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
Former research assistant
Now: research scientist and physician,
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
Undergrad researcher
NOW: In dental school,
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.