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Curriculum vitae

JOSEPH W. THORNTON, Ph.D.
Professor
Howard Hughes Medical Institute
Center for Ecology and Evolutionary Biology, Department of Biology
5289 University of Oregon
Eugene, Oregon 97403
joet@uoregon.edu


EDUCATION

Ph.D.

Columbia University, Biological Sciences, 2000, with distinction.

M. Phil

Columbia University, Biological Sciences, 1998.

M.A

Columbia University, Biological Sciences, 1997.

B.A.

Yale University, English, 1987.*


RESEARCH, TEACHING, AND PROFESSIONAL EXPERIENCE

2010-

Professor, Center for Ecology and Evolutionary Biology, Department of Biology, University of Oregon. Affiliate member, Center for Environmental Studies.

2009-

Early Career Scientist, Howard Hughes Medical Institute.

2007-2010

Associate Professor, Center for Ecology and Evolutionary Biology, Department of Biology, University of Oregon. Affiliate member, Center for Environmental Studies.

2002-2007

Assistant Professor, Center for Ecology and Evolutionary Biology, Department of Biology, University of Oregon. Affiliate member, Center for Environmental Studies.

2000-2002

Postdoctoral Research Scientist, Columbia University Earth Institute. Advisor: Darcy Kelley.

1999-2000

Lecturer, Columbia University Department of Biological Sciences.

1995-2000

Doctoral research, American Museum of Natural History, Molecular Systematics Laboratory. Advisor, Rob DeSalle.

1992-1995

Research coordinator, Greenpeace USA Toxics Campaign, Greenpeace International Chlorine Campaign

1987-1992

Research analyst, Greenpeace USA Toxics Campaign


HONORS AND AWARDS

2009

Richard T. Jones New Investigator Award, Oregon Medical Research Foundation

2009

Early Career Investigator, Howard Hughes Medical Institute

2009

Member, Faculty of 1000, Developmental Evolution Section

2008

National Institute of General Medical Sciences, Special Lecturer in Evolution and Medicine

2007

U.S. White House Presidential Early Career Award for Scientists and Engineers (PECASE)

2007-2012

University of Oregon Faculty Excellence Award

2006

Richard A. Bray Faculty Fellow, University of Oregon (for excellence in scholarship and teaching)

2006

Eric Holtzmann Memorial Lecturer, Columbia University

2006

Alfred P. Sloan Foundation Fellow (Molecular and Computational Biology)

2006

National Science Foundation CAREER Award

2002

Distinguished University Lecturer in Environmental Sustainability, Carnegie-Mellon University.

2000-2002

Columbia University Earth Institute Postdoctoral Fellowship.

2000

Distinction in Doctoral Research, Columbia University.

1999

Newberry Award for outstanding research in biological sciences, Columbia University

1998

National Science Foundation, Doctoral Dissertation Improvement Grant

1997

McGregor Award for outstanding teaching in biological sciences, Columbia University

1996

National Science Foundation Graduate Research Fellowship


GRANTS

2007-2011

National Institutes of Health. PI J. Thornton. Experimental and structural evolution of steroid hormone receptors. NIGMS 1R01-GM081592, September 2007-August 2011, $1,200,000.

2006-2011

National Science Foundation. PI J. Thornton. CAREER: Evolution of Steroid Hormone Receptor Functions and Interactions. IOB-0546906, January 15, 2006 - January 14, 2011, $911,000.

2005-2009

National Science Foundation. PI J. Thornton, co-PI J. Conery. Mixed model phylogenetic methods for evolutionarily heterogeneous data. DEB-0516530, October 1, 2005-September 30, 2009, $353,000.

2005-2007

National Science Foundation. PI J. Thornton, co-PI J. Keay. Dissertation Research: evolution of estrogen receptor functions in themollusk Octopus vulgaris. IOB-0508948, July 1, 2005-June 30, 2007, $11,908.

2005-2009

National Institutes of Health. PI J. Postlethwait, co-PIs J. Thornton, J. Conery. Resources for Teleost Gene Duplications and Human Disease. February 2005-January 2009, $3,451,237.

2004-2006

National Institutes of Health. PI J. Thornton. Estrogen receptor/ligand interactions: An Experimental Evolution System. 1R01-70792. May 2004-April 2006, ($253,237).

2004

Oregon Medical Research Foundation. PI J. Thornton. Experimental Evolution of Estrogen Receptor Structure and Function,” ($30,000).

2002-2006

National Institutes of Health. PI Rob DeSalle (Co-PIs D. Figurski, M. Siddall, J. Thornton), Genetic Transfer in the Evolution of Infectious Disease, 1 RO1 GM62351-01A1, ($936,149; $80,000 subcontract to J. Thornton).

2000-2002

Columbia University Earth Institute Postdoctoral Fellowship ($98,000).

2000

Kapor Foundation: Persistent Organic Pollutants and Public Policy ($10,000).

2000

The Beldon Fund: Persistent Organic Pollutants and Public Policy ($10,000).

1998-2000

National Science Foundation Doctoral Dissertation Improvement Grant: Molecular Evolution of the Nuclear Receptor Superfamily (DEB-9870055; $9,500).

1996

National Science Foundation Graduate Research Fellowship ($72,000).


PUBLICATIONS
Book
2000 Thornton J. Pandora's Poison: Chlorine, Health, and A New Environmental Strategy. MIT Press, 2000.

Research papers and reviews

(For pdfs, please go to Publications page)

2010

Bridgham JT, Eick G, Larroux C, Deshpande K, Harms MJ, Gauthier MEA, Ortlund EA, Degnan BM, Thornton JW (2010). Protein evolution by molecular tinkering: diversification of the nuclear receptor superfamily from a ligand-dependent ancestor. PLoS Biology 8(10): 1000497.

2010

Harms MJ, Thornton JW (2010). Analyzing protein structure and function using ancestral gene reconstruction. Current Opinion in Structural Biology 20:360-366.

2010

Hanson-Smith V, Kolaczkowski B, Thornton JW (2010). Robustness of ancestral sequence reconstruction to phylogenetic uncertainty. Molecular Biology and Evolution 27(9): 1988-1999.

2010

Eick GN, Thornton JW. Evolution of steroid receptors from an estrogen-sensitive ancestral receptor. Molecular and Cellular Endocrinology, in press.

2009

Kolaczkowski B, Thornton JW (2009) Long-Branch Attraction Bias and Inconsistency in Bayesian Phylogenetics. PLoS ONE 4(12): e7891.

2009

Bridgham JT, Ortlund EA, Thornton JW. An epistatic ratchet constrains the direction of glucocorticoid receptor evolution. Nature, 461:515-519, 2009.

2009

Keay J, Thornton JW. Hormone-activated estrogen receptors in annelid invertebrates: implications for evolution and endocrine disruption. Endocrinology 150:1731-1738, 2009.

2008

Carroll SM, Bridgham JT, Thornton JW. Evolution of hormone signaling in elasmobranchs by exploitation of promiscuous receptors. Molecular Biology and Evolution 5(12):2643-52, 2008.

2008

Bridgham JT, Brown JE, Rodriguez-Mari A, Catchen JM, Thornton JW. Evolution of a new function by degenerative mutation in cephalochordate steroid receptors. PLOS Genetics 4(9):e1000191, 2008.

2008

Kolaczkowski B, Thornton JW. A mixed model of heterotachy improves phylogenetic accuracy. Molecular Biology and Evolution 25(6):1054-1066, 2008.

2007

Ortlund EA, Bridgham JT, Redinbo MR, Thornton JT. Crystal structure of an ancient protein: evolution of a new function by conformational epistasis. Science 317:1544-1548, 2007.

2007

Dean AM, and Thornton JW. Mechanistic approaches to the study of evolution: the Functional Synthesis. Nature Reviews Genetics 8:675-688, 2007.

2007

Kolaczkowski B, Thornton JW. Effects of branch length uncertainty on Bayesian posterior probabilities for phylogenetic hypotheses. Molecular Biology and Evolution 24:2108-2118, 2007.

2007

Fox JE, Bridgham JT, Bovee TFH, Thornton JW. An evolvable oestrogen receptor activity sensor: development of a modular system for integrating multiple genes into the yeast genome. Yeast 24:379-390, 2007.

2007

Thornton JW, Bridgham JT. Using ancestral gene resurrection to understand the evolution of protein function. In: Liberles DA, ed. Ancestral Gene Reconstruction. Oxford University Press, 2007.

2007

Thornton JW. What should we do about endocrine disruption? In: Gore A, ed. Handbook of Endocrine Disrupting Chemicals. CRC Press, in press.

2006

Kolaczkowski B, Thornton, JW. Is there a star-tree paradox? Molecular Biology and Evolution 23:1819-23, 2006.

2006

Keay J, Bridgham, JT, Thornton JW. The Octopus vulgaris estrogen receptor is a constitutive transcriptional activator: evolutionary and functional implications. Endocrinology 147:3861-9, 2006

2006

Bridgham, JT, Carroll SM, Thornton JW. Evolution of Hormone-Receptor Complexity by Molecular Exploitation. Science 312:97-101, 2006.

2006

Thornton JW. Evolution of gene families. In: Evolutionary Genetics: Concepts and Case Studies, ed. C. Fox and J. Wolf. Oxford University Press, 2006.

2005

Thornton JW, Kolaczkowski B. No magic pill for phylgoenetic error. Trends in Genetics 21:310-311, 2005.

2005

Krylova IN, Sablin EP, Moore J, Xy RX, Waitt GM, Juzumiene D, Bynum JM, Montana V, Lebedeva L, McKay JA, Suzuwa M, Williams JD, Williams SP, Guy RK, Thornton JW, Fletterick RJ, Willson TM, Ingraham HA. Structural analyses of NR5 orphan receptors reveal a potential role as nuclear phosphatidyl inositol sensors. Cell 120:343-355, 2005.

2005

Krieger N, Llowy I, … Thornton JW, and 18 others. Hormone replacement therapy, cancer, controversies and women’s health: historical, epidemiological, biological, clinical and advocacy perspectives. Journal of Epidemiology and Community Health J Epidemiol Community Health 59:740–748, 2005.

2004

Kolaczkowski B, Thornton JW. Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous. Nature 431:980-984, 2004.

2004

Thornton JW. Resurrecting ancient genes: experimental analysis of extinct molecules. Nature Reviews Genetics 5:366-375, 2004.

2004

Wilson VS, Cardon MC, Thornton JW, Korte JJ, Ankley GT, Welch J, Hartig PC. Cloning and in vitro expression and characterization of the androgen receptor and isolation of estrogen receptor from the fathead minnow (Pimephales promelas). Environmental Science and Technology 38:6314-21, 2004.

2003

Thornton JW, Need E, Crews D. Resurrecting the ancestral steroid receptor: ancient origin of estrogen signaling. Science 301:1714-1717, 2003.

2003

Wu KH, Tobias MT, Thornton JW, Kelley DB. Estrogen receptors in Xenopus: Duplicate genes, splice variants, and tissue-specific expression. General and Comparative Endocrinology 133:38-49, 2003.

2003

Thornton JW. Nuclear receptor diversity: phylogeny, evolution and endocrine disruption. Pure and Applied Chemistry 75:1827–1839, 2003.

2003

Thornton JW. A precautionary approach to assessing and managing endocrine disrupting chemicals. In: Science and the Precautionary Principle, ed. J. Tickner, Island Press, 2003.

2002

Sarkar IN*, Thornton JW*, Planet PJ, Figurski D, Schierwater B, DeSalle R. An automated phylogenetic key for classifying homeoboxes. Molecular Phylogenetics and Evolution 24: 388-399, 2002 (* equal contributors).

2002

Thornton JW, DeSalle R. Gene family phylogenetics: tracing protein evolution on trees. Experientia Supplementum (EXS) 92:191-207, 2002.

2002

Thornton JW. Gene family phylogenetics: tracing protein evolution on trees. In: Techniques in Molecular Systematics, eds. DeSalle R, Giribet G, Wheeler W. Birkauser-Verlag, 2002.

2002

Thornton JW, McCally M, Houlihan J. Biomonitoring of industrial pollutants: health and policy implications of the chemical body burden. Public Health Reports 117:315-23, 2002.

2002

Thornton J, McCally M, Howard J. Body burdens of industrial chemicals in the general human population. In: Critical Condition II: Public Health and the Environment, ed. M. McCally, MIT Press, 2002.

2001

Thornton JW. Evolution of vertebrate steroid receptors from an ancestral estrogen receptor by ligand exploitation and serial genome expansions. Proceedings of the National Academy of Sciences USA 98 (10), 5671-5676, 2001.

2001

Thornton JW. Implementing green chemistry: an environmental policy for sustainability. Pure and Applied Chemistry 73:1231-1236, 2001.

2000

Hawkins MB, Thornton JW, Crews D, Skipper JK, Dotte A, Thomas P. Identification of a third distinct estrogen receptor and reclassification of estrogen receptors in teleosts. Proceedings of the National Academy of Sciences USA, 97: 10751-10756, 2000.

2000

Thornton JW, DeSalle R. Phylogenetics meets genomics: homology and evolution in gene families. Annual Review of Genomics and Human Genetics 1:43-72, 2000.

2000

Thornton JW, DeSalle R. A new test to localize and test the significance of incongruence: detecting domain shuffling in the nuclear receptor superfamily. Systematic Biology, 49:183-201, 2000.

2000

Thornton JW. Beyond risk: an ecological paradigm for persistent organic pollutants. International Journal of Occupational and Environmental Health 6:318-330, 2000.

1998

Thornton JW, Kelley DB. Evolution of the androgen receptor: structure-function implications. BioEssays 20:820-829, 1998.

1996

Thornton J, McCally M, Orris P, Weinberg J. Hospitals and plastics: dioxin prevention and medical waste incineration. Public Health Reports 111:298-313, 1996.


INVITED LECTURES AND SYMPOSIA

2009

The evolution of molecular structure and function. Darwin: The Molecular Landscape. Cold Spring Harbor Laboratory Darwin Anniversary Symposium, 2009.

2009

The evolution of molecular structure and function. Society for the Study of Evolution, 2009.

2009

Opening Darwin's Black Box. Darwin Anniversary Lecture. Columbia University, 2009.

2009

The evolution of steroid receptor structure and function. Endocrine Society, Washington DC, 2009.

2008

Hormone receptor evolution and diversity: implications for environmental health, policy, and technology. Green Chemistry and Environmental Health Sciences, Beckman Center of the National Academies, Irvine, October, 2008.

2008

Hormone receptor evolution and diversity: environmental health implications. Gordon Research Conference on Environmental Endocrine Disrupters. New Hampshire, July 2008.

2008

Evolution of protein structure and function. Evolution and Medicine Lecture Series, National Institute of General Medical Science, Bethesda, MD, 2008.

2008

Evolution of molecular complexity. Integrating Evolution, Development and Genomics 2008. University of California, Berkeley, May 2008.

2007

Evolution of glucocorticoid and mineralocorticoid receptors. Sixth International Symposium on Aldosterone and ENaC: From Gene to Disease. Zermatt, Switzerland, October, 2007..

2007

Mechanistic evolution of steroid hormone receptors. Gordon Conference on Hormone Action in Cancer and Development. July, 2007.

2006

The evolution of molecular complexity. Eric Holtzmann Memorial Lecture, Columbia University, November 2006.

2006

Evolution of complexity: insights from ancestral gene resurrection (invited sympsoium talk). Society for Molecular Biology and Evolution. Tempe, AZ, May 2006.

2006

Evolution of steroid receptor signaling. Western Regional Conference on Comparative Endocrinology. Newport, OR, March 2006..

2006

Using ancestral gene resurrection to dissect the evolution of complexity. Gordon Research Conference on Molecular Evolution. Ventura, CA, January 2006.

2005

Evolution of nuclear receptors from an ancestral liganded receptor. EMBO Nuclear receptors conference: from chromatin to disease, Lake Garda, Italy

2005

The evolution of molecular interactions: steroid hormones and their receptors. Gordon Research Conference on Ecological and Evolutionary Functional Genomics. Oxford UK

2005

Thornton J. Evolution of steroid receptors in invertebrates. International Congress on Comparative Endocrinology, Boston, MA (declined due to schedule conflict)

2005

Thornton J. Reconstructing and resurrecting ancestral steroid receptor sequences. European Science Foundation Meeting on Ancestral Gene Reconstruction, Kristineberg, Sweden

2004

Thornton J. Evolution of steroid receptors and their ligands. Nuclear Receptors Symposium, Karolinska Institute, Huddinge, Sweden

2004

Thornton J. Evolution of steroid receptors and their ligands. Endocrinology Society Annual Meeting. New Orleans

2003

Thornton J. Steroid receptor biodiversity and evolution. Gordon Research Conference on Hormones and Development, New London, CT

2002

Thornton J. Nuclear receptor biodiversity: evolution and endocrine disruption. IUPAC/SCOPE International Workshop on Environmental Endocrine Disrupters. Yokohama, Japan

2002

Thornton J. Evolution of steroid receptors and implications for endocrine disruption. Gordon Research Conference on Environmental Endocrine Disruption, June 2002 (keynote introductory lecture).

2002

Thornton J. Complexity and sustainability: towards a new environmental policy strategy. Distinguished University Lecture, Carnegie-Mellon University, February 2002 (University-wide lecture).

2001

Thornton J. Evolution of steroid receptors and implications for endocrine disruption. Environmental Hormones 2001, Tulane University, October 2001.

2001

Thornton J. The role of green chemistry in a sustainable society. International Union of Pure and Applied Chemistry, Chemrawn XIV (Chemistry Applied to World Needs) Congress, Boulder, CO

2000

Thornton J. Pandora’s Poison: Science and policy of global chemical pollution. Columbia University, (University-wide lecture)

1996

Thornton J. Hospitals, plastics, and dioxin pollution. American Public Health Association.

1995

Thornton J. A precautionary policy on chlorine chemistry. American Association for the Advancement of Science. Atlanta, GA

1992 Thornton J. The case for a chlorine phase-out. American Public Health Association. Washington DC

INVITED SEMINARS

2009 Vollum Institute, Oregon Health Sciences University.
2008 University of Wisconsin, Department of Genetics.
2008 Kavli Institute for Theoretical Physics, University of California Santa Barbara.
2008 University of California San Francisco, Department of Biochemistry.
2008 Yale University, Department of Ecology and Evolutionary Biology.
2007 Harvard University, Department of Organismal and Evolutionary Biology.
2007 University of Michigan, Departments of Molecular, Cellular, and Developmental Biology and Ecology and Evolutionary Biology.
2006 Stanford University, Department of Biological Sciences
2006 Reed College, Biology Department
2004 Bodega Bay Marine Laboratory
2003 University of Texas, Austin, Integrative Biology Section
2003 Oregon State University, Department of Zoology
2003 Oregon Institute of Marine Biology
2002 U.S. Environmental Protection Agency, Office of Research and Development
2002 Princeton University, Woodrow Wilson School , Program in Science, Technology and Enviornmental Policy
2002 Dartmouth College, Department of Biological Sciences
2002 Indiana University, Department of Biology
2002 University of Oregon, Department of Biology
2001 Columbia University, Interfaces Seminar in Science and Policy
2001 Columbia Univesity, Center for Reproductive Sciences
2001 Rockefeller University, Laboratory of Neuroendocrinology
2001 Columbia University, Center for Environmental Research and Conservation
2001 Columbia University, School of Environmental Health, Department of Environmental Health
1999 Rensallaer Polytechnic Institute, Department of Science and Technology Studies

CONTRIBUTED TALKS AND POSTERS, SCIENTIFIC MEETINGS

2003 Gordon Conference on Ecological and Evolutionary Functional Genomics, (poster)
2001

Society for the Study of Evolution/Society of Systematic Biologists, Knoxville, TN (contributed talk)

1999

EMBO Nuclear Receptors Conference, Erice, Italy (poster and abstract)

1998

Society for Social Studies of Science, Halifax, Canada

1997

EMBO Nuclear Receptors Conference, Villefranche, France (poster and abstract)

UNIVERSITY SERVICE

Biology Deparrtment Curriculum Committee 2005-2009.

Coordinator, CEEB website 2007-2009.

Coordinator, CEEB retreat, 2005.

Search committees for CEEB faculty positions in ecology, 2003-4, 2004-5, 2006-7

Search committees for CEEB faculty positions in evolution 2003-4, 2005-6, 2007-8 (chair), 2008-9 (chair)

Computer facilities coordinator, CEEB, 2002-2005

Lecturer, UO Institute of Molecular Biology introductory course for incoming grad students, 2003


SCIENTIFIC AND PUBLIC SERVICE

Grant application reviewer for: NSF Biological Sciences Division (programs in Microbiology, Ecological and Evolutionary Physiology, Quantitative Environmental and Integrative Biology, and Integrative Animal Biology, Systematic Biology, Integrative and Organismal Systems) Canadian Research Council, UK BBSRC, California Breast Cancer Research Program.

Journal reviewer for: Environmental Science and Technology, Gene, General and Comparative Endocrinology, Genome Research, Journal of Molecular Evolution, Journal of Molecular Endocrinology, Molecular Biology and Evolution, Molecular Phylogenetics and Evolution, Nature, Nature Reviews Genetics, PLOS Biology, PLOS Genetics, Science, Science STKE, Systematic Biology, Trends in Genetics, MIT Press.

Ad hoc scientific advisor, speaker, expert witness, and author on environmental health issues for: Sustainable Ecosystems Institute, Breast Cancer Action, Healthy Building Network, Environmental Health Fund, Environmental Health Sciences, SAFER, Environmental Health Strategy Center, Center for Health, Environment and Justice, Natural Resources Council of Maine, Advancing Green Chemistry, Oregon Toxics Alliance, Greenpeace USA, Forest Service Employees for Environmental Ethics, Environmental Media Services


COURSES TAUGHT

Molecular Phylogenetics, Bio 485/585, University of Oregon, Spring 2003, Winter 2005, Spring 2008.

Evolution, Bio 380, University of Oregon, Winter 2004, Spring 2005, Winter 2006, Winter 2007, Winter 2008, Winter 2009.

Molecular Evolution, Bio 484/584, University of Oregon, Spring 2006.

Biology and Politics, Bio 410/510, University of Oregon, Spring 2007, Spring 2009.

Molecular Evolution, Columbia University, Bio 3020, Spring 2000.


ADVISING

Postdocs: Dr. Jamie Bridgham (currently research scientist, University of Oregon), Dr. Geeta Eick (current), Dr. Michael Harms (current), Dr. Jennifer Fox (now senior cell biologist, Oregon Translational Research and Drug Development Institute), Dr. Bryan Kolaczkowski (now postdoctoral scientist at Dartmouth)

Graduate students: June Keay (current), Paul Cziko (current), Victor Hanson-Smith (current), David Anderson (current), Sean Carrol (now postdoctoral scientist at Harvard,) Bryan Kolaczowski (Ph.D. 2006, now postdoctoral scientist at Dartmouth)

Rotating graduate students: David Anderson (F08), Victor Hanson-Smith (F07), Sean Carroll (W04), Bill Gillis (W04), June Keay (S03)

Undergraduates: Johnlukas Webb (current), Katelyn Armstrong (current), John St. John (now graduate student in Bioegineering at UC Santa Cruz), Justine Brown (06-07, Biology Honors, now graduate student in Pathobiology at University of Washington), Anne Belusko (05-06, now in dental school at OHSU), Jesse Zaneveld (03-05, Biology honors, now in graduate school in Molecular and Cellular Biology at U. Colorado), Molly Klein-McDowell (03-04, now graduate student in Biology at SFSU)

Graduate student qualifying examination committees: Conor O'Brien (W07), Richard Jovelin (W05), Michelle Phillips (F03), June Keay (F03), Bryan Kolaczowski (W03), Craig Everroad (F02)


* This degree was awarded in 1995, but Yale lists me in the class of 1987, which is when I attended. Long story.