John R. Finnerty

E-mail:
jrf3@bu.edu

Mailing address:
Boston University
Biology Department
5 Cummington Street
Boston, MA 02215

Departmental website:
http://www.bu.edu/biology/people/faculty/finnerty/

Research Interests
Education
Academic Affiliations
Publications
Presentations
Research Support
Awards
Courses Taught
Science Education Resources

Research Interests

_Evolution and development.
_Ecological developmental biology.
_Evolutionary genomics.
_Invertebrate zoology.
_Science education.
_Development of Nematostella as a model system.

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Education
_

_Undergraduate Education:
_University of Pennsylvania
_B. A. in Biology, 1989 (Magna cum laude);

_Graduate Education:
_University of Chicago,
_Ph. D. in Organismal Biology, 1994

_Postdoctoral Training:
_University of Chicago
_Evolutionary Developmental Biology
_October 1994 - December 1998

_Additional Training:
_Comparative Functional Genomics Workshop
_Mount Desert Island Biological Laboratory, August 2000

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Academic Affiliations

_1999-present.
_Boston University
_[1] Biology Department.
_[2] Center for Ecology & Conservation Biology. [CECB]
_[3] Program in Molecular Biology, Cell Biology, and Biochemistry. [MCBB]
_[4] Bioinformatics Program.
_[5] Boston University Marine Program [BUMP].

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Publications

1992

Finnerty JR, Block BA (1992) Direct sequencing of mitochondrial DNA detects highly divergent haplotypes in blue marlin (Makaira nigricans). Mol Mar Biol Biotech 1(3): 206-214. [abstract] [download .pdf] [cited by]

1993

Block BA, Finnerty JR, Stewart AF, Kidd J (1993) Evolution of endothermy in fish: mapping physiological traits on a molecular phylogeny. Science 260: 210-214. [abstract] [download .pdf] [cited by]

1994
Block BA, Finnerty JR (1994) Endothermy in fishes - a phylogenetic analysis of constraints, predispositions, and selection pressures. Environ Biol Fish 40(3): 283-302. [abstract] [download .pdf] [cited by]

Finnerty JR, Block BA (1994) Accounting for endothermy in fishes - response. Science 265: 1250-1251. [abstract] [download .pdf] [cited by]

Finnerty JR (1994) Molecular Phylogeny of the Scombroidei (Teleostei): Implications for the Evolution of Endothermy. [Dissertation, University of Chicago, Department of Organismal Biology & Anatomy] [abstract] [download .pdf] [cited by]

1995
Finnerty JR, Block BA (1995) Evolution of cytochrome-B in the Scombroidei (Teleostei) - Molecular insights into billfish (Istiophoridae and Xiphiidae) relationships. Fish Bull 93(1): 78-96. [abstract] [download .pdf] [cited by]

1996
Finnerty JR, Master VA, Irvine S, Kourakis MJ, Warriner S, and MQ Martindale (1996) Homeobox genes in the Ctenophora: identification of paired-type and Hox homologues in the atentaculate ctenophore, Beroe ovata. Mol Mar Biol Biotechnol 5(4): 249-258. [abstract] [download .pdf] [cited by]

1997
Finnerty JR, Martindale MQ (1997) Homeoboxes in sea anemones (Cnidaria: Anthozoa): a PCR-based survey of Nematostella vectensis and Metridium senile. Biol Bull 193(1): 62-76. [abstract] [download .pdf] [cited by]

1998
Finnerty JR (1998) Homeoboxes in sea anemones and other nonbilaterian animals: implications for the evolution of the Hox cluster and the zootype. Curr Top Dev Biol 40: 211-54. [abstract] [download .pdf] [cited by]

Finnerty JR, Martindale MQ (1998) The evolution of the Hox cluster: insights from outgroups." Curr Opin Genet Dev 8(6): 681-7. [abstract] [download .pdf]

1999
Finnerty JR, Martindale MQ (1999) Ancient origins of axial patterning genes: Hox genes and ParaHox genes in the Cnidaria." Evol Dev 1(1): 16-23. [abstract] [download .pdf] [cited by]

2000
Roberts CW, Finnerty JR, Johnson JJ, Roberts F, Kyle DE, Krell T, Coggins JR, Coombs GH, Milhous WK, Tzipori S, Ferguson DJP, Chakrabarti D, McLeod R (2000) Shikimate pathway in apicomplexan parasites - Reply. Nature 397: 220-220. [abstract] [download .pdf] [cited by]

Finnerty JR (2000) Evolutionary developmental biology - Head start. Nature 408: 778-781. [abstract] [download .pdf]

Pasquinelli AE, Reinhart BJ, Slack F, Martindale MQ, Kuroda MI, Maller B, Hayward DC, Ball EE, Degnan B, Muller P, Spring J, Srinivasan A, Fishman M, Finnerty JR, Corbo J, Levine M, Leahy P, Davidson E, Ruvkun G (2000) Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA. Nature 408(6808): 86-89. [abstract]

2001
Finnerty JR (2001) Cnidarians reveal intermediate stages in the evolution of Hox clusters and axial complexity. Am Zool 41(3): 608-620. [abstract] [download .pdf] [cited by]

2002
Martindale MQ, Finnerty JR, Henry JQ (2002). The Radiata and the evolutionary origins of the bilaterian body plan. Mol Phylogenet Evol 24(3): 358-365. [abstract] [cited by]

Roberts CW, Roberts F, Lyons RE, Kirisits MJ, Mui EJ, Finnerty JR, Johnson JJ, Ferguson DJP, Coggins JR, Krell T, Coombs GH, Milhous WK, Kyle DE, Tzipori S, Barnwell J, Dame JB, Carlton J, McLeod R (2002). The shikimate pathway and its branches in apicomplexan parasites. J Infect Dis 185(Suppl.): S25-S36. [abstract]

2003
Ryan JF, Finnerty JR (2003) CnidBase: The Cnidarian Evolutionary Genomics Database. Nucl Acids Res 31(1): 159-63. [abstract] [download .pdf]

Schneider SQ, Finnerty JR, Martindale MQ (2003) Protein evolution: structure-function relationships of the oncogene beta-catenin in the evolution of multicellular animals. J Exp Zool 295B(1): 25-44. [abstract] [download .pdf]

Finnerty JR, Paulson D, Burton P, Pang K, Martindale MQ (2003). Early evolution of a homeobox gene: The ParaHox gene Gsx in the Cnidaria and the Bilateria. Evol Dev. 5: 331-345. [abstract] [download .pdf] [cited by]

Rokas A, King N, Finnerty JR, Carroll SB (2003) Conflicting Phylogenetic Signals at the Base of the Metazoan Tree. Evol Dev 5: 346-360. [abstract] [download .pdf]

Finnerty JR (2003) The origins of axial patterning in the metazoa: how old is bilateral symmetry? Int J Dev Biol 47(7-8): 523-529. [abstract] [download .pdf]

2004
Finnerty JR, Pang K, Burton P, Paulson D, Martindale MQ (2004) Homology of Bilateral Symmetry in Cnidaria and Bilateria: Axial expression of Hox genes and Dpp in the sea anemone Nematostella. Science 304: 1335-1337. [abstract] [download .pdf] [download supplemental material] [cited by]

Martindale MQ, Pang K, Finnerty JR (2004) Investigating the origins of triploblasty: "Mesodermal” gene expression in a diploblastic animal, the sea anemone, Nematostella vectensis (phylum, Cnidaria; Class Anthozoa). Development 131: 2463-2474. [abstract on PubMed] [download .pdf] [cited by]
Darling JD, Reitzel A, Finnerty JR (2004) Population genetics of the sea anemone Nematostella in New England estuaries assessed by AFLP analysis. Mol Ecol 13: 2969-2981. [abstract] [download .pdf] [cited by]

2005

Darling JD, Reitzel A, Burton P, Mazza M, Ryan JF, Sullivan JC, Finnerty (2005) A rising starlet: the starlet sea anemone, Nematostella vectensis.” BioEssays 27: 211-221. [abstract] [download .pdf] [cited by]

Finnerty JR (2005) Could bilateral symmetry have evolved due to selection for improved internal circulation?” BioEssays. 27: 1174-1180. [abstract] [download .pdf] [cited by]

Rieger RM, Ladurner P, Hobmayer B, Martindale MQ, Finnerty JR (2005). A Clue to the Origin of the Bilateria?" Science 307(5708): 353c-355c. [abstract] [download .pdf] [cited by]

Sullivan JC, O’Neill T, Finnerty JR (2005) Bringing the urban environment into the classroom: learning from an estuarine mesocosm. Urban Habitats 3(1) [download .pdf] [cited by]

2006
Darling JD, Reitzel AM, Finnerty JR (2006) Characterization of microsatellite loci in the widely introduced estuarine anemone Nematostella vectensis. Mol Ecol Notes. 6: 803-805. [abstract] [download .pdf] [cited by]

Reitzel AM, Sullivan JC, Finnerty JR (2006) Qualitative shift to indirect development in the parasitic sea anemone Edwardsiella lineata. Integ Comp Biol 46(6):827-837. [abstract] [download .pdf] [cited by]

Ryan JF, Burton PM, Mazza ME, Kwong GK, Mullikin JC, Finnerty JR (2006) The cnidarian-bilaterian ancestor possessed at least 56 homeoboxes. Evidence from the starlet sea anemone, Nematostella vectensis. Genome Biol 7: R-64. [abstract] [download .pdf] [cited by]

Sullivan JC, Ryan JF, Watson JA, Webb J, Mullikin JC, Finnerty JR (2006) StellaBase — the Nematostella vectensis genomics database. Nucl Acids Res. 34:D495-D499 [abstract] [download .pdf] [cited by]

Sullivan JC, Buscetta KJ, Michener RH, Whitaker JO, Finnerty JR, Kunz TH (2006) Models developed from 13C and 15N of skin tissue indicate non-specific habitat use by the big brown bat. Ecoscience 13: 11-22. [abstract] [download .pdf] [cited by]

Sullivan JC, Reitzel AR, Finnerty JR (2006) A large percentage of introns in human genes were present early in animal evolution—Evidence from the starlet sea anemone, Nematostella vectensis. Genome Informatics. 17(1): 219-229. [abstract] [download .pdf] [cited by]

2007

Mazza ME, Pang K, Martindale MQ, Finnerty JR (2007) Genomic organization, gene structure, and developmental expression of three clustered otx genes in the sea anemone Nematostella vectensis. J Exp Zoolog B Mol Dev Evol 308B: 494-506 [abstract] [download .pdf] [cited by]

Putnam NH, Srivastava M, Hellsten U, Dirks B, Chapman J, Salamov A, Terry A, Shapiro H, Lindquist E, Kapitonov VV, Jurka J, Genikhovich G, Gregoriev IV, Lucas SM, Steele RE, Finnerty JR, Technau U, Martindale MQ, Rokhsar DS (2007) Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor. Science 317:86-94. [abstract] [download .pdf] [cited by]

Reitzel AM, Burton P, Krone C, Finnerty JR (2007) Comparison of alternate developmental trajectories in the starlet sea anemone Nematostella vectensis (Stephenson): embryogenesis, regeneration, and two forms of asexual fission. Invert Biol 126: 99-112. [abstract] [download .pdf] [cited by]

Reitzel AM, Sullivan JC, *Brown BK, *Chin DW, *Cira EK, *Edquist SK, *Genco BM, *Joseph OC, *Kaufman CA, *Kovitvongsa K, *Muñoz MM, *Negri TL, Taffel JR, *Zuehlke RT, Finnerty JR (2007) Ecological and developmental dynamics of a host-parasite system involving a sea anemone and two ctenophores. J. Parasitology 93:1392-1402. [*students from BI547 “Marine Invertebrates,” a course in the Boston University Marine Program’s research semester] [abstract] [download .pdf] [cited by]

Ryan JF, Mazza ME, Pang K, Matus DQ, Baxevanis A, Martindale MQ, Finnerty JR (2007) Pre-bilaterian origins of the Hox cluster and the Hox code: Evidence from the sea anemone, Nematostella vectensis. PLoS ONE 2(1):e153. [abstract] [download .pdf] [cited by]

Sullivan JC, Finnerty JR (2007) A suprising abundance of human disease genes in a simple “basal” animal, the starlet sea anemone Nematostella vectensis. Genome. 50: 689-692. [abstract] [download .pdf] [cited by]

Sullivan JC, Kalaitzidis D, Gilmore TD, Finnerty JR (2007) Rel Homology domain-containing transcription factors in the Cnidarian Nematostella vectensis. Dev Genes Evol 217: 63-72. [abstract] [download .pdf] [cited by]

Sullivan JC, Ryan JF, Mullikin JC, Finnerty JR (2007) Conserved and novel Wnt clusters in the basal eumetazoan Nematostella vectensis. Dev Genes Evol 217(3): 235-239. [abstract] [download .pdf] [cited by]

2008

Moran Y, Weinberger H, Sullivan JC, Reitzel AM, Finnerty JR, Gurevitz M (2008). Concerted evolution of sea anemone neurotoxin genes is revealed through analysis of the Nematostella vectensis genome. Molecular Biology and Evolution 25:737-747. [abstract] [download .pdf] [cited by]

Moran Y, Weinberger H, Sullivan JC, Reitzel AM, Finnerty JR, and Gurevitz M (2008) Intron retention as a posttranscriptional regulatory mechanism of neurotoxin expression at early life stages of the starlet anemone Nematostella vectensis. Journal of Molecular Biology. 380:437-443. [abstract] [download .pdf] [cited by]

Reitzel AM, Darling JA, Sullivan JC, Finnerty JR (2008) Global population genetic structure of the starlet anemone Nematostella vectensis: multiple introductions and implications for conservation policy. Biological Invasions. In press. [abstract] [download .pdf] [cited by]

Reitzel AM, Sullivan JC, Traylor-Knowles N, Finnerty JR (2008) A genomic inventory of stress responsive elements in the model organism Nematostella vectensis. Biological Bulletin. In press. [abstract] [download .pdf] [cited by]

Sullivan JC, Reitzel AM, Finnerty JR (2008). Upgrades to StellaBase facilitate medical and genetic studies on the starlet sea anemone, Nematostella vectensis. Nucleic Acids Research 36, D607-D611. [abstract] [download .pdf] [cited by]

2009

Finnerty JR (2009) The starlet anemone, Nematostella vectensis. McGraw-Hill 2009 Yearbook of Science and Technology. In press.

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Invited presentations

1999

1. Society for Developmental Biology, Annual meeting, Nashville, TN.
2. University of Chicago. Symposium: The Developmental Basis of Evolutionary Change. Chicago, IL.

2000

3. Society for Integrative and Comparative Biology; Symposium: Hox Gene Evolution. Atlanta, GA.

2001

4. University of Illinois, Department of Cell and Structural Biology, Urbana, IL
5. Harvard University, Department of Organismic and Evolutionary Biology

2002

6. Cold Spring Harbor Laboratories Symposium. Evolution of Developmental Mechanisms

2003

7. Society for Developmental Biology. Boston, MA. Evolution of Development Symposium. Evolution of key bilaterian traits: Insights into axial patterning and mesoderm formation from the sea anemone Nematostella, a non-bilaterian animal. Finnerty JR, Pang K, Burton PM, and MQ Martindale.
8. International Conference of Cnidarian Biology. Lawrence, KS. Axial Patterning Symposium. Axial patterning in multiple contexts : Embryogenesis, regeneration and asexual reproduction of Nematostella. JR Finnerty.

2005

9. Northeast regional meeting of the Society for Developmental Biology, Woods Hole, MA, Inreach. A Pragmatic Plan for Bringing High School Students into Academic Laboratories. JR Finnerty. [slideshow]

2006

 10. Duke University. Department of Biology [slideshow]
11. Tufts University. Department of Biology
12. European Society for Evolutionary Developmental Biology. Prague. Symposium: Homeobox genes in Evolution and Development. [slideshow]

2007

13. Masschusetts Institute of Technology, Chemical Oceanography and Biogeochemistry Seminar
14. 4th International Symposium on Networks in Bioinformatics, Amsterdam
15. Harvard University, Radcliffe Workshop on Emerging Model Species

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Research Support


2008-2010
National Science Foundation
"Developmental Evolution of Facultative Parasitism: Mechanisms Underlying Body Plan Remodeling in the Sea Anemone Edwardsiella"
Award number: IOS 0818831; [View award abstract.]
Principal Investigator: JR Finnerty
Award Amount: $199,000.

2007-2009
National Science Foundation
"DISSERTATION RESEARCH: Microevolution of stress-response. Genetic, developmental, and molecular analyses of a unique NF-kB SNP"
Award number: DEB 0710098; [View award abstract.]
Principal Investigator: JR Finnerty (The award funds the disseration research of JC Sullivan)
Award Amount: $10,000.

2005-2008
Environmental Protection Agency / STAR Fellowship Program
"Historical Introductions and Population Dynamics of the Widely Introduced Salt Marsh Anemone, Nematostella vectensis."
Award number: F5E11155; [View award abstract.]
Principal Investigator: JR Finnerty (The award funds the disseration research of AM Reitzel)
Total Award Amount: $87,354. (including 3 year's stipend for graduate student)

2006-2007
Boston University; The Special Program for Research Initiation Grants
"Characterization of the kB stress response pathway in basal animals—Implications for the evolution of immunity, the conservation of coastal ecosystems, and the identification of novel antimicrobial agents."
Principal Investigator: JR Finnerty (with Tom Gilmore & Les Kaufman, co-PIs);
Total Award Amount: $25,000.

2003-2005
National Science Foundation, Division of Biological Infrastructure
"An automated DNA sequencer for the Department of Biology at Boston University."
Award number: DBI-0301711; [View award abstract.]
Principal Investigator: MD Sorenson (I am one of 3 co-PIs with J Celenza and C Schneider.)
Total Award Amount: $102,887.

2002-2005
National Science Foundation, Division of Integrative Organismal Systems
"Axial Patterning During Embryogenesis, Asexual Reproduction, and Regeneration."
Award number: IBN-0212773; [View award abstract.]
Principal Investigator: JR Finnerty;
Total Award Amount: $262,480.

1998-2002
National Science Foundation,
"The Structure, Evolution, and Deployment of the Hox Cluster in a Basal Cnidarian."
Principal Investigator: MQ Martdinale (I authored this grant proposal while a post-doc at the University of Chicago. For administrative reasons, Professor Martindale served as PI.);
Total Award Amount: $299,978.Award number: DEB 9727244; [View award abstract.]

1994-1996
National Institutes of Health
Developmental Biology Training Grant.
[post-doctoral fellow]

1991-1994
National Institutes of Health
Molecular Biology Training Grant.
[Ph.D. candidate]

1992
Hinds Fund Research Award
[Ph.D. candidate] University of Chicago; Award Amount: $2,500.

1990
Sigma Xi Research Award
[Ph.D. candidate]

1989-1990
Searle Fellowship
[Ph.D. candidate]

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Awards


2006
Gitner Award
for Distinguished Teaching, College of Arts and Sciences, Boston University

2004
nominated for the Metcalf Award
Boston University’s highest teaching award.

1995
Outstanding Doctoral Disseration
University of Chicago, Department of Organismal Biology

1988
Phi Beta Kappa

1986-1989
Dean's List
University of Pennsylvania.

1985
National Merit Scholarship

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Courses Taught


Spring 2004-2006
Biodiversity (CC106)
Boston University, Core Curriculum;
Responsibilities: Course coordinator, lab coordinator, curriculum design, lab design, lab
manual author, web site design and administration, lecturer, and discussion leader.
http://people.bu.edu/jrf3/cc106

Fall 2000, '01, '03, '05
Invertebrate Zoology (BI 301)

Responsibilities: Curriculum design, lab design / lab manual, web design and administration, and lectures.

Fall 2002, '06,
Marine Invertebrates (BI 547)
Boston University Marine Program
Responsibilities: Curriculum design, lab design, web design and administration, and lectures. http://people.bu.edu/jrf3/BI547

Spring 2000-2003, Fall 2004,
Evolution & Development (BI 505)
Boston University, Ecology, Behavior, and Evolutionary Biology Prog.
Responsibilities: Curriculum design, web design and administration, and lectures.
http://people.bu.edu/jrf3/BI505

Fall 1997, 1998,
Human Morphology
University of Chicago, Pritzker School of Medicine
Responsibilities: Lecturer and Laboratory Instructor.

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Science Education Resources

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