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Robert S. Coyne
Associate Professor
J. Craig Venter Institute
rcoyne@jcvi.org
9704 Medical Center Dr.
Rockville, MD 20850
301-795-7593
Overview
• Ph.D., Harvard University
• Post-Doc, Fred Hutchinson Cancer Research Center
• JCVI, 2005-present, P.I. on four major awards in this period.
• Principal research interests: genomics, post-genomics, and programmed genome
rearrangement in ciliates
• NSF Service: BIO/MCB Program Director 2002-05, 2009-10;
EPSCoR Program Director 2015-present
Appointments
J. Craig Venter Institute, 03/05 to present
Associate Professor, Department of Microbial and Environmental Genomics
• Principal Investigator on the following:
o NSF-funded project to investigate genome structure, contents and rearrangements
in Tetrahymena thermophila and related species
o NIH-funded project to develop high throughput methods for gene knockout strain
generation in Tetrahymena thermophila
o NIH-funded project to develop the means of cloning genes by complementation
of mutations in Tetrahymena thermophila
o USDA-funded project to sequence and annotate the genome of the parasitic ciliate
Ichthyophthirius multifiliis
• Coordination of annotation, EST sequencing, and analysis of Tetrahymena thermophila
macronuclear genome sequence
• Coordination of Tetrahymena comparative and micronuclear genomics through NHGRI
National Science Foundation, 11/02-03/05 and 09/09-09/10 (BIO), 1/15-present (EPSCoR)
BIO Program Director (Visiting Scientist, on leave from UVA and JCVI), Division of Molecular
and Cellular Biosciences (MCB)
• Management of “Biochemistry of Gene Expression” and “Microbial Genome
Sequencing” Programs
• Attendance and presentations at conferences and workshops: Plant and Animal Genomes
Conference, ASM/TIGR Conference on Microbial Genomes, Genomes to Life - DOE
Awardees Workshop, Systems Biology: Genomic Approaches to Transcriptional
Regulation, FASEB Ciliate Molecular Biology Conference, NSF Regional Grants
Conference, Annual Drosophila Research Conference, Protist Genomics Workshop

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• Independent Research and Development Activities: Consulting with scientists at TIGR on
assembly and annotation of the Tetrahymena thermophila whole genome sequence,
attending course on Genome Sequence Analysis at the Jackson Laboratory, Bar Harbor
• Taking part in strategic planning and assessment activities for NSF/MCB
EPSCoR Program Director (Intergovernmental Personnel Act appointee), Experimental Program
to Stimulate Competitive Research
• Management of Research Infrastructure Improvement Track-1, Track-2, and Workshop
programs, including complete review and award processes, strategic planning sessions,
reverse site visits, site visits, planning and assessment activities
• Lead coordinator of Workshop reviews, Spring 2016 Reverse Site Visits, FY 2017 Track-
2 competition, planning for biennial EPSCoR National Conference, BRAIN Initiative
Track-2 review panels
• Independent Research and Development Activities: continuation of research in ciliate
genomics, presentations at International Ciliate Molecular Biology Conference
(Camerino, Italy; July 2015) and The Allied Genetics Conference (Orlando, FL; July
2016)
Institut Jacques Monod, Paris France, 03/11-06/11
Visiting Researcher, supported by grant from "Research in Paris" program
• Research Topic: Epigenetic regulation of genome rearrangement in Paramecium
tetraurelia
University of Virginia Health Science Center, 07/01-06/04
Assistant Research Professor, Department of Biochemistry and Molecular Genetics (on leave
2002-04)
Cornell University, 06/00-06/01
Visiting Assistant Professor, Department of Molecular Biology and Genetics
Colgate University, 07/97-06/00
Assistant Professor, Department of Biology
• Teaching responsibilities: Genes: Introduction to Molecular Analysis, Genetics,
Research Tutorial ("Eukaryotic Genome Structure"), Seminar on Human Evolution
• Developed novel "real research" laboratory in which students used a yeast assay to screen
human BRCA1 sequence polymorphisms for cancer-associated loss of function, in
collaboration with scientists at the NIH; results published in Cancer Biology and Therapy
• Coordinator of Biology Department seminar series
• Member of five departmental search committees
Fred Hutchinson Cancer Research Center, 09/92-06/97
Postdoctoral Fellow in laboratory of Dr. Meng-Chao Yao
• Research interests: Genome rearrangement in Tetrahymena thermophila
Massachusetts General Hospital East, 07/91-08/92
Postdoctoral Fellow in laboratory of Dr. James Casanova

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• Research interests: Membrane protein trafficking in polarized epithelial cells, receptor-
ligand interactions
Oberlin College, 07/90-06/91
Visiting Assistant Professor in Department of Biology
• Taught advanced molecular biology, introductory cell biology/biochemistry
• Research interests: Suppression of transposon-induced mutations in Drosophila
Grants Awarded
• 5/15/12-5/14/16: NSF: “Genomics of Tetrahymena” $1,387,688
• 9/01/10-2/31/14: NIH R24: “High Throughput Gene Knockout Production in
Tetrahymena thermophila” $1,219,625
• 8/01/07-7/31/09: NIH R24: “Forward Genetics in Tetrahymena: Cloning by
Complementation” $746,258
• 9/15/07-9/14/10: NSF/USDA Microbial Genome Sequencing Program, “Genome
Sequence of the Parasitic Ciliate, Ichthyophthirius multifiliis” $887,000
• 1998-2001: NSF RUI Award: "Trans-Acting Factors in Large-Scale Genome
Rearrangement" $300,000
• 1999: NSF Instrumentation Grant (Co-PI): "Automated Sequencing at Colgate
University" $38,990
• 1999: NSF REU Supplement
• 1994-1996: NRSA Postdoctoral Fellowship
• 1982-1985: NSF Predoctoral Fellowship
Professional Service
! Reviewer for NSF Biochemistry of Gene Expression, Eukaryotic Genetics, and Microbial
Genome Sequencing grant review panels, Human Frontier Science Program, and the journals
Science, Genes and Development, Eukaryotic Cell, PloS Genetics, Microbiology and
Molecular Biology Reviews, J. Eukaryotic Microbiology, BioMedCentral Genomics,
Bioinformatics, Protist.
! Contributor to Tetrahymena Whole Genome Sequencing Project proposal (2002)
! Principal presenter of white paper to NHGRI Comparative Genome Evolution working group:
Tetrahymena Comparative Genomics Sequencing Project (2006); approved by Coordinating
Committee and Council, May 2007.
! Steering Committee Member for Joint Genome Institute-sponsored project to sequence
micronuclear genome of Tetrahymena thermophila
! Session Chair at 2003, 2011 FASEB Ciliate Molecular Biology Conference
! Co-Organizer, Tetrahymena Forward Genetics Workshop, University of California Santa
Barbara July 13-19, 2008
! Co-Organizer of 2009 FASEB Ciliate Molecular Biology Conferences
! Member, Tetrahymena Scientific Advisory Board
! Member, Arlington Virginia Public Schools Science Advisory Committee

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Education
1982-1990: Harvard University, Cambridge, MA
• Awarded Ph.D. from Department of Cellular and Developmental Biology
• Thesis title: Molecular and genetic analysis of the Drosophila alpha spectrin region
• NSF Predoctoral Fellow
• Teaching Fellow for Introductory Cell/Molecular Biology, Genetics, Biochemistry
1983, 1991: Marine Biological Laboratories, Woods Hole MA
• Summer courses in Physiology - Cellular and Molecular Biology,
Molecular Evolution
1978-1982: Allegheny College, Meadville PA
• Awarded B.S. with double major in Biology and Chemistry.
• Honors: Class valedictorian, Departmental honors in Biology, Phi Beta Kappa, Summa
cum laude, National Merit Scholar, Doane Scholar
Publications
Eileen P. Hamilton, Aurélie Kapusta, Piroska E. Huvos, Shelby L. Bidwell,
Nikhat Zafar, Haibao
Tang, Michalis Hadjithomas, Vivek Krishnakumar, Jonathan Badger, Elisabet V. Caler, Carsten
Russ, Qiandong Zeng, Lin Fan, Joshua Z. Levin, Terrance Shea, Sarah K. Young, Ryan Hegarty,
Riza Daza, Sharvari Gujja, Jennifer R. Wortman, Bruce Birren, Chad Nusbaum, Jainy Thomas,
Clayton M. Carey, Ellen J. Pritham, Cédric Feschotte, Tomoko Noto, Kazufumi Mochizuki,
Romeo Papazyan, Sean D. Taverna, Paul H. Dear, Donna M. Cassidy-Hanley, Jie Xiong, Wei
Miao, Eduardo Orias, Robert S. Coyne (senior, corresponding author). Structure of the
germline genome of Tetrahymena thermophila and its relationship to the massively rearranged
somatic genome. Submitted to eLife, favorably reviewed, revised version under review.
Lynch M, Doak T, McGrath C, Miller S, Lang F, Brami D, Hostetler JB, Joardar VS, Radune D,
Kolli P, Coyne RS The genome of a rickettsiales bacterium inhabiting the parasitic ciliate
Ichthyophthirius multifiliis (in preparation)
Yang Q, Nasir AM, Coyne RS, Forney JD (2015) Depletion of UBC9 Causes Nuclear Defects
during the Vegetative and Sexual Life Cycles in Tetrahymena thermophila. Eukaryot. Cell.
14(12):1240-52. PMID: 26453653
Papazyan R, Voronina E, Chapman JR, Luperchio TR, Gilbert TM, Meier E, Mackintosh SG,
Shabanowitz J, Tackett AJ, Reddy KL, Coyne RS, Hunt DF, Liu Y, Taverna SD (2014)
Methylation of histone H3K23 blocks DNA damage in pericentric heterochromatin during
meiosis. Elife. Aug 26;3:e02996. PMID: 25161194
Coyne RS, Stover, NA, Miao W (2012) Whole genome studies of Tetrahymena. In:
Tetrahymena thermophila, edited by K. Collins. Methods in Cell Biology.109: 53-81. PMID:
22444143

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Coyne RS, Lhuillier-Akakpo M, Duharcourt S (2012) RNA-guided DNA rearrangement in
ciliates: Is the best genome defense a good offense? Biology of the Cell. 104:309-25. PMID:
22352444
Coyne RS, Hannick L, Shanmugam D, Hostetler JB, Brami D, Joardar VS, Johnson J, Radune
D, Singh I, Kumar U, Saier M, Wang Y, Cai H, Gu J, Mather MW, Vaidya AB, Wilkes DE,
Rajagopalan V, Asai DJ, Pearson CG, Findly RC, Dickerson HW, Badger JH, Wu M, Martens C,
Van de Peer Y, Roos DS, Cassidy-Hanley DM, Clark TG (2011) Comparative genomics of the
pathogenic ciliate Ichthyophthirius multifiliis, its free-living relatives and a host species provide
insights into adoption of a parasitic lifestyle and prospects for disease control. Genome Biology.
12:R100 doi:10.1186/gb-2011-12-10-r100. PMID: 22004680
Fass JN, Joshi NA, Couvillion MT, Bowen J, Gorovsky MA, Hamilton EP, Orias E, Hong K,
Coyne RS, Eisen JA, Chalker DL, Lin D, Collins K (2011) Genome-scale analysis of
programmed DNA elimination sites in Tetrahymena thermophila. G3: Genes, Genomes,
Genetics. Nov;1(6):515-22. PMID: 22384362
Coyne RS (2011) Tetrahymena. Encyclopedia of Life Sciences.
http://www.els.net/WileyCDA/ElsArticle/refId-a0001972.html
Sun HY, Noe J, Barber J, Coyne RS, Cassidy-Hanley D, Clark TG, Findly RC, Dickerson HW
(2009) Endosymbiotic bacteria in the parasitic ciliate Ichthyophthirius multifiliis. Appl Environ
Microbiol. 75:7445-52. PMID: 19820157
Coyne RS, Thiagarajan M, Jones KM, Wortman JR, Tallon LJ, Haas BJ, Cassidy-Hanley DM,
Wiley EA, Smith JJ, Collins K, Lee SR, Liu Y, Garg J, Pearlman RE, Hamilton EP, Orias E,
Eisen JA, Methe BA (2008) Refined annotation and assembly of the Tetrahymena thermophila
genome sequence through EST analysis, comparative genomic hybridization, and targeted gap
closure. BMC Genomics. 26:562. PMID: 19036158
Yao MC, Yao CH, Halasz LM, Fuller P, Rexer CH, Wang SS, Jain R, Coyne RS, Chalker DL
(2007) Identification of novel chromatin-associated proteins involved in programmed genome
rearrangements in Tetrahymena. J. Cell Sci. 120: 1978-89. PMID: 17519286
Eisen JA, Coyne RS, Wu M, Wu D, Thiagarajan M, Wortman JR, Badger JH, Ren Q, Amedeo
P, Jones KM, Tallon LJ, Delcher AL, Salzberg SL, Silva JC, Haas BJ, Majoros WH, Farzad M,
Carlton JM, Smith RK, Garg J, Pearlman RE, Karrer KM, Sun L, Manning G, Elde NC,
Turkewitz AP, Asai DJ, Wilkes DE, Wang Y, Cai H, Collins K, Stewart BA, Lee SR, Weinberg
Z, Ruzzo WL, Wloga D, Gaertig J, Frankel J, Tsao CC, Gorovsky MA, Keeling PJ, Waller RF,
Patron NJ, Cherry JM, Stover NA, Krieger CJ, Del Toro C, Ryder HF, Williamson SC, Barbeau
RA, Hamilton EP, Orias E (2006) Macronuclear genome sequence of the ciliate Tetrahymena
thermophila, a model eukaryote. PLoS Biol. 4(9): e286. PMID: 16933976
Cervantes MD, Coyne RS, Xi X, Yao MC (2006) The condensin complex is essential for
amitotic segregation of bulk chromosomes, but not nucleoli, in the ciliate Tetrahymena

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thermophila. Mol. Cell. Biol. 26(12):4690-700. PMID: 16738332
Coyne RS, McDonald HB, Edgemon K, Brody LC (2004) Functional characterization of BRCA1
sequence variants using a yeast small colony phenotype assay. Cancer Biol. Ther. 3(5):453-7.
PMID: 15004537
Coyne R (2004) NSF’s RUI program: Perspectives from the inside. Council of Undergraduate
Research Quarterly. December 2004 issue.
Taverna S*, Coyne R* (*Joint first authors), Allis CD (2002) Methylation of histone H3 at
lysine 9 targets programmed DNA elimination in Tetrahymena. Cell 6:701-711. Featured in
Science’s Breakthrough of the Year 2002. PMID: 12297044
Coyne R*, Nikiforov M* (*Joint first authors), Smothers J, Allis CD, Yao M-C (1999) Parental
expression of the chromodomain protein Pdd1p is required for completion of programmed DNA
elimination and nuclear differentiation. Molecular Cell 4: 865-872. PMID: 10619033
Coyne R, Yao M-C (1996) Evolutionary conservation of sequences directing chromosome
breakage and rDNA palindrome formation in tetrahymenine ciliates. Genetics 144: 1479-1487.
PMID: 8978037
Madireddi M*, Coyne R* (*Joint first authors), Smothers J, Mickey K, Yao M-C, Allis CD
(1996) Pdd1p, a novel chromodomain-containing protein, links heterochromatin assembly and
DNA elimination in Tetrahymena. Cell 87: 75-84. Cover photo article. PMID: 8858150
Coyne R, Chalker D, Yao M-C (1996) Genome downsizing during ciliate development: Nuclear
division of labor through chromosome restructuring. Ann. Rev. Genetics 30: 557-578. PMID:
8982465
Coyne R, Siebrecht M, Peitsch M, Casanova J (1994) Mutational analysis of polymeric
immunoglobulin receptor/ligand interactions: evidence for the involvement of multiple CDR-
like loops in receptor domain I. J. Biol. Chem. 269: 31620-31625. PMID: 7989333
Lee J, Coyne R, Dubreuil R, Goldstein L, Branton D (1993) Cell shape and interaction defects
in alpha spectrin mutants of Drosophila melanogaster. J. Cell Biol. 123: 1797-1809. PMID:
8276898
Harrison D, Gdula D, Coyne R, Corces V (1993) A leucine zipper domain of the suppressor of
Hairy-wing protein mediates its repressive effect on enhancer function. Genes Dev. 7: 1966-
1978. PMID: 7916729
Parkhurst S, Harrison D, Remington M, Spana C, Kelly R, Coyne R, Corces V (1988) The
Drosophila su(Hw) gene, which controls the phenotypic effect of the gypsy transposable
element, encodes a putative DNA binding protein. Genes Dev. 2: 1205-1215. PMID: 2462523
References available upon request