Bhattacharya Lab - Debashish Bhattacharya


Curriculum Vitae


The breathtaking diversity of life that surrounds us is the underlying inspiration for my lab's research.
We have long-standing interests in algal/protist evolution and genomics and specific projects include
elucidating the endosymbiotic origin of photosynthetic organelles (plastids), functional genomics of
"red tide"-causing dinoflagellates, erecting the eukaryotic tree of life, and studying microRNA evolution.



Higher Education

    1984-1989 Ph.D., Biology, Simon Fraser University, Burnaby, Canada
    1981-1983 M.E.S., Environmental Sciences, Dalhousie University, Canada
    1977-1981 B.Sc. (Hons.), Biology, Dalhousie University, Halifax, Canada
  Professional and Academic Positions
    2009-present Professor, Department of Ecology, Evolution and Natural Resources, Institute of Marine and Coastal Science, Rutgers University, New Brunswick, NJ 08901.
    2005-present Adjunct Scientist, Woods Hole Oceanographic Institution, Biology Department
    2005-2009 Director, Interdisciplinary PhD Program in Genetics
    2005-2009 Faculty, Interdisciplinary PhD Program in Applied Mathematics and Computational Sciences
    2003-2009 Associate Professor, University of Iowa, Department of Biological Sciences
    1999-2009 Faculty, Interdisciplinary PhD Program in Genetics, University of Iowa
    1997-2003 Assistant Professor, University of Iowa, Department of Biological Sciences
    1994-1997 Research Scientist, Department of Biochemistry, Max Planck Institute for
      Biophysical Chemistry, Göttingen, Germany
      Habilitation Candidate, Department of Botany, University of Göttingen
    1991-1994 Humboldt Scholar, (postdoctoral position), with Michael Melkonian,
    Department of Botany, University of Cologne, Germany
    1989-1991 Alfred P. Sloan Fellow, (postdoctoral position), with Mitch Sogin, Marine Biological
      Laboratories, Woods Hole, MA

Major Honors and Awards

    2008 Darbaker Prize, Botanical Society of America
    2007 Fellow, American Association for the Advancement of Science
    1995-1997 Habilitation Stipendium and Research Grant, German Science Foundation, Göttingen, Germany
    1992-1994 Alexander von Humboldt Scholar, University of Cologne, Germany
    1991 Postdoctoral Research Grant, German Academic Exchange Service (DAAD)
    1989-1991 Alfred P. Sloan Fellow, Marine Biological Laboratories, Woods Hole, MA
    1988 Simon Fraser University Postdoctoral Fellowship
    1987 President’s Research Stipendium, Simon Fraser University, Burnaby, Canada
    1981-1983 Dalhousie Graduate Fellowship, Dalhousie University, Canada
    American Society for Microbiology
    American Association for the Advancement of Science
    International Society of Protistologists
    Phycological Society of America
    International Society for Evolutionary Protistology
    Botanical Society of America


pointer to text below Publications 2007 to present Publications prior to 2007arrow to right side


Brodie J, Ball SG, Bouget F-Y, Chan CX, De Clerck O, Cock M, Gachon C, Grossman AR, Mock T, Raven J, Saha M, Smith AG, Vardi A, Yoon HS, Bhattacharya D. 2017. Biotic interactions as drivers of algal origin and evolution. New Phytol. (Invited Tansley Review) doi:10.1111/nph.14760.

Brawley SH, Blouin NA, Ficko-Blean E, Wheeler GL, Lohr M, Goodson HV, Jenkins JW,  Blaby-Haas CE,  Helliwell KE, Xin Chan Cl, Marriage TK, Bhattacharya D, Klein AS, Badis Y, Brodie , Cao Y, Collén J, Dittam SM, Gachon CMM, Green BR, Karpowicz SJ, Kim JW, Kudahl UJ, Lin S, Michel G, Mittag M, Olson BJSC, Pangilinan JL, Peng Y, Qiu H, Shuh S, Singer JT, Smith AG, Sprecher BN, Wagner V, Wang W, Wang Z-Y, Yan J,  Yarish C, Zäuner-Rieka S, Zhuang Y, Zou Y, Lindquist EA, Grimwood J, Barry KW,  Rokhsar DH, Schmutz J, Stiller JW, Grossman AR, Prochnik SE. 2017. Insights into the red algae and eukaryotic evolution from the genome of Porphyra umbilicalis (Bangiophyceae, Rhodophyta). Proc Natl Acad Sci USA. 114:E6361-E6370.

Kim JI, Moore CE, Archibald JM, Bhattacharya D, Yi G, Yoon HS, Shin W. 2017. Evolutionary dynamics of cryptophyte plastid genomes. Genome Biol and Evol. 9:1859-1872.

Qiu H, Zelzion E, Putnam HM, Gates RD, Wagner NE, Adams DK, Bhattacharya D. 2017. Discovery of SCORs: Anciently derived, highly conserved gene-associated repeats in stony corals. Genomics. Jun 17. doi:10.1016/j.ygeno.2017.06.003. [Epub ahead of print]

Brodie J, Chan CX, De Clerck O, Cock JM, Coelho SM, Gachon C, Grossman AR, Mock T, Raven JA, Smith AG, Yoon HS, Bhattacharya D. 2017. The algal revolution. Trends Plant Sci. 22:726-738.

Tripp EA, Zhang N, Schneider H, Huang Y, Mueller GM, Hu Z, Häggblom M, Bhattacharya D. 2017. Reshaping Darwin's tree: impact of the symbiome. Trends Ecol Evol. 32:552-555.

Putnam HM, Adams DK, Zelzion E, Wagner NE, Qiu H, Mass T, Falkowski PG, Gates RD, Bhattacharya D. 2017. Divergent evolutionary histories of DNA markers in a Hawaiian population of the coral Montipora capitata. PeerJ. 5:e3319.

Price DC, Bhattacharya D. 2017. Robust Dinoflagellata phylogeny inferred from public transcriptome databases. J Phycol. 53:725-729.

Zhang R, Nowack EC, Price DC, Bhattacharya D, Grossman AR. 2017. Impact of light intensity and quality on chromatophore and nuclear gene expression in Paulinella chromatophora, an amoeba with nascent photosynthetic organelles. Plant J. 90:221-234.

Qiu H, Lee JM, Yoon HS, Bhattacharya D. 2017. Hypothesis: gene-rich plastid genomes in red algae may be an outcome of nuclear genome reduction. J Phycol. 53:715-719.

Cenci U, Bhattacharya D, Weber AP, Colleoni C, Subtil A, Ball SG. 2017. Biotic host-pathogen interactions as major drivers of plastid endosymbiosis. Trends Plant Sci. 22:316-328.

Pandey RS, Saxena G, Bhattacharya D, Qiu H, Azad RK. 2017. Using complementary approaches to identify trans-domain nuclear gene transfers in the extremophile Galdieria sulphuraria (Rhodophyta). J Phycol. 53:7-11.

Honig JA, Zelzion E, Wagner NE, Kubik C, Averello V, Vaiciunas J, Bhattacharya D, Bonos SA, Meyer WA. 2017. Microsatellite identification in perennial ryegrass using next-generation sequencing. Crop Sci. 57:1-10.


ECM Nowack, DC Price, D Bhattacharya, A Singer, M Melkonian, and AR Grossman. 2016. Gene transfers from diverse bacteria compensate for reductive genome evolution in the chromatophore of Paulinella chromatophora, PNAS 2016: 1608016113v1-201608016

Bhattacharya D, Agrawal S, Aranda M, Baumgarten S, Belcaid M, Drake JL, Erwin D, Foret S, Gates RD, Gruber DF, et al. 2016. Comparative genomics explains the evolutionary success of reef-forming corals. eLife. 5:e13288.

Ball SG, Bhattacharya D, Weber AP. 2016. EVOLUTION. Pathogen to powerhouse. Science. 351:659-660.

Ball SG, Bhattacharya D, Weber APM. 2016. Response to SB Gould, Infection and first eukaryotes. Science 27 May 2016. Vol. 352, Issue 6289, pp. 1065-1066.

Méheust R, Zelzion E, Bhattacharya D, Lopez P, Bapteste E. 2016. Protein networks identify novel symbiogenetic genes resulting from plastid endosymbiosis. Proc. Natl. Acad. Sci. USA. 113:3579-3584.

Mass T, Putnam HM, Drake JL, Zelzion E, Gates RD, Bhattacharya D, Falkowski PG. 2016. Temporal and spatial expression patterns of biomineralization proteins during early development in the stony coral Pocillopora damicornis. Proc. Biol. Sci. 283:20160322.

Stephens TG, Bhattacharya D, Ragan MA, Chan CX. 2016. PhySortR: a fast, flexible tool for sorting phylogenetic trees in R. PeerJ. 4:e2038.

Qiu H, Cai G, Luo J, Bhattacharya D, Zhang N. 2016. Extensive horizontal gene transfers between plant pathogenic fungi. BMC Biol. 14:41.

Leliaert F, Tronholm A, Lemieux C, Turmel M, DePriest MS, Bhattacharya D, Karol KG, Fredericq S, Zechman FW, Lopez-Bautista JM. 2016. Chloroplast phylogenomic analyses reveal the deepest-branching lineage of the Chlorophyta, Palmophyllophyceae class. nov. Sci. Rep. 6:25367.

Ball SG, Bhattacharya D, Qiu H, Weber AP. 2016. Commentary: Plastid establishment did not require a chlamydial partner. Front. Cell Infect Microbiol. 6:43.

Foflonker F, Ananyev G, Qiu H, Morrison A, Palenik B, Dismukes GC, Bhattacharya D. 2016. The unexpected extremophile: Tolerance to fluctuating salinity in the green alga Picochlorum. Algal Res. 16:465-472.

Lee J, Kim KM, Yang EC, Miller KA, Boo SM, Bhattacharya D, Yoon HS. 2016. Reconstructing the complex evolutionary history of mobile plasmids in red algal genomes. Sci. Rep. 6:23744.

Yang EC, Boo SM, Bhattacharya D, Saunders GW, Knoll AH, Fredericq S, Graf L, Yoon HS. 2016. Divergence time estimates and the evolution of major lineages in the florideophyte red algae. Sci. Rep. 6:21361.


Karkar S, Facchinelli F, Price DC, Weber APM, and Bhattacharya D. 2015. Metabolic connectivity as a driver of host and endosymbiont integration. Proc Natl Acad Sci USA. 112:10208-10215.

J. Luo, H. Qiu, G. Cai, N. E. Wagner, D. Bhattacharya & N. Zhang. 2015. Phylogenomic analysis uncovers the evolutionary history of nutrition and infection mode in rice blast fungus and other Magnaporthales. Sci. Rep. 5:9448.

MM Perrineau, DC Price, G Mohr, D Bhattacharya. 2015. Recent mobility of plastid encoded group II introns and twintrons in five strains of the unicellular red alga Porphyridium. 2015. PeerJ. 3:e1017.

Foflonker F, Price DC, Qiu H, Palenik B, Wang S, Bhattacharya D. 2015. Genome of the halotolerant green alga Picochlorum SENEW3 reveals strategies for thriving under fluctuating environmental conditions. Environ. Microbiol. 17:412-426.

Harel A, Karkar S, Cheng S, Falkowski PG, and Bhattacharya D. 2015. Deciphering primordial cyanobacterial genome functions from protein network analysis. Curr. Biol. 25:628-634.

Bhattacharya D, Qiu H, Price DC, Yoon HS. 2015. Why we need more algal genomes. J. Phycol. 51:1-5

Levitan O, Dinamarca J, Zelzion E, Lun DS, Guerra LT, Kim MK, Kim J, Van Mooy BA, Bhattacharya D, Falkowski PG. 2015. Remodeling of intermediate metabolism in the diatom Phaeodactylum tricornutum under nitrogen stress. Proc Natl Acad Sci USA 112(2):412-417.

H Qiu, DC Price, EC Yang, HS Yoon, D Bhattacharya. 2015. Evidence of ancient genome reduction in red algae (Rhodophyta). J. Phycol. 51:624-636.

Yang EC, Kim KM, Kim SY, Lee J, Boo GH, Lee JH, Nelson WA, Yi G, Schmidt WE, Fredericq S, Boo SM, Bhattacharya D, Yoon HS. 2015. Highly conserved mitochondrial genomes among multicellular red algae of the Florideophyceae. Genome Biol. Evol. 7:2394-2406.


Rockwell NC, Lagarias JC, and Bhattacharya D. 2014. Primary endosymbiosis and the evolution of light and oxygen sensing in photosynthetic eukaryotes. Front Ecol Evol 2:66.

Roy R, Bhattacharya D, Schliep A. 2014. Turtle: Identifying frequent k-mers with cache-efficient algorithms. Bioinformatics 30(14):1950-1957. 2014 Apr 2.
software download

Roy RS, Price DC, Schliep A, Cai G, Korobeynikov A, Yoon HS, Yang EC, Bhattacharya D. 2014. Single cell genome analysis of an uncultured heterotrophic stramenopile. 2014. Sci Rep. 2014 Apr 24;4:4780.
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Harel A, Bromberg Y, Falkowski PG, Bhattacharya D. 2014. The evolutionary history of redox metal-binding domains across the tree of life. Proc Natl Acad Sci USA 111:7042-7047.

Debashish Bhattacharya, Rajat S. Roy, Dana C. Price and Alexander Schliep. 2014. Single-cell genomics of marine plankton. Biochemist Magazine – Journal of the Biochemical Society, 36:1 February 16–22.

Rockwell NC, Duanmu D, Martin SS, Bachy C, Price DC, Bhattacharya D, Worden AZ, Lagarias JC. 2014. Eukaryotic algal phytochromes span the visible spectrum. Proc Natl Acad Sci USA. Mar 11;111(10):3871-6.

Foflonker F, Price DC, Qiu H, Palenik B, Wang S, and Bhattacharya D. 2014. Genome of the halotolerant green alga Picochlorum SENEW3 reveals strategies for thriving under fluctuating environmental conditions. Environ Microbiology in press.

Cheng S, Price DC, Karkar S, Bhattacharya D. 2014. Exploring biotic interactions within protist cell populations using network methods. J Eukaryot Microbiol 61(4):399-403.

Kim KM, Park J-H, Bhattacharya D, Yoon HS. 2014. Applications of next-generation sequencing to unravelling the evolutionary history of algae. International Journal of Systematic and Evolutionary Microbiology 64(2):333-345.

Bhattacharya D, Roy RS, Price DC, Schliep A. 2014. Single-cell genomics of marine plankton. Biochemist Magazine – Journal of the Biochemical Society, February 16–22.

MM Perrineau, E Zelzion, J Gross, DC Price, J Boyd, D Bhattacharya. Evolution of salt tolerance in a laboratory reared population of Chlamydomonas reinhardtii. 2014. Environmental Microbiology 16:1755-1766.

Perrineau MM, Gross J, Zelzion E, Price DC, Levitan O, Boyd J, Bhattacharya D. 2014. Using natural selection to explore the adaptive potential of Chlamydomonas reinhardtii. PLoS One: 9:e92533. March 21, 2014.
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Polashock J, Zelzion E, Fajardo D, Zalapa J, Georgi L, Bhattacharya D, Vorsa N. 2014. The American cranberry: first insights into the whole genome of a species adapted to bog habitat. BMC Plant Biol 14:165.

Cheng S, Karkar S, Bapteste E, Yee N, Falkowski P, Bhattacharya D. 2014. Sequence similarity network reveals the imprints of major diversification events in the evolution of microbial life. Frontiers in Ecology and Evolution 2:72.

Chan CX, Bhattacharya D. 2014. Analysis of horizontal genetic transfer in red algae in the post-genomics age. Mobile Genetic Elements 3(6): e27669 .

DePriest MS, Bhattacharya D, López-Bautista JM. 2014. The mitochondrial genome of Grateloupia taiwanensis (Halymeniaceae, Rhodophyta) and comparative mitochondrial genomics of red algae. Biol Bull 227(2):191-200.


S Nyati, D Bhattacharya, S Werth, R Honegger. Phylogenetic analysis of LSU and SSU rDNA group I introns of lichen photobionts associated with the genera Xanthoria and Xanthomendoza (Teloschistaceae, lichenized Ascomycetes). Journal of Phycology 49 (6), 1154-1166, 11 Nov 2013.

D Bhattacharya, KN Pelletreau, DC Price, KE Sarver, ME Rumpho. Genome analysis of Elysia chlorotica egg DNA provides no evidence for horizontal gene transfer into the germ line of this kleptoplastic mollusc. Molecular biology and Evolution 30(8), 1843–1852. 11 July 2013.

C. X. Chan, F. L. Baglivi, C. E. Jenkins, and D. Bhattacharya. Foreign gene recruitment to the fatty acid biosynthesis pathway in diatoms. Mobile Genetic Elements 3, e27313; September/October 2013.

Huan Qiu, Dana C. Price, Andreas P.M. Weber, Fabio Facchinelli, Hwan Su Yoon, and Debashish Bhattacharya. Assessing the bacterial contribution to the plastid proteome. Trends in Plant Science. 2013 Oct 16. S1360-1385(13)00198-2.

Huan Qiu, Dana C. Price, Andreas P.M. Weber, Valérie Reeb, Eun Chan Yang, Jun Mo Lee, Su Yeon Kim, Hwan Su Yoon, and Debashish Bhattacharya, Adaptation through horizontal gene transfer in the cryptoendolithic red alga Galdieria phlegrea. Current Biology. Oct 7;23(19):R865-6.

Ugo Cenci, Malika Chabi, Mathieu Ducatez, Catherine Tirtiaux, Jennifer Nirmal-Raj, Yoshinori Utsumi, Daiki Kobayashi, Satoshi Sasaki, Eiji Suzuki, Yasunori Nakamura, Jean-Luc Putaux, Xavier Roussel, Amandine Durand-Terrasson, Debashish Bhattacharya, Anne-Sophie Vercoutter-Edouart, Emmanuel Maes, Maria Cecilia Arias, Monica Palcic, Lyann Sim, Steven G. Ball and Christophe Colleoni. 2013. Convergent Evolution of Polysaccharide Debranching Defines a Common Mechanism for Starch Accumulation in Cyanobacteria and Plants. The Plant Cell October 2013 tpc.113.118174.

Huan Qiu, Hwan Su Yoon, and Debashish Bhattacharya. 2013. Algal endosymbionts as vectors of horizontal gene transfer in photosynthetic eukaryotes. Frontiers in Plant Science, 19 September 2013.

Depriest MS, Bhattacharya D, López-Bautista JM. 2013. The Plastid Genome of the Red Macroalga Grateloupia taiwanensis (Halymeniaceae). PLoS One. 2013 Jul 19;8(7):e68246.

Skorupa DJ, Reeb V, Castenholz RW, Bhattacharya D, McDermott TR. 2013. Cyanidiales diversity in Yellowstone National Park Lett Appl Microbiol. 2013 Jul 19. [Epub ahead of print]

Drake JL, Massa T, Haramaty L, Zelzion E, Bhattacharya D, Falkowski PG.
Reply to Ramos-Silva et al.: Regarding coral skeletal proteome. Proc Natl Acad Sci U S A. 2013 Jun 11;110(24):E2147-8.

Shoguchi E, Shinzato C, Kawashima T, Gyoja F, Mungpakdee S, Koyanagi R, Takeuchi T, Hisata K, Tanaka M, Fujiwara M, Hamada M, Seidi A, Fujie M, Usami T, Goto H, Yamasaki S, Arakaki N, Suzuki Y, Sugano S, Toyoda A, Kuroki Y, Fujiyama A, Medina M, Coffroth MA, Bhattacharya D, Satoh N. 2013. Draft Assembly of the Symbiodinium minutum Nuclear Genome Reveals Dinoflagellate Gene Structure. Curr Biol. 2013 Jul 9.

Bhattacharya D, Price DC, Chan CX, Qiu H, Rose N, Ball S, Weber AP, Cecilia Arias M, Henrissat B, Coutinho PM, Krishnan A, Zäuner S, Morath S, Hilliou F, Egizi A, Perrineau MM, Yoon HS. 2013. Genome of the red alga Porphyridium purpureum. Nat Commun. 2013 Jun 17;4:1941.

Jeferson Gross, Sana Wajid, Dana C. Price, Ehud Zelzion, Junyi Li, Cheong Xin Chan, Debashish Bhattacharya. 2013. Evidence for Widespread Exonic Small RNAs in the Glaucophyte Alga Cyanophora paradoxa. PLoS ONE 8(7): e67669.
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Tali Mass, Jeana L. Drake, Liti Haramaty, J. Dongun Kim, Ehud Zelzion, Debashish Bhattacharya, and Paul G. Falkowski. Cloning and Characterization of Four Novel Coral Acid-Rich Proteins that Precipitate Carbonates In Vitro. Current Biology, Volume 23, Issue 12, 17 June 2013, Pages 1126–1131.
doi | RU news release

Bhattacharya, D., D.C. Price, C. Bicep, E. Bapteste, M. Sarwade, V.D. Rajah, and H. S. Yoon. 2013. Identification of a marine cyanophage in a protist single cell metagenome assembly. Journal of Phycology Volume 49, Issue 1, pages 207–212, February.

Drake J.L., Mass T., Haramaty L., Zelzion E., Bhattacharya D., Falkowski P.G. 2013. Proteomic analysis of skeletal organic matrix from the stony coral Stylophora pistillata. Proc Natl Acad Sci U S A. 2013 Feb 19.
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Ball, S.G., A. Subtil, D. Bhattacharya, A. Moustafa, A.P.M. Weber, L. Gehre, C. Colleoni, M.-C. Arias, U. Cenci, and D. Dauvillée. 2013. Metabolic effectors secreted by bacterial pathogens: essential facilitators of plastid endosymbiosis? The Plant Cell January 2013 tpc.112.101329.
doi|free full text online

Facchinelli, F., M. Pribil, U. Oster, N. Ebert, D. Bhattacharya, D. Leister, and A. Weber. 2013. Proteomic analysis of the Cyanophora paradoxa muroplast provides clues on early events in plastid endosymbiosis. Planta: 2013 Feb;237(2):637-51, epub ahead of print


Steiner, J.M., D. Bhattacharya, and W. Löffelhardt. 2012. Conservative sorting in the muroplasts of Cyanophora paradoxa: a reevaluation based on the completed genome sequence. Symbiosis 57: epub ahead of print

Georgi, L., J. Johnson-Cicalese, J. Honig, S. Parankush Das, V.D. Rajah, D. Bhattacharya, N. Bassil, L.J. Rowland, J. Polashock, and N. Vorsa. 2012. The first genetic map of the American cranberry: exploration of synteny conservation and quantitative trait loci. Theoretical and Applied Genetics:  2012 Dec 8. epub ahead of print

Gross, J., and D. Bhattacharya. 2012. Evolution: Eukaryotes. Encyclopedia fo Genetics, 2nd Edition, Elsevier.

Price D.C., Chan C.X., Yoon HS, Yang E.C., Qiu H., Weber A.P., Schwacke R., Gross J., Blouin N.A., Lane C., Reyes-Prieto A., Durnford D.G., Neilson J.A., Lang F.B., Gertraud Burger G., Steiner J.M., Löffelhardt W., Meuser J.E., Posewitz M.C., Ball S., Arias M.C., Henrissat B., Coutinho P.M., Rensing S.A., Symeonidi A., Doddapaneni H., Green B.R., Rajah V.D., Boore J., and Bhattacharya D. 2012. Cyanophora paradoxa genome elucidates origin of photosynthesis in algae and plants. Science 17 February 2012: Vol. 335 no. 6070 pp. 843-847
doi|Nature news|| [German]|RU news|Cyanophora BLAST and data download|
See commentary by Spiegel FW. 2012. Contemplating the first Plantae. Science 17 February 2012: Vol. 335 no. 6070 pp. 809-810 |doi

Chan CX, Soares MB, Bonaldo MF, Wisecaver JH, Hackett JD, Anderson DM, Erdner DL, Bhattacharya D. 2012. Analysis of Alexandrium tamarense (Dinophyceae) genes reveals the complex evolutionary history of a microbial eukaryote. Journal of Phycology 48:1130-1142.

Chan CX, Bhattacharya D and Reyes-Prieto A. 2012. Endosymbiotic and horizontal gene transfer in microbial eukaryotes: impacts on cell evolution and the tree of life. Mobile Genetic Elements, 2(2)

Chan, C.X., S. Zaeuner, G. Wheeler, A.R. Grossman, S.E. Prochnik, N.A. Blouin, Y. Zhuang, C. Benning, G.M. Berg, C.Yarish, R.L. Eriksen, A.S. Klein, S. Lin, I. Levine, S.H. Brawley, and D. Bhattacharya. 2012. Analysis of Porphyra membrane transporters demonstrates gene transfer among photosynthetic eukaryotes and numerous sodium-coupled transport systems. Plant Physiology. February 2012 pp.112.193896.

Salcedo T, Upadhyay RJ, Nagasaki K, and Bhattacharya D. 2012. Dozens of toxin-related genes are expressed in a non-toxic strain of the dinoflagellate Heterocapsa circularisquama. Mol Biol Evol (2012) 29(6): 1503-1506.

Hackett JD, Wisecaver JH, Brosnahan ML, Kulis DM, Anderson DM, Bhattacharya D, Plumley FG, and Erdner DL. 2012. Evolution of saxitoxin synthesis in cyanobacteria and dinoflagellates. Mol Biol Evol first published online May 23, 2012.

Qiu H, Yang EC, Bhattacharya D, Yoon HS. 2012. Ancient gene paralogy may mislead inference of plastid phylogeny.
Mol Biol Evol. 2012 Nov;29(11):3333-43. Epub 2012 May 21.

Bhattacharya D, Price DC, Yoon HS, Yang EC, Poulton NJ, Andersen RA, Das SP. 2012. Single cell genome analysis supports a link between phagotrophy and primary plastid endosymbiosis. Sci Rep. 2012;2:356. Epub 2012 Apr 10.


Chan CX, Reyes-Prieto A, Bhattacharya D. 2011. Red and Green Algal Origin of Diatom Membrane Transporters: Insights into Environmental Adaptation and Cell Evolution. PLoS ONE 6(12): e29138.
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Chan CX and Bhattacharya D. 2011. Plastid origin and evolution. In: Encyclopedia of Life Sciences (eLS). Wiley & Sons.

Bhattacharya D. 2011. As an evolutionary biologist. Debashish Bhattacharya., Curr Biol. Sep 27;21(18):R676-7.

Yoon, H.S., D.C. Price, R. Stepanauskas, V.D. Rajah, M.E. Sieracki, W.H. Wilson, E.C. Yang, S. Duffy, and D. Bhattacharya. 2011. Single cell genomics reveals trophic interactions and evolutionary history of uncultured protists. Science 6 May 2011: Vol. 332 no. 6030 pp. 714-717.
doi|RU news article|Science Daily

Chan, CX and Bhattacharya, D (2011). Non-random sharing of Plantae genes. Communicative and Integrative Biology 4(3): 361 - 363.

Cheong Xin Chan, Jeferson Gross, Hwan Su Yoon, and Debashish Bhattacharya. 2011. Plastid Origin and Evolution: New Models Provide Insights into Old Problems. Plant Physiology 155(4):1552-1560.
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Jeferson Gross, Debashish Bhattacharya. 2011. Endosymbiont or host: who drove mitochondrial and plastid evolution? Biology Direct, 6:12. Published on 19 February 2011.
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Karen N. Pelletreau, Debashish Bhattacharya, Dana C. Price, Jared M. Worful, Ahmed Moustafa, and Mary E. Rumpho. 2011. Update on Sea Slug Kleptoplasty and Plastid Maintenance in a Metazoan. Plant Physiology 155(4):1561-1565.
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Chan CX, Yang EC, Banerjee T, Yoon HS, Martone PT, Estevez JM and Bhattacharya D (2011). Red-and-green algal monophyly and extensive gene sharing found in a rich repertoire of red algal genes. Current Biology 21(4):328-333.
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Valérie Reeb, Avraham Kolel, Timothy R. McDermott and Debashish Bhattacharya. Good to the bone: microbial community thrives within bone cavities of a bison carcass at Yellowstone National Park Environmental Microbiology (2010).

Vis ML, Yoon HS, Bhattacharya D, Lopez-Bautista JM. RedTol - The Red Algal Tree of Life. In: Why Study the Tree of Life? - Scientists Speak, (Edited by Mikkelsen P). American Paleontologist 18(3) Fall 2010 13.
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Sung Min Boo, Han Soon Kim, Woongghi Shin, Ga Hun Boo, Sung Min Cho, Bok Yeon Jo, Jee-Hwan Kim, Jin Hee Kim, Eun Chan Yang, Peter A. Siver, Alexander P. Wolfe, Debashish Bhattacharya, Robert A. Andersen and Hwan Su Yoon. 2010. Complex phylogeographic patterns in the freshwater alga Synura provide new insights into ubiquity vs. endemism in microbial eukaryotes. Molecular Ecology 19: 4328-4338.

Chan, C. X. & Bhattacharya, D. (2010) The Origin of Plastids. Nature Education 3(9):84.
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Gross J, Bhattacharya D. 2010. Uniting sex and eukaryote origins in an emerging oxygenic world.
Biol Direct. 2010 Aug 23;5:53.
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Rumpho, M. E., K. N. Pelletreau, A. Moustafa, and D. Bhattacharya. 2011. The making of a photosynthetic animal.
J Exp Biol:2011 Jan 15;214(Pt 2):303-11.

Kerry Knudsen, Valérie Reeb, Martin Westberg, Rithu Srikantha and Debashish Bhattacharya. 2010. Acarospora rosulata in Europe, North America and Asia. The Lichenologist 42)3): 291-296.

Moustafa, A., A.N. Evans, D.M. Kulis, J.D. Hackett, D.L. Erdner, D.M. Anderson, and D. Bhattacharya. Transcriptome profiling of a toxic dinoflagellate reveals a highly gene-rich protist and a major impact on gene expression due to bacterial presence. PLoS ONE.
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Reyes-Prieto, A.R., H.S. Yoon, A. Moustafa, E.C. Yang, R.A. Andersen, S.M. Boo, T. Nakayama, K.-i. Ishida, and D. Bhattacharya. 2010. Differential gene retention in plastids of common recent origin.
Mol Biol Evol. 27(7):1530-1537. 2010 Feb 1.


Borchert, G.M., B.L. Gilmore, R.M. Spengler, Y. Xing, W. Lanier, D. Bhattacharya, and B.L. Davidson. 2009. Adenosine deamination in human transcripts generates novel microRNA binding sites. Hum. Mol. Genet. 18:4801-4807.
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Rumpho, M.E., S. Pochareddy, J.M. Worful, E.J. Summer, D. Bhattacharya, K.N. Pelletreau, M.S. Tyler, J. Lee, J.R. Manhart, and K.M. Soule. 2009. Molecular characterization of the Calvin cycle enzyme phosphoribulokinase in the stramenopile alga Vaucheria litorea and the plastid hosting mollusc Elysia chlorotica. Mol. Plant 2:1384-1396.

Soares, M.B., M. de Fatima Bonaldo, J.D. Hackett, and D. Bhattacharya. 2009. Expressed sequence tags: normalization and subtraction of cDNA libraries expressed sequence tags\ normalization and subtraction of cDNA libraries. Methods Mol. Biol. 533:109-122.

Moustafa, A., B. Beszteri, U.G. Maier, C. Bowler, K. Valentin, and D. Bhattacharya. 2009. Genomic footprints of a cryptic plastid endosymbiosis in diatoms.Science 324: 1724-1726.
doi| pubmed

Gross, J., and D. Bhattacharya. 2009. Mitochondrial and plastid evolution in eukaryotes: an outsider’s perspective. Nature Rev. Genet. 10:495-505.

Reeb, V.C., M.T. Peglar, H.S. Yoon, J.R. Bai, M. Wu, P. Shiu, J.L. Grafenberg, A. Reyes-Prieto, S.E. Rümmele, J. Gross, and D. Bhattacharya. 2009. Interrelationships of chromalveolates within a broadly sampled tree of photosynthetic protists. Mol Phylogenet. Evol. 53:202-211.

Worden, A.Z., J-H. Lee, T. Mock, P. Rouzé, M.P. Simmons, A.L. Aerts, A.E. Allen, M.L. Cuvelier, E. Derelle, M.V. Everett, E. Foulon, J. Grimwood, H. Gundlach, B. Henrissat, C. Napoli, S.M. McDonald, M. Schnitzler Parker, S. Rombauts, A. Salamov, P. Von Dassow, J.H. Badger, P.M. Coutinho, E. Demir, I. Dubchak, C. Gentemann, W. Eikrem, J.E. Gready, U. John, W. Lanier, E.A. Lindquist, S. Lucas, K.F.X. Mayer, H. Moreau, F. Not, R. Otillar, O. Panaud, J. Pangilinan, I. Paulsen, B. Piegu, A. Poliakov, S. Robbens, J. Schmutz, E. Toulza, T. Wyss, A. Zelensky, K. Zhou, E.V. Armbrust, D. Bhattacharya, U.W. Goodenough, Y. Van de Peer, and I.V. Grigoriev. 2009. Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas. Science 324:268-272.
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Wu, M., J. Comeron, H.S. Yoon, and D. Bhattacharya. 2009. Unexpected dynamic gene family evolution in algal actins. Mol. Biol. Evol. 26:249-253.

Yoon, H.S, T. Nakayama, A. Reyes-Prieto, R.A. Andersen, S.M. Boo, K-i Ishida, and D. Bhattacharya. 2009. A single origin of the photosynthetic organelle in different Paulinella lineages. BMC Evol. Biol. 9:98.

Moustafa, A., J.E. Loram, J.D. Hackett, D.M. Anderson, F.G. Plumley, and D. Bhattacharya. 2009. Origin of saxitoxin biosynthetic genes in cyanobacteria. PLoS One 4:e5758.

Gross, J., and D. Bhattacharya. 2009. Revaluating the evolution of the Toc/Tic protein translocons. Trends Plant Sci. 14:13-20.


Frommolt, R., S. Werner, H. Paulsen, R. Goss, C. Wilhelm, S. Zauner, U.G. Maier, A.R. Grossman, D. Bhattacharya, and M. Lohr. 2008. Ancient recruitment by chromists of green algal genes encoding enzymes for carotenoid biosynthesis. Mol. Biol. Evol. 25:2653-2667.

Rumpho, M.E., J.M. Worful, J. Lee, K. Kannan, M.S. Tyler, D. Bhattacharya, A. Moustafa, and J.R. Manhart. 2008 . Horizontal gene transfer of the algal nuclear gene psbO to the photosynthetic sea slug Elysia chlorotica. Proc. Natl. Acad. Sci. USA 105:17867-17871.
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Gross, J., J. Meurer, and D. Bhattacharya. 2008. Evidence of a chimeric genome in the cyanobacterial ancestor of plastids. BMC Evol. Biol. 8:117.
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Grosskurth, S.E., D. Bhattacharya, Q. Wang, and J.J. Lin. 2008. Emergence of Xin demarcates a key innovation in heart evolution. PLoS ONE. 2008 Aug 6;3(8):e2857.
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Lanier, W., A. Moustafa, D. Bhattacharya, and J.M. Comeron. 2008. Analysis of Ostreococcus lucimarinus EST data shows more introns in highly expressed genes. PLoS ONE:e2171.
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Moustafa, A., and D. Bhattacharya. 2008. PhyloSort: a user-friendly phylogenetic sorting tool and its application to estimating the cyanobacterial contribution to the nuclear genome of Chlamydomonas. BMC Evol. Biol. 8:6.
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Moustafa, A., A. Reyes-Prieto, and D. Bhattacharya. 2008. Chlamydiae has contributed at least 55 genes to Plantae with predominantly plastid functions. PLoS One. 2008 May 21;3(5):e2205.
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Nosenko, T., and D. Bhattacharya. 2008. Endosymbiotic and horizontal gene transfer in chromalveolates. J. Phycol. 44:7-10.
Journal cover|doi

Phillips, N., S. Calhoun, A. Moustafa, D. Bhattacharya, and E.L. Braun. 2008. Genomic insights into evolutionary relationships among heterokont lineages emphasizing the Phaeophyceae. J. Phycol. 44:15-18.

Reyes-Prieto, A., A. Moustafa, and D. Bhattacharya. 2008. Multiple genes of apparent algal origin suggest ciliates may once have been photosynthetic. Curr Biol. 2008 Jul 8;18(13):956-62. (with accompanying commentary)
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Yoon, H.S., J. Grant, Y.I. Tekle, M. Wu, B.C. Chaon, J.C. Cole, J.M. Logsdon, D.J. Patterson, D. Bhattacharya, and L.A. Katz. 2008. Broadly sampled multigene trees of eukaryotes. BMC Evol Biol. 2008 Jan 18;8:14
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Zhang, H., D. Bhattacharya, L. Maranda, and S. Lin. 2008. Mitochondrial cob and cox1 and their mRNA editing in Dinophysis acuminata from Narragansett Bay, with special reference to the phylogenetic position of Dinophysis. Appl. Environ. Microbiol. 74:1546-1554.
doi |pubmed


Bhattacharya, D., J.M. Archibald, A.P.M. Weber, and A. Reyes-Prieto. 2007. How do endosymbionts become organelles? Understanding early events in plastid evolution. BioEssays 2007 Dec;29(12):1239-46.

Reyes-Prieto, A., and D. Bhattacharya. 2007. Phylogeny of nuclear encoded plastid targeted proteins suggests an early divergence of glaucophytes within Plantae. Mol Biol Evol. 2007 Sep 6.
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Tyra, H.M., Linka, M., Weber, A.P.M., and D. Bhattacharya. 2007. Host origin of plastid solute transporters in the first photosynthetic eukaryotes. Genome Biol. 8:R212.
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Nosenko, T., and D. Bhattacharya. 2007. Horizontal gene transfer in chromalveolates. BMC Evol. Bio. 2007 Sep 25;7(1):173
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Reyes-Prieto, A., A. Weber, and D. Bhattacharya. 2007. The origin and establishment of the plastid in algae and plants. Annu. Rev. Genet. 41:147-168.
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Hackett, J.D., H.S. Yoon, S. Li, A. Reyes-Prieto, S.E. Ruemmele, and D. Bhattacharya. 2007. Phylogenomic analysis supports the monophyly of cryptophytes and haptophytes and the association of 'Rhizaria' with chromalveolates. Mol. Biol. Evol. 24: 1702-1713.
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J.D. Hackett, H.S. Yoon, N.J. Butterfield, M.J. Sanderson, and D. Bhattacharya. 2007. Plastid endosymbiosis: sources and timing of the major events. In: Evolution of Primary Producers in the Sea, (Eds.) P. Falkowski and A. Knoll. Elsevier Academic Press. 109-133.

Nosenko, T., B. Boese, and D. Bhattacharya. 2007. Pulsed field gel electrophoresis analysis of genome size and structure in Pavlova gyrans and Diacronema sp. (Haptophyta). J. Phycol. 43:763-767.
Download this publication (PDF file)| doi This is an electronic version of an article published in Journal of Phycology ©2007,
The Phycological Society of America.

Reyes-Prieto, A., and D. Bhattacharya. 2007. Phylogeny of Calvin cycle enzymes supports Plantae monophyly. Mol. Phylogenet. Evol. 45:384-391.
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Haugen, P., D. Bhattacharya, J.D. Palmer, S. Turner, L.A. Lewis, and K.M. Pryer. 2007. Cyanobacterial ribosomal RNA genes with multiple, endonuclease-encoding group I introns. BMC Evol. Biol. 7:159.
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Reeb, V., P. Haugen, D. Bhattacharya, and F. Lutzoni. 2007. Evolution of Pleopsidium (Lichenized Ascomycota) S943 Group I Introns and the Phylogeography of an Intron-Encoded Putative Homing Endonuclease. J. Mol. Evol. 64:285-298.
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Zhang, H., S. Lin, and D. Bhattacharya. 2007. A three-gene dinoflagellate phylogeny suggests monophyly of prorocentrales and a basal position for amphidinium and heterocapsa. J. Mol. Evol. 65:463-474.
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Book Chapters


Yoon HS, Yang EC, Qiu H, Bhattacharya D. 2014. Photosynthetic Paulinella -recapitulation of primary plastid establishment. In. Endosymbiosis (ed. W. Löffelhardt) 2014, pp 151-166, Springer, Wien.

Bhattacharya D, Price DC, Chan CX, Gross J, Steiner JM, Löffelhardt W. 2014. Analysis of the genome of Cyanophora paradoxa: an algal model for understanding primary endosymbiosis. In. Endosymbiosis (ed. W. Löffelhardt) 2014, pp 135-148, Springer, Wien.


Gantt, E., G.M. Berg, D. Bhattacharya, N.A. Blouin, J.A. Brodie, C.X. Chan, J. Collén, F.X. Cunningham Jr., J. Gross, A.R. Grossman, S. Karpowicz, Y. Kitade, A.S. Klein, I.A. Levine, S. Lin, S. Lu, M. Lynch, S.C. Minocha, K. Müller, C.D. Neefus, M.C. De Oliveira, L. Rymarquis, A. Smith, J.W. Stiller, W.-K. Wu, C. Yarish, Y.Y. Zhuang, And S.H. Brawley. 2010. Porphyra: complex life histories in a harsh environment: P. umbilicalis, an intertidal red alga for genomic analysis. In: Red algae in the Genomic Age, (Eds.) J. Seckbach and D. Chapman. Cellular Origin, Life in Extreme Habitats and Astrobiology 13, 129 - 148, Springer 2010.
doi|read online

Reeb, V., and D. Bhattacharya. 2010. The thermo-acidophilic Cyanidiophyceae (Cyanidiales). In: Red Algae in the Genomic Age, (Eds.) J. Seckbach and D. Chapman. Cellular Origin, Life in Extreme Habitats and Astrobiology 13, 409–426. Springer 2010.
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Reyes-Prieto, A., H.S. Yoon, and D. Bhattacharya. 2010. Marine protist (algal) genomics and evolution. Encyclopedia of Ocean Sciences, Wiley, in press.

Yoon, H.S., G.C. Zuccarello, and D. Bhattacharya. 2010. Evolutionary history and taxonomy of red algae. In: Red algae in the genomic age, (Eds.) J. Seckbach and D. Chapman, Springer, in press.


Bhattacharya, D., H.S. Yoon, S.B. Hedges, and J.D. Hackett. 2009. Eukaryotes (Eukaryota). Timetree of Life, In: Timetree of life, (Eds.) S.B. Hedges and S. Kumar, Oxford University Press, pp. 116-120.

Yoon, H.S., R.A. Andersen, S.M. Boo, and D. Bhattacharya. 2009. Evolutionary history and diversity of Stramenopiles. Encyclopedia of Microbiology, Elsevier, pp. 721-731.


Moustafa, A., C.X. Chan, M. Danforth, D. Zear, H. Ahmed, N. Jadhav, T. Savage, and D. Bhattacharya. 2008. A phylogenomic approach for studying plastid endosymbiosis. Genome Inform. 21:165-176.


Hackett, J.D., H.S. Yoon, N.J. Butterfield, M.J. Sanderson, and D. Bhattacharya. 2007. Plastid endosymbiosis: origins and timing of events. In: Evolution of Aquatic Photoautotrophs, Eds. Falkowski, P., and A. Knoll, Elsevier, p. 109-131.

Edited Volumes

Katz, L.A., and D. Bhattacharya. 2006. Genome evolution in eukaryotic microbes. Oxford
University Press.
Book cover

Bhattacharya, D. 1997. Origins of algae and their plastids. (Editor) Springer-Verlag, Wien. Three reviews from different journals are included in the appendix to the dossier.

Electronic Publications (Invited) “Virtual” Book Bhattacharya, D. 2007. Origin and molecular evolution of the plastid. In: Understanding chloroplasts, Organizer J.K. Hoober. Henry Stewart Talks.

Invited Lectures after 2007

Plastid origin and its consequences for the eukaryote tree of life. Darwin Science Talk (Cruikshank Lecture), University of Rhode Island, Nov. 16, 2009, Kingston, RI.

Genomic approaches to understanding red tide. Darwin Public Talk (Cruikshank Lecture), University of Rhode Island, Nov. 16, 2009, Kingston, RI.

Genome based insights into the origin of the plastid in algae and plants. National Institute of Natural Resources Symposium in Honor of Darwin, Oct. 9, 2009, Seoul, South Korea.

The evolution of photosynthesis on the tree of life. PSA/ASPB, July 19, 2009, Honolulu, Hawaii. On the evolutionary origin(s) of photosynthesis, November 20, 2008, Brown & Williamson Distinguished Speaker Series, University of Louisville, Kentucky.

The genomics of extremophiles and red tides, November 21, 2008, Brown & Williamson Distinguished Speaker Series, University of Louisville, Kentucky.

Genomic methods in algal biology, June 4-7, 2008, Marine genomics exploratory workshop, Alfred Wegener Institute for Polar and Marine Research, Plenary Speaker, Bremerhaven, Germany.

Algal genomics and phylogenomics: windows into endosymbiosis and eukaryotic evolution. April 16, 2007. European Marine Genomics Exploratory Workshop, Keynote Speaker, Roscoff, France.

Unraveling the evolutionary history of eukaryotic photosynthesis through genomic and phylogenomic analyses of algae. European Phycological Congress (EPC-4), Keynote Speaker. July 26, 2007, Oviedo, Spain.

Using comparative genomics to unravel the tangled evolutionary history of photosynthesis in microbial eukaryotes. Plenary Speaker, 15th Annual International Meeting on Microbial Genomics, September 16-20, 2007, University of Maryland, College Park, MD.

Other Invited Lectures

Greening of the eukaryotic tree of life. Biological Sciences, University of Wisconsin-Milwaukee, Dec. 11, 2009, Milwaukee, WI.

Greening of the tree of life. Geosciences, Princeton University, Nov. 19, 2009, Princeton, NJ.

Hidden endosymbioses and rampant gene transfer: the impact of genomics on clarifying algal evolution. IPMB 2009, Oct. 26, 2009, St. Louis, MO.

Genomics and evolution of dinoflagellates: towards understanding the origin and spread of red tides. Bowling Green State University, Feb. 9, 2009, Bowling Green, OH.

Ancient (and a more recent) origin of photosynthesis in eukaryotes. IGERT Annual Symposium, University of Arizona, May 6, 2009, Tucson, AZ.

Endosymbiotic origin of algal plastids, July 18-22, 2009, American Society of Plant Biologists, Honolulu, Hawaii. Ancient and more recent origins of photosynthesis in eukaryotes. NSF IGERT “Deep Genomics” Symposium, May 6, 2009, University of Arizona, Tucson.

Genomics and evolution of dinoflagellates: towards understanding the origin and spread of red tides. February 9, 2009, Bowling Green State University, Bowling Green, Ohio.

Matryoshka plastids: primary, secondary, and tertiary, endosymbioses, October 20-23, 2008, Ecole Thématique, Station Biologique de Roscoff, France, CNRS Environnement et Développement Durable.

Piecing together the composition and origin of the plastid proteome in the first photosynthetic eukaryotes, June 2, 2008, American Society of Microbiology, Division X Symposium, Boston, MA.

Origin and molecular evolution of phytoplankton, June 10-19, 2008, EU Marine Genomics Summer Course in Plankton Bloom Dynamics, Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany.

The origin and spread of photosynthesis in the eukaryotic tree of life. Department of Ecology, Evolution, and Natural Resources, Rutgers University, February 13, 2008.

Cyanidiophyceae and Red Tides: Phylogenetic and Genomic Approaches to Understanding the Biology of Two Remarkable Groups of Algae. Institute of Marine and Coastal Sciences, Rutgers University, February 12, 2008.

(Re)Tracing the spread of photosynthesis in the eukaryotic tree of life. Scripps Institute of Oceanography-UCSD Marine Biology Seminar Series, January 11, 2008.

The complete genome sequence of the glaucophyte alga Cyanophora paradoxa. National Science Foundation, MGSP Meeting, January 12, 2008, San Diego, CA.

Algal genomics and phylogenomics: windows into endosymbiosis and eukaryotic evolution. Febraury 12, 2007. Dept. of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA.

Evolution of photosynthetic eukaryotes: life at both extremes. Montana State University, June 1, 2007, Bozeman, Montana.

Taxon breadth or phylogenetic marker breadth: two attempts at reconstructing the eukaryotic tree of life. Invited Lecture. Society for Molecular Biology and Evolution/Canadian Institute of Advanced Research, June 24-28, 2007, Halifax, Canada.

Endosymbiotic gene transfer and plastid origin in chromalveolate protists. Speaker and co-organizer, NSF Funded Mini-Symposium on chromalveolate evolution, Botanical Society of America Meeting, July 7-11, 2007, Chicago, IL.

From genomes to the environment: a coordinated effort to improve our understanding of Alexandrium and the formation of red tides. Biology Department, Woods Hole Oceanographic Institution, August 9, 2007, Woods Hole, MA.

Using Comparative genomic approaches to unravel the complex evolutionary history of chromalveolates. German Botanical Society Annual Meeting, Invited Lecture, September 3-7, 2007, Hamburg, Germany.

The need for a microbial genome database to spur evolutionary and applied research. US-EC Workshop on Cyberinfrastructure Resources for Genome-Enabled Research on Microbial Life and the Marine Environment. Washington, DC, September 9-11, 2007.

Understanding red tides using genomic methods. University of Iowa Biology Department Annual Retreat, November 10, 2007, Dubuque, IA.