Publications

Selected

Aerobic sister lineage of breviates has gene-rich mitochondrial genomes

Cho A, Burns JA, Woyke T, Stepanauskas R, Poulton N, Wideman JG. Current Biology. 2026.

A multicellular developmental program in a close animal relative

Olivetta M, Bhickta C, Chiaruttini N, Burns J, Dudin O. 2024.

An in situ digital synthesis strategy for the discovery and description of ocean life

Burns JA, Becker KP, Casagrande D, Daniels J, Roberts P, Orenstein E, Vogt DM, Teoh ZE, et al.. Science Advances. 2024.

Functional stress responses in Glaucophyta: Evidence of ethylene and abscisic acid functions in Cyanophora paradoxa

Genot B, Grogan M, Yost M, Iacono G, Archer SD, Burns JA. Journal of Eukaryotic Microbiology. 2024.

Gene-based predictive models of trophic modes suggest Asgard archaea are not phagocytotic

Burns JA, Pittis AA, Kim E. Nature Ecology & Evolution. 2018.

Transcriptome analysis illuminates the nature of the intracellular interaction in a vertebrate-algal symbiosis

Burns JA, Zhang H, Hill E, Kim E, Kerney R. eLife. 2017.

Recent work

year	title	description
2026	Crawling under the radar: two novel Paulinella species expand knowledge about the ecology and evolution of a primary plastid-containing amoeba lineage	Van_Etten J, Han S, Burns J, Lhee D, Willoughby A, Stephens T, Chille E, Sleith R, et al.. Journal of phycology. 2026.
2026	The Calcidiscus leptoporus genome reveals vitamin-mediated holobiont interactions	Chaux F, Vojvoda Zeljko T, Vuković BB, Burns JA, Le Perrun T, Žižek M, Bannerman BP, Mason DTB, et al.. ISME Communications. 2026.
2025	Global metagenomics reveals hidden protist diversity	Romero MF, Krinos AI, Maurer-Alcala X, Burns JA, Stepanauskas R, Woyke T, Schulz F. Preprint. 2025.
2025	High partner specificity in an algal-salamander mutualism at continental scale	Wallace SE, Burns JA, Hale RE, Kerney RR, Mott CL, Bishop CD. Frontiers in Amphibian and Reptile Science. 2025.
2025	Turf algae redefine the chemical landscape of temperate reefs, limiting kelp forest recovery	Farrell SP, Petras D, Stincone P, Yiu DS, Burns JA, Pakkir Shah AK, Hartmann AC, Brady DC, et al.. Science. 2025.
2024	Transcriptome sequencing of seven deep marine invertebrates	Burns JA, Daniels J, Becker KP, Casagrande D, Roberts P, Orenstein E, Vogt DM, Teoh ZE, et al.. Scientific Data. 2024.
2023	Long-Read–Based Genome Assembly Reveals Numerous Endogenous Viral Elements in the Green Algal Bacterivore Cymbomonas tetramitiformis	Gyaltshen Y, Rozenberg A, Paasch A, Burns JA, Warring S, Larson RT, Maurer-Alcalá XX, Dacks J, et al.. Genome Biology and Evolution. 2023.
2022	Injection of algae intoAmbystomid (salamander) embryo v1	Burns J. 2022.
2022	Organismal and cellular interactions in vertebrate–alga symbioses	Yang H, Genot B, Duhamel S, Kerney R, Burns JA. Biochemical Society Transactions. 2022.
2022	Phagocytosis underpins the biotrophic lifestyle of intracellular parasites in the class Phytomyxea (Rhizaria)	Garvetto A, Murúa P, Kirchmair M, Salvenmoser W, Hittorf M, Ciaghi S, Harikrishnan SL, Gachon CMM, et al.. 2022.
2022	Phylogenomics and the first higher taxonomy of Placozoa, an ancient and enigmatic animal phylum	Tessler M, Neumann JS, Kamm K, Osigus HJ, Eshel G, Narechania A, Burns JA, DeSalle R, et al.. Frontiers in Ecology and Evolution. 2022.
2022	Transcriptomics of a Greenlandic Snailfish Reveals Exceptionally High Expression of Antifreeze Protein Transcripts	Burns JA, Gruber DF, Gaffney JP, Sparks JS, Brugler MR. Evolutionary Bioinformatics. 2022.
2022	Transformation of the symbiotic alga Oophila amblystomatis: a new tool for animal-algae symbiosis studies	Genot B, Burns JA. Symbiosis. 2022.
2021	Experimental identification and in silico prediction of bacterivory in green algae	Bock NA, Charvet S, Burns J, Gyaltshen Y, Rozenberg A, Duhamel S, Kim E. The ISME Journal. 2021.
2021	No evidence of Phago‐mixotropy in Micromonas polaris (Mamiellophyceae), the Dominant Picophytoplankton Species in the Arctic	Jimenez V, Burns JA, Le Gall F, Not F, Vaulot D. Journal of Phycology. 2021.
2021	Relating genome completeness to functional predictions	Liu J, Williams T, Burns JA. 2021.
2021	The Bacterial Diversity Lurking in Protist Cell Cultures	Aponte A, Gyaltshen Y, Burns JA, Heiss AA, Kim E, Warring SD. American Museum Novitates. 2021.
2020	Heterotrophic Carbon Fixation in a Salamander-Alga Symbiosis	Burns JA, Kerney R, Duhamel S. 2020.
2020	Ultra-gentle soft robotic fingers induce minimal transcriptomic response in a fragile marine animal	Tessler M, Brugler MR, Burns JA, Sinatra NR, Vogt DM, Varma A, Xiao M, Wood RJ, et al.. Current Biology. 2020.
2019	Co-cultures of Oophila amblystomatis between Ambystoma maculatum and Ambystoma gracile hosts show host-symbiont fidelity	Kerney R, Leavitt J, Hill E, Zhang H, Kim E, Burns J. Symbiosis. 2019.
2019	Collect of Collodarian (Rhizaria, Radiolaria) nuclei for genomic analyses v1	Bigeard E, Pillet L, Burns J, Not F. 2019.
2019	From intent to implementation: Factors affecting public involvement in life science research	Burns JA, Korzec K, Dorris ER. 2019.
2018	Algae Living in Salamanders, Friend or foe?	Burns JA, Kerney R. TheScienceBreaker. 2018.
2018	Global transcriptome analysis of the aphelid Paraphelidium tribonemae supports the phagotrophic origin of fungi	Torruella G, Grau-Bové X, Moreira D, Karpov SA, Burns JA, Sebé-Pedrós A, Völcker E, López-García P. Communications Biology. 2018.
2018	O 6-methylguanine–induced transcriptional mutagenesis reduces p53 tumor-suppressor function	Ezerskyte M, Paredes JA, Malvezzi S, Burns JA, Margison GP, Olsson M, Scicchitano DA, Dreij K. Proceedings of the National Academy of Sciences. 2018.
2018	The Chytrid Fungus, Batrachochytrium dendrobatidis, is Widespread Among Cuban Amphibians	Cádiz A, Reytor ML, Díaz LM, Chestnut T, Burns JA, Amato G. EcoHealth. 2018.
2017	Complete mitochondrial genomes of prasinophyte algae Pyramimonas parkeae and Cymbomonas tetramitiformis	Satjarak A, Burns JA, Kim E, Graham LE. Journal of phycology. 2017.
2016	Investigating Mechanisms of Algal Entry into Salamander Cells	KERNEY R, BURNS J, KIM E. Algal and Cyanobacteria Symbioses. 2016.
2016	Nucleotide Excision Repair and Transcription-coupled DNA Repair Abrogate the Impact of DNA Damage on Transcription	Nadkarni A, Burns JA, Gandolfi A, Chowdhury MA, Cartularo L, Berens C, Geacintov NE, Scicchitano DA. Journal of Biological Chemistry. 2016.
2016	Retention of bacterivory in the dominantly photoautotrophic green alga Cymbomonas tetramitiformis is influenced by phosphate limitation	Paasch A, Burns J, Kim E. Protistology. 2016.
2016	The green alga and the salamander: a suffocating love story	Burns J, Zhang H, Hill E, Kerney R, Kim E. Protistology. 2016.
2015	Comparative Genomics of a Bacterivorous Green Alga Reveals Evolutionary Causalities and Consequences of Phago-Mixotrophic Mode of Nutrition	Burns JA, Paasch A, Narechania A, Kim E. Genome Biology and Evolution. 2015.

Earlier work

Molecular biology of transcription and DNA damage, from graduate and postdoctoral work.

year	title	description
2018	Genetic instability associated with loop or stem–loop structures within transcription units can be independent of nucleotide excision repair	Burns JA, Chowdhury MA, Cartularo L, Berens C, Scicchitano DA. Nucleic Acids Research. 2018.
2013	Are We Listening to Genomic Noise?	Burns JA. DNA and Cell Biology. 2013.
2012	RNA Polymerase II Transcription: Effects of DNA Damage and DNA Secondary Structure on Elongation and Fidelity	Burns JA. 2012.
2010	DNA Damage and Transcription Elongation: Consequences and RNA Integrity	Dreij K, Burns JA, Dimitri A, Nirenstein L, Noujnykh T, Scicchitano DA. The Chemical Biology of DNA Damage. 2010.
2010	O 6-Methylguanine induces altered proteins at the level of transcription in human cells	Burns JA, Dreij K, Cartularo L, Scicchitano DA. Nucleic Acids Research. 2010.
2008	Transcription elongation past O 6-methylguanine by human RNA polymerase II and bacteriophage T7 RNA polymerase	Dimitri A, Burns JA, Broyde S, Scicchitano DA. Nucleic acids research. 2008.