Publications

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Publications as a lead/corresponding author

(^*equal contribution; underlined=me)

2022

• Y Sun^*, D-H Oh^*, L Duan, P Ramachandran, A Bartlett, K-N Tran, G Wang, M Dassanayake, JR Dinneny (2022), Divergence in a stress regulatory network underlies differential growth control. Nat Plants 8:549-560 doi:10.1038/s41477-022-01139-5

• D-H Oh, KP Kowalski, C Wijesinghege, Q Quach, P Tanford, M Dassanayake, K Clay (2022), Novel genome characteristics contribute to the invasiveness of Phragmites australis (common reed). Mol Ecol 31:1142-1159 doi:10.1111/mec.16293

2019

• D-H Oh and M Dassanayake (2019), Landscape of gene transposition-duplication within the Brassicaceae family. DNA Res 26:21-36 doi:10.1093/dnares/dsy035

• G Wang, P Pantha, K-N Tran, D-H Oh, M Dassanayake (2019), Plant growth and agrobacterium-mediated floral-dip transformation of the extremophyte Schrenkiella parvula. J Vis Exp 143:e58544.

2015

• D-H Oh, BJ Barkla, R Vera-Estrella, O Pantoja, SY Lee, HJ Bohnert, M Dassanayake (2015), Cell type-specific responses to salinity - the epidermal bladder cell transcriptome of Mesembryanthemum crystallinum. New Phytol 207:627–644 doi:10.1111/nph.13414

2014

• D-H Oh^*, H Hong^*, SYLee, D-J Yun, HJ Bohnert, M Dassanayake (2014), Genome structures and transcriptomes signify niche adaptation for the multi-ion tolerant extremophyte Schrenkiella parvula. Plant Physiol 164:2123–2138 doi:10.1104/pp.113.233551

2010–2012: Draft reference genomes for the Arabidopsis-relative halophyte / extremophyte Thellugiella parvula (syn. Schrenkiella parvula) and Thellugiella salsuginea (syn. Eutrema salsugineum) (see circos)

• H-J Wu^*, Z Zhang^*, J-Y Wang^*, D-H Oh^*, M Dassanayake^*, B Liu^*, Q Huang^*, HX Sun, R Xia, Y Wu, Y Wang, Z Yang, Y Liu, W Zhang, H Zhang, J Chu, C Yan, S Fang, J Zhang, Y Wang, F Zhang, G Wang, SY Lee, JM Cheeseman, B Yang, B Li, J Min, L Yang, J Wang, C Chu, SY Chen, HJ Bohnert, JK Zhu, XJ Wang, Q Xie (2012), Insights into salt tolerance from the genome of Thellungiella salsuginea. Proc Natl Acad Sci USA 109:12219–12224 doi:10.1073/pnas.1209954109

• D-H Oh^*, M Dassanayake^*, HJ Bohnert and JM Cheeseman (2012), Life in the extreme: lessons from genomics. Genome Biol 13:241 doi:10.1186/gb4003

• M Dassanayake^*, D-H Oh^*, JS Haas, A Hernandez, H Hong, S Ali, D-J Yun, RA Bressan, J-K Zhu, HJ Bohnert and JM Cheeseman (2011), The genome of the extremophile crucifer Thellungiella parvula. Nat Genet 43:913–918 doi:10.1038/ng.889

• D-H Oh^*, M Dassanayake^*, JS Haas, A Kropornicka, C Wright, MP D’Urzo, H Hong, S Ali, A Hernandez, GM Lambert, G Inan, DW Galbraith, RA Bressan, D-J Yun, J-K Zhu, JM Cheeseman, and HJ Bohnert (2010), Genome structures and halophyte-specific gene expression of the extremophile Thellungiella parvula in comparison with Thellungiella salsuginea (Thellungiella halophila) and Arabidopsis. Plant Physiol 154:1040–1052 doi:10.1104/pp.110.163923

2007–2012: Studies on SOS1 (Salt-Overly-Sensitive 1) and HKT1 (High-affinity K⁺ Transporter 1) orthologs in the halophyte T. salsuginea (syn. E. salsugineum)

• Z Ali^*, A Ali^*, HC Park^*, D-H Oh^*, R Aman, A Kropornicka, H Hong, RA Bressan, HJ Bohnert, W-Y Kim, SY Lee, and D-J Yun (2012), TsHKT1;2, a HKT1 homolog from the extremophile Arabidopsis-relative Thellungiella salsuginea, shows K⁺-specificity in the presence of NaCl. Plant Physiol 158:1463–1474. doi:10.1104/pp.111.193110

• D-H Oh, SY Lee, RA Bressan, D-J Yun, and HJ Bohnert (2010), Intracellular consequences of SOS1 deficiency during salt stress. J Exp Bot 61:1205-1213 doi:10.1093/jxb/erp391

• D-H Oh, A Zahir, DJ Yun, RA Bressan, HJ Bohnert (2009), SOS1 and halophytism. Plant Signal Behav 4:1081–1083.

• D-H Oh, E Leidi, Q Zhang, S-M Hwang, Y Li, FJ Quintero, X Jiang, MP D’Urzo, SY Lee, Y Zhao, JD Bahk, RA Bressan, D-J Yun, JM Pardo, and HJ Bohnert (2009), Loss of halophytism by interference with SOS1 expression. Plant Physiol 151:210–222 doi:10.1104/pp.109.137802

• D-H Oh, Q Gong, A Ulanov, Q Zhang, Y Li, W Ma, D-J Yun, RA Bressan, and HJ Bohnert (2007), Sodium stress in the halophyte Thellungiella halophila and transcriptional changes in a thsos1-RNA interference line. J Intgr Plant Biol 49:1484–1496

2003 and before (during the PhD@KAIST)

• D-H Oh, CS Kwon, H Sano, WI Chung, N Koizumi (2003), Conservation between animals and plants of the cis-acting element involved in the unfolded protein response. Biochem Biophys Res Commun 301:225–230.

• D-H Oh, KJ Song, YU Shin, WI Chung (2000), Isolation of a cDNA encoding a 31-kDa, pathogenesis-related 5/thaumatin-like (PR5/TL) protein abundantly expressed in apple fruit (Malus domestica cv. Fuji). Biosci Biotechnol Biochem 64:355–362.

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Publications as a co-author

(^*equal contribution; underlined=me)

Preprints

• K-N Tran, G Wang, D-H Oh, JC Larkin, AP Smith, M Dassanayake (2021) Multiple paths lead to salt tolerance - pre-adaptation vs dynamic responses from two closely related extremophytes. bioRxiv doi:10.1101/2021.10.23.465591

• K-N Tran^*, P Pantha^*, G Wang^*, N Kumar^*, C Wijesinghege, D-H Oh, N Duppen, H Li, H Hong, JC Johnson, R Kelt, MG Matherne, A Clement, D Tran, C Crain, P Adhikari, Y Zhang, M Foroozani, G Sessa, JC Larkin, AP Smith, D Longstreth, P Finnegan, C Testerink, S Barak, M Dassanayake (2021) Balancing growth amidst salinity stress-lifestyle perspectives from the extremophyte model Schrenkiella parvula. bioRxiv doi:10.1101/2021.08.27.457575

2023

• X Huang^*, H Tian^*, J Park^*, D-H Oh, J Hu, R Zentella, H Qiao, M Dassanayake, T-P Sun (2023) The master growth regulator DELLA binding to histone H2A is essential for DELLA-mediated global transcription regulation. Nat Plants 9:1291–1305 doi:10.1038/s41477-023-01477-y

• P Pantha, D-H Oh, D Longstreth, M Dassanayake (2022) Living with high potassium: balance between nutrient acquisition and K-induced salt stress signaling. Phant Physiol 191:1102-1121 doi:10.1093/plphys/kiac564

2022

• DL Lindsay, J Freeland, P Gong, X Guan, NE Harms, KP Kowalski, RF Lance, D-H Oh, BT Sartain, DL Wendell (2022), Genetic analysis of North American Phragmites australis guides management approaches. Aquat Bot 184:103589 doi:10.1016/j.aquabot.2022.103589

• G Eshel^*, N Duppen^*, G Wang, D-H Oh, Y Kazachkova, P Herzyk, A Amtmann, M Gordon, V Chalifa-Caspi, MO Arland, S Bar-David, A Marshall-Colon, M Dassanayake, S Barak (2022) Positive selection and heat-response transcriptomes reveal adaptive features of the Brassicaceae desert model, Anastatica hierochuntica. New Phytol 236:1006-1026 doi:10.1111/nph.18411

2021

• G Wang G, SF DiTusa, D-H Oh, AD Herrmann, MA O’Neill, AP Smith, M Dassanayake (2021), Cross species multi-omics reveals cell wall sequestration and elevated global transcript abundance as mechanisms of boron tolerance in plants. New Phytol 230:1985–2000 doi:10.1111/nph.17295

• P Pantha, S Chalivendra, D-H Oh, B Elderd, M Dassanayake (2021), A tale of two transcriptomic responses in agricultural pests via host defenses and viral replication. Int J Mol Sci 22:3568 doi:10.3390/ijms22073568

2020

• SY Park, JH Choi, D-H Oh, JC Johnson, M Dassanayake, DH Jeong, MH Oh (2020) Genome-wide analysis of brassinosteroid responsive small RNAs in Arabidopsis thaliana. Genes Genomics 42:957–969.

• G Wang, D-H Oh, M Dassanayake (2020), GOMCL: a tool to cluster Gene Ontology based functions. BMC Bioinformatics 21:139 doi:10.1186/s12859-020-3447-4

• M Foroozani, S Zahraeifard, D-H Oh, G Wang, M Dassanayake, AP Smith (2020), Low-phosphate chromatin dynamics predict a cell wall remodeling network in rice shoots. Plant Physiol 182:1494–1509.

• MV Cruz, GM Mori, D-H Oh, M Dassanayake, MI Zucchi, RS Oliveira, AP de Souza (2020), Molecular responses to freshwater limitation in the mangrove tree Avicennia germinans (Acanthaceae). Mol Ecol 29:344–362.

2019

• MV Cruz, GM Mori, CS Müller, CC da Silva, D-H Oh, M Dassanayake, MI Zucchi, RS Oliveira, AP de Souza (2019), Local adaptation of a dominant coastal tree to freshwater availability and solar radiation suggested by genomic and ecophysiological approaches. Sci Rep 9:19936.

2018

• S Shrestha, D-H Oh, JK McKowen, M Dassanayake, CM Hart (2018), 4C-seq characterization of Drosophila BEAF binding regions provides evidence for highly variable long-distance interactions between active chromatin. PLoS One 13:e0203843.

• S Zahraeifard, M Foroozani, A Sepehri, D-H Oh, G Wang, V Mangu, B Chen, N Baisakh, M Dassanayake, AP Smith (2018), Rice H2A.Z negatively regulates genes responsive to nutrient starvation but promotes expression of key housekeeping genes. J Exp Bot 69:4907–4919.

• R Wu, L Duan, JL Pruneda-Paz, D-H Oh, M Pound, S Kay, JR Dinneny (2018), The 6xABRE synthetic promoter enables the spatiotemporal analysis of ABA-mediated transcriptional regulation. Plant Physiol 177:1650–1665.

• B Shrestha, D-H Oh, M Dassanayake, JH Ham (2018), Analysis of genome sequence variations among three us rice varieties showing differential quantitative disease resistance to bacterial panicle blight and sheath blight. Int J Genom Data Min IJGD-122.

• Q Zhang, D-H Oh, SF DiTusa, MV RamanaRao, N Baisakh, M Dassanayake, AP Smith (2018), Rice nucleosome patterns undergo remodeling coincident with stress-induced gene expression. BMC Genomics 19:97.

2017

• J Park, D-H Oh, M Dassanayake, KT Nguyen, J Ogas, G Choi, T Sun (2017), Gibberellin signaling requires chromatin remodeler pickle to promote vegetative growth and phase. Plant Physiol 173: 1463–1474 doi:10.1104/pp.16.01471

2016

• B Lambert, M Dassanayake, D-H Oh, SB Garrett, SY Lee, GS Pettis (2016), A novel phase variant of the cholera pathogen shows stress-adaptive cryptic transcriptomic signatures. BMC Genomics 17:914.

• A Ali, N Raddatz, R Aman, S Kim, HC Park, M Jan, D Baek, IU Khan, D-H Oh, SY Lee, RA Bressan, KW Lee, A Maggio, JM Pardo, HJ Bohnert, DJ Yun (2016), A single amino acid substitution in the sodium transporter HKT1 associated with plant salt tolerance. Plant Physiol 171:2112–2126.

2014

• Q Wang, CM Nowak, A Korde, D-H Oh, M Dassanayake, D Donze (2014), Compromised RNA Polymerase III complex assembly leads to local alterations of intergenic RNA Polymerase II transcription in Saccharomyces cerevisiae. BMC Biol 12:89.

• G Batelli, D-H Oh, MP D’Urzo, F Orsini, M Dassanayake, JK Zhu, HJ Bohnert, RA Bressan, A Maggio (2014), Using Arabidopsis-related model species (ARMS): growth, genetic transformation, and comparative genomics. Methods Mol Biol 1062:27–51.

2013 and before (before joining LSU)

• JI Kim, D Baek, HC Park, HJ Chun, D-H Oh, MK Lee, JY Cha, WY Kim, MC Kim, WC Chung, HJ Bohnert, SY Lee, RA Bressan, SW Lee, DJ Yun (2013), Overexpression of Arabidopsis YUCCA6 in potato results in high-auxin developmental phenotypes and enhanced resistance to water deficit. Mol Plant 6:337–349.

• RA Bressan, HC Park, F Orsini, D-H Oh, M Dassanayake, G Inan, DJ Yun, HJ Bohnert, A Maggio (2013), Biotechnology for mechanisms that counteract salt stress in extremophile species: a genome-based view. Plant Biotechnol Rep 7:27–37

• MH Oh, J Sun, D-H Oh, RE Zielinski, SD Clouse, SC Huber (2011), Enhancing Arabidopsis leaf growth by engineering the BRASSINOSTEROID INSENSITIVE1 receptor kinase. Plant Physiol 157:120–131.

• W Choi, D Baek, D-H Oh, J Park, H Hong, WY Kim, HJ Bohnert, RA Bressan, HC Park, DJ Yun (2011), NKS1, Na⁺- and K⁺-sensitive 1, regulates ion homeostasis in an SOS-independent pathway in Arabidopsis. Phytochemistry 72:330–336.

• M Dassanayake, D-H Oh, H Hong, HJ Bohnert, and JM Cheeseman (2011), Transcription strength and halophytic lifestyle. Trends Plant Sci 16:1–3.

• M Dassanayake, D-H Oh, D-J Yun, RA Bressan, JM Cheeseman, and HJ Bohnert. “The Scope of Things to Come - New Paradigms in Biotechnology” in: Plant biotechnology 2010: prospects for the 21st Century, eds. PM Hasegawa and A Altman, Elsevier, Amsterdam, Netherland (2011) (Book chapter).

• F Orsini, MP D’Urzo, G Inan, S Serra, D-H Oh, MV Mickelbart, F Consiglio, X Li, JC Jeong, D-J Yun, HJ Bohnert, RA Bressan, and A Maggio (2010), A comparative study of salt tolerance parameters in 11 wild relatives of Arabidopsis thaliana. J Exp Bot 61:3787–3798.

• SJ Noh, CS Kwon, D-H Oh, JS Moon, Chung WI (2003), Expression of an evolutionarily distinct novel BiP gene during the unfolded protein response in Arabidopsis thaliana. Gene 311:81–91.

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Grants

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Awarded

(amount awarded; PI; my role) * roles transferred to colleague by 2022 May

• 2023 – 2026 : Using an Evolutionary Perspective to Discover and Predict Stress-Associated Gene Functions ($2,700,000; José Dinneny, Stanford Univ.; Co-Investigator *)

• 2022 – 2025 : USDA-NIFA; Deciphering the role of the quorum-sensing master regulator, qsmR, in social behaviors of Burkholderia glumae for bacterial pathogenesis in rice plants ($682,232; Jong Hyun Ham, LSU; Collaborator *)

• 2022 – 2023 : DOE-JGI; Resequencing nuclear genome, mitochondrial genome and transcriptome for Brassicaceae species to facilitate stress tolerance research (Sequencing and assembly services; Song Li, Virginia Tech.; Co-PI *)

• 2020 – 2022 : COPIA Foundation, Israel; Mining seagrasses to develop salt-tolerant crops, as an international collaboration with Ben-Gurion University of the Negev ($200,000 to LSU; Simon Barak, Ben Gurion Univ., Israel; Key personnel *)

• 2019 – 2022 : DOE-BER; Discovering innovations in stress tolerance through comparative gene regulatory network analysis and cell-type specific expression maps ($2,200,000; José Dinneny, Stanford Univ., CA; Co-Investigator *)

• 2019 – 2022 : NSF-BSF-EDGE; Developing Functional Genomics Tools for Emerging Extremophyte Models ($1,000,000; Maheshi Dassanayake, LSU; Co-PI *)

• 2019 – 2022 : USGS- Great Lakes Coastal Wetland Restoration program, Cooperative Ecosystem Studies Units (CESU) G19AC0046; The Phragmites australis genome project (Not determined; Kurt Kowalski, U.S. Geological Survey; Key personnel *)

• 2017 – 2020 : USDA-NIFA; Improving the quality of rice by identifying targets to restrict arsenic accumulation ($500,000; Aaron P. Smith, LSU; Key personnel)

• 2016 – 2019 : NSF-MCB; Is abiotic stress tolerance achieved by network restructuring or invention of new genetic modules? ($900,000; Maheshi Dassanayake, LSU; Co-PI)

• 2015 – 2018 : Theragen BIO, South Korea; Consultation on the tartary buckwheat genome project ($95,000; M. Dassanayake; Key personnel)

• 2013 – 2017 : RDA-Biogreen 21, South Korea; Genomic variations for stress adaptation in extremophyte wild-relatives of crops ($300,000; Sang-Yul Lee, Gyeongsang National University, S. Korea; International collaborator)

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Tools

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Each link leads to the GitHub repository for the tool.

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PiP

• An attempt to identify functions and gene sets (e.g. Gene Ontology terms) that underwent lineage(s)-specific modifications in gene expression/regulation among multiple species, by performing Phylogenetically-informed Profiling (PiP) of gene sets. Check the re-recorded PAG2022 talk for details.

• The matrices of presence and absence of positive correlation between all pairs of species are superimposed to the species tree, for all gene sets. Variance of correlations are then ranked to find out the most significant modifications.

toggle Publication

• Y Sun^*, D-H Oh^*, L Duan, P Ramachandran, A Bartlett, K-N Tran, G Wang, M Dassanayake, JR Dinneny (2022), Divergence in a stress regulatory network underlies differential growth control. Nat Plants doi:doi.org/10.1038/s41477-022-01139-5 (^*equal contribution)

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OrthNet

• An attempt to identify ortholog groups based on synteny/co-linearity and encode the evolutionary history of each ortholog group as the topology of Ortholog Network (OrthNet), among multiple closely related genomes.

• OrthNet can (1) improve the resolution of solely sequence-based orthology inferences (e.g. OrthoFinder); (2) serve as a platform to organize and compare various -seq data for multiple species; (3) identify lineage(s)-specific events that modify ortholog copy numbers and synteny, such as duplication, transposition, deletion, and combinations of them; and more.

toggle Publication

• D-H Oh and M Dassanayake (2019), Landscape of gene transposition-duplication within the Brassicaceae family. DNA Res 26:21-36 doi:10.1093/dnares/dsy035

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Genome toolbox

• Python scripts for exploring and fixing genome assembly (.fa) and annotation (.gtf).

• Useful if you want to (1) remove chunks in the middle of sequences when there is a gene model annotation (.gtf); (2) for all gene models in a .gtf, rename transcript_id, gene_id, and gene_name fields; (3) cluster gene models from the same locus (i.e. isoforms) and select, for example, those coding for longest ORFs as “primary” gene models; (4) extract sequences for genomic regions (e.g. promoters); (5) find all sequence elements (defined as regex) in a genome; and more.

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