The University of Queensland

De novo plant transcriptome assembly and annotation using illumina RNA-seq reads

Kerr, Stephanie C., Gaiti, Federico and Tanurdzic, Milos (2019). De novo plant transcriptome assembly and annotation using illumina RNA-seq reads. Plant long non-coding RNAs: methods and protocols. (pp. 265-275) edited by Julia A. Chekanova and Hsiao-Lin V. Wang. New York, NY, United States: Springer Nature. doi: 10.1007/978-1-4939-9045-0_16

Origins of novel phenotypic variation in polyploids

Finigan, Patrick, Tanurdzic, Milos and Martienssen, Robert A. (2012). Origins of novel phenotypic variation in polyploids. Polyploidy and Genome Evolution. (pp. 57-76) edited by Pamela S. Soltis and Douglas E. Soltis. Heidelberg, Germany: Springer. doi: 10.1007/978-3-642-31442-1_4

Reverse Genetic Analyses of Gene Function in Fern Gametophytes

Rutherford, George, Tanurdzic, Milos, Hasebe, Mitsuyasu and Banks, Jo Ann (2012). Reverse Genetic Analyses of Gene Function in Fern Gametophytes. Vascular Plants and Paleobotany. (pp. 54-66) edited by Philip Stewart and Sabine Globig. Point Pleasant, NJ, United States: CRC Press. doi: 10.1201/b12226-6

Advancing tree genomics to future proof next generation orchard production

Kerr, Stephanie C., Shehnaz, Saiyara, Paudel, Lucky, Manivannan, Mekaladevi S., Shaw, Lindsay M., Johnson, Amanda, Velasquez, Jose Teodoro J., Tanurdžić, Miloš, Cazzonelli, Christopher I., Varkonyi-Gasic, Erika and Prentis, Peter J. (2024). Advancing tree genomics to future proof next generation orchard production. Frontiers in Plant Science, 14 1321555, 1-23. doi: 10.3389/fpls.2023.1321555

Genome-wide identification of accessible chromatin regions by ATAC-seq upon induction of the transcription factor bZIP11 in Arabidopsis

Hellens, Alicia M., Humphreys, Jazmine L., Fichtner, Franziska, Tanurdžić, Miloš, Beveridge, Christine A. and Barbier, François F. (2023). Genome-wide identification of accessible chromatin regions by ATAC-seq upon induction of the transcription factor bZIP11 in Arabidopsis. Scientific Data, 10 (1) 490, 490. doi: 10.1038/s41597-023-02395-6

Epigenome guided crop improvement: current progress and future opportunities

Zhang, Yan, Andrews, Haylie, Eglitis-Sexton, Judith, Godwin, Ian, Tanurdžić, Miloš and Crisp, Peter A. (2022). Epigenome guided crop improvement: current progress and future opportunities. Emerging Topics in Life Sciences, 6 (2), 141-151. doi: 10.1042/etls20210258

Horticultural innovation by viral-induced gene regulation of carotenogenesis

Paudel, Lucky, Kerr, Stephanie, Prentis, Peter, Tanurdžić, Miloš, Papanicolaou, Alexie, Plett, Jonathan M. and Cazzonelli, Christopher I. (2022). Horticultural innovation by viral-induced gene regulation of carotenogenesis. Horticulture Research, 9 uhab008, 1-19. doi: 10.1093/hr/uhab008

Profiling the endosperm, one nucleus at a time

Tanurdžić, Miloš (2021). Profiling the endosperm, one nucleus at a time. Nature Plants, 7 (6), 710-711. doi: 10.1038/s41477-021-00945-7

Loss of small-RNA-directed DNA methylation in the plant cell cycle promotes germline reprogramming and somaclonal variation

Borges, Filipe, Donoghue, Mark T.A., LeBlanc, Chantal, Wear, Emily E., Tanurdžić, Milos, Berube, Benjamin, Brooks, Ashley, Thompson, William F., Hanley-Bowdoin, Linda and Martienssen, Robert A. (2021). Loss of small-RNA-directed DNA methylation in the plant cell cycle promotes germline reprogramming and somaclonal variation. Current Biology, 31 (3), 591-600.e4. doi: 10.1016/j.cub.2020.10.098

An optimised chromatin immunoprecipitation (ChIP) method for starchy leaves of Nicotiana benthamiana to study histone modifications of an allotetraploid plant

Ranawaka, Buddhini, Tanurdzic, Milos, Waterhouse, Peter and Naim, Fatima (2020). An optimised chromatin immunoprecipitation (ChIP) method for starchy leaves of Nicotiana benthamiana to study histone modifications of an allotetraploid plant. Molecular Biology Reports, 47 (12), 9499-9509. doi: 10.1007/s11033-020-06013-1

Pre‐introduction introgression contributes to parallel differentiation and contrasting hybridization outcomes between invasive and native marine mussels

Popovic, Iva, Bierne, Nicolas, Gaiti, Federico, Tanurdžić, Miloš and Riginos, Cynthia (2020). Pre‐introduction introgression contributes to parallel differentiation and contrasting hybridization outcomes between invasive and native marine mussels. Journal of Evolutionary Biology, 34 (1) jeb.13746, 175-192. doi: 10.1111/jeb.13746

De novo transcriptome assembly and annotation for gene discovery in avocado, macadamia and mango

Chabikwa, Tinashe G., Barbier, Francois F., Tanurdzic, Milos and Beveridge, Christine A. (2020). De novo transcriptome assembly and annotation for gene discovery in avocado, macadamia and mango. Scientific Data, 7 (1) 9, 9. doi: 10.1038/s41597-019-0350-9

SDG8-mediated histone methylation and RNA processing function in the response to nitrate signaling

Li, Ying, Brooks, Matthew, Yeoh-Wang, Jenny, McCoy, Rachel M, Rock, Tara M, Pasquino, Angelo, Moon, Chang In, Patrick, Ryan M, Tanurdzic, Milos, Ruffel, Sandrine, Widhalm, Joshua R, McCombie, W Richard and Coruzzi, Gloria M (2020). SDG8-mediated histone methylation and RNA processing function in the response to nitrate signaling. Plant Physiology, 182 (1), 215-227. doi: 10.1104/pp.19.00682

A phenol/chloroform-free method to extract nucleic acids from recalcitrant, woody tropical species for gene expression and sequencing

Barbier, François F., Chabikwa, Tinashe G., Ahsan, Muhammad U., Cook, Stacey E., Powell, Rosanna, Tanurdzic, Milos and Beveridge, Christine A. (2019). A phenol/chloroform-free method to extract nucleic acids from recalcitrant, woody tropical species for gene expression and sequencing. Plant Methods, 15 (1) 62, 62. doi: 10.1186/s13007-019-0447-3

Juvenility and vegetative phase transition in tropical/subtropical tree crops

Ahsan, Muhammad Umair, Hayward, Alice, Irihimovitch, Vered, Fletcher, Stephen, Tanurdzic, Milos, Pocock, Alexander, Beveridge, Christine Anne and Mitter, Neena (2019). Juvenility and vegetative phase transition in tropical/subtropical tree crops. Frontiers in Plant Science, 10 729, 729. doi: 10.3389/fpls.2019.00729

Identification of molecular integrators shows that nitrogen actively controls the phosphate starvation response in plants

Medici, Anna, Szponarski, Wojciech, Dangeville, Pierre, Safi, Alaeddine, Dissanayake, Indeewari Madhubhashini, Saenchai, Chorpet, Emanuel, Amélie, Rubio, Vicente, Lacombe, Benoît, Ruffel, Sandrine, Tanurdzic, Milos, Rouached, Hatem and Krouk, Gabriel (2019). Identification of molecular integrators shows that nitrogen actively controls the phosphate starvation response in plants. The Plant Cell, 31 (5), 1171-1184. doi: 10.1105/tpc.18.00656

Sex determination in is accompanied by transcriptome changes that drive epigenetic reprogramming of the young gametophyte

Atallah, Nadia M., Vitek, Olga, Gaiti, Federico, Tanurdzic, Milos and Banks, Jo Ann (2018). Sex determination in is accompanied by transcriptome changes that drive epigenetic reprogramming of the young gametophyte. G3: Genes, Genomes, Genetics, 8 (7), 2205-2214. doi: 10.1534/g3.118.200292

Long non-coding regulatory RNAs in sponges and insights into the origin of animal multicellularity

Gaiti, Federico, Degnan, Bernard M and Tanurdžić, Miloš (2018). Long non-coding regulatory RNAs in sponges and insights into the origin of animal multicellularity. RNA Biology, 15 (6), 1-22. doi: 10.1080/15476286.2018.1460166

Sponge Long Non-Coding RNAs Are Expressed in Specific Cell Types and Conserved Networks

Gaiti, Federico, Hatleberg, William L., Tanurdžić, Miloš and Degnan, Bernard M. (2018). Sponge Long Non-Coding RNAs Are Expressed in Specific Cell Types and Conserved Networks. Non-Coding RNA, 4 (1) 6, 6. doi: 10.3390/ncrna4010006

Convergent microevolution of Cryptococcus neoformans hypervirulence in the laboratory and the clinic

Arras, Samantha D. M., Ormerod, Kate L., Erpf, Paige E., Espinosa, Monica I., Carpenter, Alex C., Blundell, Ross D., Stowasser, Samantha R., Schulz, Benjamin L., Tanurdzic, Milos and Fraser, James A. (2017). Convergent microevolution of Cryptococcus neoformans hypervirulence in the laboratory and the clinic. Scientific Reports, 7 (1) 17918, 1-14. doi: 10.1038/s41598-017-18106-2

Origin and evolution of the metazoan non-coding regulatory genome

Gaiti, Federico, Calcino, Andrew D., Tanurdzic, Miloš and Degnan, Bernard M. (2017). Origin and evolution of the metazoan non-coding regulatory genome. Developmental Biology, 427 (2), 193-202. doi: 10.1016/j.ydbio.2016.11.013

Sirtuins in the phylum Basidiomycota: A role in virulence in Cryptococcus neoformans

Arras, Samantha D. M., Chitty, Jessica L., Wizrah, Maha S. I., Erpf, Paige E., Schulz, Benjamin L., Tanurdzic, Milos and Fraser, James A. (2017). Sirtuins in the phylum Basidiomycota: A role in virulence in Cryptococcus neoformans. Scientific Reports, 7 (1) 46567, 46567.1-46567.14. doi: 10.1038/srep46567

Landscape of histone modifications in a sponge reveals the origin of animal cis-regulatory complexity

Gaiti, Federico, Jindrich, Katia, Fernandez-Valverde, Selene L., Roper, Kathrein E., Degnan, Bernard M. and Tanurdzic, Milos (2017). Landscape of histone modifications in a sponge reveals the origin of animal cis-regulatory complexity. Elife, 6 e22194. doi: 10.7554/eLife.22194

De novo transcriptome assembly reveals high transcriptional complexity in Pisum sativum axillary buds and shows rapid changes in expression of diurnally regulated genes

Kerr, Stephanie C., Gaiti, Federico, Beveridge, Christine A. and Tanurdzic, Milos (2017). De novo transcriptome assembly reveals high transcriptional complexity in Pisum sativum axillary buds and shows rapid changes in expression of diurnally regulated genes. BMC Genomics, 18 (1) 221, 221. doi: 10.1186/s12864-017-3577-x

Dynamic and Widespread lncRNA Expression in a Sponge and the Origin of Animal Complexity

Gaiti, Federico, Fernandez-Valverde, Selene L., Nakanishi, Nagayasu, Calcino, Andrew D., Yanai, Itai, Tanurdzic, Milos and Degnan, Bernard M. (2015). Dynamic and Widespread lncRNA Expression in a Sponge and the Origin of Animal Complexity. Molecular Biology and Evolution, 32 (9), 2367-2382. doi: 10.1093/molbev/msv117

The histone methyltransferase SDG8 mediates the epigenetic modification of light and carbon responsive genes in plants

Li, Ying, Mukherjee, Indrani, Thum, Karen E., Tanurdzic, Milos, Katari, Manpreet S., Obertello, Mariana, Edwards, Molly B., McCombie, W. Richard, Martienssen, Robert A. and Coruzzi, Gloria M. (2015). The histone methyltransferase SDG8 mediates the epigenetic modification of light and carbon responsive genes in plants. Genome Biology, 16 (79) 79, 1-15. doi: 10.1186/s13059-015-0640-2

Differential sRNA regulation in leaves and roots of sugarcane under water depletion

Thiebaut, Flavia, Grativol, Clı´cia, Tanurdzic, Milos, Carnavale-Bottino, Mariana, Vieira, Tauan, Motta, Mariana Romeiro, Rojas, Cristian, Vincentini, Renato, Chabregas, Sabrina Moutinho, Hemerly, Adriana Silva, Martienssen, Robert A. and Ferreira, Paulo Cavalcanti Gomes (2014). Differential sRNA regulation in leaves and roots of sugarcane under water depletion. PLoS One, 9 (4) e93822, e93822.1-e93822.17. doi: 10.1371/journal.pone.0093822

Integrated RNA-seq and sRNA-seq analysis identifies novel nitrate-responsive genes in Arabidopsis thaliana roots

Vidal, Elena A., Moyano, Tomás C., Krouk, Gabriel, Katari, Manpreet S., Tanurdzic, Milos, McCombie, W. Richard, Coruzzi, Gloria M. and Gutierrez, Rodrigo A. (2013). Integrated RNA-seq and sRNA-seq analysis identifies novel nitrate-responsive genes in Arabidopsis thaliana roots. BMC Genomics, 14 (1) 701, 701.1-701.15. doi: 10.1186/1471-2164-14-701

Computational identification and analysis of novel sugarcane microRNAs

Thiebaut, Flavia, Grativol, Clicia, Carnavale-Bottino, Mariana, Rojas, Cristian Antonio, Tanurdzic, Milos, Farinelli, Laurent, Martienssen, Robert A., Hemerly, Adriana Silva and Gomes Ferreira, Paulo Cavalcanti (2012). Computational identification and analysis of novel sugarcane microRNAs. BMC Genomics, 13 (1) 290, 290.1-290.14. doi: 10.1186/1471-2164-13-290

The Selaginella Genome Identifies Genetic Changes Associated with the Evolution of Vascular Plants

Banks, Jo Ann, Nishiyama, Tomoaki, Hasebe, Mitsuyasu, Bowman, John L., Gribskov, Michael, dePamphilis, Claude, Albert, Victor A., Aono, Naoki, Aoyama, Tsuyoshi, Ambrose, Barbara A., Ashton, Neil W., Axtell, Michael J., Barker, Elizabeth, Barker, Michael S., Bennetzen, Jeffrey L., Bonawitz, Nicholas D., Chapple, Clint, Cheng, Chaoyang, Correa, Luiz Gustavo Guedes, Dacre, Michael, DeBarry, Jeremy, Dreyer, Ingo, Elias, Marek, Engstrom, Eric M., Estelle, Mark, Feng, Liang, Finet, Cedric, Floyd, Sandra K., Frommer, Wolf B. ... Grigoriev, Igor V. (2011). The Selaginella Genome Identifies Genetic Changes Associated with the Evolution of Vascular Plants. Science, 332 (6032), 960-963. doi: 10.1126/science.1203810

Arabidopsis thaliana chromosome 4 replicates in two phases that correlate with chromatin state

Lee, Tae-Jin, Pascuzzi, Pete E., Settlage, Sharon B., Shultz, Randall W., Tanurdzic, Milos, Rabinowicz, Pablo D., Menges, Margit, Zheng, Ping, Main, Dorrie, Murray, James A. H., Sosinski, Bryon, Allen, George C., Martienssen, Robert A., Hanley-Bowdoin, Linda, Vaughn, Matthew W. and Thompson, William F. (2010). Arabidopsis thaliana chromosome 4 replicates in two phases that correlate with chromatin state. PLoS Genetics, 6 (6), e1000982.1-e1000982.18. doi: 10.1371/journal.pgen.1000982

Epigenetic reprogramming and small RNA silencing of transposable elements in pollen

Slotkin, R. Keith, Vaughn, Matthew, Borges, Filipe, Tanurdzic, Milos, Becker, Joerg D., Feijo, Jose A. and Martienssen, Robert A. (2009). Epigenetic reprogramming and small RNA silencing of transposable elements in pollen. Cell, 136 (3), 461-472. doi: 10.1016/j.cell.2008.12.038

Epigenomic consequences of immortalized plant cell suspension culture

Tanurdzic, Milos, Vaughn, Matthew W., Jiang, Hongmei, Lee, Tae-Jin, Slotkin, R. Keith, Sosinski, Bryon, Thompson, William F., Doerge, R. W. and Martienssen, Robert A. (2008). Epigenomic consequences of immortalized plant cell suspension culture. PLoS Biology, 6 (12), 2880-2895. doi: 10.1371/journal.pbio.0060302

ABAP1 is a novel plant Armadillo BTB protein involved in DNA replication and transcription

Masuda, Hana Paula, Cabral, Luiz Mors, De Veylder, Lieven, Tanurdzic, Milos, Engler, Janice de Almeida, Geelen, Danny, Inze, Dirk, Martienssen, Robert A., Ferreira, Paulo C. G. and Hemerly, Adriana S. (2008). ABAP1 is a novel plant Armadillo BTB protein involved in DNA replication and transcription. EMBO Journal, 27 (20), 2746-2756. doi: 10.1038/emboj.2008.191

Systems approach identifies an organic nitrogen-responsive gene network that is regulated by the master clock control gene CCA1

Gutierez, Rodrigo A., Stokes, Trevor L., Thum, Karen, Xu, Xiaodong, Obertello, Mariana, Katari, Manpreet S., Tanurdzic, Milos, Dean, Alexis, Nero, Dannion C., McClung, C. Robertson and Coruzzi, Gloria M. (2008). Systems approach identifies an organic nitrogen-responsive gene network that is regulated by the master clock control gene CCA1. Proceedings of the National Academy of Sciences of the United States of America, 105 (12), 4939-4944. doi: 10.1073/pnas.0800211105

Epigenetic natural variation in Arabidopsis thaliana

Vaughn, Matthew W., Tanurdzic, Milos, Lippman, Zachary, Jiang, Hongmei, Carrasquillo, Robert, Rabinowicz, Pablo D., Dedhia, Neilay, McCombie, W. Richard, Agier, Nicolas, Bulski, Agnes, Colot, Vincent, Doerge, R. W. and Martienssen, Robert A. (2007). Epigenetic natural variation in Arabidopsis thaliana. PloS Biology, 5 (7), 1617-1629. doi: 10.1371/journal.pbio.0050174

Replication, repair, and reactivation

Vaughn, Matthew W., Tanurdzic, Milos and Martienssen, Rob (2005). Replication, repair, and reactivation. Developmental Cell, 9 (6), 724-725. doi: 10.1016/j.devcel.2005.11.011

Construction of a bacterial artificial chromosome library from the spikemoss Selaginella moellendorffii: a new resource for plant comparative genomics

Wang, Wenming, Tanurdzic, Milos, Luo, Meizhong, Sisneros, Nicholas, Kim, Hye Ran, Weng, Jing-Ke, Kudrna, Dave, Mueller, Christopher, Arumuganathan, K., Carlson, John, Chapple, Clint, de Pamphilis, Claude, Mandoli, Dina, Tomkins, Jeff, Wing, Rod A. and Banks, Jo Ann (2005). Construction of a bacterial artificial chromosome library from the spikemoss Selaginella moellendorffii: a new resource for plant comparative genomics. BMC Plant Biology, 5 (1) 10, 10.1-10.8. doi: 10.1186/1471-2229-5-10

Functional analysis and comparative genomics of expressed sequence tags from the lycophyte Selaginella moellendorffii

Weng, Jing-Ke, Tanurdzic, Milos and Chapple, Clint (2005). Functional analysis and comparative genomics of expressed sequence tags from the lycophyte Selaginella moellendorffii. BMC Genomics, 6 (7-8) 85, 85.1-85.13. doi: 10.1186/1471-2164-6-85

A systemic gene silencing method suitable for high throughput, reverse genetic analyses of gene function in fern gametophytes

Rutherford, George, Tanurdzic, Milos, Hasebe, Mitsuyasu and Banks, Jo Ann (2004). A systemic gene silencing method suitable for high throughput, reverse genetic analyses of gene function in fern gametophytes. BMC Plant Biology, 4 6. doi: 10.1186/1471-2229-4-6

Polyglutamine-encoding microsatellite contributes to LMW GS diversity in Triticum monococcum

Tanurdzic, M., Obreht, D., Vapa, L. and Davidovic, M. (2004). Polyglutamine-encoding microsatellite contributes to LMW GS diversity in Triticum monococcum. Cereal Research Communications, 32 (3), 301-308.

Sex-determining mechanisms in land plants

Tanurdzic, Milos and Banks, Jo Ann (2004). Sex-determining mechanisms in land plants. Plant Cell, 16 (Supplement 1), S61-S71. doi: 10.1105/tpc.016667

Epigenetic inheritance and reprogramming in plants and fission yeast

Martienssen, R. A., Kloc, A., Slotkin, R. K. and Tanurdzic, M. (2008). Epigenetic inheritance and reprogramming in plants and fission yeast. 73rd Cold Spring Harbor Symposium on Quantitative Biology, Cold Spring Harbor, NY, New York, 28 May - 2 June 2008. Woodbury, NY, United States: Cold Spring Harbor Laboratory Press. doi: 10.1101/sqb.2008.73.062

Silent running: RNA interference and heterochromatic modification

Martienssen, Rob, Zaratiegui, Mikel, Irvine, Danielle, Goto, Derek, Slotkin, Keith, Tanurdzic, Milos, Lippman, Zach, Vaughn, Matt, May, Bruce, Cande, Zac, Colot, Vincent and Doerge, R. W. (2007). Silent running: RNA interference and heterochromatic modification. 16th International Chromosome Conference (ICC 16), Amsterdam, Netherlands, 25-29 August 2007. Dordrecht, Netherlands: Springer. doi: 10.1007/s10577-007-1912-9

Microarrays: Design, analysis, and applications in functional genomics

Tanurdžić, Miloš, Doerge, Rebecca and Martienssen, Robert (2005). Microarrays: Design, analysis, and applications in functional genomics. doi: 10.2298/A000503124T

Designing microarrays

Craig, B. A., Vitek, O., Black, M. A., Tanurdzic, M. and Doerge, R. W. (2001). Designing microarrays. 13th Annual Conference on Applied Statistics in Agriculture, Manhattan, Kansas, United States, April 29 - May 1, 2001. Manhattan, Kansas, United States: New Prairie Press. doi: 10.4148/2475-7772.1223