Dr Ute Baumann

Bioinformatics Group Leader

School of Agriculture, Food and Wine

Faculty of Sciences, Engineering and Technology

Eligible to supervise Masters and PhD - email supervisor to discuss availability.

Ute Baumann is the Bioinformatics Leader at the School of Agriculture, Food and Wine and also leads Program 5, Genomics for Breeding, of the ARC Industry Hub for Wheat in a Hot and Dry Climate. She manages a diverse team of highly skilled experts that is instrumental in the success of a wide range of projects and industry collaborations. The combination of a PhD in Molecular Biology and a postgraduate certificate in Bioinformatics followed by extensive research experience allows her to effectively facilitate and manage collaborations between biologists and computer scientists. Ute has a long standing international reputation and expertise in cereal bioinformatics and genomics and is frequently approached to consult on use of Next Generation Sequencing technologies and experimental design. In this capacity she was elected to be a board member of the International Wheat Genome Sequencing Consortium.

My Research
Career
Publications
Grants and Funding
Supervision
Professional Activities
Contact

Bioinformatics has become an important component in many plant research areas, from addressing topics in plant development to the elucidation of abiotic stress tolerance.

This has resulted in the participation of my research group in a large variety of research projects both at national and international level, often in close collaboration with established Australian breeders and multinational agribusiness. In my research I apply bioinformatics to investigate the genetic control of economically important traits across a range of commercial crops. My interest in genome and genetic diversity has also lead to the development of bioinformatic tools to visualise and mine genomic resources to identify allelic variation underlying loci of interest. Other projects have investigated transcriptome responses to environmental stresses like heat, drought, salt or boron, which are particularly problematic in the Australian context.

Appointments

Date	Position	Institution name
2017 - ongoing	Bioinformatics Group Leader	School of Agriculture, Food and Wine
2012 - 2016	Bioinformatics Leader	Australian Centre for Plant Functional Genomics
1991 - 1992	Consultant	Ministry for Environment

Language Competencies

Language Competency

German Can read, write, speak, understand spoken and peer review
Education

Date Institution name Country Title

University of Adelaide, Adelaide Australia PhD
Research Interests

Bioinformatics Genetics Genomics Plant Cell and Molecular Biology

Language	Competency
German	Can read, write, speak, understand spoken and peer review

Date	Institution name	Country	Title
	University of Adelaide, Adelaide	Australia	PhD

Journals

Year	Citation
2024	Pallotta, M., Okada, T., Roy, S., Pearson, A., Baumann, U., & Whitford, R. (2024). Diversity in bread and durum wheat stigma morphology and linkage of increased stigma length to dwarfing gene Rht14. Theoretical and Applied Genetics: international journal of plant breeding research, 137(7), 160-1-160-15. DOI
2024	Amalraj, A., Baumann, U., Hayes, J. E., & Sutton, T. (2024). Using RNA sequencing to unravel molecular changes underlying the defense response in chickpea induced by Phytophthora medicaginis. Physiologia Plantarum, 176(4), 12 pages. DOI
2023	Tan, J. W., Shinde, H., Tesfamicael, K., Hu, Y., Fruzangohar, M., Tricker, P., . . . Rodríguez López, C. M. (2023). Global transcriptome and gene co-expression network analyses reveal regulatory and non-additive effects of drought and heat stress in grapevine. Frontiers in Plant Science, 14, 1-15. DOI Scopus12 WoS2 Europe PMC7
2023	Selva, C., Yang, X., Shirley, N. J., Whitford, R., Baumann, U., & Tucker, M. R. (2023). HvSL1 and HvMADS16 promote stamen identity to restrict multiple ovary formation in barley. Journal of Experimental Botany, 74(17), 5039-5056. DOI Scopus3 WoS1 Europe PMC2
2023	Khan, H. A., Sharma, N., Siddique, K. H. M., Colmer, T. D., Sutton, T., & Baumann, U. (2023). Comparative transcriptome analysis reveals molecular regulation of salt tolerance in two contrasting chickpea genotypes. Frontiers in Plant Science, 14, 24 pages. DOI Scopus4 Europe PMC3
2023	Midzi, J., Jeffery, D. W., Baumann, U., Capone, D. L., Rogiers, S. Y., & Pagay, V. (2023). Evidence of Bi-Directional Volatile-Mediated Communication between Drought-Stressed and Well-Watered Grapevines (Vitis vinifera L.). Agronomy, 13(7), 1747. DOI Scopus1
2022	Midzi, J., Jeffery, D. W., Baumann, U., Rogiers, S., Tyerman, S. D., & Pagay, V. (2022). Stress-Induced Volatile Emissions and Signalling in Inter-Plant Communication. Plants, 11(19), 1-30. DOI Scopus26 WoS8 Europe PMC9
2022	Chidzanga, C., Mullan, D., Roy, S., Baumann, U., & Garcia, M. (2022). Nested association mapping-based GWAS for grain yield and related traits in wheat grown under diverse Australian environments. Theoretical and Applied Genetics, 135(12), 4437-4456. DOI Scopus11 WoS2 Europe PMC6
2022	Selva, C., Shirley, N., Houston, K., Whitford, R., Baumann, U., Li, G., & Tucker, M. R. (2022). HvLEAFY controls the early stages of floral organ specification and inhibits the formation of multiple ovaries in barley. The Plant Journal, 108(2), 509-527. DOI Scopus14 WoS7 Europe PMC10
2022	Nguyen, D. T., Hayes, J. E., Atieno, J., Li, Y., Baumann, U., Pattison, A., . . . Sutton, T. (2022). The genetics of vigour-related traits in chickpea (Cicer arietinum L.): insights from genomic data. Theoretical and Applied Genetics, 135(1), 107-124. DOI Scopus6 WoS5 Europe PMC4
2022	Schultz, C. J., Wu, Y., & Baumann, U. (2022). A targeted bioinformatics approach identifies highly variable cell surface proteins that are unique to Glomeromycotina. Mycorrhiza, 32(1), 45-66. DOI Scopus3 WoS1 Europe PMC2
2022	Laugerotte, J., Baumann, U., & Sourdille, P. (2022). Genetic control of compatibility in crosses between wheat and its wild or cultivated relatives.. Plant biotechnology journal, 20(5), 812-832. DOI Scopus16 WoS9 Europe PMC8
2022	Akpinar, B. A., Leroy, P., Watson-Haigh, N., Baumann, U., Barbe, V., & Budak, H. (2022). The complete genome sequence of elite bread wheat cultivar, "Sonmez".. F1000Research, 11, 1-9. DOI Scopus2
2021	Tiong, J., Sharma, N., Sampath, R., MacKenzie, N., Watanabe, S., Metot, C., . . . Okamoto, M. (2021). Improving nitrogen use efficiency through overexpression of alanine aminotransferase in rice, wheat, and barley. Frontiers in Plant Science, 12, 1-18. DOI Scopus38 WoS27 Europe PMC14
2021	Derkx, A., Baumann, U., Cheong, J., Mrva, K., Sharma, N., Pallotta, M., & Mares, D. (2021). A Major Locus on Wheat Chromosome 7B Associated With Late-Maturity α-Amylase Encodes a Putative ent-Copalyl Diphosphate Synthase. Front Plant Sci, 12, 1-17. DOI Scopus13 WoS8 Europe PMC9
2021	Tura, H., Edwards, J., Gahlaut, V., Garcia, M., Sznajder, B., Baumann, U., . . . Fleury, D. (2021). Correction to: QTL analysis and fine mapping of a QTL for yield‑related traits in wheat grown in dry and hot environments. Theoretical and Applied Genetics, 134(5), 1 page. DOI
2021	Chidzanga, C., Fleury, D., Baumann, U., Mullan, D., Watanabe, S., Kalambettu, P., . . . de Oliveira Santos Garcia, M. (2021). Development of an Australian bread wheat nested association mapping population, a new genetic diversity resource for breeding under dry and hot climates. International Journal of Molecular Sciences, 22(9), 4348-1-4348-18. DOI Scopus6 WoS5 Europe PMC4
2021	Menadue, D. J., Riboni, M., Baumann, U., Schilling, R. K., Plett, D. C., & Roy, S. J. (2021). Proton-pumping pyrophosphatase homeolog expression is a dynamic trait in bread wheat (Triticum aestivum). Plant Direct, 5(10), 1-16. DOI Europe PMC1
2021	Okada, T., Jayasinghe, R. M., Eckermann, P., Watson-Haigh, N. S., Warner, P., Williams, M. E., . . . Whitford, R. (2021). Genetic factors associated with favourable pollinator traits in the wheat cultivar Piko. FUNCTIONAL PLANT BIOLOGY, 48(4), 434-447. DOI Scopus4 WoS3 Europe PMC4
2021	Thomelin, P., Bonneau, J., Brien, C., Suchecki, R., Baumann, U., Kalambettu, P., . . . Fleury, D. (2021). The wheat Seven in absentia gene is associated with increases in biomass and yield in hot climates. Journal of Experimental Botany, 72(10), 3744-3791. DOI Scopus14 WoS9 Europe PMC5
2021	Serra, H., Svačina, R., Baumann, U., Whitford, R., Sutton, T., Bartoš, J., & Sourdille, P. (2021). Ph2 encodes the mismatch repair protein MSH7-3D that inhibits wheat homoeologous recombination.. Nat Commun, 12(1), 1-10. DOI Scopus50 WoS33 Europe PMC30
2020	Camp, A., Croxford, A. E., Ford, C. S., Baumann, U., Clements, P. R., Hiendleder, S., . . . Wilkinson, M. J. (2020). Dual-locus DNA metabarcoding reveals southern hairy-nosed wombats (Lasiorhinus latifrons Owen) have a summer diet dominated by toxic invasive plants.. PLoS One, 15(3), e0229390. DOI Scopus9 WoS8 Europe PMC6
2020	Amarasinghe, S., Huang, W., Watson-Haigh, N., Gilliham, M., Roy, S., & Baumann, U. (2020). AtCIPK16 Mediates Salt Stress Through Phytohormones and Transcription Factors. DOI
2020	Selva, C., Riboni, M., Baumann, U., Wurschum, T., Whitford, R., & Tucker, M. R. (2020). Hybrid breeding in wheat: how shaping the floral biology can offer new perspectives. Functional Plant Biology, 47(8), 47-8. DOI Scopus16 WoS13 Europe PMC8
2020	Tura, H., Edwards, J., Gahlaut, V., Garcia, M., Sznajder, B., Baumann, U., . . . Fleury, D. (2020). QTL analysis and fine mapping of a QTL for yield-related traits in wheat grown in dry and hot environments. Theoretical and Applied Genetics, 133(1), 239-257. DOI Scopus48 WoS40 Europe PMC24
2019	Fruzangohar, M., Kalashyan, E., Kalambettu, P., Ens, J., Wiebe, K., Pozniak, C. J., . . . Baumann, U. (2019). Novel Informatic Tools to Support Functional Annotation of the Durum Wheat Genome.. Frontiers in plant science, 10, 10 pages. DOI Scopus4 WoS4 Europe PMC3
2019	Arndell, T., Sharma, N., Langridge, P., Baumann, U., Watson-Haigh, N. S., & Whitford, R. (2019). gRNA validation for wheat genome editing with the CRISPR-Cas9 system.. BMC biotechnology, 19(1), 71. DOI Scopus57 WoS35 Europe PMC25
2019	Broad, R. C., Bonneau, J. P., Beasley, J. T., Roden, S., Philips, J. G., Baumann, U., . . . Johnson, A. A. T. (2019). Genome-wide identification and characterization of the GDP-L-galactose phosphorylase gene family in bread wheat.. BMC plant biology, 19(1), 515. DOI Scopus10 WoS8 Europe PMC7
2019	Garcia, M., Eckermann, P., Haefele, S., Satija, S., Sznajder, B., Timmins, A., . . . Fleury, D. (2019). Genome-wide association mapping of grain yield in a diverse collection of spring wheat (Triticum aestivum L.) evaluated in southern Australia. PLoS ONE, 14(2), e0211730-1-e0211730-19. DOI Scopus56 WoS36 Europe PMC33
2019	Casartelli, A., Melino, V. J., Baumann, U., Riboni, M., Suchecki, R., Jayasinghe, N. S., . . . Heuer, S. (2019). Opposite fates of the purine metabolite allantoin under water and nitrogen limitations in bread wheat. Plant Molecular Biology, 99(4-5), 477-497. DOI Scopus36 WoS31 Europe PMC22
2019	Okada, A., Arndell, T., Borisjuk, N., Sharma, N., Watson-Haigh, N. S., Tucker, E. J., . . . Whitford, R. (2019). CRISPR/Cas9-mediated knockout of Ms1 enables the rapid generation of male-sterile hexaploid wheat lines for use in hybrid seed production. Plant Biotechnology Journal, 17(10), 1905-1913. DOI Scopus126 WoS85 Europe PMC52
2019	Okada, T., Jayasinghe, R. M., Eckermann, P., Watson-Haigh, N. S., Warner, P., Hendrikse, Y., . . . Whitford, R. (2019). Effects of Rht-B1 and Ppd-D1 loci on pollinator traits in wheat. Theoretical and Applied Genetics, 132(7), 1965-1979. DOI Scopus28 WoS20 Europe PMC14
2019	Suchecki, R., Sandhu, A., Deschamps, S., Llaca, V., Wolters, P., Watson-Haigh, N., . . . Baumann, U. (2019). LNISKS: Reference-free mutation identification for large and complex crop genomes. Biorxiv. DOI
2019	Pallotta, M. A., Warner, P., Kouidri, A., Tucker, E. J., Baes, M., Suchecki, R., . . . Whitford, R. (2019). Wheat ms5 male-sterility is induced by recessive homoeologous A and D genome non-specific lipid transfer proteins. Plant Journal, 99(4), 673-685. DOI Scopus30 WoS26 Europe PMC14
2019	Balfourier, F., Bouchet, S., Robert, S., De Oliveira, R., Rimbert, H., Kitt, J., . . . Paux, E. (2019). Worldwide phylogeography and history of wheat genetic diversity. SCIENCE ADVANCES, 5(5), 10 pages. DOI WoS82 Europe PMC65
2019	Amarasinghe, S. L., Watson-Haigh, N. S., Byrt, C., James, R., Qiu, J., Berkowitz, O., . . . Baumann, U. (2019). Transcriptional variation is associated with differences in shoot sodium accumulation in distinct barley varieties. Environmental and Experimental Botany, 166, 103812-1-103812-15. DOI Scopus5 WoS3
2019	Thomelin, P., Bonneau, J., Brien, C., Suchecki, R., Baumann, U., Kalambettu, P., . . . Fleury, D. (2019). The wheat Seven in Absentia gene is associated with increases in biomass and yield in hot climates. DOI
2018	Keeble-Gagnère, G., Rigault, P., Tibbits, J., Pasam, R., Hayden, M., Forrest, K., . . . Appels, R. (2018). Optical and physical mapping with local finishing enables megabase-scale resolution of agronomically important regions in the wheat genome. Genome Biology, 19(1), 112-1-112-18. DOI Scopus19 WoS18 Europe PMC10
2018	Kouidri, A., Whitford, R., Suchecki, R., Kalashyan, E., & Baumann, U. (2018). Genome-wide identification and analysis of non-specific Lipid Transfer Proteins in hexaploid wheat. Scientific Reports, 8(1), 12 pages. DOI Scopus14 WoS11 Europe PMC7
2018	Kouidri, A., Baumann, U., Okada, T., Baes, M., Tucker, E., & Whitford, R. (2018). Wheat TaMs1 is a glycosylphosphatidylinositol-anchored lipid transfer protein necessary for pollen development. BMC Plant Biology, 18(1), 13 pages. DOI Scopus17 WoS16 Europe PMC10
2018	Watson-Haigh, N. S., Suchecki, R., Kalashyan, E., Garcia, M., & Baumann, U. (2018). DAWN: a resource for yielding insights into the diversity among wheat genomes. BMC Genomics, 19(1), 941-1-941-20. DOI Scopus18 WoS18 Europe PMC13
2018	Okada, T., Jayasinghe, R., Nansamba, M., Baes, M., Warner, P., Kouidri, A., . . . Baumann, U. (2018). Unfertilized ovary pushes wheat flower open for cross-pollination. Journal of Experimental Botany, 69(3), 399-412. DOI Scopus28 WoS22 Europe PMC18
2018	Sharma, N., Dang, T., Singh, N., Ruzicic, S., Mueller-Roeber, B., Baumann, U., & Heuer, S. (2018). Allelic variants of OsSUB1A cause differential expression of transcription factor genes in response to submergence in rice. Rice, 11(2), 1-19. DOI Scopus15 WoS12 Europe PMC8
2017	Quesneville, H., Dzale Yeumo, E., Alaux, M., Arnaud, E., Aubin, S., Baumann, U., . . . Whan, A. (2017). Developing data interoperability using standards: A wheat community use case. F1000Research, 6, 1843. DOI Scopus14 Europe PMC7
2017	Tucker, E., Baumann, U., Kouidri, A., Suchecki, R., Baes, M., Garcia, M., . . . Whitford, R. (2017). Molecular identification of the wheat male fertility gene Ms1 and its prospects for hybrid breeding. Nature Communications, 8(1), 869-1-869-10. DOI Scopus82 WoS72 Europe PMC40
2017	Suchecki, R., Watson-Haigh, N., & Baumann, U. (2017). POTAGE: A Visualisation Tool for Speeding up Gene Discovery in Wheat. Scientific Reports, 7(1), 8 pages. DOI Scopus9 WoS10 Europe PMC5
2016	Li, B., Byrt, C., Qiu, J., Baumann, U., Hrmova, M., Evrard, A., . . . Roy, S. (2016). Identification of a stelar-localized transport protein that facilitates root-to-shoot transfer of chloride in arabidopsis. Plant Physiology, 170(2), 1014-1029. DOI Scopus89 WoS72 Europe PMC46
2016	Harris, J., Sornaraj, P., Taylor, M., Bazanova, N., Baumann, U., Lovell, B., . . . Hrmova, M. (2016). Molecular interaction of the γ-clade homeodomain-leucine zipper class I transcription factors during the wheat response to water deficit. Plant Molecular Biology, 90(4), 435-452. DOI Scopus31 WoS29 Europe PMC17
2016	Schoppach, R., Taylor, J., Majerus, E., Claverie, E., Baumann, U., Suchecki, R., . . . Sadok, W. (2016). High resolution mapping of traits related to whole-plant transpiration under increasing evaporative demand in wheat. Journal of Experimental Botany, 67(9), 2847-2860. DOI Scopus49 WoS44 Europe PMC22
2016	Amarasinghe, S., Watson-Haigh, N. S., Gilliham, M., Roy, S., & Baumann, U. (2016). The evolutionary origin of CIPK16: a gene involved in enhanced salt tolerance. Molecular Phylogenetics and Evolution, 100, 135-147. DOI Scopus10 WoS7 Europe PMC7
2016	Bonneau, J., Baumann, U., Beasley, J., Li, Y., & Johnson, A. (2016). Identification and molecular characterization of the nicotianamine synthase gene family in bread wheat. Plant Biotechnology Journal, 14(12), 2228-2239. DOI Scopus51 WoS42 Europe PMC26
2016	Plett, D., Holtham, L., Baumann, U., Kalashyan, E., Francis, K., Enju, A., . . . Kaiser, B. (2016). Nitrogen assimilation system in maize is regulated by developmental and tissue-specific mechanisms. Plant Molecular Biology, 92(3), 293-312. DOI Scopus16 WoS12 Europe PMC6
2016	Plett, D., Baumann, U., Schreiber, A., Holtham, L., Kalashyan, E., Toubia, J., . . . Kaiser, B. (2016). Maize maintains growth in response to decreased nitrate supply through a highly dynamic and developmental stage-specific transcriptional response. Plant Biotechnology Journal, 14(1), 342-353. DOI Scopus17 WoS15 Europe PMC5
2015	Liu, H., Searle, I., Watson-Haigh, N., Baumann, U., Mather, D., Able, A., & Able, J. (2015). Genome-wide identification of microRNAs in leaves and the developing head of four durum genotypes during water deficit stress. PLoS One, 10(11), e0142799-1-e0142799-30. DOI Scopus47 WoS41 Europe PMC27
2014	Pallotta, M., Schnurbusch, T., Hayes, J., Hay, A., Baumann, U., Paull, J., . . . Sutton, T. (2014). Molecular basis of adaptation to high soil boron in wheat landraces and elite cultivars. Nature, 514(7520), 88-91. DOI Scopus91 WoS77 Europe PMC50
2014	Henderson, S., Baumann, U., Blackmore, D., Walker, A., Walker, R., & Gilliham, M. (2014). Shoot chloride exclusion and salt tolerance in grapevine is associated with differential ion transporter expression in roots. BMC Plant Biology, 14(1), 273-1-273-18. DOI Scopus83 WoS74 Europe PMC35
2013	Sleep, J., Schreiber, A., & Baumann, U. (2013). Sequencing error correction without a reference genome. BMC Bioinformatics, 14(1), 1-8. DOI Scopus20 WoS16 Europe PMC12
2013	Hayes, J., Pallotta, M., Baumann, U., Berger, B., Langridge, P., & Sutton, T. (2013). Germanium as a tool to dissect boron toxicity effects in barley and wheat. Functional Plant Biology, 40(6), 618-627. DOI Scopus24 WoS15 Europe PMC2
2012	Schreiber, A., Hayden, M., Forrest, K., Kong, S., Langridge, P., & Baumann, U. (2012). Transcriptome-scale homoeolog-specific transcript assemblies of bread wheat. BMC Genomics, 13(1), 1-14. DOI Scopus34 WoS33 Europe PMC27
2012	Huynh, B., Mather, D., Schreiber, A., Toubia, J., Baumann, U., Shoaei, Z., . . . Fleury, D. (2012). Clusters of genes encoding fructan biosynthesizing enzymes in wheat and barley. Plant Molecular Biology, 80(3), 299-314. DOI Scopus24 WoS18 Europe PMC9
2012	Edwards, D., Wilcox, S., Barrero, R., Fleury, D., Cavanagh, C., Forrest, K., . . . Fitzgerald, A. (2012). Bread matters: a national initiative to profile the genetic diversity of Australian wheat. Plant Biotechnology Journal, 10(6), 703-708. DOI Scopus40 WoS31 Europe PMC23
2012	Lai, K., Duran, C., Berkman, P., Lorenc, M., Stiller, J., Manoli, S., . . . Edwards, D. (2012). Single nucleotide polymorphism discovery from wheat next-generation sequence data. Plant Biotechnology Journal, 10(6), 743-749. DOI Scopus96 WoS77 Europe PMC60
2011	Schreiber, A., Shi, B., Huang, C., Langridge, P., & Baumann, U. (2011). Discovery of barley miRNAs through deep sequencing of short reads. BMC Genomics, 12(1), 1-21. DOI Scopus112 WoS98 Europe PMC68
2011	Conn, S., Gilliham, M., Athman, A., Schreiber, A., Baumann, U., Moller, I., . . . Leigh, R. (2011). Cell-specific vacuolar calcium storage mediated by CAX1 regulates apoplastic calcium concentration, gas exchange, and plant productivity in arabidopsis. Plant Cell, 23(1), 240-257. DOI Scopus211 WoS180 Europe PMC112
2011	Cotsaftis, O., Plett, D., Johnson, A., Walia, H., Wilson, C., Ismail, A., . . . Baumann, U. (2011). Root-specific transcript profiling of contrasting rice genotypes in response to salinity stress. Molecular Plant, 4(1), 25-41. DOI Scopus117 WoS99 Europe PMC60
2010	Plett, D., Toubia, J., Garnett, T., Tester, M., Kaiser, B., & Baumann, U. (2010). Dichotomy in the NRT gene families of dicots and grass species. PLoS One, 5(12), 1-10. DOI Scopus132 WoS114 Europe PMC72
2010	Schnurbusch, T., Hayes, J., Hrmova, M., Baumann, U., Ramesh, S., Tyerman, S., . . . Sutton, T. (2010). Boron toxicity tolerance in barley through reduced expression of the multifunctional aquaporin HvNIP2;1. Plant Physiology, 153(4), 1706-1715. DOI Scopus148 WoS128 Europe PMC68
2010	Burton, R., Ma, G., Baumann, U., Harvey, A., Shirley, N., Taylor, J., . . . Fincher, G. (2010). A customized gene expression microarray reveals that the brittle stem phenotype fs2 of barley is attributable to a retroelement in the HvCesA4 cellulose synthase gene. Plant Physiology, 153(4), 1716-1728. DOI Scopus37 WoS30 Europe PMC22
2010	Hassan, M., Oldach, K., Baumann, U., Langridge, P., & Sutton, T. (2010). Genes mapping to boron tolerance QTL in barley identified by suppression subtractive hybridization. Plant Cell and Environment, 33(2), 188-198. DOI Scopus10 WoS7 Europe PMC5
2009	Schreiber, A., Sutton, T., Caldo, R., Kalashyan, E., Lovell, B., Mayo, G., . . . Baumann, U. (2009). Comparative transcriptomics in the Triticeae. BMC Genomics, 10(1), 1-17. DOI Scopus54 WoS54 Europe PMC41
2009	Chen, A., Gusta, L., Brule-Babel, A., Leach, R., Baumann, U., Fincher, G., & Collins, N. (2009). Varietal and chromosome 2H locus-specific frost tolerance in reproductive tissues of barley (Hordeum vulgare L.) detected using a frost simulation chamber. Theoretical and Applied Genetics, 119(4), 685-694. DOI Scopus17 WoS17 Europe PMC8
2009	Chen, A., Reinheimer, J., Brûlé-Babel, A., Baumann, U., Pallotta, M., Fincher, G., & Collins, N. (2009). Genes and traits associated with chromosome 2H and 5H regions controlling sensitivity of reproductive tissues to frost in barley. Theoretical and Applied Genetics, 118(8), 1465-1476. DOI Scopus17 WoS15 Europe PMC11
2009	Chen, A., Baumann, U., Fincher, G., & Collins, N. (2009). Flt-2L, a locus in barley controlling flowering time, spike density, and plant height. Functional & Integrative Genomics, 9(2), 243-254. DOI Scopus36 WoS32 Europe PMC23
2009	Chen, A., Brûlé-Babel, A., Baumann, U., & Collins, N. (2009). Structure-function analysis of the barley genome: the gene-rich region of chromosome 2HL. Functional & Integrative Genomics, 9(1), 67-79. DOI Scopus14 WoS14 Europe PMC11
2008	Tran, M., Schultz, C., & Baumann, U. (2008). Conserved upstream open reading frames in higher plants. BMC Genomics, 9(1), 1-17. DOI Scopus56 WoS51 Europe PMC41
2008	Jones, C., Schwerdt, J., Bretag, T., Baumann, U., & Brown, A. (2008). GOSLING: a rule-based protein annotator using BLAST and GO. Bioinformatics, 24(22), 2628-2629. DOI Scopus12 WoS9 Europe PMC6
2007	Sutton, T., Baumann, U., Hayes, J., Collins, N., Shi, B., Schnurbusch, T., . . . Langridge, P. (2007). Boron toxicity tolerance in barley arising from efflux transporter amplification. Science, 318(5855), 1446-1449. DOI Scopus362 WoS307 Europe PMC192
2007	Jones, C., Brown, A., & Baumann, U. (2007). Estimating the annotation error rate of curated GO database sequence annotations. BMC Bioinformatics, 8(170), WWW 1-WWW 9. DOI Scopus114 WoS104 Europe PMC83
2007	Schreiber, A., & Baumann, U. (2007). A framework for gene expression analysis. Bioinformatics, 23(2), 191-197. DOI Scopus4 WoS3 Europe PMC7
2007	Whitford, R., Baumann, U., Sutton, T., Gumaelius, L., Wolters, P., Tingey, S., . . . Langridge, P. (2007). Identification of transposons, retroelements, and a gene family predominantly expressed in floral tissues in chromosome 3DS of the hexaploid wheat progenitor Aegilops tauschii. Functional & Integrative Genomics, 7(1), 37-52. DOI Scopus9 WoS8 Europe PMC5
2006	Crismani, W., Baumann, U., Sutton, T., Shirley, N., Webster, T., Spangenberg, G., . . . Able, J. (2006). Microarray expression analysis of meiosis and microsporogenesis in hexaploid bread wheat. BMC Genomics, 7(267), 1-17. DOI Scopus74 WoS62 Europe PMC42
2006	Lunde, C., Baumann, U., Shirley, N., Drew, D., & Fincher, G. (2006). Gene structure and expression pattern analysis of three monodehydroascorbate reductase (Mdhar) genes in Physcomitrella patens: Implications for the evolution of the MDHAR family in plants. Plant Molecular Biology, 60(2), 259-275. DOI Scopus53 WoS41 Europe PMC20
2006	Druka, A., Muehlbauer, G., Druka, I., Caldo, R., Baumann, U., Rostoks, N., . . . Waugh, R. (2006). An atlas of gene expression from seed to seed through barley development. Functional & Integrative Genomics, 6(3), 202-211. DOI Scopus128 Europe PMC86
2005	Jones, C., Baumann, U., & Brown, A. (2005). Automated methods of predicting the function of biological sequences using GO and BLAST. BMC Bioinformatics, 6(272), WWW 1-WWW 10. DOI Scopus40 WoS37 Europe PMC26
2005	Sprunck, S., Baumann, U., Edwards, K., Langridge, P., & Dresshaus, T. (2005). The transcript composition of egg cells changes significantly following fertilization in wheat (Triticum aestivum L.). Plant Journal, 41(5), 660-672. DOI Scopus123 WoS113 Europe PMC98
2004	Bian, X., Friedrich, A., Bai, J., Baumann, U., Hayman, D., Barker, S., & Langridge, P. (2004). High-resolution mapping of the S and Z loci of Phalaris coerulescens. Genome, 47(5), 918-930. DOI Scopus25 WoS23 Europe PMC20
2003	Sutton, T., Whitford, R., Baumann, U., Dong, C., Able, J., & Langridge, P. (2003). The Ph2 pairing homoeologous locus of wheat (Triticum aestivum): identification of candidate meiotic genes using a comparative genetics approach. Plant Journal, 36(4), 443-456. DOI Scopus64 WoS55 Europe PMC37
2002	Baumann, U., & Juttner, J. (2002). Plant thioredoxins: the multiplicity conundrum. Cellular and Molecular Life Sciences, 59(6), 1042-1057. DOI Scopus45 Europe PMC27
2000	Juttner, J., Olde, D., Langridge, P., & Baumann, U. (2000). Cloning and expression of a distinct subclass of plant thioredoxins. FEBS Journal, 267(24), 7109-7117. DOI Scopus31 WoS30 Europe PMC20
2000	Baumann, U., Juttner, J., Bian, X., & Langridge, P. (2000). Self-incompatibility in the grasses. Annals of Botany, 85(SUPPL. A), 203-209. DOI Scopus81 WoS74
1999	Langridge, P., Baumann, U., & Juttner, J. (1999). Revisiting and Revising the Self-Incompatibility Genetics of Phalaris coerulescens. Plant Cell, 11(10), 1826. DOI Scopus13 WoS21
1997	Baumann, U., & Langridge, P. (1997). A pollen-specific cDNA of Phalaris coerulescens shows homology to Zm13. Sexual Plant Reproductions, 10(2), 124-125. DOI
1993	Ramos, R. G. P., Igloi, G. L., Lichte, B., Baumann, U., Maier, D., Schneider, T., . . . Fischbach, K. F. (1993). The irregular chiasm C-roughest locus of Drosophila, which affects axonal projections and programmed cell death, encodes a novel immunoglobulin-like protein. Genes and Development, 7(12 PART B), 2533-2547. DOI Scopus152 Europe PMC112

Book Chapters

Year	Citation
2012	Evrard, A., Bargmann, B., Birnbaum, K., Tester, M., Baumann, U., & Johnson, A. (2012). Fluorescence-activated cell sorting for analysis of cell type-specific responses to salinity stress in Arabidopsis and rice. In S. Shabala, & T. Cuin (Eds.), Plant Salt Tolerance: Methods and Protocols (Vol. 913, pp. 265-276). USA: Humana Press. DOI Scopus18 Europe PMC12
2012	Fleury, D., Baumann, U., & Langridge, P. (2012). Plant genome sequencing: models for developing synteny maps and association mapping. In A. Altman, & P. M. Hasegawa (Eds.), Plant biotechnology and agriculture: Prospects for the 21st century (pp. 83-97). USA: Academic Press. DOI Scopus2
2011	Fleury, D., Baumann, U., & Langridge, P. (2011). Plant genome sequencing: Models for developing synteny maps and association mapping. In Plant Biotechnology and Agriculture: Prospects for the 21st Century (pp. 83-97). DOI Scopus1
2008	Langridge, P., & Baumann, U. (2008). Self-Incompatibility in the Grasses. In Self-Incompatibility in Flowering Plants (pp. 275-288). USA: Springer. DOI Scopus16

Conference Papers

Year	Citation
2004	Sutton, T., Whitford, R., Baumann, U., Able, J., Lazo, G., & Langridge, P. (2004). Genomics approaches to identify meiotic genes in wheat. In Plant & Animal Genome XII : conference abstracts (pp. W143). San Diego, CA.

Conference Items

Year	Citation
2018	Selva, C., Tucker, M. R., Baumann, U., & Whitford, R. (2018). Floral development in barley: characterization of multiovary mutants. Poster session presented at the meeting of International Congress on Sexual Plant Reproduction. Japan.
2017	Selva, C., Tucker, M. R., Baumann, U., & Whitford, R. (2017). The benefits of sterility: characterizing multiovary mutants for hybrid seed production. Poster session presented at the meeting of Combined biosciences - ComBio. Australia.
2015	Liu, H., Searle, I., Watson-Haigh, N., Baumann, U., Mather, D., Able, A., & Able, J. (2015). Identification of differentially expressed miRNAs and their targets in durum wheat during water deficit stress. Poster session presented at the meeting of 9th International Wheat Conference. Sydney, Australia..

Patents

Year Citation

2010 Baumann, U. (2010). US 20100281583 A1, Boron transporter. USA.

Year	Citation
2010	Baumann, U. (2010). US 20100281583 A1, Boron transporter. USA.

Datasets

Year	Citation
2015	Liu, H., Searle, I., Watson-Haigh., Baumann., Mather, D. E., Able, A. J., & Able, J. A. (2015). Genome-wide identification of differentially expressed microRNAs in leaves and the developing head of four durum genotypes during water deficit stress.
-	Fruzangohar, M., Kalashyan, E., Kalambettu, P., Ens, J., Wiebe, K., Pozniak, C., . . . Baumann, U. (n.d.). Durum Exome Capture Reference (DECaR). DOI

Filesets

Year	Citation
-	Garcia, M., Eckermann, P., Haefele, S., Satija, S., Sznajder, B., Timmins, A., . . . Fleury, D. (n.d.). Phenotypic and genotypic data from a wheat diversity panel. DOI
-	Watson-Haigh, N., Suchecki, R., Garcia, M. D. O. S., Kalashyan, E., & Baumann, U. (n.d.). Xiaoyan-54 WGS vs IWGSC RefSeq v1.0 Genome Assembly. DOI
-	Watson-Haigh, N., Suchecki, R., Garcia, M. D. O. S., Kalashyan, E., & Baumann, U. (n.d.). Alsen WGS vs IWGSC RefSeq v1.0 Genome Assembly. DOI
-	Watson-Haigh, N., Suchecki, R., Garcia, M. D. O. S., Kalashyan, E., & Baumann, U. (n.d.). Excalibur WGS vs IWGSC RefSeq v1.0 Genome Assembly. DOI
-	Watson-Haigh, N., Suchecki, R., Garcia, M. D. O. S., Kalashyan, E., & Baumann, U. (n.d.). Gladius WGS vs IWGSC RefSeq v1.0 Genome Assembly. DOI
-	Watson-Haigh, N., Suchecki, R., Garcia, M. D. O. S., Kalashyan, E., & Baumann, U. (n.d.). H-45 WGS vs IWGSC RefSeq v1.0 Genome Assembly. DOI
-	Watson-Haigh, N., Suchecki, R., Garcia, M. D. O. S., Kalashyan, E., & Baumann, U. (n.d.). RAC-875 WGS vs IWGSC RefSeq v1.0 Genome Assembly. DOI
-	Watson-Haigh, N., Suchecki, R., Garcia, M. D. O. S., Kalashyan, E., & Baumann, U. (n.d.). Volcani-DD-1 WGS vs IWGSC RefSeq v1.0 Genome Assembly. DOI
-	Watson-Haigh, N., Suchecki, R., Garcia, M. D. O. S., Kalashyan, E., & Baumann, U. (n.d.). Wyalkatchem WGS vs IWGSC RefSeq v1.0 Genome Assembly. DOI
-	Watson-Haigh, N., Suchecki, R., Garcia, M. D. O. S., Kalashyan, E., & Baumann, U. (n.d.). Yitpi WGS vs IWGSC RefSeq v1.0 Genome Assembly. DOI
-	Watson-Haigh, N., Suchecki, R., Garcia, M. D. O. S., Kalashyan, E., & Baumann, U. (n.d.). Kukri WGS vs IWGSC RefSeq v1.0 Genome Assembly. DOI
-	Watson-Haigh, N., Suchecki, R., Garcia, M. D. O. S., Kalashyan, E., & Baumann, U. (n.d.). Pastor WGS vs IWGSC RefSeq v1.0 Genome Assembly. DOI
-	Watson-Haigh, N., Suchecki, R., Garcia, M. D. O. S., Kalashyan, E., & Baumann, U. (n.d.). Westonia WGS vs IWGSC RefSeq v1.0 Genome Assembly. DOI
-	Watson-Haigh, N., Suchecki, R., Garcia, M. D. O. S., Kalashyan, E., & Baumann, U. (n.d.). Chara,AUS WGS vs IWGSC RefSeq v1.0 Genome Assembly. DOI
-	Watson-Haigh, N., Suchecki, R., Garcia, M. D. O. S., Kalashyan, E., & Baumann, U. (n.d.). Drysdale WGS vs IWGSC RefSeq v1.0 Genome Assembly. DOI
-	Watson-Haigh, N., Suchecki, R., Garcia, M. D. O. S., Kalashyan, E., & Baumann, U. (n.d.). Baxter WGS vs IWGSC RefSeq v1.0 Genome Assembly. DOI
-	Watson-Haigh, N., Suchecki, R., Garcia, M. D. O. S., Kalashyan, E., & Baumann, U. (n.d.). AC-Barrie WGS vs IWGSC RefSeq v1.0 Genome Assembly. DOI

Date	Project / No.	Investigators	Title	Funding Body
2017-2018	UA1503	C Rodriguez Lopez, E Edwards (CSIRO), U Baumann, R De Bei, P Tricker	Using the epigenetic memory of stress to prime grapevines for a changing environment	Australian Grape and Wine Authority
2016-2020	LP15010069	U Baumann, Haefele S, N Collins, S Praud [BioGemma, France]	Exploring genetic diversity to identify new heat tolerance genes in wheat.	Australian Research Council
2015-2020	IH130200027	D Fleury, U Baumann, N Borysyuk, N Collins, S Haefele, B Kaiser, P Langridge, S Miklavcic, M-J Appelbee, J Juttner, H. Kuchel, D Mullen	Genetic diversity and molecular breeding for wheat in a hot and dry climate	Australian Research Council [Industrial Transformation Research Hub]
2015-2017	AISRF33760	D Fleury, N Collins, U Baumann, S Haefele	Mining alleles for heat tolerance of wheat in Australian and Indian environments for development of heat resilient cultivars	Australia-India Strategic Research Fund
2014-2017	IRGP15	D Fleury, U Baumann, P Langridge, P Tricker, C Posniak [CDC University of Saskatchewan,Canada], C. Ceoloni [DAFNE Universita di Tuscia Italy],	Molecular diversity drive for precision-engineered wheat	SA Gov. Premier’s Research and Industry Fund’s International Research Grant Program
2013-2018	Pioneer_Hybrid	U Baumann, R Whitford, T Okada	Wheat Hybrid Program	Dupont-Pioneer, USA

Date	Project / No.	Collaborators	Title	Funding Body
2013	ABN00001	U Baumann, J Taylor, P Moolhuuijzen	Wheat Bioinformaticians' Forum	Australian Bioinformatics Connection Grant
2013	ABN00002	N Watson-Haigh, G Wilson, U Baumann, C Shang, A McGrath, P Bayer	Improving bioinformaticians' productivity through Software Carpentry	Australian Bioinformatics Connection Grant

Current Higher Degree by Research Supervision (University of Adelaide)

Date	Role	Research Topic	Program	Degree Type	Student Load	Student Name
2023	Co-Supervisor	Improving doubled haploid production in Brassica napus L. by better understanding chromosomal doubling and embryo initiation.	Doctor of Philosophy	Doctorate	Part Time	Miss Kaat Lut K Devriendt

Past Higher Degree by Research Supervision (University of Adelaide)

Date	Role	Research Topic	Program	Degree Type	Student Load	Student Name
2020 - 2023	Co-Supervisor	Inter-vine Signalling via Plant Volatiles	Doctor of Philosophy	Doctorate	Full Time	Miss Joanah Midzi
2019 - 2022	Co-Supervisor	Nested Association Mapping of wheat yield under Australian drought and heat conditions	Doctor of Philosophy	Doctorate	Full Time	Miss Charity Chidzanga
2016 - 2020	Co-Supervisor	Understanding Flower Development in Barley (Hordeum Vulgare) through Characterisation of Multiovary Mov Mutants and Their Potential Use in Hybrid Breeding	Doctor of Philosophy	Doctorate	Full Time	Miss Caterina Selva
2016 - 2018	Co-Supervisor	Genetic Mapping and Physiological Analysis of Heat Tolerance in Wheat	Master of Philosophy	Master	Full Time	Mr Mohammed Mizanur Rahman
2015 - 2019	Co-Supervisor	Genome editing in wheat with CRISPR/Cas9	Doctor of Philosophy	Doctorate	Full Time	Taj Arndell
2014 - 2018	Principal Supervisor	Wheat non-specific Lipid Transfer Proteins: identification and characterisation of nuclear-encoded fertility restorer genes	Doctor of Philosophy	Doctorate	Full Time	Mr Allan Kouidri
2014 - 2018	Principal Supervisor	Defining Transcriptional Networks Associated with Plant Salinity Tolerance	Doctor of Philosophy	Doctorate	Full Time	Ms Shanika Lakmini Amarasinghe
2012 - 2012	Co-Supervisor	Transcription Factors Important in the Regulation of Salinity Tolerance	Doctor of Philosophy	Doctorate	Full Time	Mr Michael Dow
2009 - 2013	Co-Supervisor	Cell Type-specific Transcriptional Responses of Plants to Salinity	Doctor of Philosophy under a Cotutelle Agreement with	Doctorate	Full Time	Miss Aurelie Christiane Patricia Evrard
2006 - 2007	Co-Supervisor	Using Sequence Similarity to Predict the Function of Biological Sequences	Master of Science in Mathematical and Computer Sciences	Master	Full Time	Mr Craig Jones
2005 - 2009	Co-Supervisor	Dissection of Traits Relating to Flowering and Reproductive Frost Tolerance on Chromosome 2HL of Barley (Hordeum vulgare L.)	Doctor of Philosophy	Doctorate	Full Time	Mr Andrew Chen
2005 - 2009	Co-Supervisor	Whole Genome Approaches to Identify Genes Involved in Early Meiosis	Doctor of Philosophy	Doctorate	Full Time	Mr Wayne Crismani
2004 - 2010	Co-Supervisor	Conserved Control Signals in the transcriptome of Higher Plants	Doctor of Philosophy	Doctorate	Full Time	Mr Khanh Tran
2004 - 2010	Principal Supervisor	Functional Characterisation of Plant Cytosolic Thioredoxins	Doctor of Philosophy	Doctorate	Full Time	Dr Fleur Dolman
2003 - 2008	Principal Supervisor	The Transcriptional Response of Barley (Hordeum vulgare L.) to Boron Toxicity	Doctor of Philosophy	Doctorate	Full Time	Mr Mahmood Hassan
1996 - 2003	Co-Supervisor	An Analysis of Thioredoxins h in the Grasses	Doctor of Philosophy	Doctorate	Full Time	Dr Juan Juttner

Board Memberships

Date	Role	Board name	Institution name	Country
2018 - ongoing	Member	Editorial Board	Nature Scientific Reports	United Kingdom
2018 - ongoing	Board Member	Board of Directors	International Wheat Genome Sequencing Consortium	United States

Committee Memberships

Date	Role	Committee	Institution	Country
2017 - ongoing	Member	ABACBS Conference Committee	-	Australia
2015 - ongoing	Member	International Wheat Genome Sequencing Consortium	IWGSC	-
2015 - ongoing	Member	Management Committee	Australian Center for Plant Functional Genomics	Australia
2015 - ongoing	Member	Wheat Data Interoperability Working Group	Research Data Alliance	-
2014 - ongoing	Member	Wheat Information System Expert Working Group	Wheat Initiative	-
2005 - 2014	Member	PhD student Advisory Committee	ACPFG	Australia

Position: Bioinformatics Group Leader
Phone: 83137169
Email: ute.baumann@adelaide.edu.au
Fax: 83137102
Campus: Waite
Building: Plant Genomics Centre, floor Level Two
Room: 2.02
Org Unit: Agricultural Science

Dr Ute Baumann

Appointments

Language Competencies

Education

Research Interests