Staff Members with ACPFG

Baumann, Ute
TitleDr
PositionBioinformatics Leader
E-mailute.baumann@acpfg.com.au
Phone+61 8 8313 7388
Research Interests

Ute is the group Leader for Transcriptomics and Bioinformatics at ACPFG at the University of Adelaide. She applies bioinformatic methods to investigate how cereals tolerate abiotic stresses.

Biography

Ute completed her Bachelors degree in Biological Science at the University of Freiburg, Germany. She completed her PhD at the University of Adelaide and has a Graduate Certificate in Bioinformatics from Manchester University, UK. She joined the University of Adelaide Department of Plant Science in 1997 and has led the ACPFG bioinformatics research group in Adelaide since 2003.

Publications

Plett D, Baumann U, Schreiber AW, Holtham L, Kalashyan E, Toubia J, Nau J, Beatty M, Rafalski A, Dhugga KS, Tester M, Garnett T, Kaiser BN.(2015) Maize maintains growth in response to decreased nitrate supply through a highly dynamic and developmental stage-specific transcriptional response. Plant Biotechnol J.  doi: 10.1111/pbi.12388.

Pallotta M,  Schnurbusch T, Hayes JE, Hay A, Baumann U, Paull J, Langridge, P and Sutton T (2014) Molecular basis of adaptation to high soil boron in wheat landraces and elite cultivars. Nature 514: 88-91

Henderson S, Baumann U, Blackmore DH, Walker AR, Walker RR and Gilliham M (2014) Shoot chloride exclusion and salt tolerance in grapevine is associated with differential ion transporter expression in roots. BMC Plant Biology 14:273

Sleep JA, Schreiber AW and Baumann U (2013) Sequencing error correction without a reference genome. BMC Bioinformatics 14:367

Hayes JE, Pallotta M., Baumann U, Berger B, Langridge, P and Sutton T (2013) Germanium as a tool to dissect boron toxicity effects in barley and wheat. Functional Plant Biology 40:618-627

Lai K, Duran C, Berkman PJ, Lorenc MT, Stiller J, Manoli S, Hayden M, Forrest K, Fleury D, Baumann U, Zander M, Mason A, Batley J and Edwards D (2012) Single Nucleotide Polymorphism Discovery from Wheat Next Generation Sequence Data. Plant Biotech Journal 10:743-749.

Huyn BL, Mather DE, Schreiber AW, Toubia J, Baumann U, Shoaei Z, Stein N, Stangoulis J, Edwards J, Shirley N, Langridge P and Fleury D (2012) Clusters of genes encoding fructan biosynthesizing enzymes in wheat and barley. Plant Molecular Biology 80: 299-314.

Schreiber AW, Hayden MJ, Forrest KL, Kong SL, Langridge P and Baumann U (2012) Transcriptome-scale homoeolog-specific transcript assemblies of bread wheat. BMC Genomics 13: 492.

Edwards D, Wilcox S, Barrero RA, Fleury D, Cavanagh CR, Forrest KL, Hayden MJ, Moolhuijzen P, Keeble-Gagnère G, Bellgard MI, Lorenc MT, Shang CA, Baumann U, Taylor JM, Morell MK, Langridge P, Appels R and Fitzgerald A (2012) Bread matters: A national initiative to profile the genetic diversity of Australian wheat. Plant Biotechnology Journal 10: 703-708

Schreiber AW, Shi B-J, Huang C-Y, Langridge P, Baumann U (2011) Discovery of Barley miRNAs through Deep Sequencing of Short Reads. BMC Genomics 12:129

Plett D, Toubia J, Garnett T, Tester M, Kaiser, BN , Baumann U (2010) Dichotomy in the NRT Gene Families of Dicots and Grass Species. PLOS One 5(12): e15289. doi:10.1371/journal.pone.0015289

Conn SJ, Gilliham M, Athman A, Schreiber AW, Baumann U, Moller I, Cheng N-H, Stancombe MA, , Hirschi KD, Webb AAR, Burton R, Kaiser BN, Tyerman SD, Leigh RA (2011) Cell-specific vacuolar calcium storage mediated by AtCAX1 regulates apoplastic calcium concentration, gas exchange and plant productivity. The Plant Cell 23: 240-257

Cotsaftis O, Plett D, Johnson A, Tester M, Baumann U (2010) Root-specific transcript profiling of contrasting rice genotypes in response to salinity stress. Molecular Plant doi: 10.1093/mp/ssq056

Burton RA, Ma G, Baumann U, Harvey AJ, Shirley NJ, Taylor J, Pettolino F, Bacic A, Beatty M, Simmons CR, Kanwarpal SD, Rafalski JA, Tingey SV and Fincher GB (2010) A Customized Gene Expression Microarray Reveals that the Brittle Stem Phenotype fs2 of Barley has a Retroelement in the HvCesA4 Cellulose Synthase Gene. Plant Physiol. 153(4):1716-28.

Schnurbusch T, Hayes J, Hrmova M, Baumann U, Ramesh SA, Tyerman SD, Langridge P , Sutton T (2010) Boron toxicity tolerance in barley through reduced expression of the multifunctional aquaporin HvNIP2;1. Plant Physiol. 153(4):1706-15.

Hassan M, Oldach K, Baumann U, Langridge P and Sutton T. 2010. Genes mapping to B tolerance QTL in barley identified by Suppression Subtractive Hybridization. Plant, Cell and Environment 33(2):188-98.

Schreiber AW, Sutton T, Caldo RA, Kalashyan E, Lovell B, Mayo G, Muehlbauer GJ, Druka A, Waugh R, Wise RP, Langridge P and Baumann U. 2009. Comparative transcriptomics in the Triticeae. BMC Genomics. 10:285.

Chen A, Gusta LV, Brûlé-Babel A, Leach R, Baumann U, Fincher GB and Collins NC. 2009 Varietal and locus-specific frost tolerance in barley reproductive tissues detected using a frost simulation chamber. Theor Appl Genet. 119(4):685-94.

Chen A, Baumann U, Fincher GB and Collins NC. 2009. Flt-2L, a locus in barley controlling flowering time, spike density and plant height. Funct Integr Genomics 9(2):243-54.

Chen A, Reinheimer J, Brûlé-Babel A, Baumann U, Pallotta M, Fincher GB and Collins NC. (2009) Genes and traits associated with chromosome 1 2H and 5H regions controlling sensitivity of reproductive tissues to frost in barley. Theor Appl Genet. 118(8):1465-76

Chen A, Brûlé-Babel A, Baumann U and Collins NC. (2009) Structure–function analysis of the barley genome: the gene-rich region of chromosome 2HL. Funct Integr Genomics 9(1):67-79.

Jones CE, Schwerdt J, Bretag TA, Baumann U and Brown AL (2008) GOSLING: a rule-based protein annotator using BLAST and GO. Bioinformatics doi: 10.1093/bioinformatics/btn486.

Tran MK, Schultz CJ, Baumann U. (2008) Conserved upstream open reading frames in higher plants. BMC Genomics 9:361.

Sutton, T, Baumann, U, Hayes J, Collins NC, Shi, BJ, Schnurbusch T, Hay A, Mayo, G, Palotta M, Tester M, Langridge P. (2007) Boron toxicity tolerance in barley arising from efflux transporter amplification. Science 318: 1446 – 9.

Jones C, Brown A, and Baumann, U. (2007) Estimating the annotation error rate of curated GO database sequence annotations BMC Bioinformatics 8: 170.

Schreiber AW, Baumann U. (2007) A framework for gene expression analysis. Bioinformatics 15; 23(2):191-7.

Whitford R, Baumann U, Sutton T, Gumaelius L, Wolters P, Tingey S, Able JA, 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, Funct Integr Genomics 7: 37–52.

Druka A, Muehlbauer G, Druka I, Caldo R, Baumann U, Rostoks N, Schreiber A, Wise R, Close T, Kleinhofs A, Graner A, Schulman A, Langridge P, Sato K, Hayes P, McNicol J, Marshall D, Waugh R. (2006) An atlas of gene expression from seed to seed through barley development. Funct Integr Genomics 6(3):202-11.

Crismani W , Baumann, U , Sutton T, Shirley N, Webster T, Spangenberg G, Langridge, P, and Able JA. (2006) Microarray expression analysis of meiosis and microsporogenesis in hexaploid bread wheat. BMC Genomics. 7: 267.

Lunde C, Baumann U, Shirley NJ, Drew DP, Fincher G.B. (2005) 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 Mol Biol. 60, 259-275.

Jones, C, Baumann U, Brown, F. (2005) Automated Methods of Predicting the Function of Biological Sequences using GO and BLAST. BMC Bioinformatics 6:272.

Sprunck S, Baumann U, Edwards K, Langridge P, Dresselhaus T. (2005) The transcript composition of egg cells changes significantly following fertilization in wheat (Triticum aestivum L.) Plant J. 41(5):660-72.

Robert S. and Baumann U. (1998) Resistance to the herbicide glyphosate. Nature 395, 25-26.

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