报告题目：Omics of Non-Model Species -- Opportunities and Challenge

报告人：Dr. Mingshu Cao (曹明树 博士)

           

工作单位：Senior Scientist, AgResearch, Crown Research Institute,          

             New Zealand

报告时间：2014年5月14日下午2点

报告地点： 理科楼 C303

联系人:  王秀娥, 电话: 84395308

附件: 曹明树博士简历

 

 

Mingshu Cao

     AgResearch, Grasslands Research Centre

          Tennent Drive, Private Bag 11008

        Palmerston North 4442, New Zealand

    +64-6-351-8163 (Office)

    +64-6-353-2396 (Home)

                                            mingshu.cao@agresearch.co.nz

               

Research Interests:

My grand research interest is to integrate multilevel data to understand the properties and regulations of molecular networks underlying complex traits. Current research involves developing statistical and computational methods to pre-process and analyze high-throughput data in functional genomics such as metabolomics and transcriptomics.

Employment:

  2004-present: Senior Scientist.

AgResearch, Crown Research Institute, New Zealand

  2001-2004:    Post-doctorate fellow.

Department of Agronomy, University of Missouri-Columbia, USA

  1996-2001:    Research Assistant.

Department of Agronomy, University of Missouri-Columbia, USA

  1994-1996:    Lecturer.

Cytogenetics Institute, Nanjing Agricultural University, China    

  1992-1994:    Junior Lecturer.

Cytogenetics Institute, Nanjing Agricultural University, China

 

Education:

  2001-2003: M.Sc in Computer Science. Univ. of Missouri-Columbia, USA

  1996-2001: Ph.D in Genetics and Plant Breeding. Univ. of Missouri-Columbia. USA

  1989-1992: M.Sc in Genetics and Plant Breeding. Nanjing Agri. Univ., China

  1985-1989: B.Sc in Agronomy. South Anhui Agri. College. China

Experiences in Computational Biology:

--High-throughput data mining and analysis in functional genomics, including gene expression data and mass spectrometry data from various analytical platforms.

--Data integration of transcriptomics and metabolomics; of genetics and metabolomics (mQTL). 

--Proficiency in programming languages: Java, C, Perl.

--Proficiency in statistical computing tools: R, BioConductor and Matlab.

--Experienced in enterprise information systems. Designed and implemented a web-based database system for the management of microarray and metabolomics data using open-source systems such as PostgreSQL and Apache Tomcat.

Experiences in Genetics:

--Taught Cytogenetics, Molecular Cytogenetics for senior undergraduates and

   graduate students.

--Co-authored a textbook of Cytogenetics (ISBN 7-109-05779-8).

--Developed molecular genetic markers (RFLP, RAPD and genome-specific repetitive

   DNA sequences) to research genomic relationships and gene introgression.

--Field selection of wheat and soybean breeding lines.

Professional Awards:

-- Invitation fellowship from the Japan Society for the Promotion of Science (JSPS).

    2011. (Hosted by Kazuki Saito at the RIKEN Plant Science Centre)

-- Tomorrow’s Leaders Programme. AgResearch/Waikato Management School. Oct.

    2010 – Oct. 2011.

-- Award from the Royal Society of New Zealand (2009) to participate in a joint NZ-

  China workshop and international conference on “Mathematical Models of Dynamics

  and Control of Environmental Change: Scaling from Genomes to Ecosystems”.

-- Fellowship for Ph.D student research at the Univ. of Missouri-Columbia (1996-2001)

-- Science and Technology Progress Prize (Second Rank) issued by the Ministry of    

    Agriculture of China (1995) on “The development of Powdery mildew resistant   

    translocation lines of wheat and Haynadia villosa and chromosome localization of   

    pm21 gene”.

Memberships and Services

--The editorial board of Frontiers in Plant Metabolism and Chemodiversity.

--Reviewer of journals including EJMS, Metabolomics etc.

--Examiner of Ph.D or Master theses.

--The International Society for Computational Biology. (2001-2004)

--American Society of Agronomy, Crop Science Society of America. (1997-2003)

Publications:

Journal Papers

Cao M. K. Fraser and S. Rasmussen. 2013. Computational analyses of spectral trees from electrospray multi-stage mass spectrometry to aid metabolite identification. Metabolites. 3(4):1036-1050.

Otter D, M Cao, HM Lin, K. Fraser, S. Edmunds, G. Lane and D. Rowan. 2011.  Identification of urinary biomarkers of colon inflammation in IL10^-/- mice using short-column LCMS metabolomics. Journal of Biomedicine and Biotechnology, vol. 2011, Article ID 974701, 12 pages, 2011. doi:10.1155/2011/974701

Cookson AL, M Cao, J Bennett, C Nicol, F Thomson-Carter, GT Attwood. 2010. Relationship between virulence gene profiles of atypical enteropathogenic Escherichia coli and Shiga toxin- producing E. coli isolates from cattle and sheep in New Zealand. Appl. Environ. Microbiol. 76: 3744-3747.

Koulman A*, M Cao*, M Faville, G Lane, W Mace, S. Rasmussen 2009. Semi-quantitative and structural metabolic phenotyping by direct infusion ion trap mass spectrometry and its application in genetical metabolomics. Rapid Commun. Mass Spectrom. 23(15):2253-2263. (*: equal contribution)

Rowan DD, M Cao, KL Wang, JM Cooney, DJ Jensen, PT Austin, MB Hunt, C Norling, RP Hellens, RJ Schaffer and AC Allan. 2009. Environmental regulation of leaf colour in red 35S:PAP1 Arabidopsis thaliana. New Phytologist. 182(1):102-115.

Cao M*, A Koulman*, LJ. Johnson, GA. Lane, and S Rasmussen. 2008. Advanced data-mining strategies for the analysis of direct-infusion ion trap mass spectrometry data from the association of Lolium perenne with its endophytic fungus Neotyphodium lolii. Plant Physiology. 146 (4): 1501-1514. (*: equal contribution)

Villas-Boas SG, CD Moon, SJ Noel, HM Hussein, WJ Kelly, M Cao, GA Lane, AL Cookson, GT Attwood. 2008. Phenotypic characterization of transposon-inserted mutants of Clostridium proteoclasticum B316T using extracellular metabolomics. Journal of Biotechnology 134: 55-63.

Koulman A, C Seeliger, PJB Edwards, K Fraser, W Simpson, L Johnson, M Cao, S Rasmussen, GA Lane. 2008. E/Z-Thesinine-O-4′-α-rhamnoside, pyrrolizidine conjugates produced by grasses (Poaceae). Phytochemistry, 69 (9):1927-1932.

Koulman A, BA Tapper, K Fraser, M Cao, GA Lane, S Rasmussen. 2007. High-throughput direct-infusion ion trap mass spectrometry: a new method for metabolomics. Rapid Commun.Mass Spectrom. 21: 421-428.

Software

Cao M. 2011. iontree: Data management and analysis of ion trees from ion-trap mass spectrometry. (a BioConductor package in R and Java)

            http://www.bioconductor.org/packages/release/bioc/html/iontree.html

Conference Papers

Cao M, C Jones, S Rasmussen, M Faville, K Fraser, I Verry and W Williams. 2012. The current status of metabolomics and its potential contribution to forage genetics and breeding. Proceedings of the 7^th International Symposium on the Molecular Breeding of Forage and Turf. (Ed. BS Bushman and GC Spangenberg). 9-11.

Cao M, L Johnson, R Johnson, A Koulman, GA Lane and S Rasmussen. 2007. Joint Analyses of transcriptomic and metabolomic data to probe the ryegrass-endophyte symbiosis.  Proceedings of the 6^th International Symposium on Fugal Endophytes of Grasses. (Ed. AJ Popay and ER Thom). 195-198.

Faville MJ, A Koulman, L Briggs, M Cao, C Podmore and D Abraham. 2007. Exploring endophyte compatibility in perennial ryegrass. Proceedings of the 6^th International Symposium on Fugal Endophytes of Grasses. (Ed. AJ Popay and ER Thom). 143-146.

Lane GA, M Cao, L Johnson, A Koulman, AJ Popay, S Rasmussen and BA Tapper. 2007. Anti-herbivore factors of grass endphytes: new prospects from metabolomics. Proceedings of the 6^th International Symposium on Fugal Endophytes of Grasses. (Ed. AJ Popay and ER Thom). 307-312.

Cao M, A  Koulman, D Pacheco, GA Lane and S Rasmussen. 2006. Systems Biology and Metabolomics: Experimental and Computational Challenges. Proceedings of the New Zealand Society of Animal Production 66:213-218.

Rasmussen S, M Cao, K Fraser, A Koulman, Z Park-Ng, H Xue, and GA Lane. 2006. Cold stress in white clover - An integrated view of metabolome and tranascriptome responses. Proceedings of the 13^th Australasian Plant Breeding Conference, Christchurch, New Zealand (Ed. CF Mercer). 750-757, www.apbc.org.nz

Koulman A, DD Rowan, S Gardiner, M Cao, M Faville, GA Lane and S Rasmussen. 2006. Metabolomics in QTL discovery: A powerful tool for plant breeding. Proceedings of the 13^th Australasian Plant Breeding Conference, Christchurch, New Zealand (Ed. CF Mercer). 714-720, www.apbc.org.nz

Johnson RD, S Bassett,S M Cao, M Christensen, C Gaborit, LJ Johnson, A Koulman, S Rasmussen, C Voisey, G Bryan. 2006. A multidisciplinary approach to dissect the molecular basis of the Neotyphodium lolii/ryegrass symbiosis. Proceedings of 13^th Australasian Plant Breeding Conference, Christchurch, New Zealand (Ed. CF Mercer). 537-547, www.apbc.org.nz

Lane GA, K Fraser, M Cao,  A Koulman, GP Cosgrove, A Death. 2006. Urinary biomarkers of forage feeding from ESI-MS/MS fingerprinting: exploratory studies. New ZealandSociety of Animal Production Conference, 66: 230-235.

Selected Conference Presentations

Cao M. 2011. “iontree” – an R package for data management and analysis of ion trees from ion trap mass spectrometry.7^th International Conference of the Metabolomics Society. Cairns. AU. (oral)

Cao M, D Otter, GA Lane, D Rowan, N Roy. 2010. Computational and statistical issues in biomarker discovery via mass spectrometry-based metabolomics. 4^th Asia Pacific Nutrigenomics Conference. Auckland, NZ. (oral)

Cao M, K Fraser, D Otter, S Harrison, GA Lane, S Rasmussen. 2009. A bioinformatics investigation of ion trees. 1^st Australasian Symposium on Metabolomics. Auckland, NZ. (poster)

Cao M. 2009. Genetic Metabolomics – dissecting genetic impacts on metabolic variation. Joint New Zealand and China workshop on Mathematical models: scaling from genomes to ecosystems. Shanghai, China. (Oral)

Cao M. 2008. Metabolomics – from signals to metabolites. Statistics Forum at Massey University. (Oral)

Cao M. A Koulman, GA Lane and S Rasmussen. 2007. Computational tools to aid metabolite identification in metabolomics. Australia Bioinformatics 2007. Brisbane, AU. (poster)

Cao M, M Faville, A Koulman, GA Lane, S Rasmussen. 2007. Genetical Metabolomics – a new approach to link QTL with metabolites. 3^rd New Zealand molecular mapping workshop. (Oral)

Cao M, L Johnson, A Koulman, GA Lane and S Rasmussen. 2006.  Towards understanding of the ryegrass-endophyte symbiosis through the integration of transcriptome and metabolome data.  Proceedings from the 4th International Plant Metabolomics Conference. UK. Metabolomics. 2(4):302. (poster)

Cao M, GA Lane and S Rasmussen. 2004. Building a data infrastructure for plant metabolomics. International Conference on Bioinformatics (ICoB).Auckland, NZ. (poster)

Technical Reports

Cao M. 2005. Joint analysis of transcriptome and metabolome of ryegrass-endophyte symbiosis. June 2005.

Cao M. 2005. Towards joint analysis of transcriptomic and metabolomic data - A literature review. March 2005.

Lane GA, S Rasmussen S, M Cao, A Koulman, DD Rowan, PT Austin, JM Cooney, AJ Matich. 2004. Establishing plant metabolomics forNew Zealand: Experimental and data handling protocols. September 2004.

Cao M and GA Lane. 2004.  Database design for plant metabolomics III - Linkage of transcriptome and metabolome. September 2004.

Cao M. 2004. Database design for plant metabolomics  II - Database system design and implementation. June 2004.

Cao M. 2004. Database design for plant metabolomics I - Requirement analysis. May 2004.

Publications before 2004 -- Plant Genetics

1)      Cao M, SS. Bughrara and DA. Sleper. 2003. Cytogenetic analysis of Festuca species and amphiploids between Festuca mairei and Lolium perenne. Crop Sci. 43: 1659-1662.

2)      Cao M and DA. Sleper. 2001. Use of genome-specific DNA sequences to monitor chromatin introgression from Festuca mairei into Lolium perenne. Theor. Appl. Genet. 103: 248-253.

3)      Cao M, DA. Sleper, F Dong and J Jiang. 2000. Genomic in situ hybridization (GISH) reveals high chromosome pairing affinity between Lolium perenne and Festuca mairei. Genome 43: 398-403.

4)      Cao M (coauthor) 1999.  Cytogenetics. China Agriculture Press. (textbook)

5)      Chai S, D Liu, P Chen, W Li, L Qi, M Cao. 1999. A study on species-specific DNA repeats from Leymus racemosus and Psathyrostachys juncea. I. Isolation and Identification. Journal of Northwest Agricultural University. 27(3):33-37.

6)      Chai S, D Liu, P Chen, W Li, L Qi, M Cao, J Liu. 1999. A study on species-specific DNA repeats from Leymus racemosus and Psathyrostachys juncea. II. Polymorphism among the Species of Triticea. Journal of Northwest Agricultural University. 27(4):4-9.

7)      Chen W, M Cao, H Zhang, Q Wu and D Liu. 1997. Culture of immature embryo and morphological characters of its regeneration plants from F1 hybrid of tetraploid tall fescue and Italian ryegrass. Journal ofNanjingAgricultural University. 20(1): 9-12.

8)      Qi L, M Cao, P Chen, W Li and D Liu. 1996. Identification, mapping and application of polymorphic DNA associated with resistance gene Pm21 of wheat. Genome 39: 191-197.

9)      Cao M, W Chen and D Liu. 1994. Cytogenetic studies of intergeneric hybrids and its amphiploid between Lolium multiflorum and Festuca arundinacea var. glaucescens. Scientia Agricultural Sinica. 27(5): 69-76.

10)  Qi L, P Chen, D Liu and M Cao. 1993. Isolation of molecular markers linked to gene for Powdery mildew resistance in Triticum. High Technology Letters. 3(8). 31-34.

11)  Cao M, W Chen and D Liu. 1992. Morphological, cytogenetic and isozymic characterization of intergeneric hybrid somaclones of Lolium multiflorum and Festuca arundinacea var. glaucescens (4x). Proc. of 1^st JiangsuYouth Academic Symposium.ChinaScience and Technology Press. 25-29.