Dr Sebastian Schmeier staff profile picture

Contact details +64 (09) 414 0800  ext. 43538

Dr Sebastian Schmeier PhD, MSc, BSc, NZSO

Senior Lecturer in Bioinformatics/Genomics

School of Natural and Computational Sciences

for more information please visit the lab webpage at http://sschmeier.com or  http://compbio.massey.ac.nz/schmeier

Sebastian Schmeier (http://sschmeier.com) is a research group leader and Senior Lecturer in Bioinformatics/Genomics at the Institute of Natural and Mathematical Sciences (INMS) at Massey University Auckland, the bioinformatics lead of the Massey Genome Service, and an Affiliate Investigator at the Maurice Wilkins Centre for Molecular Biodiscovery. His group combines computational methods and biology to answer questions in the fields of genomics, transcriptomics, and epigenetics, with a focus on gene regulation, non-coding RNAs, and data-driven biomedical discovery. Besides research, Sebastian is also highly interested in the computational and bioinformatics up-skilling of students and scientists. For more information see the lab webpages.

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Professional

Contact details

  • Ph: +64 9 4140800 43538
    Location: 10, OR14
    Campus: Oteha Rohe, Albany, Auckland, New Zealand

Qualifications

  • Doctor of Philosophy - University of the Western Cape (2009)
  • Master of Science - Freie University Berlin (2005)
  • Bachelor of Science - Freie University Berlin (2003)

Fellowships and Memberships

  • Member, New Zealand Society for Oncology (Full) (2017)

Prizes and Awards

  • ''Northwest Society of Colon and Rectal Surgeons Award for Clinical / Podium'' for presentation at ASCRS 2017. Purcell RV, Visnovska M, Biggs P, Schmeier S, Frizelle F. - Northwest Society of Colon and Rectal Surgeons (2017)

Research Expertise

Research Interests

  • Bioinformatics
  • Genomics
  • Transcriptomics
  • non-coding RNA (e.g. miRNA, lncRNA, etc.)
  • Epigenomics / Epigenetics
  • Biomedical data mining, text mining
  • Biological databases
  • Data integration, information extraction
  • Machine learning, artificial intelligence
  • Web technologies

Thematics

Health and Well-being

Area of Expertise

Field of research codes
Artificial Intelligence and Image Processing (080100):
Biochemistry and Cell Biology (060100): Bioinformatics (060102):
Bioinformatics Software (080301):
Biological Sciences (060000):
Computer Software (080300):
Epigenetics (incl. Genome Methylation and Epigenomics) (060404): Gene Expression (incl. Microarray and other genome-wide approaches) (060405): Genetics (060400): Genome Structure and Regulation (060407): Genomics (060408):
Information And Computing Sciences (080000):
Mathematical Sciences (010000):
Proteomics and Intermolecular Interactions (excl. Medical Proteomics) (060109): Systems Biology (060114)

Keywords

Bioinformatics, Computational Biology, Genomics, Transcriptomics, Next-generation sequencing

Research Projects

Summary of Research Projects

Position Current Completed
Project Leader 1 5

Research Outputs

Journal

Tamgue, O., Gcanga, L., Ozturk, M., Whitehead, L., Pillay, S., Jacobs, R., . . . Guler, R. (2019). Differential targeting of c-Maf, Bach-1, and Elmo-1 by microRNA-143 and microRNA-365 promotes the intracellular growth of mycobacterium tuberculosis in alternatively IL-4/IL-13 activated macrophages. Frontiers in Immunology. 10(MAR)
[Journal article]Authored by: Schmeier, S.
Denisenko, E., Guler, R., Mhlanga, M., Suzuki, H., Brombacher, F., & Schmeier, S. (2019). Transcriptionally induced enhancers in the macrophage immune response to Mycobacterium tuberculosis infection. BMC Genomics. 20(1)
[Journal article]Authored by: Schmeier, S.
Zhou, H., Visnovska, T., Gong, H., Schmeier, S., Hickford, J., & Ganley, ARD. (2019). Contrasting patterns of coding and flanking region evolution in mammalian keratin associated protein-1 genes. Molecular Phylogenetics and Evolution. 133, 352-361
[Journal article]Authored by: Schmeier, S.
Dale, R., Grüning, B., Sjödin, A., Rowe, J., Chapman, BA., Tomkins-Tinch, CH., . . . Hägglund, E. (2018). Bioconda: Sustainable and comprehensive software distribution for the life sciences. Nature Methods. 15(7), 475-476
[Journal article]Authored by: Schmeier, S.
Hoeppner, MP., Denisenko, E., Gardner, PP., Schmeier, S., & Poole, AM. (2018). An evaluation of function of multicopy noncoding RNAs in mammals using ENCODE/FANTOM data and comparative genomics. Molecular Biology and Evolution. 35(6), 1451-1462
[Journal article]Authored by: Schmeier, S.
Roy, S., Schmeier, S., Kaczkowski, B., Arner, E., Alam, T., Ozturk, M., . . . Suzuki, H. (2018). Transcriptional landscape of Mycobacterium tuberculosis infection in macrophages. Scientific Reports. 8(1)
[Journal article]Authored by: Schmeier, S.
Zhou, H., Visnovska, T., Gong, H., Schmeier, S., Hickford, J., & Ganley, ARD. (2018). Contrasting patterns of coding and flanking region evolution in mammalian keratin associated protein-1 genes.
[Journal article]Authored by: Schmeier, S.
Denisenko, E., Guler, R., Mhlanga, M., Suzuki, H., Brombacher, F., & Schmeier, S. (2018). Transcriptionally induced enhancers in the macrophage immune response to Mycobacterium tuberculosis infection.
[Journal article]Authored by: Schmeier, S.
Hon, CC., Ramilowski, JA., Harshbarger, J., Bertin, N., Rackham, OJL., Gough, J., . . . Forrest, ARR. (2017). An atlas of human long non-coding RNAs with accurate 5′ ends. Nature. 543(7644), 199-204
[Journal article]Authored by: Schmeier, S.
Denisenko, E., Guler, R., Mhlanga, MM., Suzuki, H., Brombacher, F., & Schmeier, S. (2017). Genome-wide profiling of transcribed enhancers during macrophage activation. Epigenetics and Chromatin. 10(1)
[Journal article]Authored by: Schmeier, S.
Schmeier, S., Alam, T., Essack, M., & Bajic, VB. (2017). TcoF-DB v2: Update of the database of human and mouse transcription co-factors and transcription factor interactions. Nucleic Acids Research. 45(D1), D145-D150
[Journal article]Authored by: Schmeier, S.
Purcell, RV., Visnovska, M., Biggs, PJ., Schmeier, S., & Frizelle, FA. (2017). Distinct gut microbiome patterns associate with consensus molecular subtypes of colorectal cancer. Scientific Reports. 7(1)
[Journal article]Authored by: Biggs, P., Schmeier, S.
Salhi, A., Essack, M., Alam, T., Bajic, VP., Ma, L., Radovanovic, A., . . . Bajic, VB. (2017). DES-ncRNA: A knowledgebase for exploring information about human micro and long noncoding RNAs based on literature-mining. RNA Biology. 14(7), 963-971
[Journal article]Authored by: Schmeier, S.
Denisenko, E., Ho, D., Tamgue, O., Ozturk, M., Suzuki, H., Brombacher, F., . . . Schmeier, S. (2016). IRNdb: The database of immunologically relevant non-coding RNAs. Database. 2016
[Journal article]Authored by: Schmeier, S.
Forrest, ARR., Kawaji, H., Rehli, M., Baillie, JK., De Hoon, MJL., Haberle, V., . . . Huminiecki, L. (2014). A promoter-level mammalian expression atlas. Nature. 507(7493), 462-470
[Journal article]Authored by: Schmeier, S.
Roy, S., Schmeier, S., Arner, E., Alam, T., Parihar, SP., Ozturk, M., . . . Suzuki, H. (2015). Redefining the transcriptional regulatory dynamics of classically and alternatively activated macrophages by deepCAGE transcriptomics. Nucleic Acids Research. 43(14), 6969-6982
[Journal article]Authored by: Schmeier, S.
Roy, S., Guler, R., Parihar, SP., Schmeier, S., Kaczkowski, B., Nishimura, H., . . . Suzuki, H. (2015). Batf2/Irf1 induces inflammatory responses in classically activated macrophages, lipopolysaccharides, and mycobacterial infection. Journal of Immunology. 194(12), 6035-6044
[Journal article]Authored by: Schmeier, S.
Ravasi, T., Suzuki, H., Cannistraci, CV., Katayama, S., Bajic, VB., Tan, K., . . . Hayashizaki, Y. (2010). An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man. Cell. 140(5), 744-752
[Journal article]Authored by: Schmeier, S.
Suzuki, H., Forrest, ARR., Van Nimwegen, E., Daub, CO., Balwierz, PJ., Irvine, KM., . . . Petrovsky, N. (2009). The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nature Genetics. 41(5), 553-562
[Journal article]Authored by: Schmeier, S.
Guler, R., Parihar, SP., Savvi, S., Logan, E., Schwegmann, A., Roy, S., . . . Brombacher, F. (2015). IL-4Rα-dependent alternative activation of macrophages is not decisive for Mycobacterium tuberculosis pathology and bacterial burden in mice. PLoS ONE. 10(3)
[Journal article]Authored by: Schmeier, S.
Essack, M., MacPherson, CR., Schmeier, S., & Bajic, VB. (2012). Identification of estrogen responsive genes using esophageal squamous cell carcinoma (ESCC) as a model. BMC Systems Biology. 6
[Journal article]Authored by: Schmeier, S.
Schaefer, U., Schmeier, S., & Bajic, VB. (2011). TcoF-DB: Dragon database for human transcription co-factors and transcription factor interacting proteins. Nucleic Acids Research. 39(SUPPL. 1)
[Journal article]Authored by: Schmeier, S.
Schmeier, S., Schaefer, U., MacPherson, CR., & Bajic, VB. (2011). dPORE-miRNA: Polymorphic regulation of microRNA genes. PLoS ONE. 6(2)
[Journal article]Authored by: Schmeier, S.
Schmeier, S., Schaefer, U., Essack, M., & Bajic, VB. (2011). Network analysis of microRNAs and their regulation in human ovarian cancer. BMC Systems Biology. 5
[Journal article]Authored by: Schmeier, S.
Schmeier, S., Jankovic, B., & Bajic, VB. (2011). Simplified method to predict mutual interactions of human transcription factors based on their primary structure. PLoS ONE. 6(7)
[Journal article]Authored by: Schmeier, S.
Kaur, M., MacPherson, CR., Schmeier, S., Narasimhan, K., Choolani, M., & Bajic, VB. (2011). In Silico discovery of transcription factors as potential diagnostic biomarkers of ovarian cancer. BMC Systems Biology. 5
[Journal article]Authored by: Schmeier, S.
Kowald, A., & Schmeier, S. (2011). Text mining for systems modeling.. Methods in molecular biology (Clifton, N.J.). 696, 305-318
[Journal article]Authored by: Schmeier, S.
Maqungo, M., Kaur, M., Kwofie, SK., Radovanovic, A., Schaefer, U., Schmeier, S., . . . Bajic, VB. (2011). DDPC: Dragon database of genes associated with prostate cancer. Nucleic Acids Research. 39(SUPPL. 1)
[Journal article]Authored by: Schmeier, S.
Ravasi, T., Suzuki, H., Cannistraci, CV., Katayama, S., Bajic, VB., Tan, K., . . . Hayashizaki, Y. (2010). An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man (vol 140, pg 744, 2010). CELL. 141(2), 369-369
[Journal article]Authored by: Schmeier, S.
Schmeier, S., MacPherson, CR., Essack, M., Kaur, M., Schaefer, U., Suzuki, H., . . . Bajic, VB. (2009). Deciphering the transcriptional circuitry of microRNA genes expressed during human monocytic differentiation. BMC Genomics. 10
[Journal article]Authored by: Schmeier, S.
Kaur, M., Radovanovic, A., Essack, M., Schaefer, U., Maqungo, M., Kibler, T., . . . Bajic, VB. (2009). Database for exploration of functional context of genes implicated in ovarian cancer. Nucleic Acids Research. 37(SUPPL. 1)
[Journal article]Authored by: Schmeier, S.
Essack, M., Radovanovic, A., Schaefer, U., Schmeier, S., Seshadri, SV., Christoffels, A., . . . Bajic, VB. (2009). DDEC: Dragon database of genes implicated in esophageal cancer. BMC Cancer. 9
[Journal article]Authored by: Schmeier, S.
Kaur, M., Schmeier, S., MacPherson, CR., Hofmann, O., Hide, WA., Taylor, S., . . . Bajic, VB. (2008). Prioritizing genes of potential relevance to diseases affected by sex hormones: An example of Myasthenia Gravis. BMC Genomics. 9
[Journal article]Authored by: Schmeier, S.
Toedling, J., Schmeier, S., Heinig, M., Georgi, B., & Roepcke, S. (2005). MACAT - Microarray chromosome analysis tool. Bioinformatics. 21(9), 2112-2113
[Journal article]Authored by: Schmeier, S.
Hakenberg, J., Schmeier, S., Kowald, A., Klipp, E., & Leser, U. (2004). Finding kinetic parameters using text mining. OMICS A Journal of Integrative Biology. 8(2), 131-152
[Journal article]Authored by: Schmeier, S.

Book

Kowald, A., & Schmeier, S. (2010). Text Mining for Systems Modelling.. In M. Hamacher, M. Eisenacher, & C. Stephan (Eds.) Data Mining in Proteomics. (pp. 305 - 318). : Humana Press
[Chapter]Authored by: Schmeier, S.
Bajic, VB., Schmeier, S., & MacPherson, CR. (2009). Computational methods to identify transcription factor binding sites using CAGE information. In Cap-Analysis Gene Expression (CAGE): The Science of Decoding Genes Transcription. (pp. 137 - 152).
[Chapter]Authored by: Schmeier, S.

Conference

Purcell, R., Visnovska, M., Biggs, P., Schmeier, S., & Frizelle, F.(2017, June). Consensus molecular classification of colorectal cancer and association with the colonic microbiome. Diseases of the Colon and Rectum. 60 (6)(pp. E90 - E91). 0012-3706.
[Conference]Authored by: Biggs, P., Schmeier, S.
Roy, S., Guler, R., Parihar, SP., Schmeier, S., Kaczkowski, B., Nishimura, H., . . . Suzuki, H.Batf2/Irf1 induces inflammatory responses in classically activated macrophages, LPS and mycobacterial infection.. Eur. J. Immunol. ICI 2016. (pp. 7 - 7).
[Conference]Authored by: Schmeier, S.
Roy, S., Guler, R., Parihar, SP., Schmeier, S., Kaczkowski, B., Nishimura, H., . . . Suzuki, H.(2016, August). Batf2/Irf1 induces inflammatory responses in classically activated macrophages, lipopolysaccharides, and mycobacterial infection. European Journal of Immunology. (pp. 7 - 7). 0014-2980.
[Conference]Authored by: Schmeier, S.
Schmeier, S., Hakenberg, J., Kowald, A., Klipp, E., & Leser, U.(2003, October). Text Mining for Systems Biology Using Statistical Learning Methods. .
[Conference]Authored by: Schmeier, S.

Consultancy and Languages

Consultancy

  • Jan 2017 - now - Massey Genome Service (MGS)
    Bioinformatics lead for the Massey Genome Service (MGS), IFS, Massey University
  • Dec 2012 - Dec 2017 - New Zealand Genomics Limited (NZGL)
    Affiliate of New Zealand Genomics Limited (NZGL) and its representative on the Massey Albany campus. Supervisor of bioinformatics technicians of NZGL.

Languages

  • English
    Last used: current
    Spoken ability: Excellent
    Written ability: Excellent
  • German
    Last used: current
    Spoken ability: Excellent
    Written ability: Excellent

Supervision and Teaching

Summary of Doctoral Supervision

Position Current Completed
Supervisor 2 2
Co-supervisor 4 0

Teaching

Courses

  • 203.341 Genetics and Evolution
  • 203.343 Advanced Genetics and Genomics
  • 203.203 Human Genetics
  • 203.342 Molecular Cell Biology
  • 162.760 Research Methods in Molecular Biosciences

Workshops

Please see this page for upcoming workshops. Past workshops include:

  • Software Carpentry Workshops
  • Introduction to Bioinformatics and Genomics
  • Transciptomics using Next-Generation Sequencing
  • Reproducible computational genomics research

Courses Coordinated

Current Doctoral Supervision

Supervisor of:

  • Tyler Kolisnik - Doctor of Philosophy
    Microbes distinguish colorectal cancer subtypes
  • Arielle Kae Sulit - Doctor of Philosophy
    Deciphering genotype-phenotype relationships in genomic data

Co-supervisor of:

  • Stan Wang - Doctor of Philosophy
    Decision Markets Implementation
  • Georgia Breckell - Doctor of Philosophy
    Mechanisms of epigentic inheritance in Bacteria 
  • Kiran Sreeja Jayan - Doctor of Philosophy
    Characterization of genes for the utilization of histidine and its metabolites in a human pathogenic bacterium Pseudomonas aeruginosa PAO1

Completed Doctoral Supervision

Supervisor of:

  • 2018 - Elena Denisenko - Doctor of Philosophy
    Transcriptional regulation in mouse macrophages: the role of enhancers in macrophage activation and infection
  • 2016 - Daniela Quintana Rincon - Doctor of Philosophy
    Role of the ribosomal DNA repeats on chromosome segregation of Saccharomyces cerevisiae

Media and Links

Media

  • 27 Mar 2014 - Newspaper
    Revealed: How parts of our bodies get pudgy
    Hardcopy newspaper article in the New Zealand Herald. Coverage about a co-authored publication in Nature about the most detailed catalogue of gene regulatory regions.
  • 27 Mar 2014 - Newspaper, Online
    Revealed: How parts of our bodies get pudgy
    Media coverage at the New Zealand Herald of a publication Nature on transcriptional regulation.
  • 27 Mar 2014 - Online
    Kiwi scientist helps find what makes cells differe
    Massey University news feature on a co-authored publication in Nature about gene regulatory regions.
  • 08 Jan 2015 - Newspaper
    North Shore Times news: Two Grants pave the way
    Media coverage of the Marsden grant received in the 2014 round.
  • 05 Nov 2014 - Newspaper, Online
    Marsden Fund: In search of bright ideas
    Media coverage at the New Zealand Herald of recent receipt of a grant funded through the Marsden fund.
  • 04 Apr 2014 - Newspaper
    Gene study could bring medical advances
    Auckland City harbour News feature on a co-authored publication in Nature about gene regulatory regions.

Other Links

Massey Contact Centre Mon - Fri 8:30am to 4:30pm 0800 MASSEY (+64 6 350 5701) TXT 5222 contact@massey.ac.nz Web chat Staff Alumni News Māori @ Massey