Dr Sebastian Schmeier staff profile picture

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

Dr Sebastian Schmeier

Senior Lecturer in Bioinformatics/Genomics

Institute of Natural and Mathematical Sciences

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

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

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 3 1

Research Outputs

Journal

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.
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.
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.
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., . . . Endoh, M. (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., . . . Ishihara, R. (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., . . . Orlando, V. (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.
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.
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.
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.

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.(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.

Consultancy and Languages

Consultancy

  • Dec 2012 - now - New Zealand Genomics Limited (NZGL)
    I am affiliated with New Zealand Genomics Limited (NZGL) and its representative on the Massey Albany campus. I am supervising and supporting bioinformatics technicians in their work for 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 1 1
CoSupervisor 1 0

Teaching

Courses

  • 122.231 Genes and Gene Expression
  • 203.341 Genetics and Evolution
  • 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

Current Doctoral Supervision

Supervisor of:

  • Elena Denisenko - PhD
    Understanding fundamental mechanisms of infection using systems biology

CoSupervisor of:

  • Kiran Sreeja Jayan - PhD
    Characterization of genes for the utilization of histidine and its metabolites in a human pathogenic bacterium Pseudomonas aeruginosa PAO1

Completed Doctoral Supervision

Supervisor of:

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 5:00pm 0800 MASSEY (+64 6 350 5701) TXT 5222 contact@massey.ac.nz Web chat Staff Alumni News Māori @ Massey