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Dr Nikki Freed staff profile picture

Contact details +64 (09) 414 0800  ext. 43639

Dr Nikki Freed PhD, MSc, BSc

Senior Lecturer in Genetics

School of Natural and Computational Sciences

My research involves the study of bacterial and viral pathogens. Current projects include: 

  • Using portable qPCR and sequencing devices to detect SARS-Cov2, the virus that causes COVID-19 
  • Using next-generation sequencing to identify essential genes in the bacterial pathogen Shigella flexneri
  • Using laboratory evolution to investigate genetic and epigenetic changes underlying antibiotic resistance
  • I dabble in a number of other projects that include using DNA sequencing to investigate animal diets, soil metagenomics, and bacteriophage discovery
  • I consult for a New Zealand based start-up company developing portable quantitative PCR devices. 
  • I consult for Fonterra, a large New Zealand dairy company. 

Professional

Qualifications

  • Doctor of Philosophy - Swiss Federal Institute of Technology (ETH) (2009)
  • Master of Science - University of California San Diego (2002)
  • Bachelor of Science - University of California San Diego (2000)

Prizes and Awards

  • Nominated for Lecturer of the Year award 2019 - Albany Students Association (2019)
  • Nominated for Lecturer of the Year award 2018 - Massey University (2018)
  • Nominated for Lecture of the Year award - Massey University (2016)
  • Massey University INNOVATION AND EXCELLENCE GRANT 5000$. Co-applicant with Dr. Olin Silander - Massey University (2016)
  • Massey University Research Fund grant for $12,472 - Massey University (2017)
  • 2015 Early Career Researcher Award. Title: Use of Functional Metagenomics to Identify Novel Antimicrobials. $5000 NZD. - Massey University (2015)

Research Expertise

Research Interests

    • Molecular Biology
    • Bacterial Genetics
    • Next generation DNA sequencing
    • Nanopore DNA sequencing
    • Metagenomics
    • Epigenetics

    Thematics

    Health and Well-being

    Area of Expertise

    Field of research codes
    Biological Adaptation (060303): Biological Sciences (060000): Epigenetics (incl. Genome Methylation and Epigenomics) (060404): Evolutionary Biology (060300): Gene Expression (incl. Microarray and other genome-wide approaches) (060405): Genetics (060400): Genomics (060408): Infectious Agents (060502): Microbial Ecology (060504): Microbial Genetics (060503): Microbiology (060500): Molecular Evolution (060409)

    Research Projects

    Summary of Research Projects

    Position Current Completed
    Project Leader 6 6

    Current Projects

    Project Title: Rapid diagnosis and genome sequencing to follow Cov-2019 outbreak

    Date Range: 2020 - 2020

    Funding Body: Health Research Council of New Zealand

    Project Team:

    Project Title: Microbial Community Analysis for Fonterra Stirling Membrane Bioreactor

    This project aims to assess the diversity and abundance of the microbial taxa (viral, bacterial, fungal, and protozoan) in the Fonterra Stirling wastewater treatment membrane bioreactor at various time points using metagenomics and 16S DNA sequencing
    Read Project Description Hide Project Description

    Date Range: 2019 - 2020

    Funding Body: Fonterra Co-operative Group Limited

    Project Team:

    Project Title: Development and testing biological assays

    Date Range: 2017 - 2020

    Funding Body: Ubiquitome Ltd

    Project Team:

    Research Outputs

    Journal

    Pearman, WS., Freed, NE., & Silander, OK. (2020). Testing the advantages and disadvantages of short- And long- read eukaryotic metagenomics using simulated reads. BMC Bioinformatics. 21(1)
    [Journal article]Authored by: Freed, N., Silander, O.
    Davies, CG., Wojtus, JK., Gilligan, CER., Latu, SF., Manning, TJ., Meyer, CE., . . . Hendrickson, HL. (2019). Complete genome sequences of nine mycobacteriophages from New Zealand, Beatrix, Carthage, Daegal, Dulcie, fancypants, Fenn, Inca, Naira, and Robyn. Microbiology Resource Announcements. 8(20)
    [Journal article]Authored by: Freed, N., Hendrickson, H.
    Freed, NE. (2017). Creation of a dense transposon insertion library using bacterial conjugation in enterobacterial strains such as Escherichia coli or Shigella flexneri. Journal of Visualized Experiments. 2017(127)
    [Journal article]Authored by: Freed, N.
    Butela, KA., Gurney, SMR., Hendrickson, HL., LeBlanc-Straceski, JM., Zimmerman, AM., Conant, SB., . . . Kagey, JD. (2017). Complete genome sequences of cluster a mycobacteriophages BobSwaget, Fred313, KADY, Lokk, MyraDee, Stagni, and StepMih. Genome Announcements. 5(43)
    [Journal article]Authored by: Freed, N., Hendrickson, H., Silander, O.Contributed to by: Hendrickson, H.
    Freed, NE., Bumann, D., & Silander, OK. (2016). Combining Shigella Tn-seq data with gold-standard E. coli gene deletion data suggests rare transitions between essential and non-essential gene functionality. BMC Microbiology. 16(203)
    [Journal article]Authored by: Freed, N., Silander, O.
    Freed, NE., Bumann, D., & Silander, OK. (2016). Combining Shigella Tn-seq data with gold-standard E. coli gene deletion data suggests rare transitions between essential and non-essential gene functionality. BMC Microbiology. 16(1)
    [Journal article]Authored by: Freed, N., Silander, O.
    Freed, NE., Bumann, D., & Silander, OK. (2016). Combining Shigella Tn-seq data with gold-standard E. coli gene deletion data suggests rare transitions between essential and non-essential gene functionality. bioRxiv.
    [Journal article]Authored by: Freed, N.
    Blyn, LB., Hall, TA., Libby, B., Ranken, R., Sampath, R., Rudnick, K., . . . Ecker, DJ. (2008). Rapid detection and molecular serotyping of adenovirus by use of PCR followed by electrospray ionization mass spectrometry. Journal of Clinical Microbiology. 46(2), 644-651
    [Journal article]Authored by: Freed, N.
    Ackermann, M., Stecher, B., Freed, NE., Songhet, P., Hardt, WD., & Doebeli, M. (2008). Self-destructive cooperation mediated by phenotypic noise. Nature. 454(7207), 987-990
    [Journal article]Authored by: Freed, N.
    Freed, NE., Silander, OK., Stecher, B., Böhm, A., Hardt, WD., & Ackermann, M. (2008). A simple screen to identify promoters conferring high levels of phenotypic noise. PLoS Genetics. 4(12)
    [Journal article]Authored by: Freed, N., Silander, O.
    Freed, NE., Myers, CA., Russell, KL., Walter, EA., Irvine, M., Coon, RG., . . . Metzgar, D. (2007). Diagnostic discrimination of live attenuated influenza vaccine strains and community-acquired pathogenic strains in clinical samples. Molecular and Cellular Probes. 21(2), 103-110
    [Journal article]Authored by: Freed, N.
    Vora, GJ., Lin, B., Gratwick, K., Meador, C., Hansen, C., Tibbetts, C., . . . Metzgar, D. (2006). Co-infections of adenovirus species in previously vaccinated patients. Emerging Infectious Diseases. 12(6), 921-930
    [Journal article]Authored by: Freed, N.
    Fuller, J., Hanley, K., Schultz, R., Lewis, M., Freed, NE., Ellis, M., . . . Russell, K. (2006). Surveillance for febrile respiratory infections during Cobra Gold 2003. Military Medicine. 171(5), 357-359
    [Journal article]Authored by: Freed, N.
    Russell, KL., Broderick, MP., Franklin, SE., Blyn, LB., Freed, NE., Moradi, E., . . . Ryan, MAK. (2006). Transmission dynamics and prospective environmental sampling of adenovirus in a military recruit setting. Journal of Infectious Diseases. 194(7), 877-885
    [Journal article]Authored by: Freed, N.
    Russell, KL., Ryan, MAK., Hawksworth, A., Freed, NE., Irvine, M., & Daum, LT. (2005). Effectiveness of the 2003-2004 influenza vaccine among US military basic trainees: a year of suboptimal match between vaccine and circulating strain. VACCINE. 23(16), 1981-1985
    [Journal article]Authored by: Freed, N.
    Ecker, DJ., Sampath, R., Blyn, LB., Eshoo, MW., Ivy, C., Ecker, JA., . . . Hofstadler, SA. (2005). Rapid identification and strain-typing of respiratory pathogens for epidemic surveillance. Proceedings of the National Academy of Sciences of the United States of America. 102(22), 8012-8017
    [Journal article]Authored by: Freed, N.
    Russell, KL., Ryan, MAK., Hawksworth, A., Freed, NE., Irvine, M., & Daum, LT. (2005). Effectiveness of the 2003-2004 influenza vaccine among U.S. military basic trainees: A year of suboptimal match between vaccine and circulating strain. Vaccine. 23(16), 1981-1985
    [Journal article]Authored by: Freed, N.
    Blasiole, DA., Metzgar, D., Daum, LT., Ryan, MAK., Wu, J., Wills, C., . . . Russell, KL. (2004). Molecular Analysis of Adenovirus Isolates from Vaccinated and Unvaccinated Young Adults. Journal of Clinical Microbiology. 42(4), 1686-1693
    [Journal article]Authored by: Freed, N.

    Conference

    Pearman, W., Breckell, G., Dale, J., Silander, O., & Freed, NE. (2017, August). New tools for diet analysis: nanopore sequencing of unamplified genomic DNA from stomach contents to detect with high resolution what rats are eating. Presented at Queenstown Research Week. Queenstown, New Zealand.
    [Conference Oral Presentation]Authored by: Dale, J., Freed, N., Silander, O.
    Freed, NE., Bumann, D., & Silander, OK. (2016). Combining Shigella Tn-seq data with gold-standard E. coli gene deletion data suggests rare transitions between essential and non-essential gene functionality. Poster session presented at the meeting of Society for Microbiology and Evolution Conference 2016. Gold Coast, Australia
    [Conference Poster]Authored by: Freed, N., Silander, O.
    Hendrickson, HL., Davies, C., Silander, OK., & Freed, N. (2016). From Soil to Sequencing: The isolation and characterisation of novel New Zealand Mycobacterium smegmatis bacteriophages. Poster session presented at the meeting of Janelia Laboratories, United States of America. Ashburn, United States of America
    [Conference Poster]Authored by: Freed, N., Hendrickson, H., Silander, O.Contributed to by: Hendrickson, H.
    Freed, NE., Bumann, D., & Silander, O. (2015). Combining Tn-seq with comparative genomics identifies proteins uniquely essential in Shigella flexneri. Poster session presented at the meeting of Queenstown Research Week Computational Genomics. Queenstown, New Zealand
    [Conference Poster]Authored by: Freed, N., Silander, O.
    Hofstadler, SA., Ecker, DJ., Blyn, LB., Sampath, R., Drader, J., Jiang, Y., . . . Russell, K.(2004, March). High throughput mass spectrometry for the identification and typing of biowarfare agents and pathogens associated with emerging infectious diseases: The TIGER approach.. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY. (pp. U247 - U248). 0065-7727.
    [Conference]Authored by: Freed, N.

    Consultancy and Languages

    Consultancy

    • Dec 2017-present - Ubiquitome Bio
      Development of portable qPCR devices

    Teaching and Supervision

    Teaching Statement

    2018 and 2019

    203.340 Applied Molecular Biology (Coordinator)

    246.202 Bacteriophage Discovery and Genomics (Phage Hunt New Zealand) 
    203.203 Human Genetics
    162.760 Research Methods and Communication in the Biosciences (Postgraduate)

    2017
    203.340 Applied Molecular Biology (Coordinator)

    246.202 Bacteriophage Discovery and Genomics (Phage Hunt New Zealand) 
    122.233 Metabolic Biochemistry
    203.203 Human Genetics
    162.760 Research Methods and Communication in the Biosciences (Postgraduate)

    2016
    203.340 Applied Molecular Biology

    246.301 Special Topics in Natural Sciences (Phage Hunt New Zealand) 
    122.233 Metabolic Biochemistry 
    122.102 Biochemistry of Cells (Coordinator)
    203.203 Human Genetics
    162.760 Research Methods and Communication in the Biosciences (Postgraduate)

    2015

    246.301 Special Topics in Natural Sciences (Phage Hunt New Zealand)
    122.233 Metabolic Biochemistry
    203.203 Human Genetics

     

    Courses Coordinated

    Summary of Doctoral Supervision

    Position Current Completed
    Main Supervisor 1 0
    Co-supervisor 1 1

    Current Doctoral Supervision

    Main Supervisor of:

    • Kelly Hong - Doctor of Philosophy
      Antibiotic evolution

    Co-supervisor of:

    • Andrea Sajuthi - Doctor of Philosophy
      Bacterial competition and cooperation at the single-cell level

    Completed Doctoral Supervision

    Co-supervisor of:

    • 2016 - Daniela Quintana Rincon - Doctor of Philosophy
      Role of the ribosomal DNA repeats on chromosome segregation of Saccharomyces cerevisiae

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