Doctor Mark Temple

Doctor Mark Temple

Senior Lecturer,
Life Sciences

Biography

Dr Mark Temple is a Senior Lecturer in Molecular Biology in the School of Science at the Western SydneyUniversity (WSU).

During his PhD Mark studied chromatin structure (nucleosome positioning and transcription factor binding) during gene expression and cell cycle progression. In addition he studied the interaction of anti-cancer drugs (including cisplatin and some novel analogues) with DNA in human cells. As a post-doctoral research fellow with Profressor Ian Dawes in the School of Biotechnology and Biomolecular Sciences at University of New South Wales (UNSW), Mark studied ageing and oxidative stress using bakers yeast as a model organism.

During the past few years Mark has become increasingly interested in cell biology, functional genomics and the development of bioinformatics tools for genome-wide dataset analysis. This had led Mark to explore the use of audio for analyses of biological sequence data and publication of the http://dnasonification.org/ website. During the COVID-19 lockdown Mark explored the sonification of the coronavirus genome and he produced the https://coronavirus.dnasonification.org/ website. 

When I started using audio for data analysis, I had no thought towards its use in an artistic space. I was focused solely on how the audio display could be used to help scientists understand how DNA sequences function. In many ways the original science work was intentionally robotic sounding and not particularly musical. I was quite anxious because I thought that talking about an artistic aspect to my work would distract science academics and journal reviewers forn the scientific outcomes. Over the years I became convinced that through that use of artistic considerations, such as the introduction of harmony by layering more audio data would improve the representation of the data. I then had to think like a musician rather than a scientist to tame the melody the DNA sequence made so that is was not harsh and difficult to listen to. This was the first time I thought as both a scientist and artist to make something that was greater than the sum of it's parts. To my surprise the audio displays worked as a science tool and as a generative music tool.

I have integrated my research with creative outreach and held two successful events at The Joan Sutherland Theatre in Penrith. Mark produced the "This Sounds Like Science" event at City Recital Hall with Inspiring Australia. At National Art School he produced "Science Meets Art: An evening of Sonification which was featured on ABC TV ArtWorks. In 2023 he organised the Myrtle Rust: Science meets Art Exhibition at the Australian Botanical Gardens. The exhibition featured work by Aboriginal Artists, sonification of DNA sequences, musification of critically endangered Australian Native plants and a Science Symposium 

This information has been contributed by Doctor Temple.

Qualifications

  • PhD University of New South Wales

Professional Memberships

  • Inspiring Australia NSW Executive Committee (2023 - 2024)

Awards

  • Engagement Excellence Award, SoSc, WSU 2020-01-10
  • Research Impact Award, SoSc, WSU 2019-01-10
  • Sonification, Music and Digital Art Grant, Inspiring Australia 2022-05-10

Interests

  • Bioinformatics
  • Computer Science
  • Molecular Biology
  • Music Collaboration
  • STEM Education

Organisational Unit (School / Division)

  • Life Sciences

Committees

  • Learning and Teaching Technologies Advisory Group
  • Central Provost Committee
  • Academic Program Advisor (2020)
  • Director of Academic Program (2021 - 2022)

Contact

Email: M.Temple@westernsydney.edu.au
Phone: (02) 9685 9906
Mobile:
Location: EHA.1.05
Parramatta

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Teaching

Previous Teaching Areas

  • 301406 Applied Bioinformatics, 2023
  • NATS3034 Molecular Medicine, 2023

Publications

Chapters in Books

  • Temple, M., Gelling, C., Kornfeld, G. and Dawes, I. (2013), 'Microarrays and gene regulation networks in yeast', Madame Curie Bioscience Database, Landes Bioscience 9781498713733.

Journal Articles

  • Temple, M. (2020), 'Real-time audio and visual display of the Coronavirus genome', BMC Bioinformatics, vol 21, no 1 .
  • Temple, M. (2018), 'A website to identify shared genes in Saccharomyces cerevisiae homozygous deletion library screens', BMC Bioinformatics, vol 19, no 1 .
  • Johnson, B., Burgess, M., Murray, V., Aldrich-Wright, J. and Temple, M. (2018), 'The interactions of novel mononuclear platinum-based complexes with DNA', BMC Cancer, vol 18 .
  • Temple, M. (2017), 'An auditory display tool for DNA sequence analysis', BMC Bioinformatics, vol 18, no 221 .
  • Johnson, B., Murray, V. and Temple, M. (2016), 'Characterisation of the DNA sequence specificity, cellular toxicity and cross-linking properties of novel bispyridine-based dinuclear platinum complexes', BMC Cancer, vol 16, no 1 .
  • Temple, M. (2015), 'Twenty years later, the evolution of origami DNA', Trends in Biochemical Sciences, vol 40, no 6 , pp 293 - 295.
  • Akand, E., Bain, M. and Temple, M. (2010), 'Learning with gene ontology annotation using feature selection and construction', Applied Artificial Intelligence, vol 24, no 40575 , pp 5 - 38.
  • Fong, C., Temple, M., Alic, N., Chiu, J., Durchdewald, M., Thorpe, G., Higgins, V. and Dawes, I. (2008), 'Oxidant-induced cell-cycle delay in Saccaromyces cerevisiae : the involvement of the SWI6 transcription factor', FEMS Yeast Research, vol 8, no 3 , pp 386 - 399.
  • Drakulic, T., Temple, M., Guido, R., Jarolim, S., Breitenbach, M., Attfield, P. and Dawes, I. (2005), 'Involvement of oxidative stress response genes in redox homeostasis, the level of reactive oxygen species, and ageing in Saccharomyces cerevisiae', FEMS Yeast Extract, vol 5, no 12 , pp 1215 - 1228.
  • Temple, M. and Murray, V. (2005), 'Footprinting the 'essential regulatory region' of the retinoblastoma gene promoter in intact human cells', International Journal of Biochemistry and Cell Biology, vol 37, no 3 , pp 665 - 678.
  • Temple, M., Perrone, G. and Dawes, I. (2005), 'Complex cellular responses to reactive oxygen species', Trends in Cell Biology, vol 15, no 6 , pp 319 - 326.
  • Alic, N., Felder, T., Temple, M., Gloeckner, C., Higgins, V. and Dawes, I. (2004), 'Genome-wide transcriptional responses to a lipid hydroperoxide: adaptation occurs without induction of oxidant defenses', Free Radical Biology & Medicine, vol 37, no 1 , pp 23 - 35.
  • Temple, M., Freebody, J. and Murray, V. (2004), 'Genomic and phylogenetic footprinting at the epsilon-globin silencer region in intact human cells', Biochimica et Biophysica Acta - Gene Structure and Expression, vol 1678, no 2-3 , pp 126 - 134.

Conference Papers

  • Akand, E., Bain, M. and Temple, M. (2010), 'A visual analytics approach to augmenting formal concepts with relational background knowledge in a biological domain', Australasian Ontology Workshop, Adelaide, S.A..
  • Akand, E., Bain, M. and Temple, M. (2010), 'Learning responsive cellular networks by integrating genomics and proteomics data', ILP (Conference), Belgium.
  • Akand, E., Bain, M. and Temple, M. (2007), 'Learning from ontological annotation : an application of formal concept analysis to feature construction in the gene ontology', Australasian Ontology Workshop, Gold Coast, Qld..
  • Ahsan, N., Bain, M., Potter, J., Gaeta, B., Temple, M. and Dawes, I. (2006), 'Learning causal networks from microarray data', Workshop on Intelligent Systems for Bioinformatics, Hobart, Tas..
  • Ratnakumar, A., Dawes, I. and Temple, M. (2005), 'Web-based tools for the visualisation of over-represented components of the genetic regulatory network in microarray datasets', Australian Undergraduate Students' Computing Conference, Australian National University, Canberra.

Exhibitions

  • 2023, 'Sonification of Critically Endangered Native Plants and Generative Music Made from Myrtle Rust Genomic Data'
  • 2022, 'Performance at Science Meets Art, an Evening of Sonification and Music'
  • 2021, 'This Sounds Like Science: Sounds of Coronavirus'
  • 2021, 'Molecular Music: The Sounds of Coronavirus'
  • 2021, 'Composing with DNA Sequences for Science Exhibition at Lichfield Cathedral'
  • 2018, 'The Sound of Genes'
  • 2017, 'Code: Sci-Fi Meets Reality'

Other Publications

  • 2022, 'CoronaCode Music', Recorded Work
  • 2020, 'International Strange Music Day: Coronacode Music', Recorded Work

DNA Sonification is a technique that is growing in popularity and it is gaining more credibility as a new technique to supplement visual DNA analyses. DNA Sonification refers to the use of an auditory display to convey the information content of DNA sequence data. Biological sequences contain vast amounts of data and computer algorithms play an important role in processing data for inspection. The application of sonification techniques to generate an auditory display may provide a synergistic tool to hear the data during inspection. These auditory displays use musical notes to represent scientific data.

In my approach to sonification was made with the benefit of hindsight and greater computer resources than my predecessors. I took the approach to sonify DNA with many algorithms - each of increasing complexity from sounding mono-nucleotided (bases) leading to the sonification of codons in multiple reading frames (the most complex approach). I also made use of start and stop codons to identify the beginning or end of a potential gene within a sequence. I also identify a gene sequence within a wider region of DNA using these start codons. Lastly I thought it was important to sonify three frame simultaneously and look for the open reading frame (the one that corresponds to the protein sequence). I also chose to sonify non-coding DNA sequences and identify audio differences between these and genes gene sequences. 

Given the incorporation of musical notes in the displays raises the possibility that these may be considered algorithmic music. When I first published the DNA audio in 2017 it generated quite a lot of interest in social media and in science blogs. Many people's first reaction on social media was to comment that I was making music from DNA even though I was was actually making science audio. I have picked up on this idea to actually make music out of the science audio. Music and rhythms a have powerful influence on the human mind, they enable us to envisage concepts, feel wonder, and relate to topics far removed from our own lives. The music provides a connection between the science audio data and the creative musician to create something greater than the sum of their parts.  It provides a connection from our research work to the lives of diverse groups of people, sparking peoples interest or answering common questions, "Ah so that’s what it’s all about!"  Using my research to create art provides an interesting story and a musical narrative, this makes it memorable, relatable, and infectious. 

I currently run research projects concerned with coding for the analyses of bioinformatics data and website development. 

This information has been contributed by Doctor Temple.

Current Projects

Title: Indigenous artistic and linguistic interpretation of myrtle rust and it's impacts for community awareness
Funder:
  • Australian Plant Biosecurity Science Foundation (APBSF Ltd)
Western Researchers: Mark Temple and Michelle Moffitt
Years: 2022-02-01 - 2024-03-31
ID: P00027736

Previous Projects

Title: Discovery and prediction of transcriptional regulatory networks important in the cellular responses to oxidative stress.
Funder:
  • University of Western Sydney
Western Researchers: Mark Temple
Years: 2008-09-24 - 2010-03-31
ID: P00016348

Supervision

Doctor Temple is available to be a principal supervisor for doctoral projects

Current Supervision

Thesis Title: The Formation of DNA Adducts Caused by Cisplatin and other Closely Related Platinum-Based Drugs
Field of Research:
Thesis Title: Geonome-wide Functional Ananlysis of Saccharomyces cerevisiae after peroxynitrite exposure
Field of Research:
Thesis Title: Characterisation of the Formation and Biological Impacts of DNA-Addicts caused by the Anti-Cancer Drug Cisplatin and other Clinically Important Platinum-Based Drugs
Field of Research:

Previous Supervision

Thesis Title: Analysis of High Dimensionality Yeast Gene Expression Data using Data Mining
Field of Research: Computer Science
Thesis Title: Characterisation of the Formation and Biological Impacts of DNA-Addicts caused by the Anti-Cancer Drug Cisplatin and other Clinically Important Platinum-Based Drugs
Field of Research:
Thesis Title: Characterisation of the interactions and biological impacts of cisplatin analogues and metallo-drug complexes with DNA
Field of Research: Biological Sciences, N.e.c.
Thesis Title: Geonome-wide Functional Ananlysis of Saccharomyces cerevisiae after peroxynitrite exposure
Field of Research:
Thesis Title: The Formation of DNA Adducts Caused by Cisplatin and other Closely Related Platinum-Based Drugs
Field of Research:
Thesis Title: The Formation of DNA Adducts Caused by Cisplatin and other Closely Related Platinum-Based Drugs
Field of Research: Biological Sciences, N.e.c.; Chemical Sciences, N.e.c.
Thesis Title: Analysis of High Dimensionality Yeast Gene Expression Data using Data Mining
Field of Research: Computer Science
Thesis Title: Characterisation of the interactions and biological impacts of cisplatin analogues and metallo-drug complexes with DNA
Field of Research: Biological Sciences, N.e.c.
Thesis Title: The Formation of DNA Adducts Caused by Cisplatin and other Closely Related Platinum-Based Drugs
Field of Research: Biological Sciences, N.e.c.; Other Natural And Physical Sciences; Chemical Sciences, N.e.c.

Media

Title: 2SER Radio
Description: The Sound of Science
Title: ABC TV ArtWorks
Description: Episode 28, COVID sonification
Title: BMC Series blog
Description: Sounding out the properties of DNA
Title: BMC Series blog
Description: Can science be musical?
Title: CoronaCode Music
Description: Album (Science Rock)
Title: Forbes
Description: Scientists Are Making Music
Title: IFLscience
Description: Making Music From The Genome Of SARS-CoV-2
Title: Inspiring NSW
Description: Making music from science data
Title: NewScientist
Description: The Sound of Coronavirus (Podcast)
Title: The Conversation
Description: A viral hit?
Title: The Conversation
Description: What does DNA sound like? Using music to unlock the secrets of genetic code
Title: The New York Times
Description: Content for Humans About the Content of Humans
Title: The Wire
Description: Musical Code to COVID19
Title: Wordpress Site
Description: The Art and Science of Myrtle Rust
Title: YouTube Playlist (12 videos)
Description: The Art and Science of Myrtle Rust
Title: YouTube Video
Description: Sonification of the Human Mitochondrial Genome
Title: ABC The Science Show
Description: Coronavirus becomes music
Title: Los Angeles Times
Description: The sounds of science
Title: National Public Radio
Description: COVID's genetic code was loaded into a computer and interpreted as music
Title: Nature Index
Description: The sequence of coronavirus makes surprisingly lovely music
Title: Smithsonian Magazine
Description: Why Scientists Are Turning Molecules Into Music

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