Dr Julian Zaugg
Senior Bioinformatician
Data Science Collaborative Research Platform
- More than 7 years experience in bioinformatics, specialising in microbial genomics, metagenomics, phylogenetics, and, more broadly, computational biology.
- Extensive experience in processing and analysing data from various technologies, e.g. rRNA gene amplicon, Illumina, and long-read sequencing data.
- Skilled in developing bioinformatics pipelines for isolate and metagenomic data, including assembly, binning, SNP discovery, and functional profiling.
- Proficient in statistical analysis and data visualisation using R.
- Often consults on, or leads analysis for, research projects across a variety of research areas, e.g. environmental and clinical.
- Provides supervision/mentorship to HDR students.
Book Chapter
Zaugg, Julian, Gumulya, Yosephine, Gillam, Elizabeth M. J. and Bodén, Mikael (2014). Computational tools for directed evolution: a comparison of prospective and retrospective strategies. Directed evolution library creation: methods and protocols. (pp. 315-333) edited by Elizabeth M. J. Gillam, Janine N. Copp and David F. Ackerley. New York, NY, United States: Humana Press. doi: 10.1007/978-1-4939-1053-3_21
Journal Articles
Horsman, Sara, Zaugg, Julian, Meler, Erika, Mikkelsen, Deirdre, Soares Magalhães, Ricardo J. and Gibson, Justine S. (2025). Molecular epidemiological characteristics of Staphylococcus pseudintermedius, Staphylococcus coagulans, and coagulase-negative staphylococci cultured from clinical canine skin and ear samples in Queensland. Antibiotics, 14 (1) 80, 1-25. doi: 10.3390/antibiotics14010080
Prabhu, Apoorva, Zaugg, Julian, Chan, Cheong Xin, McIlroy, Simon J. and Rinke, Chris (2025). Insights Into Phylogeny, Diversity and Functional Potential of Poseidoniales Viruses. Environmental Microbiology, 27 (1) e70017, e70017-1. doi: 10.1111/1462-2920.70017
Payne, Paige E., Knobbe, Loren N., Chanton, Patricia, Zaugg, Julian, Mortazavi, Behzad and Mason, Olivia U. (2024). Uncovering novel functions of the enigmatic, abundant, and active Anaerolineae in a salt marsh ecosystem. mSystems, 10 (1), e0116224. doi: 10.1128/msystems.01162-24
Asgharzadeh Kangachar, Shahla, Logel, Dominic Y., Trofimova, Ellina, Zhu, Hannah X., Zaugg, Julian, Schembri, Mark A., Weynberg, Karen D. and Jaschke, Paul R. (2024). Discovery and characterisation of new phage targeting uropathogenic Escherichia coli. Virology, 597 110148, 110148. doi: 10.1016/j.virol.2024.110148
Howe, Kathryn L., Zaugg, Julian and Mason, Olivia U. (2024). Novel, active, and uncultured hydrocarbon-degrading microbes in the ocean. Applied and Environmental Microbiology, 90 (9), 1-22. doi: 10.1128/aem.01224-24
Bromfield, Jacoba I., Zaugg, Julian, Straw, Rodney C., Cathie, Julia, Krueger, Annika, Sinha, Debottam, Chandra, Janin, Hugenholtz, Philip and Frazer, Ian H. (2024). Characterization of the skin microbiome in normal and cutaneous squamous cell carcinoma affected cats and dogs. mSphere, 9 (4) e0055523, e0055523. doi: 10.1128/msphere.00555-23
Wilson, Liam A., Melville, Jamie N., Pedroso, Marcelo M., Krco, Stefan, Hoelzl, Robert, Zaugg, Julian, Southam, Gordon, Virdis, Bernardino, Evans, Paul, Supper, Jenna, Harmer, Jeffrey R., Tyson, Gene, Clark, Alice, Schenk, Gerhard and Bernhardt, Paul V. (2024). Kinetic, electrochemical and spectral characterization of bacterial and archaeal rusticyanins; unexpected stability issues and consequences for applications in biotechnology. Journal of Inorganic Biochemistry, 256 112539, 1-10. doi: 10.1016/j.jinorgbio.2024.112539
Prabhu, Apoorva, Tule, Sanjana, Chuvochina, Maria, Bodén, Mikael, McIlroy, Simon J., Zaugg, Julian and Rinke, Christian (2024). Machine learning and metagenomics identifies uncharacterized taxa inferred to drive biogeochemical cycles in a subtropical hypereutrophic estuary. ISME Communications, 4 (1) ycae067, ycae067. doi: 10.1093/ismeco/ycae067
Song, Young C., Holland, Sophie I., Lee, Matthew, Chen, Gao, Zaugg, Julian, Löffler, Frank E., Manefield, Michael J., Hugenholtz, Philip and Kappler, Ulrike (2023). Corrigendum: 'A comparative genome analysis of the Bacillota (Firmicutes) class Dehalobacteriia'. Microbial Genomics, 9 (8) 001092. doi: 10.1099/mgen.0.001092
Bialasiewicz, Seweryn, May, Meryta, Tozer, Sarah, Day, Rebecca, Bernard, Anne, Zaugg, Julian, Gartrell, Kyana, Alexandersen, Soren, Chamings, Anthony, Wang, Claire Y. T., Clark, Julia, Grimwood, Keith, Heney, Claire, Schlapbach, Luregn, Ware, Robert S., Speers, David, Andrews, Ross M. and Lambert, Stephen (2023). HPeV3 diversity, recombination and clinical impact across 7-years: an Australian story. The Journal of Infectious Diseases, 227 (2), 278-287. doi: 10.1093/infdis/jiac311
Foley, Gabriel, Mora, Ariane, Ross, Connie M., Bottoms, Scott, Sützl, Leander, Lamprecht, Marnie L., Zaugg, Julian, Essebier, Alexandra, Balderson, Brad, Newell, Rhys, Thomson, Raine E. S., Kobe, Bostjan, Barnard, Ross T., Guddat, Luke, Schenk, Gerhard, Carsten, Jörg, Gumulya, Yosephine, Rost, Burkhard, Haltrich, Dietmar, Sieber, Volker, Gillam, Elizabeth M. J. and Bodén, Mikael (2022). Engineering indel and substitution variants of diverse and ancient enzymes using Graphical Representation of Ancestral Sequence Predictions (GRASP). PL o S Computational Biology, 18 (10) e1010633, e1010633. doi: 10.1371/journal.pcbi.1010633
Montgomery, Kate, Williams, Timothy J., Brettle, Merryn, Berengut, Jonathan F., Ray, Angelique E. , Zhang, Eden, Zaugg, Julian, Hugenholtz, Philip and Ferrari, Belinda C. (2022). Persistence and resistance: survival mechanisms of Candidatus Dormibacterota from nutrient‐poor Antarctic soils. Environmental Microbiology, 24 (9), 4491-4491. doi: 10.1111/1462-2920.16191
Ray, Angelique E., Zaugg, Julian, Benaud, Nicole, Chelliah, Devan S., Bay, Sean, Wong, Hon Lun, Leung, Pok Man, Ji, Mukan, Terauds, Aleks, Montgomery, Kate, Greening, Chris, Cowan, Don A., Kong, Weidong, Williams, Timothy J., Hugenholtz, Philip and Ferrari, Belinda C. (2022). Atmospheric chemosynthesis is phylogenetically and geographically widespread and contributes significantly to carbon fixation throughout cold deserts. The ISME Journal, 16 (11), 1-14. doi: 10.1038/s41396-022-01298-5
Liu, Yongqin, Ji, Mukan, Yu, Tao, Zaugg, Julian, Anesio, Alexandre M., Zhang, Zhihao, Hu, Songnian, Hugenholtz, Philip, Liu, Keshao, Liu, Pengfei, Chen, Yuying, Luo, Yingfeng and Yao, Tandong (2022). A genome and gene catalog of glacier microbiomes. Nature Biotechnology, 40 (9), 1341-1348. doi: 10.1038/s41587-022-01367-2
Krueger, Annika, Mohamed, Ahmed, Kolka, Cathryn M., Stoll, Thomas, Zaugg, Julian, Linedale, Richard, Morrison, Mark, Soyer, H. Peter, Hugenholtz, Philip, Frazer, Ian H. and Hill, Michelle M. (2022). Skin cancer-associated S. aureus strains can induce DNA damage in human keratinocytes by downregulating DNA repair and promoting oxidative stress. Cancers, 14 (9) 2143, 2143. doi: 10.3390/cancers14092143
Torquati, L., Gajanand, T., Cox, E. R., Willis, C. R. G., Zaugg, J., Keating, S. E. and Coombes, J. S. (2022). Effects of exercise intensity on gut microbiome composition and function in people with type 2 diabetes. European Journal of Sport Science, 23 (4), 1-12. doi: 10.1080/17461391.2022.2035436
Coleman, Andrea, Håkansson, Alexander, Grahn Håkansson, Eva, Cottrell, Kyra, Bialasiewicz, Seweryn, Zaugg, Julian and Cervin, Anders (2022). In vitro Inhibition of respiratory pathogens by lactobacillus and alpha haemolytic streptococci from Aboriginal and Torres Strait Islander children. Journal of Applied Microbiology, 132 (3), 2368-2378. doi: 10.1111/jam.15320
Krueger, Annika, Zaugg, Julian, Lachner, Nancy, Bialasiewicz, Seweryn, Lin, Lynlee L., Gabizon, Sharon, Sobarun, Priyamvada, Morrison, Mark, Soyer, H. Peter, Hugenholtz, Philip and Frazer, Ian H. (2022). Changes in the skin microbiome associated with squamous cell carcinoma in transplant recipients. ISME Communications, 2 (1) 13, 13. doi: 10.1038/s43705-022-00095-7
Krueger, Annika, Zaugg, Julian, Chisholm, Sarah, Linedale, Richard, Lachner, Nancy, Teoh, Siok Min, Tuong, Zewen K., Lukowski, Samuel W., Morrison, Mark, Soyer, H. Peter, Hugenholtz, Philip, Hill, Michelle M. and Frazer, Ian H. (2022). Secreted toxins from Staphylococcus aureus strains isolated from keratinocyte skin cancers mediate pro-tumorigenic inflammatory responses in the skin. Frontiers in Microbiology, 12 789042, 789042. doi: 10.3389/fmicb.2021.789042
Coleman, Andrea, Zaugg, Julian, Wood, Amanda, Cottrell, Kyra, Håkansson, Eva Grahn, Adams, Jasmyn, Brown, Matthew, Cervin, Anders and Bialasiewicz, Seweryn (2021). Upper respiratory tract microbiome of Australian Aboriginal and Torres Strait Islander children in ear and nose health and disease. Microbiology Spectrum, 9 (2) e00367-21, e0036721. doi: 10.1128/spectrum.00367-21
Montgomery, Kate, Williams, Timothy J., Brettle, Merryn, Berengut, Jonathan F., Zhang, Eden, Zaugg, Julian, Hugenholtz, Philip and Ferrari, Belinda C. (2021). Persistence and resistance: survival mechanisms of Candidatus Dormibacterota from nutrient-poor Antarctic soils. Environmental Microbiology, 23 (8), 4276-4294. doi: 10.1111/1462-2920.15610
Ji, Mukan, Williams, Timothy J., Montgomery, Kate, Wong, Hon Lun, Zaugg, Julian, Berengut, Jonathan F., Bissett, Andrew, Chuvochina, Maria, Hugenholtz, Philip and Ferrari, Belinda C. (2021). Candidatus Eremiobacterota, a metabolically and phylogenetically diverse terrestrial phylum with acid-tolerant adaptations. The ISME Journal, 15 (9), 2692-2707. doi: 10.1038/s41396-021-00944-8
Ahmed, Warish, Tscharke, Ben, Bertsch, Paul M., Bibby, Kyle, Bivins, Aaron, Choi, Phil, Clarke, Leah, Dwyer, Jason, Edson, Janette, Nguyen, Thi Minh Hong, O'Brien, Jake W., Simpson, Stuart L., Sherman, Paul, Thomas, Kevin V., Verhagen, Rory, Zaugg, Julian and Mueller, Jochen F. (2021). SARS-CoV-2 RNA monitoring in wastewater as a potential early warning system for COVID-19 transmission in the community: a temporal case study. Science of The Total Environment, 761 144216, 144216. doi: 10.1016/j.scitotenv.2020.144216
Mason, Olivia U., Chanton, Patricia, Knobbe, Loren N., Zaugg, Julian and Mortazavi, Behzad (2021). New insights into the influence of plant and microbial diversity on denitrification rates in a salt marsh. Wetlands, 41 (2) 33, 1-14. doi: 10.1007/s13157-021-01423-8
Coleman, Andrea, Bialasiewicz, Seweryn, Marsh, Robyn L., Grahn Håkansson, Eva, Cottrell, Kyra, Wood, Amanda, Jayasundara, Nadeesha, Ware, Robert S., Zaugg, Julian, Sidjabat, Hanna E., Adams, Jasmyn, Ferguson, Josephine, Brown, Matthew, Roos, Kristian and Cervin, Anders (2021). Upper respiratory microbiota in relation to ear and nose health among Australian Aboriginal and Torres Strait Islander children. Journal of the Pediatric Infectious Diseases Society, 10 (4), 468-476. doi: 10.1093/jpids/piaa141
Ahmed, Warish, Angel, Nicola, Edson, Janette, Bibby, Kyle, Bivins, Aaron, O'Brien, Jake W., Choi, Phil M., Kitajima, Masaaki, Simpson, Stuart L., Li, Jiaying, Tscharke, Ben, Verhagen, Rory, Smith, Wendy J.M., Zaugg, Julian, Dierens, Leanne, Hugenholtz, Philip, Thomas, Kevin V. and Mueller, Jochen F. (2020). First confirmed detection of SARS-CoV-2 in untreated wastewater in Australia: a proof of concept for the wastewater surveillance of COVID-19 in the community. Science of the Total Environment, 728 138764, 138764. doi: 10.1016/j.scitotenv.2020.138764
Ahmed, Warish, Bertsch, Paul M., Angel, Nicola, Bibby, Kyle, Bivins, Aaron, Dierens, Leanne, Edson, Janette, Ehret, John, Gyawali, Pradip, Hamilton, Kerry, Hosegood, Ian, Hugenholtz, Philip, Jiang, Guangming, Kitajima, Masaaki, Sichani, Homa T., Shi, Jiahua, Shimko, Katja M., Simpson, Stuart L., Smith, Wendy J. M., Symonds, Erin M., Thomas, Kevin V., Verhagen, Rory, Zaugg, Julian and Mueller, Jochen F (2020). Detection of SARS-CoV-2 RNA in commercial passenger aircraft and cruise ship wastewater: a surveillance tool for assessing the presence of COVID-19 infected travelers. Journal of Travel Medicine, 27 (5) taaa116, 1-11. doi: 10.1093/jtm/taaa116
Gagen, Emma J., Zaugg, Julian, Tyson, Gene W. and Southam, Gordon (2019). Goethite Reduction by a Neutrophilic Member of the Alphaproteobacterial Genus Telmatospirillum. Frontiers in Microbiology, 10 2938, 2938. doi: 10.3389/fmicb.2019.02938
Zaugg, Julian, Gumulya, Yosephine, Bodén, Mikael, Mark, Alan E and Malde, Alpeshkumar K (2018). Effect of Binding on Enantioselectivity of Epoxide Hydrolase. Journal of Chemical Information and Modeling, 58 (3), 630-640. doi: 10.1021/acs.jcim.7b00353
Zaugg, Julian, Gumulya, Yosephine, Malde, Alpeshkumar K and Bodén, Mikael (2017). Learning epistatic interactions from sequence-activity data to predict enantioselectivity. Journal of computer-aided molecular design, 31 (12), 1085-1096. doi: 10.1007/s10822-017-0090-x
Bernhofer, Michael, Goldberg, Tatyana, Wolf, Silvana, Ahmed, Mohamed, Zaugg, Julian, Boden, Mikael and Rost, Burkhard (2017). NLSdb-major update for database of nuclear localization signals and nuclear export signals. Nucleic Acids Research, 46 (D1), D503-D508. doi: 10.1093/nar/gkx1021
Conference Papers
Horsman, Sara, Zaugg, Julian, Mikkelsen, Deirdre, Soares Magalhaes, Ricardo J., Meler, Erika and Gibson, Justine S. (2024). Molecular epidemiological characteristics of Staphylococcus species cultured from clinical canine skin and ear samples in Queensland. Antimicrobials 2024 Annual Scientific Meeting, Sydney, NSW Australia, 15-17 February 2024.
Shah, Ayesha, Kang, Seungha, Tyson, Gene, Zaugg, Julian, Hugenholtz, Phil, Morrison, Mark and Holtmann, Gerald J. (2020). Variations of the mucosa associated microbiota along the human gastrointestinal tract in health and inflammatory bowel disease. Crohn's and Colitis Congress, Austin, TX, United States, 23-25 January 2020. Philadelphia, PA United States: Elsevier. doi: 10.1016/s0016-5085(20)32052-7
Thesis
Zaugg, Julian (2019). Computational modelling of enzymes: predicting and understanding the selectivity of an epoxide hydrolase. PhD Thesis, School of Chemistry and Molecular Biosciences, The University of Queensland. doi: 10.14264/uql.2019.300