Dr Waardenberg is a Research Fellow at the Australian Institute of Tropical Health and Medicine (AITHM) and member of the biodiscovery theme of the Centre for Molecular Therapeutics, James Cook University. His research interests are focused around the combination of high-throughput technologies (such as DNA/RNA sequencing or mass-spectrometry) and computational methods for understanding mechanisms of disease, with the view to identifying suitable diagnostic and/or treatment approaches. At AITHM, Dr Waardenberg is collaborating on projects that aim to define biomarkers from human clinical trials for malaria and other infectious diseases that can be used to guide future vaccine development.

Prior to joining AITHM, Dr Waardenberg completed his PhD in Systems Biology (2012) at CSIRO (Livestock Genomics) and Griffith University (Eskitis Institute, QLD, Australia), where he was trained in both molecular biology and bioinformatics. During his PhD, he developed methods for integrating high-throughput gene expression data and protein spatial location related to muscle development and hypertrophy. A key outcome was the discovery of an interaction between PI3K and the muscle contractile apparatus, in particular a role with Melusin (a muscle mechano-sensor). Dr Waardenberg was also involved in the Bovine Genome Consortia, contributing to the assembly annotation of the bovine genome (published in Science) and was a team recipient of the CSIRO Chairman’s Medal in 2010 for contributions to this international effort. He has since held research positions at the Victor Chang Cardiac Research Institute (Sydney), Children’s Medical Research Institute (Sydney) and European Molecular Biology Laboratory (Germany) where he has focused on the implementation and development of systems biology methods for 1) understanding genome-wide effects of transcription factor mutations relevant to congenital heart disease and 2) signalling pathways of neurotransmission utilising high-throughput phosphoproteomic mass-spectrometry. During this time Dr Waardenberg developed R/BioConductor statistical software packages implementing algorithms for prediction of kinase activity from phosphoproteomics data (KinSwingR), comparison of gene ontology pathways (compGO) and automation of RNA-seq analysis with different algorithms (consensusDE).

Dr Waardenberg has contributed significantly to the development of a bioinformatics and computational biology community in Australia. As co-founder of the Australian Bioinformatics and Computational Biology Society (ABACBS) Inc., he was tasked with incorporating and meeting constitutional requirements for ABABCS, later holding positions of Vice-President (2014-2017) and Secretary (2018). Dr Waardenberg has consulted to numerous organisations on the needs of the emerging field of bioinformatics.

Teaching

• BC5203: Advanced Bioinformatics (Level 5; TSV)

Interests

Research

• Host-pathogen interaction of infectious diseases. Neuroscience. Bioinformatics. Machine Learning. Network Biology.

Experience

• 2017 to 2018 - Research Fellow, European Molecular Biology Laboratory (Germany)
• 2015 to 2017 - Conjoint Lecturer, University of Sydney (Sydney, Australia)
• 2015 to 2017 - Research Fellow, Children's Medical Research Insitute (Sydney, Australia)
• 2012 to 2015 - Research Fellow, Victor Chang Cardiac Research Insitute (Sydney, Australia)

Research Disciplines

• Biochemistry and Cell Biology (0601)
• Immunology (1107)
• Computer Software (0803)

Socio-Economic Objectives

• Expanding Knowledge (9701)
• Clinical Health (9201)
• Computer Software and Services (8902)

Awards

• 2010 - CSIRO Chairman's Medal

These are the most recent publications associated with this author. To see a detailed profile of all publications stored at JCU, visit ResearchOnline@JCU. Hover over Altmetrics badges to see social impact.

Journal Articles

• Browne D, Brady J, Van Waardenberg A, Loiseau C and Doolan D (2020) An analytically and diagnostically sensitive RNA extraction and RT-qPCR protocol for peripheral blood mononuclear cells. Frontiers in Immunology, 11, Article: 402, DOI:10.3389/fimmu.2020.00402.
• Muruganandah V, Sathkumara H, Pai S, Rush C, Brosch R, Waardenberg A and Kupz A (2020) A systematic approach to simultaneously evaluate safety, immunogenicity, and efficacy of novel tuberculosis vaccination strategies. Science Advances, 6 (10), DOI:10.1126/sciadv.aaz1767.
• Engholm-Keller K, Waardenberg A, Müller J, Wark J, Fernando R, Arthur J, Robinson P, Dietrich D, Schoch S, Graham M, and (2019) The temporal profile of activity-dependent presynaptic phospho-signalling reveals long-lasting patterns of poststimulus regulation. PLoS Biology, 17 (3), Article: e3000170, DOI:10.1371/journal.pbio.3000170.
• Waardenberg A and Field M (2019) consensusDE: an R package for assessing consensus of multiple RNA-seq algorithms with RUV correction. PeerJ, 7, Article: e8206, pp. 1-16, DOI:10.7717/peerj.8206.
• Bottje W, Kong B, Reverter A, Waardenberg A, Lassiter K and Hudson N (2017) Progesterone signalling in broiler skeletal muscle is associated with divergent feed efficiency. BMC Systems Biology, 11, Article: 29, DOI:10.1186/s12918-017-0396-2.
• Ramialison M, Waardenberg A, Schonrock N, Doan T, de Jong D, Bouveret R and Harvey R (2017) Analysis of steric effects in DamID profiling of transcription factor target genes. Genomics, 109 (2), pp. 75-82, DOI:10.1016/j.ygeno.2017.01.006.
• Waardenberg A, Homan B, Mohamed S, Harvey R and Bouveret R (2016) Prediction and validation of protein–protein interactors from genome-wide DNA-binding data using a knowledge-based machine-learning approach. Open Biology, 6, Article: 160183, DOI:10.1098/rsob.160183.
• Bouveret R, Waardenberg A, Schonrock N, Ramialison M, Doan T, de Jong D, Bondue A, Kaur G, Mohamed S, Fonoudi H, Chen C, Wouters M, Bhattacharya S, Plachta N, Dunwoodie S, Chapman G, Blanpain C and Harvey R (2015) NKX2-5 mutations causative for congenital heart disease retain functionality and are directed to hundreds of targets. eLife, 4, Article: e06942, DOI:10.7554/eLife.06942.
• Cannon L, Yu Z, Marciniec T, Waardenberg A, Iismaa S, Nikolova-Krstevski V, Neist E, Ohanian M, Qiu M, Rainer S, Harvey R, Feneley M, Graham R and Fatkin D (2015) Irreversible triggers for hypertrophic cardiomyopathy are established in the early postnatal period. Journal of the American College of Cardiology, 65 (6), pp. 560-569, DOI:10.1016/j.jacc.2014.10.069.
• Kozlov S, Waardenberg A, Engholm-Keller K, Arthur J, Graham M and Lavin M (2015) Reactive oxygen species (ROS)-activated ATM-dependent phosphorylation of cytoplasmic substrates identified by large-scale phosphoproteomics screen. Molecular and Cellular Proteomics, 15 (3), pp. 1032-1047, DOI:10.1074/mcp.M115.055723.
• Waardenberg A, Bassett S, Bouveret R and Harvey R (2015) CompGO: an R package for comparing and visualizing gene ontology enrichment differences between DNA binding experiments. BMC Bioinformatics, 16, Article: 275, DOI:10.1186/s12859-015-0701-2.
• Sun W, Hudson N, Reverter A, Waardenberg A, Tellam R, Vuocolo T, Byrne K and Dalrymple B (2012) An always correlated gene expression landscape for ovine skeletal muscle, lessons learnt from comparison with an “equivalent” bovine landscape. BMC Research Notes, 5, Article: 632, DOI:10.1186/1756-0500-5-632.

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These Higher Degree Research projects are either current or by students who have completed their studies within the past 5 years at JCU. Linked titles show theses available within ResearchOnline@JCU.

Completed

• Molecular profiling of immunity to infectious diseases using human challenge models (2020, PhD , Secondary Advisor)

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