Dr Nikitas Koussis

Dr Nikitas Koussis

Postdoctoral Researcher

School of Medicine and Public Health

Career Summary

Biography

Dr Nikitas Koussis is a dynamic early-career researcher (ECR) based at the Mark Hughes Foundation Centre for Brain Cancer Research, University of Newcastle, Australia. I am passionate about harnessing advanced machine learning and computational imaging to transform our understanding of brain tumours and drive personalised treatment strategies.
As a proud Gamilaraay man, I am deeply committed to embedding Indigenous Data and Indigenous Knowledge into digital health and AI. Trust and transparency in the benefits that digital health can provide are paramount to real-world translation and robust improvement of clinical outcomes.
Research Journey
I began my research career at QIMR Berghofer, where I worked as a Research Assistant recruiting and scanning participants for epilepsy and aging studies. Witnessing the profound impact of neurological disorders and the limitations of conventional imaging ignited my commitment to developing novel computational tools that better characterise and predict disease progression.
My PhD in Psychology (2024) focused on multi-modal computational and imaging approaches to schizophrenia, equipping me with expertise in data integration, statistical modeling, and high-dimensional image analysis. Building on this foundation, I transitioned to brain cancer research, where I now lead projects to predict treatment response and molecular markers from imaging data.
Indigenous Research
To ensure cultural safety and data sovereignty in medical AI, I established the Indigenous Digital Health Advisory Committee at the University of Newcastle. This committee—comprised of Elders, community leaders, and digital health experts—meets regularly to advise on best practices, develop policies around Indigenous Cultural and Intellectual Property (ICIP), and embed data sovereignty principles into every stage of algorithm and product development.
High-Impact Research
  • $500K Partnership Lead: Steering a collaboration between Hunter Medical Research Institute and the Mark Hughes Foundation Centre for Brain Cancer Research to advance preoperative imaging and machine-learning applications aimed at improving survival and care outcomes.
  • Open-Source Pipeline Development: Designing automated tools for detecting tumour hypoxia and micro-haemorrhages by integrating deep learning with clinically acquired imaging and genetic markers.
Visionary Leadership & Collaboration
I thrive in multidisciplinary teams, working alongside radiologists, oncologists, behavioural scientists, educators, and data scientists. My leadership philosophy blends rigorous computational thinking with deep empathy for patients’ journeys—always striving to translate algorithmic advances into clinically trusted bedside tools.
Global Partnerships
I maintain active collaborations with the Walter and Eliza Hall Institute (WEHI) (Melbourne), The Kids Research Institute (Perth), and with leading universities in the USA, co-designing research studies and data-sharing initiatives to validate our predictive models across diverse populations.
My mission is to break through the 30-year stagnation in brain cancer survival rates by equipping researchers and clinicians with predictive, personalised models of tumour behaviour—because every patient deserves treatment that’s as unique as they are.

Qualifications

  • Doctor of Philosophy, University of Newcastle
  • Bachelor of Science, Queens University

Keywords

  • Bayesian Modelling
  • Computational Modelling
  • Imaging
  • Machine learning
  • Neuroscience
  • Software development
  • fMRI

Languages

  • English (Mother)
  • Greek (Working)

Fields of Research

Code Description Percentage
461103 Deep learning 30
461201 Automated software engineering 20
400304 Biomedical imaging 30
321102 Cancer diagnosis 20

Professional Experience

UON Appointment

Title Organisation / Department
Postdoctoral Researcher University of Newcastle
School of Medicine and Public Health
Australia

Professional appointment

Dates Title Organisation / Department
21/3/2024 - 31/12/2024 Research Assistant

  • Development of machine learning and advanced modelling algorithms to understanding the mechanisms of brain cancer progression
  • Advise on internal policy and SOP for high-performance computing and data linkage across research programs

College of Health, Medicine & Wellbeing - The University of Newcastle
Australia
20/1/2020 - 30/4/2024 Data Analyst

  • Multimodal data processing and analysis on several projects, including healthy and clinical data. My role was processing and analysing structural, diffusion and functional MRI and phenotypic data, much of which has been published in high-impact clinical and neuroscience journals.
  • Developing and integrating data-solutions with pre-existing and in-house toolboxes for novel and robust data processing and analysis.
  • Developing and applying sophisticated statistical and modelling techniques including machine learning, statistical inference, and computational models of psychosis, Alzheimer’s dementia, multiple sclerosis, and healthy brain function.

College of Engineering, Science and Environment (CESE), University of Newcastle
Australia
1/10/2018 - 31/12/2019 Research Assistant

  • Employed under an AQIP grant in partnership with Mater Hospital and Queensland University of Technology. My role was using mathematical modelling in combination with high angular resolution diffusion imaging to determine structural networks in SEEG patients with refractory epilepsy.
  • Developed a paradigm in Python for neurofeedback for use in a pilot study looking at the phenomenon of non-responders to neurofeedback treatment, using healthy subjects.

Queensland Institute of Medical Research
Australia

Invitations

Speaker

Year Title / Rationale
2024 Organization for Human Brain Mapping
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Publications

For publications that are currently unpublished or in-press, details are shown in italics.


Conference (7 outputs)

Year Citation Altmetrics Link
2023 Burgher B, Koussis N, Whybird G, Scott J, Cocchi L, Breakspear M, 'Sub-optimal modulation of gain by the cognitive control system in young adults with early psychosis', JOURNAL OF COMPUTATIONAL NEUROSCIENCE, 51, S26-S27 (2023)
Co-authors Michael Breakspear
2023 Koussis N, Burgher B, Jeganathan J, Scott J, Cocchi L, Breakspear M, 'Cognitive control system gates insula subregion processing of affective stimuli in early psychosis', JOURNAL OF COMPUTATIONAL NEUROSCIENCE, 51, S28-S28 (2023)
Co-authors Michael Breakspear
2023 Al-iedani O, Alshehri A, Koussis N, Khormi I, Lea S, Lea R, Ramadan S, Lechner-Scott J, 'Diffusion metrics changes of the cortico-thalamic-striatal tracts correlate with fatigue and disability in people with MS', MULTIPLE SCLEROSIS JOURNAL, 29, 278-278 (2023)
Co-authors Oun Aliedani, Saadallah Ramadan, Jeannette Lechnerscott
2023 Alshehri A, Al-iedani O, Koussis N, Khormi I, Lea R, Ramadan S, Lechner-Scott J, 'Longitudinal diffusion metrics stability in Australian MS cohort treated with Injectables, Fingolimod and Dimethyl Fumarate:An analysis of treatment effects', MULTIPLE SCLEROSIS JOURNAL, 29, 862-863 (2023)
Co-authors Jeannette Lechnerscott, Oun Aliedani, Saadallah Ramadan
2022 Alshehri A, Al-Iedani O, Koussis N, Khormi I, Lea R, Lechner-Scott J, Ramadan S, 'Stability of longitudinal DTI metrics in MS with treatment of injectables, fingolimod and dimethyl fumarate', MULTIPLE SCLEROSIS JOURNAL, 28, 376-376 (2022)
Co-authors Jeannette Lechnerscott, Saadallah Ramadan, Oun Aliedani
2022 Burgher B, Koussis N, Whybird G, Cocchi L, Scott JG, Breakspear M, 'THE RANZCP EARLY CAREER PSYCHIATRIST AWARD - SUB-OPTIMAL MODULATION OF GAIN BY THE COGNITIVE CONTROL SYSTEM IN YOUNG ADULTS WITH EARLY PSYCHOSIS', AUSTRALIAN AND NEW ZEALAND JOURNAL OF PSYCHIATRY, 56, 5-5 (2022)
Co-authors Michael Breakspear
2022 Burgher B, Whybird G, Koussis N, Scott JG, Cocchi L, Breakspear M, 'SUBOPTIMAL MODULATION OF GAIN BY THE COGNITIVE CONTROL SYSTEM IN YOUNG ADULTS WITH EARLY PSYCHOSIS', AUSTRALIAN AND NEW ZEALAND JOURNAL OF PSYCHIATRY, 56, 96-96 (2022)
Co-authors Michael Breakspear
Show 4 more conferences

Journal article (12 outputs)

Year Citation Altmetrics Link
2025 Jeganathan J, Koussis NC, Paton B, Phogat R, Pang J, Mansour L S, Zalesky A, Breakspear M, 'Spurious correlations in surface-based functional brain imaging', Imaging Neuroscience, 3 (2025) [C1]
DOI 10.1162/imag_a_00478
Co-authors Bryan Paton, Michael Breakspear
2025 Koussis NC, Pang JC, Phogat R, Jeganathan J, Paton B, Fornito A, Robinson PA, Misic B, Breakspear M, 'Generation of surrogate brain maps preserving spatial autocorrelation through random rotation of geometric eigenmodes', Imaging Neuroscience, 3 (2025) [C1]
DOI 10.1162/IMAG.a.71
Co-authors Bryan Paton, Michael Breakspear
2025 Momeni A, Addis DR, Feredoes E, Klepel F, Rasheed MM, Chinchani AM, Koussis NC, Woodward TS, 'Functional Brain Networks Underlying Autobiographical Event Simulation: An Update', Journal of Cognitive Neuroscience, 37, 1083-1146 (2025) [C1]

fMRI studies typically explore changes in the BOLD signal underlying discrete cognitive processes that occur over milliseconds to a few seconds. However, autobiographic... [more]

fMRI studies typically explore changes in the BOLD signal underlying discrete cognitive processes that occur over milliseconds to a few seconds. However, autobiographical cognition is a protracted process and requires fMRI tasks with longer trials to capture the temporal dynamics of the underlying brain networks. In the current study, we provided an updated analysis of the fMRI data obtained from a published autobiographical event simulation study, with a slow event-related design (34-sec trials), that involved participants recalling past, imagining past, and imagining future autobiographical events, as well as completing a semantic association control task. Our updated analysis using Constrained Principal Component Analysis for fMRI retrieved two networks reported in the original study: (1) the Default Mode Network, which activated during the autobiographical event simulation conditions but deactivated during the control condition, and (2) the Multiple Demand Network, which activated early in all conditions during the construction of the required representations (i.e., autobiographical events or semantic associates). Two novel networks also emerged: (1) the Response Network, which activated during the scale-rating phase, and (2) the Maintaining Internal Attention Network, which, while active in all conditions during the elaboration of details associated with the simulated events, was more strongly engaged during the imagination and semantic association control conditions. Our findings suggest that the Default Mode Network does not support autobiographical simulation alone, but it co-activates with the Multiple Demand Network and Maintaining Internal Attention Network, with the timing of activations depending on evolving task demands during the simulation process.

DOI 10.1162/jocn_a_02305
2025 Couvy-Duchesne B, Frouin V, Bouteloup V, Koussis N, Sidorenko J, Jiang J, Wink AM, Lorenzini L, Barkhof F, Trollor JN, Mangin JF, Sachdev PS, Brodaty H, Lupton MK, Breakspear M, Colliot O, Visscher PM, Wray NR, 'Grey-Matter Structure Markers of Alzheimer's Disease, Alzheimer's Conversion, Functioning and Cognition: A Meta-Analysis Across 11 Cohorts', Human Brain Mapping, 46 (2025) [C1]

Alzheimer's disease (AD) brain markers are needed to select people with early-stage AD for clinical trials and as quantitative endpoint measures in trials. Using 1... [more]

Alzheimer's disease (AD) brain markers are needed to select people with early-stage AD for clinical trials and as quantitative endpoint measures in trials. Using 10 clinical cohorts (N = 9140) and the community volunteer UK Biobank (N = 37,664) we performed region of interest (ROI) and vertex-wise analyses of grey-matter structure (thickness, surface area and volume). We identified 94 trait-ROI significant associations, and 307 distinct cluster of vertex-associations, which partly overlap the ROI associations. For AD versus controls, smaller hippocampus, amygdala and of the medial temporal lobe (fusiform and parahippocampal gyri) was confirmed and the vertex-wise results provided unprecedented localisation of some of the associated region. We replicated AD associated differences in several subcortical (putamen, accumbens) and cortical regions (inferior parietal, postcentral, middle temporal, transverse temporal, inferior temporal, paracentral, superior frontal). These grey-matter regions and their relative effect sizes can help refine our understanding of the brain regions that may drive or precede the widespread brain atrophy observed in AD. An AD grey-matter score evaluated in independent cohorts was significantly associated with cognition, MCI status, AD conversion (progression from cognitively normal or MCI to AD), genetic risk, and tau concentration in individuals with none or mild cognitive impairments (AUC in 0.54¿0.70, p-value < 5e-4). In addition, some of the grey-matter regions associated with cognitive impairment, progression to AD ('conversion'), and cognition/functional scores were also associated with AD, which sheds light on the grey-matter markers of disease stages, and their relationship with cognitive or functional impairment. Our multi-cohort approach provides robust and fine-grained maps the grey-matter structures associated with AD, symptoms, and progression, and calls for even larger initiatives to unveil the full complexity of grey-matter structure in AD.

DOI 10.1002/hbm.70089
Co-authors Michael Breakspear
2024 Jeganathan J, Paton B, Koussis N, Breakspear M, 'Integrating anatomical and functional landmarks for interparticipant alignment of imaging data', Imaging Neuroscience, 2, 1-16 (2024) [C1]
DOI 10.1162/imag_a_00253
Co-authors Bryan Paton, Michael Breakspear
2024 Alshehri A, Koussis N, Al-iedani O, Khormi I, Lea R, Ramadan S, Lechner-Scott J, 'Improvement of the thalamocortical white matter network in people with stable treated relapsing-remitting multiple sclerosis over time', NMR IN BIOMEDICINE, 37 (2024) [C1]
DOI 10.1002/nbm.5119
Citations Scopus - 1Web of Science - 1
Co-authors Jeannette Lechnerscott, Oun Aliedani, Saadallah Ramadan
2024 Alshehri A, Koussis N, Al-iedani O, Arm J, Khormi I, Lea S, Lea R, Ramadan S, Lechner-Scott J, 'Diffusion tensor imaging changes of the cortico-thalamic-striatal tracts correlate with fatigue and disability in people with relapsing-remitting MS', EUROPEAN JOURNAL OF RADIOLOGY, 170 (2024) [C1]
DOI 10.1016/j.ejrad.2023.111207
Citations Scopus - 3Web of Science - 1
Co-authors Jeannette Lechnerscott, Oun Aliedani, Saadallah Ramadan
2023 Borne L, Tian Y, Lupton MK, van der Meer JN, Jeganathan J, Paton B, Koussis N, Guo CC, Robinson GA, Fripp J, Zalesky A, Breakspear M, 'Functional re-organization of hippocampal-cortical gradients during naturalistic memory processes', NEUROIMAGE, 271 (2023) [C1]
DOI 10.1016/j.neuroimage.2023.119996
Citations Scopus - 8Web of Science - 8
Co-authors Michael Breakspear, Bryan Paton
2023 Koussis NC, Burgher B, Jeganathan J, Scott JG, Cocchi L, Breakspear M, 'Cognitive Control System Gates Insula Processing of Affective Stimuli in Early Psychosis', SCHIZOPHRENIA BULLETIN, 49, 987-996 (2023) [C1]

Background and Hypothesis: Impairments in the expression, experience, and recognition of emotion are common in early psychosis (EP). Computational accounts of psychosis... [more]

Background and Hypothesis: Impairments in the expression, experience, and recognition of emotion are common in early psychosis (EP). Computational accounts of psychosis suggest disrupted top-down modulation by the cognitive control system (CCS) on perceptual circuits underlies psychotic experiences, but their role in emotional deficits in EP is unknown. Study Design: The affective go/no-go task was used to probe inhibitory control during the presentation of calm or fearful faces in young persons with EP and matched controls. Computational modeling of functional magnetic resonance imaging (fMRI) data were performed using dynamic causal modeling (DCM). The influence of the CCS on perceptual and emotional systems was examined using parametric empirical bayes. Study Results: When inhibiting motor response to fearful faces, EP participants showed higher brain activity in the right posterior insula (PI). To explain this, we used DCM to model effective connectivity between the PI, regions from the CCS activated during inhibition (dorsolateral prefrontal cortex [DLPFC] and anterior insula [AI]), and a visual input region, the lateral occipital cortex (LOC). EP participants exerted a stronger top-down inhibition from the DLPFC to the LOC than controls. Within the EP cohort, increased top-down connectivity between the LOC and AI was associated with a higher burden of negative symptoms. Conclusions: Young persons with a recent onset of psychosis show a disturbance in the cognitive control of emotionally salient stimuli and the suppression of irrelevant distractors. These changes are associated with negative symptoms, suggesting new targets for the remediation of emotional deficits in young persons with EP.

DOI 10.1093/schbul/sbad010
Citations Scopus - 4Web of Science - 2
Co-authors Michael Breakspear
2023 Alshehri A, Al-iedani O, Koussis N, Khormi I, Lea R, Lechner-Scott J, Ramadan S, 'Stability of longitudinal DTI metrics in MS with treatment of injectables, fingolimod and dimethyl fumarate', NEURORADIOLOGY JOURNAL, 36, 388-396 (2023) [C1]
DOI 10.1177/19714009221140511
Citations Scopus - 4Web of Science - 4
Co-authors Oun Aliedani, Jeannette Lechnerscott, Saadallah Ramadan
2021 Burgher B, Whybird G, Koussis N, Scott JG, Cocchi L, Breakspear M, 'Sub-optimal modulation of gain by the cognitive control system in young adults with early psychosis', TRANSLATIONAL PSYCHIATRY, 11 (2021) [C1]

Executive dysfunctions in early psychosis (EP) are subtle but persistent, hindering recovery. We asked whether changes in the cognitive control system (CCS) disrupt the... [more]

Executive dysfunctions in early psychosis (EP) are subtle but persistent, hindering recovery. We asked whether changes in the cognitive control system (CCS) disrupt the response to increased cognitive load in persons with EP. In all, 30 EP and 30 control participants undertook multimodal MRI. Computational models of structural and effective connectivity amongst regions in the CCS were informed by cortical responses to the multi-source interference task, a paradigm that selectively introduces stimulus conflict. EP participants showed greater activation of CCS regions, including the superior parietal cortex, and were disproportionately slower at resolving stimulus conflict in the task. Computational models of the effective connectivity underlying this behavioral response suggest that the normative (control) group resolved stimulus conflict through an efficient and direct modulation of gain between the visual cortex and the anterior insula (AI). In contrast, the EP group utilized an indirect path, with parallel and multi-region hops to resolve stimulus conflict at the AI. Individual differences in task performance were dependent on initial linear gain modulations in the EP group versus a single nonlinear modulation in the control group. Effective connectivity in the EP group was associated with reduced structural integration amongst those connections critical for task execution. CCS engagement during stimulus conflict is hampered in EP owing to inefficient use of higher-order network interactions, with high tonic gain impeding task-relevant (phasic) signal amplification.

DOI 10.1038/s41398-021-01673-4
Citations Scopus - 7Web of Science - 7
Co-authors Michael Breakspear
2020 Sonkusare S, Nguyen VT, Moran R, van der Meer J, Ren Y, Koussis N, Dionisio S, Breakspear M, Guo C, 'Intracranial-EEG evidence for medial temporal pole driving amygdala activity induced by multi-modal emotional stimuli', CORTEX, 130, 32-48 (2020) [C1]

The temporal pole (TP) is an associative cortical region required for complex cognitive functions such as social and emotional cognition. However, mapping the TP with f... [more]

The temporal pole (TP) is an associative cortical region required for complex cognitive functions such as social and emotional cognition. However, mapping the TP with functional magnetic resonance imaging is technically challenging and thus understanding its interaction with other key emotional circuitry, such as the amygdala, remains elusive. We exploited the unique advantages of stereo-electroencephalography (sEEG) to assess the responses of the TP and the amygdala during the perception of emotionally salient stimuli of pictures, music and movies. These stimuli consistently elicited high gamma responses (70¿140 Hz) in both the TP and the amygdala, accompanied by functional connectivity in the low frequency range (2¿12 Hz). Computational analyses suggested that the TP drove this effect in the theta frequency range, modulated by the emotional valence of the stimuli. Notably, cross-frequency analysis indicated the phase of theta oscillations in the TP modulated the amplitude of high gamma activity in the amygdala. These results were reproducible across three types of sensory inputs including naturalistic stimuli. Our results suggest that multimodal emotional stimuli induce a hierarchical influence of the TP over the amygdala.

DOI 10.1016/j.cortex.2020.05.018
Citations Scopus - 1Web of Science - 10
Co-authors Michael Breakspear
Show 9 more journal articles

Preprint (2 outputs)

Year Citation Altmetrics Link
2024 Jeganathan J, Koussis NC, Paton B, Sina Mansour L, Zalesky A, Breakspear M, 'Spurious correlations in surface-based functional brain imaging.' (2024)
DOI 10.1101/2024.07.09.602799
Co-authors Michael Breakspear, Bryan Paton
2024 Koussis N, Pang J, Jeganathan J, Paton B, Fornito A, Robinson PA, Misic B, Breakspear M, 'Generation of surrogate brain maps preserving spatial autocorrelation through random rotation of geometric eigenmodes' (2024)
DOI 10.1101/2024.02.07.579070
Co-authors Bryan Paton, Michael Breakspear
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Grants and Funding

Summary

Number of grants 3
Total funding $477,500

Click on a grant title below to expand the full details for that specific grant.


20242 grants / $475,000

Enhancing patient outcomes in brain cancer through advanced brain imaging$250,000

Funding body: Mark Hughes Foundation

Funding body Mark Hughes Foundation
Project Team Associate Professor Saadallah Ramadan, Doctor Michael Fay, Professor Michael Breakspear, Doctor Nikitas Koussis
Scheme Research Funding
Role Investigator
Funding Start 2024
Funding Finish 2028
GNo G2401476
Type Of Funding Scheme excluded from IGS
Category EXCL
UON Y

Enhancing patient outcomes in brain cancer through advanced brain imaging$225,000

Funding body: Hunter Medical Research Institute

Funding body Hunter Medical Research Institute
Project Team Associate Professor Saadallah Ramadan, Doctor Michael Fay, Professor Michael Breakspear, Doctor Nikitas Koussis
Scheme Research Grant
Role Investigator
Funding Start 2024
Funding Finish 2028
GNo G2400383
Type Of Funding C3300 – Aust Philanthropy
Category 3300
UON Y

20231 grants / $2,500

Brain Neuromodulation Research Program Seed Funding$2,500

Funding body: Brain Neuromodulation Research Program, HMRI

Funding body Brain Neuromodulation Research Program, HMRI
Project Team

Michael Breakspear

Scheme Seed Funding
Role Lead
Funding Start 2023
Funding Finish 2023
GNo
Type Of Funding Grant - Aust Non Government
Category 3AFG
UON N
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Research Supervision

Number of supervisions

Completed5
Current0

Highlighted Supervision

Commenced Level of Study Research Title Program Supervisor Type
2022 Honours White matter connectivity reductions in early psychosis
A 4th year medical student research project into white matter dysfunction in first-episode psychotic individuals, I facilitated the data preprocessing and analysis, as well as the guidance of hypotheses, literature review, and report writing.
Medical Science, College of Health, Medicine & Wellbeing - The University of Newcastle Co-Supervisor

Past Supervision

Year Level of Study Research Title Program Supervisor Type
2024 Honours Metacognitive processes in noisy environments Psychology, School of Psychological Sciences Co-Supervisor
2023 Honours White matter connectivity reductions in early psychosis Medical Science, College of Health, Medicine & Wellbeing - The University of Newcastle Co-Supervisor
2023 Honours White matter connectivity reductions in early psychosis Medical Science, College of Health, Medicine & Wellbeing - The University of Newcastle Co-Supervisor
2023 Honours White matter connectivity reductions in early psychosis Medical Science, College of Health, Medicine & Wellbeing - The University of Newcastle Co-Supervisor
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Dr Nikitas Koussis

Position

Postdoctoral Researcher
School of Medicine and Public Health
College of Health, Medicine and Wellbeing

Contact Details

Email nikitas.koussis@newcastle.edu.au
Phone 0240420981
Link Twitter
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