Matiss Ozols

Matiss Ozols
Wellcome Sanger Institute · Human Genetics Programme

PhD Bioinformatics, Data science and Biomedical engineering
Senior Bioinformatics Data Scientist at Wellcome Sanger Institute

About

31
Publications
7,371
Reads
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220
Citations
Introduction
Passionate about data science, machine learning, AI, database and software development, full stack web development applied to proteomics and genomics data to reveal underlying biology of disease and ageing, and contribute to drug discovery. Developed, host and maintain database and web-application: http://www.manchesterproteome.manchester.ac.uk/#/
Additional affiliations
June 2015 - July 2015
Ma Chung University
Position
  • Intern
September 2014 - September 2018
The University of Manchester
Position
  • PhD Student
Education
September 2014 - September 2018
The University of Manchester
Field of study
  • Bioinformatics, Medicine, Biochemistry
September 2011 - June 2014
University of Bradford
Field of study
  • Medical Engineering

Publications

Publications (31)
Article
The extracellular matrices (ECMs) of mammalian tissues play important roles in mediating and maintaining tissue function. However, aberrant and progressive remodelling of ECM components is a key feature in the pathology and ageing of many organs, including skin. Crucially, these degradative processes not only impair function, but may also release p...
Article
During ageing, the glomerular and tubular basement membranes (BM) of the kidney undergo a progressive decline in function that is underpinned by histological changes, including glomerulosclerosis and tubular interstitial fibrosis and atrophy. This BM-specific ageing is thought to result from damage accumulation to long-lived extracellular matrix (E...
Preprint
Full-text available
The exogenous application of small peptides can beneficially affect clinical skin appearance (wrinkles) and architecture (collagen and elastic fibre deposition and epidermal thickness). However, the discovery of new bioactive peptides has not been underpinned by any guiding hypothesis. As endogenous extracellular matrix (ECM)-derived peptides produ...
Article
Full-text available
The paper’s main contributions are twofold: to demonstrate how to apply the general European Union’s High-Level Expert Group’s (EU HLEG) guidelines for trustworthy AI in practice for the domain of healthcare; and to investigate the research question of what does “trustworthy AI” mean at the time of the COVID-19 pandemic. To this end, we present the...
Article
Full-text available
Extracellular matrix (ECM) in the intervertebral disc (IVD), lung and artery are thought to undergo the age-dependant accumulation of damage by chronic exposure to mechanisms such as reactive oxygen species, proteases and glycation. It is unknown whether this damage accumulation is species-dependant (via differing lifespans and hence cumulative exp...
Article
Full-text available
Extracellular matrix (ECM) proteins confer biomechanical properties, maintain cell phenotype and mediate tissue repair (via release of sequestered cytokines and proteases). In contrast to intracellular proteomes, where proteins are monitored and replaced over short time periods, many ECM proteins function for years (decades in humans) without repla...
Article
Full-text available
Proteases and protease inhibitors (P/PIs) are involved in many biological processes in human skin, yet often only specific families or related groups of P/PIs are investigated. Proteomics approaches, such as mass spectrometry, can define proteome signatures (including P/PIs) in tissues; however, they struggle to detect low-abundance proteins. To ov...
Preprint
Full-text available
Extracellular matrix (ECM) in the intervertebral disc (IVD), lung and artery are thought to undergo the age-dependant accumulation of damage by chronic exposure to mechanisms such as reactive oxygen species, proteases and glycation. It is unknown whether this damage accumulation is species-dependant (via differing lifespans and hence cumulative exp...
Article
Full-text available
In ageing tissues, long-lived extracellular matrix (ECM) proteins are susceptible to the accumulation of structural damage due to diverse mechanisms including glycation, oxidation and protease cleavage. Peptide location fingerprinting (PLF) is a new mass spectrometry (MS) analysis technique capable of identifying proteins exhibiting structural diff...
Preprint
In ageing tissues, long-lived extracellular matrix (ECM) proteins are susceptible to the accumulation of structural damage due to diverse mechanisms including glycation, oxidation and protease cleavage. Peptide location fingerprinting (PLF) is a new mass spectrometry (MS) analysis technique capable of identifying proteins exhibiting structural diff...
Article
Full-text available
Artificial Intelligence (AI) has the potential to greatly improve the delivery of healthcare and other services that advance population health and wellbeing. However, the use of AI in healthcare also brings potential risks that may cause unintended harm. To guide future developments in AI, the High-Level Expert Group on AI set up by the European Co...
Article
Full-text available
This paper documents how an ethically aligned co-design methodology ensures trustworthiness in the early design phase of an artificial intelligence (AI) system component for healthcare. The system explains decisions made by deep learning networks analyzing images of skin lesions. The co-design of trustworthy AI developed here used a holistic approa...
Article
Chronic UVR exposure of human skin can result in photo-ageing which manifests both externally and internally (as remodelling of skin layers including the extracellular matrix-rich dermis). However, the intermittent nature of UVR exposure over a timescale of decades combined with the longevity of many structural dermal proteins makes the identificat...
Article
Full-text available
Ozols and Eckersley are equally contributing joint first authors. Although dysfunctional protein homeostasis (proteostasis) is a key factor in many age‐related diseases, the untargeted identification of structurally modified proteins remains challenging. Peptide location fingerprinting is a proteomic analysis technique capable of identifying struct...
Article
Full-text available
Both protease- and reactive oxygen species (ROS)-mediated proteolysis are thought to be key effectors of tissue remodeling. We have previously shown that comparison of amino acid composition can predict the differential susceptibilities of proteins to photo-oxidation. However, predicting protein susceptibility to endogenous proteases remains challe...
Preprint
Full-text available
Age, disease, and exposure to environmental factors can induce tissue remodelling and alterations in protein structure and abundance. In the case of human skin, ultraviolet radiation (UVR)-induced photo-ageing has a profound effect on dermal extracellular matrix (ECM) proteins. We have previously shown that ECM proteins rich in UV-chromophore amino...
Chapter
Full-text available
Age-related changes in elastin refer to modifications such as nonenzymatic cross-linking and/ or proteolytic degradation, which adversely affect the mechanical and biochemical properties of elastin-rich tissues and organs. Elastin (in combination with other extracellular matrix components) forms elastic fibers. These structures are primarily respon...
Preprint
Full-text available
Although dysfunctional protein homeostasis (proteostasis) is a key factor in many age-related diseases, the untargeted identification of structural modifications in proteins remains challenging. Peptide location fingerprinting is a proteomic analysis technique capable of identifying structural modification-associated differences in mass spectrometr...
Article
Full-text available
In contrast to the dynamic intracellular environment, structural extracellular matrix (ECM) proteins with half-lives measured in decades, are susceptible to accumulating damage. Whilst conventional approaches suchas histology, immunohistochemistry and mass spectrometry are able to identify age- and disease-relatedchanges in protein abundance or dis...
Article
Circadian rhythms are daily oscillations that, in mammals, are driven by both a master clock, located in the brain, and peripheral clocks in cells and tissues. Approximately 10% of the transcriptome, including extracellular matrix components, is estimated to be under circadian control. Whilst it has been established that certain collagens and extra...
Chapter
In this chapter we discuss the molecular composition and structure of the epidermis, dermal-epidermal junction, dermis and hypodermis. We highlight the contribution of long-lived dermal collagens, elastic fibres, proteoglycans and hyaluronic acid to skin function and also consider the role of apparently “minor” skin components. In order to characte...
Article
Full-text available
Defining protein composition is a key step in understanding the function of both healthy and diseased biological systems. There is currently little consensus between existing published proteomes in tissues such as the aorta, cartilage and organs such as skin. Lack of agreement as to both the number and identity of proteins may be due to issues in p...
Article
Full-text available
Although the composition and structure of cartilaginous tissues is complex, collagen II fibrils and aggrecan are the most abundant assemblies in the articular cartilage (AC) and nucleus pulposus (NP) of the intervertebral disc (IVD). Whilst structural heterogeneity of intact (three globular domain) aggrecan is well characterised, the extent of aggr...
Article
Full-text available
High performance liquid chromatography (HPLC) equipped with photodiode array (PDA) detection from 190-800 nm spectral range has been a method in great demand in analytical chemistry of natural products that offers three-dimensional data set. This data set presents simultaneously the retention time of identified compounds over the spectral range of...

Questions

Questions (4)
Question
I want to understand what is the calculation to derive a number 120.9 for SS Subjects (matching) in
ANOVA table in two ways RM ANOVA with matches values on row.
Question
In mixed anova with repeated measures on 1 factor how do I calculate the SS_subjects DF_subjects and and MS_subjects? And how do i adjust the residual values?
Question
Hi I have analysed a dataset in Graphpad prism with a 2 Way Anova.
1) In the experimental design i select "Each column represents a different time point, so matched values are spread accross the row."
2) Then in Multiple Comparisons tab we select "With each column, compare rows".
3) And then we correct for multiple comparisons using Bonferroni.
Eventually i get a p value for each row comparing different treatments.
I can not seem to be able to replicate same results or even same pattern programmatically.
So far I have tried pipelines:
Question
Searching for a conference to present my work and get insights in the cutting edge research in my field.

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