Former group members
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DPhil Student in Clinical Medicine |
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DPhil Student in Clinical Medicine I am a DPhil student in the labs of Julian Knight and Alex Mentzer, where I work on the functional genomics of sepsis and related infections including COVID-19. |
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I am currently a first year DPhil student in Genomic Medicine and Statistics and am undertaking my 3 rotations in different research groups. |
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My particular interest is identifying genetic variants underlying epilepsy and severe infectious diseases with the aim of translation into clinical medicine. |
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I am an MSc student at Knight Group, my research focuses on functional characterization of novel variants associated with Sepsis identified by Whole Exome Sequencing. |
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Lahiru Handunnetthi aims to understand how brain infections contribute to the development of psychiatric and neurological complications. His research programme leverages the power of big data, genetic information and stem cell derived model systems. |
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As a research assistant in the Julian Knight group, I work on a number of different projects. |
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I am working as a post-doctoral bioinformatician focusing on host-pathogen genomics. My current work focuses on how -omic variation in host and pathogen modulate the response to infection in the context of sepsis and COVID-19. I also have an interest in the linkage and integration of routinely collected hospital data and -omic data, with the goal of identifying associations between biomarkers and -omic signatures of the dysregulated response to infection. |
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Dysregulation of the innate immune system leads to a variety of diseases ranging from sepsis to autoinflammatory states. Previous work in the group demonstrated that regulatory genetic variation plays an important role in driving individual differences in extreme innate immune response phenotypes.
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Dr Justin P. Whalley was a senior bioinformatician in the Knight Group from 2017 to 2022 and Research Member of Common Room at Kellogg College. He was the lead for the Extreme Response Functional Genomics project, as well as the head of Integration (Tensors) working group for the COVID-19 Multi-omic Blood Atlas (COMBAT).
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Inappropriate immune responses underpin various diseases and auto-inflammatory states including sepsis. Our current research goal is to define and characterise extreme immune response phenotypes which should resolve functional alleles, mechanisms of gene regulation and pathophysiology. |
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Significant heterogeneity in individual patient response in sepsis has posed great challenges for identifying appropriate therapeutic strategies and makes it urgent to now develop personalized therapy. Former work of the group has distinguished two response groups among sepsis patients through transcriptomic profiling, and identified specific sepsis regulatory genetic variation (eQTL) involving the immune and metabolic response. |
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Sepsis is a life threatening condition with high morbidity and mortality and few therapeutic options. Understanding the biological basis of this deleterious host response to infection is the main aim of my research. I am looking to further our understanding of the cell type specificity underlying disease endotypes that the group has previously established through transcriptomic analyses of peripheral blood in septic patients. |
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Ankylosing spondylitis (AS) is a chronic inflammatory arthritis affecting 1-2% of people in the UK. It is a polygenic disease, with over 40 associated genetic loci identified by genome-wide association studies. My research focus is to determine which particular single nucleotide polymorphisms (SNPs) play a causative role... |
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I am an anaesthetic registrar and academic clinical fellow working in Oxford and the surrounding areas, with clinical interests in perioperative medicine and pain. Major surgery and major illness can cause... |
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I am working as a Senior Bioinformatician in Integrative Analysis at the COVID-19 Multi-omics Blood ATlas (COMBAT) consortium at the University of Oxford using multi-omics techniques in combination with the cutting-edge bioinformatic approaches and statistical methods to explore the pathogenesis of COVID-19...
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The majority of regulatory variants identified by Genome-Wide Association Studies (GWAS) occur in non-coding regions of the genome, often at considerable distances...
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The ULTRA-DD is a European-wide consortium comprising both academics and industry, aiming to validate new protein targets for drug discovery by generating chemical probes (and antibodies) in clinically based models... |
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My work focuses on using genomic data (e.g. GWAS and eQTL) to develop bioinformatic pipelines for drug target prediction and prioritization. I'm aiming to aggregate existing drug data- target, type, development stage, etc.- in order to understand the underlying genetic factors... |
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Ankylosing spondylitis (AS) is an autoimmune disease characterized by chronic inflammation, new bone formation, and fusion of joints. Though much of its aetiology is unknown, our current understanding is that AS is largely a genetic disorder. Previous studies have associated it with... |
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As a clinician in Intensive Care Medicine, I have a special interest in sepsis, a disease that represents a major public health burden worldwide. Community acquired pneumonia is the commonest cause of sepsis and... |
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Ankylosing spondylitis (AS) is a chronic inflammatory disease causing arthropathy of the spine. The exact cause for the disease development in not known, but there are genetic components associated with AS... |
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The field of research I am currently working for my DPhil involves the chronic inflammatory disease of the skin known as psoriasis. Psoriasis is influenced by environmental factors but an important genetic susceptibility has also been revealed by... |
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Spondyloarthritis is a common chronic inflammatory rheumatic disease with a strong genetic component with over 50 susceptibility loci already identified. How these variants confer disease predisposition is however poorly understood. Convergent data suggest... |
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Using a functional genomics approach to explore heterogeneity in inflammatory and infectious disease... |
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Now (January 2018) a Postdoctoral Fellow at The Raychaudhuri Lab, Harvard University, Boston Functional genomics of the response to infection. My research uses a functional genomics approach to identify genetic determinants... |
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DPhil awarded 2014 Epstein-Barr Virus (EBV) is a ubiquitous herpesvirus which infects over 95% of adult human population. It has been implicated in aetiology of Infectious Mononucleosis and oncogenesis of lymphoid and epithelial... |
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Now (January 2018): MRC Intermediate Research Fellow in Computational Biology and Epidemiology, Faculty of Medicine, School of Public Health, Imperial College, London. Functional genomics of Vitamin D. I am interested in... |
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Nicholas Hasle MBiochem final year student |
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Sepsis is the systemic inflammatory response to infection. The pathophysiology of sepsis is complex and poorly understood. This is reflected in the limited treatment options available for sepsis and the poor clinical... |
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Single nucleotide polymorphisms (SNPs) are single base changes that occur approximately once in every thousand bases in human DNA. These small changes are hypothesised to be responsible for 90% of the 1% variation in DNA... |
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Cardiac surgery continues to be associated with a significant mortality and a considerable risk of postoperative complications. Much of this morbidity and mortality is related to a dysfunctional host inflammatory response... |
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My main research interest is the genetics of autoimmune diseases, focusing on their prime genetic factor, the human Major Histocompatibility Complex (MHC). My work is situated at the interface of mutifactorial genetics... |
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Rachael Dellar MBiochem final year student |
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My central research interest is in the molecular genetic mechanisms of immune-mediated disease and phenomena in humans, with special emphasis on infectious diseases and allergic disorders. I am also interested in radiation... |
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Currently (January 2018): Research Associate, Division of Infection, Immunity & Respiratory Medicine, Manchester University The genes of the tumor necrosis factor (TNF) superfamily in the class III region of the MHC are tightly... |
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We are using functional genomic approaches to define genetic variants that are responsible for the association of genetic variation in the Major... |
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I am working on the GenExpressID project, which aims to characterise gene expression in patients of various autoimmune diseases within different immune cell types. We are hoping to determine unique expression signatures that ... |
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Currently (January 2018): Laboratory Associate, Eurofins Clinical Genetics KK, Tokyo Inflammation is dependent on a number of innate immune cell types. Transcriptome analysis on differentially developed primary lymphocytes will ... |
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I am currently working with samples from Abu Dhabi trying to understand the underlying genetic reasons for a high incidence of Type 2 Diabetes in the Emiratis ... |
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Gene expression in sepsis. As part of my MBiochem degree, I am undertaking a research project looking studying the changes in monocyte gene expression in sepsis. Sepsis is abnormal inflammatory response in response to ... |
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Functional genomics of ankylosing spondylitis - We are using functional genomics to understand the mechanism of ankylosing spondylitis (AS), a chronic imflammatory disease with strong genetic predisposition. Recent research ... |
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Genome-Wide Association Studies (GWAS) reveal that 90% of SNPs associated with disease are located in non-coding DNA, highlighting the importance of regulatory variants for disease. Establishing the ... |
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The Strep Gene Project. For my 4th year research project, I am investigating how certain SNPs (Single Nucleotide Polymorphisms) may affect susceptibility to bacterial infection by Streptococcus group A. SNPs represent small ... |
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My current project involves investigating the effects of HLA typing on gene expression across a variety of cell types; this involves using genotype and expression (microarray) ... |
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We are using functional genomic approaches to define genetic variants that are responsible for the association of genetic variation in the Major Histocompatibility Complex (MHC) with ... |
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I am in the final term of my MSc in Integrated Immunology and will be carrying out a 14 week project within the group, focusing on sepsis. Sepsis is defined as a dysregulated immune and inflammatory response to infection ... |
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My active interest is the characterization of genetic and epigenetic variation in the human major histocompatibility complex (MHC) from high throughput sequencing for transcript ... |
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The syndrome of pneumonia is the most common infectious cause of death in children under five years of age across the globe. A large range of organisms can ... |
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Functional Genomics - As a research assistant I am currently working with Dr Benjamin Fairfax. Our main project involves the analysis of methylation changes in specific cells under different conditions. I am also ... |
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I am supported by a Wellcome for MB PhD postdoctoral Fellowship. I am a clinical trainee in Medical Oncology and a Senior Research Fellow at Worcester College. I studied the molecular interactions and determinants of ... |
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Currently (2018) working in medical communications at AMICULUM UK - Functional genomics of ankylosing spondylitis. Understanding the molecular mechanisms involved in disease pathogenesis is vital in developing tailored ... |
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Understanding the role of regulatory elements in driving allelic associations with differences in gene expression in human leukocytes for different cellular contexts Inappropriate immune activity and associated inflammation are ... |