Group news

  • 30 October 2018: Congratulations to Katie Burnham and everyone involved from our group and the UK Genomic Advances in Sepsis Investigators

    following the publication of the American Journal of Respiratory and Critical Care Medicine (AJRCCM) paper “Transcriptomic Signatures in Sepsis and a Differential Response to Steroids: From the VANISH Randomized Trial  PubMed: 30365341

    We have demonstrated that sepsis response signatures (SRS)/sepsis endotypes are associated with different responses to treatment. Genome-wide gene expression profiling was performed and SRS endotype was determined using a previously established model with seven discriminant genes. We concluded that transcriptomic profile at onset of septic shock was associated with response to corticosteroids. Those with the immuno-competent SRS2 endotype had significantly higher mortality when given corticosteroids compared to placebo.

  • 5 October 2018 - DNA Manipulation Workshop at Abingdon School

    A strong contingent from the Knight group (Justin, Andrew, Alice, Ola, Harindra, Giuseppe and Julie) went to Abingdon School to run a DNA manipulation workshop, based on identifying and using DNA sequence variants, as part of the Abingdon Science Partnership. Students from four schools (Carterton Community College, Europa School, Sir William Borlase's Grammar School and John Mason School) came together to learn how to work with DNA and small volumes. They carried out a PCR reaction which produced a product, 2,000 bases long, which was subsequently manipulated with molecular scissors (restriction enzymes) that cut the product into two smaller fragments, but only if a certain variant in the DNA was present at the 300th base. Each group loaded their own sample into a gel electrophoresis system and ten minutes later they could see if the DNA was cut into 300 base and 1700 base fragments, and all of them successfully confirmed that the variant was present. The practical part was interspersed with a talk on genome editing with CRISP-R and several career path talks. In the afternoon we played a stimulating “whispering game” which showed how we can use the presence of variants in bioinformatics. As a six word message spreads through a group it gets corrupted (mutated) and starts to gather variants in the message. By recording the changes in the message as it spreads through the group, the students reconstructed how the message was disseminated. In genetics we can similarly use the variants a pathogen gains in its genome as it replicates, to work out how an infectious disease spreads through a population. The Knight group really enjoyed the day out with many interesting questions and discussions about our work with the students.

  • 5 May 2018: Congratulations to Julie Osgood on the publication of her review paper "Translating GWAS in rheumatic disease: approaches to establishing mechanism and function for genetic associations with ankylosing spondylitis"

    Julie A Osgood, Julian C Knight, Briefings in Functional Genomics, 2018, ely015

    Ankylosing spondylitis (AS) is a highly heritable chronic inflammatory arthritis characterized by osteoproliferation, fusion of affected joints and systemic manifestations. Many disease associations for AS have been reported through genome-wide association studies; however, identifying modulated genes and functional mechanism remains challenging. This review summarizes current genetic associations involving AS and describes strategic approaches for functional follow-up of disease-associated variants.

          • 3 May 2018 - Our Genomic Future, preview of a new play at the Oxford University Museum of Natural History

            "If you had the chance to know whether your life will be affected by disease, would you take it? What if you could change the colour of your unborn child's eyes? Or rid the world of a disability? Our medical records will soon be open to pharmaceutical companies able to tailor their advertising to our individual frailties. So, as we enter an age of unprecedented bodily insight and choice, where do we draw the line?"
          • “Reading between the Lines” Theatre Companywith Oxford University present some preview scenes with accompanying discussion of their fascinating new play, exploring the impacts and issues raised by the most significant medical development in recent history.
            This play was developed in partnership with Wellcome Centre researcher Dr George Busby; the play preview was followed by a lively panel discussion on the topics raised by it – this included Prof Julian Knight (centre), Dr Jason Torres, and Prof Nina Hallowell.
  • Genetic Lines at the Oxford University Museum of Natural History, 19 April 2018

    Justin recently told the story of his life in science as part of an evening of storytelling and music at the Oxford University Museum of Natural History. Along with Brian Mackenwells, George Busby, Cath Green and folk band Threepenny Bit, Justin performed under the T-rex in the Main Court to a packed audience. The stories and music were very well received and everyone left knowing a little more about throwing up in zero gravity, genetics and wolf poo, how medical research can affect one’s love life and why us scientists have the best and the worst job in the world.

  • Congratulations to Katie following her DPhil viva on 22nd February 2018, successfully defending the thesis “Functional Genomics of the Sepsis Response” 

  • 8 December 2017 - Christmas dinner after Away-Day meeting at Merton College

    This is becoming something of a tradition within the Knight group: an Away-Day at the TS Eliot Theatre complex at Merton College, Oxford presenting the highlights of current research projects running within the group, mixed with lively discussions about current trends in functional genomics and topped by an evening with great food and great laughter!
  • 12 July 2017 - Genome based activity at local primary school: have the cake and eat it!

    Kate, Katie and Alicia from our group visited St Joseph’s Catholic Primary School, Oxford in July to talk to Year 1 pupils about genetics.  The children were asked about what makes us different and think about what they have inherited from their parents.  The human genome was explained using a cake recipe as an example and how this would have to be expanded to make all of the instructions needed to make a human.  The children were very excited that the printed out human instructions, the genome, would stretch from their school all the way to France.  Taste strips were used to show how some of the differences in our DNA can cause differences we cannot see, but taste.  The afternoon finished with making DNA bracelets and eating the cake.  The children were very engaged and excited and it was thoroughly enjoyable all round.

  • 4-16 July 2017 - Meeting a STEM+ Challenge in China!

    Addressing systemic poverty and the rich-poor gap are the main objectives of Inclusive Business Lab and Foundation (IBLF), an organization targeting rural China and Hong Kong. One of their programmes- the Global Inclusive Leadership Programme- aims to empower the next generation of leaders by cultivating a passion for STEM+ subjects in students aged 14-17 (Science, Technology, Engineering, Mathematics, with the + signifying well-roundedness as demonstrated by the arts, humanities, business, etc.). One of the ways they go about doing this is by hosting week-long challenges for students to work through in teams of five, inspiring participants to weave together STEM, creativity, leadership, and teamwork.

    Bogdan Knezevic, a second-year D.Phil. student in our group, got in touch with IBLF when an email went around the Wellcome Trust Centre’s social list, calling for people interested in designing a STEM challenge and working with kids who would be completing it. Bogdan designed, organized, implemented, and judged the biotechnology innovation challenge (which he focused on the genome editing technique CRISPR/Cas-9) and, along with four other university students and four IBLF staff, he ran two sets of five day challenges: one in Hong Kong and one in Zhenjiang, China. In total, approximately 700 students worked through each of the activities over the span of the two-week period. The event culminated in a final day challenge that the top eight teams participated in, at the end of which each team presented their work in front of a 400-person auditorium consisting of students, teachers, politicians, and many others.

    When asked about his experience, Bogdan had nothing but praise. “The kids were an inspiration to work with” he noted. “They were full of wonderfully creative ideas, they were engaging and excited, and, most importantly, they exhibited tremendous personal growth throughout the week”.                                      Photography by

  • 10th June 2017 Cheltenham Science Festival

    Gabriele Migliorini from the Knight Group helped the Oxford Science Team run a stall for a day at the 2017 Cheltenham Science Festival. This involved a number of activities designed to make genomics accessible to the public, ranging from understanding the large impact of small genetic changes using a scrabble game to extracting DNA from frozen strawberries using concentrated pineapple juice and alcohol. The activities built on the success of the stall at the Oxford Science Festival 2016 (’

  • 27 March 2017: Congratulations to Cyndi Goh on the publication of her review paper "Enhanced understanding of the host-pathogen interaction in sepsis: new opportunities for omic approaches"

    Goh CKnight JC, Lancet Respir Med. 2017 Mar;5(3):212-223. doi: 10.1016/S2213-2600(17)30045-0.

    Omics-based approaches have facilitated understanding of the heterogeneous sepsis disease phenotype, but they are themselves currently limited by this heterogeneity. In this review article, we explore how unique characteristics attributable to individual pathogens affect the nature and consequences of interaction with the host in sepsis. We propose that achieving the goal of personalised treatment for individuals with sepsis will require researchers and clinicians to integrate studies of both pathogen and host.

  • 'Research Down The Road' at Banbury Town Hall, 18th March 2017

    Michael and Julian from the Knight lab manned a stall at the Medical Science Division ‘family fun day’ in Banbury Town Hall, explaining aspects of our work on human disease genomics and in particular the European Research Council (ERC) funded programme of work relating to human leukocyte antigen (HLA) that we have recently completed at the Wellcome Trust Centre for Human Genetics, University of Oxford. The prodigious capacity of strawberries to yield DNA, each cell nucleus containing 8 copies of the chromosome set instead of the 2 copies found in humans, proved popular with our Genetics in the Kitchen approach to DNA extraction using a combination of salt, washing up liquid and very cold methylated spirits.

  • 30 December 2016: A late Christmas present! Congratulations to Katie Burnham and everyone involved from our group and the UK Genomic Advances in Sepsis Investigators

    following the publication of the new paper Shared and Distinct Aspects of the Sepsis Transcriptomic Response to Fecal Peritonitis and Pneumonia. Burnham KL, Davenport EE, Radhakrishnan J, Humburg P, Gordon AC, Hutton P, Svoren-Jabalera E, Garrard C, Hill AV, Hinds CJ, Knight JC. American Journal of Respiratory and Critical Care Medicine, online pre-print December 2016 PMID: 28036233                

    Sepsis is a highly heterogeneous syndrome, in which we have applied genomic approaches to gain insight into the individual response to infection. This paper describes the gene expression response to abdominal sepsis, investigating individual and temporal variation in the gene expression patterns observed, and comparing this to pneumonia. We found that sepsis response signature (SRS) subgroups were present in faecal peritonitis, replicating the association of relative immunosuppression with increased early mortality previously described in pneumonia. Differences according to source of infection were less pronounced, but changes in gene expression over time were noted. These findings highlight the opportunity for personalised medicine in sepsis.

  • Well done to Hai, Bogdan and Katie for their Genomic Medicine paper describing a new tool developed in the Knight Group for enhanced interpretation of genomic summary data, 13 December 2016

    Our paper describes XGR (eXploring Genomic Relations), released as an R package and web-app enabling downstream knowledge discovery from genomic summary data. XGR utilises ontology and network information to perform enrichment, network, similarity, and annotation analyses, supporting interpretation of sets of genes, SNPs, or genomic regions. In short, XGR is software designed for enhanced interpretation necessary for working with big data science in genomics.

  • Experimental design: An exhibition of prints, 9-22 November 2016

    A collaboration between the Oxford Printmakers Co-operative and the Wellcome Trust Centre for Human Genetics.

    Sixteen WTCHG researchers have been paired with sixteen OPC artists to produce sixteen different works based on the research.  Three pieces were inspired by the research work done by DPhil students Anna Sanniti, Alicia Leedo Lara and Bogdan Knezevic from the Julian Knight group.

    These pieces were exhibited at the Fusion Arts Centre, Cowley Road, Oxford, from the 9th to the 22nd November 2016.

    Follow this link to the Twitter account KnightGenetics to see pictures of the art.

  • A question of taste: using PCR to investigate human evolution. Members of the Knight group help with DNA workshops at the Oxford University Museum of Natural History, 4-20 October 2016

    The Oxford University Museum of Natural History runs periodical workshops aimed at Key Stage 5 (A level) students from the state school sector.  In this workshop students learn something new about themselves. The workshop gives students the chance to analyse and compare their version of a bitter taste receptor gene (their genotype) to their ability to taste PTC (their phenotype). Students learn about molecular biology techniques by using research-quality equipment and find out whether they are homozygous or heterozygous for the gene variant that confers the ability to taste this bitter compound. Researchers Daniel Wong and Giuseppe Scozzafava were helpers for the day sharing their knowledge of molecular biology with students from Poole Grammar School and from Lord Williams’ School.

  • 11 October 2016, NDM Graduate Prizes – Congratulations to Emma Davenport!

    The Nuffield Department of Medicine (NDM) awards Graduate Prizes to its graduate research students for various achievements, including success in terms of discoveries and published work, significant achievements in establishing infrastructure, success in strongly collaborative projects, and involvement in public engagement and other departmental activities.

    Emma Davenport has been awarded a prestigious NDM graduate prize for the high impact and resulting publication record of her doctoral research, conducted in the Knight lab. Emma investigated the genetic determinants of variation in the human response to both common and rare infection. Her key discovery was the determination of a gene expression signature, identifying sepsis patients with an immunosuppressed phenotype associated with higher early mortality. This led to a first author publication in The Lancet Respiratory Medicine. She is currently continuing her research career as a postdoctoral fellow at Harvard Medical School and the Broad Institute in Professor Soumya Raychaudhuri's group. Emma is interested in how genetics can be used to understand the mechanism of action of drugs and improve the treatment of patients; the overarching strategy in developing precision medicine.

  • Science enrichment lesson at Princes Risborough School, 21 September 2016

    Many thanks to Princes Risborough School (Princes Risborough, Buckinghamshire) for inviting us into their science lesson. Giuseppe, Julie and Daniel from the Knight Lab had a great time talking genetics and extracting DNA from strawberries, finding out whether the pupils were PCT tasters or not (a bitter compound similar to that found in brussels sprout and cabbage, the taste receptor being under the control of TAS2R38 gene on Chromosome 7) and where the students fell on the Tree of Life according to some simple genetic based traits (can you roll your tongue?).

  • 29 July 2016 “YER A WIZARD HARRY” 

    Science for the People, Canadian syndicated radio show, podcast #380

    Our group head  Julian Knight is interviewed about his Christmas special BMJ paper that looks to genetics for the origins of magic in the Harry Potter universe and uses this to illustrate the basics of genetics (from minute 40:22 in this podcast).

  • METHOD IN THE MOTION, A DANCED LECTURE, Oxfordshire Science Festival, 25 June 2016

    Hear Irina Pulyakhina from the Wellcome Trust Centre for Human Genetics (JKnight group) talk about her work as her science is interpreted by FLUX, a dance company specialising in translating scientific principles into theatrical form.

    A unique event combining a scientific talk with inspirational dance.


  • 25 April 2016: Congratulations to Emma Davenport, Katie Burnham and everyone involved from our group and the UK Genomic Advances in Sepsis Investigators

    following the publication of the Lancet RespiratoryMedicine paper “Genomic landscape of the individual host response and outcomes in sepsis: a prospective cohort study”, The Lancet Respiratory Medicine, 4, 259-271 (2016).

    This paper describes how an integrated functional genomics approach uncovered differences in the host response to pneumonia, identifying opportunities for personalised treatment. Following admission to intensive care, we found that transcriptomic analysis of peripheral blood leucocytes defines two distinct sepsis response signatures (SRS1 and SRS2). We resolved that a predictive set of seven genes enabled the classification of patients as SRS1 or SRS2. This has potential value as a biomarker as patients in the SRS1 group have a worse outcome.

  • Group retreat in the Brecon Beacons National Park, Wales, 17-18 February 2016

    The group spent two days thinking about science in the day and food in the evening, not forgetting to put in a couple of treks, the photo showing the top of Sugar Loaf Mountain.

    Thanks to all who took part in good spirits to make it such a memorable trip despite the cold!

  • Christmas dinner - after Away-Day meeting at Merton College

    A fantastic Friday evening on 4th December 2015, right after a very stimulating session in TS Eliot Theatre complex presenting the current research projects running within the group.
  • Heart and Head - a night of storytelling and music at the Museum of Natural History of Oxford on 10th October 2015

    Researchers from WTCHG and CRUK were telling real life stories about special moments in their scientific everyday lives, accompanied by life music. Congratulations Irina on a really wonderful performance.

  • Genetics in your kitchen! - 2015 Cheltenham Science Festival

    On 4th June 2015, more than 600 visitors of all ages tested their bitter taste perception, made bracelets based on their own genetic variants, put their names on our trait tree and extracted DNA from strawberries at our stall in the Discover Zone, run together with the Taylor group.
  • Congratulations to Witold and Emma following their DPhil viva

    Witold did his viva on 29th October 2014 and Emma on 16th January 2015.

  • Science paper published describing context specific eQTL related to innate immunity

    Fairfax BP, Humburg P, Makino S, Naranbhai V, Wong D, Lau E, Jostins L, Plant K, Andrews R, McGee C and Knight JC. 2014 Innate Immune Activity Conditions Effects of Regulatory Variants upon Monocyte Gene Expression. Science 343: 1246949. doi:1246910.1241126/science.1246949

    View in PubMed Hyperlink Overview of work reported

  • A Night at the Museum on 26th September 2014

    Kat, Peter, Anna and Julian hosted a stall at Science Uncovered in the Natural History Museum in London.

  • Knight Group at the Cheltenham Science Festival on 6th June 2014

    DNA as it never tasted before, designer bracelets based on one of your eye colour genes, a trait tree and extracting DNA from strawberries all made for an exciting day with over 400 visitors to the stand.

  • Congratulations to Antonio following his DPhil viva on 30th Jan 2014

  • Congratulations to Seiko following her DPhil viva on 9th Jan 2014

    The Doctor is ready for some more Kayaking!