Staff Profile

New sequencing technologies such as spatial transcriptomic (ST) and single-cell (SC) techniques have the potential to revolutionise our understanding of disease and human development.

By developing new develop bioinformatics methods I aim to:

1) Create tools to understand spatial components of gene regulation;

2) Study transitions between states using naturally occurring cellular;

3) Investigate analysis methods for new sequencing technologies with the potential to capture additional information about genetic changes. 

• Articles

  • Walls GM, Ghita M, Queen R, Edgar KS, Gill EK, Kuburas R, Grieve DJ, Watson CJ, McWilliam A, Van Herk M, Williams KJ, Cole AJ, Jain S, Butterworth KT. Spatial Gene Expression Changes in the Mouse Heart After Base-targeted Irradiation. International Journal of Radiation Oncology*Biology*Physics 2023, 115(2), 453-463.
  • Collin J, Hasoon MSR, Zerti D, Hammadi S, Dorgau B, Clarke L, Steel D, Hussain R, Coxhead J, Lisgo S, Queen R, Lako M. Single-cell RNA sequencing reveals transcriptional changes of human choroidal and retinal pigment epithelium cells during fetal development, in healthy adult and intermediate age-related macular degeneration. Human Molecular Genetics 2023, 32(10), 1698-1710.
  • Chichagova V, Georgiou M, Carter M, Dorgau B, Hilgen G, Collin J, Queen R, Chung G, Ajeian J, Moya-Molina M, Kustermann S, Pognan F, Hewitt P, Schmitt M, Sernagor E, Armstrong L, Lako M. Incorporating microglia-like cells in human induced pluripotent stem cell-derived retinal organoids. Journal of Cellular and Molecular Medicine 2023, epub ahead of print.
  • Kurzawa-Akanbi M, Whitfield P, Burte F, Bertelli PM, Pathak V, Doherty M, Hilgen B, Gliaudelyte L, Platt M, Queen R, Coxhead J, Porter A, Oberg M, Fabrikova D, Davey T, Beh CS, Georgiou M, Collin J, Boczonadi V, Hartlova A, Taggart M, Al-Aama J, Korolchuk VI, Morris CM, Guduric-Fuchs J, Steel DH, Medina RJ, Armstrong L, Lako M. Retinal pigment epithelium extracellular vesicles are potent inducers of age-related macular degeneration disease phenotype in the outer retina. Journal of Extracellular Vesicles 2022, 11(12), 12295.
  • Rozanska A, Cerna R, Queen R, Collin J, Zerti D, Dorgau B, Beh C, Davey T, Coxhead J, Hussain R, Alaama J, Steel D, Benvenisty N, Armstrong L, Parulekar M, Lako M. pRB-depleted pluripotent stem cell retinal organoids recapitulate cell state transitions of retinoblastoma development and suggest an important role for pRB in retinal cell differentiation. Stem Cell Translational Medicine 2022, 11(4), 415-433.
  • Johnson K, Leary PJ, Govaere O, Barter MJ, Charlton SH, Cockell SJ, Tiniakos D, Zatorska M, Bedossa P, Brosnan MJ, Cobbold JF, Ekstedt M, Aithal GP, Clement K, Schattenberg JM, Boursier J, Ratziu V, Bugianesi E, Anstee QM, Daly AK, LITMUS Consortium Investigators. Increased serum miR-193a-5p during non-alcoholic fatty liver disease progression: Diagnostic and mechanistic relevance. JHEP Reports 2022, 4(2), 100409.
  • Dorgau B, Georgiou M, Chaudhary A, Molina M, Collin J, Queen R, Hilgen G, Davey T, Hewitt P, Schmitt M, Kustermann S, Pognan F, Steel D, Sernagor E, Armstrong L, Lako M. Human Retinal Organoids Provide a Suitable Tool for Toxicological Investigations: A Comprehensive Validation Using Drugs and Compounds Affecting the Retina. Stem Cell Translational Medicine 2022, 11(2), 159-177.
  • Jackson RM, Hatton CF, Spegarova JS, Georgiou M, J Collin, E Stephenson, B Verdon, IJ Haq, R Hussain, JM Coxhead, H-S Mudhar, B Wagner, M Hasoon, T Davey, P Rooney, A Khan, C Ward, M Brodlie, M Haniffa, S Hambleton, L Armstrong, F Figueiredo, Queen R, Duncan CJ, Lako M. Conjunctival epithelial cells resist productive SARS-CoV-2 infection. Stem Cell Reports 2022, 17(7), 1699-1713.
  • Muus C, Queen R, Lako M, Zerti D, HCA Lung Biological Network. Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics. Nature Medicine 2021, 27, 546-559.
  • Armstrong L, Collin J, Mostafa I, Queen R, Figueiredo F, Lako M. In the eye of the storm: SARS-CoV-2 infection and replication at the ocular surface?. Stem Cells Translational Medicine 2021, 10(7), 976-986.
  • Collin J, Queen R, Zerti D, Steel D, Bowen C, Parulekar M, Lako M. Dissecting the transcriptional and chromatin accessibility heterogeneity of proliferating cone precursors in human retinoblastoma tumours by single cell sequencing- opening pathways to new therapeutic strategies?. Investigative Ophthalmology & Visual Science (IOVS) 2021, 62(6).
  • Jardine L, Webb S, Goh I, Quiroga Londono M, Reynolds G, Mather M, Olabi B, Stephenson E, Botting RA, Horsfall D, Engelbert J, Maunder D, Mende N, Murnane C, Dann E, McGrath J, King H, Kucinski I, Queen R, Carey CD, Shrubsole C, Poyner E, Acres M, Jones C, Ness T, Coulthard R, Elliott N, O'Byrne S, Haltalli MLR, Lawrence JE, Lisgo S, Balogh P, Meyer KB, Prigmore E, Ambridge K, Jain MS, Efremova M, Pickard K, Creasey T, Bacardit J, Henderson D, Coxhead J, Filby A, Hussain R, Dixon D, McDonald D, Popescu D-M, Kowalczyk MS, Li B, Ashenberg O, Tabaka M, Dionne D, Tickle TL, Slyper M, Rozenblatt-Rosen O, Regev A, Behjati S, Laurenti E, Wilson NK, Roy A, Gottgens B, Roberts I, Teichmann SA, Haniffa M. Blood and immune development in human fetal bone marrow and Down syndrome. Nature 2021, 598, 327-331.
  • Collin J, Queen R, Zerti D, Figueiredo F, Armstrong L, Lako M. A single cell atlas of human cornea that defines its development, limbal progenitor cells and their interactions with the immune cells. The Ocular Surface Journal 2021, 21, 279-298.
  • Khasawneh RR, Kist R, Queen R, Hussain R, Coxhead J, Schneider JE, Mohun TJ, Zaffran S, Peters H, Phillips HM, Bamforth SD. Msx1 haploinsufficiency modifies the Pax9-deficient cardiovascular phenotype. BMC Developmental Biology 2021, 21, 14.
  • O'Keefe H, Queen R, Lord P, Elson JL. What can a comparative genomics approach tell us about the pathogenicity of mtDNA mutations in human populations?. Evolutionary Applications 2020, 12(10), 1912-1930.
  • Govaere O, Cockell S, Tiniakos D, Queen R, Younes R, Vacca M, Alexander L, Ravaioli F, Palmer J, Petta S, Boursier J, Rosso C, Johnson K, Wonders K, Day CP, Ekstedt M, Oresic M, Darlay R, Cordell H, Marra F, Vidal-Puig A, Bedossa P, Schattenberg JM, Clément K, Allison M, Bugianesi E, Ratziu V, Daly AK, Anstee QM. Transcriptomic profiling across the nonalcoholic fatty liver disease spectrum reveals gene signatures for steatohepatitis and fibrosis. Science Translational Medicine 2020, 12(572), eaba4448.
  • Sungnak W, Huang N, Bécavin C, Berg M, Queen R, Litvinukova M, Talavera-López C, Maatz H, Reichart D, Sampaziotis F, Worlock KB, Yoshida M, Barnes JL, HCA Lung Biological Network, Lako M. SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes. Nature Medicine 2020, 26, 681-687.
  • Sungnak W, Huang N, Becavin C, Berg M, Queen R, Litvinukova M, Talavera-Lopez C, Maatz H, Reichart D, Sampaziotis F, Worlock KB, Yoshida M, Barnes JL, Banovich NE, Barbry P, Brazma A, Collin J, Desai TJ, Duong TE, Eickelberg O, Falk C, Farzan M, Glass I, Gupta RK, Haniffa M, Horvath P, Hubner N, Hung D, Kaminski N, Krasnow M, Kropski JA, Kuhnemund M, Lako M, Lee H, Leroy S, Linnarson S, Lundeberg J, Meyer KB, Miao Z, Misharin AV, Nawijn MC, Nikolic MZ, Noseda M, Ordovas-Montanes J, Oudit GY, Pe'er D, Powell J, Quake S, Rajagopal J, Tata PR, Rawlins EL, Regev A, Reyfman PA, Rozenblatt-Rosen O, Saeb-Parsy K, Samakovlis C, Schiller HB, Schultze JL, Seibold MA, Seidman CE, Seidman JG, Shalek AK, Shepherd D, Spence J, Spira A, Sun X, Teichmann SA, Theis FJ, Tsankov AM, Vallier L, van den Berge M, Whitsett J, Xavier R, Xu Y, Zaragosi L-E, Zerti D, Zhang H, Zhang K, Rojas M, Figueiredo F. SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes. Nature Medicine 2020, 26, 681-687.
  • Cytlak U, Resteu A, Pagan S, Green K, Milne P, Maisuria S, McDonald D, Hulme G, Filby A, Carpenter B, Queen R, Hambleton S, Hague R, Lango Allen H, Thaventhiran JED, Doody G, Collin M, Bigley V. Differential IRF8 Transcription Factor Requirement Defines Two Pathways of Dendritic Cell Development in Humans. Immunity 2020, 53(2), 353-370.
  • Collin J, Queen R, Zerti D, Dorgau B, Georgiou M, Djidrovski I, Hussain R, Coxhead JM, Joseph A, Rooney P, Lisgo S, Figueiredo FC, Armstrong L, Lako M. Co-expression of SARS-CoV-2 entry genes in the superficial adult human conjunctival, limbal and corneal epithelium suggests an additional route of entry via the ocular surface. The Ocular Surface 2020, 19, 190-200.
  • Mellough CB, Collin J, Queen R, Hilgen G, Dorgau B, Zerti D, Felemban M, White K, Sernagor E, Lako M. Systematic Comparison of Retinal Organoid Differentiation from Human Pluripotent Stem Cells Reveals Stage Specific, Cell Line, and Methodological Differences. STEM CELLS Translational Medicine 2019, 8(7), 694-706.
  • Collin J, Queen R, Zerti D, Dorgau B, Hussain R, Coxhead J, Cockell S, Lako M. Deconstructing Retinal Organoids: Single cell RNA-Seq reveals the cellular components of human pluripotent stem cell-derived retina. Stem Cells (Durham) 2019, 37(5), 593-598.
  • Collin J, Zerti D, Queen R, SantoFerreira T, Bauer R, Coxhead J, Hussain R, Steel D, Mellough C, Ader M, Sernagor E, Armstrong L, Lako M. CRX Expression in Pluripotent Stem Cell‐Derived Photoreceptors Marks a Transplantable Subpopulation of Early Cones. Stem Cells (Durham) 2019, 37(5), 609-622.
  • O'Keefe H, Queen RA, Meldau S, Lord P, Elson JL. Haplogroup Context is Less Important in the Penetrance of Mitochondrial DNA Complex I Mutations Compared to mt-tRNA Mutations. Journal of Molecular Evolution 2018, 86(6), 395-403.
  • Bojic S, Hallam D, Alcada N, Ghareeb A, Queen R, Pervinder S, Buck H, Lange AA, Figueiredo G, Rooney P, Stojkovic M, Shortt A, Figueiredo FC, Lako M. CD200 expression marks a population of quiescent limbal epithelial stem cells with holoclone forming ability. Stem Cells 2018, 36(11), 1723-1735.
  • Queen RA, Steyn JS, Lord P, Elson JL. Mitochondrial DNA sequence context in the penetrance of mitochondrial t-RNA mutations: A study across multiple lineages with diagnostic implications. PLOS ONE 2017, 12(11), e0187862.

• Review

  • Zerti Z, Collin J, Queen R, Cockell SJ, Lako M. Understanding the complexity of retinal and pluripotent stem cell derived retinal organoids with single cell RNA sequencing: current progress, remaining challenges and future prospectives. Current Eye Research 2020, 45(3), 385-396.