Publications
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Commentaries and Outreach

Translational genomics

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Fairbrother-Browne et al. (includes T Xenakis)

Molecular and cellular signatures differentiate Parkinson’s disease from Parkinson’s disease with dementia

bioRxiv​

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Budinger et al.

An in vivo and in vitro spatiotemporal atlas of human midbrain development

bioRxiv​

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McGlacken-Byrne et al. (includes T Xenakis)

Mapping the anatomical and transcriptional landscape of early human fetal ovary development

bioRxiv

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McGlacken-Byrne et al. (includes T Xenakis)

Single-nucleus RNA-sequencing reveals novel potential mechanisms of ovarian insufficiency in 45,X Turner Syndrome

bioRxiv

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Hall and Castellano

Dawnn: single-cell differential abundance with neural networks

bioRxiv

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Loukogeorgakis et al. (includes T Xenakis)

Prenatal VEGF Nano-Delivery Reverses Congenital Diaphragmatic Hernia-Associated Pulmonary Abnormalities

bioRxiv

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Hall GT

Portable-CELLxGENE: standalone executables of CELLxGENE for easy installation

GIGAbyte​ (2025)

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Buddle et al.

Clinical metagenomics for detection of viruses using short-read, long-read and targeted approaches

Genome Medicine, ​16, 11 (2024)

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Gerli et al. (includes T Xenakis)

Single cell-guided prenatal derivation of primary epithelial organoids from the human amniotic and tracheal fluids

Nature Medicine, 30, 875–887 (2024)​

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​Puigdevall et al.

Somatic mutations alter the differentiation outcomes of iPSC-derived neurons

Cell Genomics, 3, 100280 (2023)

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Morfopoulou et al.

Genomic investigations of acute hepatitis of unknown aetiology in children

Nature, 617, 564–573 (2023)​

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Bea-Mascato et al.

Loss of the centrosomal protein ALMS1 alters lipid metabolism and the regulation of extracellular matrix-related processes

Biology Direct, 18, 84 (2023)

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Jayarajan et al.

Short-term keratinocyte Rho-associated kinase inhibitor treatment accelerates primary keratinocyte growth while preserving stem cell characteristics

Cells, 12, 346 (2023)

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Michelozzi et al.

Enhanced functionality of low-affinity CD19 CAR T-cells is associated with activation priming and a polyfunctional cytokine phenotype

Blood Advances, 7, 1725–1738 (2023)

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Wilkinson et al.

CD14+ monocyte-derived oxidised mitochondrial DNA amplifies the inflammatory interferon type 1 signature in Juvenile Dermatomyositis

Annals of the Rheumatic Diseases, 82, 658-669 (2023)

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Aggarwal et al. (including COG-UK).

The role of genomics in understanding COVID-19 outbreaks in long term care facilities 

The Lancet Microbe, 3, e151-e158 (2022)

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Snell et al. (including COG-UK). 

Combined epidemiological and genomic analysis of nosocomial SARS-CoV-2 transmission identifies community social distancing as the dominant intervention reducing outbreaks

Clinical Microbiology and Infection, 28, 93–100 (2022)

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Sánchez-Corrales, Pohle, Castellano and Giustacchini

Taming Cell-to-Cell Heterogeneity in Acute Myeloid Leukaemia With Machine Learning

Frontiers in Oncology, 11, 1411 (2021)

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Lythgoe et al. (including COG-UK)

SARS-CoV-2 within host diversity and transmission

Science, 372, eabg0821 (2021)

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Parker et al. (including COG-UK)

Subgenomic RNA identification in SARS-CoV-2 genomic sequencing data

Genome research, 31, 645-658 (2021)

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Stirrup et al. (including COG-UK). 

Rapid feedback on hospital onset SARS-CoV-2 infections combining epidemiological and sequencing data

Elife, 10, e65828 (2021)

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Thomson et al. (including COG-UK)

Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity

Cell, 184, 1171-1187 (2021)

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Hosie et al. (including COG-UK). Detection of SARS‐CoV‐2 in respiratory samples from cats in the UK associated with human‐to‐cat transmission. 

Veterinary Record, 188, 8 (2021)

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du Plessis et al. (including COG-UK)

Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK

Science, 371, 708-712 (2021)

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Volz et al. (including COG-UK)

Evaluating the effects of SARS-CoV-2 spike mutation D614G on transmissibility and pathogenicity

Cell, 184, 64-75 (2021)

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O'Toole et al. (including COG-UK)

Tracking the international spread of SARS-CoV-2 lineages B. 1.1. 7 and B. 1.351/501Y-V2 with grinch

Wellcome open research, 6 (2021)

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Page et al. (including COG-UK)

Large-scale sequencing of SARS-CoV-2 genomes from one region allows detailed epidemiology and enables local outbreak management

Microbial genomics, 7 (2021)

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Da Silva et al. (including COG-UK)

Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland

Nature Microbiology, 6, 112-122 (2021)

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The COVID-19 Genomics UK consortium (COG-UK)

An integrated national scale SARS-CoV-2 genomic surveillance network

The Lancet Microbe, 1, e99–e100 (2020)

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Ancient genomics

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Martin, Jay, Castellano and Slatkin

Determination of genetic relatedness from low-coverage human genome sequences using pedigree simulations

Molecular Ecology, 26, 4145-4157 (2017)

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De Manuel et al.

Chimpanzee genomic diversity reveals ancient admixture with bonobos

Science, 354, 477-481 (2016)

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Mendez, Poznik, Castellano and Bustamante

The divergence of Neandertal and modern human Y chromosomes

The American Journal of Human Genetics, 98, 728-734 (2016)

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Kuhlwilm et al.

Ancient gene flow from early modern humans into Eastern Neanderthals

Nature, 530, 429-433 (2016)

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Lazaridis et al.

Ancient human genomes suggest three ancestral populations for present-day Europeans

Nature, 513, 409-413 (2014)

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Castellano et al.

Patterns of coding variation in the complete exomes of three Neandertals

PNAS, 111, 6666-6671 (2014)

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Fu et al.

A revised timescale for human evolution based on ancient mitochondrial genomes

Current Biology, 23, 553-559 (2013)

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Micronutrient genomics

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Rees et al.
Ancient loss of catalytic selenocysteine spurred convergent adaptation in a mammalian oxidoreductase

Genome Biology and Evolution, 16, 3 (2024)

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Sarangi et al.

Distinct Patterns of Selection in Selenium-Dependent Genes between Land and Aquatic Vertebrates

Molecular Biology and Evolution, 35, 1744-1756 (2018)

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Davy and Castellano

The genomics of selenium: Its past, present and future

Biochimica et Biophysica Acta, 1862, 2427-2432 (2018).

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Sarangi, White and Castellano

Genetic adaptation and Selenium uptake in vertebrates.

In Encyclopedia of the Life Sciences. Wiley (2018)

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Castellano.

Selenium strikes back at fungi

Nature Microbiology, 4, 726-727 (2018)

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Gladyshev et al.

Selenoprotein Gene Nomenclature

The Journal of Biological Chemistry, 291, 24036-24040 (2016)

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White and Castellano

The role of selenium in human evolution

In D. Hatfield and V. Gladyshev (Eds.), Selenium: Its molecular biology and role in human health (4th ed., pp. 59-71). Springer (2016)

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White et al.

Genetic adaptation to levels of dietary selenium in recent human history

Molecular Biology and Evolution, 32, 1507-1518 (2015)

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Romagné et al.

SelenoDB 2.0: Annotation of selenoprotein genes in animals and their genetic diversity in humans

Nucleic Acids Research, 42, D437-D443 (2014)

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White and Castellano

Evolutionary basis for the use of selenocysteine

In DL Hatfield, MJ Berry and VN Gladyshev (Eds.), Selenium: Its Molecular Biology and Role in Human Health (3, pp. 85-93). New York. Springer (2012)

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Castellano

On the unique function of selenocysteine - insights from the evolution of selenoproteins

Biochimica et Biophysica Acta, 1790, 1463-1470 (2009) - In special issue on selenoprotein expression and function

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Castellano et al.

Low exchangeability of selenocysteine, the 21st amino acid, in vertebrate proteins

Molecular Biology and Evolution, 26, 2031-2040 (2009)

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Castellano, Gladyshev, Guigó and Berry

SelenoDB 1.0: A database of selenoprotein genes, proteins and SECIS elements

Nucleic Acids Research, 36, D332-D338 (2008)

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Castellano

Little biological and statistical support for hundreds of selenoproteins in mouse pseudo-messenger RNAs 

Reader response - A critical assessment of PLoS Genetics, 2, e3 (2006). PLoS Genetics (2006)

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Castellano et al.

Diversity and functional plasticity of eukaryotic selenoproteins: Identification and characterization of the SelJ family

PNAS, 102, 16188-16193 (2005)

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Taskov et al.

The use of the selenocysteine insertion system to decode one codon in an animal genome?

Nucleic Acids Research, 33, 2227-2238 (2005)

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International Chicken Genome Sequencing Consortium

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

Nature, 432, 695-716 (2004)

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Jaillon et al.

Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype

Nature, 431, 946-957 (2004)

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Castellano

Towards the characterization of the eukaryotic selenoproteome: a computational approach

PhD Thesis (2004)

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Castellano et al. 

Reconsidering the evolution of eukaryotic selenoproteins: A novel nonmammalian family with scattered phylogenetic distribution

EMBO Reports, 5, 71-77 (2004)

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Kryukov et al.

Characterization of mammalian selenoproteomes

Science, 300, 1439-1443 (2003)

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Castellano et al.

In silico identification of novel selenoproteins in the Drosophila melanogaster genome

EMBO Reports, 2, 697-702 (2001)

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Computational genomics

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Abril and Castellano 

Genome Annotation

In Encyclopedia of Bioinformatics and Computational Biology

Elsevier (2018)

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Population genomics

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Rees, Castellano and Andrés

The Genomics of Human Local Adaptation

Trends in Genetics, 36, 415-428 (2018)