Publications
191 results found
Chang JJ-Y, Gleeson J, Rawlinson D, et al., 2022, Long-Read RNA Sequencing Identifies Polyadenylation Elongation and Differential Transcript Usage of Host Transcripts During SARS-CoV-2 <i>In Vitro</i> Infection, FRONTIERS IN IMMUNOLOGY, Vol: 13, ISSN: 1664-3224
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- Citations: 3
Zhang M, Jia C, Li F, et al., 2022, Critical assessment of computational tools for prokaryotic and eukaryotic promoter prediction, BRIEFINGS IN BIOINFORMATICS, Vol: 23, ISSN: 1467-5463
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- Citations: 8
Steinig E, Duchene S, Aglua I, et al., 2022, Phylodynamic Inference of Bacterial Outbreak Parameters Using Nanopore Sequencing, MOLECULAR BIOLOGY AND EVOLUTION, Vol: 39, ISSN: 0737-4038
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- Citations: 5
Schlapbach LJ, Coin L, 2022, Understanding Detrimental Host Response to Infection-The Promise of Transcriptomics, PEDIATRIC CRITICAL CARE MEDICINE, Vol: 23, Pages: 133-135, ISSN: 1529-7535
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- Citations: 1
Ganesamoorthy D, Robertson AJ, Chen W, et al., 2022, Whole genome deep sequencing analysis of cell-free DNA in samples with low tumour content, BMC CANCER, Vol: 22
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- Citations: 4
Li F, Dong S, Leier A, et al., 2022, Positive-unlabeled learning in bioinformatics and computational biology: a brief review, BRIEFINGS IN BIOINFORMATICS, Vol: 23, ISSN: 1467-5463
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- Citations: 17
Li F, Guo X, Xiang D, et al., 2022, Computational analysis and prediction of PE_PGRS proteins using machine learning, COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL, Vol: 20, Pages: 662-674, ISSN: 2001-0370
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- Citations: 9
Zhang S, Li X, Wu J, et al., 2021, Molecular Methods for Pathogenic Bacteria Detection and Recent Advances in Wastewater Analysis, WATER, Vol: 13
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- Citations: 7
Li F, Guo X, Jin P, et al., 2021, Porpoise: a new approach for accurate prediction of RNA pseudouridine sites, BRIEFINGS IN BIOINFORMATICS, Vol: 22, ISSN: 1467-5463
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- Citations: 30
Li X, Kulandaivelu J, Zhang S, et al., 2021, Data-driven estimation of COVID-19 community prevalence through wastewater-based epidemiology, SCIENCE OF THE TOTAL ENVIRONMENT, Vol: 789, ISSN: 0048-9697
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- Citations: 36
De T, Goncalves A, Speed D, et al., 2021, Signatures of TSPAN8 variants associated with human metabolic regulation and diseases, iScience, Vol: 24, ISSN: 2589-0042
Here, with the example of common copy number variation (CNV) in the TSPAN8 gene, we present an important piece of work in the field of CNV detection, that is, CNV association with complex human traits such as 1H NMR metabolomic phenotypes and an example of functional characterization of CNVs among human induced pluripotent stem cells (HipSci). We report TSPAN8 exon 11 (ENSE00003720745) as a pleiotropic locus associated with metabolomic regulation and show that its biology is associated with several metabolic diseases such as type 2 diabetes (T2D) and cancer. Our results further demonstrate the power of multivariate association models over univariate methods and define metabolomic signatures for variants in TSPAN8.
Parry R, Gifford RJ, Lytras S, et al., 2021, No evidence of SARS-CoV-2 reversetranscription and integration as the origin of chimeric transcripts in patient tissues, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol: 118, ISSN: 0027-8424
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- Citations: 17
Irwin AD, Coin LJM, Harris PNA, et al., 2021, Optimising Treatment Outcomes for Children and Adults Through Rapid Genome Sequencing of Sepsis Pathogens. A Study Protocol for a Prospective, Multi-Centre Trial (DIRECT), FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY, Vol: 11, ISSN: 2235-2988
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- Citations: 4
Chang JJ-Y, Rawlinson D, Pitt ME, et al., 2021, Transcriptional and epi-transcriptional dynamics of SARS-CoV-2 during cellular infection, CELL REPORTS, Vol: 35, ISSN: 2211-1247
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- Citations: 17
Bainomugisa A, Meumann EM, Rajahram GS, et al., 2021, Genomic epidemiology of tuberculosis in eastern Malaysia: insights for strengthening public health responses, MICROBIAL GENOMICS, Vol: 7, ISSN: 2057-5858
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- Citations: 4
Halliday A, Jain P, Hoang L, et al., 2021, New technologies for diagnosing active TB: the VANTDET diagnostic accuracy study, Efficacy and Mechanism Evaluation, Vol: 8, Pages: 1-160, ISSN: 2050-4365
<jats:sec id="abs1-1"> <jats:title>Background</jats:title> <jats:p>Tuberculosis (TB) is a devastating disease for which new diagnostic tests are desperately needed.</jats:p> </jats:sec> <jats:sec id="abs1-2"> <jats:title>Objective</jats:title> <jats:p>To validate promising new technologies [namely whole-blood transcriptomics, proteomics, flow cytometry and quantitative reverse transcription-polymerase chain reaction (qRT-PCR)] and existing signatures for the detection of active TB in samples obtained from individuals with suspected active TB.</jats:p> </jats:sec> <jats:sec id="abs1-3"> <jats:title>Design</jats:title> <jats:p>Four substudies, each of which used samples from the biobank collected as part of the interferon gamma release assay (IGRA) in the Diagnostic Evaluation of Active TB study, which was a prospective cohort of patients recruited with suspected TB.</jats:p> </jats:sec> <jats:sec id="abs1-4"> <jats:title>Setting</jats:title> <jats:p>Secondary care.</jats:p> </jats:sec> <jats:sec id="abs1-5"> <jats:title>Participants</jats:title> <jats:p>Adults aged ≥ 16 years presenting as inpatients or outpatients at 12 NHS hospital trusts in London, Slough, Oxford, Leicester and Birmingham, with suspected active TB.</jats:p> </jats:sec> <jats:sec id="abs1-6"> <jats:title>Interventions</jats:title> <jats:p>New tests using genome-wide gene expression microarray
Gliddon H, Kaforou M, Alikian M, et al., 2021, Identification of reduced host transcriptomic signatures for tuberculosis disease and digital PCR-based validation and quantification, Frontiers in Immunology, Vol: 12, ISSN: 1664-3224
Recently, host whole blood gene expression signatures have been identified for diagnosis of tuberculosis (TB). Absolute quantification of the concentrations of signature transcripts in blood have not been reported, but would facilitate diagnostic test development. To identify minimal transcript signatures, we applied a transcript selection procedure to microarray data from African adults comprising 536 patients with TB, other diseases (OD) and latent TB (LTBI), divided into training and test sets. Signatures were further investigated using reverse transcriptase (RT)—digital PCR (dPCR). A four-transcript signature (GBP6, TMCC1, PRDM1, and ARG1) measured using RT-dPCR distinguished TB patients from those with OD (area under the curve (AUC) 93.8% (CI95% 82.2–100%). A three-transcript signature (FCGR1A, ZNF296, and C1QB) differentiated TB from LTBI (AUC 97.3%, CI95%: 93.3–100%), regardless of HIV. These signatures have been validated across platforms and across samples offering strong, quantitative support for their use as diagnostic biomarkers for TB.
Nguyen SH, Cao MD, Coin LJM, 2021, Real-time resolution of short-read assembly graph using ONT long reads, PLOS COMPUTATIONAL BIOLOGY, Vol: 17, ISSN: 1553-734X
Murigneux V, Rai SK, Furtado A, et al., 2020, Comparison of long-read methods for sequencing and assembly of a plant genome, GIGASCIENCE, Vol: 9, ISSN: 2047-217X
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- Citations: 39
Borghesi A, Trück J, Asgari S, et al., 2020, Whole-exome sequencing for the identification of rare variants in primary immunodeficiency genes in children with sepsis - a prospective population-based cohort study., Clinical Infectious Diseases, Vol: 71, Pages: e614-e623, ISSN: 1058-4838
BACKGROUND: The role of primary immunodeficiencies (PID) in susceptibility to sepsis remains unknown. It is unclear whether children with sepsis benefit from genetic investigations. We hypothesized that sepsis may represent the first manifestation of underlying PID. We applied whole-exome sequencing (WES) to a national cohort of children with sepsis to identify rare, predicted pathogenic variants in PID genes. METHODS: Multicenter population-based prospective study including previously healthy children ≥28 days and <17 years admitted with blood culture-proven sepsis. Using a stringent variant filtering procedure, analysis of WES data was restricted to rare, predicted pathogenic variants in 240 PID genes for which increased susceptibility to bacterial infection has been reported. RESULTS: 176 children presenting with 185 sepsis episodes underwent WES (median age 52 months, IQR 15.4-126.4). 41 unique predicted pathogenic PID variants (1 homozygous, 5 hemizygous, and 35 heterozygous) were found in 35/176 (20%) patients, including 3/176 (2%) patients carrying variants which were previously reported to lead to PID. The variants occurred in PID genes across all 8 PID categories as defined by the International Union of Immunological Societies. We did not observe a significant correlation between clinical or laboratory characteristics of patients and the presence or absence of PID variants. CONCLUSIONS: Applying WES to a population-based cohort of previously healthy children with bacterial sepsis detected Variants of Uncertain Significance in PID genes in one out of five children. Future studies need to investigate the functional relevance of these variants to determine whether variants in PID genes contribute to pediatric sepsis susceptibility.
Zhou C, Olukolu B, Gemenet DC, et al., 2020, Assembly of whole-chromosome pseudomolecules for polyploid plant genomes using outbred mapping populations, NATURE GENETICS, Vol: 52, Pages: 1256-+, ISSN: 1061-4036
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- Citations: 7
Pitt ME, Nguyen SH, Duarte TPS, et al., 2020, Complete Genome Sequences of Clinical <i>Pandoraea fibrosis</i> Isolates, MICROBIOLOGY RESOURCE ANNOUNCEMENTS, Vol: 9, ISSN: 2576-098X
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- Citations: 1
Pitt ME, Nguyen SH, Duarte TPS, et al., 2020, Evaluating the genome and resistome of extensively drug-resistant <i>Klebsiella pneumoniae</i> using native DNA and RNA Nanopore sequencing, GIGASCIENCE, Vol: 9, ISSN: 2047-217X
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- Citations: 18
Zhang P, Ganesamoorthy D, Nguyen SH, et al., 2020, Nanopore sequencing as a scalable, cost-effective platform for analyzing polyclonal vector integration sites following clinical T cell therapy, JOURNAL FOR IMMUNOTHERAPY OF CANCER, Vol: 8
Gemenet DC, Pereira GDS, De Boeck B, et al., 2020, Quantitative trait loci and differential gene expression analyses reveal the genetic basis for negatively associated β-carotene and starch content in hexaploid sweetpotato [<i>Ipomoea batatas</i> (L.) Lam.], THEORETICAL AND APPLIED GENETICS, Vol: 133, Pages: 23-36, ISSN: 0040-5752
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- Citations: 39
Raftery LJ, Howard CB, Grewal YS, et al., 2019, Retooling phage display with electrohydrodynamic nanomixing and nanopore sequencing, LAB ON A CHIP, Vol: 19, Pages: 4083-4092, ISSN: 1473-0197
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- Citations: 4
Xu J, Falconer C, Nguyen Q, et al., 2019, Genotype-free demultiplexing of pooled single-cell RNA-seq, GENOME BIOLOGY, Vol: 20, ISSN: 1474-760X
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- Citations: 28
Wang X, Nijman R, Camuzeaux S, et al., 2019, Plasma lipid profiles discriminate bacterial from viral infection in febrile children, Scientific Reports, Vol: 9, ISSN: 2045-2322
Fever is the most common reason that children present to Emergency Departments. Clinical signs and symptoms suggestive of bacterial infection are often non-specific, and there is no definitive test for the accurate diagnosis of infection. The ‘omics’ approaches to identifying biomarkers from the host-response to bacterial infection are promising. In this study, lipidomic analysis was carried out with plasma samples obtained from febrile children with confirmed bacterial infection (n=20) and confirmed viral infection (n=20). We show for the first time that bacterial and viral infection produces distinct profile in the host lipidome. Some species of glycerophosphoinositol, sphingomyelin, lysophosphatidylcholine and cholesterol sulfate were higher in the confirmed virus infected group, while some species of fatty acids, glycerophosphocholine, glycerophosphoserine, lactosylceramide and bilirubin were lower in the confirmed virus infected group when compared with confirmed bacterial infected group..A combination of three lipids achieved an area under the receiver operating characteristic (ROC) curve of 0.911 (95% CI 0.81 to 0.98). This pilot study demonstrates the potential of metabolic biomarkers to assist clinicians in distinguishing bacterial from viral infection in febrile children, to facilitate effective clinical management and to the limit inappropriate use of antibiotics.
Alves AC, De Silva NMG, Karhunen V, et al., 2019, GWAS on longitudinal growth traits reveals different genetic factors influencing infant, child, and adult BMI, Science Advances, Vol: 5, ISSN: 2375-2548
Early childhood growth patterns are associated with adult health, yet the genetic factors and the developmental stages involved are not fully understood. Here we combine genome-wide association studies with modelling of longitudinal growth traits to study the genetics of infant and child growth, followed by functional, pathway, genetic correlation, risk score and co-localization analyses to determine how developmental timings, molecular pathways and genetic determinants of these traits overlap with those of adult health. We found a robust overlap between the genetics of child and adult BMI, with variants associated with adult BMI acting as early as 4-6 years old. However, we demonstrated a completely distinct genetic makeup for peak BMI during infancy, influenced by variation at the LEPR/LEPROT locus. These findings suggest that different genetic factors control infant and child BMI. In light of the obesity epidemic, these findings are important to inform the timing and targets of prevention strategies.
Shimizu C, Kim J, Eleftherohorinou H, et al., 2019, HLA-C variants associated with amino acid substitutions in the peptide binding groove influence susceptibility to Kawasaki disease, Human Immunology, Vol: 80, Pages: 731-738, ISSN: 0198-8859
Kawasaki disease (KD) is a pediatric vasculitis caused by an unknown trigger in genetically susceptible children. The incidence varies widely across genetically diverse populations. Several associations with HLA Class I alleles have been reported in single cohort studies. Using a genetic approach, from the nine single nucleotide variants (SNVs) associated with KD susceptibility in children of European descent, we identified SNVs near the HLA-C (rs6906846) and HLA-B genes (rs2254556) whose association was replicated in a Japanese descent cohort (rs6906846 p = 0.01, rs2254556 p = 0.005). The risk allele (A at rs6906846) was also associated with HLA-C*07:02 and HLA-C*04:01 in both US multi-ethnic and Japanese cohorts and HLA-C*12:02 only in the Japanese cohort. The risk A-allele was associated with eight non-conservative amino acid substitutions (amino acid positions); Asp or Ser (9), Arg (14), Ala (49), Ala (73), Ala (90), Arg (97), Phe or Ser (99), and Phe or Ser (116) in the HLA-C peptide binding groove that binds peptides for presentation to cytotoxic T cells (CTL). This raises the possibility of increased affinity to a "KD peptide" that contributes to the vasculitis of KD in genetically susceptible children.
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