Publications

vissE.cloud: a webserver to visualise higher order molecular phenotypes from enrichment analysis
vissE.Cloud is a web-server that can help identify, visualise and explore higher-order biological processes from the results of a gene-set enrichment analysis (GSEA). It provides end-to-end analysis of scRNA-seq (10x Chromium) and spatial transcriptomics (10x Visium, 10x Xenium, and NanoString CosMx) datasets.
Ahmed Mohamed, Dharmesh D Bhuva, Sam Lee, Ning Liu, Chin Wee Tan, Melissa J Davis
Cite Code DOI Web tool Bioconductor Workshop
vissE.cloud: a webserver to visualise higher order molecular phenotypes from enrichment analysis
Transcriptomic profiling of cardiac tissues from SARS-CoV-2 patients identifies DNA damage
Abstract The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is known to present with pulmonary and extra-pulmonary organ …
Arutha Kulasinghe, NingLiu, Chin WeeTan, James Monkman, Jane E Sinclair, Dharmesh D Bhuva, David Godbolt, Liuliu Pan, Andy Nam, Habib Sadeghirad, Kei Sato, Gianluigi Li Bassi, Ken O'Byrne, Camila Hartmann, Anna Flavia Ribeiro dos Santos Miggiolaro, Gustavo Lenci Marques, Lidia ZytynskiMoura, Derek Richard, Mark Adams, Lucia de Noronha, Cristina Pellegrino Baena, Jacky Y Suen, Rakesh Arora, Gabrielle T Belz, Kirsty R Short, Melissa J Davis, Fernando Souza-Fonseca Guimaraes, John F Fraser
Cite Code DOI Bioconductor
Transcriptomic profiling of cardiac tissues from SARS-CoV-2 patients identifies DNA damage
Profiling of lung SARS-CoV-2 and influenza virus infection dissects virus-specific host responses and gene signatures
Background: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) which emerged in late 2019 has spread globally, causing a …
Arutha Kulasinghe, Chin Wee Tan, Anna Flavia Ribeiro dos Santos Miggiolaro, James Monkman, Habib Sadeghirad, Dharmesh D Bhuva, Jarbas da Silva Motta Junior, Caroline Busatta Vaz de Paula, Seigo Nagashima, Cristina Pellegrino Baena, Paulo Souza-Fonseca-Guimaraes, Lucia de Noronha, Timothy McCulloch, Gustavo Rodrigues Rossi, Caroline Cooper, Benjamin Tang, Kirsty R Short, Melissa J Davis, Fernando Souza-Fonseca Guimaraes, Gabrielle T Belz, Ken O'Byrne
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Profiling of lung SARS-CoV-2 and influenza virus infection dissects virus-specific host responses and gene signatures
Computational Screening of Anti-Cancer Drugs Identifies a New BRCA Independent Gene Expression Signature to Predict Breast Cancer Sensitivity to Cisplatin
In this work, we developed models to predict drug response in cancer patients using cell line models
Jean Berthelet, Momeneh Foroutan, Dharmesh D Bhuva, Holly J Whitfield, Farrah El-Saafin, Joseph Cursons, Antonin Serrano, Michal Merdas, Elgene Lim, Emmanuelle Charafe-Jauffret, Christophe Ginestier, Matthias Ernst, Frédéric Hollande, Robin L Anderson, Bhupinder Pal, Belinda Yeo, Melissa J Davis, Delphine Merino
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Computational Screening of Anti-Cancer Drugs Identifies a New BRCA Independent Gene Expression Signature to Predict Breast Cancer Sensitivity to Cisplatin
vissE: A versatile tool to identify and visualise higher-order molecular phenotypes from functional enrichment analysis
vissE is a tool that can help identify, visualise and explore higher-order biological processes from the results of a gene-set enrichment analysis (GSEA)
Dharmesh D Bhuva, Chin Wee Tan, Ning Liu, Holly J Whitfield, Nicholas Papachristos, Sam Lee, Malvika Kharbanda, Ahmed Mohamed, Melissa J Davis
PDF Cite Code DOI Web tool Bioconductor Workshop
vissE: A versatile tool to identify and visualise higher-order molecular phenotypes from functional enrichment analysis
Systems pharmacogenomics identifies novel targets and clinically actionable therapeutics for medulloblastoma
Background: Medulloblastoma (MB) is the most common malignant paediatric brain tumour and a leading cause of cancer-related mortality …
Laura Genovesi, Amanda Millar, Elissa Tolson, Matthew Singleton, Emily Hassall, Marija Kojic, Caterina Brighi, Emily Girard, Clara Andradas, Mani Kuchibhotla, Dharmesh D Bhuva, Raelene Endersby, Nicholas G Gottardo, Anne Bernard, Christelle Adolphe, James M Olson, Melissa J Davis, Brandon J Wainwright
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Systems pharmacogenomics identifies novel targets and clinically actionable therapeutics for medulloblastoma
Stable gene expression for normalisation and single-sample scoring
This work proposes an extension to our robust single-sample molecular phenotyping method, singscore, that works on targeted transcriptomic panels with as few as 5 endogenous control genes, thus taking the approach a step closer to the clinic.
Dharmesh D Bhuva, Joseph Cursons, Melissa J Davis
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Stable gene expression for normalisation and single-sample scoring
Differential co-expression-based detection of conditional relationships in transcriptional data: comparative analysis and application to breast cancer
dcanr is a method that helps infer differential regulatory networks from high-througput ‘omics data
Dharmesh D Bhuva, Joseph Cursons, Gordon K Smyth, Melissa J Davis
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Differential co-expression-based detection of conditional relationships in transcriptional data: comparative analysis and application to breast cancer
Using singscore to predict mutation status in acute myeloid leukemia from transcriptomic signatures
This workflow demonstrates the versatility of singscore by applying it to infer mutation status in cancer
Dharmesh D Bhuva, Momeneh Foroutan, Yi Xie, Ruqian Lyu, Joseph Cursons, Melissa J Davis
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Using singscore to predict mutation status in acute myeloid leukemia from transcriptomic signatures
Single sample scoring of molecular phenotypes
singscore is a robust rank-based method to compute molecular phenotypes scores for individual samples such as those originating from an individual patient in the clinic
Momeneh Foroutan, Dharmesh D Bhuva, Ruqian Lyu, Kristy Horan, Joseph Cursons, Melissa J Davis
PDF Cite Code Video DOI Bioconductor Workshop
Single sample scoring of molecular phenotypes