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The Short Chain Fatty Acid Butyrate Imprints an Antimicrobial Program in Macrophages

Immunity (Cambridge, Mass.), 2019-02, Vol.50 (2), p.432-445.e7

2019

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Genome sequencing of the extinct Eurasian wild aurochs, Bos primigenius, illuminates the phylogeography and evolution of cattle

Genome Biology, 2015-10, Vol.16 (1), p.234-234, Article 234

2015

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Plasma Metabolomics Implicates Modified Transfer RNAs and Altered Bioenergetics in the Outcomes of Pulmonary Arterial Hypertension

Circulation (New York, N.Y.), 2017-01, Vol.135 (5), p.460-475

2017

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RNA sequencing provides exquisite insight into the manipulation of the alveolar macrophage by tubercle bacilli

Scientific reports, 2015-09, Vol.5 (1), p.13629-13629, Article 13629

2015

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Invasive Salmonella exploits divergent immune evasion strategies in infected and bystander dendritic cell subsets

Nature communications, 2018-11, Vol.9 (1), p.4883-17, Article 4883

2018

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High-throughput transcriptomics reveals common and strain-specific responses of human macrophages to infection with Mycobacterium abscessus Smooth and Rough variants

BMC genomics, 2015-12, Vol.16 (1), p.1046-1046, Article 1046

2015

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TreeSummarizedExperiment: a S4 class for data with hierarchical structure [version 2; peer review: 3 approved]

F1000 research, 2021, Vol.9, p.1246-1246

2021

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TreeSummarizedExperiment: a S4 class for data with hierarchical structure [version 1; peer review: 2 approved, 1 approved with reservations]

F1000 research, 2020, Vol.9, p.1246

2020

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Panpipes: a pipeline for multiomic single-cell and spatial transcriptomic data analysis

Genome Biology, 2024-07, Vol.25 (1), p.1-20, Article 181

2024

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iSEE: Interactive SummarizedExperiment Explorer

F1000 research, 2018, Vol.7, p.741-741

2018

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GOexpress: an R/Bioconductor package for the identification and visualisation of robust gene ontology signatures through supervised learning of gene expression data

BMC bioinformatics, 2016-03, Vol.17 (1), p.126-126, Article 126

2016

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Comparative 'omics analyses differentiate Mycobacterium tuberculosis and Mycobacterium bovis and reveal distinct macrophage responses to infection with the human and bovine tubercle bacilli

Microbial genomics, 2018-03, Vol.4 (3)

2018

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RNA-seq Transcriptional Profiling of Peripheral Blood Leukocytes from Cattle Infected with Mycobacterium bovis

Frontiers in immunology, 2014-08, Vol.5, p.396-396

2014

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Whole-transcriptome, high-throughput RNA sequence analysis of the bovine macrophage response to Mycobacterium bovis infection in vitro

BMC genomics, 2013-04, Vol.14 (1), p.230-230, Article 230

2013

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RNA Sequencing (RNA-Seq) Reveals Extremely Low Levels of Reticulocyte-Derived Globin Gene Transcripts in Peripheral Blood From Horses ( Equus caballus ) and Cattle ( Bos taurus )

Frontiers in genetics, 2018-08, Vol.9, p.278-278

2018

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RNA-Seq Transcriptome Analysis of Peripheral Blood From Cattle Infected With Mycobacterium bovis Across an Experimental Time Course

Frontiers in veterinary science, 2021-05, Vol.8, p.662002-662002

2021

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Comparative functional genomics and the bovine macrophage response to strains of the mycobacterium genus

Frontiers in immunology, 2014, Vol.5, p.536

2014

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Orchestrating single-cell analysis with Bioconductor

Nature methods, 2020-02, Vol.17 (2), p.137

2020

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Capture-C: a modular and flexible approach for high-resolution chromosome conformation capture

Nature protocols, 2022-02, Vol.17 (2), p.445-475

2022

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Author Correction: Capture-C: a modular and flexible approach for high-resolution chromosome conformation capture

Nature protocols, 2023-10, Vol.18 (10), p.3155-3155

2023

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Experimental infection of cattle with Mycobacterium tuberculosis isolates shows the attenuation of the human tubercle bacillus for cattle

Scientific reports, 2018-01, Vol.8 (1), p.894-13, Article 894

2018

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The bovine alveolar macrophage DNA methylome is resilient to infection with Mycobacterium bovis

Scientific reports, 2019-02, Vol.9 (1), p.1510-1510, Article 1510

2019

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Correlation of disorder between S. cerevisiae interacting proteinsPublished as part of a Molecular BioSystems themed issue on Intrinsically Disordered Proteins: Guest Editor M. Madan Babu.Electronic supplementary information (ESI) available. See DOI: 10.1039/c1mb05214d

2011-12

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Integrated computational prediction and experimental validation identifies promiscuous T cell epitopes in the proteome of Mycobacterium bovis

Microbial genomics, 2016-08, Vol.2 (8), p.e000071-e000071

2016

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The Short Chain Fatty Acid Butyrate Imprints an Antimicrobial Program in Macrophages

Genome sequencing of the extinct Eurasian wild aurochs, Bos primigenius, illuminates the phylogeography and evolution of cattle

Plasma Metabolomics Implicates Modified Transfer RNAs and Altered Bioenergetics in the Outcomes of Pulmonary Arterial Hypertension

RNA sequencing provides exquisite insight into the manipulation of the alveolar macrophage by tubercle bacilli

Invasive Salmonella exploits divergent immune evasion strategies in infected and bystander dendritic cell subsets

High-throughput transcriptomics reveals common and strain-specific responses of human macrophages to infection with Mycobacterium abscessus Smooth and Rough variants

TreeSummarizedExperiment: a S4 class for data with hierarchical structure [version 2; peer review: 3 approved]

TreeSummarizedExperiment: a S4 class for data with hierarchical structure [version 1; peer review: 2 approved, 1 approved with reservations]

Panpipes: a pipeline for multiomic single-cell and spatial transcriptomic data analysis

iSEE: Interactive SummarizedExperiment Explorer

GOexpress: an R/Bioconductor package for the identification and visualisation of robust gene ontology signatures through supervised learning of gene expression data

Comparative 'omics analyses differentiate Mycobacterium tuberculosis and Mycobacterium bovis and reveal distinct macrophage responses to infection with the human and bovine tubercle bacilli

RNA-seq Transcriptional Profiling of Peripheral Blood Leukocytes from Cattle Infected with Mycobacterium bovis

Whole-transcriptome, high-throughput RNA sequence analysis of the bovine macrophage response to Mycobacterium bovis infection in vitro

RNA Sequencing (RNA-Seq) Reveals Extremely Low Levels of Reticulocyte-Derived Globin Gene Transcripts in Peripheral Blood From Horses ( Equus caballus ) and Cattle ( Bos taurus )

RNA-Seq Transcriptome Analysis of Peripheral Blood From Cattle Infected With Mycobacterium bovis Across an Experimental Time Course

Comparative functional genomics and the bovine macrophage response to strains of the mycobacterium genus

Orchestrating single-cell analysis with Bioconductor

IL-1-driven stromal-neutrophil interactions define a subset of patients with inflammatory bowel disease that does not respond to therapies

Capture-C: a modular and flexible approach for high-resolution chromosome conformation capture

Author Correction: Capture-C: a modular and flexible approach for high-resolution chromosome conformation capture

Experimental infection of cattle with Mycobacterium tuberculosis isolates shows the attenuation of the human tubercle bacillus for cattle

The bovine alveolar macrophage DNA methylome is resilient to infection with Mycobacterium bovis

Correlation of disorder between S. cerevisiae interacting proteinsPublished as part of a Molecular BioSystems themed issue on Intrinsically Disordered Proteins: Guest Editor M. Madan Babu.Electronic supplementary information (ESI) available. See DOI: 10.1039/c1mb05214d

Integrated computational prediction and experimental validation identifies promiscuous T cell epitopes in the proteome of Mycobacterium bovis

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