Publications

This page lists my research publications, organised by employment. Expect some overlap in years for publications arising from transitions between positions.

Sims Group (2020–present)

Learning and teaching biological data science in the Bioconductor community. 2025

Drnevich J, Tan FJ, Almeida-Silva F, Castelo R, Culhane AC, Davis S, Doyle MA, Geistlinger L, Ghazi AR, Holmes S, Lahti L, Mahmoud A, Nishida K, Ramos M, Rue-Albrecht K, Shih DJH, Gatto L, Soneson C.

Paper · DOI · PubMed

Eleven quick tips for writing a Bioconductor package 2025

Charlotte Soneson; B.F. Francis Ouellette; Lori Shepherd; Marcel Ramos; Kevin Rue-Albrecht; Johannes Rainer; Hervé Pagès; Vincent J. Carey

Paper · DOI · PubMed

Panpipes: a pipeline for multiomic single-cell and spatial transcriptomic data analysis. 2024

Curion F, Rich-Griffin C, Agarwal D, Ouologuem S, Rue-Albrecht K, May L, Garcia GEL, Heumos L, Thomas T, Lason W, Sims D, Theis FJ, Dendrou CA.

Paper · DOI · PubMed

Capture-C: a modular and flexible approach for high-resolution chromosome conformation capture. 2022

Downes DJ, Smith AL, Karpinska MA, Velychko T, Rue-Albrecht K, Sims D, Milne TA, Davies JOJ, Oudelaar AM, Hughes JR.

Paper · DOI · PubMed

TreeSummarizedExperiment: a S4 class for data with hierarchical structure. 2020

Huang R, Soneson C, Ernst FGM, Rue-Albrecht KC, Yu G, Hicks SC, Robinson MD.

Paper · DOI · PubMed

Sansom Group (2017–2020)

The transcriptional repressor AEBP2 is indispensable for the epigenetic control of mimetic thymic epithelial cell differentiation and central self-tolerance induction 2025

Wei Wu; Kevin Rue-Albrecht; Qian Cheng; Fatima Dhalla; Mary Deadman; Rongyu Zang; Stephen Sansom; Yiyan Zheng; Georg Hollander

Paper · DOI

IL-1-driven stromal-neutrophil interactions define a subset of patients with inflammatory bowel disease that does not respond to therapies 2021

Friedrich M, Pohin M, Jackson MA, Korsunsky I, Bullers SJ, Rue-Albrecht K, Christoforidou Z, Sathananthan D, Thomas T, Ravindran R, Tandon R, Peres RS, Sharpe H, Wei K, Watts GFM, Mann EH, Geremia A, Attar M; Oxford IBD Cohort Investigators; Roche Fibroblast Network Consortium; McCuaig S, Thomas L, Collantes E, Uhlig HH, Sansom SN, Easton A, Raychaudhuri S, Travis SP, Powrie FM.

Paper · DOI · PubMed

Orchestrating single-cell analysis with Bioconductor. 2019

Amezquita RA, Lun ATL, Becht E, Carey VJ, Carpp LN, Geistlinger L, Marini F, Rue-Albrecht K, Risso D, Soneson C, Waldron L, Pagès H, Smith ML, Huber W, Morgan M, Gottardo R, Hicks SC.

Paper · DOI · PubMed

The Short Chain Fatty Acid Butyrate Imprints an Antimicrobial Program in Macrophages. 2019

Schulthess J, Pandey S, Capitani M, Rue-Albrecht KC, Arnold I, Franchini F, Chomka A, Ilott NE, Johnston DGW, Pires E, McCullagh J, Sansom SN, Arancibia-Cárcamo CV, Uhlig HH, Powrie F.

Paper · DOI · PubMed

iSEE: Interactive SummarizedExperiment Explorer 2018

Rue-Albrecht K, Marini F, Soneson C, Lun ATL

Paper · DOI · PubMed

Ratcliffe Group (2016–2017)

This publication arose from a collaboration started during a short-term research position in the group of Prof. David Mole and Prof. Sir Peter Ratcliffe at the University of Oxford.

Invasive Salmonella exploits divergent immune evasion strategies in infected and bystander dendritic cell subsets. 2018

Aulicino A, Rue-Albrecht KC, Preciado-Llanes L, Napolitani G, Ashley N, Cribbs A, Koth J, Lagerholm BC, Ambrose T, Gordon MA, Sims D, Simmons A.

Paper · DOI · PubMed

Wilkins Group (2015–2016)

These publications arose from my first postdoctoral research position in the group of Prof. Martin Wilkins at Imperial College London.

Whole-genome sequencing of a sporadic primary immunodeficiency cohort. 2020

Thaventhiran JED, Lango Allen H, Burren OS, Rae W, Greene D, Staples E, Zhang Z, Farmery JHR, Simeoni I, Rivers E, Maimaris J, Penkett CJ, Stephens J, Deevi SVV, Sanchis-Juan A, Gleadall NS, Thomas MJ, Sargur RB, Gordins P, Baxendale HE, Brown M, Tuijnenburg P, Worth A, Hanson S, Linger RJ, Buckland MS, Rayner-Matthews PJ, Gilmour KC, Samarghitean C, Seneviratne SL, Sansom DM, Lynch AG, Megy K, Ellinghaus E, Ellinghaus D, Jorgensen SF, Karlsen TH, Stirrups KE, Cutler AJ, Kumararatne DS, Chandra A, Edgar JDM, Herwadkar A, Cooper N, Grigoriadou S, Huissoon AP, Goddard S, Jolles S, Schuetz C, Boschann F; Primary Immunodeficiency Consortium for the NIHR Bioresource; Lyons PA, Hurles ME, Savic S, Burns SO, Kuijpers TW, Turro E, Ouwehand WH, Thrasher AJ, Smith KGC.

Paper · DOI · PubMed

Bi-allelic Loss-of-Function CACNA1B Mutations in Progressive Epilepsy-Dyskinesia. 2019

Gorman KM, Meyer E, Grozeva D, Spinelli E, McTague A, Sanchis-Juan A, Carss KJ, Bryant E, Reich A, Schneider AL, Pressler RM, Simpson MA, Debelle GD, Wassmer E, Morton J, Sieciechowicz D, Jan-Kamsteeg E, Paciorkowski AR, King MD, Cross JH, Poduri A, Mefford HC, Scheffer IE, Haack TB, McCullagh G; Deciphering Developmental Disorders Study; UK10K Consortium; NIHR BioResource; Millichap JJ, Carvill GL, Clayton-Smith J, Maher ER, Raymond FL, Kurian MA.

Paper · DOI · PubMed

Plasma Metabolomics Implicates Modified Transfer RNAs and Altered Bioenergetics in the Outcomes of Pulmonary Arterial Hypertension. 2016

Rhodes CJ, Ghataorhe P, Wharton J, Rue-Albrecht KC, Hadinnapola C, Watson G, Bleda M, Haimel M, Coghlan G, Corris PA, Howard LS, Kiely DG, Peacock AJ, Pepke-Zaba J, Toshner MR, Wort SJ, Gibbs JS, Lawrie A, Gräf S, Morrell NW, Wilkins MR.

Paper · DOI · PubMed

PhD Research (2011–2015)

These publications arose from my doctoral research and collaborations, jointly supervised by Prof. David MacHugh and Prof. Stephen Gordon, at University College Dublin.

RNA-Seq Transcriptome Analysis of Peripheral Blood From Cattle Infected With Mycobacterium bovis Across an Experimental Time Course. 2021

McLoughlin KE, Correia CN, Browne JA, Magee DA, Nalpas NC, Rue-Albrecht K, Whelan AO, Villarreal-Ramos B, Vordermeier HM, Gormley E, Gordon SV, MacHugh DE.

Paper · DOI · PubMed

The bovine alveolar macrophage DNA methylome is resilient to infection with Mycobacterium bovis. 2019

O’Doherty AM, Rue-Albrecht KC, Magee DA, Ahting S, Irwin RE, Hall TJ, Browne JA, Nalpas NC, Walsh CP, Gordon SV, Wojewodzic MW, MacHugh DE.

Paper · DOI · PubMed

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). 2018

Correia CN, McLoughlin KE, Nalpas NC, Magee DA, Browne JA, Rue-Albrecht K, Gordon SV, MacHugh DE.

Paper · DOI · PubMed

High-throughput transcriptomics reveals common and strain-specific responses of human macrophages to infection with Mycobacterium abscessus Smooth and Rough variants 2015

Aulicino A, Dinan AM, Miranda-CasoLuengo AA, Browne JA, Rue-Albrecht K, MacHugh DE, Loftus BJ.

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Genome sequencing of the extinct Eurasian wild aurochs, Bos primigenius, illuminates the phylogeography and evolution of cattle. 2015

Park SD, Magee DA, McGettigan PA, Teasdale MD, Edwards CJ, Lohan AJ, Murphy A, Braud M, Donoghue MT, Liu Y, Chamberlain AT, Rue-Albrecht K, Schroeder S, Spillane C, Tai S, Bradley DG, Sonstegard TS, Loftus BJ, MacHugh DE.

Paper · DOI · PubMed

RNA sequencing provides exquisite insight into the manipulation of the alveolar macrophage by tubercle bacilli. 2015

Nalpas NC, Magee DA, Conlon KM, Browne JA, Healy C, McLoughlin KE, Rue-Albrecht K, McGettigan PA, Killick KE, Gormley E, Gordon SV, MacHugh DE.

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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 2016

Rue-Albrecht K, McGettigan PA, Hernández B, Nalpas NC, Magee DA, Parnell AC, Gordon SV, MacHugh DE.

Paper · DOI · PubMed

Shields Group (2010)

This publication arose from a summer internship in the group of Prof. Denis Shields, under the supervision of Dr. Nora Khaldi.

Correlation of disorder between S. cerevisiae interacting proteins 2012

Rue-Albrecht K, Shields DC, Khaldi N.

Paper · DOI · PubMed