O’Keeffe P, Nouri Y, Saw HS, Moore Z, Baldwin TM, Olechnowicz SWZ, Jabbari JS, Squire DM, Leslie S, Wang C, You Y, Ritchie ME, Cross RS, Jenkins MR, Audiger C, Naik SH, Whittle JR, Freytag S, Best SA, Hickey PF, Amann-Zalcenstein D, Bowden R, Brown DV. TIRE-seq simplifies transcriptomics via integrated RNA capture and library preparation. Scientific Reports. 2025;15(1):10.1038/s41598-025-98282-8
Du MRM, Wang C, Law CW, Amann-Zalcenstein D, Anttila CJA, Ling L, Hickey PF, Sargeant CJ, Chen Y, Ioannidis LJ, Rajasekhar P, Yip RKH, Rogers KL, Hansen DS, Bowden R, Ritchie ME. Benchmarking spatial transcriptomics technologies with the multi-sample SpatialBenchVisium dataset. Genome Biology. 2025;26(1):10.1186/s13059-025-03543-4
Yip RKH, Hawkins ED, Bowden R, Rogers KL. Towards deciphering the bone marrow microenvironment with spatial multi-omics. Seminars in Cell and Developmental Biology. 2025;167:10.1016/j.semcdb.2025.01.001
Brown DV, Swierczak A, You Y, You Y, Amann-Zalcenstein D, Hickey P, Hsu A, Ritchie ME, Alhamdoosh M, Field J, Bowden R. A dataset examining technical factors on fixed white blood cell single-cell RNA-seq. Data in Brief. 2024;57:10.1016/j.dib.2024.111096
Zeglinski K, Montellese C, Ritchie ME, Alhamdoosh M, Vonarburg C, Bowden R, Jordi M, Gouil Q, Aeschimann F, Hsu A. An optimized protocol for quality control of gene therapy vectors using nanopore direct RNA sequencing.Genome Research. 2024;34(11):10.1101/gr.279405.124
Baldi A, Braat S, Hasan MI, Bennett C, Barrios M, Jones N, Abdul Azeez I, Wilcox S, Roy PK, Bhuiyan MSA, Ataide R, Clucas D, Larson LM, Hamadani J, Zimmermann M, Bowden R, Jex A, Biggs B-A, Pasricha S-R. Effects of iron supplements and iron-containing micronutrient powders on the gut microbiome in Bangladeshi infants: a randomized controlled trial. Nature Communications. 2024;15(1):10.1038/s41467-024-53013-x
Kadambari S, Harvala H, Nguyen D, Sadarangani M, Martin NG, Al-Rawahi GN, Sekirov I, Defres S, Solomon T, Golubchik T, Bowden R, Pollard AJ, Simmonds P. Characterising the molecular epidemiology of human parechovirus in young infants in the UK and Canada. Journal of Clinical Virology. 2024;174:10.1016/j.jcv.2024.105715
Mayne R, Secret S, Geoghegan C, Trebes A, Kean K, Reid K, Lin G-L, Ansari MA, de Cesare M, Bonsall D, Elliott I, Piazza P, Brown A, Bray J, Knight JC, Harvala H, Breuer J, Simmonds P, Bowden RJ, Golubchik T. Castanet: a pipeline for rapid analysis of targeted multi-pathogen genomic data. Bioinformatics. 2024;40(10):10.1093/bioinformatics/btae591
Baldi A, Braat S, Imrul Hasan M, Bennett C, Barrios M, Jones N, Moir-Meyer G, Abdul Azeez I, Wilcox S, Saiful Alam Bhuiyan M, Ataide R, Clucas D, Harrison LC, Arifeen SE, Bowden R, Biggs B-A, Jex A, Pasricha S-R. Community use of oral antibiotics transiently reprofiles the intestinal microbiome in young Bangladeshi children. Nature Communications. 2024;15(1):10.1038/s41467-024-51326-5
Chiou S, Al-Ani AH, Pan Y, Patel KM, Kong IY, Whitehead LW, Light A, Young SN, Barrios M, Sargeant C, Rajasekhar P, Zhu L, Hempel A, Lin A, Rickard JA, Hall C, Gangatirkar P, Yip RK, Cawthorne W, Jacobsen AV, Horne CR, Martin KR, Ioannidis LJ, Hansen DS, Day J, Wicks IP, Law C, Ritchie ME, Bowden R, Hildebrand JM, O’Reilly LA, Silke J, Giulino-Roth L, Tsui E, Rogers KL, Hawkins ED, Christensen B, Murphy JM, Samson AL. An immunohistochemical atlas of necroptotic pathway expression. EMBO Molecular Medicine. 2024;16(7):10.1038/s44321-024-00074-6
