Molania R, Foroutan M, Gagnon-Bartsch JA, Gandolfo LC, Jain A, Sinha A, Olshansky G, Dobrovic A, Papenfuss AT, Speed TP. Removing unwanted variation from large-scale RNA sequencing data with PRPS. Nat Biotechnol. 2023 41(1):82-95. PMID: 36109686.
Runx3 drives a CD8+ T cell tissue residency program that is absent in CD4+ T cells. Fonseca R, Burn TN, Gandolfo LC, Devi S, Park SL, Obers A, Evrard M, Christo SN, Buquicchio FA, Lareau CA, McDonald KM, Sandford SK, Zamudio NM, Zanluqui NG, Zaid A, Speed TP, Satpathy AT, Mueller SN, Carbone FR, Mackay LK. Nat Immunol. 2022 23(8):1236-1245.
PMID: 35882933.
RUV-III-NB: normalization of single cell RNA-seq data. Salim A, Molania R, Wang J, De Livera A, Thijssen R, Speed TP. Nucleic Acids Res. 2022 50(16):e96. PMID: 35758618.
Removing unwanted variation with CytofRUV to integrate multiple CyTOF datasets
Marie Trussart, Charis E Teh, Tania Tan, Lawrence Leong, Daniel H Gray Terence P Speed. Elife 2020 9:e59630. PMID: 32894218.
Using long-read sequencing to detect imprinted DNA methylation. Gigante S, Gouil Q, Lucattini A, Keniry A, Beck T, Tinning M, Gordon L, Woodruff C, Speed TP, Blewitt ME, Ritchie ME. Nucleic Acids Res. 2019 47(8):e46. PMID: 30793194.