Sundaresh A*, Meistermann D*, Lampela R, Yang Z, Woldegebriel R, Ganna A, Puigdevall P, Kilpinen H. Characterization of cortical neurodevelopment in vitro using gene expression and morphology profiles from single cells. bioRxiv 2023 https://doi.org/10.1101/2023.12.03.569583
Gynter A, Meistermann D, Lähdesmäki H, Kilpinen H. DeconV: Probabilistic Cell Type Deconvolution from Bulk RNA-sequencing Data. bioRxiv 2023 https://doi.org/10.1101/2023.12.07.570524
Puigdevall P, Jerber J, Danecek P, Castellano S, Kilpinen H. Effects of somatic mutations on cellular differentiation in iPSC models of neurodevelopment. Cell Genomics 2023 Mar 23;3(4): 100280.
Saukkonen A, Kilpinen H*, Hodgkinson A*. PAC: Highly accurate quantification of allelic gene expression for population and disease genetics. Genome Res. 2022 Jul 6;32(8):1565-72.
Bonder MJ, Smail C, Gloudemans MJ, Frésard L, Jakubosky D, D’Antonio M, Li X, Ferraro NM, Carcamo-Orive I, Mirauta B, Seaton DD, Cai N, Vakili D, Horta D, Zhao C, Zastrow DB, Bonner DE; HipSci Consortium; iPSCORE consortium; Undiagnosed Diseases Network; PhLiPS consortium, Wheeler MT, Kilpinen H, Knowles JW, Smith EN, Frazer KA, Montgomery SB, Stegle O. Identification of rare and common regulatory variants in pluripotent cells using population-scale transcriptomics. Nat Genet. 2021 Mar;53(3):313-321.
Mirauta B, Seaton DD, Bensaddek D, Brenes A, Bonder MJ, Kilpinen H, HipSci consortium, Stegle O, Lamond A. Population-scale proteome variation in human induced pluripotent stem cells. eLife 2020 Aug 10;9:e57390.
Schwartzentruber J, Foskolou S, Kilpinen H, Rodrigues J, Alasoo K, Knights AJ, Patel M, Goncalves A, Ferreira R, Benn CL, Wilbrey A, Bictash M, Impey E, Cao L, Lainez S, Loucif AJ, Whiting PJ, HIPSCI Consortium, Gutteridge A, Gaffney DJ. Molecular and functional variation in iPSC-derived sensory neurons. Nat Genet. 2018 Jan;50(1):54-61.
Kilpinen H*, Goncalves A*, Leha A, Afzal V, Ashford S, Bala S, Bensaddek D, Casale FP, Culley O, Danecek P, Faulconbridge A, Harrison P, McCarthy D, McCarthy SA, Meleckyte R, Memari Y, Moens N, Soares F, Streeter I, Chukwuma AA, Alderton A, Nelson R, Harper S, Patel M, Clarke L, Halai R, Kirton CM, Kolb-Kokocinski A, Beales P, Birney E, Danovi D, Lamond AI, Ouwehand WH, Vallier L, Watt FM, Durbin R, Stegle O, Gaffney DJ. Common genetic variation drives molecular heterogeneity in human iPSCs. Nature 2017 Jun 15;546(7658):370-375.
Waszak SM*, Delaneau O*, Gschwind AR, Kilpinen H, Raghav SK, Witwicki RM, Orioli A, Wiederkehr M, Panousis NI, Yurovsky A, Romano-Palumbo L, Planchon A, Bielser D, Padioleau I, Udin G, Thurnheer S, Hacker D, Hernandez N, Reymond A, Deplancke B, Dermitzakis ET. Population Variation and Genetic Control of Modular Chromatin Architecture in Humans. Cell. 2015 Aug 27;162(5):1039-50.
Waszak SM, Kilpinen H, Gschwind AR, Orioli A, Raghav SK, Witwicki RM, Migliavacca E, Yurovsky A, Lappalainen T, Hernandez N, Reymond A, Dermitzakis ET, Deplancke B. Identification and removal of low-complexity sites in allele-specific analysis of ChIP-seq data. Bioinformatics. 2014 Jan 15;30(2):165-71.
Kilpinen H*, Waszak SM*, Gschwind AR*, Raghav SK, Witwicki RM, Orioli A, Migliavacca E, Wiederkehr M, Gutierrez-Arcelus M, Panousis NI, Yurovsky A, Lappalainen T, Romano-Palumbo L, Planchon A, Bielser D, Bryois J, Padioleau I, Udin G, Thurnheer S, Hacker D, Core LJ, Lis JT, Hernandez N, Reymond A, Deplancke B, Dermitzakis ET. Coordinated effects of sequence variation on DNA binding, chromatin structure, and transcription. Science. 2013 Nov 8;342(6159):744-7.