Selected publications and preprints:
2024
, , , , , , , , , , , An in vivo and in vitro spatiotemporal atlas of human midbrain development. bioRxiv 2024. doi: https://doi.org/10.1101/2024.09.25.613908
2023
Gynter A, Meistermann D, Lähdesmäki H, Kilpinen H#. DeconV: Probabilistic Cell Type Deconvolution from Bulk RNA-sequencing Data. bioRxiv 2023. doi: https://doi.org/10.1101/2023.12.07.570524.
https://github.com/lutrarutra/deconv
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. doi: https://doi.org/10.1101/2023.12.03.569583.
P Puigdevall#, J Jerber, P Danecek, S Castellano, H Kilpinen#. Effects of somatic mutations on cellular differentiation in iPSC models of neurodevelopment. Cell Genomics 2023 Mar 23;3(4): 100280.
A Neaverson, Andersson MHL, Arshad OA, Foulser L, Goodwin-Trotman M, Hunter A, Newman B, Patel M, Roth C, Thwaites T, Kilpinen H, Hurles ME, Day A, Gerety SS. Differentiation of human induced pluripotent stem cells into cortical neural stem cells. Front Cell Dev Biol. 2023 Jan 5:10:1023340.
2022
A Saukkonen, H Kilpinen#, A Hodgkinson#. PAC: Highly accurate quantification of allelic gene expression for population and disease genetics. Genome Res. 2022 Jul6;32(8):1565-72.
https://github.com/anna-saukkonen/PAC
2021
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.
2020
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 Aug10;9:e57390.
2018
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.
2017
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.
2015
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.
2014
Rossi M*, Kilpinen H*, Muona M, Surakka I, Ingle C, Lahtinen J, Hennah W, Ripatti S, Hovatta I. Allele-specific regulation of DISC1 expression by miR-135b-5p. Eur J Hum Genet. 2014 Jun;22(6):840-3.
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.
2013
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.
Kilpinen H and Barrett JC. How next-generation sequencing is transforming complex disease genetics. Trends Genet. 2013 Jan;29(1):23-30.
2012
Kilpinen H and Dermitzakis ET. Genetic and epigenetic contribution to complex traits. Hum Mol Genet. 2012 Oct 15;21(R1):R24-8.
2009 and earlier
Kilpinen H, Ylisaukko-oja T, Rehnström K, Gaál E, Turunen JA, Kempas E, von Wendt L, Varilo T, Peltonen L. Linkage and Linkage Disequilibrium Scan for Autism Loci in an Extended Pedigree from Finland. Hum Mol Genet. 2009 Aug 1;18(15):2912-21.
Kilpinen H, Ylisaukko-oja T, Hennah W, Palo OM, Varilo T, Vanhala R, Nieminen-von Wendt T, von Wendt L, Paunio T, Peltonen L. Association of DISC1 with autism and Asperger syndrome. Mol Psychiatry 2008 Feb; 13(2):187-96.
Kilpinen lab 