Dr Helena Kilpinen | Career Development Fellow

Kilpinen, Helena

Helena is interested in the functional effects of genetic variation in human induced pluripotent stem cells (iPSC). Her research combines computational and experimental methods in iPSC-based models to understand the cellular mechanisms that lead to rare human diseases.

Helena is a human geneticist who leads a research group at the UCL Great Ormond Street Institute of Child Health. She is a MRC eMedLab career development fellow (www.emedlab.ac.uk) and holds an appointment also at the Wellcome Trust Sanger Institute. Helena received her PhD from the University of Helsinki, where she studied the genetic mechanisms underlying autism spectrum disorders. She then transitioned to functional genomics, using diverse next-generation sequencing -based assays to study how DNA sequence variation influences different levels of gene regulation in human cells, first at the University of Geneva, and then at the EMBL-EBI. She joined the Human Induced Pluripotent Stem Cells Initiative (www.hipsci.org) in 2014 and has since focused on the functional characterization of genetic variation in human iPS cells from hundreds of donors. The long-term goal of her research is to combine high-dimensional molecular data from iPSCs and iPSC-derived cell types with clinical data to comprehensively model the cellular mechanisms that lead to rare human diseases.


  • Common genetic variation drives molecular heterogeneity in human iPSCs.

    Kilpinen H, Goncalves A, Leha A, Afzal V, Alasoo K et al.

    Nature 2017;546;7658;370-375

  • Population Variation and Genetic Control of Modular Chromatin Architecture in Humans.

    Waszak SM, Delaneau O, Gschwind AR, Kilpinen H, Raghav SK et al.

    Cell 2015;162;5;1039-50

  • Identification and removal of low-complexity sites in allele-specific analysis of ChIP-seq data.

    Waszak SM, Kilpinen H, Gschwind AR, Orioli A, Raghav SK et al.

    Bioinformatics (Oxford, England) 2014;30;2;165-71

  • Coordinated effects of sequence variation on DNA binding, chromatin structure, and transcription.

    Kilpinen H, Waszak SM, Gschwind AR, Raghav SK, Witwicki RM et al.

    Science (New York, N.Y.) 2013;342;6159;744-7

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Helena's Timeline

Group leader and career development fellow (MRC eMedLab) at University College London and the Wellcome Trust Sanger Institute, Cambridge


Post-doctoral fellow at the EMBL-EBI, Cambridge, UK


Post-doctoral fellow (EMBO) at the University of Geneva, Switzerland


PhD student at the Institute of Molecular Medicine Finland (FIMM), Helsinki


MSc student at the Institute of Molecular Medicine Finland (FIMM), Helsinki