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Lappalainen Lab

Tuuli Lappalainen’s lab studies functional genetic variation in human populations. It is particularly interested in regulatory variation affecting the transcriptome, as well as cellular mechanisms underlying genetic associations to disease. The lab integrates computational analysis of genomic and transcriptomic data with population genetic and experimental analysis.

The lab is also affiliated with the Department of Systems Biology at Columbia University.

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    Tuuli Lappalainen


    Tuuli Lappalainen, PhD, is a Core Member and Assistant Investigator at the New York Genome Center. She holds a joint appointment as Assistant Professor in the Department of Systems Biology at Columbia University.

    Her research focuses on functional genetic variation in human populations and its contribution to traits and diseases. Dr. Lappalainen has pioneered the integration of large-scale genome and transcriptome sequencing data to understand how genetic variation affects gene expression, providing insight to cellular mechanisms underlying genetic risk for disease. The work of her research group at NYGC links computational and population genomics to experimental molecular biology.

    Dr. Lappalainen received her PhD in Genetics from the University of Helsinki, Finland in 2009, followed by postdoctoral research at the University of Geneva, Switzerland and Stanford University. She has made important contributions to several international research consortia in human genomics, including the 1000 Genomes Project and the Genotype Tissue Expression (GTEx) Project, and led the RNA-sequencing work of the Geuvadis Consortium. GenomeWeb profiled her in their 2013 feature on promising young investigators.

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    • Lappalainen T, Hemmluth-Kim S.

      Concerted Genetic Function in Blood Traits

      ScienceDirect. 2016 Nov 14.

    • Joshi RS, Garg P, Zaitlen N, Lappalainen T, Watson CT, Azam N, Ho D, Li X, Antonarakis SE, Brunner HG, Buiting K, Cheung SW, Coffee B, Eggermann T, Francis D, Geraedts JP, Gimelli G, Jacobson SG, Le Caignec C, de Leeuw N, Liehr T, Mackay DJ, Montgomery SB, Pagnamenta AT, Papenhausen P, Robinson DO, Ruivenkamp C, Schwartz C, Steiner B, Stevenson DA, Surti U, Wassink T, Sharp AJ.

      DNA Methylation Profiling of Uniparental Disomy Subjects Provides a Map of Parental Epigenetic Bias in the Human Genome.

      Am J Hum Genet. 2016 Sep 1. PMID: 27569549

    • Castel SE, Mohammadi P, Chung WK, Shen Y, Lappalainen T.

      Rare variant phasing and haplotypic expression from RNA sequencing with phASER.

      Nat Commun. 2016 Sep 8. PMID: 27605262

    • Lappalainen T, Sammeth M, Friedlander M, ‘t Hoen PAC, Rivas MA, Monlong J, Gonzalez-Porta M, Kurbatova N, Griebel T, Ferreira P, Barann M, Wieland T, Greger L, van Iterson M, Almlof J, Ribeca P, Pulyakhina I, Esser D, Giger T, Sultan M, Bertier G, MacArthur DG, Lek M, Lizano E, Buermans H, Padioleau I, Strom T, Schwartzmayer T, Pirinen M, Karlberg O, Betran Agullo S, Gut M, Amstislavskiy V, Montgomery SB, Donnelly P, McCarthy M, The Geuvadis Consortium, Lehrach H, Schreiber S, Sudbrak R, Carracedo Alvarez A, Flicek P, Antonarakis S, Hasler R, Syvanen A-C, van Ommen G-J, Brazma A, Meitinger T, Rosenstiel P, Guigo R, Gut I, Estivill X, Dermitzakis ET.

      Transcriptome and genome sequencing uncovers human functional variation.

      (2013) Nature 501: 506-511

    • ’t Hoen PAC, Friedländer MR, Almlöf J, Sammeth M, Pulyakhina I, Anvar SY, Laros JFJ, Karlberg O, The GEUVADIS Consortium, Syvänen AC, Guigó R, Estivill X, den Dunnen JT, van Ommen GJB, Dermitzakis ET, Lappalainen T (2013)

      Reproducible transcriptome sequencing across different laboratories.

      Nature Biotechnology 31:1015—1022. (2013)

    • Lappalainen T, Montgomery SB, Nica AC, Dermitzakis ET (2011)

      Epistatic selection between coding and regulatory variation in human evolution and disease

      Am J Hum Genet. 89:459-63 (2011)

    • Khurana E, Fu Y, Colonna V, Mu XJ, Kang HM, Lappalainen T, Lochovsky L, Chen J, Abyzov A, Balasubramanian S, Challis D, Chen Y, Clarke D, Clarke L, Das J, Dermatzikis ET, Evani U, Fragoza R, Garrison E, Gibbs R, Harmanci A, Herrero J, Kitabayashi N, Kong Y, Lage K, Lipkin S, MacArthur DG, Muzni D, Pers T, Rosenfeld JA, Rubin M, Sboner A, Sisu C, Wei X, Wilson M, Xue Y, Yu H, Yu F, 1000 Genomes Project Consortium, Tyler-Smith C, Gerstein M. (2013)

      Integrative Annotation of Variants from 1092 Humans: Application to Cancer Genomics.

      Science 342: (2013)


This work was partially supported by a gift from the Simons Foundation.