Zou J, Hormozdiari F, Jew B, Castel SE, Lappalainen T, Ernst J, Sul JH, Eskin E. Leveraging allelic imbalance to refine fine-mapping for eQTL studies . PLoS Genet. 2019 Dec 13;15(12):e1008481. doi: 10.1371/journal.pgen.1008481. eCollection 2019 Dec.

Mohammadi P, Castel SE, Cummings BB, Einson J, Sousa C, Hoffman P, Donkervoort S, Jiang Z, Mohassel P, Foley AR, Wheeler HE, Im HK, Bonnemann CG, MacArthur DG, Lappalainen T. Genetic regulatory variation in populations informs transcriptome analysis in rare disease . Science. 2019 Oct 18;366(6463):351-356. doi: 10.1126/science.aay0256. Epub 2019 Oct 10.

Brandt M, Lappalainen T. SnapShot: Discovering Genetic Regulatory Variants by QTL Analysis. Cell. 2017 Nov 2;171(4):980-980.e1. 

Mohammadi P, Castel SE, Brown AA, Lappalainen T. Quantifying the regulatory effect size of cis-acting genetic variation using allelic fold change.  Genome Res. 2017 Nov;27(11):1872-1884. Epub 2017 Oct 11.

Tukiainen T, Villani AC, Yen A, Rivas MA, Marshall JL, Satija R, Aguirre M, Gauthier L, Fleharty M, Kirby A, Cummings BB, Castel SE, Karczewski KJ, Aguet F, Byrnes A; GTEx Consortium; Laboratory, Data Analysis &Coordinating Center (LDACC)—Analysis Working Group; Statistical Methods groups—Analysis Working Group; Enhancing GTEx (eGTEx) groups; NIH Common Fund; NIH/NCI; NIH/NHGRI; NIH/NIMH; NIH/NIDA; Biospecimen Collection Source Site—NDRI; Biospecimen Collection Source Site—RPCI; Biospecimen Core Resource—VARI; Brain Bank Repository—University of Miami Brain Endowment Bank; Leidos Biomedical—Project Management; ELSI Study; Genome Browser Data Integration &Visualization—EBI; Genome Browser Data Integration &Visualization—UCSC Genomics Institute, University of California Santa Cruz, Lappalainen T, Regev A, Ardlie KG, Hacohen N, MacArthur DG. Landscape of X chromosome inactivation across human tissues.  Nature. 2017 Oct 11.

GTEx Consortium (Lappalainen T); GTEx Consortium (including Lappalainen T). Genetic effects on gene expression across human tissues. Nature. 2017 Oct 11.

Kim-Hellmuth S, Bechheim M, Pütz B, Mohammadi P, Nédélec Y, Giangreco N, Becker J, Kaiser V, Fricker N, Beier E, Boor P, Castel SE, Nöthen MM, Barreiro LB, Pickrell JK, Müller-Myhsok B, Lappalainen T, Schumacher J, Hornung V. Genetic regulatory effects modified by immune activation contribute to autoimmune disease associations. Nat Commun. 2017 Aug 16.

Lappalainen T, Greally JM. Associating cellular epigenetic models with human phenotypes. Nat Rev Genet. 2017 Jul;18(7):441-451. Epub 2017 May 30. Review.

Fort A, Panousis NI, Garieri M, Antonarakis SE, Lappalainen T, Dermitzakis ET, Delaneau O. MBV: a method to solve sample mislabeling and detect technical bias in large combined genotype and sequencing assay datasets. Bioinformatics. 2017 Jun 15;33(12):1895-1897.

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.  Nature 2013 Sep 26;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 Reproducible transcriptome sequencing across different laboratories . Nat Biotechnol. 2013 Nov;31(11):1015-22.

Lappalainen T, Montgomery SB, Nica AC, Dermitzakis ET Epistatic selection between coding and regulatory variation in human evolution and disease . Am J Hum Genet. 2011 Sep 9;89(3):459-63.

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. Integrative Annotation of Variants from 1092 Humans: Application to Cancer Genomics . Science. 2013 Oct 4;342(6154):1235587.

The 1000 Genomes Consortium. An integrated map of genetic variation from 1,092 human genomes . Nature. 2012 Nov 1;491(7422):56-65.

Gutierrez-Arcelus M, Lappalainen T , Montgomery SB, Buil A, Ongen H, Yurovsky A, Bryois J, Giger T, Romano L, Planchon A, Falconnet E, Bielser D, Gagnebin M, Padioleau I, Borel C, Letourneau A, Makrythanasis P, Guipponi M, Gehrig C, Antonarakis SE, Dermitzakis ET. Passive and active DNA methylation and the interplay with genetic variation in gene regulation . Elife. 2013 Jun 4;2:e00523.