Selected publications and preprints

  • Fang H, Jiang L, da Veiga Leprevost F, Jian R, Chan J, Glinos D, Lappalainen T, Nesvizhskii AI, Reiner AP, Consortium G, Snyder MP, Tang H (2025) Regulation of protein abundance in normal human tissues. mexRxiv doi: 10.1101/2025.01.10.25320181.

  • Coorens THH, Guillaumet-Adkins A, Kovner R, Linn RL, Roberts VHJ, Sule A, Van Hoose PM; dGTEx Consortium (2025) Nature 637(8046):557-564

  • Kämpe A, Gudmundsson S, Walsh CP, Lindblad-Toh K, Johansson Å, Clareborn A, Ameur A, Edsjö A, Fioretos T, Ehrencrona H, Eriksson D, Fall T, Franks PW, Gyllensten U, Haag M, Hagwall A, Johansson Soller M, Lehtiö J, Lu Y, Magnusson PKE, Melen E, Melin B, Michaelsson K, Nordgren A, Nordlund J, Saal LH, Schwenk JM, Sikora P, Sundström J, Taylan F, Van Guelpen B, Wadelius M, Wedell A, Wirta V, Östling P, Jacobsson B, Sjöblom T, Persson B, Rosenquist R, Lindstrand A, Lappalainen T (2024)  Precision Omics Initiative Sweden (PROMISE): a new model for biomedical research. SSRN

  • Domingo J, Minaeva M, Morris JA, Ziosi M, Sanjana NE, Lappalainen T (2024) Non-linear transcriptional responses to gradual modulation of transcription factor dosage. eLife13:RP100555

  • Minaeva M, Domingo J, Rentzsch P, Lappalainen T (2023) Specifying cellular context of transcription factor regulons for exploring context-specific gene regulation programs. NAR Genom Bioinform 7(1):lqae178. doi: 10.1093/nargab/lqae178.

  • Gudmundsson S, Singer-Berk M, Stenton SL, Goodrich JK, Wilson MW, Einson J, Watts NA; Genome Aggregation Database Consortium; Lappalainen T, Rehm HL, MacArthur DG, O'Donnell-Luria A (2024) Exploring penetrance of clinically relevant variants in over 800,000 humans from the Genome Aggregation Database. doi: 10.1101/2024.06.12.593113.

  • Rentzsch P, Kollotzek A, Mohammadi P, Lappalainen T (2024) Recalibrating differential gene expression by genetic dosage variance prioritizes functionally relevant genes. bioRxiv; doi: 10.1101/2024.04.10.588830.

  • Lappalainen T, Li YA, Ramachandran S, Gusev A (2024). Genetic and molecular architecture of complex traits. Cell 187(5):1059-1075

  • Kasela S, Aguet F, Kim-Hellmuth S, Brown BC, Nachun DC, Tracy RP, Durda P, Liu Y, Taylor KD, Johnson WC, Van Den Berg D, Gabriel S, Gupta N, Smith JD, Blackwell TW, Rotter JI, Ardlie KG, Manichaikul A, Rich SE, Barr RG, Lappalainen T (2024) Interaction molecular QTL mapping discovers cellular and environmental modifiers of genetic regulatory effects. The American Journal of Human Genetics, 111(1): 133-149. https://doi.org/10.1016/j.ajhg.2023.11.013.

  • Einson J, Minaeva M, Rafi F, Lappalainen T (2024) The impact of genetically controlled splicing on exon inclusion and protein structure. PLoS ONE 19(3):e0291960. 

  • George SHL, Medina-Rivera A, Idaghdour Y, Lappalainen T, Gallego Romero I. (2023) Increasing diversity of functional genetics studies to advance biological discovery and human health. Am J Hum Genet. 110(12):1996-2002. doi: 10.1016/j.ajhg.2023.10.012.

  • Brown BC, Morris JA, Lappalainen T, Knowles DA (2023) Large-scale causal discovery using interventional data sheds light on the regulatory network architecture of blood traits. bioRxiv. doi: 10.1101/2023.10.13.562293.

  • Martorella M, Kasela S, Garcia-Flores R, Gokden A, Castel SE, Lappalainen T (2023) Evaluation of noninvasive biospecimens for transcriptome studies. BMC Genomics. 24(1):790. doi: 10.1186/s12864-023-09875-4.

  • Aguet F, Alasoo K, Yang IL, Battle A, Im HK, Montgomery SB, Lappalainen T (2023). Molecular quantitative trait loci. Nature Reviews Methods Primers 3:4.

  • Li X, Lappalainen T, Bussemaker HJ (2023) Identifying Genetic Regulatory Variants that Affect Transcription Factor Activity. Cell Genomics 3,100382.

  • Flynn E, Lappalainen T. (2022) Functional Characterization of Genetic Variant Effects on Expression. Annu Rev Biomed Data Sci. 2022 Apr 28. doi: 10.1146/annurev-biodatasci-122120-010010.

  • Brown BC, Wang C, Kasela S, Aguet F, Nachun DC, Taylor KD, Tracy RP, Durda P, Liu Y, Johnson WC, VanDenBerg DJ, Gupta N, Gabriel S, Smith JD, Gerzsten R, Clish C, Wong Q, Papanicolau G, Blackwell TW, Rotter JI, Rich SS, Ardlie KG, Knowles DA*, Lappalainen T* (2023) Multiset correlation and factor analysis enables exploration of multi-omic data. Cell Genomics 3(8):100359.

  • Morris JA,  Daniloski Z,  Domingo J, Barry T, Ziosi M, Glinos DA, Hao S, Mimitou EP, Smibert P,  Roeder K, Katsevich E, Lappalainen T#, Sanjana NE# (2023) Discovery of target genes and pathways of blood trait loci using pooled CRISPR screens and single cell RNA sequencing. Science 380(6646):eadh7699, doi: 10.1126/science.adh7699

  • Einson J,  Glinos D, Boerwinkle E, Castaldi P, Darbar D, de Andrade M, Ellinor P, Fornage M, Gabriel S, Germer S, Gibbs R, Hersh CP, Johnsen J, Kaplan R, Konkle BA, Kooperberg C, Nassir R, Loos RJF, Meyers DA, Mitchell BA, Psaty B, Vasan RS, Rich SS, Rienstra M, Rotter JI, Saferali A, Shoemaker MB, Silverman E, Smith AV, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Mohammadi P, Castel SE, Iossifov I, Lappalainen T (2023) Genetic control of mRNA splicing as a potential mechanism for incomplete penetrance of rare coding variants. Genetics 224(4):iyad115

  • Glinos DA*, Garborcauskas G*, Hoffman P, Ehsan N, Jiang L, Gokden A, Dai X, Aguet F, Brown KL, Garimella K, Bowers T, Costello M, Ardlie K, Jian R, Tucker NR, Ellinor PT, Harrington ED, Tang H, Snyder M, Juul S, Mohammadi P, MacArthur D, Lappalainen T#, Cummings B# (2022). Transcriptome variation in human tissues revealed by long-read sequencing. Nature 608(7922):353-359.

  • Flynn ED, Tsu AL, Kasela S, Kim-Hellmuth S, Aguet F, Ardlie KG, Bussemaker HJ, Mohammadi P, Lappalainen T (2021). Transcription factor regulation of eQTL activity across individuals and tissues. PLoS Genet. 18(1):e1009719. doi: 10.1371/journal.pgen.1009719. 

  • Kasela S, Daniloski Z, Bollepalli S, Jordan TX, tenOever BR, Sanjana NE, Lappalainen T# (2021) Integrative approach identifies SLC6A20 and CXCR6 as putative causal genes for the COVID-19 GWAS signal in the 3p21.31 locus. Genome Biology 22, 242 (2021).

  • Lappalainen T#, MacArthur DG (2021) From variant to function in human disease genetics. Science 373(6562):1464-1468

  • Brandt M, Kim-Hellmuth S, Ziosi M, Gokden A, Wolman A, Lam, N, Recinos Y, Daniloski Z, Morris JA, Hornung V, Schumacher J, Lappalainen T (2021) An autoimmune disease risk variant: a trans master regulatory effect mediated by IRF1 under immune stimulation? PLoS Genetics 17(7):e1009684 

  • de Goede OM, Ferraro NM, Nachun DC, Rao AS, Aguet F, Barbeira AN, Castel SE, Kim-Hellmuth S, Park Y, Scott AJ, Strober BJ, GTEx Consortium, Brown CD, Wen X, Hall IM, Battle A, Lappalainen T, Im HK, Ardlie KG, Quertermous T, Kirkegaard K, Montgomery SB (2021) Long non-coding RNA gene regulation and trait associations across human tissues. Cell 184(10):2633-2648.e19

  • Uffelmann E, Huang QQ, Munung NS, de Vries J, Okada Y, Martin AR, Martin HC, Lappalainen T, Danielle Posthuma (2021). Genome-wide association studies. Nature Reviews Methods Primers 1, 59.

  • Kasela S, Ortega VE, Martorella M, Garudadri S, Nguyen J, Ampleford E, Pasanen A, Nerella S, Buschur K L, Barjaktarevic I Z, Barr RG, Bleecker ER, Bowler RP, Comellas AP, Cooper CB, Couper DJ, Criner GJ, Curtis JL, Han, M K, … , Woodruff, PG, Lappalainen, T#, Christenson, SA# (2021) Genetic and non-genetic factors affecting the expression of COVID-19 relevant genes in the large airway epithelium. Genome Medicine 13(1):66

  • Barbeira AN,  Bonazzola R, Gamazon ER, Liang Y, Park Y, Kim-Hellmuth S, Wang G, Jiang Z, Zhou D, Hormozdiari F, Liu B, Rao A, Hamel AR, DPividori M, Aguet F, GTEx GWAS Working Group, Bastarache L, Jordan DM, Verbanck M, Do R, GTEx Consortium, Stephens M, Ardlie K, McCarthy M, Montgomery SB, Segrè AV, Brown CD, Lappalainen T, Wen X, Im HK (2021) Exploiting the GTEx resources to decipher the mechanisms at GWAS loci. Genome Biology 22(1):49. doi: 10.1186/s13059-020-02252-4

  • Daniloski Z, Jordan TX, Wessels H-H, Hoagland DA, Kasela S, Legut M, Maniatis S, Mimitou EP, Lu l, Geneer E, Danziger O, Rosenberg BR, Phatnani H, Smibert P, Lappalainen T, tenOever BR, Sanjana NE (2020) Identification of required host factors for SARS-CoV-2 infection in human cells. Cell. https://doi.org/10.1016/j.cell.2020.10.030.

  • Kim-Hellmuth S, Aguet F, Oliva M, Munoz-Aguirre M, Wucher V,  Kasela S, Castel SE, Hamel A, Vinuela A, Roberts AL, Mangul S, Wen X, Wang G, Barbeira A, Garrido-Martin D, Nadel B, Zou Y, Bonazzola R, Quan J, Brown A, Martinez-Perez A, Soria JM, The GTEx Consortium, Getz G, Dermitzakis E, Small KS, Stephens M, Xi HS, Im HK, Guigo R, Segre A, Stranger B, Ardlie K,  Lappalainen T# (2019) Cell type specific genetic regulation of gene expression across human tissues. Science 369(6509):eaaz8528.

  • Ferraro NM, Strober BJ, Einson J, Li X, Aguet F, Barbeira AN, Castel SE, Davis JR, Hilliard AT, Kotis B, Park Y, Scott AJ, Smail C, Tsang EK, Ardlie KG, Assimes TL, Hall I, Im HK, GTEx Consortium, Lappalainen T, Mohammadi P#, Montgomery SB#, Battle A# (2019) Diverse transcriptomic signatures across human tissues identify functional rare genetic variation. Science 369(6509):eaaz5900

  • Oliva M, Muñoz-Aguirre M, Kim-Hellmuth S, Wucher V, Gewirtz ADH, Cotter DJ, Parsana P, Kasela S, Balliu B, Viñuela A, Castel SE, Mohammadi P, Aguet F, Zou Y, Khramtsova EA, Skol AD, Garrido-Martín D, Reverter F, Brown A, Evans P, Gamazon ER, Payne A, Bonazzola R, Barbeira AN, Hamel AR, Martinez-Perez A, Soria JM; GTEx Consortium, Pierce BL, Stephens M, Eskin E, Dermitzakis ET, Segrè AV, Im HK, Engelhardt BE, Ardlie KG, Montgomery SB, Battle AJ, Lappalainen T, Guigó R, Stranger BE (2020) The impact of sex on gene expression across human tissues. Science 369(6509):eaba3066

  • The GTEx Consortium (2019) The GTEx Consortium atlas of genetic regulatory effects across human tissues. Science 369(6509):1318-1330. [Lappalainen T#: last & co-corresponding author]

  • Brandt M, Gokden A, Ziosi M, Lappalainen T# (2019) A polyclonal allelic expression assay for detecting regulatory effects of transcript variants. Genome Medicine 12(79) doi:10.1186/s13073-020-00777-8

  • Castel SE, Aguet F, Mohammadi P, GTEx Consortium, Lappalainen T (2019) A vast resource of allelic expression data spanning human tissues. Genome Biology 21(1):234.

  • Sanford JA, Nogiec CD, Lindholm ME, Adkins JN, Amar D, Dasari S, Drugan JK, Fernández FM, Radom-Aizik S, Schenk S, Snyder MP, Tracy RP, Vanderboom P, Trappe S, Walsh MJ; Molecular Transducers of Physical Activity Consortium (2020) Molecular Transducers of Physical Activity Consortium (MoTrPAC): Mapping the Dynamic Responses to Exercise. Cell 181(7):1464-1474. 

  • Lappalainen T#, Scott AJ, Brandt M, Hall IM# (2019) Genomic analysis in the age of human genome sequencing. Cell 177(1):70-84.

  • Mohammadi P, Castel SE, Cummings BB, Einson J, Sousa C, Hoffman P, Donkervoort S, Mohassel P, Foley R, Wheeler HE, Im HK, Bonnemann C, MacArthur DG, Lappalainen T (2019) Genetic regulatory variation in populations informs transcriptome analysis in rare disease. Science 366(6463):351-356

  • Castel SE, Cervera A, Mohammadi P, Aguet F, Reverter F, Wolman A, Guigo R, Vasileva A, Lappalainen T (2018) Modified penetrance of coding variants by cis-regulatory variation shapes human traits. Nature Genetics 50 1327–1334.

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

  • Lappalainen T#, Greally J# (2017). Associating cellular epigenetic models with human phenotypes. Nature Reviews Genetics. 18(7):441-451

  • GTEx Consortium (2017). Genetic effects on gene expression across human tissues (2017) Nature 550(7675):204-213. [Lappalainen T is the last author of the eQTL working group]

  • Kim-Hellmuth S, Bechheim M, Puetz B, Mohammadi P, Nedelec Y, Giangreco N, Becker J, Kaiser V, Fricker N, Beier E, Boor P, Castel S, Noethen MM, Barreiro LB, Pickrell JK, Mueller-Myhsok B, Lappalainen T#, Schumacher J#, Hornung V# (2017) Genetic regulatory effects modified by immune activation contribute to autoimmune disease associations. Nature Communications 8:226.

  • Castel SE, Mohammadi P, Chung WK, Shen Y, Lappalainen T (2016) phASER: Long range phasing and haplotypic expression from RNA sequencing. Nature Communications 7:12817

  • Castel S, Levy-Moonshine A, Mohammadi P, Banks E, Lappalainen T (2015) Tools and best practices for data processing in allelic expression analysis. Genome Biology 16(1):195.

  • Lappalainen T (2015) Functional genomics bridges the gap between quantitative genetics and molecular biology. Genome Res. 25:1427-31

  • Baran Y, Subramaniam M, Biton A, Tukiainen T, Tsang EK, Rivas MA, Pirinen M, Gutierrez-Arcelus M, Smith KS, Kukurba KR, Zhang R, Eng C, Torgerson DG, Urbanek C; GTEx Consortium, Li JB, Rodriguez-Santana JR, Burchard EG, Seibold MA, MacArthur DG, Montgomery SB, Zaitlen NA#, Lappalainen T# (2015) The landscape of genomic imprinting across diverse adult human tissues. Genome Research 25:927-936

  • Rivas MA, Pirinen M, Conrad DF, Lek M, Tsang EK, Karczewski KJ, Maller JB, Kukurba KR, DeLuca D, Fromer M, Ferreira P, Smith KS, Zhang R, Zhao F, Banks E, Poplin R, Ruderfer D, Stenson PD, Cooper DN, Consortium TG, Consortium TG, Bustamante CD, Li JB, Daly MJ, Guigo R, Donnelly P, Ardlie K, Sammeth M, Dermitzakis ET, McCarthy MI, Montgomery SB, Lappalainen T#, MacArthur DG# (2015) Impact of predicted protein-truncating genetic variants on the human transcriptome. Science 348:666-669

  • GTEx Consortium (2015) The Genotype-Tissue Expression (GTEx) pilot analysis of multi-tissue gene regulation in humans. Science 348:648-660.

  • Pirinen M, Lappalainen T, Zaitlen NA; GTEx Consortium, Dermitzakis ET, Donnelly P, McCarthy MI, Rivas MA. (2015) Assessing allele-specific expression across multiple tissues from RNA-seq read data. Bioinformatics 31:2497-504.

  • Gutierrez-Arcelus MG, Ongen H#, Lappalainen T#, Montgomery SB#, Buil AB, Yurovsky A, Bryois J, Padioleau I, Romano L, Planchon A, Falconnet E, Bielser D, Gagnebin M, Giger T, Borel C, Letourneau A, Makrythanasis P, Guipponi M, Gehrig C, Antonarakis SE, Dermitzakis ET (2015) Tissue-specific effects of genetic and epigenetic variation on gene regulation and splicing. PLoS Genetics 11(1):e1004958.

  • Panousis N, Gutierrez-Arcelus M, Dermitzakis ET#, Lappalainen T# (2014) Allelic mapping bias in RNA-sequencing is not a major confounder in eQTL studies. Genome Biology 15(9):467

  • 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# (2013) Transcriptome and genome sequencing uncovers human functional variation. 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.

  • 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 (2013) Passive and active DNA methylation and the interplay with genetic variation in gene regulation. eLife 2013;2:e00523

  • The 1000 Genomes Consortium (2012) An integrated map of genetic variation from 1,092 human genomes. Nature 491, 56–65.

  • 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

  • Montgomery SB, Lappalainen T, Gutierrez-Arcelus M, Dermitzakis ET (2011) Rare and common regulatory variation in population-scale sequenced human genomes. Plos Genetics 7(7): e1002144.

  • Lappalainen T, Salmela E, Andersen PM, Dahlman-Wright K, Sistonen P, Savontaus M-L, Schreiber S, Lahermo P, Kere J (2010) Genomic landscape of positive natural selection in Northern European populations. European Journal of Human Genetics, 18:471-8

  • Salmela E#, Lappalainen T#, Fransson I, Andersen P, Dahlman-Wright K, Fiebig A, Sistonen P, Savontaus M-L, Kere J, Lahermo P (2008) Genome-wide analysis of single nucleotide polymorphisms uncovers population structure in Northern Europe. PLoS ONE, 3:e3519.

See our github and respective papers for tools and code!