Selected publications

• Domingo J, Minaeva M, Morris JA, Ziosi M, Sanjana NE, Lappalainen T (2024) Non-linear transcriptional responses to gradual modulation of transcription factor dosage. bioRxiv; doi: https://doi.org/10.1101/2024.03.01.582837

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

• 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.

• 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.

• 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.

• 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.

• 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. Science380(6646):eadh7699, doi: 10.1126/science.adh7699

• 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.

• 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. bioRxiv 2023.01.31.526505; doi: https://doi.org/10.1101/2023.01.31.526505

• Einson J, Minaeva M, Rafi F, Lappalainen T (2022) The impact of genetically controlled splicing on exon inclusion and protein structure. bioRxiv https://doi.org/10.1101/2022.12.05.518915 .

• Li X, Lappalainen T, Bussemaker HJ (2022) Identifying Genetic Regulatory Variants that Affect Transcription Factor Activity. bioRxiv 2022.10.21, 513166; doi: https://doi.org/10.1101/2022.10.21.513166

• Martorella M, Kasela S, Garcia-Flores R, Gokden A, Castel SE, Lappalainen T (2022) Noninvasive, low-cost RNA-sequencing enhances discovery potential of transcriptome studies. bioRxiv 2022.09.06, 506813; doi: https://doi.org/10.1101/2022.09.06.506813

• 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 (2022) Multiset correlation and factor analysis enables exploration of multi-omic data. bioRxiv 2022.07.18, 500246; doi:https://doi.org/10.1101/2022.07.18.500246

• 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.

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

• 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. 

• 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#, 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). https://doi.org/10.1186/s13059-021-02454-4

• 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

• 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# (2021) Discovery of target genes and pathways of blood trait loci using pooled CRISPR screens and single cell RNA sequencing. bioRxiv 2021.04.07.438882; doi: https://doi.org/10.1101/2021.04.07.438882 

• 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# (2021). Transcriptome variation in human tissues revealed by long-read sequencing. BioRxiv, 2021.01.22.427687.

• Xutong Zhao, Dandi Qiao , Chaojie Yang, Silva Kasela, …, Tuuli Lappalainen, Elizabeth C Oelsner, Goncalo R Abecasis, Edwin K Silverman, R Graham Barr, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium; TOPMed Lung Working Group; Michael H Cho, Ani Manichaikul. Whole genome sequence analysis of pulmonary function and COPD in 19,996 multi-ethnic participants. Nat Commun. 2020 Oct 14;11(1):5182. doi: 10.1038/s41467-020-18334-7

• Kasela S, Ortega VE, Martorella M, Garudadri S, Nguyen J, Ampleford E, Pasanen A, Nerella S, Buschur KL, 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# (2020) Genetic and non-genetic factors affecting the expression of COVID-19 relevant genes in the large airway epithelium. Genome Medicine 13(1):66

• The GTEx Consortium (2020) The GTEx Consortium atlas of genetic regulatory effects across human tissues. Science. 369 (1318-1330) [Lab contributions Castel SE, Kasela S, Kim-Hellmuth S: lead analysts; Flynn E: analyst; Hoffman P, Einson J: Manuscript working group; Lappalainen T#: last & co-corresponding author]

• 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# (2020) Cell type specific genetic regulation of gene expression across human tissues. Science 369(6509):eaaz8528.

• Brandt M, Gokden A, Ziosi M, Lappalainen T# (2020) A polyclonal allelic expression assay for detecting regulatory effects of transcript variants. Genome Medicine. 12(79)

• Castel SE#, Aguet F, Mohammadi P, GTEx Consortium, Lappalainen T# (2020) A vast resource of allelic expression data spanning human tissues. Genome Biology. 21(234).

• 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# (2020) 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

• 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 eaay0256, DOI: 10.1126/science.aay0256

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

• 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.

• GTEx Consortium (2017). Genetic effects on gene expression across human tissues (2017) Nature 550(7675):204-213.

• 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 8:266

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

• Kim-Hellmuth S, Lappalainen T# (2016) Concerted Genetic Function in Blood Traits. Cell 167:1167–1169

• Castel SE#, Mohammadi P, Chung WK, Shen Y, Lappalainen T#. (2016) . Rare variant phasing and haplotypic expression from RNA sequencing with phASER. Nature Communications 12817

• Lappalainen T# (2015) Functional genomics bridges the gap between quantitative genetics and molecular biology. Genome Research 25: 1427-1431

• Castel SE#, Levy-Moonshine A, Mohammadi P, Banks E, Lappalainen T# (2015) . Tools and best practices for data processing in allelic expression analysis. Genome Biology 6:195

• Lappalainen T. (2015) From trainee to tenure-track: Ten tips. Genome Biology16:132

• Rivas MA#*, Pirinen M, Conrad DF, Lek M, Tsang EK, Karczewski KJ, Maller JB, Kukurba KR, DeLuca DS, Fromer M, Ferreira PG, Smith KS, Zhang R, Zhao F, Banks E, Poplin R, Ruderfer DM, Purcell SM, Tukiainen T, Minikel EV, Stenson PD, Cooper DN, Huang KH, Sullivan TJ, Nedzel J; GTEx Consortium; Geuvadis Consortium, 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) Effect of predicted protein-truncating genetic variants on the human transcriptome. Science 348:666-9

• 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 DOI: 10.1101/gr.192278.115

• The GTEx Consortium (2015) The genotype-tissue expression (GTEx) pilot analysis: Multitissue gene regulation in humans. Science 348: 648-660

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

• 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

• 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.

• 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

• 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.

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