Selected publications and preprints

Lab members in bold.  # Corresponding author.  * Equal contribution

• 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# (2016) Genetic regulatory effects modified by immune activation contribute to autoimmune disease associations. biorXiv116376; doi:https://doi.org/10.1101/116376
• Kim-Hellmuth S, Lappalainen T# (2016) Concerted Genetic Function in Blood Traits. Cell 167:1167–1169
• Aguet F*, Brown AA*, Castel SE*, Davis JR*, Mohammadi P*, Segre AV*, Zappala Z*, Abell NS, Fresard L, Gamazon ER, Gelfand E, Gloudemans MJ, He Y, Hormozdiari F, Li X, Li X, Liu B, Garrido-Martin D, Ongen H, Palowitch JJ, Park Y, Peterson CB, Quon G, Ripke S, Shabalin AA, Shimko TC, Strober BJ, Sullivan TJ, Teran NA, Tsang EK, Zhang H, Zhou Y, Battle A, Bustamonte CD, Cox NJ, Engelhardt BE, Eskin E, Getz G, Kellis M, Li G, MacArthur DG, Nobel AB, Sabbati C, Wen X, Wright FA, GTEx Consortium, Lappalainen T, Ardlie KG, Dermitzakis ET, Brown CD, Montgomery SB (2016). Local genetic effects on gene expression across 44 human tissues. bioRxiv 074450; doi: http://dx.doi.org/10.1101/074450
• Mohammadi P#, Castel SE, Brown AA, Lappalainen T# (2016) Quantifying the regulatory effect size of cis-acting genetic variation using allelic fold change. BioRxiv doi: http://dx.doi.org/10.1101/078717
• 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 Biology 16:132
• 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.