The paper identifies USP18 as a negative regulator of interferon response at a lupus risk locus through trans-eQTL analysis in lymphoblastoid cell lines.

Nature Communications · Oct 2, 2025Peer-reviewedGenetic & Genomic Medicine

OTTERS: A powerful TWAS framework leveraging summary-level reference data

Qile Dai, Geyu Zhou, Hongyu Zhao, Urmo Võsa, Lude Franke, Alexis J. Battle, Alexander Teumer, Terho J. Lehtimäki, Olli Tuomas Raitakari, Tõnu Esko, Mawussé D. T. Agbessi, Habibul Ahsan, Isabel Alves, Anand Kumar Andiappan, Wibowo Arindrarto, , Jingjing Yang

OTTERS is a TWAS framework that uses summary-level eQTL reference data to estimate eQTL weights and perform omnibus TWAS, showing improved power and applicability.

Nature Communications · Mar 7, 2023Peer-reviewedGenetics

Unraveling the polygenic architecture of complex traits using blood eQTL meta-analysis

Urmo Võsa, Annique Claringbould, Harm-Jan Westra, Marc Jan Bonder, Patrick Deelen, Biao Zeng, Holger Kirsten, Ashis Saha, Roman Kreuzhuber, Seyhan Yazar, Harm Brugge, Roy Oelen, Dylan H. de Vries, Monique G.P. van der Wijst, Silva Kasela, , Bruce M. Psaty

The paper uses blood eQTL meta-analysis to explore the polygenic architecture of complex traits, finding that trans-eQTLs are more informative for identifying causal genes than cis-eQTLs.

Nature Genetics · Sep 1, 2021Peer-reviewedGenomics

Mendelian Randomization integrating GWAS and eQTL data reveals genetic determinants of complex and clinical traits

Eleonora Porcu, Sina Rüeger, Kaido Lepik, Mawussé D. T. Agbessi, Habibul Ahsan, Isabel Alves, Anand Kumar Andiappan, Wibowo Arindrarto, Philip Awadalla, Alexis J. Battle, Frank Beutner, Marc Jan Bonder, Dorret Irene Boomsma, Mark W. Christiansen, Annique Claringbould, , René Luijk

This paper introduces TWMR, a Mendelian Randomization method that identifies gene-trait associations by integrating GWAS and eQTL data, revealing 3,913 novel associations across 43 human phenotypes.

Nature Communications · Jul 24, 2019Peer-reviewedGenetics

AluMine: alignment-free method for the discovery of polymorphic Alu element insertions

Tarmo Puurand, Viktorija Kukushkina, Fanny‐Dhelia Pajuste, Maido Remm

AluMine identifies polymorphic Alu element insertions in personal genomes using alignment-free methods, achieving high genotype concordance.

Mobile DNA · Jul 18, 2019Peer-reviewedGenomics

The genetic architecture of sporadic and recurrent miscarriage

Triin Laisk, Ana Gonçalves Soares, Teresa Cruz Ferreira, Jodie N. Painter, Samantha Laber, Jonas Bačelis, Chia‐Yen Chen, Maarja Lepamets, Kuang Lin, SiYang Maggie Liu, Iona Y. Millwood, Avinash Ramu, Jennifer H. Southcombe, Marianne Andersen, Ling Yang, , Cecilia M. Lindgren

This study identifies genetic variants associated with sporadic and recurrent miscarriage through large-scale association analyses and Mendelian randomization.

bioRxiv · Mar 12, 2019 · PreprintGenetics

Endometrial receptivity revisited: endometrial transcriptome adjusted for tissue cellular heterogeneity

Marina Suhorutshenko, Viktorija Kukushkina, Agne Velthut‐Meikas, Signe Altmäe, Maire Peters, Reedik Mägi, Kaarel Krjutškov, Mariann Koel, Francisco M. Codoñer, Juan Francisco Martínez-Blanch, Felipe Vilella, Carlos Simón, Andres Salumets, Triin Laisk

The paper investigates how cellular composition affects endometrial gene expression profiles and shows that adjusting for cell proportions changes differential expression results.

Human Reproduction · Sep 26, 2018Peer-reviewedGenomics

Novel susceptibility loci and genetic regulation mechanisms for type 2 diabetes

Angli Xue, Yang Wu, Zhihong Zhu, Futao Zhang, Kathryn E. Kemper, Zhili Zheng, Loïc Yengo, Luke R. Lloyd‐Jones, Julia Sidorenko, Yeda Wu, Mawussé D. T. Agbessi, Habibul Ahsan, Isabel Alves, Anand Kumar Andiappan, Philip Awadalla, , Jian Yang

This study identifies 139 common and 4 rare genetic variants associated with type 2 diabetes through GWAS and integrates gene expression and epigenomic data to highlight potential functional genes and regulatory mechanisms.

Nature Communications · Jul 23, 2018Peer-reviewedGenetics

Identifying gene targets for brain-related traits using transcriptomic and methylomic data from blood

Ting Qi, Yang Wu, Jian Zeng, Futao Zhang, Angli Xue, Longda Jiang, Zhihong Zhu, Kathryn E. Kemper, Loïc Yengo, Zhili Zheng, Mawussé D. T. Agbessi, Habibul Ahsan, Isabel Alves, Anand Kumar Andiappan, Philip Awadalla, , Jian Yang

The paper identifies gene targets for brain-related traits using transcriptomic and methylomic data from blood, finding strong correlations between genetic effects in brain and blood tissues.

Nature Communications · Jun 5, 2018Peer-reviewedGenetics