This study evaluates variability in kidney organoid structure development across different culture approaches and iPSC lines using high-throughput methods.

Methods and Protocols · Oct 19, 2025Peer-reviewedDevelopmental Biology

Effects of alcohol on the transcriptome, methylome, and metabolome of in vitro gastrulating human embryonic cells

Essi Wallén, K. Rämö, Jussi Vehvilainen, Joonas Sokka, Marko Lehtonen, Timo Otonkoski, Ras Trokovic, Pauliina Auvinen, Olli K. Kärkkäinen, Nina Kaminen‐Ahola

This study examines how alcohol exposure affects the transcriptome, methylome, and metabolome of human embryonic cells during gastrulation, identifying key gene and metabolic changes linked to fetal alcohol spectrum disorders.

Disease Models & Mechanisms · May 22, 2025Peer-reviewedGenetics

A Comprehensive Human Embryogenesis Reference Tool using Single-Cell RNA-Sequencing Data

Cheng Zhao, Álvaro Plaza Reyes, John Paul Schell, Jere Weltner, N. M. Ortega, Yi Zheng, Åsa K. Björklund, Laura Baqué-Vidal, Joonas Sokka, Ras Trokovic, Brian Cox, Janet Rossant, Jianping Fu, Sophie Petropoulos A, Fredrik Lanner

The paper develops a comprehensive reference tool for human embryogenesis using integrated single-cell RNA-sequencing data to benchmark embryo models.

Nature Methods · Nov 14, 2024Peer-reviewedDevelopmental Biology

Chromatin remodeler developmental pluripotency associated factor 4 (DPPA4) is a candidate gene for alcohol-induced developmental disorders

Pauliina Auvinen, Jussi Vehvilainen, Heidi Marjonen, Vijayachitra Modhukur, Joonas Sokka, Essi Wallén, K. Rämö, L. Ahola, Andres Salumets, Timo Otonkoski, Heli Skottman, Miina Ollikainen, Ras Trokovic, Hanna K. Kahila, Nina Kaminen‐Ahola

The paper investigates the effects of alcohol exposure on placental DNA methylation and identifies DPPA4 as a candidate gene for alcohol-induced developmental disorders.

BMC Medicine · Dec 29, 2022Peer-reviewedGenetic & Genomic Medicine