FEHAT automatically detects heart rates in Medaka fish embryos from high-resolution videos, showing reliable performance across temperature perturbations.

Bioinformatics · Nov 6, 2024Peer-reviewedBioinformatics

The Medaka Inbred Kiyosu-Karlsruhe (MIKK) Panel

Tomas W. Fitzgerald, Ian Brettell, Adrien Léger, Nadeshda Wolf, Natalja Kusminski, Jack Monahan, Carl Barton, Cathrin Herder, Narendar Aadepu, Jakob Gierten, Clara Becker, Omar T. Hammouda, Eva Hasel, Colin Q. Lischik, Katharina Lust, , Felix Loosli

The paper introduces the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel, a vertebrate genetic resource for genotype-to-phenotype studies, enabling controlled experiments on complex traits.

Genome biology · Feb 21, 2022Peer-reviewedGenomics

Genomic variations and epigenomic landscape of the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel

Adrien Léger, Ian Brettell, Jack Monahan, Carl Barton, Nadeshda Wolf, Natalja Kusminski, Cathrin Herder, Narendar Aadepu, Clara Becker, Jakob Gierten, Omar T. Hammouda, Eva Hasel, Colin Q. Lischik, Katharina Lust, Natalia Sokolova, , Tomas W. Fitzgerald

The paper analyzes genomic and epigenomic variation in the MIKK panel using long-read sequencing and pan-genome graphs, revealing novel structural variants and methylation patterns.

Genome biology · Feb 21, 2022Peer-reviewedGenomics

In vivo identification and validation of novel potential predictors for human cardiovascular diseases

Omar T. Hammouda, Meng Yue Wu, Verena Kaul, Jakob Gierten, Thomas Thumberger, Joachim Wittbrodt

The paper identifies and validates 16 GWAS candidates with potential predictive power for human cardiovascular diseases using CRISPR/Cas9 in medaka.

PLoS ONE · Dec 17, 2021Peer-reviewedGenetics

Automated high-throughput heart rate measurement in medaka and zebrafish embryos under physiological conditions

Jakob Gierten, Christian Pylatiuk, Omar T. Hammouda, Christian Schock, Johannes Stegmaier, Joachim Wittbrodt, Jochen Gehrig, Felix Loosli

The paper develops an automated high-throughput method for measuring heart rate in medaka and zebrafish embryos without anesthesia or fluorescent reporters.

Scientific Reports · Feb 6, 2020Peer-reviewedDevelopmental Biology

Swift Large-scale Examination of Directed Genome Editing (SLEDGE Hammer)

Omar T. Hammouda, Frank Böttger, Joachim Wittbrodt, Thomas Thumberger

The paper introduces a low-cost DIY method for rapid nucleic acid extraction using cellulose filter discs in pipet tips, enabling fast and reliable genotyping of diverse samples.

PLoS ONE · Mar 5, 2019Peer-reviewedMolecular Biology