The paper fills a gap in 3D spatial transcriptomics by providing data from E9.5 and E11.5 mouse embryos, enabling detailed analysis of organogenesis with a new open-access database.

bioRxiv · Aug 17, 2024 · PreprintDevelopmental Biology

Evolution of the Growth Hormone Gene Duplication in Passerine Birds

Shauna A. Rasband, Peri E. Bolton, Qi Fang, Philip L. F. Johnson, Michael J. Braun

The paper investigates the molecular evolution of duplicated growth hormone genes in passerine birds, finding evidence of positive selection and functional divergence.

Genome Biology and Evolution · Feb 27, 2023Peer-reviewedMolecular Biology

Genome of an iconic Australian bird: Chromosome-scale assembly and linkage map of the superb fairy-wren (Malurus cyaneus)

Joshua V. Peñalba, Yuan Deng, Qi Fang, Leo Joseph, Craig C. Moritz, Andrew Cockburn

The paper presents a chromosome-scale genome assembly and genetic map for the superb fairy-wren, along with gene and repeat annotations, providing a new reference for avian comparative genomics.

Molecular Ecology Resources · Dec 10, 2019Peer-reviewedGenomics

Progressive alignment with Cactus: a multiple-genome aligner for the thousand-genome era

Joel C. Armstrong, Glenn Hickey, Mark Diekhans, Alden Deran, Qi Fang, Duo Xie, Shaohong Feng, Josefin Stiller, Diane P. Genereux, Jeremy Johnson, Voichita Dana Marinescu, David H. Haussler, Jessica Alföldi, Kerstin Lindblad‐Toh, Elinor K. Karlsson, , Benedict Paten

The paper improves the Cactus multiple-genome aligner to handle large numbers of vertebrate genomes with high accuracy and better orthology resolution.

bioRxiv · Oct 15, 2019 · PreprintGenomics