[HTML][HTML] The zebrafish reference genome sequence and its relationship to the human genome

…, M Dunn, C Johnson, J Wood, S Clark, S Pelan… - Nature, 2013 - nature.com
Zebrafish have become a popular organism for the study of vertebrate gene function 1 , 2 .
The virtually transparent embryos of this species, and the ability to accelerate genetic studies …

[HTML][HTML] Towards complete and error-free genome assemblies of all vertebrate species

…, I Gut, J Ghurye, E Garrison, Y Sims, J Collins, S Pelan… - Nature, 2021 - nature.com
High-quality and complete reference genome assemblies are fundamental for the application
of genomics to biology, disease, and biodiversity conservation. However, such assemblies …

Significantly improving the quality of genome assemblies through curation

K Howe, W Chow, J Collins, S Pelan, DL Pointon… - …, 2021 - academic.oup.com
Genome sequence assemblies provide the basis for our understanding of biology.
Generating error-free assemblies is therefore the ultimate, but sadly still unachieved goal of a …

Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly

…, J Collins, G Harden, T Hubbard, S Pelan… - Genome …, 2017 - genome.cshlp.org
The human reference genome assembly plays a central role in nearly all aspects of today's
basic and clinical research. GRCh38 is the first coordinate-changing assembly update since …

[HTML][HTML] Modernizing reference genome assemblies

…, J Wood, J Collins, P Heath, G Griffiths, S Pelan… - PLoS …, 2011 - journals.plos.org
The availability of a high quality human genome assembly has revolutionized biomedical
research. Genomics has now entered the realm of clinical genetics, with many groups using …

[PDF][PDF] Population genomics of the critically endangered kākāpō

…, AM Phillippy, J Korlach, K Howe, W Chow, S Pelan… - Cell Genomics, 2021 - cell.com
The kākāpō is a flightless parrot endemic to New Zealand. Once common in the archipelago,
only 201 individuals remain today, most of them descending from an isolated island …

[HTML][HTML] Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci

…, FCP Navarro, DT Odom, N Park, S Pelan… - Nature …, 2018 - nature.com
We report full-length draft de novo genome assemblies for 16 widely used inbred mouse strains
and find extensive strain-specific haplotype variation. We identify and characterize 2,567 …

[PDF][PDF] An improved germline genome assembly for the sea lamprey Petromyzon marinus illuminates the evolution of germline-specific chromosomes

…, B Haase, JR Balacco, G Formenti, S Pelan… - Cell reports, 2023 - cell.com
Programmed DNA loss is a gene silencing mechanism that is employed by several
vertebrate and nonvertebrate lineages, including all living jawless vertebrates and songbirds. …

Reference genome and demographic history of the most endangered marine mammal, the vaquita

…, W Musser, S Paez, S Pelan… - Molecular Ecology …, 2021 - Wiley Online Library
The vaquita is the most critically endangered marine mammal, with fewer than 19 remaining
in the wild. First described in 1958, the vaquita has been in rapid decline for more than 20 …

[HTML][HTML] Ancient diversity in host-parasite interaction genes in a model parasitic nematode

…, JL Hall, M Kieninger, A Kloch, S Pelan… - Nature …, 2023 - nature.com
Host-parasite interactions exert strong selection pressures on the genomes of both host and
parasite. These interactions can lead to negative frequency-dependent selection, a form of …