Recent Publications

Best practices for collecting and preserving marine mammal biological samples in the ‘omics era. Van Cise, Amy M., Alexandra D. Switzer, Amy Apprill, Cory D. Champagne, Paul M. Chittaro, Natasha K. Dudek, Mackenzie R. Gavery et al. Marine Mammal Science (2024): e13148.

A DNA barcoding framework for taxonomic verification in the Darwin Tree of Life Project. Twyford, Alex D., Jordan Beasley, Ian Barnes, Heather Allen, Freja Azzopardi, David Bell, Mark L. Blaxter et al. Wellcome Open Research 9 (2024): 339.

COPO-Managing sample metadata for biodiversity: considerations from the Darwin Tree of Life project. Shaw, Felix, Alice Minotto, Seanna McTaggart, Aaliyah Providence, Peter Harrison, Joana Paupério, Jeena Rajan et al. Wellcome Open Research 7, no. 279 (2024): 279.

Informed Choices, Cohesive Future: Decisions and Recommendations for ERGA. Narayan, Jitendra. Peer Community in Genomics 1 (2024): 100298.

Contextualising samples: supporting reference genomes of European biodiversity through sample and associated metadata collection. Böhne, Astrid, Rosa Fernández, Jennifer A. Leonard, Ann M. McCartney, Seanna McTaggart, José Melo-Ferreira, Rita Monteiro, Rebekah A. Oomen, Olga Vinnere Pettersson, and Torsten H. Struck. npj Biodiversity 3, no. 1 (2024): 26.

The Genomics for Australian Plants (GAP) framework initiative–developing genomic resources for understanding the evolution and conservation of the Australian flora. Simpson, Lalita, David Cantrill, Margaret Byrne, Theodore Allnutt, Graham King, Mabel Lum, Ziad Al Bkhetan et al. (2024).

Genomes on a Tree (GoaT): a versatile, scalable search engine for genomic and sequencing project metadata across the eukaryotic tree of life. Challis, Richard, Sujai Kumar, Cibele Sotero-Caio, Max Brown, and Mark Blaxter. Wellcome Open Research 8 (2023).

The BioGenome Portal: a web-based platform for biodiversity genomics data management. Righi, Emilio, and Roderic Guigo. bioRxiv (2023): 2023-12.

MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads. Uliano-Silva, Marcela, João Gabriel RN Ferreira, Ksenia Krasheninnikova, Giulio Formenti, Linelle Abueg, James Torrance, Eugene W. Myers, Richard Durbin, Mark Blaxter, and Shane A. McCarthy. BMC bioinformatics 24, no. 1 (2023): 288.

Standards recommendations for the earth BioGenome project. Lawniczak, Mara KN, Richard Durbin, Paul Flicek, Kerstin Lindblad-Toh, Xiaofeng Wei, John M. Archibald, William J. Baker et al. Proceedings of the National Academy of Sciences 119, no. 4 (2022): e2115639118.

Squalomix: shark and ray genome analysis consortium and its data sharing platform. Nishimura, Osamu, John Rozewicki, Kazuaki Yamaguchi, Kaori Tatsumi, Yuta Ohishi, Tazro Ohta, Masaru Yagura et al. F1000Research 11 (2022).

dartR v2: An accessible genetic analysis platform for conservation, ecology and agriculture. Mijangos, Jose Luis, Bernd Gruber, Oliver Berry, Carlo Pacioni, and Arthur Georges. Methods in Ecology and Evolution 13, no. 10 (2022): 2150-2158.

Ten simple rules for getting started with command-line bioinformatics. Brandies, Parice A., and Carolyn J. Hogg. PLoS Computational Biology 17, no. 2 (2021): e1008645.

Progressive Cactus is a multiple-genome aligner for the thousand-genome era. Armstrong, Joel, Glenn Hickey, Mark Diekhans, Ian T. Fiddes, Adam M. Novak, Alden Deran, Qi Fang et al. Nature 587, no. 7833 (2020): 246-251.