Publications

Caio A. Leal-Dutra, Joel Vizueta, Dr. Tobias Baril, Pepijn W. Kooij, Asta Rødsgaard-Jørgensen, Benjamin H. Schantz-Conlon, Daniel Croll, Jonathan Z. Shik (2024). Genomic Signatures of Domestication in a Fungus Obligately Farmed by Leafcutter Ants. Molecular Biology and Evolution.

Hélène Mayeur, Jake Leyhr, John Mulley, Nicolas Leurs, Léo Michel, Kanika Sharma, Ronan Lagadec, Jean-Marc Aury, Owen Osborne, Peter Mulhair, Julie Poulain, Sophie Mangenot, Dan Mead, Michelle Smith, Craig Corton, Karen Oliver, Jason Skelton, Emma Betteridge, Jale Dolucan, Olga Dudchenko, Arina Omer, David Weisz, Erez Lieberman-Aiden, Shane McCarthy, Ying Sims, James Torrance, Alan Tracey, K Howe, Dr. Tobias Baril, Alexander Hayward, Camille Matinand-Mari, Sophie Sanchez, Tatjana Haitina, Kyle Martin, Sigrun Korsching, Sylvie Mazan, Melanie Debiais-Thibaud (2024). The sensory shark: high-quality phenotypic, genomic and transcriptomic data for the small spotted catshark Scyliorhinus canicula reveal the molecular bases of sensory organ evolution in jawed vertebrates. BioRxiv.

Dr. Tobias Baril, James Galbraith, Alex Hayward (2024). Earl Grey: a fully automated user-friendly transposable element annotation and analysis pipeline. Molecular Biology and Evolution.

Gabriel David, Alicia Bertolotti, Ryan Layer, Douglas Scofield, Alexander Hayward, Dr. Tobias Baril, Hamish A Burnett, Erik Gudmunds, Henrik Jensen, Arild Husby (2024). Calling structural variants with confidence from short-read data in wild bird populations. Genome Biology and Evolution.

Dr. Tobias Baril, Daniel Croll (2023). A pangenome-guided manually curated library of transposable elements for Zymoseptoria tritici. BMC Research Notes.

Dr. Tobias Baril, Adam Pym, Chris Bass, Alexander Hayward (2023). Transposon accumulation at xenobiotic gene family loci in aphids. Genome Research.

Ivy H T Lee, Wenyan Nong, Wai Lok So, Chris K H Cheung, Yichun Xie, Dr. Tobias Baril, Ho Yin Yip, Thomas Swale, Simon K F Chan, Yingying Wei, Nathan Lo, Alexander Hayward, Ting Fung Chan, Hon-ming Lam, Jerome H L Hui (2023). The genome and sex-dependent responses to temperature in the common yellow butterfly, Eurema hecabe. BMC Biology.

Thomas D Brekke, Alexander S T Papadopulos, Eva Julia, Oscar Fornas, Beiyuan Fu, Fengtang Yang, Roberto de la Fuente, Jesus Page, Dr. Tobias Baril, Alex Hayward, John F Mulley (2023). A New Chromosome-Assigned Mongolian Gerbil Genome Allows Characterization of Complete Centromeres and a Fully Heterochromatic Chromosome. Molecular Biology and Evolution.

Toby Doyle, Eva Jimenez‐Guri, Will LS Hawkes, Richard Massy, Federica Mantica, Jon Permanyer, Luca Cozzuto, Toni Hermoso Pulido, Dr. Tobias Baril, Alex Hayward, Manuel Irimia, Jason W Chapman, Chris Bass, Karl R Wotton (2022). Genome-wide transcriptomic changes reveal the genetic pathways involved in insect migration. Molecular Ecology.

Alexander Mackintosh, Dominik R Laetsch, Dr. Tobias Baril, Sam Ebdon, Paul Jay, Roger Vila, Alex Hayward, Konrad Lohse (2022). The genome sequence of the scarce swallowtail, Iphiclides podalirius. G3.

Sean TS Law, Wenyan Nong, Wai Lok So, Dr. Tobias Baril, Thomas Swale, Chi Bun Chan, Stephen S Tobe, Zhen-peng Kai, William G Bendena, Alexander Hayward, Jerome HL Hui (2022). Chromosomal-level reference genome of the moth Heortia vitessoides (Lepidoptera: Crambidae), a major pest of agarwood-producing trees. Genomics.

Alexander Mackintosh, Dominik Laetsch, Dr. Tobias Baril, Robert Foster, Vlad Dincă, Roger Vila, Alex Hayward, Konrad Lohse (2022). The genome sequence of the lesser marbled fritillary, Brenthis ino, and evidence for a segregating neo-Z chromosome. G3.

Wai Lok So, Wenyan Nong, Yichun Xie, Dr. Tobias Baril, Hai-yao Ma, Zhe Qu, Jasmine Haimovitz, Thomas Swale, Juan Diego Gaitan-Espitia, Kwok Fai Lau, Stephen S Tobe, William G Bendena, Zhen-peng Kai, Alexander Hayward, Jerome HL Hui (2022). Myriapod genomes reveal ancestral horizontal gene transfer and hormonal gene loss in millipedes. Nature Communications.

Dr. Tobias Baril, Alex Hayward (2022). Migrators within migrators: exploring transposable element dynamics in the monarch butterfly, Danaus plexippus. Mobile DNA.

Wenyan Nong, Yifei Yu, Madeleine E Aase-Remedios, Yichun Xie, Wai Lok So, Yiqian Li, Cheuk Fung Wong, Dr. Tobias Baril, Sean TS Law, Sheung Yee Lai, Jasmine Haimovitz, Thomas Swale, Shan-shan Chen, Zhen-peng Kai, Xi Sun, Zhongdao Wu, Alexander Hayward, David EK Ferrier, Jerome HL Hui (2022). Genome of the ramshorn snail Biomphalaria straminea—an obligate intermediate host of schistosomiasis. GigaScience.

Alex Hayward, Roger Vila, Dominik R Laetsch, Konrad Lohse, Dr. Tobias Baril, Wellcome Sanger Institute Tree of Life, Darwin Tree of Life Consortium (2021). The genome sequence of the heath fritillary, Melitaea athalia (Rottemburg, 1775). Wellcome Open Research.

Mathilde Dupeyron, Dr. Tobias Baril, Alexander Hayward (2021). Broadscale evolutionary analysis of eukaryotic DDE transposons. BioRxiv.

Wenyan Nong, Zhe Qu, Yiqian Li, Tom Barton-Owen, Annette YP Wong, Ho Yin Yip, Hoi Ting Lee, Satya Narayana, Dr. Tobias Baril, Thomas Swale, Jianquan Cao, Ting Fung Chan, Hoi Shan Kwan, Sai-Ming Ngai, Gianni Panagiotou, Pei-Yuan Qian, Jian-Wen Qiu, Kevin Y Yip, Noraznawati Ismail, Siddhartha Pati, Akbar John, Stephen S Tobe, William G Bendena, Siu Gin Cheung, Alexander Hayward, Jerome HL Hui (2021). Horseshoe crab genomes reveal the evolution of genes and microRNAs after three rounds of whole genome duplication. Communications Biology.

Yiqian Li, Wenyan Nong, Dr. Tobias Baril, Ho Yin Yip, Thomas Swale, Alexander Hayward, David EK Ferrier, Jerome HL Hui (2020). Reconstruction of ancient homeobox gene linkages inferred from a new high-quality assembly of the Hong Kong oyster (Magallana hongkongensis) genome. BMC Genomics.

Zhe Qu, Wenyan Nong, Yifei Yu, Dr. Tobias Baril, Ho Yin Yip, Alexander Hayward, Jerome HL Hui (2020). Genome of the four-finger threadfin Eleutheronema tetradactylum (Perciforms: Polynemidae). BMC Genomics.

Zhe Qu, Wenyan Nong, Wai Lok So, Tom Barton-Owen, Yiqian Li, Thomas CN Leung, Chade Li, Dr. Tobias Baril, Annette YP Wong, Thomas Swale, Ting Fung Chan, Alexander Hayward, Sai-Ming Ngai, Jerome HL Hui (2020). Millipede genomes reveal unique adaptations during myriapod evolution. PLoS Biology.

Mathilde Dupeyron, Dr. Tobias Baril, Chris Bass, Alexander Hayward (2020). Phylogenetic analysis of the Tc1/mariner superfamily reveals the unexplored diversity of pogo-like elements. Mobile DNA.

Wenyan Nong, Sean TS Law, Annette YP Wong, Dr. Tobias Baril, Thomas Swale, Lee Man Chu, Alexander Hayward, David TW Lau, Jerome HL Hui (2020). Chromosomal-level reference genome of the incense tree Aquilaria sinensis. Molecular Ecology Resources.

Rute R Da Fonseca, Alvarina Couto, Andre M Machado, Brona Brejova, Carolin B Albertin, Filipe Silva, Paul Gardner, Dr. Tobias Baril, Alex Hayward, Alexandre Campos, Ângela M Ribeir, Inigo Barrio-Hernandez, Henk-Jan Hoving, Ricardo Tafur-Jimenez, Chong Chu, Barbara Frazão, Bent Petersen, Fernando Peñaloza, Francesco Musacchia, Graham C Alexander Jr, Hugo Osório, Inger Winkelmann, Oleg Simakov, Simon Rasmussen, M Ziaur Rahman, Davide Pisani, Jakob Vinther, Erich Jarvis, Guojie Zhang, Jan M Strugnell, L Filipe C Castro, Olivier Fedrigo, Mateus Patricio, Qiye Li, Sara Rocha, Agostinho Antunes, Yufeng Wu, Bin Ma, Remo Sanges, Tomas Vinar, Blagoy Blagoev, Thomas Sicheritz-Ponten, Rasmus Nielsen, M Thomas P Gilbert (2020). A draft genome sequence of the elusive giant squid, Architeuthis dux. GigaScience.