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Latest publications

  • Assembly of female and male hihi genomes (stitchbird; Notiomystis cincta) enables characterization of the W chromosome and resources for conservation genomics 

    Published Papers
    Issue date:

    Bailey, Sarah; Guhlin, Joseph; Senanayake, Dinindu S.; Scherer, Phoebe; Brekke, Patricia; Ewen, John G.; Santure, Anna W.; Whibley, Annabel    

    Molecular Ecology Resources
    https://onlinelibrary.wiley.com/doi/full/10.1111/1755-0998.13823

  • Capturing species‐wide diversity of the gut microbiota and its relationship with genomic variation in the critically endangered kākāpō    

    Published Papers
    Issue date:

    West, Annie G.; Digby, Andrew; Santure, Anna W.; Guhlin, Joseph G.; Dearden, Peter; Team, Kākāpō Recovery; Taylor, Michael W.; Urban, Lara    
    Molecular Ecology
    https://onlinelibrary.wiley.com/doi/10.1111/mec.16999

  • Formalin fixed paraffin embedded (FFPE) samples help to investigate transcriptomic responses in wildlife disease

    Published Papers
    Issue date:

    Miller, Allison K.; Brosnahan, Cara L.; Pande, Anjali; Baker, Cindy F.; Geoghegan, Jemma L.; Kitson, Jane; Gemmell, Neil J.; Dowle, Edwina J.
    Molecular Ecology Resources
    https://onlinelibrary.wiley.com/doi/10.1111/1755-0998.13805

  • Rapid dissemination of host-metabolism-manipulating transposon-like entities via integrative and conjugative elements    

    Published Papers
    Issue date:

    Colombi, Elena; Bertels, Frederic; Doulcier, Guilhem; McConnell, Ellen; Pichugina, Tatyana; Sohn, Kee Hoon; Straub, Christina; McCann, Honour; Rainey, Paul B.    
    bioRxiv
    https://www.biorxiv.org/content/10.1101/2023.04.24.538000v1

  • Transcriptomic identification of differentially expressed genes in Levonorgestrel resistant endometrial cancer cell lines

    Published Papers
    Issue date:

    Dore, Molly; Faya, Ngonidzashe; Filoche, Sara; Henry, Claire    
    Molecular Carcinogenesis
    https://onlinelibrary.wiley.com/doi/10.1002/mc.23544

  • GALBA: Genome Annotation with Miniprot and AUGUSTUS  

    Published Papers
    Issue date:

    Brůna, Tomáš; Li, Heng; Guhlin, Joseph; Honsel, Daniel; Herbold, Steffen; Stanke, Mario; Nenasheva, Natalia; Ebel, Matthis; Gabriel, Lars; Hoff, Katharina J.    
    bioRxiv
    https://www.biorxiv.org/content/10.1101/2023.04.10.536199v1

  • Building pangenome graphs 

    Published Papers
    Issue date:

    Garrison, Erik; Guarracino, Andrea; Heumos, Simon; Villani, Flavia; Bao, Zhigui; Tattini, Lorenzo; Hagmann, Jörg; Vorbrugg, Sebastian; Marco-Sola, Santiago; Kubica, Christian; Ashbrook, David G.; Thorell, Kaisa; Rusholme-Pilcher, Rachel L.; Liti, Gianni; Rudbeck, Emilio; Nahnsen, Sven; Yang, Zuyu; Moses, Mwaniki N.; Nobrega, Franklin L.; Wu, Yi; Chen, Hao; de Ligt, Joep; Sudmant, Peter H.; Soranzo, Nicole; Colonna, Vincenza; Williams, Robert W.; Prins, Pjotr    
    bioRxiv
    https://www.biorxiv.org/content/10.1101/2023.04.05.535718v1

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

    Published Papers
    Issue date:

    Timoshevskaya, Nataliya; Esşkut, Kaan i.; Timoshevskiy, Vladimir A.; Robb, Sofia M.C.; Holt, Carson; Hess, Jon E.; Parker, Hugo J.; Baker, Cindy F.; Miller, Allison K.; Saraceno, Cody; Yandell, Mark; Krumlauf, Robb; Narum, Shawn R.; Lampman, Ralph T.; Gemmell, Neil J.; Mountcastle, Jacquelyn; Haase, Bettina; Balacco, Jennifer R.; Formenti, Giulio; Pelan, Sarah; Sims, Ying; Howe, Kerstin; Fedrigo, Olivier; Jarvis, Erich D.; Smith, Jeramiah J.   
    Cell Reports
    https://www.cell.com/cell-reports/fulltext/S2211-1247(23)00274-7

  • The promise and challenges of characterizing genome‐wide structural variants: A case study in a critically endangered parrot    

    Published Papers
    Issue date:

    Wold, Jana R.; Guhlin, Joseph G.; Dearden, Peter K.; Santure, Anna W.; Steeves, Tammy E.
    Molecular Ecology Resources
    https://onlinelibrary.wiley.com/doi/10.1111/1755-0998.13783

  • Divergent sensory and immune gene evolution in sea turtles with contrasting demographic and life histories 

    Published Papers
    Issue date:

    Bentley, Blair P.; Carrasco-Valenzuela, Tomás; Ramos, Elisa K. S.; Pawar, Harvinder; Arantes, Larissa Souza; Alexander, Alana; Banerjee, Shreya M.; Masterson, Patrick; Kuhlwilm, Martin; Pippel, Martin; Mountcastle, Jacquelyn; Haase, Bettina; Uliano-Silva, Marcela; Formenti, Giulio; Howe, Kerstin; Chow, William; Tracey, Alan; Sims, Ying; Pelan, Sarah; Wood, Jonathan; Yetsko, Kelsey; Perrault, Justin R.; Stewart, Kelly; Benson, Scott R.; Levy, Yaniv; Todd, Erica V.; Shaffer, H. Bradley; Scott, Peter; Henen, Brian T.; Murphy, Robert W.; Mohr, David W.; Scott, Alan F.; Duffy, David J.; Gemmell, Neil J.; Suh, Alexander; Winkler, Sylke; Thibaud-Nissen, Françoise; Nery, Mariana F.; Marques-Bonet, Tomas; Antunes, Agostinho; Tikochinski, Yaron; Dutton, Peter H.; Fedrigo, Olivier; Myers, Eugene W.; Jarvis, Erich D.; Mazzoni, Camila J.; Komoroske, Lisa M.    
    Proceedings of the National Academy of Sciences of the United States of America
    https://www.pnas.org/doi/10.1073/pnas.2201076120

  • Genomic signatures of inbreeding depression for a threatened Aotearoa New Zealand passerine

    Published Papers
    Issue date:

    Duntsch, Laura; Whibley, Annabel; Villemereuil, Pierre; Brekke, Patricia; Bailey, Sarah; Ewen, John G.; Santure, Anna W.    
    Molecular Ecology
    https://onlinelibrary.wiley.com/doi/10.1111/mec.16855

  • The mycobiota of faeces from the critically endangered kākāpō and associated nest litter     

    Published Papers
    Issue date:

    West, Annie G.; Digby, Andrew; Team, Kākāpō Recovery; Consortium, Kākāpō Aspergillosis Research; Taylor, Michael W.       
    New Zealand Journal of Zoology
    https://www.tandfonline.com/doi/full/10.1080/03014223.2023.2170428

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