Research
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Nanopore sequencing, AI, and One Health
We leverage the real-time, portable, long-read, low upfront-investment, and atomic resolution properties of nanopore sequencing technology together with computational genomic and machine learning approaches for rapid and in-depth One Health surveillance. We have established nanopore sequencing for freshwater and air monitoring, biodiversity monitoring in Zambia, and in situ surveillance of the critically endangered kākāpō as well as de novo genome generation of the critically endangered Māui dolphin in Aotearoa New Zealand. We have collaborated with clinical partners for pathogen and drug resistance profiling in the human health setting, and with veterinarians for virome profiling (with a focus on avian influenza virus) along globally significant avian flyways. We have also started exploring the promise of AI-based nanopore raw data analysis for inferring, amongst others, the virulence and dormancy of pathogens and the genomic context of resistance genes in complex metagenomic data.
veaf010.pdfPerlas, A., Reska, T., (...), Urban, L. (2025) Improvements in RNA and DNA nanopore sequencing allow for rapid genetic characterization of avian influenza. Virus Evolution.
s41467-024-49851-4.pdfSauerborn, E., Corredor, C., Reska, T., Perlas, A., Atum, S., (...), Urban, L. (2024) Detection of hidden antibiotic resistance through real-time genomics. Nature Communications.
ycae099.pdfReska, T., Pozdniakova, S., (...), Urban, L. (2024) Air monitoring by nanopore sequencing. ISME Communications.
Molecular Systems Biology - 2023 - Urban - Real‐time genomics for One Health.pdfUrban, L., (...), van Oosterhout, C. (2023) Real-time Genomics for One Health. Molecular Systems Biology.
2024.06.10.598221v1.full.pdfUrel, H., Benassou, S., Reska, T.,(...), Urban, L. Nanopore- and AI- empowered metagenomic viability inference. Preprint, with GigaScience.
84553-v1.pdfUrban, L., (...), Digby, A. (2023) Non-invasive real-time genomic monitoring of the critically endangered kākāpō. eLife.
elife-61504-v1-2.pdfUrban, L., Holzer, A. (…), Stammnitz, M. R. (2021) Freshwater monitoring with nanopore sequencing. eLife.
Gygax_eDNA.pdfGygax, D. ,(...), Urban, L. Evaluation of nanopore sequencing for increasing accessibility of eDNA studies in biodiverse countries. Preprint, with PLOS One.
Amir.pdfVarzandi, A., (...), Urban, L., (...), Ferroglio, E. (2025) Environmental screening through nanopore native sequencing leads to the detection of Batrachochytrium dendrobatidis in La Mandria Regional Park, Italy. Global Ecology and Conservation.
1-s2.0-S1472648321001449-main.pdfOberle, A.* & Urban, L.*, Falch, S., Nagai, Y., Ulm, P. A., Hengstschläger, M., Feichtinger, M (2021) 16S rRNA long-read nanopore sequencing is feasible and reliable for endometrial microbiome analysis. RBMO
Alana.pdfCostes, S., (...), Urban, L., Alana, A. (2024) Leveraging synteny to generate reference genomes for conservation: Assembling the genomes of Hector’s and Māui dolphins. Molecular Ecology Resources.
Conservation Genomics with a focus on critically endangered species
We analyzed the genomes and microbiomes of critically endangered species such as the Aotearoa New Zealand kākāpō, takahē, and tuatara to try and contribute to their conservation and recovery; this work was based on extensive collaborations and fieldwork with the national Department of Conservation and its recovery teams as well as with Ngāi Tahu as kaitiaki or guardians of these taonga or treasured species.
We have further contributed to environmental DNA studies for biodiversity monitoring, and to global efforts of leveraging genomic data for conservation.
Molecular Ecology - 2023 - West - Capturing species%E2%80%90wide diversity of the gut microbiota and its relationship with genomic.pdfWest, A., (...), Taylor, M. W., Urban, L. (2023) Capturing species-wide diversity of the gut microbiota and its relationship with genomic variation in the critically endangered kākāpō. Molecular Ecology.
journal.pbio.3002755.pdfUrban, L., (...), Morales, H. (2023) The genetic basis of the kākāpō structural color polymorphism suggests balancing selection by an extinct apex predator. PLOS Biology.
s41559-023-02165-y.pdfGuhlin, H., (...), Urban, L., (...), Dearden, P. (2023) Species-wide genomics of kakapo provides tools to accelerate recovery. Nature Ecology & Evolution.
s41587-022-01261-x.pdfCheng, H., (...), Urban, L., (...)., Li, H. (2022) Haplotype-resolved assembly of diploid individuals without parental data. Nature Biotechnology.
takahe_report_lu_2024.pdfUrban, L., Greaves, G., Digby, A., et al. First report on the Takahē Genome Project.
peerj-14675.pdfDigby, A., (...), Urban, L., (...), Kākāpō Recovery Team. (2023) Hidden impacts of conservation management on fertility of the critically endangered kākāpō. PeerJ.
Elusive aetiology of exudative cloacitis in the critically endangered k k p .pdfWest, A.,(...), Urban, L., Taylor, M. (2024) Elusive aetiology of exudative cloacitis in the critically endangered kākāpō. New Zealand Journal of Zoology.
Theissinger.pdfhttps://www.cell.com/trends/genetics/fulltext/S0168-9525(23)00020-3
s42523-022-00204-w.pdfWest, A., (...), Kākāpō Aspergillosis Research Consortium (incl. Urban, L.), Taylor, M. (2022) Influence of management practice on the microbiota of a critically endangered species: a longitudinal study of kākāpō chick faeces and associated nest litter. Animal microbiome.
Molecular Ecology Resources - 2022 - Pearman - Commonly used Hardy Weinberg equilibrium filtering schemes impact population.pdfPearman, W., Urban, L., Alexander, L. (2022) Commonly used Hardy–Weinberg equilibrium filtering schemes impact population structure inferences using RADseq data. Molecular Ecology Resources.
s42003-020-01639-0.pdfMacey, J. R., (…), Urban, L., (…), Gemmell, N. G. (2021) Evidence of wo deeply divergent co-existing mitochondrial genomes in the Tuatara. Nature Communications Biology 4, 116.
Zoo Biology - 2024 - Martin - Sonification of Genomic Data to Represent Genetic Load in Zoo Populations.pdfMartin, E., (...), Urban, L., van Oosterhout (2024) Sonification of genomic data to represent genetic load in zoo populations. Zoo Biology.
BMCBio.pdfGould, G., (...), Urban, L., (...), Parker, T. (2025) Same data, different analysts: variation in effect sizes due to analytical decisions in ecology and evolutionary biology. BMC Biology.
Evidence of two deeply divergent co-existing mitochondrial genomes in the Tuatara reveals an extremely complex genomic organization.pdfFormenti, G., (...), Urban, L., (...)., Bálint, M. (2022) The era of reference genomes in conservation genomics. Trends in Ecology & Evolution 37, 3: 197-202.
Adams_eDNA.pdfhttps://academic.oup.com/icesjms/article/80/4/953/7058017
fulltextRepo.pdfvan Oosterhout, C., (...), Urban, L., (...), Morales, H. (2022) Genomic erosion in the assessment of species extinction risk and recovery potential. bioRxiv.
filter_feeder_eDNA.pdfhttps://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.13754
515425.pdfEdgecombe, J., Urban, L., Todd, E. V., Gemmell, N. J. (2021) Might gene duplication and neofunctionalization contribute to the sexual lability observed in fish? Sexual Development 15, 122-133.
d41586-023-02229-w.pdfEuropean Reference Genome Atlas Council (incl. Urban, L., 2023) Biodiversity: an atlas of European reference genome. Nature.
b3087b_36ec86422d4c421586053a670355b391.pdfJeunen, G.* & Urban, L.*, (…), Gemmell, N. (2020) Marine environmental DNA (eDNA) for biodiversity assessments: a one-to-one comparison between eDNA and baited remote underwater video (BRUV) surveys. Authorea.
Statistical Genomics with a focus on human cancer and single-cell technology
Lara's PhD research on leveraging statistical genomics, big data, AI, and new methodology for single-cell analysis to understand gene regulation in various human cancers.
s41586-020-1970-0.pdfPCAWG Transcriptome Core Group (incl. Urban, L.*), (...), Zhang, Z. (2020): Genomic basis for RNA alterations in cancer. Nature 578, 129–136.
s41586-020-1969-6.pdfThe ICGC/TCGA PCAWG Consortium (incl. Urban, L.) (2020): Pan-cancer analysis of whole genomes. Nature 578, 82–93.
s13059-019-1644-0.pdfLinker, S.M., Urban, L., Clark, S.J. et al. (2019) Combined single-cell profiling of expression and DNA methylation reveals splicing regulation and heterogeneity. Genome Biol 20, 30.
s41587-019-0140-0.pdfAvsec, Z., (…), Urban, L., (…), Gagneur, J. (2019): The Kipoi repository accelerates community exchange and reuse of predictive models for genomics. Nature Biotechnology 37, 592-600.
s41467-020-18151-y.pdfBailey, M.H., Meyerson, W.U., Dursi, L.J.,PCAWG Consortium (incl. Urban, L.), et al. (2020) Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples. Nat Commun 11, 4748.
s41467-020-17359-2.pdfLi, C.H., Prokopec, S.D., Sun, R.X.,PCAWG Consortium (incl. Urban, L.), et al. (2020) Sex differences in oncogenic mutational processes. Nat Commun 11, 4330.
225441v1.full.pdfCalabrese, C.* & Lehmann, K. V.* & Urban, L.*, (...), Stegle O. (2017) Assessing the Gene Regulatory Landscape in 1,188 Human Tumors. bioRxiv preprint.
s13104-020-04946-1.pdfUrban, L., Remmele, C.W., Dittrich, M. et al. (2020) covRNA: discovering covariate associations in large-scale gene expression data. BMC Res Notes 13, 92.
Evaluation of the scientific publishing system
Lara's involvement in the eLife movement to change the scientific publication system to be fairer, more transparent, less hierarchical, and not-for-profit.
elife-84816-v1.pdfUrban, L., (...), Elkheir, L. (2022) eLife’s new model and its impact on science communication. eLife.
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