Publications

Selected publications [see here for all]

2024.06.10.598221v1.full.pdf

Urel, H., Benassou, S., Reska, T.,(...),  Urban, L. (2024) Nanopore- and AI- empowered metagenomic viability inference. Preprint, with PLOS Computational Biology.

2024.02.28.582540v2.full.pdf

Perlas, A., Reska, T., (...), Urban, L. (2024) Latest RNA and DNA nanopore sequencing allows for rapid avian influenza profiling. Preprint, with Virus Evolution.

2023.12.19.572325v1.full.pdf

Reska, T., Pozdniakova, S., (...), Urban, L. (2023) Air monitoring by nanopore sequencing.  Preprint, with ISME Communications.

v1_covered_68071ef4-fbe8-404d-b973-c03b26c1c6ff.pdf

Sauerborn, E., Corredor, C., Reska, T., Perlas, A., Atum, S., (...), Urban, L. (2023) Detection of hidden antibiotic resistance through real-time genomics. Accepted at Nature Communications.

2023.09.25.559367v2.full-2.pdf

Urban, L., (...),  Morales, H. (2023) The ghost of selection past: evolution and conservation relevance of the kākāpō color polymorphism. Preprint, with PLOS Biology.

84553-v1.pdf
gould_etal_20231031.pdf

Gould, G., (...), Urban, L., (...), Parker, T. (2023) Same data, different analysts: variation in effect sizes due to analytical decisions in ecology and evolutionary biology. preprint, with BMC Biology.

s41559-023-02165-y.pdf

Guhlin, H., (...), Urban, L., (...), Dearden, P. (2023) Species-wide genomics of kakapo provides tools to accelarate recovery. Nature Ecology & Evolution.

d41586-023-02229-w.pdf

European Reference Genome Atlas Council (incl. Urban, L., 2023) Biodiversity: an atlas of European reference genome. Nature.

Molecular Systems Biology - 2023 - Urban - Real‐time genomics for One Health.pdf

Urban, L., (...), van Oosterhout, C. (2023) Real-time Genomics for One Health. Molecular Systems Biology. 

Molecular Ecology - 2023 - West - Capturing species%E2%80%90wide diversity of the gut microbiota and its relationship with genomic.pdf

Urban, L. & Mehta, D. (2023) 

Nature correspondence letter -> -> -> 

Original behind paywall here: https://www.nature.com/articles/d41586-023-01005-0

peerj-14675.pdf

Digby, A., (...), Urban, L., (...), Kākāpō Recovery Team. (2023) Hidden impacts of conservation management on fertility of the critically endangered kākāpō. PeerJ.

elife-84816-v1.pdf

Urban, L., (...), Elkheir, L. (2022) eLife’s new model and its impact on science communication. eLife.

fulltextRepo.pdf

van Oosterhout, C., (...), Urban, L., (...), Morales, H. (2022) Genomic erosion in the assessment of species extinction risk and recovery potential. bioRxiv.

Molecular Ecology Resources - 2022 - Pearman - Commonly used Hardy Weinberg equilibrium filtering schemes impact population.pdf
s42523-022-00204-w.pdf

West, 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.

elife-61504-v1-2.pdf

Urban, L.*, (…), Stammnitz, M. R. (2021) Freshwater monitoring with nanopore sequencing. eLife 10:e61504.

s41587-022-01261-x.pdf

Cheng, H., (...), Urban, L., (...)., Li, H. (2022) Haplotype-resolved assembly of diploid individuals without parental data. Nature Biotechnology.

s41586-020-1970-0.pdf

PCAWG Transcriptome Core Group (incl. Urban, L.*), (...), Zhang, Z. (2020): Genomic basis for RNA alterations in cancer. Nature 578, 129–136.

Evidence of two deeply divergent co-existing mitochondrial genomes in the Tuatara reveals an extremely complex genomic organization.pdf

Formenti, G., (...), Urban, L., (...)., Bálint, M. (2022) The era of reference genomes in conservation genomics. Trends in Ecology & Evolution 37, 3: 197-202.

1-s2.0-S1472648321001449-main.pdf

Oberle, 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 

s42003-020-01639-0.pdf

Macey, 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.

s41586-020-1969-6.pdf

The ICGC/TCGA PCAWG Consortium (incl. Urban, L.) (2020): Pan-cancer analysis of whole genomes. Nature 578, 82–93.

s13059-019-1644-0.pdf
515425.pdf

Edgecombe, 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.

s41467-020-18151-y.pdf

Bailey, 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.pdf

Li, 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. 

s13104-020-04946-1.pdf

Urban, L., Remmele, C.W., Dittrich, M. et al. (2020) covRNA: discovering covariate associations in large-scale gene expression data. BMC Res Notes 13, 92. 

s41587-019-0140-0.pdf

Avsec, Z., (…), Urban, L., (…), Gagneur, J. (2019): The Kipoi repository accelerates community exchange and reuse of predictive models for genomics. Nature Biotechnology 37, 592-600.

225441v1.full.pdf

Calabrese, C.* & Lehmann, K. V.* & Urban, L.*, (...), Stegle O. (2017) Assessing the Gene Regulatory Landscape in 1,188 Human Tumors. bioRxiv preprint.

b3087b_36ec86422d4c421586053a670355b391.pdf

Jeunen, 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; under review at Molecular Ecology Resources.