Publications

A few selected publications:

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. anim microbiome.

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.

s41587-022-01261-x.pdf

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

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.

elife-61504-v1-2.pdf

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

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

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.

s41586-020-1969-6.pdf

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

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.

b3087b_36ec86422d4c421586053a670355b391.pdf

Preprint: 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.

s13059-019-1644-0.pdf
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.