Dr. Lara Urban

Lara is interested in how genomics research can benefit and be incorporated into conservation management. During her PhD at the University of Cambridge, UK, and the EMBL - European Bioinformatics Institute (EBI), she applied and developed methodology in the fields of statistical genomics and single-cell genetics. Lara is now combining this expertise in genomics with her background in both applied and theoretical ecology to investigate how these approaches can be combined with established applications from population and evolutionary genomics to inform the fledgling field of conservation genomics. While Lara's postdoctoral research concentrates on two critically endangered avian species endemic to New Zealand, the takahē and the kākāpo, she is also engaged in metagenomics and biodiversity (eDNA) research in the Gemmell lab.

Lara is a Humboldt Research Fellow, funded by a two-year Feodor Lynen Research Fellowship.

Lara is also co-founder and -organiser of the UK-based organisation PuntSeq, which employs real-time nanopore sequencing for freshwater monitoring.

 

Contact Details: 

Mobile phone: +64 (0) 288 510 3595

Email: This email address is being protected from spambots. You need JavaScript enabled to view it.This email address is being protected from spambots. You need JavaScript enabled to view it.

ORCiD: 0000-0002-5445-9314

 

Publications: 

First author publications

Urban, L.*, (...), Stammnitz, M. R. (2020): Freshwater monitoring with nanopore sequencing. bioRxiv preprint: http://dx.doi.org/10.1101/2020.02.06.936302; under review at eLife.

 

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 preprinthttps://www.authorea.com/doi/full/10.22541/au.160278512.26241559/v1; under review at Molecular Ecology Resources.

 

PCAWG Transcriptome Core Group* (incl. Urban, L.*), (...), Zhang, Z. (2020):Genomic basis for RNA alterations revealed by whole- genome analyses of 27 cancer types. Nature 578, 129–136.https://doi.org/10.1038/s41586-020-1970-0.


Urban, L.*, (...), Mueller, T. (2020):covRNA: discovering covariate associations in large-scale gene expression data.BMC Research Notes, 13:92. https://doi.org/10.1186/s13104-020-04946-1.

 

Feichtinger, M.*, Urban, L.*, (...), Oberle, A. (2020); Oxford Nanopore Sequenzierung zur Bestimmung des Endometrium-Mikrobioms. Geburtshilfe und Frauenheilkunde, 80(06). doi: 10.1055/s-0040-1713190.

 

Linker, S.*,Urban, L.*, (...), Bonder, M. J. (2019):Combined single cell profiling of expression and DNA methylation reveals splicing regulation and heterogeneity. Genome Biology, 20:30.https://doi.org/10.1186/s13059-019-1644-0.

 

Calabrese, C.*, Lehmann, K. V.*,Urban, L.*, (...), Stegle O. (2017)Assessing the Gene Regulatory Landscape in 1,188 Human Tumors.bioRxiv,https://doi.org/10.1101/225441.

 

Co-author publications

Macey, J. R., (...), Urban, L., (...), Gemmell, N. J. (2020): Two deeply divergent co-existing mitochondrial genomes in the Tuatara. Accepted at Nature Communications Biology.

 

The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium (including Urban, L.) (2020): Pan-cancer analysis of whole genomes. Nature 578, 82–93.https://doi.org/10.1038/s41586-020-1969-6.

 

Bailey, M. H., (…), Urban, L., (…), PCAWG Consortium (2020) Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples. Nature Communications, 11:4748. https://doi.org/10.1038/s41467-020-18151-y.

 

Li, C. H., (…), Urban, L., (…), PCAWG Consortium (2020) Sex differences in oncogenic mutational processes. Nature Communications, 11:4330. https://doi.org/10.1038/s41467-020-17359-2.

 

Avsec, Z., (...),Urban, L., Kundaje, A., Stegle, O., Gagneur, J. (2019):The Kipoi repository accelerates community exchange and reuse of predictive models for genomics. Nature Biotechnology 37, 592-600.https://doi.org/10.1038/s41587-019-0140-0.

 

 

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Media Highlights: 

Conservation genomics

 

 

Metagenomics

 

Participation in the Lindau Nobel Laureate Meeting

 

Machine learning