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's postdoctoral research is funded by a Feodor Lynen Research Fellowship by the Alexander von Humboldt Foundation.

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

 

Media Highlights: 

Conservation genomics

https://www.wolfson.cam.ac.uk/about/news/using-genomics-bring-rare-bird-back-brink

 

Metagenomics

https://www.bbc.co.uk/news/uk-england-beds-bucks-herts-47426790?fbclid=IwAR0cx1CyTgAwNT7ZaVsndQgKUMgHeGFrJFBmX6yQlu5My1Me7bdKbauUfWA

TV interview: https://youtu.be/-r0Ic9uZHrM

Radio interview: https://cambridge105.co.uk/breakfast-09-04-2019/

 

Participation in the Lindau Nobel Laureate Meeting

https://www.lindau-nobel.org/blog-women-in-research-at-lino18-lara-urban-from-germany/

 

https://womeninresearchblog.wordpress.com/2018/06/10/lara-germany/?fbclid=IwAR3VyFaaSzI0L9lC_iExPpABGSaqXG7Oe5SmccOGPJVt4ePntmT40XRmcCY

 

//medium.com/@wolfsoncambridge/thirty-nine-laureates-600-young-scientists-and-me-b5fed50d47b7


https://www.lindau-nobel.org/blog-young-scientists-report-about-lino18/

 

Machine learning

EMBL Heidelberg (https://issuu.com/embl/docs/issue92): 'An in silico hope for biology: machine learning'

 

Publications: 

First author publications

PCAWG Transcriptome Core Group* (Calabrese, C.*, Davidson, N. R.*, Fonseca, N. A.*, He, Y.*, Kahles, A.*, Lehmann, K. V.*, Liu, F.*, Shiraishi, Y.*, Soulette, C. M.*,Urban, L.*), (...), Stegle, O., Zhang, Z. (2020):Genomic basis for RNA alterations revealed by whole- genome analyses of 27 cancer types.Nature578, 129–136.https://doi.org/10.1038/s41586-020-1970-0.

 

Urban, L.*, Holzer, A.*, Baronas, J., Hall, M., Braeuninger-Weimer, P., Scherm, M. J., Kunz, D. J., Perera, S. P., Martin-Herranz, D. E., Tipper, E. T., Salter, S. J., Stammnitz, M. R. (2020)Freshwater monitoring with nanopore sequencing.bioRxiv,http://dx.doi.org/10.1101/2020.02.06.936302.

 

Urban, L.*, Remmele, C., Dittrich, M., Schwarz, R. F., 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.

Linker, S.*,Urban, L.*, Clark, S., Chhatriwala, M., Amatya, S., McCarthy, D., Ebersberger, I., Vallier, L., Reik, W., Stegle, O., 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

The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium (includingUrban, L.) (2020): Pan-cancer analysis of whole genomes.Nature578, 82–93.https://doi.org/10.1038/s41586-020-1969-6.

 

Avsec, Z., Kreuzhuber, R., Israeli, J., Xu, N., Cheng, J., Shrikumar, A., Banerjee, A., Kim, D. S., Beier, T.,Urban, L., Kundaje, A., Stegle, O., Gagneur, J. (2019):The Kipoi repository accelerates community exchange and reuse of predictive models for genomics.Nature Biotechnology37, 592-600.https://doi.org/10.1038/s41587-019-0140-0.