Genomics and AI for
Research group led by Lara Urban
We study how genomics, portable technology, statistical analysis, and machine learning can benefit environmental health and nature conservation in the context of One Health, which affirms that human health and our planet's health are inextricably linked. We combine environmental microbiome research, biodiversity monitoring, and real-time genomic pathogen analysis; we bring together the latest real-time genomic technologies with portable embedded AI machines, tailored computational analyses, and remote-sensing to assess environmental diversity and its interaction with anthropogenic impacts and human health.
This research group is funded by a Helmholtz Principal Investigator Grant awarded to Lara together with a Principal Investigator position at the Helmholtz AI institute and the Helmholtz Pioneer Campus and, and a faculty position at the Technical University of Munich School of Life Sciences. Until 2022, Lara's research has focused on how genomics can support the recovery of critically endangered wildlife in her role as an Independent Humboldt Research Fellow in Aotearoa New Zealand.
We support fair and responsible research assessments, discourage the inappropriate use of proxies such as journal impact factors, and value research outputs based on their intrinsic merit. Our group is a signatory of the San Francisco Declaration on Research Assessment (DORA).
Group diary 2023
02-24 Latest updates Linus, who was a Master's student in our lab working on population genomics with a focus on Takahe, successfully defended his thesis. We wish him the best in his future goals. Additionally, we are excited to welcome Valentin, who has joined our lab as an intern. He will be developing deep learning models to contribute to One Health. Finally, we had the opportunity to join Munich Nanopore Day, which was a great way to meet and network with other ONT community in Germany.
01-24 Lara off to Chile Lara has been invited by the Senate of Chile to present at their annual Congreso futuro, discuss One Health issues with Chilenian politicians including the president, and conduct fieldwork in collaboration with Oxford Nanopore Technologies in the remote Atacama desert and Patagonia to showcase ten years of portable sequencing – find a short video here. In addition, Lara has received a grant by the Humboldt foundation, has been invited to join the SciLifeLab-Wallenberg Data-Driven Life Science advisory committee, has officially started her role as a scientific advisor of the German One Health Platform – and has just been asked to also join the Germany Governmental One Health Council.
12-23 Albert, Ela and Tim are pushing! Albert as main PI and Lara as co-PI have received a major European Union's Horizon Europe ISIDORe project grant (100k €) to effectively monitor avian influenza virus and investigate its adaptation and transmission to wild birds and mammals. Ela and Tim have both meanwhile published their first research on AMR and air monitoring, respectively.
10-23 The group continues to be busy... While we have focused on wrapping up several manuscripts, we have also engaged heaps with our scientific community (also see Media). Ela and Tim gave their first public talks in front of a large audience, Camila has started her Ecuador RNA virome project in our group, and Albert and Tim have been busy for two weeks sampling air at vulture restaurants and in urban areas in Spain – with our collaborators at ISGlobal Barcelona and IREC in Ciudad Real, and with support by collaborators at ETH Zurich, especially Fabian Roger and Kristy Deiner.
09-23 Group successes this month! We are very happy to welcome PhD student Samir Vargas in our group, and to be hosting Assistant Professor Camila Acosta! Dani has defended his Master thesis, and is now ready to start his PhD with us – congratulations, Dani! Lara, Harika, and Amit successfully presented our research at BC2 in Basel, and Ela won the best poster prize at DGHM for her application of real-time genomics in the clinic – very well done! Lara has further become an eLife editor for One Health research, has been invited to the Senate of Chile's Congreso Futuro, and has been elected to join the German Governmental One Health Platform Scientific Advisory Board. Last but not least, we very much enjoyed our first Real-time Genomics for One Health symposium in the Alps with many dear collaborators – thank you for the fantastic discussions (see photo on the right)! What a month...
04-08-23 Lara receives BMBF grant as coordinator and main PI of "AI for biodiversity research" This grant of initially € 100k will allow us to combine our research on pathogen detection, environmental monitoring, and AI for squiggle data analysis, and can be extended to more than € 1M in subsequent years.
01-08-23 Medical doctor Ela joins our group! We are more than happy that Dr med Ela Djamila Sauerborn will bring her expertise in antimicrobial resistance research to the team while learning about genomics and computational approaches during her PhD with Lara as primary supervisor. A very warm welcome, Ela!
24-07-23 Our group presents their research at SMBE 2023 Albert, Dani, and Lara traveled to Ferrara, Italy, to discuss our research with the worldwide Molecular Biology community. Lara gave a talk on the main stage and organized a symposium on conservation genomics.
16-06-23 Our first group article Real-time Genomics for One Health has been published by the EMBO journal Molecular Systems Biology We are delighted that this extensive interdisciplinary and international effort – led by Lara as corresponding and first author and supported by several of our group members – is now published. You can also watch Lara's latest big-stage keynote speech here to get an overview of the topic of this publication.
01-06-23 We are excited to host three fantastic researchers in our group from this summer onwards Fazal Adnan, Associate Professor from Pakistan, Camila Acosta-López, Associate Professor from Ecuador, and Samir Vargas da Fonseca Atum, PhD student from Brazil – funded by altogether three Helmholtz HIDA and a Humboldt CAPES fellowship. A very warm welcome to this new addition to our global One Health research group. Check out our entire team here.
24-05-23 New conservation genomics publication Lara published her last-author paper "Capturing species-wide diversity of the gut microbiota and its relationship with genomic variation in the critically endangered kākāpō" in Molecular Ecology. Congratulations, Lara! Stay tuned for further exciting research updates from our team!
15 to 20-05-23 The entire team is in Cambridge and London to present their research! Lara is, for example, a keynote speaker at the biggest annual nanopore conference, London Calling 2023 (see here), and an invited speaker at Wolfson College and at the University of Cambridge One Health Society to talk about One Health Research: Genomics, AI, and Equity (see here). Follow @LaraUrban42 on Twitter to receive all updates.
02-05-23 The first graduate of our group Anastasiia has been working on applications of nanopore sequencing to freshwater monitoring in our group; she has now (very!) successfully defended her Master's thesis. She will continue her work with us for a few months, focusing on glacier ice microbiome studies for assessing the risk of thawing-induced zoonotic disease incl. some exciting glacier fieldwork in July. Congrats again, Anastasiia!
26-04-23 Bursary Recipients: Daniel Gygax and Harika Urel We're delighted to announce that our Master student Daniel Gygax and PhD student Harika Urel have been awarded bursaries by Oxford Nanopore Technologies for their poster presentations at international conferences (SMBE and BC2).
03-04-23 Young Scientist of the Year Lara attends the Gala of German Science in Berlin to receive her award (see Jan 16th '23 announcement) and showcase our group with a short movie, see here.
27-03-23 Invited panelist at the eLife Sense of Belonging Circle event Lara is invited to speak on the "Sense of Belonging Circle: Women in Science" panel. The recording is now available here.
17-03-23 EU-INTERACT Grant Recipients: Lara Urban and Anastasiia Grekova We're delighted to announce that Lara and our Master's student Anastasiia have been awarded the EU-INTERACT grant to pursue their exciting new research project: "Holistic glacier ice microbiome studies for assessing the risk of thawing-induced zoonotic disease". This project aims to study glacier ice microbiomes by deploying portable nanopore sequencing technology coupled with in situ Artificial Intelligence (AI) at Hintereis Research Station. Congratulations Anastasia and Lara for this great success!
02-03-23 Invited panelist at US COGR (Council on Governmental Relations) "Publisher's Perspectives on Open Access Initiatives" As leadership representative of the eLife Early-Career Advisory Group, Lara discusses the U.S. White House Office of Science and Technology Policy’s memorandum on "Ensuring Free, Immediate, and Equitable Access to Federally Funded Research" with journal publishers and editors.
01-03-23 Invited keynote panelist at the Mobile World Congress 2023 Lara is invited to speak on the keynote stage in Barcelona this week upon invitation by the Digital Future Society and the First Vice President of the Government of Spain; she will share the stage with the First Vice President Nadia Calviño and representatives of UNICEF and the global health companies Ayudame3D and UniversalDoctor, and many more. Be in touch with Lara if you want to chat on-site! The recording from the keynote stage and the full video of the congress is available here.
23-02-23 Invited talk about equity in science Lara is invited to the Inspiring Women series by Helmholtz Munich STEM-Tisch; she talks about "Your Career, Your Life, Your Choice". For further information on participating online here (in-person participation is unfortunately booked out); the recording will be made available here shortly.
08-02-23 Invited talk "Real-time Genomics for One Health" at WSL Zurich Lara showcases several examples where she and the group have leveraged real-time genomics through portable nanopore sequencing in the realms of biodiversity, infectious disease, and water and air quality research. See here for abstract and online participation. The recorded talk is now available here.
02-02-23 Group celebration Our entire group of now nine (!) people had a fantastic social evening out in Munich; see more here.
26-01-23 Invited talk "Non-invasive real-time genomic monitoring of the critically endangered kākāpō" Lara gives an online seminar upon invitation by Oxford Nanopore Technologies. For more information, click here. The recording is available here; thanks to the more than 600 online participants!
16-01-23 "Nachwuchswissenschaftler" Award Lara has been declared Young Investigator of the Year 2022 by the German Association of University Professors and Lecturers (DHV) and academia/ZEIT for her lasting positive impact on science and research through outstanding commitment. For more information, click here for the original announcement and find the Helmholtz announcements in the English language here (Helmholtz AI), here (Pioneer Campus), or here (Helmholtz Munich).
09-01-23 New group members The beginning of 2023 has added two new members to our team, postdocs Amit and Albert. We look forward to having these two excellent and motivated researchers work with us, and to welcoming them properly at the next big group dinner on Feb 2nd. For more information, click here.
01-09-22 Invited Talk "Real-time Genomics for One Health" Lara gives an invited keynote talk on Genomics for One Health at the European Conference on Computational Biology 2022. The recorded talk is available here.