Genomics and AI for

One Health

Research group led by Lara Urban

We study how genomics technology and AI can help us better understand One Health and improve health on a global and holistic level. Our core funding is provided by a Helmholtz Principal Investigator Grant awarded to Lara together with a Principal Investigator position at the Helmholtz AI Institute and Helmholtz Pioneer Campus, and a faculty position at the Technical University of Munich. Our group supports fair and responsible research assessments, discourages the inappropriate use of proxies such as journal impact factors, and values research outputs based on their intrinsic merit; we are a signatory of the San Francisco Declaration on Research Assessment (DORA).

Group diary

18-06-24 Preprint updates before maternity leave Shortly before Lara is starting her maternity leave, we have uploaded/updated some preprints: Harika discusses viability-resolved metagenomics leveraging freely available nanopore raw data, Tim explores the surprisingly stable location-specific urban air microbiome using nanopore metagenomics, and Lara investigates the conservation relevance of the kākāpō color polymorphism (postdoc project). Besides, we are very happy to indirectly welcome Anastasia back to the group as she is joining TUM as a PhD student under Lara's supervision as part of her EMBL Predoctoral Fellowship with Peer Bork. 

16-05-24 Grant, papers, presentations, and new group members! April and May have been exciting months for the group: Samir joined our group as a postdoc after having spent a year with us as a CAPES fellow from Brazil. Ela received an Oxford Nanopore bursary to give an oral presentation (see right) and panel discussion at the ECCMID European Congress (where she won a top-rated abstract ribbon), followed by her manuscript being accepted by Nature Comm. Albert and Lara received a Horizon Europe Isidore grant (100k ; featured by Helmholtz Munich) and a One Health Platform Pilot Project Grant (50k ) for zoonosis surveillance fieldwork this summer; Albert was also invited to give a talk at the Wildlife Congress EWDA, and his paper was recommended for publication in Virus Evolution! Lara's research and invitation to join the German Governmental One Health Council have been featured by the Helmholtz Association, and after organizing a fun Computational Health Center Lab afternoon (see right), part of the team is now off to London Calling 2024 to present their research.

06-03-24  Antimicrobial Resistance (AMR) Conference in Basel Invited by Lothar Wieler and the Global AMR Research & Development Hub, Lara has discussed how real-time genomics and AI can inform antibiotic usage under the light of the World Health Organisation Global AMR Action Plan. Great to see a lot of interest – not only in clinical surveillance but also in the broader implications of One Health! It's very exciting that Samir and Lara have just been invited to join the XPRIZE challenge (see here) as part of the BioDivX team at ETH Zurich to use some of this knowledge in pathogen, resistance and virulence monitoring at the intersection of biodiversity and human health research.  

02-24  New group happenings! Linus, who has been a Master's student in our lab working on conservation genomics with a focus on the critically endangered takahē, successfully defended his thesis with flying colors. We wish him the best for his future goals! Additionally, we are excited to welcome Valentin, who has joined our group as a math student and intern; he will be developing deep-learning models to support our nanopore data analyses. All of us had the opportunity to join the Munich Nanopore Day, which was a great way to meet and network with the nanopore community in Germany. Finally, our postdoc and team lead Albert has published his first preprint on rapid AIV profiling from the latest DNA- and RNA-nanopores (see here); he is now on his way to Barcelona to conduct experiments at IRTA-CReSA funded by our 100k € ISIDORe grant!

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 and Harika 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 welcoming them properly at the next 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