Methods in Medical Informatics

News & Events

2024

2024-DecJacqueline successfully defended her Ph.D. thesis. Congratulations Jacqueline.
2024-NovTobias was awarded the Reinhold and Maria Teufel Foundation's annual prize for outstanding PhD theses.
2024-SepOur PhD Students participated in the IBMI PhD Retreat 2024 in Stuttgart.
Nico and Florian attended the EuCARE Annual Scientific Board Meeting in Vilnius.
2024-JulOur lab attended the 6th Annual Cluster Conference "Machine Learning in Science" 2024 in Tübingen.
2024-JunOur lab participated in TüBMI 2024, our annual Bioinformatics and Medical Informatics Day.
2024-MayAttending the annual workshop for Center for Innovative Care (Zentrum für Innovative Versorgung/ZIV) in Heidelberg.
Nico, Mete and Cem attending the PrivateAIM Workshop in Leipzig.
Nico, Elham, Nurhan and Florian attending the AREVIR Meeting / EuCARE Mid-Year Consortium Meeting 2024 in Cologne.
2024-AprMarc and Pascal attended DMEA 2024 in Berlin.
2024-JanJonas successfully defended his Ph.D. thesis. Congratulations Jonas.

2023

2023-DecSofiane co-organized the AI for Africa Conference (AIFA'23) in conjunction with the African Startup Conference in Algiers, and also gave a workshop at the 1st Artificial Intelligence, Generative AI and AI Ethics Conference: Pushing the Boundaries of Innovation in Algeria (DZGENAI'23) conference in Béni Abbes, Algeria.
2023-NovHosted our 1st Boehringer Ingelheim AI & Data Science Postdoc Fellows Event in Tübingen.
2023-OctNico, Elham and Florian attended the EuCARE annual meeting in Lisbon.
Our lab members attended the MIRACUM-DIFUTURE-Symposium 2023 in Erlangen.
Nico gave a keynote at the 1st MOPRED Symposium for multimodal data integration at University Hospital Frankfurt.
2023-SepOur PhD Students participated in the IBMI PhD Retreat 2023 in Stuttgart.
Nico attended the German Center for Infection Research (DZIF) Annual Meeting 2023 in Hannover.
Sofiane presented a poster at the International Max Planck Research School for Intelligent Systems (IMPRS-IS) 2023 Boot Camp titled Robust Representation Learning for Privacy-Preserving Machine Learning: A Multi-Objective Autoencoder Approach.
2023-AugAli presented our paper ppAURORA: Privacy Preserving Area Under Receiver Operating Characteristic and Precision-Recall Curves at NSS-SocialSec2023 (17th International Conference on Network and System Security + 9th International Symposium on Security and Privacy in Social Networks and Big Data) in Canterbury, UK.
2023-Jul

Nico and Elham participated in the 53rd annual workshop StatComp2023 of the working groups Statistical Computing (GMDS/IBS-DR) and Klassifikation und Datenanalyse in den Biowissenschaften (GfKl):

 

- Nico's keynote: Efficient privacy-preserving machine learning for precision medicine,

- Elham's talk: Assessing the impact of vaccination and predicting the emergence of the Omicron-Variant: Modeling the dynamics of COVID-19 in the Omicron wave

Nico, Jonas, Nicolas, Florian, Mete, Julia, Jacqueline, Sven participated in the 31st Annual Intelligent Systems For Molecular Biology and the 22nd Annual European Conference on Computational Biology (ISMB/ECCB2023) in Lyon, FR.
 

Jonas's talk titled COmic: Convolutional Kernel Networks for Interpretable End-to-End Learning on (Multi-)Omics Data was awarded 2nd place/Honorable Mention of the Ian Lawson Van Toch Memorial Award for Outstanding Student Paper.

 

Posters presented: 

- Interpretable multi-view dimensionality reduction for biologically meaningful sample representation by Nicolas,

- Identifying risk factors for disease progression of COVID-19 using statistical machine learning by Florian

Sofiane attended the 40th International Conference on Machine Learning (ICML2023) in Honolulu, Hawaiʻi, USA.
Our lab attended the 5th Annual Cluster Conference "Machine Learning in Science" 2023 in Tübingen.
Nico co-organized a workshop for the AI & Data Science Fellowship Program at Boehringer Ingelheim's Biberach site.
2023-Jun

Our lab participated in TüBMI 2023, our annual Bioinformatics and Medical Informatics Day.
 

Jonas's talk was titled Inherently Interpretable Kernel Networks in Healthcare.
 

Posters presented: 

- FHAUC: Privacy Preserving AUC Calculation for Federated Learning using Fully Homomorphic Encryption by Cem,

- HCV 2k/1b Variant Detection with Machine Learning Methods by Nurhan,

Efficient and Secure Multi-party Sorting by Şeyma

Nico presented Privacy preserving AI-based solutions at Brocher Foundation & EuCARE's panel Law & Ethics of Post-Pandemic Health Data Sharing – Data privacy, data property, and data sharing: an interdisciplinary dialogue for post-pandemic transnational research in Geneva, CH.

Nico, Elham, and Florian attended the GMDS/IBS-DR joint workshop on Computational Models in Biology and Medicine 2023 in Stuttgart.

Elham's talk was titled A COVID-19 informed neural network with adaptive weighting during variants of concern in Germany.

2023-MayMarius gave a talk titled Secure Distributed Medical Analytics for German Healthcare institutions using the Personal Health Train (PHT-meDIC) and Marc also participated at the 1st Heidelberg Spring Symposium Medical Informatics.
Nico attended the Strategy Retreat at the Controlling Microbes to Fight Infections (CMFI) Cluster of Excellence.
2023-Apr

Nico, Elham, Nurhan and Florian attended the AREVIR Meeting / EuCARE session in Cologne.

- Nurhan's talk was titled HCV Saint Petersburg Variant Detection with Machine Learning Methods.
- Florian's talk was titled AI Models to Predict Clinical Outcome.

Marc attended DMEA 2023 in Berlin.
Hosting a project workshop with our Centre of Innovative Care (Zentrum für Innovative Versorgung/ZIV) partners from the university hospitals of Freiburg, Heidelberg, Mannheim, Tübingen and Ulm.
2023-MarMarius attended the AMIA 2023 Informatics Summit in Seattle with a systems demonstration titled Secure analysis of large-scale, distributed data using the PHT-meDIC.
Anna successfully defended her Ph.D. thesis. Congratulations Anna.
2023-FebNico and Florian attended the annual Rettenstein Symposium, where Florian gave a talk titled AI for EuCARE.

2022

2022-NovNico and Marc attended the annual event Forum Gesundheitsstandort Baden Württemberg.
Lisa successfully defended her Ph.D. thesis. Congratulations Lisa.
2022-SepNico and Sofiane attended the International Max Planck Research School for Intelligent Systems (IMPRS-IS) 2022 Boot Camp where Nico also gave his faculty talk.
Nico attended the 21st European Conference on Computational Biology (ECCB 2022).
Nico, Elham and Florian attended the EuCARE annual meeting in Lisbon.
2022-JulAli successfully defended his Ph.D. thesis. Congratulations Ali.
Nico is now a full member of the IMPRS-IS Faculty.
Jonas presented a poster on Extending Deep Kernel Approaches – Improving Prediction and Understanding in Precision Medicine at the Machine Learning in Science 2022 Cluster Conference.
Mete gave a talk at the 8th International ScaDS.AI (Center for Scalable Data Analytics and Artificial Intelligence) Summer School 2022 on Privacy-preserving collaborative training of kernel-based machine learning methods.
Our researchers attended the IBMI Kick-Off Meeting 2022.
2022-JunOur PhD Students attended the Tübingen Bioinformatics and Medical Informatics Day (TüBMI).
Nico, Jacqueline and Florian attended the German Society of Infectious Diseases (DGI) and German Center for Infection Research (DZIF) Joint Annual Meeting 2022 in Stuttgart.
2022-MayNico, Florian and Nurhan attended the AREVIR Meeting / EuCARE session in Cologne.

2021

2021-NovWe hosted a Center for Innovative Care (Zentrum für Innovative Versorgung/ZIV) event with our clinical partners across Baden-Württemberg where Nico and Alisa gave talks on Digitale Infrastrukturen für Patient:innen-zentrierte Versorgungslösungen.
Nico attended the Horizon Europe funded European Cohorts of Patients and Schools to Advance Response to Epidemics (EuCARE) Project Kick-off to present our contributions to SARS-CoV-2/COVID-19 research across Europe, Kenya, Mexico, Russia and Vietnam.
2021-OctMarius published an article on the Federation of European Biochemical Societies' (FEBS) Network site titled The Personal Health Train - Secure analysis of large-scale, distributed biomedical data.
Congratulations to Dr. Mete Akgün and Ali Burak Ünal on boarding our new interdisciplinary research group in Medical Data Privacy and Privacy-preserving Machine Learning on healthcare data (MDPPML) funded by the BMBF.
Kicking off our new research project European Cohorts of Patients and Schools to Advance Response to Epidemics (EuCARE) funded by the European Commission.
2021-AugThe AIMe standard and registry for reporting AI results in medicine and biomedical research is out in Nature Methods.
2021-JulMarius's talk on a Machine Learning framework titled Bringing the Algorithms to the Data – Secure Distributed Medical Analytics using the Personal Health Train presented at ISCB's ISMB/ECCB 2021 TransMed.
Nico updated the participants of TÜBIT 2021 (Tübingen Medical and Bioinformatics Day) on our research, and Jacqueline presented her project on Predicting malaria vaccine efficacy from anti-plasmodial antibody profile(s).
Nico is on the Steering Committee of AIMe Registry where you can report publication of biomedical Artificial Intelligence technologies to facilitate their application in clinical practice: https://aime-registry.org
Jonas's talk Extending Deep Kernel Approaches for Better Prediction and Understanding of ADME Phenotypes and Related Drug Response was featured in the Spotlight Presentations of the 3rd Cluster Conference "Machine Learning in Science" 2021.

Bernhard's poster on Machine Learning for prediction of drug resistance in Mycobacterium tuberculosis strains was presented in the ePoster Review at the 31st European Congress of Clinical Microbiology & Infectious Diseases (ECCMID 2021).

New publication Evaluation of a rapid antigen test to detect SARS-CoV-2 infection and identify potentially infectious individuals by Michael Korenkov, Nareshkumar Poopalasingam, Matthias Madler, Kanika Vanshylla, Ralf Eggeling, Maike Wirtz, Irina Fish, Felix Dewald, Lutz Gieselmann, Clara Lehmann, Gerd Fätkenheuer, Henning Gruell, Nico Pfeifer, Eva Heger, and Florian Klein accepted by Journal of Clinical Microbiology.
2021-JunPresenting our results on genotypic prediction of tuberculosis drug resistance with Machine Learning and Precision Medicine in the final CARE research meeting.
We are happy to announce that starting our Master's degree program Medical Informatics will now be open both in the winter and summer semesters.
2021-MayAdrin successfully defended his Ph.D. thesis. Congratulations Adrin.
2021-MarNew Medical Informatics (or Bioinformatics) Master's Thesis template now available for download under our Thesis Topics.
2021-FebNew paper Adapting the geno2pheno[coreceptor] tool to HIV-1 subtype CRF01_AE by phenotypic validation using clinical isolates from South-East Asia by Nina Marty, Siriphan Saeng-Aroon, Eva Heger, Alexander Thielen, Martin Obermeier, Nico Pfeifer, Rolf Kaiser, Thomas Klimkait published in Journal of Clinical Virology.
2021-JanNew paper DNA-binding properties of the MADS-domain transcription factor SEPALLATA3 and mutant variants characterized by SELEX-seq by S. Käppel, R. Eggeling, F. Rümpler, M. Groth, R. Melzer, G. Theißen published in Plant Molecular Biology.

2020

2020-DecOur manuscript ESCAPED: Efficient Secure and Private Dot Product Framework for Kernel-based Machine Learning Algorithms with Applications in Healthcare (by Ali, Mete and Nico) was just accepted at AAAI 2021.
2020-OctCongratulations to our Ph.D. Student Jonas who is now Representative of Early Career Researchers at the Cluster of Excellence Machine Learning: New Perspectives for Science!
2020-JulOur manuscript on Longitudinal isolation of potent near-germline SARS-CoV-2-neutralizing antibodies from COVID-19 patients published at Cell.
2020-MayJonas's new paper Perturbation-evoked potentials can be classified from single-trial EEG accepted for publication in Journal of Neural Engineering.
2020-MarCOVID-19 keeps us busy: we have initiatied and joined various projects to contribute to documenting and investigating the current coronavirus developments.
New paper Privacy-preserving SVM on Outsourced Genomic Data via Secure Multi-party Computation by Huajie Chen, Ali Burak Ünal, Mete Akgün, and Nico Pfeifer published (IWSPA '20: Proceedings of the Sixth International Workshop on Security and Privacy Analytics).
2019
2019-NovNora successfully defended her Ph.D. thesis. Congratulations Nora.
2019-SepResults of our latest collaborative research project (from our side: Ralf and Nico) have just been accepted for publication at Nature Medicine (go to paper).
2019-JulLisa presented our domain adaptation paper at ISMB/ECCB 2019 (go to recording).
2019-JunSarvesh successfully defended his Ph.D. thesis. Congratulations Sarvesh.
2019-MayOur web server web-rMKL has been accepted for publication at the web server issue of Nucleic Acids Research (contributions by Benedict, Nicolas, Marius, Nora, and Nico).
2019-AprMatthias successfully defended his Ph.D. thesis. Congratulations Matthias.
Our domain adaptation paper “Weighted Elastic Net for Unsupervised Domain Adaptation with Application to Age Prediction from DNA Methylation Data” (including authors Lisa, Ralf and Nico) has just been accepted for presentation at ISMB/ECCB 2019 and will be published in Bioinformatics at the time of the conference.
2018
2018-SepOur proposal for an excellence cluster ‘Machine Learning: New Perspectives for Science’ where Nico is the PI for Machine Learning in Medicine got accepted, so we will have the excellence cluster in Tübingen starting January 1st 2019. See press release of the University of Tübingen. Go to cluster webpage
2018-AugOur latest research on data from a bNAbs trial was just accepted for publication at Nature Medicine (go to paper)
Our H2020 grant proposal CARE: “COMMON ACTION AGAINST HIV/TB/HCV ACROSS THE REGIONS OF EUROPE” accepted
2018-JulOur latest analyses on data from a bNAbs trial were just accepted for publication at Nature (go to paper)
2018-AprOur geno2pheno[ngs-freq] paper just got accepted at NAR (first author Matthias, last author Nico): [go to website]
2018-MarNico gave a keynote talk at the Workshop on Computational Models in Biology and Medicine 2018 in Regensburg
2017
2017-NovOur (Anna and Nico) PLOS Comp Bio paper got the front cover of the November 2017 issue (predicting, visualizing and analyzing bNAbs resistance against HIV)
2017-OctOur (Anna and Nico) paper on predicting, visualizing and analyzing bNAbs resistance against HIV published at PLOS Comp Bio.
2017-SepOur proposal for an excellence cluster ‘Machine Learning: New Perspectives for Science’ where Nico is the PI for Machine Learning in Medicine made it to the next round. See press release of University of Tübingen.
2017-AugSarvesh presented our latest work on machine learning methods for classification problems with variable length sequences at WABI.
2017-JulThe proposal of our consortium (DIFUTURE) within the medical informatics initiative of the BMBF was evaluated successfully: BMBF Website
2017-MayNico's talk at the Arevir meeting in Cologne.
2017-AprOur paper on predicting long-range chromatin interactions (first author Sarvesh, last author Nico) just got published.
2017-MarNico gave a keynote talk at the 1st European Virus Bioinformatics Center meeting (http://evbc.uni-jena.de/meetings/1st-evbc-meeting/).
2017-JanOur latest analysis of the 10-1074 trial was just published at Nature Medicine: Antibody 10-1074 suppresses viremia in HIV-1-infected individuals.
Nico is now full professor for ‘Methods in Medical Informatics’ at the Department of Computer Science of the University of Tübingen.
2016
2016-DecOur work (first author Matthias, last author Nico) on HIV-2 coreceptor usage prediction has just been published at Retrovirology: go to journal homepage
Our latest analysis of the 10-1074 trial was just accepted at Nature Medicine.
Nora's spotlight presentation at the NIPS workshop on Machine Learning for Health.
2016-JunOur Nature paper (co-authors Anna and Nico) was just published: HIV-1 antibody 3BNC117 suppresses viral rebound in humans during treatment interruption
Nico presented the 2016 research project funded by the supporting members of the Max Planck Society during the annual meeting of the Max Planck Society.
Our manuscript submitted to Nature just got accepted. More details after the press embargo.
2016-MayOur Nature Medicine paper was just published: Impact of Pre-adapted HIV Transmission
Our Science paper (co-authors Anna and Nico) was just published: HIV-1 therapy with monoclonal antibody 3BNC117 elicits host immune responses against HIV-1
2016-AprThe new semester started. Check out our lecture on Statistical Learning in Computational Biology.
2016-FebOur paper on HLA footprints in transmitted HIV sequences got accepted at Nature Medicine.
2015
2015 was a new max for program committee memberships. Nico was PC member of ISMB/ECCB 2015 (Disease models & Epidemiology track), ISMB/ECCB 2015 (Applied Bioinformatics track), MLCB 2015, GCB 2015, PSB 2016 (Precision Medicine track) , and Recomb 2016