Department of Computer Science

News

2021

2021-Oct Marius 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 German Aerospace Center (DLR).

Kicking off our new research project European Cohorts of Patients and Schools to Advance Response to Epidemics (EuCARE) funded by the European Commission.
2021-Aug

The AIMe standard and registry for reporting AI results in medicine and biomedical research is out in Nature Methods.

2021-Jul Marius'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 (Tübingen Medical and Bioinformatics Day, 21.07.2021) 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-Jun Presenting 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-May Adrin successfully defended his Ph.D. thesis. Congratulations Adrin.
2021-Mar

New Medical Informatics (or Bioinformatics) Master's Thesis template now available for download under our Thesis Topics.

2021-Feb New 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-Jan

New 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-Dec Our manuscript ESCAPED: Efficient Secure and Private Dot Product Framework for Kernel-based Machine Learning Algorithms with Applications in Healthcare (from Ali, Mete and Nico) was just accepted at AAAI 2021.
2020-Oct Congratulations 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-Jul Our manuscript on "Longitudinal isolation of potent near-germline SARS-CoV-2-neutralizing antibodies from COVID-19 patients" published at Cell.
2020-May Jonas's new paper Perturbation-evoked potentials can be classified from single-trial EEG accepted for publication in Journal of Neural Engineering.
2020-Mar COVID-19 keeps us busy: we have initiatied and joined various projects to contribute to documenting and investigating the current coronavirus developments.
2020-Mar

New paper Privacy-preserving SVM on Outsourced Genomic Data via Secure Multi-party Computationby Huajie Chen, Ali Burak Ünal, Mete Akgün, and Nico PfeiferIWSPA '20: Proceedings of the Sixth International Workshop on Security and Privacy Analytics).

2019
2019-Nov-11 Nora successfully defended her Ph.D. thesis. Congratulations Nora.
2019-Sep-4 Results 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-Jul-24 Lisa presented our domain adaptation paper at ISMB/ECCB 2019 (go to recording).
2019-Jun-24 Sarvesh successfully defended his Ph.D. thesis. Congratulations Sarvesh.
2019-May-03 Our 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-Apr-30 Matthias successfully defended his Ph.D. thesis. Congratulations Matthias.
2019-Apr-09 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-Sep-27 Our 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-Aug-16 Our latest research on data from a bNAbs trial was just accepted for publication at Nature Medicine (go to paper)
2018-Aug-03 Our H2020 grant proposal CARE: “COMMON ACTION AGAINST HIV/TB/HCV ACROSS THE REGIONS OF EUROPE” accepted
2018-Jul-30 Our latest analyses on data from a bNAbs trial were just accepted for publication at Nature (go to paper)
2018-Apr-21 Our geno2pheno[ngs-freq] paper just got accepted at NAR (first author Matthias, last author Nico): [go to website]
2018-Mar-08 Nico gave a keynote talk at the Workshop on Computational Models in Biology and Medicine 2018 in Regensburg
2017
  Our (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-Oct-24 Our (Anna and Nico) paper on predicting, visualizing and analyzing bNAbs resistance against HIV published at PLOS Comp Bio.
2017-Sep-29 Our 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-Aug-22 Sarvesh presented our latest work on machine learning methods for classification problems with variable length sequences at WABI.
2017-Jul-10 The proposal of our consortium (DIFUTURE) within the medical informatics initiative of the BMBF was evaluated successfully: BMBF Website
2017-May-06 Nico's talk at the Arevir meeting in Cologne.
2017-Apr-18 Our paper on predicting long-range chromatin interactions (first author Sarvesh, last author Nico) just got published.
2017-Mar-07 Nico gave a keynote talk at the 1st European Virus Bioinformatics Center meeting (http://evbc.uni-jena.de/meetings/1st-evbc-meeting/).
2017-Jan-16 Our latest analysis of the 10-1074 trial was just published at Nature Medicine: Antibody 10-1074 suppresses viremia in HIV-1-infected individuals.
2017-Jan-01 Nico is now full professor for ‘Methods in Medical Informatics’ at the Department of Computer Science of the University of Tübingen.
2016
2016-Dec-20 Our work (first author Matthias, last author Nico) on HIV-2 coreceptor usage prediction has just been published at Retrovirology: go to journal homepage
2016-Dec-13 Our latest analysis of the 10-1074 trial was just accepted at Nature Medicine.
2016-Dec-09 Nora's spotlight presentation at the NIPS workshop on Machine Learning for Health.
2019-Jun-22 Our Nature paper (co-authors Anna and Nico) was just published: HIV-1 antibody 3BNC117 suppresses viral rebound in humans during treatment interruption
2016-Jun-16 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.
2016-Jun-15 Our manuscript submitted to Nature just got accepted. More details after the press embargo.
2016-May-16 Our Nature Medicine paper was just published: Impact of Pre-adapted HIV Transmission
2016-May-05 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
  The new semester started. Check out our lecture on Statistical Learning in Computational Biology.
2016-Feb-27 Our 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