2022
Direct Antimicrobial Resistance Prediction from clinical MALDI-TOF mass spectra using Machine Learning
Caroline Weis, Aline Cuénod, Bastian Rieck, Olivier Dubuis, Susanne Graf, Claudia Lang, Michael Oberle, Maximilian Brackmann, Kirstine K. Soegaard, Michael Osthoff, Karsten Borgwardt†, Adrian Egli†. Nature Medicine, January 2022. BibTex. github.
2020
Topological and kernel-based microbial phenotype prediction from MALDI-TOF mass spectra
Caroline Weis†, Max Horn†, Bastian Rieck†, Aline Cuénod, Adrian Egli, and Karsten Borgwardt. Accepted for presentation at ISMB 2020; to appear also in OUP Bioinformatics. BibTex. github.
Comorbidities, clinical signs and symptoms, laboratory findings, imaging features, treatment strategies, and outcomes in adult and pediatric patients with COVID-19: A systematic review and meta-analysis
Catherine R. Jutzeler†, Lucie Bourguignon†, Caroline V. Weis, Bobo Tong, Cyrus Wong, Bastian Rieck, Hans Pargger, Sarah Tschudin-Sutter, Adrian Egli, Karsten Borgwardt‡ and Matthias Walter‡. medRxiv, May 2020.
Machine learning for microbial identification and antimicrobial susceptibility testing on MALDI-TOF mass spectra: a systematic review
Caroline V. Weis†, Catherine R. Jutzeler†, Karsten Borgwardt. Clinical Microbiology and Infection, March 2020. BibTex.
2017
Phylogenetic Tools for Generalized HIV-1 Epidemics: Findings from the PANGEA-HIV Methods Comparison
Oliver Ratmann, Emma B. Hodcroft, Michael Pickles, Anne Cori, Matthew Hall,
Samantha Lycett, Caroline Colijn, Bethany Dearlove, Xavier Didelot,
Simon Frost, A.S. Md Mukarram Hossain, Jeffrey B. Joy,
Michelle Kendall, Denise Kühnert, Gabriel E. Leventhal, Richard
Liang, Giacomo Plazzotta, Art F.Y. Poon, David A. Rasmussen, Tanja
Stadler, Erik Volz, Caroline Weis, Andrew J. Leigh Brown,
Christophe Fraser, on behalf of the PANGEA-HIV Consortium. Molecular Biology and Evolution, Jan 2017.
Hybrid Methods Reveal Multiple Flexibly Linked DNA Polymerases within the Bacteriophage T7 Replisome
Jamie R. Wallen, Hao Zhang, Caroline Weis, Weidong Cui, Brittni M. Foster, Chris M. W. Ho, Michal Hammel, John A. Tainer, Michael L. Gross, Tom Ellenberger. Structure, Jan 2017.