A study of accuracy, precision in oligonucleotide arrays: extracting more signal at large concentrations. - Felix Naef; Nicholas D. Socci; Marcelo Magnasco (Bioinform., 2003)

Few crucial links assure checkpoint efficiency in the yeast cell-cycle network. - Gautier Stoll; Jacques Rougemont; Felix Naef (Bioinform., 2006)

Probabilistic base calling of Solexa sequencing data. - Jacques Rougemont; Arnaud Amzallag; Christian Iseli; Laurent Farinelli; Ioannis Xenarios; Felix Naef (BMC Bioinform., 2008)

Modeling an Evolutionary Conserved Circadian Cis-Element. - Eric R. Paquet; Guillaume Rey; Felix Naef (PLoS Comput. Biol., 2008)

A Self-regulatory System of Interlinked Signaling Feedback Loops Controls Mouse Limb Patterning. - Jean-Denis Benazet; Mirko Bischofberger; Eva Tiecke; Alexandre Gonalves; James F. Martin; Aime Zuniga; Felix Naef; Rolf Zeller (RECOMB, 2010)

Information processing in cells and tissues (IPCAT'2009): From small scale dynamics to understanding systems behavior. - Attila Egri-Nagy; Brigitte Galliot; Felix Naef; Chrystopher L. Nehaniv (Biosyst., 2010)

Stabilizing patterning in the Drosophila segment polarity network by selecting models in silico. - Gautier Stoll; Mirko Bischofberger; Jacques Rougemont; Felix Naef (Biosyst., 2010)

Towards improving full-length ribosome density prediction by bridging sequence and graph-based representations. - Mohan Vamsi Nallapareddy; Francesco Craighero; Cédric Gobet; Felix Naef; Pierre Vandergheynst (MLCB, 2024)

Sequence models for continuous cell cycle stage prediction from brightfield images. - Louis-Alexandre Leger; Maxine Leonardi; Andrea Salati; Felix Naef; Martin Weigert (CoRR, 2025)