Shrimps: Occurrence, Scaling and Relevance. - Ruedi Stoop; Stefan Martignoli; Philipp Benner; Ralph Lukas Stoop; Yoko Uwate (Int. J. Bifurc. Chaos, 2012)

Point estimates in phylogenetic reconstructions. - Philipp Benner; Miroslav Bacák; Pierre-Yves Bourguignon (Bioinform., 2014)

Combining prior information for the prediction of transcription factor binding sites. - Philipp Benner (2016)

Predicting enhancers in mammalian genomes using supervised hidden Markov models. - Tobias Zehnder; Philipp Benner; Martin Vingron (BMC Bioinform., 2019)

ModHMM: A Modular Supra-Bayesian Genome Segmentation Method. - Philipp Benner; Martin Vingron (J. Comput. Biol., 2020)

Computing Leapfrog Regularization Paths with Applications to Large-Scale K-mer Logistic Regression. - Philipp Benner (J. Comput. Biol., 2021)

Matbench Discovery - An evaluation framework for machine learning crystal stability prediction. - Janosh Riebesell; Rhys E. A. Goodall; Anubhav Jain 001; Philipp Benner; Kristin A. Persson; Alpha A. Lee (CoRR, 2023)

SynCoTrain: A Dual Classifier PU-learning Framework for Synthesizability Prediction. - Sasan Amariamir; Janine George; Philipp Benner (CoRR, 2024)