Parametric modeling of cellular state transitions as measured with flow cytometry. - Saumyadipta Pyne; Steven B. Haase; Hsiu J. Ho; Tsung-I Lin (ICCABS, 2011)

A generalized model for multi-marker analysis of cell cycle progression in synchrony experiments. - Michael B. Mayhew; Joshua W. Robinson; Boyoun Jung; Steven B. Haase; Alexander J. Hartemink (Bioinform., 2011)

Parametric modeling of cellular state transitions as measured with flow cytometry. - Hsiu J. Ho; Tsung-I Lin; Hannah H. Chang; Steven B. Haase; Sui Huang; Saumyadipta Pyne (BMC Bioinform., 2012)

Close Encounters of the Collaborative Kind. - Michael B. Mayhew; Xin Guo; Steven B. Haase; Alexander J. Hartemink (Computer, 2012)

Design and analysis of large-scale biological rhythm studies: a comparison of algorithms for detecting periodic signals in biological data. - Anastasia Deckard; Ron C. Anafi; John B. Hogenesch; Steven B. Haase; John Harer (Bioinform., 2013)

Branching process deconvolution algorithm reveals a detailed cell-cycle transcription program. - Xin Guo; Allister Bernard; David A. Orlando; Steven B. Haase; Alexander J. Hartemink (Proc. Natl. Acad. Sci. USA, 2013)

SW1PerS: Sliding windows and 1-persistence scoring; discovering periodicity in gene expression time series data. - Jose A. Perea; Anastasia Deckard; Steven B. Haase; John Harer (BMC Bioinform., 2015)

Hyperparameter Optimization of Topological Features for Machine Learning Applications. - Francis C. Motta; John Harer; Nick Leiby; Franco Marinozzi; Scott Novotney; Gabe Rocklin; Jed Singer; Devin Strickland; Matt Vaughn; Christopher J. Tralie; Rossella Bedini; Fabiano Bini; et al. (ICMLA, 2019)

Improved datasets and evaluation methods for the automatic prediction of DNA-binding proteins. - Alexander Zaitzeff; Nick Leiby; Francis C. Motta; Steven B. Haase; Jed Singer (Bioinform., 2021)

Conservation of dynamic characteristics of transcriptional regulatory elements in periodic biological processes. - Francis C. Motta; Robert C. Moseley; Bree Cummins; Anastasia Deckard; Steven B. Haase (BMC Bioinform., 2022)

Experimental guidance for discovering genetic networks through hypothesis reduction on time series. - Breschine Cummins; Francis C. Motta; Robert C. Moseley; Anastasia Deckard; Sophia Campione; Marcio Gameiro; Tomás Gedeon; Konstantin Mischaikow; Steven B. Haase (PLoS Comput. Biol., 2022)