Extracting Diffusive States of Rho GTPase in Live Cells: Towards In Vivo Biochemistry. - Peter K. Koo; Matthew Weitzman; Chandran R. Sabanaygam; Kenneth L. van Golen; Simon G. J. Mochrie (PLoS Comput. Biol., 2015)

Representation learning of genomic sequence motifs with convolutional neural networks. - Peter K. Koo; Sean R. Eddy (PLoS Comput. Biol., 2019)

Improving representations of genomic sequence motifs in convolutional networks with exponential activations. - Peter K. Koo; Matt Ploenzke (Nat. Mach. Intell., 2021)

Global importance analysis: An interpretability method to quantify importance of genomic features in deep neural networks. - Peter K. Koo; Antonio Majdandzic; Matthew Ploenzke; Praveen Anand; Steffan B. Paul (PLoS Comput. Biol., 2021)

Selecting deep neural networks that yield consistent attribution-based interpretations for genomics. - Antonio Majdandzic; Chandana Rajesh; Ziqi Tang; Shushan Toneyan; Ethan L. Labelson; Rohit K. Tripathy 001; Peter K. Koo (MLCB, 2022)

Evaluating histopathology transfer learning with ChampKit. - Jakub R. Kaczmarzyk; Tahsin M. Kurç; Shahira Abousamra; Rajarsi Gupta 001; Joel H. Saltz; Peter K. Koo (CoRR, 2022)

Evaluating deep learning for predicting epigenomic profiles. - Shushan Toneyan; Ziqi Tang; Peter K. Koo (Nat. Mac. Intell., 2022)

Learning single-cell chromatin accessibility profiles using meta-analytic marker genes. - Risa Karakida Kawaguchi; Ziqi Tang; Stephan Fischer; Chandana Rajesh; Rohit Tripathy 001; Peter K. Koo; Jesse A. Gillis (Briefings Bioinform., 2023)

End-to-end learning of multiple sequence alignments with differentiable Smith-Waterman. - Samantha Petti; Nicholas Bhattacharya; Roshan Rao; Justas Dauparas; Neil Thomas; Juannan Zhou; Alexander M. Rush; Peter K. Koo; Sergey Ovchinnikov 001 (Bioinform., 2023)

ChampKit: A framework for rapid evaluation of deep neural networks for patch-based histopathology classification. - Jakub R. Kaczmarzyk; Rajarsi Gupta 001; Tahsin M. Kurç; Shahira Abousamra; Joel H. Saltz; Peter K. Koo (Comput. Methods Programs Biomed., 2023)

Interpreting cis-regulatory mechanisms from genomic deep neural networks using surrogate models. - Evan Seitz; David M. McCandlish; Justin B. Kinney; Peter K. Koo (Nat. Mac. Intell., 2024)

EvoAug-TF: extending evolution-inspired data augmentations for genomic deep learning to TensorFlow. - Yiyang Yu; Shivani Muthukumar; Peter K. Koo (Bioinform., 2024)

Reusable specimen-level inference in computational pathology. - Jakub R. Kaczmarzyk; Rishul Sharma; Peter K. Koo; Joel H. Saltz (CoRR, 2025)