| The tethering of chromatin to the nuclear envelope supports nuclear mechanics SM Schreiner, PK Koo, Y Zhao, SGJ Mochrie, MC King Nature Communications 6 (1), 1-13, 2015 | 282 | 2015 |
| Representation learning of genomic sequence motifs with convolutional neural networks PK Koo, SR Eddy PLoS computational biology 15 (12), e1007560, 2019 | 131 | 2019 |
| A demonstration of unsupervised machine learning in species delimitation S Derkarabetian, S Castillo, PK Koo, S Ovchinnikov, M Hedin Molecular Phylogenetics and Evolution 139, 106562, 2019 | 126 | 2019 |
| Improving representations of genomic sequence motifs in convolutional networks with exponential activations PK Koo, M Ploenzke Nature Machine Intelligence 3, 258–266, 2021 | 95* | 2021 |
| Global importance analysis: An interpretability method to quantify importance of genomic features in deep neural networks PK Koo, A Majdandzic, M Ploenzke, P Anand, S Paul PLoS Computational Biology 17 (5), e1008925, 2021 | 90 | 2021 |
| Deep learning for inferring transcription factor binding sites PK Koo, M Ploenzke Current Opinion in Systems Biology 19, 16-23, 2020 | 88 | 2020 |
| Evaluating deep learning for predicting epigenomic profiles S Toneyan, Z Tang, PK Koo Nature machine intelligence 4 (12), 1088-1100, 2022 | 66 | 2022 |
| Single-molecule fluorescence spectroscopy using phospholipid bilayer nanodiscs A Nath, AJ Trexler, P Koo, AD Miranker, WM Atkins, E Rhoades Methods in Enzymology 472, 89-117, 2010 | 66 | 2010 |
| Interpreting Potts and Transformer Protein Models Through the Lens of Simplified Attention N Bhattacharya, N Thomas, R Rao, J Dauparas, PK Koo, D Baker, ... PACIFIC SYMPOSIUM ON BIOCOMPUTING 2022, 34-45, 2022 | 64* | 2022 |
| ZBED2 is an antagonist of interferon regulatory factor 1 and modifies cell identity in pancreatic cancer TDD Somerville, Y Xu, XS Wu, D Maia-Silva, SK Hur, LMN de Almeida, ... Proceedings of the National Academy of Sciences 117 (21), 11471-11482, 2020 | 61 | 2020 |
| End-to-end learning of multiple sequence alignments with differentiable Smith-Waterman S Petti, N Bhattacharya, R Rao, J Dauparas, N Thomas, J Zhou, AM Rush, ... Bioinformatics 39 (1), 2021 | 50 | 2021 |
| Correcting gradient-based interpretations of deep neural networks for genomics A Majdandzic, C Rajesh, PK Koo Genome Biology 24 (1), 109, 2023 | 49 | 2023 |
| Allosteric effects on substrate dissociation from cytochrome P450 3A4 in nanodiscs observed by ensemble and single-molecule fluorescence spectroscopy A Nath, PK Koo, E Rhoades, WM Atkins Journal of the American Chemical Society 130 (47), 15746-15747, 2008 | 49 | 2008 |
| WASP family proteins regulate the mobility of the B cell receptor during signaling activation I Rey-Suarez, BA Wheatley, P Koo, A Bhanja, Z Shu, S Mochrie, W Song, ... Nature Communications 11, 2020 | 48 | 2020 |
| Evaluating the representational power of pre-trained DNA language models for regulatory genomics Z Tang, N Somia, Y Yu, PK Koo Genome Biology, 2024 | 46* | 2024 |
| Systems-level approach to uncovering diffusive states and their transitions from single particle trajectories PK Koo, SGJ Mochrie arXiv preprint arXiv:1608.01419, 2016 | 46 | 2016 |
| EvoAug: improving generalization and interpretability of genomic deep neural networks with evolution-inspired data augmentations NK Lee, Z Tang, S Toneyan, PK Koo Genome Biology 24 (1), 105, 2023 | 41 | 2023 |
| Extracting diffusive states of Rho GTPase in live cells: towards in vivo biochemistry PK Koo, M Weitzman, CR Sabanaygam, KL van Golen, SGJ Mochrie PLoS Computational Biology 11 (10), e1004297, 2015 | 39 | 2015 |
| ETV6 dependency in Ewing sarcoma by antagonism of EWS-FLI1-mediated enhancer activation Y Gao, XY He, XS Wu, YH Huang, S Toneyan, T Ha, JJ Ipsaro, PK Koo, ... Nature cell biology 25 (2), 298-308, 2023 | 37 | 2023 |
| Interpreting cis-regulatory mechanisms from genomic deep neural networks using surrogate models EE Seitz, DM McCandlish, JB Kinney, PK Koo Nature machine intelligence 6 (6), 701-713, 2024 | 31 | 2024 |
