Peter K Koo

Publication Activity (10 Years)

Years Active: 2019-2024
Publications (10 Years): 33

Top Topics

Circulating Tumor Cells

Top Venues

bioRxiv : the preprint server for biology

Nature cell biology

Nature genetics

This page only lists publications with an associated author ORCID identifier.

Publications

Mike Thompson, Mariano Martín, Trinidad Sanmartín Olmo, Chandana Rajesh, Peter K Koo, Benedetta Bolognesi, Ben Lehner
Interpretably deep learning amyloid nucleation by massive experimental quantification of random sequences. bioRxiv : the preprint server for biology (2024)
Shushan Toneyan, Peter K Koo
Interpreting cis-regulatory interactions from large-scale deep neural networks. Nature genetics (2024)
Yiyang Yu, Shivani Muthukumar, Peter K Koo
EvoAug-TF: extending evolution-inspired data augmentations for genomic deep learning to TensorFlow. Bioinformatics (Oxford, England) 40 (3) (2024)
Mike Thompson, Mariano Martín, Trinidad Sanmartín Olmo, Chandana Rajesh, Peter K Koo, Benedetta Bolognesi, Ben Lehner
Interpretably deep learning amyloid nucleation by massive experimental quantification of random sequences. bioRxiv : the preprint server for biology (2024)
Yiyang Yu, Shivani Muthukumar, Peter K Koo
EvoAug-TF: Extending evolution-inspired data augmentations for genomic deep learning to TensorFlow. bioRxiv : the preprint server for biology (2024)
Yiyang Yu, Shivani Muthukumar, Peter K Koo
EvoAug-TF: Extending evolution-inspired data augmentations for genomic deep learning to TensorFlow. bioRxiv : the preprint server for biology (2024)
Ziqi Tang, Peter K Koo
Evaluating the representational power of pre-trained DNA language models for regulatory genomics. bioRxiv : the preprint server for biology (2024)
Yiyang Yu, Shivani Muthukumar, Peter K Koo
EvoAug-TF: Extending evolution-inspired data augmentations for genomic deep learning to TensorFlow. bioRxiv : the preprint server for biology (2024)
Ziqi Tang, Peter K Koo
Evaluating the representational power of pre-trained DNA language models for regulatory genomics. bioRxiv : the preprint server for biology (2024)
Yiyang Yu, Shivani Muthukumar, Peter K Koo
EvoAug-TF: extending evolution-inspired data augmentations for genomic deep learning to TensorFlow. Bioinformatics (Oxford, England) 40 (3) (2024)
Yiyang Yu, Shivani Muthukumar, Peter K Koo
EvoAug-TF: Extending evolution-inspired data augmentations for genomic deep learning to TensorFlow. bioRxiv : the preprint server for biology (2024)
Yuan Gao, Xue-Yan He, Xiaoli S Wu, Yu-Han Huang, Shushan Toneyan, Taehoon Ha, Jonathan J Ipsaro, Peter K Koo, Leemor Joshua-Tor, Kelly M Bailey, Mikala Egeblad, Christopher R Vakoc
ETV6 dependency in Ewing sarcoma by antagonism of EWS-FLI1-mediated enhancer activation. Nature cell biology (2023)
Nicholas Keone Lee, Ziqi Tang, Shushan Toneyan, Peter K Koo
EvoAug: improving generalization and interpretability of genomic deep neural networks with evolution-inspired data augmentations. Genome biology 24 (1) (2023)
Yuan Gao, Xue-Yan He, Xiaoli S Wu, Yu-Han Huang, Shushan Toneyan, Taehoon Ha, Jonathan J Ipsaro, Peter K Koo, Leemor Joshua-Tor, Kelly M Bailey, Mikala Egeblad, Christopher R Vakoc
ETV6 dependency in Ewing sarcoma by antagonism of EWS-FLI1-mediated enhancer activation. Nature cell biology 25 (2) (2023)
Antonio Majdandzic, Chandana Rajesh, Peter K Koo
Correcting gradient-based interpretations of deep neural networks for genomics. Genome biology 24 (1) (2023)
Nicholas Keone Lee, Ziqi Tang, Shushan Toneyan, Peter K Koo
EvoAug: improving generalization and interpretability of genomic deep neural networks with evolution-inspired data augmentations. Genome biology 24 (1) (2023)
Yuan Gao, Xue-Yan He, Xiaoli S Wu, Yu-Han Huang, Shushan Toneyan, Taehoon Ha, Jonathan J Ipsaro, Peter K Koo, Leemor Joshua-Tor, Kelly M Bailey, Mikala Egeblad, Christopher R Vakoc
ETV6 dependency in Ewing sarcoma by antagonism of EWS-FLI1-mediated enhancer activation. Nature cell biology 25 (2) (2023)
Antonio Majdandzic, Chandana Rajesh, Peter K Koo
Correcting gradient-based interpretations of deep neural networks for genomics. Genome biology 24 (1) (2023)
Nicholas Keone Lee, Ziqi Tang, Shushan Toneyan, Peter K Koo
EvoAug: improving generalization and interpretability of genomic deep neural networks with evolution-inspired data augmentations. Genome biology 24 (1) (2023)
Yuan Gao, Xue-Yan He, Xiaoli S Wu, Yu-Han Huang, Shushan Toneyan, Taehoon Ha, Jonathan J Ipsaro, Peter K Koo, Leemor Joshua-Tor, Kelly M Bailey, Mikala Egeblad, Christopher R Vakoc
ETV6 dependency in Ewing sarcoma by antagonism of EWS-FLI1-mediated enhancer activation. Nature cell biology 25 (2) (2023)
Evan E Seitz, David M McCandlish, Justin B Kinney, Peter K Koo
Interpreting cis -regulatory mechanisms from genomic deep neural networks using surrogate models. bioRxiv : the preprint server for biology (2023)
Nicholas Keone Lee, Ziqi Tang, Shushan Toneyan, Peter K Koo
EvoAug: improving generalization and interpretability of genomic deep neural networks with evolution-inspired data augmentations. Genome biology 24 (1) (2023)
Yuan Gao, Xue-Yan He, Xiaoli S Wu, Yu-Han Huang, Shushan Toneyan, Taehoon Ha, Jonathan J Ipsaro, Peter K Koo, Leemor Joshua-Tor, Kelly M Bailey, Mikala Egeblad, Christopher R Vakoc
ETV6 dependency in Ewing sarcoma by antagonism of EWS-FLI1-mediated enhancer activation. Nature cell biology (2023)
Nicholas Keone Lee, Ziqi Tang, Shushan Toneyan, Peter K Koo
EvoAug: improving generalization and interpretability of genomic deep neural networks with evolution-inspired data augmentations. Genome biology 24 (1) (2023)
Yuan Gao, Xue-Yan He, Xiaoli S Wu, Yu-Han Huang, Shushan Toneyan, Taehoon Ha, Jonathan J Ipsaro, Peter K Koo, Leemor Joshua-Tor, Kelly M Bailey, Mikala Egeblad, Christopher R Vakoc
ETV6 dependency in Ewing sarcoma by antagonism of EWS-FLI1-mediated enhancer activation. Nature cell biology 25 (2) (2023)
Nicholas Keone Lee, Ziqi Tang, Shushan Toneyan, Peter K Koo
EvoAug: improving generalization and interpretability of genomic deep neural networks with evolution-inspired data augmentations. Genome biology 24 (1) (2023)
Shushan Toneyan, Peter K Koo
Interpreting Cis -Regulatory Interactions from Large-Scale Deep Neural Networks for Genomics. bioRxiv : the preprint server for biology (2023)
Antonio Majdandzic, Chandana Rajesh, Peter K Koo
Correcting gradient-based interpretations of deep neural networks for genomics. Genome biology 24 (1) (2023)
Antonio Majdandzic, Chandana Rajesh, Peter K Koo
Correcting gradient-based interpretations of deep neural networks for genomics. Genome biology 24 (1) (2023)
Ziqi Tang, Shushan Toneyan, Peter K Koo
Current approaches to genomic deep learning struggle to fully capture human genetic variation. Nature genetics (2023)
Peter K Koo, Antonio Majdandzic, Matthew Ploenzke, Praveen Anand, Steffanie Paul
Global importance analysis: An interpretability method to quantify importance of genomic features in deep neural networks. PLoS computational biology 17 (5) (2021)
Tim D D Somerville, Yali Xu, Xiaoli S Wu, Diogo Maia-Silva, Stella K Hur, Larissa M N de Almeida, Jonathan B Preall, Peter K Koo, Christopher R Vakoc
ZBED2 is an antagonist of interferon regulatory factor 1 and modifies cell identity in pancreatic cancer. Proceedings of the National Academy of Sciences of the United States of America 117 (21) (2020)
Peter K Koo, Sean R Eddy
Representation learning of genomic sequence motifs with convolutional neural networks. PLoS computational biology 15 (12) (2019)