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Peter Koo
Peter Koo
Assistant Professor, Cold Spring Harbor Laboratory
Dirección de correo verificada de cshl.edu - Página principal
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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
2282015
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
1032019
Representation learning of genomic sequence motifs with convolutional neural networks
PK Koo, SR Eddy
PLoS computational biology 15 (12), e1007560, 2019
1022019
Improving representations of genomic sequence motifs in convolutional networks with exponential activations
PK Koo, M Ploenzke
Nature Machine Intelligence 3, 258–266, 2021
82*2021
Deep learning for inferring transcription factor binding sites
PK Koo, M Ploenzke
Current Opinion in Systems Biology 19, 16-23, 2020
722020
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
682021
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
662010
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
512020
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
47*2022
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
462008
Evaluating deep learning for predicting epigenomic profiles
S Toneyan, Z Tang, PK Koo
Nature machine intelligence 4 (12), 1088-1100, 2022
422022
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
392020
Systems-level approach to uncovering diffusive states and their transitions from single-particle trajectories
PK Koo, SGJ Mochrie
Physical Review E 94 (5), 052412, 2016
392016
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
362015
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
342021
Inferring sequence-structure preferences of rna-binding proteins with convolutional residual networks
PK Koo, P Anand, SB Paul, SR Eddy
bioRxiv, 418459, 2018
31*2018
Dynamics of cadmium sulfide nanoparticles within polystyrene melts
WS Jang, P Koo, K Bryson, S Narayanan, A Sandy, TP Russell, ...
Macromolecules 47 (18), 6483-6490, 2014
282014
Correcting gradient-based interpretations of deep neural networks for genomics
A Majdandzic, C Rajesh, PK Koo
Genome Biology 24 (1), 109, 2023
26*2023
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
212023
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
192023
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Artículos 1–20