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Peter Koo
Peter Koo
Assistant Professor, Cold Spring Harbor Laboratory
Verified email at cshl.edu - Homepage
Title
Cited by
Cited by
Year
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
2122015
Representation learning of genomic sequence motifs with convolutional neural networks
PK Koo, SR Eddy
PLoS computational biology 15 (12), e1007560, 2019
922019
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
892019
Improving representations of genomic sequence motifs in convolutional networks with exponential activations
PK Koo, M Ploenzke
Nature Machine Intelligence 3, 258–266, 2021
69*2021
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
Deep learning for inferring transcription factor binding sites
PK Koo, M Ploenzke
Current Opinion in Systems Biology 19, 16-23, 2020
642020
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
532021
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
472008
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
432020
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
372016
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
36*2022
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
352020
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
332015
Evaluating deep learning for predicting epigenomic profiles
S Toneyan, Z Tang, PK Koo
Nature machine intelligence 4 (12), 1088-1100, 2022
312022
Inferring sequence-structure preferences of rna-binding proteins with convolutional residual networks
PK Koo, P Anand, SB Paul, SR Eddy
bioRxiv, 418459, 2018
30*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
272014
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
252021
Robust Neural Networks are More Interpretable for Genomics
PK Koo, S Qian, G Kaplun, V Volf, D Kalimeris
bioRxiv, 657437, 2019
16*2019
The architecture of the 12RSS in V (D) J recombination signal and synaptic complexes
M Ciubotaru, MD Surleac, LA Metskas, P Koo, E Rhoades, AJ Petrescu, ...
Nucleic Acids Research 43 (2), 917-931, 2015
162015
Correcting gradient-based interpretations of deep neural networks for genomics
A Majdandzic, C Rajesh, PK Koo
Genome Biology 24 (1), 109, 2023
15*2023
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Articles 1–20