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Representation learning of genomic sequence motifs with convolutional neural networks

PLoS computational biology, 2019-12, Vol.15 (12), p.e1007560-e1007560

2019

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Correcting gradient-based interpretations of deep neural networks for genomics

Genome Biology, 2023-05, Vol.24 (1), p.109-109, Article 109

2023

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Global importance analysis: An interpretability method to quantify importance of genomic features in deep neural networks

PLoS computational biology, 2021-05, Vol.17 (5), p.e1008925-e1008925

2021

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EvoAug: improving generalization and interpretability of genomic deep neural networks with evolution-inspired data augmentations

Genome Biology, 2023-05, Vol.24 (1), p.105-105, Article 105

2023

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The tethering of chromatin to the nuclear envelope supports nuclear mechanics

Nature communications, 2015-06, Vol.6 (1), p.7159-7159, Article 7159

2015

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ZBED2 is an antagonist of interferon regulatory factor 1 and modifies cell identity in pancreatic cancer

Proceedings of the National Academy of Sciences - PNAS, 2020-05, Vol.117 (21), p.11471-11482

2020

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EvoAug-TF: extending evolution-inspired data augmentations for genomic deep learning to TensorFlow

Bioinformatics (Oxford, England), 2024-03, Vol.40 (3)

2024

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Current approaches to genomic deep learning struggle to fully capture human genetic variation

Nature genetics, 2023-12, Vol.55 (12), p.2021-2022

2023

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A demonstration of unsupervised machine learning in species delimitation

Molecular phylogenetics and evolution, 2019-10, Vol.139, p.106562-106562, Article 106562

2019

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Extracting Diffusive States of Rho GTPase in Live Cells: Towards In Vivo Biochemistry

PLoS computational biology, 2015-10, Vol.11 (10), p.e1004297-e1004297

2015

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Improved Determination of Subnuclear Position Enabled by Three-Dimensional Membrane Reconstruction

Biophysical journal, 2016-07, Vol.111 (1), p.19-24

2016

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Deep learning for inferring transcription factor binding sites

Current opinion in systems biology, 2020-02, Vol.19, p.16-23

2020

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ResidualBind: Uncovering Sequence-Structure Preferences of RNA-Binding Proteins with Deep Neural Networks

Methods in molecular biology (Clifton, N.J.), 2023, Vol.2586, p.197

2023

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ChampKit: A framework for rapid evaluation of deep neural networks for patch-based histopathology classification

Computer methods and programs in biomedicine, 2023-09, Vol.239, p.107631-107631, Article 107631

2023

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Learning single-cell chromatin accessibility profiles using meta-analytic marker genes

Briefings in bioinformatics, 2023-01, Vol.24 (1)

2023

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ETV6 dependency in Ewing sarcoma by antagonism of EWS-FLI1-mediated enhancer activation

Nature cell biology, 2023-02, Vol.25 (2), p.298

2023

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Applying Perturbation Expectation-Maximization to Protein Trajectories of Rho GTPases

Methods in molecular biology (Clifton, N.J.), 2018, Vol.1821, p.57

2018

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Interpreting Potts and Transformer Protein Models Through the Lens of Simplified Attention

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, 2022, Vol.27, p.34

2022

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Systems-level approach to uncovering diffusive states and their transitions from single-particle trajectories

Physical review. E, 2016-11, Vol.94 (5-1), p.052412-052412, Article 052412

2016

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Allosteric Effects on Substrate Dissociation from Cytochrome P450 3A4 in Nanodiscs Observed by Ensemble and Single-Molecule Fluorescence Spectroscopy

Journal of the American Chemical Society, 2008-11, Vol.130 (47), p.15746-15747

2008

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Extracting Diffusive States of Rho GTPase in Live Cells: Towards In Vivo Biochemistry: e1004297

PLoS computational biology, 2015-10, Vol.11 (10)

2015

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Chromatin Association with the Nuclear Envelope Supports Stable Nuclear Mechanics

Biophysical journal, 2015-01, Vol.108 (2), p.494a-494a

2015

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Novel optical-based methods and analyses for elucidating cellular mechanics and dynamics

Koo, Peter K

2015

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The Lancet Commission on lessons for the future from the COVID-19 pandemic

The Lancet (British edition), 2022-10, Vol.400 (10359), p.1224-1280

2022

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Quantification of Heterogeneous Degradation in Li‐Ion Batteries

Advanced energy materials, 2019-07, Vol.9 (25), p.n/a

2019

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Representation learning of genomic sequence motifs with convolutional neural networks

Correcting gradient-based interpretations of deep neural networks for genomics

Global importance analysis: An interpretability method to quantify importance of genomic features in deep neural networks

EvoAug: improving generalization and interpretability of genomic deep neural networks with evolution-inspired data augmentations

The tethering of chromatin to the nuclear envelope supports nuclear mechanics

ZBED2 is an antagonist of interferon regulatory factor 1 and modifies cell identity in pancreatic cancer

EvoAug-TF: extending evolution-inspired data augmentations for genomic deep learning to TensorFlow

Current approaches to genomic deep learning struggle to fully capture human genetic variation

A demonstration of unsupervised machine learning in species delimitation

Extracting Diffusive States of Rho GTPase in Live Cells: Towards In Vivo Biochemistry

Improved Determination of Subnuclear Position Enabled by Three-Dimensional Membrane Reconstruction

Deep learning for inferring transcription factor binding sites

ResidualBind: Uncovering Sequence-Structure Preferences of RNA-Binding Proteins with Deep Neural Networks

ChampKit: A framework for rapid evaluation of deep neural networks for patch-based histopathology classification

Learning single-cell chromatin accessibility profiles using meta-analytic marker genes

ETV6 dependency in Ewing sarcoma by antagonism of EWS-FLI1-mediated enhancer activation

Applying Perturbation Expectation-Maximization to Protein Trajectories of Rho GTPases

Interpreting Potts and Transformer Protein Models Through the Lens of Simplified Attention

Systems-level approach to uncovering diffusive states and their transitions from single-particle trajectories

Allosteric Effects on Substrate Dissociation from Cytochrome P450 3A4 in Nanodiscs Observed by Ensemble and Single-Molecule Fluorescence Spectroscopy

Extracting Diffusive States of Rho GTPase in Live Cells: Towards In Vivo Biochemistry: e1004297

Chromatin Association with the Nuclear Envelope Supports Stable Nuclear Mechanics

Novel optical-based methods and analyses for elucidating cellular mechanics and dynamics

The Lancet Commission on lessons for the future from the COVID-19 pandemic

Quantification of Heterogeneous Degradation in Li‐Ion Batteries

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