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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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Interpreting cis-regulatory interactions from large-scale deep neural networks

Nature genetics, 2024-09

2024

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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-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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Correcting gradient-based interpretations of deep neural networks for genomics

Genome Biology, 2023-05, Vol.24 (1), p.109-13, Article 109

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

Genome Biology, 2023-05, Vol.24 (1), p.105-14, 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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Improving representations of genomic sequence motifs in convolutional networks with exponential activations

Nature machine intelligence, 2021-03, Vol.3 (3), p.258-266

2021

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Evaluating deep learning for predicting epigenomic profiles

Nature machine intelligence, 2022-12, Vol.4 (12), p.1088-1100

2022

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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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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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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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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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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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E2F8 Induces Cell Proliferation and Invasion through the Epithelial-Mesenchymal Transition and Notch Signaling Pathways in Ovarian Cancer

International journal of molecular sciences, 2020-08, Vol.21 (16), p.5813

2020

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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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WASP family proteins regulate the mobility of the B cell receptor during signaling activation

Nature communications, 2020-01, Vol.11 (1), p.439-439, Article 439

2020

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Interpreting cis-regulatory mechanisms from genomic deep neural networks using surrogate models

Nature machine intelligence, 2024-06, Vol.6 (6), p.701-713

2024

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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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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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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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Randomized Clinical Trial of the Effectiveness of a Self-Care Intervention to Improve Cancer Pain Management

Journal of clinical oncology, 2004-05, Vol.22 (9), p.1713-1720

2004

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Representation learning of genomic sequence motifs with convolutional neural networks

Interpreting cis-regulatory interactions from large-scale deep neural networks

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

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

Correcting gradient-based interpretations of deep neural networks for genomics

A demonstration of unsupervised machine learning in species delimitation

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

Improving representations of genomic sequence motifs in convolutional networks with exponential activations

Evaluating deep learning for predicting epigenomic profiles

Deep learning for inferring transcription factor binding sites

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

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

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

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

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

E2F8 Induces Cell Proliferation and Invasion through the Epithelial-Mesenchymal Transition and Notch Signaling Pathways in Ovarian Cancer

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

WASP family proteins regulate the mobility of the B cell receptor during signaling activation

Interpreting cis-regulatory mechanisms from genomic deep neural networks using surrogate models

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

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

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

Randomized Clinical Trial of the Effectiveness of a Self-Care Intervention to Improve Cancer Pain Management

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