greenelab/deep-review

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A collaboratively written review paper on deep learning, genomics, and precision medicine

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Forks: 270
Open beginner issues: 0
Indexed issues: 421

Dominant language: HTML
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Last GitHub push: Dec 28, 2021
Latest indexed: Sep 17, 2026
Contributing guide: Contributing guide
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Beginner labels: help wanted
PR merge metrics: No merged PRs in 30d

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421 open issues indexed

A deep learning framework for modeling structural features of RNA-binding protein targets Open

backlog paper study unsupervised

greenelab/deep-review#15 · 5 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Microscopy cell counting and detection with fully convolutional regression networks Open

backlog paper

greenelab/deep-review#34 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Deep Motif: Visualizing Genomic Sequence Classifications Open

backlog paper

greenelab/deep-review#36 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Deep biomarkers of human aging: Application of deep neural networks to biomarker development Open

backlog paper supervised

greenelab/deep-review#37 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
DeepCyTOF: Automated Cell Classification of Mass Cytometry Data by Deep Learning and Domain Adaptation Open

backlog paper

greenelab/deep-review#41 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Classifying and segmenting microscopy images with deep multiple instance learning Open

backlog paper

greenelab/deep-review#42 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
DeepLNC, a long non-coding RNA prediction tool using deep neural network Open

backlog paper

greenelab/deep-review#44 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
MiRTDL: a deep learning approach for miRNA target prediction Open

backlog paper supervised

greenelab/deep-review#49 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
MUST-CNN: A Multilayer Shift-and-Stitch Deep Convolutional Architecture for Sequence-based Protein Structure Prediction Open

backlog

greenelab/deep-review#58 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Opening up the blackbox: an interpretable deep neural network-based classifier for cell-type specific enhancer predictions Open

backlog paper supervised

greenelab/deep-review#60 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Predicting DNA Methylation State of CpG Dinucleotide Using Genome Topological Features and Deep Networks Open

backlog paper study supervised

greenelab/deep-review#68 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
A Short Review of Deep Learning Neural Networks in Protein Structure Prediction Problems Open

review

greenelab/deep-review#69 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Efficient Multi-Scale 3D CNN with Fully Connected CRF for Accurate Brain Lesion Segmentation Open

backlog

greenelab/deep-review#73 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Modeling translation elongation dynamics by deep learning reveals new insights into the landscape of ribosome stalling Open

backlog study

greenelab/deep-review#74 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Discover regulatory DNA elements using chromatin signatures and artificial neural network. Open

backlog paper study supervised

greenelab/deep-review#76 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Deep Computational Phenotyping Open

backlog

greenelab/deep-review#77 · 1 comment · 0 reactions · 1 assignee · Indexed Sep 17, 2026
DeepWAS: Directly integrating regulatory information into GWAS using deep learning supports master regulator MEF2C as risk factor for major depressive disorder Open

backlog

greenelab/deep-review#80 · 2 comments · 2 reactions · 0 assignees · Indexed Sep 17, 2026
Deep Learning and Association Rule Mining for Predicting Drug Response in Cancer Open

backlog paper supervised treat

greenelab/deep-review#84 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
IPMiner: hidden ncRNA-protein interaction sequential pattern mining with stacked autoencoder for accurate computational prediction Open

backlog

greenelab/deep-review#96 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Deep Kalman Filters Open

greenelab/deep-review#100 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Convolutional LSTM Networks for Subcellular Localization of Proteins Open

greenelab/deep-review#103 · 3 comments · 1 reaction · 0 assignees · Indexed Sep 17, 2026
Automatic chemical design using a data-driven continuous representation of molecules Open

treat

greenelab/deep-review#104 · 1 comment · 0 reactions · 1 assignee · Indexed Sep 17, 2026
The precision-oncology illusion Open

greenelab/deep-review#105 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
FIDDLE: An integrative deep learning framework for functional genomic data inference Open

paper study supervised

greenelab/deep-review#110 · 6 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Multi-omics integration accurately predicts cellular state in unexplored conditions for Escherichia coli Open

study

greenelab/deep-review#112 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Predicting drug-target interactions using restricted Boltzmann machines Open

treat

greenelab/deep-review#113 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Deep Learning for Metagenomics and Nanopore Sequencing? Open

paper study supervised

greenelab/deep-review#114 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
CGBVS-DNN: Prediction of Compound-protein Interactions Based on Deep Learning Open

paper supervised treat

greenelab/deep-review#117 · 9 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Leveraging uncertainty information from deep neural networks for disease detection Open

categorize paper supervised

greenelab/deep-review#122 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Automating Morphological Profiling with Generic Deep Convolutional Networks Open

study

greenelab/deep-review#129 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Predicting Enhancer-Promoter Interaction from Genomic Sequence with Deep Neural Networks Open

paper study supervised

greenelab/deep-review#130 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
RNA-protein binding motifs mining with a new hybrid deep learning based cross-domain knowledge integration approach Open

paper study supervised

greenelab/deep-review#132 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Deep Learning Automates the Quantitative Analysis of Individual Cells in Live-Cell Imaging Experiments Open

paper study

greenelab/deep-review#133 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Deep learning with feature embedding for compound-protein interaction prediction Open

paper treat

greenelab/deep-review#137 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
A Deep Boosting Based Approach for Capturing the Sequence Binding Preferences of RNA-Binding Proteins from High-Throughput CLIP-Seq Data Open

paper study

greenelab/deep-review#138 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 17, 2026
DIET NETWORKS: THIN PARAMETERS FOR FAT GENOMICS Open

greenelab/deep-review#140 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Low Data Drug Discovery with One-shot Learning Open

paper treat

greenelab/deep-review#141 · 4 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Protein Secondary Structure Prediction Using Deep Multi-scale Convolutional Neural Networks and Next-Step Conditioning Open

paper study

greenelab/deep-review#142 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
RCK: accurate and efficient inference of sequence- and structure-based protein–RNA binding models from RNAcompete data Open

paper study

greenelab/deep-review#144 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Deep Residual Learning for Image Recognition Open

paper

greenelab/deep-review#145 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Gradient Boosted Trees (XGBoost) Open

greenelab/deep-review#146 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Computational Modeling of β-Secretase 1 (BACE-1) Inhibitors Using Ligand Based Approaches Open

paper treat

greenelab/deep-review#148 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
DeeperBind: Enhancing Prediction of Sequence Specificities of DNA Binding Proteins Open

paper study

greenelab/deep-review#149 · 1 comment · 1 reaction · 0 assignees · Indexed Sep 17, 2026
Development and Validation of a Deep Learning Algorithm for Detection of Diabetic Retinopathy in Retinal Fundus Photographs Open

categorize paper

greenelab/deep-review#151 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Deepr: A Convolutional Net for Medical Records Open

categorize paper

greenelab/deep-review#152 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Removal of Batch Effects using Distribution-Matching Residual Networks Open

paper study

greenelab/deep-review#153 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
EP-DNN: A Deep Neural Network-Based Global Enhancer Prediction Algorithm Open

paper study

greenelab/deep-review#154 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Cox-nnet: an artificial neural network Cox regression for prognosis prediction Open

categorize paper

greenelab/deep-review#155 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 17, 2026
DeepCancer: Detecting Cancer through Gene Expressions via Deep Generative Learning Open

discussion paper

greenelab/deep-review#157 · 5 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Deep learning is effective for the classification of OCT images of normal versus Age-related Macular Degeneration Open

categorize paper

greenelab/deep-review#158 · 5 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026

greenelab/deep-review

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