Research graph
References from Predicting 3D chromatin interactions from DNA sequence using Deep Learning. Local targets link to admitted publications; unresolved targets remain external evidence.
10.1101/gad.281964.116
10.1101/gad.281964.116 · External reference
10.1126/science.1181369
10.1126/science.1181369 · External reference
10.1002/jcb.22116
10.1002/jcb.22116 · External reference
10.1038/cr.2016.137
10.1038/cr.2016.137 · External reference
10.1038/nmeth.3999
10.1038/nmeth.3999 · External reference
Too many transcription factors: positive and negative interactions
1990 · External reference
Exploring 3d chromatin contacts in gene regulation: The evolution of approaches for the identification of functional enhancer-promoter interaction
10.1016/j.csbj.2020.02.013 · 2020 · External reference
10.1038/s41576-019-0122-6
10.1038/s41576-019-0122-6 · External reference
Modeling enhancer-promoter interactions with attention-based neural networks
2017 · External reference
10.1016/j.cell.2014.11.021
10.1016/j.cell.2014.11.021 · External reference
10.1371/journal.pbio.1001046
10.1371/journal.pbio.1001046 · External reference
10.1038/nature14248
10.1038/nature14248 · External reference
10.1101/2021.09.04.458817
10.1101/2021.09.04.458817 · External reference
10.1093/nar/gkx1081
10.1093/nar/gkx1081 · External reference
A curated benchmark of enhancer-gene interactions for evaluating enhancer-target gene prediction methods
2020 · External reference
10.1093/nar/gky955
10.1093/nar/gky955 · External reference
10.1093/nar/gkq603
10.1093/nar/gkq603 · External reference
10.1101/103614
10.1101/103614 · External reference
10.1038/s41592-020-0958-x
10.1038/s41592-020-0958-x · External reference
10.1016/j.molcel.2020.03.003
10.1016/j.molcel.2020.03.003 · External reference
10.1016/j.cell.2017.09.043
10.1016/j.cell.2017.09.043 · External reference
10.1038/s41592-020-0960-3
10.1038/s41592-020-0960-3 · External reference
10.1038/ng.3646
10.1038/ng.3646 · External reference
10.1038/nature11247
10.1038/nature11247 · External reference
10.1101/813618
10.1101/813618 · External reference
10.1101/gr.220202.117
10.1101/gr.220202.117 · External reference
10.1101/2021.05.19.444847
10.1101/2021.05.19.444847 · External reference
Unresolved reference
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10.3390/genes12091385
10.3390/genes12091385 · External reference
EPIHC: Improving enhancer-promoter interaction prediction by using hybrid features and communicative learning
2021 · External reference
10.1186/s13059-021-02453-5
10.1186/s13059-021-02453-5 · External reference
10.1016/j.cell.2015.11.024
10.1016/j.cell.2015.11.024 · External reference
DeepTACT: predicting 3D chromatin contacts via bootstrapping deep learning
2019 · External reference
10.1016/j.cell.2016.09.037
10.1016/j.cell.2016.09.037 · External reference
10.1038/nature12787
10.1038/nature12787 · External reference
10.1093/nar/gku1010
10.1093/nar/gku1010 · External reference
10.1186/s13059-016-0992-2
10.1186/s13059-016-0992-2 · External reference
DeepMILO: a deep learning approach to predict the impact of non-coding sequence variants on 3d chromatin structure
2020 · External reference
10.1126/science.aad9024
10.1126/science.aad9024 · External reference
Prediction of enhancer-promoter interactions using the cross-cell type information and domain adversarial neural network
2020 · External reference
10.1007/s40484-019-0154-0
10.1007/s40484-019-0154-0 · External reference
10.1093/bioinformatics/btz694
10.1093/bioinformatics/btz694 · External reference
Predicting enhancer-promoter interactions by deep learning and matching heuristic
2020 · External reference
10.1016/j.ymeth.2012.05.001
10.1016/j.ymeth.2012.05.001 · External reference
Hi-c analysis: from data generation to integration
2018 · External reference
10.1101/gr.185272.114
10.1101/gr.185272.114 · External reference
10.1016/j.cell.2015.05.048
10.1016/j.cell.2015.05.048 · External reference
Promoter capture hi-c: High-resolution, genome-wide profiling of promoter interactions
10.3791/57320 · 2018 · External reference
Chromatin interaction analysis with paired-end tag (chia-pet) sequencing technology and application
10.1186/1471-2164-15-s12-s11 · 2014 · External reference
10.1371/journal.pcbi.1000598
10.1371/journal.pcbi.1000598 · External reference
Visualization of genomic data with the hilbert curve
10.1093/bioinformatics/btp152 · 2009 · External reference
Unresolved reference
External reference
Unresolved reference
External reference
Unresolved reference
External reference
Application of the residue number system to reduce hardware costs of the convolutional neural network implementation
10.1016/j.matcom.2020.04.031 · 2020 · External reference
10.1162/neco.1997.9.8.1735
10.1162/neco.1997.9.8.1735 · External reference
10.1049/cp:19991218
10.1049/cp:19991218 · External reference
Bidirectional recurrent neural networks
10.1109/78.650093 · 1997 · External reference
Deep Learning
2016 · External reference
10.1016/s0893-6080(03)00115-1
10.1016/s0893-6080(03)00115-1 · External reference
10.1016/j.devcel.2011.06.008
10.1016/j.devcel.2011.06.008 · External reference
10.1038/ng.3539
10.1038/ng.3539 · External reference
10.1101/gad.924301
10.1101/gad.924301 · External reference
10.1371/journal.pone.0118432
10.1371/journal.pone.0118432 · External reference
10.1038/s41556-019-0273-x
10.1038/s41556-019-0273-x · External reference
Unresolved reference
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10.1109/cvpr.2016.319
10.1109/cvpr.2016.319 · External reference
HOCOMOCO: a comprehensive collection of human transcription factor binding sites models
10.1093/nar/gks1089 · 2012 · External reference
Unresolved reference
External reference
10.1016/j.cell.2013.03.036
10.1016/j.cell.2013.03.036 · External reference
10.1038/s41467-021-20940-y
10.1038/s41467-021-20940-y · External reference
10.1016/j.cell.2015.07.048
10.1016/j.cell.2015.07.048 · External reference
10.1038/ng.2653
10.1038/ng.2653 · External reference
10.1016/j.cell.2019.08.007
10.1016/j.cell.2019.08.007 · External reference
Transposable elements contribute to cell and species-specific chromatin looping and gene regulation in mammalian genomes
2020 · External reference
10.1038/s41588-021-00913-z
10.1038/s41588-021-00913-z · External reference
10.1534/genetics.114.167791
10.1534/genetics.114.167791 · External reference
10.1016/j.molp.2017.11.005
10.1016/j.molp.2017.11.005 · External reference
10.1093/jxb/eraa220
10.1093/jxb/eraa220 · External reference
10.1016/j.molcel.2017.07.022
10.1016/j.molcel.2017.07.022 · External reference
10.1016/j.cell.2014.09.030
10.1016/j.cell.2014.09.030 · External reference