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Deep Learning for Shallow Sequencing
Johnny Israeli Nvidia Genomics Group GTC 2018
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Talk Outline
- A Study of Breast Cancer
- Sequencing Technologies
- Deep Learning for Genomics
- Enhancing Sequencing with Deep Learning
Deep Learning for Shallow Sequencing Johnny Israeli Nvidia - - PowerPoint PPT Presentation
Deep Learning for Shallow Sequencing Johnny Israeli Nvidia - - PowerPoint PPT Presentation
Deep Learning for Shallow Sequencing Johnny Israeli Nvidia Genomics Group GTC 2018 1 Talk Outline A Study of Breast Cancer Sequencing Technologies Deep Learning for Genomics Enhancing Sequencing with Deep Learning 2 100 Pa
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25 μm
100 Pa 2000 Pa
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ATAC-seq profiling of genomic elements controlling gene expression
Map to genome
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Control elements activated in stiff cells reveal the SP1 DNA motif
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Knock down of SP1 in stiff cells removes invasive phenotype Soft Stiff SP1 Knock down
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Sequencing Technologies
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Genome Analyzer IIx HiSeq 2500 MinION SmidgeION
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Sequencers as Counting Devices
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Sequencers as Counting Devices
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Sequencers as Counting Devices
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Sequencers as Counting Devices
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Diverse sequencing-based technologies
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Growth of single cell sequencing
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Deep Learning for Genomics
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DL4Genomics takes off 2015
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DeepSEA (2015): Predicting effects of variations in the non-coding genome with deep learning
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DeepVariant (2016): Detection of single nucleotide genomic variations and insertions/deletions with deep learning
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Chiron (2017): Translating MinION measurements into DNA Sequence with Deep Learning
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1,700 Models!
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Enhancing Sequencing with Deep Learning
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Is this the same ATAC-seq signal?
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Is this the same ATAC-seq signal?
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50M DNA Reads 5M DNA Reads
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Enhancing ATAC-seq with Deep Learning
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50M DNA Reads 5M DNA Reads
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50M DNA Reads 5M DNA Reads
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Enhancing ATAC-seq with Deep Learning
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50M DNA Reads 5M DNA Reads
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50M DNA Reads 5M DNA Reads Linear Model Enhancement
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Enhancing ATAC-seq with Deep Learning
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50M DNA Reads 5M DNA Reads Linear Model Enhancement Deep Learning Enhancement 50M DNA Reads 5M DNA Reads
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Enhancing ATAC-seq with Deep Learning
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50M DNA Reads 5M DNA Reads
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50M DNA Reads 5M DNA Reads Linear Model Enhancement Deep Learning Enhancement
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Enhancing ATAC-seq with Deep Learning
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50M DNA Reads 5M DNA Reads
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5M DNA Reads Signal Enhanced by DL ~ 20M Signal!
Enhancing ATAC-seq with Deep Learning
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More Sequencing Data Better Deep Learning Models Cheaper Signal Generation Better Data Enhancement
Augmenting Sequencers with Deep Learning
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Genomics @ Nvidia (we are hiring!)
Joint work with
- Nvidia AI Infrastructure
- Nvidia Research
- Nvidia Healthcare
Nikolai Yakovenko