Machine learning for integrating data in biology and medicine: principles, practice, and opportunities

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An integrated encyclopedia of DNA elements in the human genome

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"Why Should I Trust You?": Explaining the Predictions of Any Classifier

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On a Method to Measure Supervised Multiclass Model’s Interpretability: Application to Degradation Diagnosis (Short Paper)

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Comprehensive molecular portraits of human breast tumours

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TensorFlow: Large-Scale Machine Learning on Heterogeneous Distributed Systems

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A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

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Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

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Comprehensive molecular portraits of human breast tumours

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Integrated Genomic Analysis Identifies Clinically Relevant Subtypes of Glioblastoma Characterized by Abnormalities in PDGFRA, IDH1, EGFR, and NF1

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Massively parallel digital transcriptional profiling of single cells

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High-Resolution Profiling of Histone Methylations in the Human Genome

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Topological domains in mammalian genomes identified by analysis of chromatin interactions

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“Why Should I Trust You?”: Explaining the Predictions of Any Classifier

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Integrative analysis of 111 reference human epigenomes

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A general framework for estimating the relative pathogenicity of human genetic variants

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The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups

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Lanthanum Chloride Inhibits LPS Mediated Expressions of Pro-Inflammatory Cytokines and Adhesion Molecules in HUVECs: Involvement of NF-κB-Jmjd3 Signaling

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The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans

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A Maximization Technique Occurring in the Statistical Analysis of Probabilistic Functions of Markov Chains

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FIMO: scanning for occurrences of a given motif

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Genome-wide maps of chromatin state in pluripotent and lineage-committed cells

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Stacked Denoising Autoencoders: Learning Useful Representations in a Deep Network with a Local Denoising Criterion

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Potential etiologic and functional implications of genome-wide association loci for human diseases and traits

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mRNA-Seq whole-transcriptome analysis of a single cell

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2015 IEEE Conference on Computer Vision and Pattern Recognition (CVPR)

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The Human Transcription Factors

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Simultaneous epitope and transcriptome measurement in single cells

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ToppGene Suite for gene list enrichment analysis and candidate gene prioritization

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Genome-Wide Mapping of in Vivo Protein-DNA Interactions

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Statistical Inference for Probabilistic Functions of Finite State Markov Chains

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Genomic DNA methylation: the mark and its mediators.

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ChromHMM: automating chromatin-state discovery and characterization

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Relating protein pharmacology by ligand chemistry

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The ENCODE (ENCyclopedia Of DNA Elements) Project

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Single-cell chromatin accessibility reveals principles of regulatory variation

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Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning

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The human cell atlas

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Similarity network fusion for aggregating data types on a genomic scale

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Integrated genomic characterization of pancreatic ductal adenocarcinoma

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Diagnosing the decline in pharmaceutical R&D efficiency

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Explainable machine-learning predictions for the prevention of hypoxaemia during surgery

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PathSim

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Mass-spectrometry-based draft of the human proteome

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The Emergence of lncRNAs in Cancer Biology

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An oestrogen-receptor-α-bound human chromatin interactome

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Understanding Black-box Predictions via Influence Functions

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Modeling polypharmacy side effects with graph convolutional networks

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Multiplatform Analysis of 12 Cancer Types Reveals Molecular Classification within and across Tissues of Origin

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The Human Cell Atlas

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Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing

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Transcriptional enhancers: from properties to genome-wide predictions

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A Proteome-Scale Map of the Human Interactome Network

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A Closer Look at Memorization in Deep Networks

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Higher-order organization of complex networks

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A Bayesian Networks Approach for Predicting Protein-Protein Interactions from Genomic Data

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Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing

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A global genetic interaction network maps a wiring diagram of cellular function

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Intertumoral Heterogeneity within Medulloblastoma Subgroups

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Single-cell sequencing-based technologies will revolutionize whole-organism science

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Integrative omics for health and disease

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HiChIP: efficient and sensitive analysis of protein-directed genome architecture

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Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity

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