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D. Himmelstein and S. Chen, Calculating molecular similarities between DrugBank compounds, 2015.

D. Himmelstein and C. Chung, Computing consensus transcriptional profiles for LINCS L1000 perturbations, 2015.

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D. Himmelstein and M. Gilson, Integrating drug target information from BindingDB, 2015.
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D. Himmelstein, B. Good, P. Khankhanian, and A. Ratner, Brainstorming future directions for Hetionet, 2016.
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D. Himmelstein, B. Good, T. Oprea, A. Mccoy, and A. Lizee, How should we construct a catalog of drug indications? ThinkLab, 2015.

D. Himmelstein, C. Greene, and S. Baranzini, Renaming "Heterogeneous Networks" to a More Concise and Catchy Term, 2015.
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D. Himmelstein, C. Greene, and L. J. Jensen, Positive correlations between knockdown and overexpression profiles from LINCS L1000, 2016.
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D. Himmelstein, C. Greene, V. Malladi, F. Bastian, and S. Baranzini, Gene-Ontology: Initial Zenodo Release, 2015.

D. Himmelstein, C. Greene, V. Malladi, and F. Bastian, Compiling Gene Ontology annotations into an easy-touse format, 2015.
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D. Himmelstein, C. Greene, and A. Pico, Using Entrez Gene as our gene vocabulary, 2015.
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D. Himmelstein, D. Hadley, and A. Schepanovski, Dhimmel/Stargeo V1.0: Differentially Expressed Genes For 48 Diseases From Stargeo, 2016.

D. Himmelstein, D. Hadley, and A. Strokach, Creating a catalog of protein interactions, 2015.

D. Himmelstein, C. Hessler, and P. Khankhanian, Predictions of whether a compound treats a disease, 2016.

D. Himmelstein, L. J. Jensen, and P. Khankhanian, Data nomenclature: naming and abbreviating our network types, 2016.
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D. Himmelstein, L. J. Jensen, M. Smith, K. Fortney, and C. Chung, Integrating resources with disparate licensing into an open network, 2015.
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D. Himmelstein and L. J. Jensen, Gene-Tissue Relationships From The Tissues Database, 2015.

D. Himmelstein and L. J. Jensen, The TISSUES resource for the tissue-specificity of genes, 2015.

D. Himmelstein and L. J. Jensen, Processing the DISEASES resource for disease-gene relationships, 2015.
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D. Himmelstein and L. J. Jensen, One network to rule them all, 2015.
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D. Himmelstein, K. Keough, M. Vysotskiy, J. Kim, B. Norgeot et al., Workshop to analyze LINCS data for the Systems Pharmacology course at UCSF, 2016.
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D. Himmelstein, P. Khankhanian, and C. Hessler, Expert curation of our indication catalog for disease-modifying treatments, 2015.

D. Himmelstein, P. Khankhanian, C. S. Hessler, A. J. Green, and S. Baranzini, PharmacotherapyDB 1.0: the open catalog of drug therapies for disease, 2016.
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D. Himmelstein, P. Khankhanian, and A. Lizee, Transforming DWPCs for hetnet edge prediction, 2016.

D. Himmelstein, P. Khankhanian, A. Pico, L. J. Jensen, and S. Morris, Visualizing the top epilepsy predictions in Cytoscape, 2017.
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D. Himmelstein and R. Khare, Processing LabeledIn to extract indications, 2015.
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D. Himmelstein and T. S. Li, Unifying disease vocabularies, 2015.
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D. Himmelstein, A. Lizee, C. Hessler, L. Brueggeman, S. Chen et al., Rephetio: Repurposing drugs on a hetnet, 2015.

. Thinklab, , 2017.

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. Thinklab, , 2017.

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. Thinklab, , 2017.

D. Himmelstein and A. Lizee, Computing standardized logistic regression coefficients, 2016.
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D. Himmelstein and A. Lizee, Estimating the complexity of hetnet traversal, 2016.

D. Himmelstein and A. Lizee, Measuring user contribution and content creation, 2016.
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D. Himmelstein and A. Pankov, Mining knowledge from MEDLINE articles and their indexed MeSH terms, 2015.
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D. Himmelstein and R. Partha, Selecting informative ERC (evolutionary rate covariation) values between genes, 2015.
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D. Himmelstein and S. C. Protein, Protein (target, carrier, transporter, and enzyme) interactions in DrugBank, 2015.
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D. Himmelstein, M. Sirota, and G. Way, Calculating genomic windows for GWAS lead SNPs, 2015.
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D. Himmelstein, O. Ursu, M. Gilson, P. Khankhanian, and T. Oprea, Incorporating DrugCentral data in our network, 2016.
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D. Himmelstein, Incomplete Interactome licensing, 2015.
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D. Himmelstein, Unifying drug vocabularies, 2015.
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D. Himmelstein, Extracting side effects from SIDER 4, 2015.
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D. Himmelstein, MSigDB licensing, 2015.
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D. Himmelstein, Disease Ontology feature requests, 2015.
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D. Himmelstein, Processing DisGeNET for disease-gene relationships, 2017.
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D. Himmelstein, Functional disease annotations for genes using DOAF, 2015.
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D. Himmelstein, Extracting disease-gene associations from the GWAS Catalog, 2015.
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D. Himmelstein, Disease similarity from MEDLINE topic co-occurrence, 2015.
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D. Himmelstein, Extracting indications from the ehrlink resource, 2015.
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D. Himmelstein, LINCS L1000 licensing. ThinkLab, 2015.
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D. Himmelstein, Permuting hetnets and implementing randomized edge swaps in cypher, 2015.
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D. Himmelstein, Using the neo4j graph database for hetnets, 2015.

D. Himmelstein, Assessing the informativeness of features, 2015.

D. Himmelstein, Announcing PharmacotherapyDB: the Open Catalog of Drug Therapies for Disease, 2016.

D. Himmelstein, Assessing the effectiveness of our hetnet permutations, 2016.

D. Himmelstein, Assessing the imputation quality of gene expression in LINCS L1000, 2016.

D. Himmelstein, Cataloging drug-disease therapies in the ClinicalTrials.gov database, 2016.

D. Himmelstein, Decomposing predictions into their network support, 2016.
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D. Himmelstein, Decomposing the DWPC to assess intermediate node or edge contributions, 2016.
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D. Himmelstein, dhimmel/hetio v0.2.0: Neo4j export, Cypher query creation, hetnet stats, and other enhancements, 2016.

D. Himmelstein, Edge dropout contamination in hetnet edge prediction, 2016.
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D. Himmelstein, Hosting Hetionet in the cloud: creating a public Neo4j instance, 2016.

D. Himmelstein, Exploring the power of Hetionet: a Cypher query depot, 2016.

D. Himmelstein, Our hetnet edge prediction methodology: the modeling framework for Project Rephetio, 2016.

D. Himmelstein, Dhimmel/Hetionet V1.0.0: Hetionet V1.0 In Json, Tsv, And Neo4J Formats, 2017.
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D. Himmelstein, Dhimmel/Learn V1.0: The Machine Learning Repository For Project Rephetio, 2017.

D. Himmelstein, Why we predicted ictogenic tricyclic compounds treat epilepsy? ThinkLab, 2017.
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D. S. Himmelstein and S. E. Baranzini, Heterogeneous Network Edge Prediction: A Data Integration Approach to Prioritize Disease-Associated Genes, PLOS Computational Biology, vol.11, p.26158728, 2015.
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D. S. Himmelstein and S. E. Baranzini, Dhimmel/Gwas-Catalog V1.0: Extracting Gene-Disease Associations From The Gwas Catalog, 2016.

D. S. Himmelstein and S. E. Baranzini, Dhimmel/Ppi V1.0: Compiling A Human Protein Interaction Catalog, 2016.

D. S. Himmelstein and L. J. Jensen, Dhimmel/Diseases V1.0: Processing The Diseases Database Of Gene-Disease Associations, 2016.

D. S. Himmelstein, P. Khankhanian, C. S. Hessler, A. J. Green, and S. E. Baranzini, Dhimmel/Indications V1.0. Pharmacotherapydb: The Open Catalog Of Drug Therapies For Disease, 2016.

D. S. Himmelstein, A. Lizee, C. Hessler, L. Brueggeman, S. L. Chen et al., Systematic integration of biomedical knowledge prioritizes drugs for repurposing, 2016.
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D. S. Himmelstein and J. Piñ, Dhimmel/Disgenet V1.0: Processing The Disgenet Database Of Gene-Disease Associations, 2016.

D. S. Himmelstein and A. R. Pico, Dhimmel/Pathways V2.0: Compiling Human Pathway Gene Sets, 2016.

D. S. Himmelstein, User-Friendly Extensions To The Disease Ontology V1.0, 2016.

D. S. Himmelstein, User-Friendly Extensions To Mesh V1.0, 2016.

D. S. Himmelstein, User-Friendly Extensions Of The Drugbank Database V1.0, 2016.

D. S. Himmelstein, Extracting Tidy And User-Friendly Tsvs From Sider 4.1, 2016.
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D. S. Himmelstein, Processed Entrez Gene Datasets For Humans V1, 2016.

D. S. Himmelstein, User-Friendly Anatomical Structures Data From The Uberon Ontology V1.0, 2016.

D. S. Himmelstein, Dhimmel/Doaf V1.0: Processing The Doaf Database Of Gene-Disease Associations, 2016.

D. S. Himmelstein, Dhimmel/Medline V1.0: Disease, Symptom, And Anatomy Cooccurence In Medline, 2016.

D. S. Himmelstein, Dhimmel/Erc V1.0: Processing Human Evolutionary Rate Covaration Data, 2016.

R. A. Hodos, B. A. Kidd, K. Shameer, B. P. Readhead, and J. T. Dudley, silico methods for drug repurposing and pharmacology, vol.8, p.27080087, 2016.
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