Search filters

List of works by Charles Tapley Hoyt

A Case Study on the Parametric Occurrence of Multiple Steady States

scientific article published in 2017

A Computational Approach for Mapping Heme Biology in the Context of Hemolytic Disorders

scientific article published on 06 March 2020

A Review of Biomedical Datasets Relating to Drug Discovery: A Knowledge Graph Perspective

preprint published on 02 April 2021

A Simple Standard for Ontological Mappings 2022: Updates of data model and outlook ⬇️

Conference paper

A Simple Standard for Sharing Ontological Mappings (SSSOM)

preprint published on 15 December 2021

A Systems Biology Approach for Hypothesizing the Effect of Genetic Variants on Neuroimaging Features in Alzheimer’s Disease

scientific article

A Unified Framework for Rank-based Evaluation Metrics for Link Prediction in Knowledge Graphs

preprint published on 16 March 2022

A computational approach for mapping heme biology in the context of hemolytic disorders

scholarly article

A review of biomedical datasets relating to drug discovery: a knowledge graph perspective

A simple standard for ontological mappings 2023: updates on data model, collaborations and tooling ⬇️

scientific article published on 14 December 2023

A systematic approach for identifying shared mechanisms in epilepsy and its comorbidities

preprint

A systematic approach for identifying shared mechanisms in epilepsy and its comorbidities

scientific article

An Open Challenge for Inductive Link Prediction on Knowledge Graphs

preprint published on 04 March 2022

An Open-Source Knowledge Graph Ecosystem for the Life Sciences

preprint published on 13 July 2023

An open source knowledge graph ecosystem for the life sciences

scientific article published in 2024

BEL Commons: an environment for exploration and analysis of networks encoded in Biological Expression Language

preprint

BEL Commons: an environment for exploration and analysis of networks encoded in Biological Expression Language

scholarly article

BEL2ABM: agent-based simulation of static models in Biological Expression Language

scientific article published in July 2018

BioKEEN: A library for learning and evaluating biological knowledge graph embeddings

preprint

BioKEEN: a library for learning and evaluating biological knowledge graph embeddings

scholarly article

Biomappings

repository of community curated and predicted equivalences and related mappings between named biological entities that are not available from primary sources.

Biopragmatics Stack

A collection of interlinked software packages that provide the infrastructure for biomedical semantics and pragmatics

Bringing Light Into the Dark: A Large-scale Evaluation of Knowledge Graph Embedding Models Under a Unified Framework

preprint published on 25 June 2020 that uses PyKEEN for large-scale reproduction and benchmarking

CLEP: A Hybrid Data- and Knowledge- Driven Framework for Generating Patient Representations

preprint published on 04 November 2020

CLEP: a hybrid data- and knowledge-driven framework for generating patient representations

scientific article published in 2021

Challenges of Integrative Disease Modeling in Alzheimer's Disease

scholarly article

ChemicalX: A Deep Learning Library for Drug Pair Scoring

preprint published on 11 February 2022

ChemicalX: A Deep Learning Library for Drug Pair Scoring

ComPath: An ecosystem for exploring, analyzing, and curating mappings across pathway databases

preprint

ComPath: an ecosystem for exploring, analyzing, and curating mappings across pathway databases

scholarly article

Computational Tools and Data Integration to Accelerate Vaccine Development: Challenges, Opportunities, and Future Directions

Preprint

Corrigendum: The Impact of Pathway Database Choice on Statistical Enrichment Analysis and Predictive Modeling

scientific article published on 29 April 2020

Democratising Knowledge Representation with BioCypher

scientific article published on 27 December 2022

Democratizing knowledge representation with BioCypher

Do-calculus enables estimation of causal effects in partially observed biomolecular pathways

scientific article published on 14 April 2022

Eliater: A Python package for estimating outcomes of perturbations in biomolecular networks

scientific article published on 26 August 2024

Erratum: Publisher Correction: ComPath: an ecosystem for exploring, analyzing, and curating mappings across pathway databases

scientific article published on 07 March 2019

Experimental design for causal query estimation in partially observed biomolecular networks

preprint published on 30 November 2022

Extension of Roles in the ChEBI Ontology

scholarly article

Generation and Applications of Knowledge Graphs in Systems and Networks Biology ⬇️

PhD thesis

Gilda: biomedical entity text normalization with machine-learned disambiguation as a service

preprint published on 11 September 2021

Gilda: biomedical entity text normalization with machine-learned disambiguation as a service

scientific article published on 07 May 2022

GuiltyTargets: Prioritization of Novel Therapeutic Targets with Deep Network Representation Learning

preprint

GuiltyTargets: Prioritization of Novel Therapeutic Targets with Deep Network Representation Learning

scientific article published on 19 June 2020

Identifying Drug Repositioning Candidates using Comparative Mechanism Enrichment in Neurodegenerative Diseases ⬇️

conference poster

Identifying Drug Repositioning Candidates using Representation Learning on Heterogeneous Networks ⬇️

conference poster

Identifying the parametric occurrence of multiple steady states for some biological networks

Improving reproducibility and reusability in the Journal of Cheminformatics

scientific article published on 30 June 2023

Integrating multi-omics data reveals function and therapeutic potential of deubiquitinating enzymes

preprint published on 09 August 2021

Integrating multi-omics data reveals function and therapeutic potential of deubiquitinating enzymes

scientific article published on 23 June 2022

Integration of Structured Biological Data Sources using Biological Expression Language

BioRxiv scholarly article describing Bio2BEL

Knowledge Assembly in Systems and Networks Biology ⬇️

conference poster

Leveraging Structured Biological Knowledge for Counterfactual Inference: A Case Study of Viral Pathogenesis

scientific article published on 26 January 2021

Leveraging Structured Biological Knowledge for Counterfactual Inference: a Case Study of Viral Pathogenesis ⬇️

preprint published on 14 January 2021

Maintenance and Enrichment of Disease Maps in Biological Expression Language ⬇️

conference poster

Mondo: Unifying diseases for the world, by the world

Ontology Development Kit: a toolkit for building, maintaining, and standardising biomedical ontologies

preprint published on 06 July 2022

Optimal adjustment sets for causal query estimation in partially observed biomolecular networks

scientific article published in 2023

PS4DR: a multimodal workflow for identification and prioritization of drugs based on pathway signatures

preprint

PS4DR: a multimodal workflow for identification and prioritization of drugs based on pathway signatures

scientific article published on 05 June 2020

PathMe: Merging and exploring mechanistic pathway knowledge

PathMe: merging and exploring mechanistic pathway knowledge

scholarly article

Predicting Missing Links Using PyKEEN ⬇️

conference paper

Prediction and Curation of Missing Biomedical Identifier Mappings with Biomappings

preprint published on 02 December 2022

Prediction and curation of missing biomedical identifier mappings with Biomappings

scientific article published in 2023

ProtSTonKGs: A Sophisticated Transformer Trained on Protein Sequences, Text, and Knowledge Graphs ⬇️

PyBEL

Python library for Biological Expression Language

PyBEL: a Computational Framework for Biological Expression Language

scientific article published on 18 October 2017

PyBioPAX: biological pathway exchange in Python

scientific article published on 11 March 2022

PyKEEN 1.0: A Python Library for Training and Evaluating Knowledge Graph Embeddings ⬇️

scientific article

PyOBO

Tool for unified, ontology-like access to ontologies and databases

Quantifying mechanisms in neurodegenerative diseases (NDDs) using candidate mechanism perturbation amplitude (CMPA) algorithm

scientific article published on 11 October 2019

RatVec: A General Approach for Low-dimensional Distributed Vector Representations via Domain-specific Rational Kernels ⬇️

Conference paper

Re-curation and Rational Enrichment of Knowledge Graphs in Biological Expression Language

BioRxiv article

Re-curation and rational enrichment of knowledge graphs in Biological Expression Language.

scientific article

Repurposing human PDE4 inhibitors for neglected tropical diseases: design, synthesis and evaluation of cilomilast analogues as Trypanosoma brucei PDEB1 inhibitors

scientific article

STonKGs: A Sophisticated Transformer Trained on Biomedical Text and Knowledge Graphs

preprint published on 18 August 2021

STonKGs: A Sophisticated Transformer Trained on Biomedical Text and Knowledge Graphs

scientific article published on 5 January 2022

SeMRA

Python software package

The Bioregistry

An open source, community curated registry, meta-registry, and compact identifier resolver.

The Human Brain Pharmacome: An Overview ⬇️

conference poster

The Human Phenotype Ontology in 2024: phenotypes around the world

scientific article published in 2023

The Impact of Pathway Database Choice on Statistical Enrichment Analysis and Predictive Modeling

preprint

The Impact of Pathway Database Choice on Statistical Enrichment Analysis and Predictive Modeling

scientific article published on 22 November 2019

The KEEN Universe

scientific article published in October 2019

The KEEN Universe - An Ecosystem for Knowledge Graph Embeddings with a Focus on Reproducibility and Transferability

a scientific article published at ISWC 2019

The Minimum Information about a Molecular Interaction Causal Statement (MI2CAST)

scientific article published on 30 June 2020

The O3 guidelines: open data, open code, and open infrastructure for sustainable curated scientific resources

preprint published November 16th, 2023

The O3 guidelines: open data, open code, and open infrastructure for sustainable curated scientific resources

scientific article published on 29 May 2024

The role of metadata in reproducible computational research

preprint published on 16 June 2020

Towards a mechanism-based taxonomy of Alzheimer’s and Parkinson’s disease ⬇️

conference poster

Understanding the Performance of Knowledge Graph Embeddings in Drug Discovery

preprint published on 08 June 2021

Unifying the Identification of Biomedical Entities with the Bioregistry ⬇️

preprint published on 10 July 2022

Unifying the identification of biomedical entities with the Bioregistry ⬇️

scientific article published on 19 November 2022

Wavelet-Packet Powered Deepfake Image Detection

preprint published on 18 June 2021

curies

Python package for conversion between URIs and compact URIs (CURIEs)

ptwt - The PyTorch Wavelet Toolbox ⬇️

Scholarly article

Paulina is supported by:

About Paulina

Help