Lista de obras - Charles Tapley Hoyt - Dominio Público Uruguay

A Case Study on the Parametric Occurrence of Multiple Steady States

artículo científico publicado en 2017

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

artículo científico publicado en 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)

artículo científico publicado en 2022

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

artículo científico publicado en 2021

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

artículo científico

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 ⬇️

artículo científico publicado en 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

artículo científico publicado en 2018

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

artículo científico publicado en 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

artículo científico publicado en 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

repositorio de equivalencias y relaciones entre bases de datos biológicas

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

artículo científico publicado en 2020

Democratising Knowledge Representation with BioCypher

artículo científico publicado en 2022

Democratizing knowledge representation with BioCypher

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

artículo científico publicado en 2022

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

artículo científico publicado en 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

artículo científico publicado en 2020

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

artículo científico publicado en 2022

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

preprint

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

artículo científico publicado en 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

artículo científico publicado en 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

artículo científico publicado en 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

artículo científico publicado en 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

artículo científico publicado en 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

artículo científico publicado en 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

artículo científico publicado en 2017

PyBioPAX: biological pathway exchange in Python

artículo científico publicado en 2022

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

artículo científico publicado en 2021

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 ⬇️

artículo científico publicado en 2019

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.

artículo científico publicado en 2019

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

artículo científico publicado en 2014

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

artículo científico publicado en 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

artículo científico publicado en 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

artículo científico publicado en 2019

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

artículo científico publicado en 2019

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

artículo científico publicado en 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

artículo científico publicado en 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 ⬇️

artículo científico publicado en 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 ⬇️

artículo científico publicado en 2024

Lista de obras de Charles Tapley Hoyt

A Case Study on the Parametric Occurrence of Multiple Steady States

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

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

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

A Simple Standard for Sharing Ontological Mappings (SSSOM)

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

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

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

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 ⬇️

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

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

An Open Challenge for Inductive Link Prediction on Knowledge Graphs

An Open-Source Knowledge Graph Ecosystem for the Life Sciences

An open source knowledge graph ecosystem for the life sciences

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

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

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

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

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

Biomappings

Biopragmatics Stack

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

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

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

Challenges of Integrative Disease Modeling in Alzheimer's Disease

ChemicalX: A Deep Learning Library for Drug Pair Scoring

ChemicalX: A Deep Learning Library for Drug Pair Scoring

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

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

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

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

Democratising Knowledge Representation with BioCypher

Democratizing knowledge representation with BioCypher

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

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

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

Experimental design for causal query estimation in partially observed biomolecular networks

Extension of Roles in the ChEBI Ontology

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

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

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

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

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

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

Identifying Drug Repositioning Candidates using Representation Learning on Heterogeneous Networks ⬇️

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

Improving reproducibility and reusability in the Journal of Cheminformatics

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

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

Integration of Structured Biological Data Sources using Biological Expression Language

Knowledge Assembly in Systems and Networks Biology ⬇️

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

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

Maintenance and Enrichment of Disease Maps in Biological Expression Language ⬇️

Mondo: Unifying diseases for the world, by the world

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

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

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

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

PathMe: Merging and exploring mechanistic pathway knowledge

PathMe: merging and exploring mechanistic pathway knowledge

Predicting Missing Links Using PyKEEN ⬇️

Prediction and Curation of Missing Biomedical Identifier Mappings with Biomappings

Prediction and curation of missing biomedical identifier mappings with Biomappings

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

PyBEL

PyBEL: a Computational Framework for Biological Expression Language

PyBioPAX: biological pathway exchange in Python

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

PyOBO

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

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

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

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

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

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

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

SeMRA