Assembly and reasoning over semantic mappings at scale for biomedical data integration
Summary
other
Work
Northeastern University
US
→
Harvard Medical School
US
Publications
Assembly and reasoning over semantic mappings at scale for biomedical data integration
Summary
preprint
Nociceptor-immune interactomes reveal insult-specific immune signatures of pain
Published by
Nature Immunology
Summary
journal-article
The O3 guidelines: open data, open code, and open infrastructure for sustainable curated scientific resources
Published by
Scientific Data
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journal-article
Beyond protein lists: AI-assisted interpretation of proteomic investigations in the context of evolving scientific knowledge
Published by
Nature Methods
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journal-article
Automated assembly of molecular mechanisms at scale from text mining and curated databases
Published by
Molecular Systems Biology
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journal-article
Nociceptor neuroimmune interactomes reveal cell type- and injury-specific inflammatory pain pathways
Summary
preprint
Prediction and curation of missing biomedical identifier mappings with Biomappings
Published by
Bioinformatics
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journal-article
STonKGs: a sophisticated transformer trained on biomedical text and knowledge graphs
Published by
Bioinformatics
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journal-article
Gilda: biomedical entity text normalization with machine-learned disambiguation as a service
Published by
Bioinformatics Advances
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journal-article
Prediction and Curation of Missing Biomedical Identifier Mappings with Biomappings
Summary
preprint
NDEx IQuery: a multi-method network gene set analysis leveraging the Network Data Exchange
Summary
preprint
Automated assembly of molecular mechanisms at scale from text mining and curated databases
Summary
preprint
Integrating multi-omics data reveals function and therapeutic potential of deubiquitinating enzymes
Published by
eLife
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journal-article
PyBioPAX: biological pathway exchange in Python
Published by
Journal of Open Source Software
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journal-article
Automated Network Assembly of Mechanistic Literature for Informed Evidence Identification to Support Cancer Risk Assessment
Published by
Environmental Health Perspectives
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journal-article
Gilda: biomedical entity text normalization with machine-learned disambiguation as a service
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other
Integrating multi-omics data reveals function and therapeutic potential of deubiquitinating enzymes
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From knowledge to models: Automated modeling in systems and synthetic biology
Published by
Current Opinion in Systems Biology
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journal-article
STonKGs: A Sophisticated Transformer Trained on Biomedical Text and Knowledge Graphs
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other
Robustness and parameter geography in post-translational modification systems
Published by
PLOS Computational Biology
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journal-article
Adeft: Acromine-based Disambiguation of Entities from Text with applications to the biomedical literature
Published by
Journal of Open Source Software
Summary
journal-article
A resource for exploring the understudied human kinome for research and therapeutic opportunities
Summary
preprint
Assembling a corpus of phosphoproteomic annotations using ProtMapper to normalize site information from databases and text mining
Summary
preprint
Re-curation and Rational Enrichment of Knowledge Graphs in Biological Expression Language
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Robustness and parameter geography in post-translational modification systems
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Re-curation and rational enrichment of knowledge graphs in Biological Expression Language
Published by
Database
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journal-article
FamPlex: a resource for entity recognition and relationship resolution of human protein families and complexes in biomedical text mining
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other
From word models to executable models of signaling networks using automated assembly
Published by
Molecular Systems Biology
Summary
journal-article
From word models to executable models of signaling networks using automated assembly
Summary
preprint
Simulation-guided parameter synthesis for chance-constrained optimization of control systems
Published by
2015 IEEE/ACM International Conference on Computer-Aided Design (ICCAD)
Summary
conference-paper
Hypothesis testing for Markov chain Monte Carlo
Published by
Stat Comput
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journal-article
Approximate Probabilistic Verification of Hybrid Systems
Published by
Hybrid Systems Biology
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Parallelized Parameter Estimation of Biological Pathway Models
Published by
Hybrid Systems Biology
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other
OpenComet: An automated tool for comet assay image analysis
Published by
Redox Biology
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journal-article
Statistical Model Checking Based Calibration and Analysis of Bio-pathway Models
Published by
Computational Methods in Systems Biology
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other