Deanne M. Taylor

ddkg.skill: A Compositional Agent Skill for Translating Biomedical and Bioinformatics Questions into Cypher for the Data Distillery Knowledge Graph

ddkg.skill translates biomedical questions into Cypher queries for the DDKG, improving accuracy through structured references and validation.

MOSAIC: Learning Graph Node Embeddings from Spectrally Isolated Dominant Subspaces of Accumulated Diffusion Operators

MOSAIC learns graph node embeddings by analyzing dominant spectral components of diffusion operators, outperforming existing methods in biomedical graph tasks.

BiomarkerKB: An Integrated Knowledgebase Supporting Biomarker-Centric Exploration of Biomedical Data

BiomarkerKB integrates and standardizes biomarker data from multiple sources to enable structured exploration and discovery of biomarker-disease relationships.

BIFO: A Biological Information Flow Ontology for Directed Propagation in Heterogeneous Biomedical Knowledge Graphs

The paper introduces BIFO, an ontology that specifies biologically admissible directed transformations in biomedical knowledge graphs to enable meaningful signal propagation.

An integrated single cell and spatial omics atlas of human prenatal development

Human Developmental Cell Atlas integrates ~4.6 million cells/nuclei from 4-22 post-conception weeks into 454 refined cell types and maps 114 spatial niches across 6PCW whole-embryo sections.

The Common Fund Data Ecosystem (CFDE)

The paper describes the Common Fund Data Ecosystem (CFDE), which integrates NIH Common Fund data resources to enable discovery, analysis, and collaboration across heterogeneous datasets.

Rapid cyclic stretching induces synthetic, proinflammatory phenotypes in cultured human intestinal smooth muscle, with the potential to alter signaling to adjacent bowel cells

The Data Distillery: A Graph Framework for Semantic Integration and Querying of Biomedical Data

The paper introduces a knowledge graph framework for integrating and querying biomedical data across domains, demonstrating its utility in eight use cases.

ndufs2-/- zebrafish have impaired survival, neuromuscular activity, morphology, and one-carbon metabolism treatable with folic acid

This study generates ndufs2-/- zebrafish with CI deficiency, showing metabolic and neuromuscular defects treatable by folic acid.

Leukemia confers a durable imprint on healthy hematopoietic stem and progenitor cells

This study shows that healthy hematopoietic stem and progenitor cells (HSPCs) retain long-term transcriptomic and epigenetic changes after exposure to acute myeloid leukemia (AML) blasts, leading to enhanced inflammatory and metabolic responses upon secondary challenge.

The Open Pediatric Cancer Project

The paper introduces OpenPedCan, a harmonized multi-omic dataset of pediatric cancer patients, providing integrated genomic, transcriptomic, and proteomic data for research and clinical applications.

Playbook Workflow Builder: Interactive Construction of Bioinformatics Workflows from a Network of Microservices

The paper introduces a web-based platform for building bioinformatics workflows using APIs, enabling hypothesis generation across multiple data sources.

Positioning Genomic Features in Biomedical Knowledge Graphs using the Homo sapiens Chromosomal Location Ontology for GRCh38 (HSCLO38)

The paper develops HSCLO38, a framework for connecting genomic features in a knowledge graph, and evaluates its performance with large-scale genomic data.

The glucocorticoid response element near the sphingosine-1-phopshate receptor 3 gene mitigates inflammatory processes and maladaptive behavior in females and stressed males

This study shows that GR-induced S1PR3 expression reduces social anxiety and stress-induced inflammation by affecting neural coherence in rats.

Petagraph: A large-scale unifying knowledge graph framework for integrating biomolecular and biomedical data

Petagraph integrates biomolecular data into a unified knowledge graph using UMLS ontologies to enable efficient multi-omics analysis across multiple datasets.

ReproTox-KG: Toxicology Knowledge Graph for Structural Birth Defects

The paper constructs a reproductive toxicity knowledge graph (ReproTox-KG) to link birth defects, drugs, and genes, identifying potential molecular mechanisms for drug-induced birth defects.

The interplay between lncRNAs, RNA-binding proteins and viral genome during SARS-CoV-2 infection reveals strong connections with regulatory events involved in RNA metabolism and immune response.

The paper identifies a lncRNA signature associated with SARS-CoV-2 infection through transcriptomic analysis and functional correlation studies.

Targeted Down Regulation Of Core Mitochondrial Genes During SARS-CoV-2 Infection

This study investigates how SARS-CoV-2 infection affects mitochondrial gene expression in different tissues and disease stages, finding targeted inhibition in some organs and upregulation in others.

Betacoronavirus-specific alternate splicing

The paper investigates differential alternative splicing in cells infected by betacoronaviruses and finds characteristic patterns linked to viral load and gene function.

Fusion-oncogenes are associated with increased metastatic capacity and persistent disease in pediatric thyroid cancers

This study shows that genetic subtypes of pediatric thyroid cancer, particularly RET/NTRK fusions, are linked to worse clinical outcomes compared to RAS- or BRAF-mutant subtypes.

The Great Deceiver: miR-2392's Hidden Role in Driving SARS-CoV-2 Infection

The paper identifies miR-2392 as a miRNA involved in SARS-CoV-2 infection, showing its role in inflammation, glycolysis, and hypoxia, and develops a miRNA-based therapeutic targeting it.

NASA GeneLab RNA-Seq Consensus Pipeline: Standardized Processing of Short-Read RNA-Seq Data

The paper describes a standardized RNA-Seq pipeline for spaceflight data, enabling reproducible analysis of gene expression changes in astronauts and organisms exposed to spaceflight.

Scedar: a scalable Python package for single-cell RNA-seq exploratory data analysis

Scedar is a Python package for scRNA-seq exploratory analysis, offering visualization, imputation, rare profile detection, and clustering on large datasets efficiently and without distribution assumptions.

Modeling metabolic variation with single-cell expression data

The paper develops a method to simulate cellular metabolism using scRNA-seq data and validates it with NAD+ biosynthesis flux measurements in mouse tissues.

The role of SRSF3 splicing factor in generating circular RNAs

The paper investigates the role of SRSF3 in circRNA biogenesis and identifies its impact on circRNA production and potential involvement in hematologic malignancies.

RNA-Seq 2G: Online Analysis Of Differential Gene Expression With Comprehensive Options Of Statistical Methods

RNA-Seq 2G provides a web portal with 25 differential expression methods for RNA-seq data, showing that data distribution assumptions significantly affect results.

GSA-Genie: a web application for gene set analysis

GSA-Genie provides a web tool for gene set analysis with over 2.3 million gene sets and 16 statistical methods.