A Comprehensive Dataset of Pharmacokinetic Parameters for Recommended Doses of Drugs:
Enabling Drug Repositioning and Pharmacological Analysis
Discover a unique dataset of pharmacokinetic parameters for over 600 drugs, designed to bridge the gap between in vitro efficacy and in vivo dosage. This poster details how this centralized resource, developed in collaboration with NCATS, facilitates drug repositioning and pharmacological analysis by providing crucial connections between PK properties, molecular descriptors, and recommended doses.
Poster: Society of Toxicology 64th Annual Meeting, 2025
Automated Extraction of Biotransformation Data from Metabolic Schemas Using Geometric Criteria and Large Language Models
Discover how we're revolutionizing the digitization of biotransformation data. This poster, a collaboration with Procter & Gamble, details a novel pipeline combining geometric criteria and Large Language Models to automatically extract metabolic pathways from complex schemas, enabling faster, more accurate data analysis for improved safety assessments and predictive modeling.
Poster: Society of Toxicology 64th Annual Meeting, 2025
Harnessing Human Omics Data and ML, Combined with Human Insights, to Revolutionize Gene Target Safety Evaluation
Discover how combining human omics data, machine learning, and expert insights can accelerate and enhance safety assessments. This poster, a collaboration with Johnson & Johnson Innovative Medicine, explores a study comparing a novel ML algorithm (TRAP) with expert-curated literature reviews, revealing the power of integrated approaches in predicting potential adverse event risks.
Poster: Society of Toxicology 64th Annual Meeting, 2025
The Critical Role of Single-Cell Data Science in Advancing Biomedical Research
Dive into the future of biomedical research! In this paper we discuss how The Single-Cell Data Science Consortium (SCDS) is using data to transform disease understanding and drug development.
HDinHD: A Comprehensive Data Portal for Advancing Huntington’s Disease Research
HDinHD is an open-access portal that integrates Huntington Disease experimental data with visualization and analysis tools. The latest release includes CHDI studies characterizing genetic models and power calculations for key models and assays.
Poster: 20th Annual HD Therapeutic Conference, 2025
Exploratory analysis of PENK as an early marker of HD onset and progression
CSF PENK: A Promising Biomarker for Huntington’s Disease? A validated penKid assay confirms significant PENK reduction in HDClarity CSF, correlating with disease progression and clinical scores. Findings support PENK’s potential as an early biomarker for HD onset and progression, complementing existing markers like mHTT and NfL.
Poster: 20th Annual HD Therapeutic Conference, 2025
Identify proliferative and immune-modulatory drivers of small cell lung cancer (SCLC)
This work with Genentech demonstrates how transforming large amounts of disparate multi-omics data into an interoperable resource enable researchers to drive insights.
Poster: American Association for Cancer Research Annual Meeting, 2025
Phenotype Reversal Calculation for ATAC-seq Data
Quantify treatment efficacy at the chromatin level. This novel method adapts phenotype reversal calculations, previously used for RNA-seq and proteomics, to ATAC-seq data. Analyze how treatments impact chromatin accessibility independent of transcriptional changes, enabling a deeper understanding of therapeutic mechanisms and facilitating the development of targeted interventions for diseases like Huntington's.
Poster: 20th Annual HD Therapeutic Conference, 2025
Gene Regulatory Network Analysis of Transcriptomics Data Suggests Common and Diverse Regulators Across HD Model Systems and Perturbations
HD transcriptomics: RegEnrich GRNs reveal key regulators across mouse models, linking disease progression & rescue. Analysis of allelic series & perturbations identifies common/diverse regulators, correlating with human HD data. Reveals potential therapeutic targets & mechanisms.
Poster: 20th Annual HD Therapeutic Conference, 2025
The relationship between CAG repeat expansions, mutant huntingtin protein levels, and a new HTT1a isoform which appears in mutant protein. Their findings provide a deeper understanding of the molecular mechanisms driving Huntington’s disease progression and offer valuable guidance for therapeutic strategies targeting HTT isoforms.
Publication: Brain Communications, Oxford University Press
WEBINAR: Integrating Single-Cell Transcriptomics at Scale for Mechanistic Drug Discovery
BenevolentAI and Rancho Biosciences discuss how single-cell transcriptomics data at scale is helping to revolutionize drug discovery by providing deeper insights into cellular mechanisms.
A comparison of data visualization tools: A case study in health-related research
Publication: Sage Journals
Using Literature-Based Knowledge Extraction to Develop a Disease Ontology for Skin Dysbiosis
Poster: BioTechX EU, October 2024
Large scale proteomics to enable precision medicine for Alzheimers disease
Poster: AAIC Conference, 2024
Identification and Annotation of Publicly Available Single Cell RNA-sequencing Data
Poster: BioTechX USA, September 2024
Spatial Innovation Initiative Delivering Harmonized Analysis-Ready Datasets
Poster: BioTechX USA, September 2024
Accelerating Biomedical Discovery with Public Data: Single-Cell Data Science Consortium Harnesses Collective Expertise to Deliver Even More High Value Harmonized Datasets in Year 3
Poster: BioTechX USA, September 2024
Application of an AI-Powered Terminology Management Solution (TMS) in the Real-World Data (RWD) FAIRification process
Poster: BioTechX USA, September 2024
Enhancing Single-Cell Data Integration and Discovery through Knowledge Graph Extraction from scGPT Embeddings
Poster: BioTechX USA, September 2024
WEBINAR: Explore recent advancements in biopharmaceutical manufacturing with a keen focus on data structures and CMC ontologies that fuel GenAl models, the promise to accelerate insights based off large language (LLM) models.
CREdb: A comprehensive database of Cis-Regulatory Elements and their activity in human cells and tissues
Publication: Epigenetics & Chromatin
Quality Data and Creative Approaches Drive GenAI’s Transformative Journey in Biopharma
Poster: PRISME Forum, May 2024
PERCEPTION predicts patient response and resistance to treatment using Single-Cell transcriptomics of their tumors.
Journal: Nature Cancer, April 2024
A CAG repeat threshold for therapeutics targeting somatic instability in Huntington's disease
Journal: BRAIN 2024
Spatial Innovation Initiative Delivering Harmonized Analysis-Ready Datasets.
Poster: BioIT World Conference & Expo, April 2024
Integrative Approach to Data Harmonization: Empowering Biomedical Research with Rancho Biosciences' Terminology Management Solution (TMS)
Poster: BioIT World Conference & Expo, April 2024
Accelerating Biomedical Discovery with Public Data Single-Cell Data Science Consortium Harnesses Collective Expertise to Deliver Even More High Value Harmonized Datasets in Year 3
Poster: BioIT World Conference & Expo, April 2024
Utilizing NIIMBL and ISA-88 Framework to Create a Proof of Concept Pharmaceutical Manufacturing Ontology
Poster: BioIT World Conference & Expo, April 2024
Streamlined Flow Cytometry Data QC Through Interactive Visualization
Poster: BioIT World Conference & Expo, April 2024
A Digital Platform That Transforms Tox Safety Knowledge Into Insights
Poster: SOT 63rd Annual Meeting, March 2024
Extraction of High Content Toxicity Biomarkers Data from Scientific Literature
Poster: SOT 63rd Annual Meeting, March 2024
HDinHD: An Online Data Portal for Huntington's Disease Research
Poster: 19th Annual Huntington's Disease Therapeutics Conference, February 2024
Unleashing Data’s Full Potential through Integrated Data Marts
Poster: BioIT World Conference & Expo, April 2024
Early intervention to lower mHTT in the adult zQ175 mouse model results in superior efficacy compared to later intervention.
Poster: 19th Annual Huntington's Disease Therapeutics Conference, February 2024
Immune heterogeneity in small-cell lung cancer and vulnerability to immune checkpoint blockade.
Journal: Cancer Cell March 2024
Single-Cell Data Science Consortium Enables Rapid Analysis of High Value Public Datasets
Poster: Pistoia Alliance Conference, 2023
Analysis and classification of transcriptome dysregulation signals over the course of Huntington’s disease progression in mouse model systems
Poster: 19th Annual Huntington's Disease Therapeutics Conference, February 2024
Stress-free cell aggregation by using the CEPT cocktail enhances embryoid body and organoid fitness.
Journal: Biofabrication 2023
Single-Cell Data Science Consortium Enables Rapid Analysis of High Value Public Datasets.
Poster: 2023 BioTechX Conference, October 4 – 6, Basel, Switzerland
Identification and Annotation of Publicly Available Single-Cell RNA-sequencing Data.
Poster: 2023 Festival of Genomics & Biodata, October 4 – 5, Boston, MA
NF Research Tools Central: A disease-specific knowledgebase of experimental tools.
Poster: 2023 NF Conference, June 24–27, Fairmont Scottsdale Princess, Arizona,
Unpacking Unstructured Data: A Pilot Study on Extracting Insights from Neuropathological Reports of Parkinson’s Disease Patients using Large Language Models
Journal: bioRxiv, September 2023
Jovanovic et al., A defined roadmap of radial glia and astrocyte differentiation from human pluripotent stem cells.
Journal: Stem Cell Reports (2023)
Unpacking Unstructured Data: Large Language Models used to extract insights from Neuropathological Reports of Parkinson's Patients
Poster: Bio-IT World Conference in Boston May 16-18 2023
Single-Cell Data Science Consortium Enables Rapid Analysis of High Value Public Datasets
Poster: Bio-IT World Conference in Boston May 16-18 2023
Using Graph Technologies and Artificial Intelligence to Power Terminology Management
Poster: Bio-IT World Conference in Boston May 16-18 2023
Association of nuclear shape in the tumor epithelium with response to atezolizumab in NSCLC.
Publication: ASCO 2023 Annual Meeting https://meetings.asco.org/abstracts-presentations/223107
HDinHD: A Data Portal for Huntington's Disease Research 2023
Poster: CHDI 2023 HD Therapeutics Conference Dubrovnik, Croatia
Using Artificial Intelligence to Enhance Terminology Mapping Workflow from Data Collection to Standardization.
Poster: 2023 BioTechX Conference, October 4 – 6, Basel, Switzerland
Stage-Specific Disease Genes in the Cortex and Striatum
Poster: CHDI HD Therapeutics Conference 2022
Effect of Small Molecule Splicing Modulators on proteome and transcriptome of HD stem cell derived neurons
Poster: CHDI HD Therapeutics Conference 2022
NCATS FRDB: Fast Response DataBase for Drug Repositioning
Poster: BioIT World Conference and Expo 2022
SEQUIN: rapid and reproducible analysis of RNA-seq data in R/Shiny
Journal: bioRxiv 2022
Measuring Disease Phenotype Reversal of HD Related Genomics Signatures in Response to Therapeutic and Genetic Perturbations Using Posterior Probabilities
Poster: CHDI HD Therapeutics Conference 2022
An automated 13.5 hour system for scalable diagnosis and acute management guidance for genetic diseases.
Journal: Nature Communications July 2022
NCATS Inxight Drugs: a comprehensive and curated portal for translational research
Journal: Nucleic Acids Research 2022
PerturbDB: A Database of Huntington's Disease Perturbation Studies https://www.hdinhd.org/
Poster: CHDI HD Therapeutics Conference 2022
HDinHD: A Data Portal for Huntington's Disease Research https://www.hdinhd.org/
Poster: CHDI HD Therapeutics Conference 2022
Enhancing the Fitness of Embryoid Bodies and Organoids by Chemical Cytoprotection
Journal: bioRxiv 2022
Mapping of UK Biobank clinical codes: Challenges and possible solutions
Journal: PLOS ONE 2022
A Workflow of Integrated Resources to Catalyze Network Pharmacology Driven COVID-19 Research
Journal: Journal of Chemical Information and Modeling 2022
SINGLE-CELL RNA-SEQ OF hPSC-DERIVED NEURAL CELL TYPES REVEALS EARLY GLIA-SPECIFIC DIFFERENTIATION TRAJECTORIES
Poster: NCATS 2022
Benefits of global mutant huntingtin lowering diminish over time in a Huntington’s disease mouse model.
Publication: JCI Insight 2022
Predicting patient treatment response and resistance via Single-Cell transcriptomics of their tumors.
Publication: ASCO 2022 Annual Meeting https://meetings.asco.org/abstracts-presentations/207511
Mapping brain gene co expression in daytime transcriptomes unveils diurnal molecular networks and deciphers perturbation gene signatures
Journal: Neuron 2022
The Hidden Pandemic of COVID-19-Induced Organizing Pneumonia
Journal:Pharmaceuticals, December 2022
Circulating microRNA associated with future relapse status in major depressive disorder
Journal: Frontiers in Psychiatry, August 2022
Prediction of standard cell types and functional markers from textual descriptions of flow cytometry gating definitions using machine learning.
Journal: Wiley Clinical Cytometry 2022
Towards a comprehensive view of diagnoses in UK Biobank by data curation and aggregation.
Journal: Bio-IT World Conference & Expo 2021
HDinHD: A Rich Data Portal for Huntington’s Disease Research
Journal: Journal of Huntington’s Disease 2021
Quantitation of CD137 and Nectin-4 expression across multiple tumor types to support indication selection for BT7480, a Bicycle tumor-targeted immune cell agonist™ (Bicycle TICA™)
Poster: SITC Conference 2021
NCATS- Directed Differentiation of Human Pluripotent Stem Cells into Radial Glia and Astrocytes Bypasses Neurogenesis
Journal: BioRxiv 2021
Building towards a computational infrastructure to aid in the interpretation of Bicycle® toxin conjugate response profiles.
Poster: BioIT World 2021
Implementation of the FAIR Data Principles for Exploratory Biomarker Data from Clinical trials.
Journal: Data Intelligence 2021
Molecular-based enrichment strategy for Nectin-4 targeted Bicycle toxin conjugate BT8009
Poster: American Association for Cancer Research April 2021
Housekeeping genes involved in non-malignant breast phenotypes are widely expressed in multiple cancers and provide novel biomarkers of tumor classification
Journal: Brazilian Journal of Medical and Biological Research, February 2021
HD Mouse Striatum RNA and Protein Disease Signatures
Poster : CHDI Annual Conference 2021
Application of MCAT questions as a testing tool and evaluation metric for knowledge graph based reasoning systems.
Journal: Clinical and Translational Science 2021
Lung Fibrosis after COVID-19: Treatment Prospects
Journal: Pharmaceuticals, August 2021
Assessing the use of telemetric devices in preclinical safety studies in non-human primates - data aggregation step
Journal: Bio-IT World Conference & Expo 2021
Multiple cereblon genetic changes are associated with acquired resistance to lenalidomide or pomalidomide in multiple myeloma
Poster : Blood American Society Of Hematology 2021
HD Phenocopy Disease Share Dysregulated Genes with HD
Poster : CHDI Annual Conference 2021
Searching for Genomic Biomarkers for Major
Depressive Disorder in Peripheral Immune Cells
Journal: Biological Psychiatry 2020
An integrative knowledge graph for rare diseases, derived from the Genetic and Rare Diseases Information Center (GARD)
Journal: Journal of Biomedical Semantics 2020
HTT protein nomenclature: The challenge with variable domains
Poster: CHDI Conference 2020
Global Substance Registration System: consistent scientific descriptions for substances related to health
Journal: Nucleic Acids Research 2020
Gene Expression and Genomic Markers Identify a Subpopulation of Poor Prognosis t(4;14) Patients in Newly Diagnosed Multiple Myeloma.
Journal: Blood American Society Of Hematology 2019
Multiple Myeloma DREAM Challenge reveals epigenetic regulator PHF19 as marker of aggressive disease
Journal: Leukemia 2019
Large-Scale Analysis of Relapsed/Refractory Multiple Myeloma Genome Reveals Increased Prevalence of High-Risk Molecular Features and Oncogenic Drivers
Journal: Blood American Society Of Hematology 2019
Genetic and Transcript Changesin Cereblon in IMiD-Treated Myeloma Patients
Journal: Blood American Society Of Hematology 2019
A predictor of pathological complete response to neoadjuvant chemotherapy stratifies triple negative breast cancer patients with high risk of recurrence
Journal: Scientific Reports 2019
NCATS Stitcher: Data integration and guided Curation tool
Meeting: BioIT 2019
The NCATS BioPlanet - an integrated platform for exploring the universe of cellular signaling pathways for toxicology, systems biology, and chemical genomics
Journal: Frontiers in Pharmacology 2019
Aggregation and integration of UKbiobank phenotypes data for downstream analysis
Meeting: BioIT 2019
Expression concordance of 325 novel RNA biomarkers between data generated by NanoString nCounter and Affymetrix GeneChip
Journal: Disease Markers 2019
Major Depressive Disorder Is Associated With Differential Expression of Innate Immune and Neutrophil-Related Gene Networks in Peripheral Blood: A Quantitative Review of Whole-Genome Transcriptional Data From Case-Control Studies
Journal: Biological Psychiatry 2019
A novel panel of 80 RNA biomarkers with differential expression in multiple human solid tumors against healthy blood samples
Journal: International Journal of Molecular Sciences 2019
Data deluge: challenges and solutions in implementing a precision medicine approach to create the TRACK-TBI information Commons
Meeting: BioIT 2019
Identification of novel mutational drivers reveals oncogene dependencies in multiple myeloma
Journal: Blood American Society Of Hematology 2018
A high-risk, Double-Hit, group of newly diagnosed myeloma identified by genomic analysis
Journal: Leukemia 2018
Replicable and coupled changes in innate and adaptive immune gene expression into case-control studies of blood Microarrays in major depressive disorder
Journal: Biological Psychiatry 2017
Crowdsourcing a High-Risk Classifier for Multiple Myeloma Patients
Journal: Blood American Society Of Hematology 2017
Expression analysis of Huntington disease mouse models reveals robust striatum disease signatures.
Journal: bioRxiv.org Preprint 2022