Rancho Publications

Immune heterogeneity in small-cell lung cancer and vulnerability to immune checkpoint blockade.

Journal: Cancer Cell March 2024

A CAG repeat threshold for therapeutics targeting somatic instability in Huntington's disease.

Journal: Brain March 2024

Single Cell Data Science Consortium Enables Rapid Analysis of High Value Public Datasets

Poster: Pistoia Alliance Conference, 2023

Stress-free cell aggregation by using the CEPT cocktail enhances embryoid body and organoid fitness.

Journal: Biofabrication 2023

Using Artificial Intelligence to Enhance Terminology Mapping Workflow from Data Collection to Standardization.

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

Single Cell Data Science Consortium Enables Rapid Analysis of High Value Public Datasets.

Poster: 2023 BioTechX Conference, October 4 – 6, Basel, Switzerland

NF Research Tools Central: A disease-specific knowledgebase of experimental tools.

Poster: 2023 NF Conference, June 24–27, Fairmont Scottsdale Princess, Arizona,

Jovanovic et al., A defined roadmap of radial glia and astrocyte differentiation from human pluripotent stem cells.

Journal: Stem Cell Reports (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

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

Using Graph Technologies and Artificial Intelligence to Power Terminology Management

Poster: Bio-IT World Conference in Boston May 16-18 2023

HDinHD: A Data Portal for Huntington's Disease Research 2023

Poster: CHDI 2023 HD Therapeutics Conference Dubrovnik, Croatia

Prediction of standard cell types and functional markers from textual descriptions of flow cytometry gating definitions using machine learning.

Journal: Wiley Clinical Cytometry 2022

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

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

Stage-Specific Disease Genes in the Cortex and Striatum

Poster: CHDI HD Therapeutics Conference 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

SEQUIN: rapid and reproducible analysis of RNA-seq data in R/Shiny

Journal: bioRxiv 2022

PerturbDB: A Database of Huntington's Disease Perturbation Studies https://www.hdinhd.org/

Poster: CHDI HD Therapeutics Conference 2022

NCATS Inxight Drugs: a comprehensive and curated portal for translational research

Journal: Nucleic Acids Research 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

Expression analysis of Huntington disease mouse models reveals robust striatum disease signatures.

Journal: bioRxiv.org Preprint 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

An automated 13.5 hour system for scalable diagnosis and acute management guidance for genetic diseases.

Journal:  Nature Communications July 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

An integrative knowledge graph for rare diseases, derived from the Genetic and Rare Diseases Information Center (GARD)

Journal: Journal of Biomedical Semantics 2020

Searching for Genomic Biomarkers for Major
Depressive Disorder in Peripheral Immune Cells

Journal: Biological Psychiatry 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

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

NCATS Stitcher: Data integration and guided Curation tool

Meeting: BioIT 2019

Data deluge: challenges and solutions in implementing a precision medicine approach to create the TRACK-TBI information Commons

Meeting: BioIT 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

A predictor of pathological complete response to neoadjuvant chemotherapy stratifies triple negative breast cancer patients with high risk of recurrence

Journal: Scientific Reports 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

Crowdsourcing a High-Risk Classifier for Multiple Myeloma Patients

Journal: Blood American Society Of Hematology 2017

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