Daniel J. B. Clarke

发表

Connecting omics signatures of diseases, drugs, and mechanisms of actions with iLINCS

Vasileios Stathias, Amar Koleti, Mario Medvedovic, 2019, bioRxiv.

An open-source framework for the interactive exploration of Big Data: Applications in understanding health care

A. Ravishankar Rao, Daniel J. B. Clarke, A. Rao, 2017, 2017 International Joint Conference on Neural Networks (IJCNN).

FAIRshake: toolkit to evaluate the findability, accessibility, interoperability, and reusability of research digital resources

Michel Dumontier, Denis Torre, Avi Ma'ayan, 2019, bioRxiv.

Perspectives on emerging directions in using IoT devices in blockchain applications

Daniel J. B. Clarke, A. Ravishankar Rao, A. Rao, 2020, Internet Things.

eXpression2Kinases (X2K) Web: linking expression signatures to upstream cell signaling networks

Denis Torre, Avi Ma'ayan, Zichen Wang, 2018, Nucleic Acids Res..

Making Common Fund data more findable: catalyzing a data ecosystem

Daniel J. B. Clarke, Robert E. Schuler, K. Chard, 2021, bioRxiv.

PrismExp: Predicting Human Gene Function by Partitioning Massive RNA-seq Co-expression Data

Daniel J. B. Clarke, Avi Ma’ayan, Alexander Lachmann, 2021, bioRxiv.

Modulating the transcriptional landscape of SARS-CoV-2 as an effective method for developing antiviral compounds

Daniel J. B. Clarke, Megan L. Wojciechowicz, Avi Ma’ayan, 2020, bioRxiv.

The COVID-19 Gene and Drug Set Library

Kathleen M. Jagodnik, Daniel J. B. Clarke, Maxim V. Kuleshov, 2020, Research square.

Connecting omics signatures and revealing biological mechanisms with iLINCS

Nicholas A. Clark, Daniel J. B. Clarke, D. Vidovic, 2022, Nature Communications.

Transforming L1000 profiles to RNA-seq-like profiles with deep learning

Daniel J. B. Clarke, Megan L. Wojciechowicz, Minji Jeon, 2022, BMC Bioinformatics.

Getting Started with LINCS Datasets and Tools

Kathleen M. Jagodnik, Daniel J. B. Clarke, Sherry L. Jenkins, 2022, Current protocols.

A multi-omic analysis of MCF10A cells provides a resource for integrative assessment of ligand-mediated molecular and phenotypic responses

Mark A. Dane, Laura M. Heiser, Daniel J. B. Clarke, 2022, Communications Biology.

ReproTox-KG: Toxicology Knowledge Graph for Structural Birth Defects

Tudor I. Oprea, Jeremy J. Yang, Daniel J. B. Clarke, 2022, bioRxiv.

Predicting Lyme Disease From Patients' Peripheral Blood Mononuclear Cells Profiled With RNA-Sequencing

Daniel J. B. Clarke, Sherry L. Jenkins, Alison W. Rebman, 2021, Frontiers in Immunology.

Gene Set Knowledge Discovery with Enrichr

Kathleen M. Jagodnik, Daniel J. B. Clarke, Sherry L. Jenkins, 2021, Current protocols.

Drugmonizome and Drugmonizome-ML: integration and abstraction of small molecule attributes for drug enrichment analysis and machine learning

Kathleen M. Jagodnik, Daniel J. B. Clarke, Maxim V. Kuleshov, 2021, Database J. Biol. Databases Curation.

Interoperable RNA-Seq analysis in the cloud.

Denis Torre, Avi Ma'ayan, Daniel J B Clarke, 2020, Biochimica et biophysica acta. Gene regulatory mechanisms.

LINCS Data Portal 2.0: next generation access point for perturbation-response signatures

Vasileios Stathias, Amar Koleti, Raymond Terryn, 2019, Nucleic Acids Res..

DrugShot: querying biomedical search terms to retrieve prioritized lists of small molecules

Kathleen M. Jagodnik, Daniel J. B. Clarke, Alexander Lachmann, 2022, BMC Bioinform..

Getting Started with the IDG KMC Datasets and Tools

Tudor I. Oprea, Keith J. Kelleher, Jeremy J. Yang, 2022, Current protocols.

Appyters: Turning Jupyter Notebooks into data-driven web apps

Avi Ma'ayan, Kathleen M. Jagodnik, Minji Jeon, 2021, Patterns.

The COVID-19 Drug and Gene Set Library

Kathleen M. Jagodnik, Avi Ma’ayan, Daniel J. Stein, 2020, Patterns.

Gene set predictor for post-treatment Lyme disease

Daniel J. B. Clarke, Alison W. Rebman, Avi Ma’ayan, 2022, Cell reports. Medicine.

lncHUB2: aggregated and inferred knowledge about human and mouse lncRNAs

Daniel J. B. Clarke, Maxim V. Kuleshov, Megan L. Wojciechowicz, 2023, Database J. Biol. Databases Curation.

PrismEXP: gene annotation prediction from stratified gene-gene co-expression matrices

Daniel J. B. Clarke, Alexander Lachmann, Minji Jeon, 2023, PeerJ.

SigCom LINCS: data and metadata search engine for a million gene expression signatures

Kathleen M. Jagodnik, Daniel J. B. Clarke, Maxim V. Kuleshov, 2022, Nucleic Acids Res..

GeneRanger and TargetRanger: processed gene and protein expression levels across cells and tissues for target discovery

Daniel J. B. Clarke, Avi Ma’ayan, E. Deng, 2023, Nucleic Acids Res..

FAIRshake: Toolkit to Evaluate the FAIRness of Research Digital Resources.

Daniel J Cooper, Kathleen M Jagodnik, Denis Torre, 2019, Cell systems.

Enrichr-KG: bridging enrichment analysis across multiple libraries

Daniel J. B. Clarke, Avi Ma’ayan, J. E. Evangelista, 2023, Nucleic Acids Res..

Computational screen to identify potential targets for immunotherapeutic identification and removal of senescence cells

Daniel J. B. Clarke, Avi Ma’ayan, E. Deng, 2023, Aging cell.

Toxicology knowledge graph for structural birth defects

Tudor I. Oprea, Jeremy J. Yang, Daniel J. B. Clarke, 2023, Communications medicine.

Rummagene: Mining Gene Sets from Supporting Materials of PMC Publications

Daniel J. B. Clarke, Avi Ma’ayan, J. E. Evangelista, 2023, bioRxiv.

Pan-cancer proteogenomics characterization of tumor immunity

Jeffrey R. Whiteaker, Matthew A. Wyczalkowski, Ratna R. Thangudu, 2024, Cell.

RummaGEO: Automatic Mining of Human and Mouse Gene Sets from GEO

Daniel J. B. Clarke, Avi Ma’ayan, Giacomo B. Marino, 2024, bioRxiv.

EnrichrBot: Twitter bot tracking tweets about human genes

Kathleen M Jagodnik, Avi Ma'ayan, Kathleen M. Jagodnik, 2020, Bioinform..