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Diabetes Data and Hypothesis Hub (D2H2)

Description: The Diabetes Data and Hypothesis Hub (D2H2) will develop a data-driven hypothesis-generation platform to advance our knowledge about type-2 diabetes and related metabolic disorders. The work will identify, with experimental validation, targets and drugs that may lead to new treatments.
Funding type: research
Funder scheme: RC2
Start date: 2022-07-01
End date: 2025-06-30
Investigator: ALAN D ATTIE
Institution: ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI
Funded outputs count: 25
Funder award ID: RC2DK131995
OpenAlex ID: G3307749245
GSFM: A gene set foundation model pre-trained on a massive collection of diverse gene sets
2026 · Daniel J.B. Clarke, Giacomo B. Marino, et al. · Patterns
GSFM source code snapshot from 03212026
2026 · Ma'ayan, Avi, Clarke, Daniel J. B., et al. · Figshare
A Gene Set Foundation Model Pre-Trained on a Massive Collection of Diverse Gene Sets
2025 · Daniel J. B. Clarke, Giacomo B. Marino, et al. · bioRxiv (Cold Spring Harbor Laboratory)
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L2S2: chemical perturbation and CRISPR KO LINCS L1000 signature search engine
2025 · Giacomo B Marino, John E Evangelista, et al. · Nucleic Acids Research · 17
Playbook workflow builder: Interactive construction of bioinformatics workflows
2025 · Daniel J.B. Clarke, John Erol Evangelista, et al. · PLoS Computational Biology · 5
lncRNAlyzr: Enrichment Analysis for lncRNA Sets
2025 · John Erol Evangelista, Tahleel Ali-Nasser, et al. · Journal of Molecular Biology · 6
GeneSetCart: assembling, augmenting, combining, visualizing, and analyzing gene sets
2025 · Giacomo B Marino, Stephanie Olaiya, et al. · GigaScience · 5
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sc2DAT: workflow for targeting tumor subpopulations of single cells
2024 · Giacomo B Marino, Anna I Byrd, et al. · Bioinformatics Advances
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Harmonizome 3.0: integrated knowledge about genes and proteins from diverse multi-omics resources
2024 · Ido Diamant, Daniel J B Clarke, et al. · Nucleic Acids Research · 141
RummaGEO: Automatic mining of human and mouse gene sets from GEO
2024 · Giacomo B. Marino, Daniel J.B. Clarke, et al. · Patterns · 21
Rummagene: massive mining of gene sets from supporting materials of biomedical research publications
2024 · Daniel J. B. Clarke, Giacomo B. Marino, et al. · Communications Biology · 26
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Rummagene gene sets with description 01172024
2024 · Clarke, Daniel J. B., Marino, Giacomo, et al. · Figshare · 1
Dex-Benchmark: datasets and code to evaluate algorithms for transcriptomics data analysis
2023 · Zhuorui Xie, Clara Chen, et al. · PeerJ · 3
Rummagene: Mining Gene Sets from Supporting Materials of PMC Publications
2023 · Daniel J. B. Clarke, Giacomo B. Marino, et al. · bioRxiv (Cold Spring Harbor Laboratory) · 5
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Systems immunology-based drug repurposing framework to target inflammation in atherosclerosis
2023 · Letizia Amadori, Claudia Calcagno, et al. · Nature Cardiovascular Research · 31
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Enrichr-KG: bridging enrichment analysis across multiple libraries
2023 · John Erol Evangelista, Zhuorui Xie, et al. · Nucleic Acids Research · 235
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GeneRanger and TargetRanger: processed gene and protein expression levels across cells and tissues for target discovery
2023 · Giacomo B Marino, Michael Ngai, et al. · Nucleic Acids Research · 11
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Computational screen to identify potential targets for immunotherapeutic identification and removal of senescence cells
2023 · Eden Z. Deng, Reid H. Fleishman, et al. · Aging Cell · 8
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PrismEXP: gene annotation prediction from stratified gene-gene co-expression matrices
2023 · Alexander Lachmann, Kaeli A. Rizzo, et al. · PeerJ · 14
lncHUB2: aggregated and inferred knowledge about human and mouse lncRNAs
2023 · Giacomo B Marino, Megan L Wojciechowicz, et al. · Database · 21
D2H2: diabetes data and hypothesis hub
2023 · Giacomo B Marino, Nasheath Ahmed, et al. · Bioinformatics Advances · 2
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Transforming L1000 profiles to RNA-seq-like profiles with deep learning
2022 · Minji Jeon, Zhuorui Xie, et al. · BMC Bioinformatics · 28
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