John Erol Evangelista

The share of this author’s assessed papers carrying a ⚑ flag. A concentration is a prompt for expert review — never, on its own, a determination about the person.

Collaborators, sized by shared output and coloured by their own reproducibility (green = high, red = low). Click a node to open their card. A pattern is a prompt for review, never a determination.

How this author’s assessed papers reproduced — the outcome of reproduction attempts, not a judgement of the person. Coverage is partial and grows over time.

Assessed papers (1)

• GeneSetCart: assembling, augmenting, combining, visualizing, and analyzing gene sets.⚑
  2025 L1 76/100 ⚑

1 assessed by us (1 reproduced) · 53 not yet assessed — every PubMed paper on record, linked below.

• The CFDE Workbench: Integrating Metadata and Processed Data from Common Fund Programs ↗

  Journal of Molecular Biology · 2026 · PMID 41506317
  not yet assessed
• The Common Fund Data Ecosystem (CFDE) ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2026 · PMID 41993383
  not yet assessed
• BiomarkerKB: An Integrated Knowledgebase Supporting Biomarker-Centric Exploration of Biomedical Data ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2026
  not yet assessed
• 248P LANTERN2: Inter-relationship between PDL1 expression, IASLC histological pattern and tumor stage in a perspective real world NSCLC population ↗

  ESMO Open · 2026
  not yet assessed
• ChEA-KG and ChEA-KG-TS: a network-based transcription factor enrichment analysis tool with an accompanying time-series workflow ↗

  Nucleic Acids Research · 2026 · PMID 42163770
  not yet assessed
• Cerebellar microRNA-206 tunes Purkinje neuron firing dynamics to control sensorimotor gating ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2026 · PMID 42427608
  not yet assessed
• L2S2: chemical perturbation and CRISPR KO LINCS L1000 signature search engine ↗

  Nucleic Acids Research · 2025 · PMID 40308216
  not yet assessed
• Playbook workflow builder: Interactive construction of bioinformatics workflows ↗

  PLoS Computational Biology · 2025 · PMID 40179105
  not yet assessed
• GeneSetCart: assembling, augmenting, combining, visualizing, and analyzing gene sets⚑

  GigaScience · 2025 · PMID 40208796
  L1 76/100 ⚑
• Creating an Interactive Web Interface for Networks Stored in Knowledge Graph Databases ↗

  Current Protocols · 2025 · PMID 40956607
  not yet assessed
• lncRNAlyzr: Enrichment Analysis for lncRNA Sets ↗

  Journal of Molecular Biology · 2025 · PMID 40133794
  not yet assessed
• The Data Distillery: A Graph Framework for Semantic Integration and Querying of Biomedical Data ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2025 · PMID 40832351
  not yet assessed
• The CFDE Workbench: Integrating Metadata and Processed Data from Common Fund Programs ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2025
  not yet assessed
• ChEA-KG: Human Transcription Factor Regulatory Network with a Knowledge Graph Interactive User Interface ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2025 · PMID 40832173
  not yet assessed
• Abstract 6305: hGRN-ChEAR: human transcription factor regulatory network with a knowledge graph interactive user interface ↗

  Cancer Research · 2025
  not yet assessed
• Abstract 1079: L2S2: Chemical perturbation and CRISPR KO LINCS L1000 signature search engine ↗

  Cancer Research · 2025
  not yet assessed
• Network analysis of NRG1 variants of uncertain significance (VUSes) in advanced non-small-cell lung cancer and their prognostic role in EGFR-mutant patients treated with first-line osimertinib ↗

  ESMO Open · 2025 · PMID 40885102
  not yet assessed
• EP.06.64 ISET CTC-DNA shows higher sensitivity then ctDNA in early stage lung cancer patients ↗

  Journal of Thoracic Oncology · 2025
  not yet assessed
• Harmonizome 3.0: integrated knowledge about genes and proteins from diverse multi-omics resources ↗

  Nucleic Acids Research · 2024 · PMID 39565209
  not yet assessed
• Pan-cancer proteogenomics characterization of tumor immunity ↗

  Cell · 2024 · PMID 38359819
  not yet assessed
• Rummagene: massive mining of gene sets from supporting materials of biomedical research publications ↗

  Communications Biology · 2024 · PMID 38643247
  not yet assessed
• Regulatory elements in SEM1-DLX5-DLX6 (7q21.3) locus contribute to genetic control of coronal nonsyndromic craniosynostosis and bone density-related traits ↗

  Genetics in Medicine Open · 2024 · PMID 39345948
  not yet assessed
• Playbook Workflow Builder: Interactive Construction of Bioinformatics Workflows from a Network of Microservices ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2024
  not yet assessed
• Rummagene gene sets with descriptions 01172024 ↗

  Figshare · 2024
  not yet assessed
• Rummagene gene sets with description 01172024 ↗

  Figshare · 2024
  not yet assessed
• Rummagene gene sets with descriptions 01172024 ↗

  Figshare · 2024
  not yet assessed
• Enrichr-KG: bridging enrichment analysis across multiple libraries ↗

  Nucleic Acids Research · 2023 · PMID 37166973
  not yet assessed
• Toxicology knowledge graph for structural birth defects ↗

  Communications Medicine · 2023 · PMID 37460679
  not yet assessed
• Rummagene: Mining Gene Sets from Supporting Materials of PMC Publications ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2023
  not yet assessed
• 1289TiP LANTERN study: A multi-omics digital human avatar for integrating precision medicine into clinical practice for lung cancer patients ↗

  Annals of Oncology · 2023
  not yet assessed
• EP07.04-07 Early-Stage Low Malignant Potential Adenocarcinomas: A Histological Category With A Significantly Better Prognosis ↗

  Journal of Thoracic Oncology · 2023
  not yet assessed
• P2.20-01 A Precision Medicine Approach by Performing Comprehensive Cancer Genome Profiling of Thymomas and Recurrent Thymomas ↗

  Journal of Thoracic Oncology · 2023
  not yet assessed
• SigCom LINCS: data and metadata search engine for a million gene expression signatures ↗

  Nucleic Acids Research · 2022 · PMID 35524556
  not yet assessed
• Getting Started with LINCS Datasets and Tools ↗

  Current Protocols · 2022 · PMID 35876555
  not yet assessed
• A multi-omic analysis of MCF10A cells provides a resource for integrative assessment of ligand-mediated molecular and phenotypic responses ↗

  Communications Biology · 2022 · PMID 36207580
  not yet assessed
• Transforming L1000 profiles to RNA-seq-like profiles with deep learning ↗

  BMC Bioinformatics · 2022 · PMID 36100892
  not yet assessed
• Gene and drug landing page aggregator ↗

  Bioinformatics Advances · 2022 · PMID 35368424
  not yet assessed
• Predicting the Biological Classification of Cell-Cycle Regulated Genes of Saccharomyces cerevisiae using Community Detection Algorithms on Gene Co-expression Networks ↗

  arXiv (Cornell University) · 2022
  not yet assessed
• ReproTox-KG: Toxicology Knowledge Graph for Structural Birth Defects ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2022
  not yet assessed
• Gene Set Knowledge Discovery with Enrichr ↗

  Current Protocols · 2021 · PMID 33780170
  not yet assessed
• KEA3: improved kinase enrichment analysis via data integration ↗

  Nucleic Acids Research · 2021 · PMID 34019655
  not yet assessed
• Appyters: Turning Jupyter Notebooks into data-driven web apps ↗

  Patterns · 2021 · PMID 33748796
  not yet assessed
• Drugmonizome and Drugmonizome-ML: integration and abstraction of small molecule attributes for drug enrichment analysis and machine learning ↗

  Database · 2021 · PMID 33787872
  not yet assessed
• Predicting Lyme Disease From Patients' Peripheral Blood Mononuclear Cells Profiled With RNA-Sequencing ↗

  Frontiers in Immunology · 2021 · PMID 33763080
  not yet assessed
• CPTAC Pancancer Phosphoproteomics Kinase Enrichment Analysis with ProKAP Provides Insights into Immunogenic Signaling Pathways ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2021
  not yet assessed
• The COVID-19 Drug and Gene Set Library ↗

  Patterns · 2020 · PMID 32838343
  not yet assessed
• The COVID-19 Gene and Drug Set Library ↗

  Research Square · 2020 · PMID 32702729
  not yet assessed
• The COVID-19 Gene and Drug Set Library ↗

  SSRN Electronic Journal · 2020
  not yet assessed
• LINCS Data Portal 2.0: next generation access point for perturbation-response signatures ↗

  Nucleic Acids Research · 2019 · PMID 31701147
  not yet assessed
• PepSquad: A Tool for Finding Compact Structural Motifs from Peptides ↗

  2018
  not yet assessed
• De Novo Transcriptome Assembly and Differential Expression Analysis of Coconut ( Cocos nucifera ) Endocarp for Subsequent Mining of Genes Related to Shell Thickness

  2015
  not yet assessed
• RNA-Seq Analysis of Cocos nucifera Catigan Dwarf Variety via De Novo Transcriptome Assembly for Functional Genomics Studies

  2015
  not yet assessed
• Draft assembly and analysis of the leaf transcriptome from three coconut tall varieties

  2015
  not yet assessed
• Differential Expression analysis of Cocos nucifera High and Low Copra Yielding Population using RNA-Seq and Real Time PCR to determine Copra Production Related Genes

  2015
  not yet assessed