| Gene set knowledge discovery with Enrichr Z Xie, A Bailey, MV Kuleshov, DJB Clarke, JE Evangelista, SL Jenkins, ... Current protocols 1 (3), e90, 2021 | 2404 | 2021 |
| LINCS Data Portal 2.0: next generation access point for perturbation-response signatures V Stathias, J Turner, A Koleti, D Vidovic, D Cooper, M Fazel-Najafabadi, ... Nucleic acids research 48 (D1), D431-D439, 2020 | 151 | 2020 |
| KEA3: improved kinase enrichment analysis via data integration MV Kuleshov, Z Xie, ABK London, J Yang, JE Evangelista, A Lachmann, ... Nucleic acids research 49 (W1), W304-W316, 2021 | 106 | 2021 |
| Appyters: Turning Jupyter Notebooks into data-driven web apps DJB Clarke, M Jeon, DJ Stein, N Moiseyev, E Kropiwnicki, C Dai, Z Xie, ... Patterns 2 (3), 2021 | 99 | 2021 |
| Enrichr-KG: bridging enrichment analysis across multiple libraries JE Evangelista, Z Xie, GB Marino, N Nguyen, DJB Clarke, A Ma’ayan Nucleic acids research 51 (W1), W168-W179, 2023 | 72 | 2023 |
| The COVID-19 drug and gene set library MV Kuleshov, DJ Stein, DJB Clarke, E Kropiwnicki, KM Jagodnik, A Bartal, ... Patterns 1 (6), 2020 | 60 | 2020 |
| SigCom LINCS: data and metadata search engine for a million gene expression signatures JE Evangelista, DJB Clarke, Z Xie, A Lachmann, M Jeon, K Chen, ... Nucleic acids research 50 (W1), W697-W709, 2022 | 56 | 2022 |
| Pan-cancer proteogenomics characterization of tumor immunity F Petralia, W Ma, TM Yaron, FP Caruso, N Tignor, JM Wang, ... Cell 187 (5), 1255-1277. e27, 2024 | 32 | 2024 |
| Gene set knowledge discovery with Enrichr., 2021, 1, p. e90 Z Xie, A Bailey, MV Kuleshov, DJB Clarke, JE Evangelista, SL Jenkins, ... DOI: https://doi. org/10.1002/cpz1 90, 0 | 24 | |
| Drugmonizome and Drugmonizome-ML: integration and abstraction of small molecule attributes for drug enrichment analysis and machine learning E Kropiwnicki, JE Evangelista, DJ Stein, DJB Clarke, A Lachmann, ... Database 2021, baab017, 2021 | 23 | 2021 |
| A multi-omic analysis of MCF10A cells provides a resource for integrative assessment of ligand-mediated molecular and phenotypic responses SM Gross, MA Dane, RL Smith, KL Devlin, IC McLean, DS Derrick, ... Communications biology 5 (1), 1066, 2022 | 21 | 2022 |
| The COVID-19 gene and drug set library MV Kuleshov, DJB Clarke, E Kropiwnicki, KM Jagodnik, A Bartal, ... Research Square, 2020 | 20 | 2020 |
| Getting started with LINCS datasets and tools Z Xie, E Kropiwnicki, ML Wojciechowicz, KM Jagodnik, I Shu, A Bailey, ... Current protocols 2 (7), e487, 2022 | 16 | 2022 |
| Transforming L1000 profiles to RNA-seq-like profiles with deep learning M Jeon, Z Xie, JE Evangelista, ML Wojciechowicz, DJB Clarke, A Ma’ayan BMC bioinformatics 23 (1), 374, 2022 | 15 | 2022 |
| Predicting lyme disease from patients' peripheral blood mononuclear cells profiled with RNA-sequencing DJB Clarke, AW Rebman, A Bailey, ML Wojciechowicz, SL Jenkins, ... Frontiers in immunology 12, 636289, 2021 | 12 | 2021 |
| Toxicology knowledge graph for structural birth defects JE Evangelista, DJB Clarke, Z Xie, GB Marino, V Utti, SL Jenkins, ... Communications Medicine 3 (1), 98, 2023 | 7 | 2023 |
| Towards intelligent integration and sharing of stem cell research data K Borziak, T Qi, JE Evangelista, DJB Clarke, A Ma’ayan, J Finkelstein The Importance of Health Informatics in Public Health during a Pandemic, 334-337, 2020 | 7 | 2020 |
| Rummagene: massive mining of gene sets from supporting materials of biomedical research publications DJB Clarke, GB Marino, EZ Deng, Z Xie, JE Evangelista, A Ma’ayan Communications Biology 7 (1), 482, 2024 | 6 | 2024 |
| Rummagene: Mining gene sets from supporting materials of PMC publications DJB Clarke, GB Marino, EZ Deng, Z Xie, JE Evangelista, A Ma’ayan BioRxiv, 2023.10. 03.560783, 2023 | 5 | 2023 |
| Harmonizome 3.0: integrated knowledge about genes and proteins from diverse multi-omics resources I Diamant, DJB Clarke, JE Evangelista, N Lingam, A Ma’ayan Nucleic Acids Research 53 (D1), D1016-D1028, 2025 | 3 | 2025 |
