| 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 |
| 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 |
| 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 |
| 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 | |
| Interoperable RNA-Seq analysis in the cloud A Lachmann, DJB Clarke, D Torre, Z Xie, A Ma'ayan Biochimica et Biophysica Acta (BBA)-Gene Regulatory Mechanisms 1863 (6), 194521, 2020 | 23 | 2020 |
| 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 |
| blitzGSEA: efficient computation of gene set enrichment analysis through gamma distribution approximation A Lachmann, Z Xie, A Ma’ayan Bioinformatics 38 (8), 2356-2357, 2022 | 20 | 2022 |
| 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 |
| lncHUB2: aggregated and inferred knowledge about human and mouse lncRNAs GB Marino, ML Wojciechowicz, DJB Clarke, MV Kuleshov, Z Xie, M Jeon, ... Database 2023, baad009, 2023 | 9 | 2023 |
| 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 |
| 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 |
| GeneRanger and TargetRanger: processed gene and protein expression levels across cells and tissues for target discovery GB Marino, M Ngai, DJB Clarke, RH Fleishman, EZ Deng, Z Xie, N Ahmed, ... Nucleic Acids Research 51 (W1), W213-W224, 2023 | 6 | 2023 |
| DrugShot: querying biomedical search terms to retrieve prioritized lists of small molecules E Kropiwnicki, A Lachmann, DJB Clarke, Z Xie, KM Jagodnik, A Ma’ayan BMC bioinformatics 23 (1), 76, 2022 | 6 | 2022 |
| 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 |
| Elysium: RNA-seq Alignment in the Cloud A Lachmann, Z Xie, A Ma’ayan bioRxiv, 382937, 2018 | 5 | 2018 |
| Computational screen to identify potential targets for immunotherapeutic identification and removal of senescence cells EZ Deng, RH Fleishman, Z Xie, GB Marino, DJB Clarke, A Ma'ayan Aging Cell 22 (6), e13809, 2023 | 3 | 2023 |
| D2H2: diabetes data and hypothesis hub GB Marino, N Ahmed, Z Xie, KM Jagodnik, J Han, DJB Clarke, ... Bioinformatics Advances 3 (1), vbad178, 2023 | 2 | 2023 |
