| Gene set knowledge discovery with Enrichr Z Xie, A Bailey, MV Kuleshov, DJB Clarke, JE Evangelista, SL Jenkins, ... Current protocols 1 (3), e90, 2021 | 2446 | 2021 |
| eXpression2Kinases (X2K) Web: linking expression signatures to upstream cell signaling networks DJB Clarke, MV Kuleshov, BM Schilder, D Torre, ME Duffy, AB Keenan, ... Nucleic acids research 46 (W1), W171-W179, 2018 | 191 | 2018 |
| 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 | 152 | 2020 |
| 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 | 80 | 2023 |
| Perspectives on emerging directions in using IoT devices in blockchain applications AR Rao, D Clarke Internet of Things 10, 100079, 2020 | 65 | 2020 |
| Connecting omics signatures and revealing biological mechanisms with iLINCS M Pilarczyk, M Fazel-Najafabadi, M Kouril, B Shamsaei, J Vasiliauskas, ... Nature communications 13 (1), 4678, 2022 | 64 | 2022 |
| FAIRshake: Toolkit to evaluate the FAIRness of research digital resources DJB Clarke, L Wang, A Jones, ML Wojciechowicz, D Torre, KM Jagodnik, ... Cell systems 9 (5), 417-421, 2019 | 63 | 2019 |
| The COVID-19 drug and gene set library MV Kuleshov, DJ Stein, DJB Clarke, E Kropiwnicki, KM Jagodnik, A Bartal, ... Patterns 1 (6), 2020 | 61 | 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 | 60 | 2022 |
| Connecting omics signatures of diseases, drugs, and mechanisms of actions with iLINCS M Pilarczyk, M Kouril, B Shamsaei, J Vasiliauskas, W Niu, N Mahi, ... BioRxiv, 826271, 2019 | 43 | 2019 |
| 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 | 33 | 2024 |
| A fully integrated open-source toolkit for mining healthcare big-data: architecture and applications AR Rao, D Clarke 2016 IEEE international conference on healthcare informatics (ICHI), 255-261, 2016 | 31 | 2016 |
| Modulating the transcriptional landscape of SARS-CoV-2 as an effective method for developing antiviral compounds DA Hoagland, DJB Clarke, R Møller, Y Han, L Yang, ML Wojciechowicz, ... Biorxiv, 2020.07. 12.199687, 2020 | 30 | 2020 |
| Development of an embedded system course to teach the Internet-of-Things AR Rao, D Clarke, M Bhadiyadra, S Phadke 2018 IEEE Integrated STEM Education Conference (ISEC), 154-160, 2018 | 25 | 2018 |
| 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 |
| 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 |
| 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 |
