| Learning important features through propagating activation differences A Shrikumar, P Greenside, A Kundaje International conference on machine learning, 3145-3153, 2017 | 4833 | 2017 |
| A next generation connectivity map: L1000 platform and the first 1,000,000 profiles A Subramanian, R Narayan, SM Corsello, DD Peck, TE Natoli, X Lu, ... Cell 171 (6), 1437-1452. e17, 2017 | 2851 | 2017 |
| An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues MR Corces, AE Trevino, EG Hamilton, PG Greenside, ... Nature methods 14 (10), 959-962, 2017 | 2029 | 2017 |
| Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution MR Corces, JD Buenrostro, B Wu, PG Greenside, SM Chan, JL Koenig, ... Nature genetics 48 (10), 1193-1203, 2016 | 1138 | 2016 |
| Not just a black box: Learning important features through propagating activation differences A Shrikumar, P Greenside, A Shcherbina, A Kundaje arXiv preprint arXiv:1605.01713, 2016 | 853 | 2016 |
| Discovery of common and rare genetic risk variants for colorectal cancer JR Huyghe, SA Bien, TA Harrison, HM Kang, S Chen, SL Schmit, ... Nature genetics 51 (1), 76-87, 2019 | 484 | 2019 |
| Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements MR Mumbach, AT Satpathy, EA Boyle, C Dai, BG Gowen, SW Cho, ... Nature genetics 49 (11), 1602-1612, 2017 | 481 | 2017 |
| Genetic control of chromatin states in humans involves local and distal chromosomal interactions F Grubert, JB Zaugg, M Kasowski, O Ursu, DV Spacek, AR Martin, ... Cell 162 (5), 1051-1065, 2015 | 381 | 2015 |
| Evaluation of RNAi and CRISPR technologies by large-scale gene expression profiling in the Connectivity Map I Smith, PG Greenside, T Natoli, DL Lahr, D Wadden, I Tirosh, R Narayan, ... PLoS biology 15 (11), e2003213, 2017 | 218 | 2017 |
| Landscape of cohesin-mediated chromatin loops in the human genome F Grubert, R Srivas, DV Spacek, M Kasowski, M Ruiz-Velasco, ... Nature 583 (7818), 737-743, 2020 | 161 | 2020 |
| Molecular definition of a metastatic lung cancer state reveals a targetable CD109–Janus kinase–Stat axis CH Chuang, PG Greenside, ZN Rogers, JJ Brady, D Yang, RK Ma, ... Nature medicine 23 (3), 291-300, 2017 | 161 | 2017 |
| Intertumoral heterogeneity in SCLC is influenced by the cell type of origin D Yang, SK Denny, PG Greenside, AC Chaikovsky, JJ Brady, Y Ouadah, ... Cancer discovery 8 (10), 1316-1331, 2018 | 136 | 2018 |
| Impact of regulatory variation across human iPSCs and differentiated cells NE Banovich, YI Li, A Raj, MC Ward, P Greenside, D Calderon, PY Tung, ... Genome research 28 (1), 122-131, 2018 | 136 | 2018 |
| Mitigation of off-target toxicity in CRISPR-Cas9 screens for essential non-coding elements J Tycko, M Wainberg, GK Marinov, O Ursu, GT Hess, BK Ego, Aradhana, ... Nature communications 10 (1), 4063, 2019 | 122 | 2019 |
| Proceedings of the 34th International Conference on Machine Learning A Shrikumar, P Greenside, A Kundaje, P Doina, WT Yee vol. 70 of Proceedings of Machine Learning Research, 3145-3153, 2017 | 110 | 2017 |
| An Arntl2-driven secretome enables lung adenocarcinoma metastatic self-sufficiency JJ Brady, CH Chuang, PG Greenside, ZN Rogers, CW Murray, ... Cancer cell 29 (5), 697-710, 2016 | 100 | 2016 |
| Deciphering regulatory DNA sequences and noncoding genetic variants using neural network models of massively parallel reporter assays R Movva, P Greenside, GK Marinov, S Nair, A Shrikumar, A Kundaje PLoS One 14 (6), e0218073, 2019 | 97 | 2019 |
| Discovering epistatic feature interactions from neural network models of regulatory DNA sequences P Greenside, T Shimko, P Fordyce, A Kundaje Bioinformatics 34 (17), i629-i637, 2018 | 91 | 2018 |
| Accelerating bayesian optimization for biological sequence design with denoising autoencoders S Stanton, W Maddox, N Gruver, P Maffettone, E Delaney, P Greenside, ... International Conference on Machine Learning, 20459-20478, 2022 | 89 | 2022 |
| Reverse-complement parameter sharing improves deep learning models for genomics A Shrikumar, P Greenside, A Kundaje BioRxiv, 103663, 2017 | 64 | 2017 |
