| 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 | 456 | 2017 |
| Learning important features through propagating activation differences A Shrikumar, P Greenside, A Kundaje Proceedings of the 34th International Conference on Machine Learning-Volume …, 2017 | 449 | 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, 2016 | 333 | 2016 |
| 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 | 221 | 2015 |
| 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 | 207 | 2017 |
| 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, 2017 | 138 | 2017 |
| 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 | 134 | 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 | 48 | 2019 |
| 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 | 48 | 2017 |
| 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, 2017 | 48 | 2017 |
| 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 | 43 | 2018 |
| Relating chemical structure to cellular response: an integrative analysis of gene expression, bioactivity, and structural data across 11,000 compounds B Chen, P Greenside, H Paik, M Sirota, D Hadley, AJ Butte CPT: pharmacometrics & systems pharmacology 4 (10), 576-584, 2015 | 39 | 2015 |
| 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 | 23 | 2018 |
| 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 | 22 | 2016 |
| 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 | 17 | 2018 |
| Not just a black box: Interpretable deep learning by propagating activation differences A Shrikumar, P Greenside, A Shcherbina, A Kundaje arXiv preprint arXiv:1605.01713 4, 2016 | 14 | 2016 |
| Identification of a novel interspecific hybrid yeast from a metagenomic spontaneously inoculated beer sample using Hi‐C C Smukowski Heil, JN Burton, I Liachko, A Friedrich, NA Hanson, ... Yeast 35 (1), 71-84, 2018 | 13 | 2018 |
| Reverse-complement parameter sharing improves deep learning models for genomics A Shrikumar, P Greenside, A Kundaje bioRxiv, 103663, 2017 | 11 | 2017 |
| 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), 2019 | 10 | 2019 |
| Prediction of protein-ligand interactions from paired protein sequence motifs and ligand substructures. P Greenside, M Hillenmeyer, A Kundaje PSB, 20-31, 2018 | 9 | 2018 |
