| 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 | 1903 | 2017 |
| HiChIP: efficient and sensitive analysis of protein-directed genome architecture MR Mumbach, AJ Rubin, RA Flynn, C Dai, PA Khavari, WJ Greenleaf, ... Nature methods 13 (11), 919-922, 2016 | 1008 | 2016 |
| Multimodal analysis of composition and spatial architecture in human squamous cell carcinoma AL Ji, AJ Rubin, K Thrane, S Jiang, DL Reynolds, RM Meyers, MG Guo, ... Cell 182 (2), 497-514. e22, 2020 | 699 | 2020 |
| Measuring the activity of BioBrick promoters using an in vivo reference standard JR Kelly, AJ Rubin, JH Davis, CM Ajo-Franklin, J Cumbers, MJ Czar, ... Journal of biological engineering 3, 1-13, 2009 | 495 | 2009 |
| 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 | 469 | 2017 |
| Design, construction and characterization of a set of insulated bacterial promoters JH Davis, AJ Rubin, RT Sauer Nucleic acids research 39 (3), 1131-1141, 2011 | 421 | 2011 |
| Lineage-specific dynamic and pre-established enhancer–promoter contacts cooperate in terminal differentiation AJ Rubin, BC Barajas, M Furlan-Magaril, V Lopez-Pajares, MR Mumbach, ... Nature genetics 49 (10), 1522-1528, 2017 | 295 | 2017 |
| Coupled single-cell CRISPR screening and epigenomic profiling reveals causal gene regulatory networks AJ Rubin, KR Parker, AT Satpathy, Y Qi, B Wu, AJ Ong, MR Mumbach, ... Cell 176 (1), 361-376. e17, 2019 | 258 | 2019 |
| A novel ATAC-seq approach reveals lineage-specific reinforcement of the open chromatin landscape via cooperation between BAF and p63 X Bao, AJ Rubin, K Qu, J Zhang, PG Giresi, HY Chang, PA Khavari Genome biology 16, 1-17, 2015 | 157 | 2015 |
| Transcript-indexed ATAC-seq for precision immune profiling AT Satpathy, N Saligrama, JD Buenrostro, Y Wei, B Wu, AJ Rubin, ... Nature medicine 24 (5), 580-590, 2018 | 128 | 2018 |
| 7SK-BAF axis controls pervasive transcription at enhancers RA Flynn, BT Do, AJ Rubin, E Calo, B Lee, H Kuchelmeister, M Rale, ... Nature structural & molecular biology 23 (3), 231-238, 2016 | 112 | 2016 |
| HiChIRP reveals RNA-associated chromosome conformation MR Mumbach, JM Granja, RA Flynn, CM Roake, AT Satpathy, AJ Rubin, ... Nature methods 16 (6), 489-492, 2019 | 82 | 2019 |
| CSNK1a1 regulates PRMT1 to maintain the progenitor state in self-renewing somatic tissue X Bao, Z Siprashvili, BJ Zarnegar, RM Shenoy, EJ Rios, N Nady, K Qu, ... Developmental cell 43 (2), 227-239. e5, 2017 | 56 | 2017 |
| The dynamic, combinatorial cis-regulatory lexicon of epidermal differentiation DS Kim, VI Risca, DL Reynolds, J Chappell, AJ Rubin, N Jung, ... Nature genetics 53 (11), 1564-1576, 2021 | 52 | 2021 |
| Retinoic acid and BMP4 cooperate with p63 to alter chromatin dynamics during surface epithelial commitment JM Pattison, SP Melo, SN Piekos, JL Torkelson, E Bashkirova, ... Nature genetics 50 (12), 1658-1665, 2018 | 49 | 2018 |
| Genome-wide meta-analysis identifies eight new susceptibility loci for cutaneous squamous cell carcinoma KY Sarin, Y Lin, R Daneshjou, A Ziyatdinov, G Thorleifsson, A Rubin, ... Nature communications 11 (1), 820, 2020 | 40 | 2020 |
| Divergent effects of canonical and non‐canonical TGF‐β signalling on mixed contractile‐synthetic smooth muscle cell phenotype in human Marfan syndrome aortic root aneurysms AJ Pedroza, T Koyano, J Trojan, A Rubin, I Palmon, K Jaatinen, G Burdon, ... Journal of Cellular and Molecular Medicine 24 (3), 2369-2383, 2020 | 36 | 2020 |
| Omni-ATAC-seq: improved ATAC-seq protocol MR Corces, SW Cho, HY Chang, WJ Greenleaf, TJ Montine, PA Khavari, ... | 17 | 2017 |
| Single-cell and spatial transcriptomic analysis of human skin delineates intercellular communication and pathogenic cells K Thrane, MCG Winge, H Wang, L Chen, MG Guo, A Andersson, ... Journal of Investigative Dermatology 143 (11), 2177-2192. e13, 2023 | 8 | 2023 |
| Chronic metabolic stress drives developmental programs and loss of tissue functions in non-transformed liver that mirror tumor states and stratify survival CN Tzouanas, MS Sherman, JES Shay, AJ Rubin, BE Mead, TT Dao, ... Biorxiv, 2023 | 2 | 2023 |
