| Suboptimization of developmental enhancers EK Farley, KM Olson, W Zhang, AJ Brandt, DS Rokhsar, MS Levine Science 350 (6258), 325-328, 2015 | 330 | 2015 |
| Large-scale profiling reveals the influence of genetic variation on gene expression in human induced pluripotent stem cells C DeBoever, H Li, D Jakubosky, P Benaglio, J Reyna, KM Olson, ... Cell stem cell 20 (4), 533-546. e7, 2017 | 177 | 2017 |
| Syntax compensates for poor binding sites to encode tissue specificity of developmental enhancers EK Farley, KM Olson, W Zhang, DS Rokhsar, MS Levine Proceedings of the National Academy of Sciences 113 (23), 6508-6513, 2016 | 172 | 2016 |
| 3D genomics across the tree of life reveals condensin II as a determinant of architecture type C Hoencamp, O Dudchenko, AMO Elbatsh, S Brahmachari, ... Science 372 (6545), 984-989, 2021 | 171 | 2021 |
| A global transcriptional network connecting noncoding mutations to changes in tumor gene expression W Zhang, A Bojorquez-Gomez, DO Velez, G Xu, KS Sanchez, JP Shen, ... Nature genetics 50 (4), 613-620, 2018 | 148 | 2018 |
| Enhancer grammar in development, evolution, and disease: dependencies and interplay GA Jindal, EK Farley Developmental cell 56 (5), 575-587, 2021 | 100 | 2021 |
| Doublesex and mab-3–related transcription factor 5 promotes midbrain dopaminergic identity in pluripotent stem cells by enforcing a ventral-medial progenitor fate N Gennet, E Gale, X Nan, E Farley, K Takacs, B Oberwallner, ... Proceedings of the National Academy of Sciences 108 (22), 9131-9136, 2011 | 42 | 2011 |
| Regulatory principles governing tissue specificity of developmental enhancers EK Farley, KM Olson, MS Levine Cold Spring Harbor symposia on quantitative biology 80, 27-32, 2015 | 26 | 2015 |
| Functional genomic approaches to elucidate the role of enhancers during development GE Ryan, EK Farley Wiley Interdisciplinary Reviews: Systems Biology and Medicine 12 (2), e1467, 2020 | 19 | 2020 |
| Identifying DNase I hypersensitive sites as driver distal regulatory elements in breast cancer M D′ Antonio, D Weghorn, A D′ Antonio-Chronowska, F Coulet, ... Nature communications 8 (1), 436, 2017 | 19 | 2017 |
| Affinity-optimizing enhancer variants disrupt development F Lim, JJ Solvason, GE Ryan, SH Le, GA Jindal, P Steffen, SK Jandu, ... Nature 626 (7997), 151-159, 2024 | 15 | 2024 |
| Single-nucleotide variants within heart enhancers increase binding affinity and disrupt heart development GA Jindal, AT Bantle, JJ Solvason, JL Grudzien, A D’Antonio-Chronowska, ... Developmental Cell 58 (21), 2206-2216. e5, 2023 | 13 | 2023 |
| Diverse logics and grammar encode notochord enhancers BP Song, MF Ragsac, K Tellez, GA Jindal, JL Grudzien, SH Le, EK Farley Cell reports 42 (2), 2023 | 11 | 2023 |
| Affinity-optimizing variants within the ZRS enhancer disrupt limb development F Lim, GE Ryan, SH Le, JJ Solvason, P Steffen, EK Farley BioRxiv, 2022.05. 27.493789, 2022 | 9 | 2022 |
| HOT DNAs: a novel class of developmental enhancers E Farley, M Levine Genes & Development 26 (9), 873-876, 2012 | 9 | 2012 |
| Effects of in ovo electroporation on endogenous gene expression: genome-wide analysis EK Farley, E Gale, D Chambers, M Li Neural Development 6, 1-13, 2011 | 7 | 2011 |
| Conserved enhancers control notochord expression of vertebrate Brachyury CL Kemmler, J Smolikova, HR Moran, BJ Mannion, D Knapp, F Lim, ... Nature communications 14 (1), 6594, 2023 | 5 | 2023 |
| Gene transfer in developing chick embryos: in ovo electroporation EK Farley Neural Development: Methods and Protocols, 141-150, 2013 | 5 | 2013 |
| EUGENe: A Python toolkit for predictive analyses of regulatory sequences A Klie, H Stites, T Jores, JJ Solvason, EK Farley, H Carter bioRxiv, 2022.10. 24.513593, 2022 | 4 | 2022 |
| Predictive analyses of regulatory sequences with EUGENe A Klie, D Laub, JV Talwar, H Stites, T Jores, JJ Solvason, EK Farley, ... Nature Computational Science 3 (11), 946-956, 2023 | 3 | 2023 |
