| The 4D nucleome project J Dekker, AS Belmont, M Guttman, VO Leshyk, JT Lis, S Lomvardas, ... Nature 549 (7671), 219, 2017 | 653 | 2017 |
| Chromatin conformation remains stable upon extensive transcriptional changes driven by heat shock J Ray, PR Munn, A Vihervaara, JJ Lewis, A Ozer, CG Danko, JT Lis Proceedings of the National Academy of Sciences 116 (39), 19431-19439, 2019 | 96 | 2019 |
| Compatibility rules of human enhancer and promoter sequences DT Bergman, TR Jones, V Liu, J Ray, E Jagoda, L Siraj, HY Kang, ... Nature 607 (7917), 176-184, 2022 | 86 | 2022 |
| Live-cell imaging of Pol II promoter activity to monitor gene expression with RNA IMAGEtag reporters I Shin, J Ray, V Gupta, M Ilgu, J Beasley, L Bendickson, S Mehanovic, ... Nucleic acids research 42 (11), e90-e90, 2014 | 55 | 2014 |
| Light-up and FRET aptamer reporters; evaluating their applications for imaging transcription in eukaryotic cells M Ilgu, J Ray, L Bendickson, T Wang, IM Geraskin, GA Kraus, ... Methods 98, 26-33, 2016 | 42 | 2016 |
| Aptamer-based molecular imaging T Wang, J Ray Protein & cell 3, 739-754, 2012 | 31 | 2012 |
| RNA aptamer capture of macromolecular complexes for mass spectrometry analysis J Ray, A Kruse, A Ozer, T Kajitani, R Johnson, M MacCoss, M Heck, JT Lis Nucleic Acids Research 48 (15), e90-e90, 2020 | 6 | 2020 |
| Aptamer-enabled uptake of small molecule ligands SL Auwardt, YJ Seo, M Ilgu, J Ray, RR Feldges, S Shubham, ... Scientific Reports 8 (1), 15712, 2018 | 3 | 2018 |
| IMAGEtags: Quantifying mRNA transcription in real time with multiaptamer reporters J Ray, I Shin, M Ilgu, L Bendickson, V Gupta, GA Kraus, ... Methods in enzymology 572, 193-213, 2016 | 2 | 2016 |
| Methods for capture and analysis of macromolecular complexes J Ray, O Abdullah, J Lis US Patent App. 17/167,991, 2021 | 1 | 2021 |
| Detecting cells in time varying intensity images in confocal microscopy for gene expression studies in living cells D Mitra, R Boutchko, J Ray, M Nilsen-Hamilton Medical Imaging 2015: Digital Pathology 9420, 254-257, 2015 | 1 | 2015 |
| CRISPRi of regulatory elements upon degron operation (CRUDO) P Guckelberger, BR Doughty, G Munson, CP Fulco, DT Bergman, J Ray, ... | | 2024 |
| Nanoscale photobiotinylation, pulldown and sequencing of region-specific DNA from intact cells TC Roberts, M Kushner, JC Crowley, A Ozer, J Wang, J Ray, JT Lis, ... bioRxiv, 2023 | | 2023 |
| The Impact of Genomic Variation on Function (IGVF) Consortium I Consortium arXiv preprint arXiv:2307.13708, 2023 | | 2023 |
| Nanoscale photobiotinylation, pulldown and sequencing of region-specific DNA from intact cells. W Zipfel, T Roberts, M Kushner, JC Crowley, A Ozer, J Wang, J Ray, ... bioRxiv, 2023.12. 04.569951, 2023 | | 2023 |
| Femto-Seq: A New Nonlinear Microcopy Approach for Elucidating Chromatin Structure at the Single Gene Level M Kushner, J Wang, A Ozer, J Ray, H Lin, J Lis, WR Zipfel Novel Techniques in Microscopy, NS2B. 5, 2019 | | 2019 |
| High-Resolution Locus-Specific Mapping of Chromatin Contacts using Two-Photon Photoactivated DNA Cross-Linking M Kushner, J Wang, A Ozer, J Ray, J Lis, W Zipfel Biophysical Journal 114 (3), 255a, 2018 | | 2018 |
| Aptamer-enabled uptake of small molecule ligands S Liyamali Auwardt, YJ Seo, M Ilgu, J Ray, R Feldges, M Nilsen-Hamilton, ... | | 2018 |
| Methods of Enzymology: Chapter 8-IMAGEtags: Quantifying mRNA Transcription in Real Time with Multiaptamer Reporters J Ray, I Shin, L Bendickson, V Gupta, G Kraus, M Nilsen-Hamilton Ames Lab., Ames, IA (United States), 2016 | | 2016 |
| Light-up and FRET aptamer reporters; evaluating their applications for imaging transcription in eukaryotic cells M Nilsen-Hamilton, M Ilgu, J Ray, L Bendickson, T Wang, G Kraus, ... | | 2016 |
