| High-resolution mapping of chromatin packaging in mouse embryonic stem cells and sperm BR Carone, JH Hung, SJ Hainer, MT Chou, DM Carone, Z Weng, ... Developmental cell 30 (1), 11-22, 2014 | 233 | 2014 |
| Intergenic transcription causes repression by directing nucleosome assembly SJ Hainer, JA Pruneski, RD Mitchell, RM Monteverde, JA Martens Genes & development 25 (1), 29-40, 2011 | 205 | 2011 |
| Profiling of pluripotency factors in single cells and early embryos SJ Hainer, A Bošković, KN McCannell, OJ Rando, TG Fazzio Cell 177 (5), 1319-1329. e11, 2019 | 178 | 2019 |
| High‐resolution chromatin profiling using CUT&RUN SJ Hainer, TG Fazzio Current protocols in molecular biology 126 (1), e85, 2019 | 95 | 2019 |
| Genomic methods in profiling DNA accessibility and factor localization DC Klein, SJ Hainer Chromosome Research 28 (1), 69-85, 2020 | 92 | 2020 |
| Suppression of pervasive noncoding transcription in embryonic stem cells by esBAF SJ Hainer, W Gu, BR Carone, BD Landry, OJ Rando, CC Mello, TG Fazzio Genes & development 29 (4), 362-378, 2015 | 86 | 2015 |
| The Paf1 complex represses SER3 transcription in Saccharomyces cerevisiae by facilitating intergenic transcription-dependent nucleosome occupancy of the SER3 promoter JA Pruneski, SJ Hainer, KO Petrov, JA Martens Eukaryotic cell 10 (10), 1283-1294, 2011 | 74 | 2011 |
| Super-resolution imaging reveals the evolution of higher-order chromatin folding in early carcinogenesis J Xu, H Ma, H Ma, W Jiang, CA Mela, M Duan, S Zhao, C Gao, ER Hahm, ... Nature communications 11 (1), 1899, 2020 | 72 | 2020 |
| The classic metal-sensing transcription factor MTF1 promotes myogenesis in response to copper C Tavera-Montañez, SJ Hainer, D Cangussu, SJV Gordon, Y Xiao, ... The FASEB Journal 33 (12), 14556, 2019 | 54 | 2019 |
| Identification of histone mutants that are defective for transcription-coupled nucleosome occupancy SJ Hainer, JA Martens Molecular and cellular biology 31 (17), 3557-3568, 2011 | 54 | 2011 |
| Regulation of nucleosome architecture and factor binding revealed by nuclease footprinting of the ESC genome SJ Hainer, TG Fazzio Cell reports 13 (1), 61-69, 2015 | 49 | 2015 |
| Identification of Mutant Versions of the Spt16 Histone Chaperone That Are Defective for Transcription-Coupled Nucleosome Occupancy in Saccharomyces cerevisiae SJ Hainer, BA Charsar, SB Cohen, JA Martens G3: Genes| Genomes| Genetics 2 (5), 555-567, 2012 | 41 | 2012 |
| KAT-independent gene regulation by Tip60 promotes ESC self-renewal but not pluripotency D Acharya, SJ Hainer, Y Yoon, F Wang, I Bach, JA Rivera-Pérez, ... Cell Reports 19 (4), 671-679, 2017 | 38 | 2017 |
| DNA methylation directs genomic localization of Mbd2 and Mbd3 in embryonic stem cells SJ Hainer, KN McCannell, J Yu, LS Ee, LJ Zhu, OJ Rando, TG Fazzio Elife 5, e21964, 2016 | 34 | 2016 |
| Building and sustaining mentor interactions as a mentee S Sarabipour, SJ Hainer, FN Arslan, CM De Winde, E Furlong, N Bielczyk, ... The FEBS Journal, 2021 | 33 | 2021 |
| Transcription factor chromatin profiling genome-wide using uliCUT&RUN in single cells and individual blastocysts BJ Patty, SJ Hainer Nature protocols 16 (5), 2633-2666, 2021 | 30 | 2021 |
| Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet C Viner, CA Ishak, J Johnson, NJ Walker, H Shi, MK Sjöberg-Herrera, ... bioRxiv, 043794, 2022 | 27 | 2022 |
| Non-coding RNAs and nucleosome remodeling complexes: an intricate regulatory relationship BJ Patty, SJ Hainer Biology 9 (8), 213, 2020 | 26 | 2020 |
| Transcription of ncDNA: Many roads lead to local gene regulation SJ Hainer, JA Martens Transcription 2 (3), 120-123, 2011 | 19 | 2011 |
| Chromatin regulation and dynamics in stem cells DC Klein, SJ Hainer Current topics in developmental biology 138, 1-71, 2020 | 18 | 2020 |
