| 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 | 210 | 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 | 197 | 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 | 144 | 2019 |
| 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 | 79 | 2015 |
| Genomic methods in profiling DNA accessibility and factor localization DC Klein, SJ Hainer Chromosome Research 28 (1), 69-85, 2020 | 71 | 2020 |
| 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 | 71 | 2011 |
| High‐Resolution Chromatin Profiling Using CUT&RUN SJ Hainer, TG Fazzio Current protocols in molecular biology 126 (1), e85, 2019 | 66 | 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 | 53 | 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), 1-17, 2020 | 51 | 2020 |
| 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 | 43 | 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 |
| 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), 14556-14574, 2019 | 33 | 2019 |
| 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 | 32 | 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 | 31 | 2016 |
| 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 | 19 | 2022 |
| Profiling of pluripotency factors in individual stem cells and early embryos SJ Hainer, A Bošković, OJ Rando, TG Fazzio bioRxiv, 286351, 2018 | 17 | 2018 |
| Unbiased chromatin accessibility profiling by RED-seq uncovers unique features of nucleosome variants in vivo PB Chen, LJ Zhu, SJ Hainer, KN McCannell, TG Fazzio BMC genomics 15 (1), 1-18, 2014 | 17 | 2014 |
| Transcription of ncDNA: Many roads lead to local gene regulation SJ Hainer, JA Martens Transcription 2 (3), 120-123, 2011 | 17 | 2011 |
| Non-Coding RNAs and nucleosome remodeling complexes: An intricate regulatory relationship BJ Patty, SJ Hainer Biology 9 (8), 213, 2020 | 15 | 2020 |
| 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 | 14 | 2021 |
