| Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells A Marson, SS Levine, MF Cole, GM Frampton, T Brambrink, S Johnstone, ... Cell 134 (3), 521-533, 2008 | 1763 | 2008 |
| Systematic discovery of Xist RNA binding proteins C Chu, QC Zhang, ST Da Rocha, RA Flynn, M Bharadwaj, JM Calabrese, ... Cell 161 (2), 404-416, 2015 | 1035 | 2015 |
| Divergent transcription from active promoters AC Seila, JM Calabrese, SS Levine, GW Yeo, PB Rahl, RA Flynn, ... science 322 (5909), 1849-1851, 2008 | 1016 | 2008 |
| Quantitative analysis of Argonaute protein reveals microRNA-dependent localization to stress granules AKL Leung, JM Calabrese, PA Sharp Proceedings of the National Academy of Sciences 103 (48), 18125-18130, 2006 | 479 | 2006 |
| Topoisomerases facilitate transcription of long genes linked to autism IF King, CN Yandava, AM Mabb, JS Hsiao, HS Huang, BL Pearson, ... Nature 501 (7465), 58-62, 2013 | 455 | 2013 |
| RNA sequence analysis defines Dicer's role in mouse embryonic stem cells JM Calabrese, AC Seila, GW Yeo, PA Sharp Proceedings of the National Academy of Sciences 104 (46), 18097-18102, 2007 | 382 | 2007 |
| SHAPE reveals transcript-wide interactions, complex structural domains, and protein interactions across the Xist lncRNA in living cells MJ Smola, TW Christy, K Inoue, CO Nicholson, M Friedersdorf, JD Keene, ... Proceedings of the National Academy of Sciences 113 (37), 10322-10327, 2016 | 228 | 2016 |
| Site-specific silencing of regulatory elements as a mechanism of X inactivation JM Calabrese, W Sun, L Song, JW Mugford, L Williams, D Yee, J Starmer, ... Cell 151 (5), 951-963, 2012 | 204 | 2012 |
| Functional classification of long non-coding RNAs by k-mer content JM Kirk, SO Kim, K Inoue, MJ Smola, DM Lee, MD Schertzer, JS Wooten, ... Nature genetics 50 (10), 1474-1482, 2018 | 198 | 2018 |
| Detection of RNA–protein interactions in living cells with SHAPE MJ Smola, JM Calabrese, KM Weeks Biochemistry 54 (46), 6867-6875, 2015 | 191 | 2015 |
| A latent pro-survival function for the mir-290-295 cluster in mouse embryonic stem cells GXY Zheng, A Ravi, JM Calabrese, LA Medeiros, O Kirak, LM Dennis, ... PLoS genetics 7 (5), e1002054, 2011 | 115 | 2011 |
| lncRNA-induced spread of polycomb controlled by genome architecture, RNA abundance, and CpG island DNA MD Schertzer, KCA Braceros, J Starmer, RE Cherney, DM Lee, G Salazar, ... Molecular cell 75 (3), 523-537. e10, 2019 | 102 | 2019 |
| Content and performance of the minimuga genotyping array: a new tool to improve rigor and reproducibility in mouse research JS Sigmon, MW Blanchard, RS Baric, TA Bell, J Brennan, GA Brockmann, ... Genetics 216 (4), 905-930, 2020 | 59 | 2020 |
| Characterization of the short RNAs bound by the P19 suppressor of RNA silencing in mouse embryonic stem cells JM Calabrese, PA Sharp Rna 12 (12), 2092-2102, 2006 | 54 | 2006 |
| Analysis of RNA–protein networks with RNP-MaP defines functional hubs on RNA CA Weidmann, AM Mustoe, PB Jariwala, JM Calabrese, KM Weeks Nature biotechnology 39 (3), 347-356, 2021 | 52 | 2021 |
| fourSig: a method for determining chromosomal interactions in 4C-Seq data RL Williams Jr, J Starmer, JW Mugford, JM Calabrese, P Mieczkowski, ... Nucleic acids research 42 (8), e68-e68, 2014 | 48 | 2014 |
| The mouse DXZ4 homolog retains Ctcf binding and proximity to Pls3 despite substantial organizational differences compared to the primate macrosatellite AH Horakova, JM Calabrese, CR McLaughlin, DC Tremblay, T Magnuson, ... Genome biology 13 (8), 1-16, 2012 | 48 | 2012 |
| A piggyBac-based toolkit for inducible genome editing in mammalian cells MD Schertzer, E Thulson, KCA Braceros, DM Lee, ER Hinkle, RM Murphy, ... Rna 25 (8), 1047-1058, 2019 | 37 | 2019 |
| SWI/SNF remains localized to chromatin in the presence of SCHLAP1 JR Raab, KN Smith, CC Spear, CJ Manner, JM Calabrese, T Magnuson Nature genetics 51 (1), 26-29, 2019 | 32 | 2019 |
| Differentiation-Driven Nucleolar Association of the Mouse Imprinted Kcnq1 Locus AM Fedoriw, JM Calabrese, W Mu, D Yee, T Magnuson G3: Genes| Genomes| Genetics 2 (12), 1521-1528, 2012 | 30 | 2012 |
