| An integrated encyclopedia of DNA elements in the human genome ENCODE Project Consortium Nature 489 (7414), 57, 2012 | 13857 | 2012 |
| A user's guide to the encyclopedia of DNA elements (ENCODE) ENCODE Project Consortium PLoS Biol 9 (4), e1001046, 2011 | 1443 | 2011 |
| Dynamic DNA methylation across diverse human cell lines and tissues KE Varley, J Gertz, KM Bowling, SL Parker, TE Reddy, F Pauli-Behn, ... Genome research 23 (3), 555-567, 2013 | 789 | 2013 |
| Widespread plasticity in CTCF occupancy linked to DNA methylation H Wang, MT Maurano, H Qu, KE Varley, J Gertz, F Pauli, K Lee, ... Genome research 22 (9), 1680-1688, 2012 | 642 | 2012 |
| The lingering mysteries of metastatic recurrence in breast cancer AI Riggio, KE Varley, AL Welm British journal of cancer 124 (1), 13-26, 2021 | 376 | 2021 |
| Analysis of DNA methylation in a three-generation family reveals widespread genetic influence on epigenetic regulation J Gertz, KE Varley, TE Reddy, KM Bowling, F Pauli, SL Parker, KS Kucera, ... PLoS genetics 7 (8), e1002228, 2011 | 348 | 2011 |
| Distinct properties of cell-type-specific and shared transcription factor binding sites J Gertz, D Savic, KE Varley, EC Partridge, A Safi, P Jain, GM Cooper, ... Molecular cell 52 (1), 25-36, 2013 | 326 | 2013 |
| Method for multiplexed nucleic acid patch polymerase chain reaction RM Mitra, KE Varley US Patent 8,586,310, 2013 | 307 | 2013 |
| CTCF/cohesin-mediated DNA looping is required for protocadherin α promoter choice Y Guo, K Monahan, H Wu, J Gertz, KE Varley, W Li, RM Myers, T Maniatis, ... Proceedings of the National Academy of Sciences 109 (51), 21081-21086, 2012 | 281 | 2012 |
| Quantification of rare allelic variants from pooled genomic DNA TE Druley, FLM Vallania, DJ Wegner, KE Varley, OL Knowles, JA Bonds, ... Nature methods 6 (4), 263-265, 2009 | 225 | 2009 |
| Effects of sequence variation on differential allelic transcription factor occupancy and gene expression TE Reddy, J Gertz, F Pauli, KS Kucera, KE Varley, KM Newberry, ... Genome research 22 (5), 860-869, 2012 | 184 | 2012 |
| Nested Patch PCR enables highly multiplexed mutation discovery in candidate genes KE Varley, RD Mitra Genome research 18 (11), 1844-1850, 2008 | 170 | 2008 |
| Recurrent read-through fusion transcripts in breast cancer KE Varley, J Gertz, BS Roberts, NS Davis, KM Bowling, MK Kirby, ... Breast cancer research and treatment 146, 287-297, 2014 | 168 | 2014 |
| A human breast cancer-derived xenograft and organoid platform for drug discovery and precision oncology KP Guillen, M Fujita, AJ Butterfield, SD Scherer, MH Bailey, Z Chu, ... Nature cancer 3 (2), 232-250, 2022 | 164 | 2022 |
| Genistein and bisphenol A exposure cause estrogen receptor 1 to bind thousands of sites in a cell type-specific manner J Gertz, TE Reddy, KE Varley, MJ Garabedian, RM Myers Genome research 22 (11), 2153-2162, 2012 | 153 | 2012 |
| Single-cell transcriptomes distinguish stem cell state changes and lineage specification programs in early mammary gland development RR Giraddi, CY Chung, RE Heinz, O Balcioglu, M Novotny, CL Trejo, ... Cell reports 24 (6), 1653-1666. e7, 2018 | 137 | 2018 |
| Expression of the MHC class II pathway in triple-negative breast cancer tumor cells is associated with a good prognosis and infiltrating lymphocytes A Forero, Y Li, D Chen, WE Grizzle, KL Updike, ND Merz, E Downs-Kelly, ... Cancer immunology research 4 (5), 390-399, 2016 | 126 | 2016 |
| Transposase mediated construction of RNA-seq libraries J Gertz, KE Varley, NS Davis, BJ Baas, IY Goryshin, R Vaidyanathan, ... Genome research 22 (1), 134-141, 2012 | 118 | 2012 |
| Early de novo DNA methylation and prolonged demethylation in the muscle lineage K Tsumagari, C Baribault, J Terragni, KE Varley, J Gertz, S Pradhan, ... Epigenetics 8 (3), 317-332, 2013 | 101 | 2013 |
| Intra-tumor heterogeneity of MLH1 promoter methylation revealed by deep single molecule bisulfite sequencing KE Varley, DG Mutch, TB Edmonston, PJ Goodfellow, RD Mitra Nucleic acids research 37 (14), 4603-4612, 2009 | 91 | 2009 |
