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| Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation G Li, X Ruan, RK Auerbach, KS Sandhu, M Zheng, P Wang, HM Poh, ... Cell 148 (1), 84-98, 2012 | 1364 | 2012 |
| Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project MB Gerstein, ZJ Lu, EL Van Nostrand, C Cheng, BI Arshinoff, T Liu, ... Science 330 (6012), 1775-1787, 2010 | 1133 | 2010 |
| A User's Guide to the Encyclopedia of DNA Elements (ENCODE) B Wold, A Mortazavi, B Williams, G Marinov, D Trout, B King, K McCue, ... PLoS Biology 9 (4), Art. No. e1001046, 2011 | 868 | 2011 |
| PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls J Rozowsky, G Euskirchen, RK Auerbach, ZD Zhang, T Gibson, ... Nature biotechnology 27 (1), 66, 2009 | 708 | 2009 |
| A user's guide to the encyclopedia of DNA elements (ENCODE) RM Myers, J Stamatoyannopoulos, M Snyder, I Dunham, RC Hardison, ... PLoS biology 9 (4), 2011 | 677 | 2011 |
| The real cost of sequencing: higher than you think! A Sboner, XJ Mu, D Greenbaum, RK Auerbach, MB Gerstein Genome biology 12, 1-10, 2011 | 522 | 2011 |
| Comparative analysis of the transcriptome across distant species MB Gerstein, J Rozowsky, KK Yan, D Wang, C Cheng, JB Brown, ... Nature 512 (7515), 445-448, 2014 | 336 | 2014 |
| Diverse roles and interactions of the SWI/SNF chromatin remodeling complex revealed using global approaches GM Euskirchen, RK Auerbach, E Davidov, TA Gianoulis, G Zhong, ... PLoS genetics 7 (3), e1002008, 2011 | 274 | 2011 |
| Mapping accessible chromatin regions using Sono-Seq RK Auerbach, G Euskirchen, J Rozowsky, N Lamarre-Vincent, ... Proceedings of the National Academy of Sciences 106 (35), 14926-14931, 2009 | 274 | 2009 |
| Genome-Wide Identification of Binding Sites Defines Distinct Functions for Caenorhabditis elegans PHA-4/FOXA in Development and Environmental Response M Zhong, W Niu, ZJ Lu, M Sarov, JI Murray, J Janette, D Raha, ... PLoS genetics 6 (2), e1000848, 2010 | 218 | 2010 |
| Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer T Pearson, P Giffard, S Beckstrom-Sternberg, R Auerbach, H Hornstra, ... BMC biology 7, 1-14, 2009 | 209 | 2009 |
| Phylogeography of Francisella tularensis: Global Expansion of a Highly Fit Clone AJ Vogler, D Birdsell, LB Price, JR Bowers, SM Beckstrom-Sternberg, ... Journal of bacteriology 191 (8), 2474-2484, 2009 | 208 | 2009 |
| SWI/SNF chromatin-remodeling factors: multiscale analyses and diverse functions G Euskirchen, RK Auerbach, M Snyder Journal of Biological Chemistry 287 (37), 30897-30905, 2012 | 207 | 2012 |
| Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing P Lefrançois, GM Euskirchen, RK Auerbach, J Rozowsky, T Gibson, ... BMC genomics 10, 1-18, 2009 | 200 | 2009 |
| Genomic islands from five strains of Burkholderia pseudomallei A Tuanyok, BR Leadem, RK Auerbach, SM Beckstrom-Sternberg, ... BMC genomics 9, 1-14, 2008 | 122 | 2008 |
| A Horizontal Gene Transfer Event Defines Two Distinct Groups within Burkholderia pseudomallei That Have Dissimilar Geographic Distributions A Tuanyok, RK Auerbach, TS Brettin, DC Bruce, AC Munk, JC Detter, ... Journal of bacteriology 189 (24), 9044-9049, 2007 | 119 | 2007 |
| Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data ZJ Lu, KY Yip, G Wang, C Shou, LDW Hillier, E Khurana, A Agarwal, ... Genome research 21 (2), 276-285, 2011 | 83 | 2011 |
| Relating genes to function: identifying enriched transcription factors using the ENCODE ChIP-Seq significance tool RK Auerbach, B Chen, AJ Butte Bioinformatics 29 (15), 1922-1924, 2013 | 82 | 2013 |
| Complete genomic characterization of a pathogenic A. II strain of Francisella tularensis subspecies tularensis SM Beckstrom-Sternberg, RK Auerbach, S Godbole, JV Pearson, ... PloS one 2 (9), e947, 2007 | 73 | 2007 |
