| An integrated encyclopedia of DNA elements in the human genome ENCODE Project Consortium Nature 489 (7414), 57, 2012 | 13822 | 2012 |
| Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project Management Group Liefer Laura A. 51 Wetterstrand Kris A. 51 Good Peter J. 51 ... nature 447 (7146), 799-816, 2007 | 5995 | 2007 |
| The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression T Derrien, R Johnson, G Bussotti, A Tanzer, S Djebali, H Tilgner, ... Genome research 22 (9), 1775-1789, 2012 | 5267 | 2012 |
| ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia SG Landt, GK Marinov, A Kundaje, P Kheradpour, F Pauli, S Batzoglou, ... Genome research 22 (9), 1813-1831, 2012 | 2195 | 2012 |
| The developmental transcriptome of Drosophila melanogaster BR Graveley, AN Brooks, JW Carlson, MO Duff, JM Landolin, L Yang, ... Nature 471 (7339), 473-479, 2011 | 1670 | 2011 |
| Measuring reproducibility of high-throughput experiments Q Li, JB Brown, H Huang, PJ Bickel | 1095 | 2011 |
| Diversity and dynamics of the Drosophila transcriptome JB Brown, N Boley, R Eisman, GE May, MH Stoiber, MO Duff, BW Booth, ... Nature 512 (7515), 393-399, 2014 | 719 | 2014 |
| Long noncoding RNAs are rarely translated in two human cell lines B Bánfai, H Jia, J Khatun, E Wood, B Risk, WE Gundling, A Kundaje, ... Genome research 22 (9), 1646-1657, 2012 | 454 | 2012 |
| Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic … S MacArthur, XY Li, J Li, JB Brown, HC Chu, L Zeng, BP Grondona, ... Genome biology 10, 1-26, 2009 | 396 | 2009 |
| 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 | 327 | 2014 |
| Modeling gene expression using chromatin features in various cellular contexts X Dong, MC Greven, A Kundaje, S Djebali, JB Brown, C Cheng, ... Genome biology 13, 1-17, 2012 | 321 | 2012 |
| Iterative random forests to discover predictive and stable high-order interactions S Basu, K Kumbier, JB Brown, B Yu Proceedings of the National Academy of Sciences 115 (8), 1943-1948, 2018 | 316 | 2018 |
| Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors KY Yip, C Cheng, N Bhardwaj, JB Brown, J Leng, A Kundaje, J Rozowsky, ... Genome biology 13, 1-22, 2012 | 296 | 2012 |
| Genome-wide analysis of promoter architecture in Drosophila melanogaster RA Hoskins, JM Landolin, JB Brown, JE Sandler, H Takahashi, ... Genome research 21 (2), 182-192, 2011 | 276 | 2011 |
| Global patterns of tissue-specific alternative polyadenylation in Drosophila P Smibert, P Miura, JO Westholm, S Shenker, G May, MO Duff, D Zhang, ... Cell reports 1 (3), 277-289, 2012 | 261 | 2012 |
| Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome EH Margulies, GM Cooper, G Asimenos, DJ Thomas, CN Dewey, A Siepel, ... Genome research 17 (6), 760-774, 2007 | 248 | 2007 |
| De novo Identification of DNA Modifications Enabled by Genome-Guided Nanopore Signal Processing M Stoiber, J Quick, R Egan, J Eun Lee, S Celniker, RK Neely, N Loman, ... BioRxiv, 094672, 2016 | 243 | 2016 |
| Low-frequency and rare exome chip variants associate with fasting glucose and type 2 diabetes susceptibility J Wessel, AY Chu, SM Willems, S Wang, H Yaghootkar, JA Brody, ... Nature communications 6 (1), 5897, 2015 | 225 | 2015 |
| Sparse linear modeling of next-generation mRNA sequencing (RNA-Seq) data for isoform discovery and abundance estimation JJ Li, CR Jiang, JB Brown, H Huang, PJ Bickel Proceedings of the National Academy of Sciences 108 (50), 19867-19872, 2011 | 183 | 2011 |
| Centromere and kinetochore gene misexpression predicts cancer patient survival and response to radiotherapy and chemotherapy W Zhang, JH Mao, W Zhu, AK Jain, K Liu, JB Brown, GH Karpen Nature communications 7 (1), 12619, 2016 | 175 | 2016 |
