| Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation C Trapnell, BA Williams, G Pertea, A Mortazavi, G Kwan, MJ Van Baren, ... Nature biotechnology 28 (5), 511-515, 2010 | 14981 | 2010 |
| Mapping and quantifying mammalian transcriptomes by RNA-Seq A Mortazavi, BA Williams, K McCue, L Schaeffer, B Wold Nature methods 5 (7), 621-628, 2008 | 14754 | 2008 |
| An integrated encyclopedia of DNA elements in the human genome ENCODE Project Consortium Nature 489 (7414), 57-74, 2012 | 13822 | 2012 |
| Landscape of transcription in human cells S Djebali, CA Davis, A Merkel, A Dobin, T Lassmann, A Mortazavi, ... Nature 489 (7414), 101-108, 2012 | 5473 | 2012 |
| Genome-wide mapping of in vivo protein-DNA interactions DS Johnson, A Mortazavi, RM Myers, B Wold Science 316 (5830), 1497-1502, 2007 | 3530 | 2007 |
| A survey of best practices for RNA-seq data analysis A Conesa, P Madrigal, S Tarazona, D Gomez-Cabrero, A Cervera, ... Genome biology 17, 1-19, 2016 | 2996 | 2016 |
| A comparative encyclopedia of DNA elements in the mouse genome F Yue, Y Cheng, A Breschi, J Vierstra, W Wu, T Ryba, R Sandstrom, Z Ma, ... Nature 515 (7527), 355-364, 2014 | 1896 | 2014 |
| A user's guide to the encyclopedia of DNA elements (ENCODE) ENCODE Project Consortium PLoS biology 9 (4), e1001046, 2011 | 1442 | 2011 |
| 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 | 1330 | 2012 |
| Expanded encyclopaedias of DNA elements in the human and mouse genomes JE Moore, MJ Purcaro, HE Pratt, CB Epstein, N Shoresh, J Adrian, T Kawli, ... Nature 583 (7818), 699-710, 2020 | 1153 | 2020 |
| iPSC-Derived Human Microglia-like Cells to Study Neurological Diseases EM Abud, RN Ramirez, ES Martinez, LM Healy, CHH Nguyen, ... Neuron 94 (2), 278-293. e9, 2017 | 856 | 2017 |
| Assessment of transcript reconstruction methods for RNA-seq T Steijger, JF Abril, PG Engström, F Kokocinski, M Akerman, T Alioto, ... Nature methods 10 (12), 1177-1184, 2013 | 765 | 2013 |
| Computation for ChIP-seq and RNA-seq studies S Pepke, B Wold, A Mortazavi Nature methods 6 (Suppl 11), S22-S32, 2009 | 753 | 2009 |
| Regeneration of fat cells from myofibroblasts during wound healing MV Plikus, CF Guerrero-Juarez, M Ito, YR Li, PH Dedhia, Y Zheng, ... Science 355 (6326), 748-752, 2017 | 523 | 2017 |
| An encyclopedia of mouse DNA elements (Mouse ENCODE) JA Stamatoyannopoulos, M Snyder, R Hardison, B Ren, T Gingeras, ... Genome Biology 13 (8), 418, 2012 | 369 | 2012 |
| Dynamic Transformations of Genome-wide Epigenetic Marking and Transcriptional Control Establish T Cell Identity JA Zhang, A Mortazavi, BA Williams, BJ Wold, EV Rothenberg Cell 149 (2), 467-482, 2012 | 357 | 2012 |
| SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification M Tardaguila, L de la Fuente, C Marti, C Pereira, FJ Pardo-Palacios, ... Genome research 28 (3), 396-411, 2018 | 329 | 2018 |
| 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 |
| Comparative genomics modeling of the NRSF/REST repressor network: from single conserved sites to genome-wide repertoire A Mortazavi, ECL Thompson, ST Garcia, RM Myers, B Wold Genome research 16 (10), 1208-1221, 2006 | 190 | 2006 |
| 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 |
