| Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation ME Dinger, PP Amaral, TR Mercer, KC Pang, SJ Bruce, BB Gardiner, ... Genome research 18 (9), 1433-1445, 2008 | 847 | 2008 |
| The eukaryotic genome as an RNA machine PP Amaral, ME Dinger, TR Mercer, JS Mattick science 319 (5871), 1787-1789, 2008 | 728 | 2008 |
| MEN ε/β nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles H Sunwoo, ME Dinger, JE Wilusz, PP Amaral, JS Mattick, DL Spector Genome research 19 (3), 347-359, 2009 | 617 | 2009 |
| lncRNAdb: a reference database for long noncoding RNAs PP Amaral, MB Clark, DK Gascoigne, ME Dinger, JS Mattick Nucleic acids research 39 (suppl_1), D146-D151, 2011 | 600 | 2011 |
| Noncoding RNA in development PP Amaral, JS Mattick Mammalian genome 19 (7), 454-492, 2008 | 532 | 2008 |
| The reality of pervasive transcription MB Clark, PP Amaral, FJ Schlesinger, ME Dinger, RJ Taft, JL Rinn, ... PLoS biology 9 (7), e1000625, 2011 | 459 | 2011 |
| RNA regulation of epigenetic processes JS Mattick, PP Amaral, ME Dinger, TR Mercer, MF Mehler Bioessays 31 (1), 51-59, 2009 | 397 | 2009 |
| Genome mapping and expression analyses of human intronic noncoding RNAs reveal tissue-specific patterns and enrichment in genes related to regulation of transcription HI Nakaya, PP Amaral, R Louro, A Lopes, AA Fachel, YB Moreira, ... Genome biology 8 (3), 1-25, 2007 | 252 | 2007 |
| Complex architecture and regulated expression of the Sox2ot locus during vertebrate development PP Amaral, C Neyt, SJ Wilkins, ME Askarian-Amiri, SM Sunkin, ... Rna 15 (11), 2013-2027, 2009 | 218 | 2009 |
| Pervasive transcription of the eukaryotic genome: functional indices and conceptual implications ME Dinger, PP Amaral, TR Mercer, JS Mattick Briefings in Functional Genomics and Proteomics 8 (6), 407-423, 2009 | 195 | 2009 |
| Genomic positional conservation identifies topological anchor point RNAs linked to developmental loci PP Amaral, T Leonardi, N Han, E Viré, DK Gascoigne, R Arias-Carrasco, ... Genome biology 19 (1), 1-21, 2018 | 102 | 2018 |
| Non-coding RNAs in homeostasis, disease and stress responses: an evolutionary perspective PP Amaral, ME Dinger, JS Mattick Briefings in functional genomics 12 (3), 254-278, 2013 | 98 | 2013 |
| Androgen responsive intronic non-coding RNAs R Louro, HI Nakaya, PP Amaral, F Festa, MC Sogayar, AM da Silva, ... BMC biology 5 (1), 1-14, 2007 | 94 | 2007 |
| Pinstripe: a suite of programs for integrating transcriptomic and proteomic datasets identifies novel proteins and improves differentiation of protein-coding and non-coding genes DK Gascoigne, SW Cheetham, PB Cattenoz, MB Clark, PP Amaral, ... Bioinformatics 28 (23), 3042-3050, 2012 | 80 | 2012 |
| RNA modifications detection by comparative Nanopore direct RNA sequencing A Leger, PP Amaral, L Pandolfini, C Capitanchik, F Capraro, V Miano, ... Nature Communications 12 (1), 1-17, 2021 | 66 | 2021 |
| The non-coding snRNA 7SKcontrols transcriptional termination, poising, and bidirectionality in embryonic stem cells G Castelo-Branco, PP Amaral, PG Engström, SC Robson, SC Marques, ... Genome biology 14 (9), 1-18, 2013 | 51 | 2013 |
| Long noncoding RNAs are involved in multiple immunological pathways in response to vaccination DS de Lima, LE Cardozo, V Maracaja-Coutinho, A Suhrbier, K Mane, ... Proceedings of the National Academy of Sciences 116 (34), 17121-17126, 2019 | 39 | 2019 |
| A lncRNA fine tunes the dynamics of a cell state transition involving Lin28, let-7 and de novo DNA methylation MA Li, PP Amaral, P Cheung, JH Bergmann, M Kinoshita, T Kalkan, ... Elife 6, e23468, 2017 | 25 | 2017 |
| The Evx1/Evx1as gene locus regulates anterior-posterior patterning during gastrulation CC Bell, PP Amaral, A Kalsbeek, GW Magor, KR Gillinder, P Tangermann, ... Scientific reports 6 (1), 1-11, 2016 | 23 | 2016 |
| Re-place your BETs: the dynamics of super enhancers PP Amaral, AJ Bannister Molecular cell 56 (2), 187-189, 2014 | 17 | 2014 |
