| An Integrated Encyclopedia of DNA Elements in the Human Genome J Khatun Nature, 2012 | 10989* | 2012 |
| 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 | 3570 | 2012 |
| Long noncoding RNAs with enhancer-like function in human cells UA Ørom, T Derrien, M Beringer, K Gumireddy, A Gardini, G Bussotti, ... Cell 143 (1), 46-58, 2010 | 1612 | 2010 |
| 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 | 1222 | 2014 |
| CARMEN, a human super enhancer-associated long noncoding RNA controlling cardiac specification, differentiation and homeostasis S Ounzain, R Micheletti, C Arnan, I Plaisance, D Cecchi, B Schroen, ... Journal of molecular and cellular cardiology 89, 98-112, 2015 | 139 | 2015 |
| Quantitative gene profiling of long noncoding RNAs with targeted RNA sequencing MB Clark, TR Mercer, G Bussotti, T Leonardi, KR Haynes, J Crawford, ... Nature methods 12 (4), 339-342, 2015 | 115 | 2015 |
| Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures JF Taly, C Magis, G Bussotti, JM Chang, P Di Tommaso, I Erb, ... Nature protocols 6 (11), 1669-1682, 2011 | 99 | 2011 |
| Exploring the gonad transcriptome of two extreme male pigs with RNA-seq A Esteve-Codina, R Kofler, N Palmieri, G Bussotti, C Notredame, ... BMC genomics 12 (1), 552, 2011 | 97 | 2011 |
| Multiple sequence alignment modeling: methods and applications M Chatzou, C Magis, JM Chang, C Kemena, G Bussotti, I Erb, ... Briefings in bioinformatics 17 (6), 1009-1023, 2016 | 89 | 2016 |
| Modulation of aneuploidy in Leishmania donovani during adaptation to different in vitro and in vivo environments and its impact on gene expression F Dumetz, H Imamura, M Sanders, V Seblova, J Myskova, P Pescher, ... MBio 8 (3), 2017 | 71 | 2017 |
| Enhanced transcriptome maps from multiple mouse tissues reveal evolutionary constraint in gene expression DD Pervouchine, S Djebali, A Breschi, CA Davis, PP Barja, A Dobin, ... Nature communications 6 (1), 1-11, 2015 | 58 | 2015 |
| T-Coffee: tree-based consistency objective function for alignment evaluation C Magis, JF Taly, G Bussotti, JM Chang, P Di Tommaso, I Erb, ... Multiple Sequence Alignment Methods, 117-129, 2014 | 51 | 2014 |
| Haplotype selection as an adaptive mechanism in the protozoan pathogen Leishmania donovani PP Barja, P Pescher, G Bussotti, F Dumetz, H Imamura, D Kedra, ... Nature ecology & evolution 1 (12), 1961-1969, 2017 | 48 | 2017 |
| BlastR—fast and accurate database searches for non-coding RNAs G Bussotti, E Raineri, I Erb, M Zytnicki, A Wilm, E Beaudoing, P Bucher, ... Nucleic acids research 39 (16), 6886-6895, 2011 | 33 | 2011 |
| Leishmania genome dynamics during environmental adaptation reveal strain-specific differences in gene copy number variation, karyotype instability, and telomeric amplification G Bussotti, E Gouzelou, MC Boité, I Kherachi, Z Harrat, N Eddaikra, ... MBio 9 (6), 2018 | 30 | 2018 |
| Intron retention-dependent gene regulation in Cryptococcus neoformans S Gonzalez-Hilarion, D Paulet, KT Lee, CC Hon, P Lechat, E Mogensen, ... Scientific reports 6 (1), 1-13, 2016 | 30 | 2016 |
| Using tertiary structure for the computation of highly accurate multiple RNA alignments with the SARA-Coffee package C Kemena, G Bussotti, E Capriotti, MA Marti-Renom, C Notredame Bioinformatics 29 (9), 1112-1119, 2013 | 25 | 2013 |
| A novel, noncanonical mechanism of cytoplasmic polyadenylation operates in Drosophila embryogenesis O Coll, A Villalba, G Bussotti, C Notredame, F Gebauer Genes & development 24 (2), 129-134, 2010 | 25 | 2010 |
| Detecting and comparing non-coding RNAs in the high-throughput era G Bussotti, C Notredame, AJ Enright International journal of molecular sciences 14 (8), 15423-15458, 2013 | 23 | 2013 |
| Use of ChIP-Seq data for the design of a multiple promoter-alignment method I Erb, JR Gonzalez-Vallinas, G Bussotti, E Blanco, E Eyras, C Notredame Nucleic acids research 40 (7), e52-e52, 2012 | 22 | 2012 |
