| Year |
Citation |
Score |
| 2024 |
Serra F, Nieto-Aliseda A, Fanlo-Escudero L, Rovirosa L, Cabrera-Pasadas M, Lazarenkov A, Urmeneta B, Alcalde-Merino A, Nola EM, Okorokov AL, Fraser P, Graupera M, Castillo SD, Sardina JL, Valencia A, et al. p53 rapidly restructures 3D chromatin organization to trigger a transcriptional response. Nature Communications. 15: 2821. PMID 38561401 DOI: 10.1038/s41467-024-46666-1 |
0.461 |
|
| 2023 |
Armaos A, Serra F, Núñez-Carpintero I, Seo JH, Baca SC, Gustincich S, Valencia A, Freedman ML, Cirillo D, Giambartolomei C, Tartaglia GG. The PENGUIN approach to reconstruct protein interactions at enhancer-promoter regions and its application to prostate cancer. Nature Communications. 14: 8084. PMID 38057321 DOI: 10.1038/s41467-023-43767-1 |
0.686 |
|
| 2023 |
Tomás-Daza L, Rovirosa L, López-Martí P, Nieto-Aliseda A, Serra F, Planas-Riverola A, Molina O, McDonald R, Ghevaert C, Cuatrecasas E, Costa D, Camós M, Bueno C, Menéndez P, Valencia A, et al. Low input capture Hi-C (liCHi-C) identifies promoter-enhancer interactions at high-resolution. Nature Communications. 14: 268. PMID 36650138 DOI: 10.1038/s41467-023-35911-8 |
0.472 |
|
| 2022 |
Galan S, Serra F, Marti-Renom MA. Identification of chromatin loops from Hi-C interaction matrices by CTCF-CTCF topology classification. Nar Genomics and Bioinformatics. 4: lqac021. PMID 35274099 DOI: 10.1093/nargab/lqac021 |
0.683 |
|
| 2021 |
Richart L, Lapi E, Pancaldi V, Cuenca-Ardura M, Pau EC, Madrid-Mencía M, Neyret-Kahn H, Radvanyi F, Rodríguez JA, Cuartero Y, Serra F, Le Dily F, Valencia A, Marti-Renom MA, Real FX. STAG2 loss-of-function affects short-range genomic contacts and modulates the basal-luminal transcriptional program of bladder cancer cells. Nucleic Acids Research. PMID 34648034 DOI: 10.1093/nar/gkab864 |
0.509 |
|
| 2021 |
Di Stefano M, Castillo D, Serra F, Farabella I, Goodstadt MN, Marti-Renom MA. Analysis, Modeling, and Visualization of Chromosome Conformation Capture Experiments. Methods in Molecular Biology (Clifton, N.J.). 2157: 35-63. PMID 32820398 DOI: 10.1007/978-1-0716-0664-3_4 |
0.363 |
|
| 2020 |
Di Stefano M, Stadhouders R, Farabella I, Castillo D, Serra F, Graf T, Marti-Renom MA. Transcriptional activation during cell reprogramming correlates with the formation of 3D open chromatin hubs. Nature Communications. 11: 2564. PMID 32444798 DOI: 10.1038/S41467-020-16396-1 |
0.393 |
|
| 2020 |
Sati S, Bonev B, Szabo Q, Jost D, Bensadoun P, Serra F, Loubiere V, Papadopoulos GL, Rivera-Mulia JC, Fritsch L, Bouret P, Castillo D, Gelpi JL, Orozco M, Vaillant C, et al. 4D Genome Rewiring during Oncogene-Induced and Replicative Senescence. Molecular Cell. PMID 32220303 DOI: 10.1016/J.Molcel.2020.03.007 |
0.424 |
|
| 2018 |
Beekman R, Chapaprieta V, Russiñol N, Vilarrasa-Blasi R, Verdaguer-Dot N, Martens JHA, Duran-Ferrer M, Kulis M, Serra F, Javierre BM, Wingett SW, Clot G, Queirós AC, Castellano G, Blanc J, et al. The reference epigenome and regulatory chromatin landscape of chronic lymphocytic leukemia. Nature Medicine. PMID 29785028 DOI: 10.1038/S41591-018-0028-4 |
0.317 |
|
| 2018 |
Stadhouders R, Vidal E, Serra F, Di Stefano B, Le Dily F, Quilez J, Gomez A, Collombet S, Berenguer C, Cuartero Y, Hecht J, Filion GJ, Beato M, Marti-Renom MA, Graf T. Transcription factors orchestrate dynamic interplay between genome topology and gene regulation during cell reprogramming. Nature Genetics. PMID 29335546 DOI: 10.1038/S41588-017-0030-7 |
0.415 |
|
| 2017 |
Serra F, Baù D, Goodstadt M, Castillo D, Filion G, Marti-Renom MA. Automatic analysis and 3D-modelling of Hi-C data using TADbit reveals structural features of the fly chromatin colors. Plos Computational Biology. 13: e1005665. PMID 28723903 DOI: 10.1371/Journal.Pcbi.1005665 |
0.429 |
|
| 2016 |
Huerta-Cepas J, Serra F, Bork P. ETE 3: Reconstruction, analysis and visualization of phylogenomic data. Molecular Biology and Evolution. PMID 26921390 DOI: 10.1093/Molbev/Msw046 |
0.355 |
|
| 2016 |
Lüke L, Tourmente M, Dopazo H, Serra F, Roldan ER. Selective constraints on protamine 2 in primates and rodents. Bmc Evolutionary Biology. 16: 21. PMID 26801756 DOI: 10.1186/S12862-016-0588-1 |
0.691 |
|
| 2016 |
Vilarrasa-Blasi R, Queirós AC, Beekman R, Russiñol N, Castellano G, Blanc J, Serra F, Beà S, Kulis M, Verdaguer-Dot N, Enjuanes A, Bergmann A, Salaverria I, Werken HJGvd, Datta A, et al. Aberrant Expression of the SOX11 Oncogene in Mantle Cell Lymphoma Is Associated with Activation and De Novo 3D Looping of a Distant Enhancer Element Blood. 128: 459-459. DOI: 10.1182/Blood.V128.22.459.459 |
0.348 |
|
| 2015 |
Serra F, Di Stefano M, Spill YG, Cuartero Y, Goodstadt M, Baù D, Marti-Renom MA. Restraint-based three-dimensional modeling of genomes and genomic domains. Febs Letters. PMID 25980604 DOI: 10.1016/J.Febslet.2015.05.012 |
0.371 |
|
| 2015 |
Santpere G, Carnero-Montoro E, Petit N, Serra F, Hvilsom C, Rambla J, Heredia-Genestar JM, Halligan DL, Dopazo H, Navarro A, Bosch E. Analysis of Five Gene Sets in Chimpanzees Suggests Decoupling between the Action of Selection on Protein-Coding and on Noncoding Elements. Genome Biology and Evolution. 7: 1490-505. PMID 25977458 DOI: 10.1093/Gbe/Evv082 |
0.711 |
|
| 2015 |
Trussart M, Serra F, Baù D, Junier I, Serrano L, Marti-Renom MA. Assessing the limits of restraint-based 3D modeling of genomes and genomic domains. Nucleic Acids Research. 43: 3465-77. PMID 25800747 DOI: 10.1093/Nar/Gkv221 |
0.365 |
|
| 2014 |
Le Dily F, Baù D, Pohl A, Vicent GP, Serra F, Soronellas D, Castellano G, Wright RH, Ballare C, Filion G, Marti-Renom MA, Beato M. Distinct structural transitions of chromatin topological domains correlate with coordinated hormone-induced gene regulation. Genes & Development. 28: 2151-62. PMID 25274727 DOI: 10.1101/Gad.241422.114 |
0.426 |
|
| 2013 |
Mensch J, Serra F, Lavagnino NJ, Dopazo H, Hasson E. Positive selection in nucleoporins challenges constraints on early expressed genes in Drosophila development. Genome Biology and Evolution. 5: 2231-41. PMID 24171912 DOI: 10.1093/Gbe/Evt156 |
0.732 |
|
| 2013 |
Serra F, Becher V, Dopazo H. Neutral Theory Predicts the Relative Abundance and Diversity of Genetic Elements in a Broad Array of Eukaryotic Genomes Plos One. 8. PMID 23798991 DOI: 10.1371/Journal.Pone.0063915 |
0.694 |
|
| 2012 |
Lavagnino N, Serra F, Arbiza L, Dopazo H, Hasson E. Evolutionary Genomics of Genes Involved in Olfactory Behavior in the Drosophila melanogaster Species Group. Evolutionary Bioinformatics Online. 8: 89-104. PMID 22346339 DOI: 10.4137/Ebo.S8484 |
0.742 |
|
| 2012 |
Gonçalves LG, Borges N, Serra F, Fernandes PL, Dopazo H, Santos H. Evolution of the biosynthesis of di-myo-inositol phosphate, a marker of adaptation to hot marine environments. Environmental Microbiology. 14: 691-701. PMID 22026421 DOI: 10.1111/J.1462-2920.2011.02621.X |
0.715 |
|
| 2011 |
Lüke L, Vicens A, Serra F, Luque-Larena JJ, Dopazo H, Roldan ER, Gomendio M. Sexual selection halts the relaxation of protamine 2 among rodents. Plos One. 6: e29247. PMID 22216223 DOI: 10.1371/Journal.Pone.0029247 |
0.684 |
|
| 2011 |
Sánchez R, Serra F, Tárraga J, Medina I, Carbonell J, Pulido L, de María A, Capella-Gutíerrez S, Huerta-Cepas J, Gabaldón T, Dopazo J, Dopazo H. Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing. Nucleic Acids Research. 39: W470-4. PMID 21646336 DOI: 10.1093/Nar/Gkr408 |
0.66 |
|
| 2011 |
Martín-Trillo M, Grandío EG, Serra F, Marcel F, Rodríguez-Buey ML, Schmitz G, Theres K, Bendahmane A, Dopazo H, Cubas P. Role of tomato BRANCHED1-like genes in the control of shoot branching. The Plant Journal : For Cell and Molecular Biology. 67: 701-14. PMID 21554455 DOI: 10.1111/J.1365-313X.2011.04629.X |
0.724 |
|
| 2011 |
Serra F, Arbiza L, Dopazo J, Dopazo H. Natural selection on functional modules, a genome-wide analysis. Plos Computational Biology. 7: e1001093. PMID 21390268 DOI: 10.1371/Journal.Pcbi.1001093 |
0.751 |
|
| 2011 |
Marigorta UM, Lao O, Casals F, Calafell F, Morcillo-Suárez C, Faria R, Bosch E, Serra F, Bertranpetit J, Dopazo H, Navarro A. Recent human evolution has shaped geographical differences in susceptibility to disease. Bmc Genomics. 12: 55. PMID 21261943 DOI: 10.1186/1471-2164-12-55 |
0.672 |
|
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