| Nextflow enables reproducible computational workflows P Di Tommaso, M Chatzou, EW Floden, PP Barja, E Palumbo, ... Nature biotechnology 35 (4), 316-319, 2017 | 4145 | 2017 |
| The nf-core framework for community-curated bioinformatics pipelines PA Ewels, A Peltzer, S Fillinger, H Patel, J Alneberg, A Wilm, MU Garcia, ... Nature biotechnology 38 (3), 276-278, 2020 | 3416 | 2020 |
| T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension P Di Tommaso, S Moretti, I Xenarios, M Orobitg, A Montanyola, JM Chang, ... Nucleic acids research 39 (suppl_2), W13-W17, 2011 | 1393 | 2011 |
| TCS: a new multiple sequence alignment reliability measure to estimate alignment accuracy and improve phylogenetic tree reconstruction JM Chang, P Di Tommaso, C Notredame Molecular biology and evolution 31 (6), 1625-1637, 2014 | 232 | 2014 |
| AMPA: an automated web server for prediction of protein antimicrobial regions M Torrent, P Di Tommaso, D Pulido, MV Nogués, C Notredame, E Boix, ... Bioinformatics 28 (1), 130-131, 2012 | 198 | 2012 |
| The impact of Docker containers on the performance of genomic pipelines P Di Tommaso, E Palumbo, M Chatzou, P Prieto, ML Heuer, C Notredame PeerJ 3, e1273, 2015 | 179 | 2015 |
| Accurate multiple sequence alignment of transmembrane proteins with PSI-Coffee JM Chang, P Di Tommaso, JF Taly, C Notredame BMC bioinformatics 13 (Suppl 4), S1, 2012 | 147 | 2012 |
| 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 | 125 | 2011 |
| 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, 2013 | 86 | 2013 |
| PSI/TM-Coffee: a web server for fast and accurate multiple sequence alignments of regular and transmembrane proteins using homology extension on reduced databases EW Floden, PD Tommaso, M Chatzou, C Magis, C Notredame, JM Chang Nucleic acids research 44 (W1), W339-W343, 2016 | 82 | 2016 |
| TCS: a web server for multiple sequence alignment evaluation and phylogenetic reconstruction JM Chang, P Di Tommaso, V Lefort, O Gascuel, C Notredame Nucleic Acids Research 43 (W1), W3-W6, 2015 | 67 | 2015 |
| Workflows community summit 2022: A roadmap revolution RF Da Silva, RM Badia, V Bala, D Bard, PT Bremer, I Buckley, ... arXiv preprint arXiv:2304.00019, 2023 | 49 | 2023 |
| Scalable workflows and reproducible data analysis for genomics F Strozzi, R Janssen, R Wurmus, MR Crusoe, G Githinji, P Di Tommaso, ... Evolutionary Genomics: Statistical and Computational Methods, 723-745, 2019 | 42 | 2019 |
| Cloud-Coffee: implementation of a parallel consistency-based multiple alignment algorithm in the T-Coffee package and its benchmarking on the Amazon Elastic-Cloud P Di Tommaso, M Orobitg, F Guirado, F Cores, T Espinosa, C Notredame Bioinformatics 26 (15), 1903-1904, 2010 | 42 | 2010 |
| Large multiple sequence alignments with a root-to-leaf regressive method E Garriga, P Di Tommaso, C Magis, I Erb, L Mansouri, A Baltzis, ... Nature biotechnology 37 (12), 1466-1470, 2019 | 40 | 2019 |
| Empowering bioinformatics communities with Nextflow and nf-core BE Langer, A Amaral, MO Baudement, F Bonath, M Charles, PK Chitneedi, ... Genome Biology 26 (1), 228, 2025 | 39 | 2025 |
| Workflows community summit: Bringing the scientific workflows community together RF da Silva, H Casanova, K Chard, D Laney, D Ahn, S Jha, C Goble, ... arXiv preprint arXiv:2103.09181, 2021 | 31 | 2021 |
| nf-core/rnaseq: nf-core/rnaseq v3. 14.0-Hassium Honey Badger H Patel, P Ewels, A Peltzer, J Manning, O Botvinnik, G Sturm, MU Garcia, ... Zenodo, 2024 | 27 | 2024 |
| nf-core/rnaseq: nf-core/rnaseq v3. 0-Silver Shark H Patel, P Ewels, A Peltzer, R Hammarén, O Botvinnik, G Sturm, ... Zenodo, 2020 | 21 | 2020 |
| nf-core/rnaseq: nf-core/rnaseq v3. 12.0-Osmium Octopus H Patel, P Ewels, A Peltzer, O Botvinnik, G Sturm, D Moreno, P Vemuri, ... Zenodo, 2023 | 20 | 2023 |
Cedric NotredameCentre for Genomic Regulation, SpainVerified email at crg.eu
