Publications

The complete list of publications is available at these databases:

• Europe PubMed Central (profile),
• Google Scholar,
• ORCID,
• Scopus.

Find below a selection organised by themes:

• Ensembl and TreeFam methods
• Genomicus and ancestral genome reconstruction
• Quest for Orthologs consortium
• Tree of Life Informatics Infrastructure
• Genome analysis
• Ensembl yearly NAR updates

Ensembl and TreeFam methods

Scripting Analyses of Genomes in Ensembl Plants.

Contreras-Moreira B, Naamati G, Rosello M, Allen JE, Hunt SE, Muffato M, et al.
Methods in molecular biology (Clifton, N.J.), 2443, pages 27-55, 2022
DOI: 10.1007/978-1-0716-2067-0_2

ncRNA orthologies in the vertebrate lineage.

Pignatelli M, Vilella AJ, Muffato M, Gordon L, White S, Flicek P, Herrero J.
Database : the journal of biological databases and curation, 2016, bav127
DOI: 10.1093/database/bav127

Ensembl comparative genomics resources.

Herrero J, Muffato M, et al.
Database : the journal of biological databases and curation, 2016, bav096
DOI: 10.1093/database/bav096

Current Methods for Automated Filtering of Multiple Sequence Alignments Frequently Worsen Single-Gene Phylogenetic Inference.

Tan G, Muffato M, Ledergerber C, Herrero J, Goldman N, Gil M, Dessimoz C.
Systematic biology, 64 (5), pages 778-791, 2015 Sep
DOI: 10.1093/sysbio/syv033

TreeFam v9: a new website, more species and orthology-on-the-fly.

Schreiber F, Patricio M, Muffato M, Pignatelli M, Bateman A.
Nucleic acids research, 42 (Database issue), pages D922-5, 2014 Jan
DOI: 10.1093/nar/gkt1055

Genomicus and ancestral genome reconstruction

Reconstruction of hundreds of reference ancestral genomes across the eukaryotic kingdom.

Muffato M, Louis A, Nguyen NTT, Lucas J, Berthelot C, Roest Crollius H.
Nature ecology & evolution, 7 (3), pages 355-366, 2023 Mar
DOI: 10.1038/s41559-022-01956-z

The 3D organization of chromatin explains evolutionary fragile genomic regions.

Berthelot C, Muffato M, Abecassis J, Roest Crollius H.
Cell reports, 10 (11), pages 1913-1924, 2015 Mar
DOI: 10.1016/j.celrep.2015.02.046

Genomicus update 2015: KaryoView and MatrixView provide a genome-wide perspective to multispecies comparative genomics.

Louis A, Nguyen NT, Muffato M, Roest Crollius H.
Nucleic acids research, 43 (Database issue), pages D682-9, 2015 Jan
DOI: 10.1093/nar/gku1112

PhylDiag: identifying complex synteny blocks that include tandem duplications using phylogenetic gene trees.

Lucas JM, Muffato M, Roest Crollius H.
BMC bioinformatics, 15, pages 268, 2014 Aug
DOI: 10.1186/1471-2105-15-268

Genomicus: five genome browsers for comparative genomics in eukaryota.

Louis A, Muffato M, Roest Crollius H.
Nucleic acids research, 41 (Database issue), pages D700-5, 2013 Jan
DOI: 10.1093/nar/gks1156

Genomicus: a database and a browser to study gene synteny in modern and ancestral genomes.

Muffato M, Louis A, Poisnel CE, Roest Crollius H.
Bioinformatics (Oxford, England), 26 (8), pages 1119-1121, 2010 Apr
DOI: 10.1093/bioinformatics/btq079

Paleogenomics in vertebrates, or the recovery of lost genomes from the mist of time.

Muffato M, Roest Crollius H.
BioEssays : news and reviews in molecular, cellular and developmental biology, 30 (2), pages 122-134, 2008 Feb
DOI: 10.1002/bies.20707

Quest for Orthologs consortium

Ten Years of Collaborative Progress in the Quest for Orthologs.

Linard B et al.
Molecular biology and evolution, 38 (8), pages 3033-3045, 2021 Jul
DOI: 10.1093/molbev/msab098

The Quest for Orthologs benchmark service and consensus calls in 2020.

Altenhoff AM et al.
Nucleic acids research, 48 (W1), pages W538-W545, 2020 Jul
DOI: 10.1093/nar/gkaa308

Advances and Applications in the Quest for Orthologs.

Glover N et al.
Molecular biology and evolution, 36 (10), pages 2157-2164, 2019 Oct
DOI: 10.1093/molbev/msz150

Gearing up to handle the mosaic nature of life in the quest for orthologs.

Forslund K, Pereira C, Capella-Gutierrez S, da Silva AS, Altenhoff A, Huerta-Cepas J, Muffato M, et al.
Bioinformatics (Oxford, England), 34 (2), pages 323-329, 2018 Jan
DOI: 10.1093/bioinformatics/btx542

Standardized benchmarking in the quest for orthologs.

Altenhoff AM et al.
Nature methods, 13 (5), pages 425-430, 2016 May
DOI: 10.1038/nmeth.3830

Quest for Orthologs Entails Quest for Tree of Life: In Search of the Gene Stream.

Boeckmann B, Marcet-Houben M, Rees JA, Forslund K, Huerta-Cepas J, Muffato M, et al.
Genome biology and evolution, 7 (7), pages 1988-1999, 2015 Jul
DOI: 10.1093/gbe/evv121

Big data and other challenges in the quest for orthologs.

Sonnhammer EL et al.
Bioinformatics (Oxford, England), 30 (21), pages 2993-2998, 2014 Nov
DOI: 10.1093/bioinformatics/btu492

Toward community standards in the quest for orthologs.

Dessimoz C et al.
Bioinformatics (Oxford, England), 28 (6), pages 900-904, 2012 Mar
DOI: 10.1093/bioinformatics/bts050

Tree of Life Informatics Infrastructure

Automated Discovery of Container Executables

Vanessa Sochat, Matthieu Muffato, Audrey Stott, Marco De La Pierre, Georgia Stuart
Journal of Open Research Software, 11, 2023
DOI: 10.5334/jors.451

Genome analysis

A chromosome-level reference genome for the critically endangered Southern Corroboree frog (Pseudophryne corroboree)

Kosch TA et al.
Wellcome Open Res, 2025-04-30
DOI: 10.12688/wellcomeopenres.23820.1

Hagfish genome elucidates vertebrate whole-genome duplication events and their evolutionary consequences.

Yu D, Ren Y, Uesaka M, Beavan AJS, Muffato M, et al.
Nature ecology & evolution, 8 (3), pages 519-535, 2024 Mar
DOI: 10.1038/s41559-023-02299-z

The tuatara genome reveals ancient features of amniote evolution.

Gemmell NJ et al.
Nature, 584 (7821), pages 403-409, 2020 Aug
DOI: 10.1038/s41586-020-2561-9

The comparative genomics and complex population history of Papio baboons.

Rogers J et al.
Science advances, 5 (1), pages eaau6947, 2019 Jan
DOI: 10.1126/sciadv.aau6947

Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes.

Thybert D et al.
Genome research, 28 (4), pages 448-459, 2018 Apr
DOI: 10.1101/gr.234096.117

LaGomiCs-Lagomorph Genomics Consortium: An International Collaborative Effort for Sequencing the Genomes of an Entire Mammalian Order.

Fontanesi L et al.
The Journal of heredity, 107 (4), pages 295-308, 2016 Jul
DOI: 10.1093/jhered/esw010

Gibbon genome and the fast karyotype evolution of small apes.

Carbone L et al.
Nature, 513 (7517), pages 195-201, 2014 Sep
DOI: 10.1038/nature13679

The zebrafish reference genome sequence and its relationship to the human genome.

Howe K, Clark MD, Torroja CF, Torrance J, Berthelot C, Muffato M, et al.
Nature, 496 (7446), pages 498-503, 2013 Apr
DOI: 10.1038/nature12111

Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution.

Smith JJ et al.
Nature genetics, 45 (4), pages 415-21, 421e1-2, 2013 Apr
DOI: 10.1038/ng.2568

Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate.

Denoeud F et al.
Science (New York, N.Y.), 330 (6009), pages 1381-1385, 2010 Dec
DOI: 10.1126/science.1194167

Ensembl yearly NAR updates

Ensembl (Vertebrates)

2022, 2021, 2020, 2019, 2018, 2017, 2016, 2015, 2014, 2013, 2012

Ensembl Genomes

2022, 2020