Complete list

Our public list of source data:     FIGSHARE

2016

Arnau Sebé-Pedrós, Marcia Ivonne Peña, Salvador Capella-Gutiérrez, Meritxell Antó, Toni Gabaldón, Iñaki Ruiz-Trillo & Eduard Sabidó. (2016)
High-Throughput Proteomics Reveals the Unicellular Roots of Animal Phosphosignaling and Cell Differentiation.
Developmental Cell 39 (2):  p186–197.

Alicia S. Arroyo, David López-Escardó, Colomban de Vargas & Iñaki Ruiz-Trillo. (2016)
Hidden diversity of Acoelomorpha revealed through metabarcoding.
Biology Letters 12: 20160674.  doi.org/10.1098/rsbl.2016.0674
Access supplementary material

Arnau Sebé-Pedrós & Iñaki Ruiz-Trillo. (2016)
Evolution and Classification of the T-Box Transcription Factor Family.
Current Topics in Developmental Biology (in press)

-Maureen A. O’Malley, Jeremy G. Wideman & Iñaki Ruiz-Trillo. (2016)
Losing complexity: the role of simplification in macroevolution.
Trends in Ecology and Evolution 31 (8): 608–621

Sebastián R. Najle, María Celeste Molina, Iñaki Ruiz-Trillo & Antonio D. Uttaro. (2016)
Sterol metabolism in the filasterean Capsaspora owczarzaki has features that resemble both fungi and animals. 
Open Biology 6: 160029.

Arnau Sebé-Pedrós, Cecillia Ballaré, Helena Parra-Acero, Cristina Chiva, Juan J. Tena, Eduard Sabidó, José Luis Gómez-Skarmeta, Luciano Di Croce, Iñaki Ruiz-Trillo. (2016)
The Dynamic Regulatory Genome of Capsaspora and the Origin of Animal Multicellularity.
Cell  165 (5): 1224–1237. doi: 10.1016/j.cell.2016.03.034
(see Nature’s news and views). Watch video abstract:

-Mariona Esquerdo, Xavier Grau-Bové, Alejandro Garanto, Vasileios Toulis, Sílvia Garcia-Monclús, Erica Millo, Mª José López-Iniesta, Víctor Abad-Morales, Iñaki Ruiz-Trillo, Gemma Marfany. (2016)
Expression atlas of the deubiquitinating enzymes in the adult mouse retina, their evolutionary diversification and phenotypic roles.
Plos One 11(3): e0150364.  doi:10.1371/journal.pone.0150364

-David A. Gold, Jonathan Grabenstatter, Alex de Mendoza, Ana Riesgo, Iñaki Ruiz-Trillo and Roger E. Summons. (2016)
Sterol and genomic analyses validate the sponge biomarker hypothesis.
Proceedings National Academic of Sciences USA 113(10): 2684-2689 doi: 10.1073/pnas.1512614113

Iñaki Ruiz-Trillo (2016)
What are the genomes of the premetazoan lineages telling us about the origins of metazoa?
Multicellularity: Origins and Evolution ISBN: 9780262034159

-Iñaki Ruiz-Trillo & Jordi Paps. (2016)
Acoelomorpha: earliest-branching bilaterians or deuterostomes?
Organisms Diversity and Evolution 16: 391. doi:10.1007/s13127-015-0239-1


2015

Alex de MendozaHiroshi Suga, Jon Permanyer, Manuel Irimia, Iñaki Ruiz-Trillo. (2015)
Complex transcriptional regulation and independent evolution of fungal-like traits in a relative of animals.
eLife 2015;10.7554/eLife.08904
(see also 
http://dx.doi.org/10.6084/m9.figshare.1403592)

Guifré Torruella, Alex de Mendoza, Xavier Grau-Bové, Meritxell Antó, Mark A. Chaplin, Javier del Campo, Laura Eme, Gregorio Pérez-Cordón, Christopher M. Whipps, Krista M. Nichols, Richard Paley, Andrew J. Roger, Ariadna Sitjà-Bobadilla, Stuart Donachie, and Iñaki Ruiz-Trillo. (2015)
Phylogenomics reveals convergent evolution of lifestyles in close relatives of animals and fungi.

Current Biology 25(18):2404-10.

Xavier 
Grau-BovéIñaki Ruiz-Trillo, & Francisco Rodriguez-Pascual. (2015)
Origin and evolution of lysyl oxidases.
Scientific Reports5, 10568. doi:10.1038/srep10568 

-Kamil J. Alzayady, Arnau Sebé-Pedrós, Rahul Chandrasekhar, Liwei Wang, Iñaki Ruiz- Trillo, David I. Yule. (2015)
Tracing the Evolutionary History of Inositol, 1, 4, 5-trisphosphate receptor: Insights from Analyses of Capsaspora owczarzaki Ca2+ Release Channel Orthologs.
Molecular Biology and Evolution 32 (9): 2236-2253.  doi: 10.1093/molbev/msv098Evolutionary transitions to multicell life

Iñaki Ruiz-Trillo & Aurora Nedelcu (editors). (2015)
Evolutionary transitions to multicellular life: principles and mechanisms
Advances in Marine Genomics Series. Springer.

Hiroshi Suga and Iñaki Ruiz-Trillo. (2015)
Unraveling the origin of animal multicellularity.
Jikken Igaku (Experimental Medicine) vol.33, no.6, pp968-973.

Javier del Campo, Diego Mallo, Ramon Massana, Colomban de Vargas, Tom A. Richards & Iñaki Ruiz-Trillo. (2015)
Diversity and distribution of unicellular opisthokonts along the European coast analyzed using high-throughput sequencing. 
Environmental Microbiology 17: 3195–3207. doi:10.1111/1462-2920.12759


2014

Xavier Grau-BovéArnau Sebé-Pedrós & Iñaki Ruiz-Trillo. (2014)
The eukaryotic ancestor had a complex ubiquitin signalling system of archaeal origin.
Molecular Biology and Evolution 32 (3): 726-739.

Alex de Mendoza & Iñaki Ruiz-Trillo. (2014)
Forward genetics for back-in-time questions.
eLife 3:e04070. doi: 10.7554/eLife.04070

Javier del Campo, Michael E. Sieracki, Robert Molestina, Patrick Keeling, Ramon Massana & Iñaki Ruiz-Trillo. (2014)
The others: our biased perspective of eukaryotic genomics.
Trends in Ecology and Evolution 29(5): 252-259.

-Alex de MendozaArnau Sebé-Pedrós Iñaki Ruiz-Trillo. (2014)
The evolution of the GPCR signalling system in eukaryotes: modularity, conservation and the transition to metazoan multicellularity.molecular bio and evo
Genome Biology and Evolution 6(3):606-19.

Arnau Sebé-PedrósXavier Grau-Bové, Thomas A. Richards & Iñaki Ruiz-Trillo. (2014)
Evolution and classification of myosins, a paneukaryotic whole genome approach.
Genome Biology and Evolution 6(2):290-305.
Access myosins dataset

Hiroshi SugaGuifré Torruella, Gertraud Burger, Matthew W. Brown & Iñaki Ruiz-Trillo. (2014)
Earliest holozoan expansion of phosphotyrosine signaling.
Molecular Biology and Evolution 31 (3): 517-528.

Bénédicte Desvoyes, Alex de Mendoza, Iñaki Ruiz-Trillo and Crisanto Gutierrez. (2014)
Novel roles of plant RETINOBLASTOMA-RELATED (RBR) protein in cell proliferation and asymmetric cell division.
Journal of Experimental Botany 65(10): 2657-66.


2013

Arnau Sebé-Pedrós, Manuel Irimia, Javier del CampoHelena Parra-Acero, Carsten Russ, Chad Nusbaum, Benjamin J. Blencowe & Iñaki Ruiz-Trillo. (2013)
Regulated aggregative multicellularity in a close unicellular relative of Metazoa.
eLife 2013;2:e01287
Access RNAseq data (FPKMs).

Alex de MendozaArnau Sebé-Pedrós, Martin Sebastijan Šestak, Marija Matejčić,Guifré Torruella, Tomislav Domazet-Lošo & Iñaki Ruiz-Trillo. (2013)
Transcription factor evolution in eukaryotes and the assembly of the regulatory toolkit in multicellular lineages.
Proceedings National Academic of Sciences USA 110 (50) E4858-E4866.

Arnau Sebé-Pedrós, Ana Ariza-Cosano, Matthew T. Weirauch, Sven Leininger, Ally Yang, Guifré Torruella, Marcin Adamski, Maja Adamska, Timothy R. Hughes, José Luis Gómez-Skarmeta & Iñaki Ruiz-Trillo. (2013)
Early evolution of the T-box transcription factor family.
Proceedings National Academic of Sciences USA 110(40):16050-5.

Arnau Sebé-Pedrós, Pawel Burkhardt, Núria Sánchez-Pons, Stephen R. Fairclough, B. Franz Lang, Nicole King & Iñaki Ruiz-Trillo. (2013)
Insights into the origin of metazoan filopodia and microvilli.
Molecular Biology and Evolution 30(9):2013-23.

-Hiroshi Suga, Zehua Chen, Alex de MendozaArnau Sebé-Pedrós, Matthew W. Brown, Eric Kramer, Martin Carr, Pierre Kerner, Michel Vervoort, Núria Sánchez-PonsGuifré TorruellaRomain Derelle, Gerard Manning, B. Franz. Lang, Carsten Russ, Brian J. Haas, Andrew J. Roger, Chad Nusbaum & Iñaki Ruiz-Trillo. (2013)
The Capsaspora genome reveals a complex unicellular prehistory of animals.
Nature Communications 4: 2325 doi: 10.1038/ncomms3325 (2013).

-José M. Martín-Durán, Alex de Mendoza, Arnau Sebé-PedrósIñaki Ruiz-Trillo & Andreas Hejnol. (2013)
A broad genomic survey reveals multiple origins and frequent losses in the evolution of respiratory hemerythrins and hemocyanins. 
Genome Biology and Evolution 5(7):1435-42.

Xavier Grau-BovéArnau Sebé-Pedrós & Iñaki Ruiz-Trillo. (2013)
A genomic survey of HECT ubiquitin ligases in eukaryotes reveals independent expansions of the HECT system in several lineages.
Genome Biology and Evolution 5(5):833-47. doi: 10.1093/gbe/evt052.
Access supplementary data
Access alignments
.

Javier del Campo & Iñaki Ruiz-Trillo. (2013)
Environmental survey meta-analysis reveals hidden diversity among unicellular opisthokonts.el oriden de la milticelularidad
Molecular Biology and Evolution 30(4): 802-805.
Access alignment.

Alex de MendozaArnau Sebé-Pedrós & Iñaki Ruiz-Trillo. (2013)
El origen de la multicelularidad.
Investigación y Ciencia, Febrero 2013 pp.32-39.

Hiroshi Suga & Iñaki Ruiz-Trillo. (2013)
Development of ichthyosporeans sheds light on the origin of metazoan multicellularity.
Developmental Biology 377, 284-292.

Jordi PapsLuis A. Medina-Chacón, Wyth Marshall, Hiroshi Suga & Iñaki Ruiz-Trillo. (2013)
Molecular phylogeny of Unikonts: new insights into the position of apusomonads and ancyromonads and the internal relationships of opisthokonts.
Protist 164(1):2-12.
Access sequences
Concatenated alignment


2012

-Kira P. Schultheiss, Hiroshi SugaIñaki Ruiz-Trillo & W. Todd Miller. (2012)
Lack of Csk-mediated negative regulation in a unicellular Src kinase.
Biochemistry 51 (41), pp 8267–8277.science signaling

Hiroshi Suga, Michael Dacre, Alex de Mendoza, Kamran Shalchian-Tabrizi, Gerard Manning & Iñaki Ruiz-Trillo. (2012)
Genomic Survey of Premetazoans Shows Deep Conservation of Cytoplasmic Tyrosine Kinases and Multiple Radiations of Receptor Tyrosine Kinases.
Science Signaling 5 (222), ra35 [DOI: 10.1126/scisignal.2002733] (see electronic reprint)
(listen to Science Signaling Podcast)

-Naiara Rodríguez-Ezpeleta, David Moreira, Iñaki Ruiz-Trillo. (2012)
Amoebozoos, Cromalveolados, Rizarios y Excavados.
In “El árbol de la vida: sistemática y evolución de los seres vivos”, Zardoya R. & Vargas P. eds.

Iñaki Ruiz-Trillo. (2012)
Eucariotas.
In “El árbol de la vida: sistemática y evolución de los seres vivos”, Zardoya R. & Vargas P. eds.

-Marta Riutort, Jordi PapsIñaki Ruiz-Trillo. (2012)
Bilaterales.
In “El árbol de la vida: sistemática y evolución de los seres vivos”, Zardoya R. & Vargas P. eds.

Arnau Sebé-PedrósYonggang Zheng, Iñaki Ruiz-Trillo & Duojia Pan. (2012)
Premetazoan origin of the Hippo signaling pathway.
Cell Reports 1(1): 13-20. doi:10.1016/j.cel- rep.2011.11.004
(see news in Cell Reports) (chosen among the Best of Cell Reports articles of 2012).
Access sequences

Guifré TorruellaRomain Derelle, Jordi Paps, B. Franz Lang, Andrew J Roger, Kamran Shalchian-Tabrizi & Iñaki Ruiz-Trillo. (2012)
Phylogenetic relationships within the Opisthokonta based on phylogenomic analyses of conserved single copy protein domains.
Molecular Biology and Evolution 29(2): 531-544.
Access matrix

John D. L. Shadwick Iñaki Ruiz-Trillo. (2012)
A genomic survey shows that the haloarchaeal type Tyrosyl-Synthetase is not a Synapomorphy of Opisthokonts.
European Journal of Protistology 48(1):89-93. 


2011

Alex de Mendoza & Iñaki Ruiz-Trillo(2011)
New genomes, new taxa and deep questions in the eukaryotic tree of life: a meeting report on the EMBO comparative genomics conference
Evodevo 2(1):22. 

-Agatha Schlüter, Iñaki Ruiz-Trillo & Aurora Pujol. (2011)
Phylogenomic evidence for a myxococcal contribution to the mitochondrial fatty acid beta-oxidation
Plos ONE 6(7): e21989. doi:10.1371/journal.pone.0021989

Alex de Mendoza & Iñaki Ruiz-Trillo. (2011)
The mysterious Evolutionary Origin for the GNE gene and the root of Bilateria
Molecular Biology and Evolution 28(11): 2987-91.
Access alignments

-Susan Young, D. Diolaiti, M. Conacci-Sorrell, Iñaki Ruiz-Trillo, R. M. Eisenman & Nicole King. (2011)
Premetazoan Ancestry of the Myc-Max Network.
Molecular Biology and Evolution 28(10): 2961-71.

Arnau Sebé-PedrósAlex de Mendoza, B. Franz Lang, Bernie M. Degnan & Iñaki Ruiz-Trillo. (2011)
Unexpected repertoire of metazoan transcription factors in the unicellular holozoan Capsaspora owczarzaki
Molecular Biology and Evolution 28(3): 1241-54. 


2010

-Maria José Barberà*, Iñaki Ruiz-Trillo*, Julia Y. A. Tufts, Bery Amandine, Jeffrey D. Silberman & Andrew J. Roger. (*co-authors) (2010)
Sawyeria marylandensis (Heterolobosea) has a hydrogenosome with novel metabolic properties. 
Eukaryotic Cell 9(12):1913-24.

Jordi PapsIñaki Ruiz-Trillo. (2010)
Animals and their unicellular ancestors.
In: Encyclopedia of Life Sciences 2010, John Wiley & Sons, Ltd: Chichester.

Arnau Sebé-PedrósIñaki Ruiz-Trillo. (2010)
The integrin-mediated adhesion complex: cooption of signaling systems at the dawn of Metazoa.
Communicative & Integrative Biology 3:5 1-3.

Alex de Mendoza, Hiroshi SugaIñaki Ruiz-Trillo. (2010)evoloution of multicell organisms
Evolution of the MAGUK protein gene family in premetazoan lineages.
BMC Evolutionary Biology 10(1): 93.
Alignments

Arnau Sebé-Pedrós, Andrew J. Roger, Franz B. Lang, Nicole King & Iñaki Ruiz-Trillo. (2010)
Ancient origin of integrin-mediated adhesion and signaling machinery. 
Proceedings National Academic of Sciences USA 107(22): 10142-7.

Iñaki Ruiz-Trillo. (2010)
Animales y sus ancestros unicelulares. Una visión filogenómica. 
In “Adaptación y Evolución. 150 años después del Origen de las Especies SESBE 2009”. Dopazo. & Navarro. eds, Obrapropia Editorial, Valencia.
2010


2009

Guifré Torruella, Hiroshi Suga, Marta Riutort, Juli Peretó & Iñaki Ruiz-Trillo. (2009)
The evolutionary history of lysine biosynthesis pathways within eukaryotes.
Journal of Molecular Evolution 69(3): 240-248.
Access alignments


2008

Iñaki Ruiz-Trillo, Andrew J. Roger, Gertraud Burger, Michael W. Gray & B. Franz Lang. (2008)
A phylogenomic investigation into the origin of Metazoa.
Molecular Biology and Evolution 25 (4): 664-672.
Access alignments

-E. Bapteste, E. Susko, J. Leigh, I. Ruiz-Trillo, J. Bucknam & W. F. Doolittle.(2008)
Alternative Methods for Concatenation of Core Genes Indicate a Lack of Resolution in Deep Nodes of the Prokaryotic Phylogeny. 
Molecular Biology and Evolution 25(1): 83-91.


2007

Iñaki Ruiz-Trillo, Gertraud Burger, Peter W. H. Holland, Nicole King, B. Franz Lang, Andrew J. Roger & Michael W. Gray. (2007)
The origins of multicellularity: a multi-taxon genome initiative. 
Trends in Genetics 23(3): 113-118.

-Maria J. Barberà, Iñaki Ruiz-Trillo, Jessica Leigh, Laura A. Hug & Andrew J. Roger. (2007)
The diversity of mitochondrion-related organelles amongst eukaryotic microbes. 
In “Origins of Mitochondria and Hydrogenosomes”, Martin W. ed., Springer, Heidelberg.


2006

Iñaki Ruiz-Trillo, Christopher E. Lane, John M. Archibald & Andrew J. Roger. (2006)
Insights into the evolutionary origin and genome architecture of the unicellular opisthokonts Capsaspora owczarzaki and Sphaeroforma arctica
Journal of Eukaryotic Microbiology 53(5): 1-6.

-Sina M. Adl, Iñaki Ruiz-Trillo & Melanie L. Wilson. (2006)
Observations on a Geocentrophora sp. (Lecitoepitheliata) flatworm from forest soils in Nova Scotia. 
Journal of Natural History 40 (23-24): 1381-1387.


2004

Iñaki Ruiz-Trillo, Yuji Inagaki, Lesley A. Davis, Sigmund Sperstad, Bjarne Landfald & Andrew J. Roger. (2004)
Capsaspora owczarzaki is an independent opisthokont lineage. 
Current Biology 14: R946-R947.

Iñaki Ruiz-Trillo, Marta Riutort, H. Matthew Fourcade, Jaume Baguñà & Jeffrey L. Boore. (2004)
Mitochondrial genome data support the basal position of Acoelomorpha and the polyphyly of the Platyhelminthes. 
Molecular Phylogenetics and Evolution 33: 321- 332, 2004.


2002

I. Ruiz-Trillo, J. Paps, M. Loukota, C. Ribera, U. Jondelius, J. Baguñà & M. Riutort. (2002)
A phylogenetic analysis of Myosin Heavy Chain type II sequences corroborates Acoela and Nemertodermatida are basal bilaterians. 
Proceedings National Academic of Sciences USA 99: 11246-11251.

-Jaume Baguñà, Iñaki Ruiz-Trillo, Jordi Paps & Marta Riutort. (2002)
Origen y evolución de los ejes corporales y la simetría bilateral en animales. 
In “Evolución: la base de la Biología” (M.Soler ed.), Proyecto Sur Editorial.

-U. Jondelius, I. Ruiz-Trillo, J. Baguñà & M. Riutort. (2002)
The Nemertodermatida are basal bilaterians and not members of the Platyhelminthes. 
Zoologica Scripta 31: 201-215.


2001

Iñaki Ruiz-Trillo. (2001)
Acoela. 
In “McGraw-Hill Encyclopedia of Science and Technology, 2001 Yearbook of Science & Technology”. McGraw-Hill, New York.

-J. Baguñà, I. Ruiz-Trillo, J. Paps, M. Loukota, C.s Ribera, U. Jondelius & M. Riutort. (2001)
The first bilaterian organisms: simple or complex? New molecular evidence.  
International Journal of Developmental Biology 45: S133-S134.


2000

-J. Baguñà, S. Carranza, J. PapsI. Ruiz-Trillo & M. Riutort. (2000)
Molecular taxonomy and phylogeny of Tricladida. 
In “Interrelationships of the Platyhelminthes”, Littlewood & Bray Ed., Taylor & Francis, London.


1999

I. Ruiz-Trillo, M. Riutort, D. T. J. Littlewood, E. A. Herniou & J. Baguñà. (1999)
Acoel flatworms: earliest extant bilaterian metazoans, not members of the Platyhelminthes. 
Science 283: 1919-1923.