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Items: 1 to 50 of 75

1.

Cell cycle transcriptomics of Capsaspora provides insights into the evolution of cyclin-CDK machinery.

Pérez-Posada A, Dudin O, Ocaña-Pallarès E, Ruiz-Trillo I, Ondracka A.

PLoS Genet. 2020 Mar 16;16(3):e1008584. doi: 10.1371/journal.pgen.1008584. eCollection 2020 Mar.

2.

Origin Recognition Complex (ORC) Evolution Is Influenced by Global Gene Duplication/Loss Patterns in Eukaryotic Genomes.

Ocaña-Pallarès E, Vergara Z, Desvoyes B, Tejada-Jimenez M, Romero-Jurado A, Galván A, Fernández E, Ruiz-Trillo I, Gutierrez C.

Genome Biol Evol. 2020 Feb 1;12(2):3878-3889. doi: 10.1093/gbe/evaa011.

3.

A unicellular relative of animals generates a layer of polarized cells by actomyosin-dependent cellularization.

Dudin O, Ondracka A, Grau-Bové X, Haraldsen AA, Toyoda A, Suga H, Bråte J, Ruiz-Trillo I.

Elife. 2019 Oct 28;8. pii: e49801. doi: 10.7554/eLife.49801.

4.

Reconstruction of protein domain evolution using single-cell amplified genomes of uncultured choanoflagellates sheds light on the origin of animals.

López-Escardó D, Grau-Bové X, Guillaumet-Adkins A, Gut M, Sieracki ME, Ruiz-Trillo I.

Philos Trans R Soc Lond B Biol Sci. 2019 Nov 25;374(1786):20190088. doi: 10.1098/rstb.2019.0088. Epub 2019 Oct 7.

5.

A global metabarcoding analysis expands molecular diversity of Platyhelminthes and reveals novel early-branching clades.

Mitsi K, Arroyo AS, Ruiz-Trillo I.

Biol Lett. 2019 Sep 27;15(9):20190182. doi: 10.1098/rsbl.2019.0182. Epub 2019 Sep 11.

6.

Reticulate evolution in eukaryotes: Origin and evolution of the nitrate assimilation pathway.

Ocaña-Pallarès E, Najle SR, Scazzocchio C, Ruiz-Trillo I.

PLoS Genet. 2019 Feb 21;15(2):e1007986. doi: 10.1371/journal.pgen.1007986. eCollection 2019 Feb.

7.

Concepts of the last eukaryotic common ancestor.

O'Malley MA, Leger MM, Wideman JG, Ruiz-Trillo I.

Nat Ecol Evol. 2019 Mar;3(3):338-344. doi: 10.1038/s41559-019-0796-3. Epub 2019 Feb 18. Review.

PMID:
30778187
8.

The Expansion of Inosine at the Wobble Position of tRNAs, and Its Role in the Evolution of Proteomes.

Rafels-Ybern À, Torres AG, Camacho N, Herencia-Ropero A, Roura Frigolé H, Wulff TF, Raboteg M, Bordons A, Grau-Bove X, Ruiz-Trillo I, Ribas de Pouplana L.

Mol Biol Evol. 2019 Apr 1;36(4):650-662. doi: 10.1093/molbev/msy245.

PMID:
30590541
9.

Revision of the Capsaspora genome using read mating information adjusts the view on premetazoan genome.

Denbo S, Aono K, Kai T, Yagasaki R, Ruiz-Trillo I, Suga H.

Dev Growth Differ. 2019 Jan;61(1):34-42. doi: 10.1111/dgd.12587. Epub 2018 Dec 25.

PMID:
30585312
10.

Unicellular Origin of the Animal MicroRNA Machinery.

Bråte J, Neumann RS, Fromm B, Haraldsen AAB, Tarver JE, Suga H, Donoghue PCJ, Peterson KJ, Ruiz-Trillo I, Grini PE, Shalchian-Tabrizi K.

Curr Biol. 2018 Oct 22;28(20):3288-3295.e5. doi: 10.1016/j.cub.2018.08.018. Epub 2018 Oct 11.

11.

Origin of exon skipping-rich transcriptomes in animals driven by evolution of gene architecture.

Grau-Bové X, Ruiz-Trillo I, Irimia M.

Genome Biol. 2018 Sep 17;19(1):135. doi: 10.1186/s13059-018-1499-9.

12.

Metabarcoding analysis on European coastal samples reveals new molecular metazoan diversity.

López-Escardó D, Paps J, de Vargas C, Massana R, Ruiz-Trillo I, Del Campo J.

Sci Rep. 2018 Jun 14;8(1):9106. doi: 10.1038/s41598-018-27509-8.

13.

Decoupling of Nuclear Division Cycles and Cell Size during the Coenocytic Growth of the Ichthyosporean Sphaeroforma arctica.

Ondracka A, Dudin O, Ruiz-Trillo I.

Curr Biol. 2018 Jun 18;28(12):1964-1969.e2. doi: 10.1016/j.cub.2018.04.074. Epub 2018 Jun 7.

14.

Transfection of Capsaspora owczarzaki, a close unicellular relative of animals.

Parra-Acero H, Ros-Rocher N, Perez-Posada A, Kożyczkowska A, Sánchez-Pons N, Nakata A, Suga H, Najle SR, Ruiz-Trillo I.

Development. 2018 May 23;145(10). pii: dev162107. doi: 10.1242/dev.162107.

15.

Characterization of a group I Nme protein of Capsaspora owczarzaki-a close unicellular relative of animals.

Ćetković H, Bosnar MH, Perina D, Mikoč A, Deželjin M, Belužić R, Bilandžija H, Ruiz-Trillo I, Harcet M.

Lab Invest. 2018 Mar;98(3):304-314. doi: 10.1038/labinvest.2017.134. Epub 2018 Feb 5.

16.

Capsaspora owczarzaki.

Ferrer-Bonet M, Ruiz-Trillo I.

Curr Biol. 2017 Sep 11;27(17):R829-R830. doi: 10.1016/j.cub.2017.05.074.

17.

Evaluation of single-cell genomics to address evolutionary questions using three SAGs of the choanoflagellate Monosiga brevicollis.

López-Escardó D, Grau-Bové X, Guillaumet-Adkins A, Gut M, Sieracki ME, Ruiz-Trillo I.

Sci Rep. 2017 Sep 8;7(1):11025. doi: 10.1038/s41598-017-11466-9.

18.

Codon adaptation to tRNAs with Inosine modification at position 34 is widespread among Eukaryotes and present in two Bacterial phyla.

Rafels-Ybern À, Torres AG, Grau-Bove X, Ruiz-Trillo I, Ribas de Pouplana L.

RNA Biol. 2018;15(4-5):500-507. doi: 10.1080/15476286.2017.1358348. Epub 2017 Sep 26.

19.

Parvularia atlantis gen. et sp. nov., a Nucleariid Filose Amoeba (Holomycota, Opisthokonta).

López-Escardó D, López-García P, Moreira D, Ruiz-Trillo I, Torruella G.

J Eukaryot Microbiol. 2018 Mar;65(2):170-179. doi: 10.1111/jeu.12450. Epub 2017 Aug 12.

20.

Dynamics of genomic innovation in the unicellular ancestry of animals.

Grau-Bové X, Torruella G, Donachie S, Suga H, Leonard G, Richards TA, Ruiz-Trillo I.

Elife. 2017 Jul 20;6. pii: e26036. doi: 10.7554/eLife.26036.

21.

The origin of Metazoa: a unicellular perspective.

Sebé-Pedrós A, Degnan BM, Ruiz-Trillo I.

Nat Rev Genet. 2017 Aug;18(8):498-512. doi: 10.1038/nrg.2017.21. Epub 2017 May 8. Review.

PMID:
28479598
22.

Evolution and Classification of the T-Box Transcription Factor Family.

Sebé-Pedrós A, Ruiz-Trillo I.

Curr Top Dev Biol. 2017;122:1-26. doi: 10.1016/bs.ctdb.2016.06.004. Epub 2016 Jul 25. Review.

PMID:
28057261
23.

High-Throughput Proteomics Reveals the Unicellular Roots of Animal Phosphosignaling and Cell Differentiation.

Sebé-Pedrós A, Peña MI, Capella-Gutiérrez S, Antó M, Gabaldón T, Ruiz-Trillo I, Sabidó E.

Dev Cell. 2016 Oct 24;39(2):186-197. doi: 10.1016/j.devcel.2016.09.019. Epub 2016 Oct 13.

24.

Hidden diversity of Acoelomorpha revealed through metabarcoding.

Arroyo AS, López-Escardó D, de Vargas C, Ruiz-Trillo I.

Biol Lett. 2016 Sep;12(9). pii: 20160674.

25.

Sterol metabolism in the filasterean Capsaspora owczarzaki has features that resemble both fungi and animals.

Najle SR, Molina MC, Ruiz-Trillo I, Uttaro AD.

Open Biol. 2016 Jul;6(7). pii: 160029. doi: 10.1098/rsob.160029.

26.

Losing Complexity: The Role of Simplification in Macroevolution.

O'Malley MA, Wideman JG, Ruiz-Trillo I.

Trends Ecol Evol. 2016 Aug;31(8):608-621. doi: 10.1016/j.tree.2016.04.004. Epub 2016 May 19.

PMID:
27212432
27.

The Dynamic Regulatory Genome of Capsaspora and the Origin of Animal Multicellularity.

Sebé-Pedrós A, Ballaré C, Parra-Acero H, Chiva C, Tena JJ, Sabidó E, Gómez-Skarmeta JL, Di Croce L, Ruiz-Trillo I.

Cell. 2016 May 19;165(5):1224-1237. doi: 10.1016/j.cell.2016.03.034. Epub 2016 Apr 21.

28.

Expression Atlas of the Deubiquitinating Enzymes in the Adult Mouse Retina, Their Evolutionary Diversification and Phenotypic Roles.

Esquerdo M, Grau-Bové X, Garanto A, Toulis V, Garcia-Monclús S, Millo E, López-Iniesta MJ, Abad-Morales V, Ruiz-Trillo I, Marfany G.

PLoS One. 2016 Mar 2;11(3):e0150364. doi: 10.1371/journal.pone.0150364. eCollection 2016.

29.

Sterol and genomic analyses validate the sponge biomarker hypothesis.

Gold DA, Grabenstatter J, de Mendoza A, Riesgo A, Ruiz-Trillo I, Summons RE.

Proc Natl Acad Sci U S A. 2016 Mar 8;113(10):2684-9. doi: 10.1073/pnas.1512614113. Epub 2016 Feb 22.

30.

Complex transcriptional regulation and independent evolution of fungal-like traits in a relative of animals.

de Mendoza A, Suga H, Permanyer J, Irimia M, Ruiz-Trillo I.

Elife. 2015 Oct 14;4:e08904. doi: 10.7554/eLife.08904.

31.

Phylogenomics Reveals Convergent Evolution of Lifestyles in Close Relatives of Animals and Fungi.

Torruella G, de Mendoza A, Grau-Bové X, Antó M, Chaplin MA, del Campo J, Eme L, Pérez-Cordón G, Whipps CM, Nichols KM, Paley R, Roger AJ, Sitjà-Bobadilla A, Donachie S, Ruiz-Trillo I.

Curr Biol. 2015 Sep 21;25(18):2404-10. doi: 10.1016/j.cub.2015.07.053. Epub 2015 Sep 10.

32.

Origin and evolution of lysyl oxidases.

Grau-Bové X, Ruiz-Trillo I, Rodriguez-Pascual F.

Sci Rep. 2015 May 29;5:10568. doi: 10.1038/srep10568.

33.

Tracing the Evolutionary History of Inositol, 1, 4, 5-Trisphosphate Receptor: Insights from Analyses of Capsaspora owczarzaki Ca2+ Release Channel Orthologs.

Alzayady KJ, Sebé-Pedrós A, Chandrasekhar R, Wang L, Ruiz-Trillo I, Yule DI.

Mol Biol Evol. 2015 Sep;32(9):2236-53. doi: 10.1093/molbev/msv098. Epub 2015 Apr 23.

34.

Diversity and distribution of unicellular opisthokonts along the European coast analysed using high-throughput sequencing.

Del Campo J, Mallo D, Massana R, de Vargas C, Richards TA, Ruiz-Trillo I.

Environ Microbiol. 2015 Sep;17(9):3195-207. doi: 10.1111/1462-2920.12759. Epub 2015 Feb 14.

35.

The eukaryotic ancestor had a complex ubiquitin signaling system of archaeal origin.

Grau-Bové X, Sebé-Pedrós A, Ruiz-Trillo I.

Mol Biol Evol. 2015 Mar;32(3):726-39. doi: 10.1093/molbev/msu334. Epub 2014 Dec 17.

36.

Forward genetics for back-in-time questions.

de Mendoza A, Ruiz-Trillo I.

Elife. 2014 Nov 4;3. doi: 10.7554/eLife.05218.

37.

The others: our biased perspective of eukaryotic genomes.

del Campo J, Sieracki ME, Molestina R, Keeling P, Massana R, Ruiz-Trillo I.

Trends Ecol Evol. 2014 May;29(5):252-9. doi: 10.1016/j.tree.2014.03.006. Epub 2014 Apr 11.

38.

The evolution of the GPCR signaling system in eukaryotes: modularity, conservation, and the transition to metazoan multicellularity.

de Mendoza A, Sebé-Pedrós A, Ruiz-Trillo I.

Genome Biol Evol. 2014 Mar;6(3):606-19. doi: 10.1093/gbe/evu038.

39.

Evolution and classification of myosins, a paneukaryotic whole-genome approach.

Sebé-Pedrós A, Grau-Bové X, Richards TA, Ruiz-Trillo I.

Genome Biol Evol. 2014 Feb;6(2):290-305. doi: 10.1093/gbe/evu013.

40.

Regulated aggregative multicellularity in a close unicellular relative of metazoa.

Sebé-Pedrós A, Irimia M, Del Campo J, Parra-Acero H, Russ C, Nusbaum C, Blencowe BJ, Ruiz-Trillo I.

Elife. 2013 Dec 24;2:e01287. doi: 10.7554/eLife.01287.

41.

Novel roles of plant RETINOBLASTOMA-RELATED (RBR) protein in cell proliferation and asymmetric cell division.

Desvoyes B, de Mendoza A, Ruiz-Trillo I, Gutierrez C.

J Exp Bot. 2014 Jun;65(10):2657-66. doi: 10.1093/jxb/ert411. Epub 2013 Dec 9.

42.

Earliest Holozoan expansion of phosphotyrosine signaling.

Suga H, Torruella G, Burger G, Brown MW, Ruiz-Trillo I.

Mol Biol Evol. 2014 Mar;31(3):517-28. doi: 10.1093/molbev/mst241. Epub 2013 Dec 3.

43.

Transcription factor evolution in eukaryotes and the assembly of the regulatory toolkit in multicellular lineages.

de Mendoza A, Sebé-Pedrós A, Šestak MS, Matejcic M, Torruella G, Domazet-Loso T, Ruiz-Trillo I.

Proc Natl Acad Sci U S A. 2013 Dec 10;110(50):E4858-66. doi: 10.1073/pnas.1311818110. Epub 2013 Nov 25.

44.

Early evolution of the T-box transcription factor family.

Sebé-Pedrós A, Ariza-Cosano A, Weirauch MT, Leininger S, Yang A, Torruella G, Adamski M, Adamska M, Hughes TR, Gómez-Skarmeta JL, Ruiz-Trillo I.

Proc Natl Acad Sci U S A. 2013 Oct 1;110(40):16050-5. doi: 10.1073/pnas.1309748110. Epub 2013 Sep 16.

45.

The Capsaspora genome reveals a complex unicellular prehistory of animals.

Suga H, Chen Z, de Mendoza A, Sebé-Pedrós A, Brown MW, Kramer E, Carr M, Kerner P, Vervoort M, Sánchez-Pons N, Torruella G, Derelle R, Manning G, Lang BF, Russ C, Haas BJ, Roger AJ, Nusbaum C, Ruiz-Trillo I.

Nat Commun. 2013;4:2325. doi: 10.1038/ncomms3325.

46.

A broad genomic survey reveals multiple origins and frequent losses in the evolution of respiratory hemerythrins and hemocyanins.

Martín-Durán JM, de Mendoza A, Sebé-Pedrós A, Ruiz-Trillo I, Hejnol A.

Genome Biol Evol. 2013;5(7):1435-42. doi: 10.1093/gbe/evt102.

47.

Insights into the origin of metazoan filopodia and microvilli.

Sebé-Pedrós A, Burkhardt P, Sánchez-Pons N, Fairclough SR, Lang BF, King N, Ruiz-Trillo I.

Mol Biol Evol. 2013 Sep;30(9):2013-23. doi: 10.1093/molbev/mst110. Epub 2013 Jun 14.

48.

A genomic survey of HECT ubiquitin ligases in eukaryotes reveals independent expansions of the HECT system in several lineages.

Grau-Bové X, Sebé-Pedrós A, Ruiz-Trillo I.

Genome Biol Evol. 2013;5(5):833-47. doi: 10.1093/gbe/evt052.

49.

Development of ichthyosporeans sheds light on the origin of metazoan multicellularity.

Suga H, Ruiz-Trillo I.

Dev Biol. 2013 May 1;377(1):284-92. doi: 10.1016/j.ydbio.2013.01.009. Epub 2013 Jan 18.

50.

Environmental survey meta-analysis reveals hidden diversity among unicellular opisthokonts.

del Campo J, Ruiz-Trillo I.

Mol Biol Evol. 2013 Apr;30(4):802-5. doi: 10.1093/molbev/mst006. Epub 2013 Jan 16.

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