Journal covers
Full list of publications: https://scholar.google.com/citations?hl=ca&user=i5EWfDsAAAAJ&view_op=list_works&sortby=pubdate
2026
C. Marín-García & A Ruiz-Herrera*. The evolutionary impact of Robertsonian fusions: linking genomic architecture, recombination and reproduction. Journal of Evolutionary Biology. In press.
C.E. McDonough-Goldstein, S. E. Young, M. Neiman, S. Paez, N. Valenzuela, C. G. Sotero-Caio, D.l L. Jeffries, O. M. Palacios-Gimenez, J. K. Abbott, C. Benvenuto, A. K.Huylmans, S. Calhim, J. A. Baeza, A. J. Mongue, E.L. Larson, L.Andjel, R.Melzer, A. Ruiz-Herrera, Tree of Sex Consortium. Navigating the semantic labyrinth of “sex” in the study of reproductive trait evolution. Integrative and Comparative Biology. 2026: 22:icag093. doi: 10.1093/icb/icag093.
N.G. Simonet, J. K. Thackray, A. Guitart-Solanes, B. Kesner, F. Serra, M. Espinosa-Alcantud, A. Lappala, L. Marín-Gual, C. Marín-García, U. Weissbein, J. Castelló-García, D. Wang, L. Rovirosa, J. Tischfield, L. Serrano, B. Payer, A. Ruiz-Herrera, B.N. Vazquez, B. M. Javierre, A. Vaquero, and J. T. Lee. Sirtuin 7 regulates dosage compensation and safeguards the female X-chromosome. Nature. 655(8124):1079-1090, 2026
L. Marín-Gual, L. Álvarez-González, A. M. Milton, L. Gonzalez-Rodelas, M. Renfree, P. D Waters, A. Ruiz-Herrera*. Divergent 3D genome architecture of male germ cells across vertebrates. Nature Communications. 17, 7805, 2026
S. Schlebusch, V. Trifonov, Z. Halenkova, M. Klianitskaya, D. Dedukh, A. Ruiz Herrera, L. Alvarez-Gonzalez, G. Pujol Infantes, E. Hribova, L. Andjel, O. Bartos, P. Pajer, T. Tichopad, D. Kulik, J. Kotusz, M. Dolezalkova-Kastankova, Astrid Bohne, A. Marta, P. Horna, R. Reifova, Y. Guiguen, J. Paces, K. Janko. Sex Chromosome Turnover and Structural Interspecific Genome Divergence Shapes Meiotic Outcomes in Hybridizing Cobitis. GigaScience, giag031, 2026
W.R. Thomas, T. M. Lama, C. Baldoni, L. Marín-Gual, D. Moreno Santillán, M. Farré, L. Abueg, J. Balacco, O. Fedrigo, G. Formenti, N. Jain, J. Mountcastle, T. Tilley, A. Tracey, D. Ray, D. von Elverfeldt, J. Nieland, A. P. Corthals, A. Ruiz-Herrera, D. K. N. Dechmann,, E. Jarvis, L. M. Dávalos. Genomic comparisons shed light on the adaptive basis of brain size plasticity and chromosomal instability in the Eurasian common shrew. Molecular Biology and Evolution, 43(2):msag006, 2026
C. Kirkland, X. Wang, C. Canedo-Ribeiro, L. Álvarez-González, D. Weisz, A. Mena, J. St Leger, O. Dudchenko, E. Lieberman-Aiden, A. Ruiz-Herrera, R. Heller, T. King, M. Farré. Chromosome-level genomics and historical museum collections reveal new insights into the population structure and chromosome evolution of waterbuck. Molecular Ecology, 35:e70218, 2026
A. M. Burgos Ruíz, M. F. Geng, G. Pujol, E. Sanabria, T. Brethouwer, M. Almuedo-Castillo, A. Ruiz-Herrera, J. J. Tena, O. Bogdanovic. A single-cell multiomics roadmap of zebrafish spermatogenesis reveals regulatory principles of male germline formation. Molecular System Biology, 22(1):42-68, 2026
B. J. Hanrahan, J. K. Chang, A. M. Milton, N. C. Lister, D. S.B. Dissanayake, J. M. Hammond, A. L.M. Reis, I. W. Deveson, A. Ruiz-Herrera, H. R. Patel, J. A. M. Graves, A. Georges, P. D. Waters. Partial sex chromosome dosage compensation in Bassiana duperreyi, a sex reversing skink. BMC Genomics 27, 72, 2026
M. Zhang, S. Steckenborn, M. Castellani, L. Marin-Gual, A. Souza Camara, L.A. Robledillo, L. Maria-Parteka, N. Sargheini, M. Marek, E. Chacón-Madrigal, A. Aria Gatica, A. L. L. Vanzela, A. Pedrosa-Harand, W. W. Thomas, B. Huettel, A. Pedros-Harand, J. T. Lovell, A. L.L. Vanzela, A. Ruiz-Herrera, A. Marques. Holocentric karyotype plasticity alters recombination through changes in synapsis and chromatin configuration. Under review. BioRxiv https://doi.org/10.64898/2026.01.17.700048
G. Formenti, D. Absolon, L. Abueg, F. Ackerman, A. Antunes, J.-N. Audet, J. Balacco, A. Beavan, M. Blaxter, T. Brown, G. Butler, S. Cao, E. Charvel, Y. Chen, H. Clawson, H. Conceiçāo, M. Couture, A. Crawford, H. Roest Crollius, M. Daigavane, H W. Detrich III, R. Durbin, E. Duarte, O. Fedrigo, P. Galante, E. Garrison, M.P.T. Gilbert, F. Giudicelli, S. Gable, A. Guarracino, B. Haase, M. Hiller, K. Horan, K. Howe, D. Jackson, N. Jain, V. Joardar, L. Kang, B. June Ko, B. Koo, S. Koren, D. Lariviere, C. Lee, Y.-H. Lee, H. Lewin, D.Lim, N. Lou, K. Makova, K. McCaffrey, S. McCarthy, L. Marín-Gual, J. Medico, P. Michalak, S. Mirarab, P. A. Morin, J. Mountcastle, T. Murphy, E. W. Myers, A. Nekrutenko, M. J. O’Connell, B. O’Toole, B. Paten, S. Paez, M. Paulini, S. Pelan, Andreas Pfenning, Adam M. Phillippy, Martin Pippel, B. Pinto, A. Rhie, A. Ruiz-Herrera, Y. Safonova, C. A. Santos, M. C. Schatz, S. Secomandi, L. Shalmiyev, J. Smith, M. Sollitto, C. G. Sotero-Caio, P.Sudmant, S. Talbot, F. Thibaud-Nissen, T. Tilley, N.Timoshevskaya, Patrick Traore, M. Uliano-Silva, C. Whelan, S. Winkler, M. Wilson, J, M.D. Wood, G. Zhao, E. D. Jarvis*, and the Vertebrate Genomes Project Phase I. The Vertebrate Genomes Project Phase I: A global reference genome resource. Under review. BioRxiv. doi: 10.64898/2026.06.24.732306
2025
G. Pujol, L. Marín-Gual, L. González-Rodelas, F. Chauvigné, J. Cerdà, M. Teles, N. Roher, A Ruiz-Herrera*. Short-term polystyrene nanoplastic exposure alters zebrafish male and female germ line and reproductive outcomes, unveiling pollutant-impacted molecular pathways. Journal of Hazardous Materials 481, 136529 (2025). DOI: https://doi.org/10.1016/j.jhazmat.2024.136529
G. Arrey, X. Liang, Y. Qin, L. Álvarez-González, M.C. Tümmler, J. Ma, S. Holt, P. Han, Y. Luo, A. Ruiz-Herrera, H. Pilegaard, B. Regenberg.Atlas of eccDNA reveals protection of age-dependent transcription-induced eccDNA by intron and isoform gene densities. Nature Communications, 16:1872 (2025). DOI: 10.1038/s41467-025-57042-y
M. Coulée, C. Gobé, M. Blanco, A. de la Iglesia, C. Lapoujade, C. Ialy-Radio, L. Alvarez-Gonzalez, A. Ruiz-Herrera, G. Meurice, P. Fouchet, J. Cocquet, L. El Khattabi. Chromatin Environment-Dependent Effects of DOT1L on Gene Expression in Male Germ Cells. Communication Biology, 8:138 (2025). DOI: 10.1038/s42003-024-07393-x
L. Álvarez-González & A Ruiz-Herrera*. Evolution of 3D Chromatin Folding. Annual Review of Animal Biosciences, 13(1):49-71 (2025). DOI:10.1146/annurev-animal-111523-102233
M. Brasó-Vives, D. A. Hartasánchez, C. F. Bucao, M. Furlan-Magaril, P. Majic, J. Phipps-Tan Sheng Yi, T. F. Rogers, A. Ruiz-Herrera, G. Santos-Rodriguez, N. Vellnow, J. J. S. Wilcox, J. A. Rodríguez. Unlocking the hidden dimensions of genomic diversity within species. Genome Biology & Evolution. 17(11):evaf204, 2025
L. Marín-Gual, R. Sainz-Urruela, C. Vara, Y. Cuartero, L. Álvarez-Gonzalez, N. Felipe-Medina, F. Garcia, E. Llano, M. A. Marti-Renom, A. M. Pendás, A. Ruiz-Herrera*. RAD21L depletion alters 3D genome architecture and landscape of transcriptional activity in the male germ line. Science Advances. 11(40):eadv2283, 2025
H. R. Patel, K. Alreja, A. L. M. Reis, J King Chang, Zahra A. Chew, H. Jung, J. M. Hammond, I. W. Deveson, A. Ruiz-Herrera, L. Marin-Gual, C. Holleley, X. Zhang, N. C. Lister, S. Whiteley, Lei Xiong, D. Dissanayake, P. D. Waters, A. Georges. A near-telomere to telomere phased genome assembly and annotation for the Australian central bearded dragon Pogona vitticeps. GigaScience 14, giaf085, 2025
D. Jeffries, C. Benvenuto, A. Böhne, C. Fraisse, S. Garcia, P. Jay, L. Kratochvíl, C. McDonough-Goldstein, A. Ruiz-Herrera, C. Sotero-Caio, M. A. Wilson, Tree of Sex Consortium, K. S. Jaron. The Tree of Sex consortium: A global initiative for studying the evolution of reproduction in eukaryotes. Journal of Evolutionary Biology 38(7):861-886, 2025
C. Vargas-Chávez, L. Benítez, G. I. Martínez-Redondo, L. Álvarez-González, J. Salces-Ortiz, K. Eleftheriadi, N. Escudero, N. Guiglielmoni, J.-F. Flot, M. Novo, A. Ruiz-Herrera, A. McLysaght, R. Fernández. A punctuated burst of massive genomic rearrangements by chromosome shattering and the origin of non-marine annelids. Nature Ecology and Evolution, 9(7):1263-1279, 2025
L. Marín-Gual, C. J. Hogg, J. K. Chang, A. J. Pask, M. B. Renfree, P. D Waters, A. Ruiz-Herrera*. Meiotic dynamics in a unique Australian marsupial provide new insights into the evolution of neo-sex chromosomes in the early stages of differentiation. Frontiers in Cell and Developmental Biology 13:1562403, 2025
2024
C. J. Hogg, R. J. Edwards, K. A. Farquharson, L. W. Silver, P. Brandies, E. Peel, M. Escalona, F. R. Jaya, R. Thavornkanlapachai, K. Batley, T. M. Bradford, J. K. Chang, Z. Chen, N. Deshpande, M. Dziminski, K. M. Ewart, O. W. Griffith, L. Marin-Gual, K. L. Moon, K. J. Travouillon, P. Waters, C. M. Whittington, M. R. Wilkins, K. M. Helgen, N. Lo, S. Y. W. Ho, A. Ruiz Herrera, R. Paltridge, J. A. M. Graves, M. Renfree, B. Shapiro, K. Ottewell, K. Rangers, K. Belov. Extant and extinct bilby genomes combined with Indigenous knowledge improve conservation of a unique Australian marsupial. Nature Ecology and Evolution 8, 311–1326 (2024). DOI: 10.1038/s41559-024-02436-2
B. Bista#, L. González-Rodelas#, L. Álvarez-González, Z.Q. Wu, E.E. Montiel, L.S. Lee, D.B. Badenhorst, S. Radhakrishnan, R. Literman, B. Navarro-Rodriguez, J.B. Iverson, A. Ruiz-Herrera*, N. Valenzuela*.De novo genome assemblies of two cryptodiran turtles with ZZ/ZW and XX/XY sex chromosomes provide insights into patterns of genome reshuffling and uncover novel 3D genome folding in amniotes. Genome Research 34(10):1553-1569, 2024. DOI: doi/10.1101/gr.279443.124
C. Marín-Garcia, L. Álvarez-González, S. Casillas, L. Marín-Gual, J. Picón, K. Yam, M. Garcias-Ramis, C. Vara, J. Ventura, A. Ruiz-Herrera*. Multiple genomic landscapes of recombination and genomic divergence in wild populations of mouse mice with chromosomal fusions. Mol Biol Evol 41(4):msae063 (2024). DOI: 10.1093/molbev/msae063
A. M. Milton, L. Marin-Gual, B. J. Hanrahan, A. Ruiz-Herrera, P. D. Waters. Imprinted X chromosome inactivation in marsupials: the paternal X arrives at the egg with a silent DNA methylation profile. Proc Natl Acad Sci U S A 121 (36), e2412185121, (2024). DOI: 10.1073/pnas.2412185121
N.C. Lister, A.M. Milton, B.J. Hanrahan, H.R. Patel, K.L. McIntyre, W.B. Horspool. A. M. Livernois, S.A. Waters, L. Kian Wee, A. Ruiz-Herrera, P.D. Waters. Incomplete transcriptional dosage compensation of chicken and platypus sex chromosomes is balanced by post-transcriptional compensation. Proc Natl Acad Sci U S A 21(32):e2322360121 (2024). DOI: doi.org/10.1073/pnas.2322360121
M. Corominas, T. Marquès-Bonet, M. A. Arnedo, M. Bayés, J. Belmonte, H. Escrivà, R. Fernández, T. Gabaldón, T. Garnatje, J. Germain, M. Niell, F. Palero, J. Pons, P. Puigdomènech, The Catalan Initiative for the Earth BioGenome Project (including A. Ruiz-Herrera), V. Arroyo, C. Cuevas-Caballé, J. Ferrer Obiol, I. Gut, M. Gut, O. Hidalgo, G. Izquierdo-Arànega, L. Pérez-Sorribes, E. Righi, M. Riutort, J. Vallès, J. Rozas, T. Alioto, R. Guigó. The Catalan initiative for the Earth BioGenome Project: contributing local data to global biodiversity genomics. NAR Genomics and Bioinformatics 6, lqae075 (2024). DOI:doi.org/10.1093/nargab/lqae075
O. Massafret, M. Barragán, L. Álvarez, B. Aran, B. Martín, A. Esteve, A. Ruiz-Herrera, R. Vassena, E. Ibañez, J. Santaló. The pluripotency state of human Embryonic Stem Cells derived from single blastomeres of eight-cell embryos. Cells & Development 22:203935 (2024). DOI: doi.org/10.1016/j.cdev.2024.203935
M. Sandoval- Velasco, O. Dudchenko, J. A. Rodríguez, C. Perez Estrada, M.Dehasque, C. Fontsere1, S. S.T. Mak, V.Plotnikov, R. Khan, D.Weisz, V.G. Contessoto, A.B. Oliveira Junior, A. Kalluchi, S. S. Batra, M. S. Shamim, N.C. Durand, B. O’Connell, R. E. Green, B.Shapiro, A.L. Roca, A. Gnirke, I.Garcia-Treviño, R.Coke, J. P. Flanagan, K. Pletch, A. Ruiz-Herrera, E. S. Lander, J. Rowley, J.N. Onichic, L. Dalén, M.A. Marti-Renom, M. T. P. Gilbert, E. Lieberman Aiden. Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample. Cell 187, 3541–3562 (2024). DOI: 10.1016/j.cell.2024.06.002
2023
S. Alonso-Alonso, A. Esteve-Codina, B. Martin-Mur, L. Álvarez-González, A. Ruiz-Herrera, J. Santaló, E. Ibáñez. Blastomeres of 8-cell mouse embryos differ in their ability to generate stem cells and produce lines with different transcriptional signatures. Frontiers in Cell and Developmental Biology 11:1274660 (2023) doi: 10.3389/fcell.2023.1274660
P.D. Waters, J.A.M. Graves, S.L. Whiteley, A. Georges, A. Ruiz-Herrera. The three dimensions of thermolabile sex determination. Bioessays 45 (2), 2200123. DOI: 10.1002/bies.202200123
F. J. Valero-Regalón, M. Solé, P. López-Jiménez, M. Valerio-de Arana, M. Martín-Ruiz, R. de la Fuente, L. Marín-Gual, M. B. Renfree, G. Shaw, S. Berríos, R.Fernández-Donoso, P. D. Waters, A. Ruiz-Herrera, R. Gómez, J. Page. Divergent patterns of meiotic double strand breaks and synapsis initiation dynamics suggest an evolutionary shift in the meiosis program between American and Australian marsupials. Frontiers in Cell and Developmental Biology 11:1147610
2022
Lucía Álvarez-González, Cristina Arias-Sardá, Laia Montes-Espuña, Laia Marín-Gual, Covadonga Vara, Nicholas C Lister, Yasmina Cuartero, Francisca Garcia, Janine Deakin, Marilyn B Renfree, Terence J Robinson, Marc A Martí-Renom, Paul D Waters, Marta Farré, Aurora Ruiz-Herrera. Principles of 3D chromosome folding and evolutionary genome reshuffling in mammals. Cell Reports 41, 111839. https://doi.org/10.1016/j.celrep.2022.111839
Lucía Álvarez-González, Frances Burden, Dadakhalandar Doddamani, Roberto Malinverni, Emma Leach, Cristina Marín-García, Laia Marín-Gual, Albert Gubern, Covadonga Vara, Andreu Paytuví-Gallart, Marcus Buschbeck, Peter JI Ellis, Marta Farré, Aurora Ruiz-Herrera. 3D chromatin remodelling in the germ line modulates genome evolutionary plasticity. Nature Communications 13 (2608). https://www.nature.com/articles/s41467-022-30296-6
Aurora Ruiz-Herrera, Paul D Waters. Fragile, unfaithful and persistent Ys—on how meiosis can shape sex chromosome evolution. Heredity 129 (1), 22-30. https://www.nature.com/articles/s41437-022-00532-2
Laia Marín-Gual, Laura González-Rodelas, Gala Pujol, Covadonga Vara, Marta Martín-Ruiz, Soledad Berríos, Raúl Fernández-Donoso, Andrew Pask, Marilyn B Renfree, Jesús Page, Paul D Waters, Aurora Ruiz-Herrera. Strategies for meiotic sex chromosome dynamics and telomeric elongation in Marsupials. PLoS Genetics 18 (2), e1010040. https://doi.org/10.1371/journal.pgen.1010040
Covadonga Vara, Aurora Ruiz-Herrera. Unpacking chromatin remodelling in germ cells: implications for development and evolution. Trends in Genetics, 38(5), pp. 422–425. https://doi.org/10.1016/j.tig.2021.10.007
2021
Paul D Waters, Hardip R Patel, Aurora Ruiz-Herrera, Lucía Álvarez-González, Nicholas C Lister, Oleg Simakov, Tariq Ezaz, Parwinder Kaur, Celine Frere, Frank Grützner, Arthur Georges, Jennifer A Marshall Graves. Microchromosomes are building blocks of bird, reptile, and mammal chromosomes. Proceedings of the National Academy of Sciences 118 (45), e2112494118. https://doi.org/10.1073/pnas.2112494118
Covadonga Vara, Andreu Paytuví-Gallart, Yasmina Cuartero, Lucía Álvarez-González, Laia Marín-Gual, Francisca Garcia, Beatriu Florit-Sabater, Laia Capilla, Rosa Ana Sanchéz-Guillén, Zaida Sarrate, Riccardo Aiese Cigliano, Walter Sanseverino, Jeremy B Searle, Jacint Ventura, Marc A Marti-Renom, François Le Dily, Aurora Ruiz-Herrera. The impact of chromosomal fusions on 3D genome folding and recombination in the germ line. Nature communications 12 (1), 2981. https://www.nature.com/articles/s41467-021-23270-1
Terence J Robinson, Halina Cernohorska, Svatava Kubickova, Miluse Vozdova, Petra Musilova, Aurora Ruiz-Herrera. Chromosomal evolution in Raphicerus antelope suggests divergent X chromosomes may drive speciation through females, rather than males, contrary to Haldane‘s rule. Scientific Reports 11 (1), 3152. https://www.nature.com/articles/s41598-021-82859-0