Journal covers
2024
2024. 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. Preprint: https://doi.org/10.1101/2023.06.30.547175
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. https://www.researchsquare.com/article/rs-3723914/v1
2024. 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. https://papers.ssrn.com/sol3/papers.cfm?abstract_id=4634357
2024. 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 (in press) DOI: 10.1093/molbev/msae063
2023
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 (2023) doi: 10.3389/fcell.2023.1274660
2023. 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
2023. N.C. Lister, A.M. Milton, H. R. Patel, S. Waters, B. J. Hanrahan, K. L. McIntyre, A. M. Livernois, L.K. Wee, A. R. Ringel, S. Mundlos, M. I. Robson, L. Shearwin-Whyatt, F. Grutzner, J. A. Marshall Graves, A. Ruiz-Herrera, P. D. Waters. Incomplete transcriptional dosage compensation of vertebrate sex chromosomes is balanced by post-transcriptional compensation. https://www.biorxiv.org/content/10.1101/2023.02.23.529605v1.abstract
2023. Francisco Javier Valero-Regalón, Mireia Solé, Pablo López-Jiménez, María Valerio-de Arana, Marta Martín-Ruiz, Roberto de la Fuente, Laia Marín-Gual, Marilyn B Renfree, Geoff Shaw, Soledad Berrís, Raul Fernández-Donoso, Paul D Waters, Aurora Ruiz-Herrera, Rocio Gómez, Jesus 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
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
2022. 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
2022. 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
2022. 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
2022. 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
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
2021. 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
2021. 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
2020
- 2020, Marta Farré and Aurora Ruiz-Herrera. The Plasticity of Genome Architecture. Genes, Special Issue Mechanisms Driving Karyotype Evolution and Genomic Architecture 11
- 2020, Marta Godia, Alex Clop, Armand Sánzhez, Anna Castelló, Joan E. Rogríguez-Gila, Aurora Ruiz-Herrera, and Joaquim Casellas. Whole genome sequencing identifies Allelic Ratio Distortion in sperm involving genes related to spermatogenesis in a swine model.. DNA Research 27
- 2020, Francisca Garcia, Aurora Ruiz-Herrera, Jose A. Godoy, Francisco Cortés, Albert Lozano, Jacinto Román, Javier Calzada, and Luis Biedma. Chromosomal differentiation in genetically isolated populations of the marsh-specialist Crocidura suaveolens (Mammalia: Soricidae). Genes 11
- 2020, Paul D. Waters and Aurora Ruiz-Herrera. Meiotic Executioner Genes Protect the Y from Extinction. Trends in Genetics 36
2019
- 2019, Eleonora Cappelletti, Elena Giulotto, Aurora Ruiz-Herrera, Solomon G. Nergadze, Kevin F. Sullivan, Teri A. Masterson, Covadonga Vara, Marco Santagostino, Marina Bambi, Claudia Badiale, and Francesca M. Piras. CENP-A binding domains and recombination patterns in horse spermatocytes.
- 2019, Deakin, Janine E, Ezaz, Tariq, Wapstra, Erik, Srikulnath, Kornsorn, Rovatsos, Michail, Miura, Ikuo, Kratochvíl, Lukáš, Grutzner, Frank, Griffin, Darren, Marshall Graves, Jennifer A, Fukui, Kichi, Eldridge, Mark D B, Cioffi, Marcelo B, Ruiz-Herrera, Aurora, O’Neill, Rachel, and Potter, Sally. Chromosomics: Bridging the Gap between Genomes and Chromosomes.. Genes (Basel) 10
- 2019, Ruiz-Herrera, Aurora, Vara, Covadonga, Marti-Renom, Marc A, Waters, Paul D, Heyn, Holger, Pendás, Alberto M, Fornas, Oscar, Sanseverino, Walter, Aiese Cigliano, Riccardo, Moutinho, Catia, Julià, Eva, Gómez-H, Laura, Salvà-Castro, Judit, Garcia, Francisca, Le Dily, François, Cuartero, Yasmina, and Paytuví-Gallart, Andreu. Three-Dimensional Genomic Structure and Cohesin Occupancy Correlate with Transcriptional Activity during Spermatogenesis.. Cell Rep 28 352-367.e9
- 2019, Vara, C, Ruiz-Herrera, A, Mathias, ML, Searle, JB, Ventura, J, Bello-Rodríguez, J, Florit-Sabater, B, Albert-Lizandra, G, Gabriel, SI, Sánchez-Guillén, RA, Ledda, A, Ferretti, L, and Capilla, L. PRDM9 diversity at fine geographical scale reveals contrasting evolutionary patterns and functional constraints in natural populations of house mice. Molecular Biology and Evolution
- 2019, Shunxin Wang, Liangran Zhang, Nancy Kleckner, Zijiang Chen, Denise Zickler, Hongbin Liu, Yongliang Shang, Aurora Ruiz-Herrera, Fei Sun, and Carl Veller. Per-Nucleus Crossover Covariation and Implications for Evolution. Cell 177 1-13
2018
- 2018, Ruiz-Herrera, A, Ventura, J, Searle, JB, Albert-Lizandra, G, Vara, C, and Capilla, A. The plasticity of meiotic recombination and its implications for mammalian genome evolution. COMPARATIVE CYTOGENETICS
2017
- 2017, Ruiz-Herrera, Aurora, Rubes, J, Robinson, Terence J, Sipek, Jaroslav, Hernández-Marsal, Adrià, Vara, Covadonga, Frohlich, Jan, Capilla, Laia, Sebestova, Hana, Fernández, Jonathan, and Vozdova, Miluse. Recombination correlates with synaptonemal complex length and chromatin loop size in bovids—insights into mammalian meiotic chromosomal organization. Chromosoma doi: 10.1007/s00412-016-0624-3
- 2017, Vicente-Salvador, David, Cáceres, Mario, Ignacio Lucas-Lledó, José, Aguado, Cristina, Estivill, Xavier, Ruiz-Herrera, Aurora, Martínez-Fundichely, Alexander, Izquierdo, David, Noguera, Isaac, Giner-Delgado, Carla, Pacheco, Sarai, Gayà-Vidal, Magdalena, and Puig, Marta. Detailed analysis of inversions predicted between two human genomes: errors, real polymorphisms, and their origin and population distribution. Human Molecular Genetics 26(3):567-581
2016
- 2016, Godoy, JL, Alioto, T, Gabaldón, T, Albà, MM, Mailund, T, Notredame, C, Roma, G, Marques-Bonet, T, Ruiz-Herrera, A, Murphy, WJ, Guigó, R, García, JL, Gut, I, Valencia, A, López-Otín, C, Andrés-Nieto, M, Lorente-Galdos, B, Gut, M, Blanc, J, Galán, B, Derdak, S, Arango, JR, Soriano, L, Casas-Marce, M, Reverter, F, Ruiz-Orera, J, Rodriguez-Ales, JL, Tress, ML, Erb, I, Cozzuto, L, Lawry, E, Camara, F, Rodríguez, JM, Capella-Gutiérrez, S, Abascal, F, Ribeca, P, Frías, L, Rubio-Camarillo, M, García, F, Li, G, Quilez, J, Quesada, V, Prieto, P, Cheng, JY, Martínez-Cruz, B, Marcet-Houben, M, Vlasova, A, Villanueva-Cañas, JL, Cruz, F, and Carvelo, A. Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx. Genome Biology 17
- 2016, Laia Capilla, Aurora Ruiz-Herrera, Denis M Larkin, Jacint Ventura, Roberto Malinverni, Andreu Paytuví-Gallart, Marta Farré, and Rosa Ana Sánchez-Guillén. Mammalian comparative genomics reveals genetic and epigenetic features associated with genome reshuffling in Rodentia. Genome Biology and Evolution 8(12):3703-3717
- 2016, LS Stevison, JD Wall, MF Hammer, CD Bustamante, Great Ape Genome Project, KF McManus, KR Veeramah, JL Kelley, JM Kidd, and AE Woerner. The Time Scale of Recombination Rate Evolution in Great Apes. Mol Biol Evol 33(4):928-45.
- 2016, Laia Capilla, Aurora Ruiz-Herrera, and Montserrat Garcia-Caldés. Meiotic recombination in mammals: a toolbox for evolution. Cytogenetics and Genome Research 150 1-16
- 2016, Miluse Vozdova, Jiri Rubes, Svatava Kubickova, Hana Sebestova, Jan Frohlich, Halina Cernohorska, Jonathan Fernandez, and Aurora Ruiz-Herrera. Meiotic behaviour of evolutionary sex-autosome translocations in Bovidae. Chromosome Research 24 325-338
- 2016, Reig-Viader, Rita, Aurora Ruiz-Herrera, and Garcia-Caldes, Montserrat. Telomere homeostasis in mammalian germ cells: a review. Chromosoma 125 337-351
2015
- 2015, Aurora Ruiz-Herrera. Chromosomal Rearrangements in Primates. eLS (in press)
- 2015, Marta Farrè, Aurora Ruiz-Herrera, and Terence J Robinson. An Integrative Breakage Model of Genome Architecture, Reshuffling and Evolution. BioEssays 37(5):479-88
- 2015, JM Argyris, J Garcia-Mas, S. Ramos-Onsins, M Pujol, J Morata, W Sanseverino, P Madriz Masis, and A. Ruiz-Herrera. Targeted SNP selection for improving the anchoring of the melon ( Cucumis melo L.) scaffold genome assembly. BMC Genomics 16(1):4.
- 2015, RA Sánchez-Guillén, A. Ruiz-Herrera, Ventura, J, M Andrés-Nieto, C Pardo-Camacho, M Martínez-Plana, R. Reig-Viader, and L. Capilla. On the origin of Robertsonian fusions in nature: evidence of telomere shortening in wild house mice. Journal of Evolutionary Biology 28(1):241-9
2014
- 2014, R. Reig-Viader, A. Ruiz-Herrera, M. Garcia-Caldes, Aguita, B, F. Garcia, Vila-Cejudo, M, and L. Capilla. Telomere homeostasis is compromised in spermatocytes from patients with idiopathic infertility. Fertility and Sterility
- 2014, L. Capilla, A. Ruiz-Herrera, Ventura, J, M. Oliver-Bonet, Alemany-Schmidt, A, and Medarde, N. Genetic recombination variation in wild Robertsonian mice: on the role of chromosomal fusions and Prdm9 allelic backgound.. Proceedings of the Royal Society B
- 2014, Reig-Viader, Rita, Aurora Ruiz-Herrera, Montserrat Garcia-Caldés, Elena Giulotto, Sabaté, Montserrat, Buscà, Rafael, Vitelli, Valerio, and Vila-Cejudo, Marta. Telomeric repeat-containing RNA (TERRA) and telomerase are components of telomeres during mammalian gametogenesis. Biology of Reproduction
- 2014, M. Farré and A. Ruiz-Herrera. Role of chromosomal reorganisations in the human-chimpanzee speciation. eLS
- 2014, Aguado, C, et al, Villatoro, S, and Gayá-Vidal, M. Large-scale validation and genotyping of human polymorphic inversions mediated by inverted repeats a high degree of recurrence. PLOS Genet 10(3)
2013
- 2013, F. Hormozdiari, et al, J Prado-Martinez, and MK Konkel. Rates and patterns of great ape retrotransposition. Proc Natl Acad Sci U S A 110(33)
- 2013, J. Segura, A. Ruiz-Herrera, M. Garcia-Caldés, T. J. Robinson, H. Fernández-Bellon, M. Oliver-Bonet, F. Reis, M. Farré, L. Capilla, S. Ramos-Onsins, and L. Ferretti. Insights into the mechanisms that affect meiotic recombination rates and crossover interference in eutherian mammals. Proc. R. Soc. B 280 (1771): 1471-2954
- 2013, Javier Prado-Martinez, et al, Aurora Ruiz-Herrera, Tiago Carvalho, Cristina Camprubí, [….], Joanna L. Kelley, Heng Li, Jeffrey M. Kidd, and Peter H. Sudmant. Great ape genetic diversity and population history. Nature 99(7459):471-5
- 2013, Marta Farré, Aurora Ruiz-Herrera, and Diego Micheletti. Recombination rates and genomic shuffling in human and chimpanzee – a new twist in the speciation theory. Molecular Biology and Evolution Apr;30(4):853-64 30(4)
- 2013, R. Reig-Viader, A. Ruiz-Herrera, M. Garcia-Caldés, E. Giulotto, L. Khoriauli, Ll. Cabero, Toran, N, and Brieño-Enríquez, MA. Telomeric repeat-containing RNA and telomerase in human fetal oocytes.. Human Reproduction Feb;28(2):414-22 28
2012
- 2012, Aurora Ruiz-Herrera, Montserrat Garcia-Caldés, and Francisca Garcia. Radiobiology and reproduction – what can we learn from mammalian females?. Genes 3(3): 521-544 Special Issue
- 2012, A. Ruiz-Herrera, T. J. Robinson, and M. Farré. Molecular cytogenetic and genomic insights to chromosomal evolution. Heredity 108(1):28-36 Special issue on Molecular Cytogenetics: Karyotype evolution, Phylogenomics and Future prospects
2011
- 2011, Brieño-Enríquez, MA, Garcia Caldés, M, Roig, I, Martínez, F, Toran, N, Cabero, L, and Reig, R. Gene expression is altered after Bisphenol A exposure in human fetal oocytes in vitro. Mol Hum Reprod-Nov 25. [Epub ahead of print]
- 2011, M. Farre, A. Ruiz-Herrera, M. Ponsà, F. López-Giráldez, and M. Bosch. Assessing the Role of Tandem Repeats in Shaping the Genomic Architecture of Great Apes. PLOS One 6(11):e27239
- 2011, R. Garcia-Cruz, M. Garcia-Caldés*, A. Ruiz-Herrera*, M. Mudry, E. Steinberg, M.A. Brieño, and S. Pacheco. A comparative study of the recombination pattern in three species of Platyrrhini monkeys (Primates). Chromosoma 120(5):521-30
- 2011, Elena Raimondi, Elena Giulotto, Leopoldo Ianuzzi, Montserrat Ponsà, Aurora Ruiz-Herrera, Giulia Pia Di Meo, Solomon G. Nergadze, and Francesca M. Piras. Polymorphic organization of constitutive heterochromatin in Equus asinus (2n = 62) chromosome 1. Hereditas 148(3):110-113
- 2011, A. Ruiz-Herrera, E. Giulotto, C. Mondello, S.G. Nergadze, L. Khoriauli, and A. Smirnova. Gene amplification in human cells knocked down for RAD54. Genome Integrity 2:5
2010
- 2010, T. J. Robinson and A. Ruiz-Herrera. Mammalian Chromosomal Evolution: From Ancestral States to Evolutionary Regions. Evolutionary Biology – Concepts, Molecular and Morphological Evolution 143-158
- 2010, A. Ruiz-Herrera, T. J. Robinson, M. Ponsà, and M. Farré. Selection against Robertsonian fusions involving housekeeping genes in the house mouse: integrating data from gene expression arrays and chromosome evolution.. Chromosome Research 18(7) 801-808
2009
- 2009, A. Salzano, E. Giulotto, C. Mondello, A. Ruiz-Herrera, A. Smirnova, L. Khoriauli, S.G. Nergadze, and N. Kochiashvili. Enhanced gene amplification in human cells knocked down for DNA-PKcs. DNA Repair 8(1):19-28
2008
- 2008, JL Deuve, T. J. Robinson, J. Britton-Davidian, P.D. Waters, A. Ruiz-Herrera, and N.C. Bennett. Dissection of a Y-autosome translocation in an African mole-rat, Cryptomys hottentotus (Rodentia, Bathyergidae).. Chromosoma 117(2):211-7
- 2008, A. Ruiz-Herrera and T. J. Robinson. Evolutionary plasticity and cancer breakpoint in human chromosome 3: a review.. Bioessays 30
- 2008, T. J. Robinson and A. Ruiz-Herrera. Defining the ancestral eutherian karyotype: a cladistic interpretation of chromosome painting and genome sequence assembly data.. Chromosome Research 16(8):1133-41
- 2008, T. J. Robinson, J.C. Avise, and A. Ruiz-Herrera. Hemiplasy and homoplasy in the karyotypic phylogenies of mammals.. Proc Natl Acad Sci U S A 105
- 2008, A. Ruiz-Herrera, E. Giulotto, M. Santagostino, and S.G. Nergadze. Telomeric repeats far from the ends: mechanisms of origin and role in evolution.. Cytogenetics and Genome Research, special issue on Telomeres and Telomerase 122
2007
- 2007, P.D. Waters, T. J. Robinson, M. Garcia, G. Dobigny, and A. Ruiz-Herrera. Sex chromosomes of basal placental mammals.. Chromosoma 116
- 2007, A. Ruiz-Herrera and T. J. Robinson. Afrotherian fragile sites, evolutionary breakpoints and phylogenetic inference from genomic assemblies.. BMC Evolutionary Biology 7
2006
- 2006, N. Camats, M. Garcia, F. García, E. Giulotto, P. Payá, M. Acien, J.J. Parrilla, and A. Ruiz-Herrera. Genomic instability in rat: breakpoints induced by ionizing radiation and interstitial telomeric-like sequences.. Mutation Research 595
- 2006, T. J. Robinson, L. Fröenicke, and A. Ruiz-Herrera. Dissecting the mammalian genome – new insights into chromosomal evolution.. Trends in Genetics 22
- 2006, A. Ruiz-Herrera, T. J. Robinson, and J. Castresana. Is mammalian chromosomal evolution driven by regions of genome fragility?. Genome Biology 7