2024 Publications

Albacete S, Sancho G, Azpiazu C, Sgolastra F, Rodrigo A, Bosch J. 2024. Exposure to sublethal levels of insecticide-fungicide mixtures affect reproductive success and population growth rates in the solitary bee Osmia cornuta. Environment International, 190(July):108919. DOI:10.1016/j.envint.2024.108919

Alfonso P, Butković A, Fernández R, Riesgo A, Elena SF. 2024. Unveiling the hidden viromes across the animal tree of life: insights from a taxonomic classification pipeline applied to invertebrates of 31 metazoan phyla. mSystems, 9(5). DOI:10.1128/msystems.00124-24

Allentoft ME, Sikora M, Refoyo-Martínez A, Irving-Pease EK, Fischer A, Barrie W, Ingason A, Stenderup J, Sjögren KG, Pearson A, Sousa da Mota B, Schulz Paulsson B, Halgren A, Macleod R, Jørkov MLS, Demeter F, Sørensen L, Nielsen PO, Henriksen RA, Vimala T, McColl H, Margaryan A, Ilardo M, Vaughn A, Fischer Mortensen M, Nielsen AB, Ulfeldt Hede M, Johannsen NN, Rasmussen P, Vinner L, Renaud G, Stern A, Jensen TZT, Scorrano G, Schroeder H, Lysdahl P, Ramsøe AD, Skorobogatov A, Schork AJ, Rosengren A, Ruter A, Outram A, Timoshenko AA, Buzhilova A, Coppa A, Zubova A, Silva AM, Hansen AJ, Gromov A, Logvin A, Gotfredsen AB, Henning Nielsen B, González-Rabanal B, Lalueza-Fox C, McKenzie CJ, Gaunitz C, Blasco C, Liesau C, Martinez-Labarga C, Pozdnyakov DV, Cuenca-Solana D, Lordkipanidze DO, En'shin D, Salazar-García DC, Price TD, Borić D, Kostyleva E, Veselovskaya EV, Usmanova ER, Cappellini E, Brinch Petersen E, Kannegaard E, Radina F, Eylem Yediay F, Duday H, Gutiérrez-Zugasti I, Merts I, Potekhina I, Shevnina I, Altinkaya I, Guilaine J, Hansen J, Aura Tortosa JE, Zilhão J, Vega J, Buck Pedersen K, Tunia K, Zhao L, Mylnikova LN, Larsson L, Metz L, Yepiskoposyan L, Pedersen L, Sarti L, Orlando L, Slimak L, Klassen L, Blank M, González-Morales M, Silvestrini M, Vretemark M, Nesterova MS, Rykun M, Rolfo MF, Szmyt M, Przybyła M, Calattini M, Sablin M, Dobisíková M, Meldgaard M, Johansen M, Berezina N, Card N, Saveliev NA, Poshekhonova O, Rickards O, Lozovskaya OV, Gábor O, Uldum OC, Aurino P, Kosintsev P, Courtaud P, Ríos P, Mortensen P, Lotz P, Persson P, Bangsgaard P, de Barros Damgaard P, Vang Petersen P, Martinez PP, Włodarczak P, Smolyaninov RV, Maring R, Menduiña R, Badalyan R, Iversen R, Turin R, Vasilyev S, Wåhlin S, Borutskaya S, Skochina S, Sørensen SA, Andersen SH, Jørgensen T, Serikov YB, Molodin VI, Smrcka V, Merts V, Appadurai V, Moiseyev V, Magnusson Y, Kjær KH, Lynnerup N, Lawson DJ, Sudmant PH, Rasmussen S, Korneliussen TS, Durbin R, Nielsen R, Delaneau O, Werge T, Racimo F, Kristiansen K, Willerslev E. 2024. Population genomics of post-glacial western Eurasia. Nature, 625(7994):301-311. DOI:10.1038/s41586-023-06865-0

Aranda S, Muntané G, Vilella E. 2024. Coexpression network analysis of the adult brain sheds light on the pathogenic mechanism of DDR1 in schizophrenia and bipolar disorder. Translational Psychiatry, 14(1):112. DOI:10.1038/s41398-024-02823-0

Balart-García P, Bradford TM, Beasley-Hall PG, Polak S, Cooper SJB, Fernández R. 2024. Highly dynamic evolution of the chemosensory system driven by gene gain and loss across subterranean beetles. Molecular Phylogenetics and Evolution, 194(February):108027. DOI:10.1016/j.ympev.2024.108027

Barquera R, Del Castillo-Chávez O, Nägele K, Pérez-Ramallo P, Hernández-Zaragoza DI, Szolek A, Rohrlach AB, Librado P, Childebayeva A, Bianco RA, Penman BS, Acuña-Alonzo V, Lucas M, Lara-Riegos JC, Moo-Mezeta ME, Torres-Romero JC, Roberts P, Kohlbacher O, Warinner C, Krause J. 2024. Ancient genomes reveal insights into ritual life at Chichén Itzá. Nature, 630(March 2023). DOI:10.1038/s41586-024-07509-7

Barrios-Núñez I, Martínez-Redondo GI, Medina-Burgos P, Cases I, Fernández R, Rojas AM. 2024. Decoding functional proteome information in model organisms using protein language models. NAR Genomics and Bioinformatics, 6(3):1-25. DOI:10.1093/nargab/lqae078

Benvenuto G, Leone S, Astoricchio E, Bormke S, Jasek S, D'Aniello E, Kittelmann M, McDonald K, Hartenstein V, Baena V, Escrivà H, Bertrand S, Schierwater B, Burkhardt P, Ruiz-Trillo I, Jékely G, Ullrich-Lüter J, Lüter C, D'Aniello S, Arnone MI, Ferraro F. 2024. Evolution of the ribbon-like organization of the Golgi apparatus in animal cells. Cell Reports, 43(3):113791. DOI:10.1016/j.celrep.2024.113791

Bista B, González-Rodelas L, Álvarez-González L, Wu ZQ, Montiel EE, Lee LS, Badenhorst DB, Radhakrishnan S, Literman R, Navarro-Dominguez B, Iverson JB, Orozco-Arias S, González J, Ruiz-Herrera A, Valenzuela N. 2024. 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, 1-17. DOI:10.1101/gr.279443.124

Böhne A, Fernández R, Leonard JA, McCartney AM, McTaggart S, Melo-Ferreira J, Monteiro R, Oomen RA, Vinnere Pettersson O, Struck TH. 2024. Contextualising samples: supporting reference genomes of European biodiversity through sample and associated metadata collection. npj Biodiversity, 3(1):26. DOI:10.1038/s44185-024-00053-7

Bonacolta AM, Visscher PT, del Campo J, White III RA. 2024. The eukaryome of modern microbialites reveals distinct colonization across aquatic ecosystems. npj Biofilms and Microbiomes, 10(1):78. DOI:10.1038/s41522-024-00547-z

Bonacolta AM, Krause-Massaguer J, Smit NJ, Sikkel PC, del Campo J. 2024. A new and widespread group of fish apicomplexan parasites. Current Biology, 34(12):2748-2755.e3. DOI:10.1016/j.cub.2024.04.084

Boscaro V, James ER, Fiorito R, Del Campo J, Scheffrahn RH, Keeling PJ. 2024. Updated classification of the phylum Parabasalia. Journal of Eukaryotic Microbiology, 71(4). DOI:10.1111/jeu.13035

Bulduk BK, Tortajada J, Torres-Egurrola L, Valiente-Pallejà A, Martínez-Leal R, Vilella E, Torrell H, Muntané G, Martorell L. 2024. High frequency of mitochondrial DNA rearrangements in the peripheral blood of adults with intellectual disability. Journal of Intellectual Disability Research, 1-16. DOI:10.1111/jir.13197

Bulduk BK, Tortajada J, Valiente-Pallejà A, Callado LF, Torrell H, Vilella E, Meana JJ, Muntané G, Martorell L. 2024. High number of mitochondrial DNA alterations in postmortem brain tissue of patients with schizophrenia compared to healthy controls. Psychiatry Research, 337(February):115928. DOI:10.1016/j.psychres.2024.115928

Burriel-Carranza B, Talavera A, Mochales-Riaño G, Al Hashmi S, Al Busaidi A, Els J, Carranza S. 2024. First record of dermal fluorescence in the desert-adapted Stenodactylus and Trigonodactylus geckos. Journal of Arid Environments, 222(April):105161. DOI:10.1016/j.jaridenv.2024.105161

Burriel-Carranza B, Mochales-Riaño G, Talavera A, Els J, Estarellas M, Al Saadi S, Urriago Suarez JD, Olsson PO, Matschiner M, Carranza S. 2024. Clinging on the brink: Whole genomes reveal human‐induced population declines and severe inbreeding in the Critically Endangered Emirati Leaf‐toed Gecko ( Asaccus caudivolvulus ). Molecular Ecology, 33(15). DOI:10.1111/mec.17451

Burriel-Carranza B, Tejero-Cicuéndez H, Carné A, Mochales-Riaño G, Talavera A, Al Saadi S, Els J, Šmíd J, Tamar K, Tarroso P, Carranza S. Integrating genomics and biogeography to unravel the origin of a mountain biota: The case of a reptile endemicity hotspot in Arabia. Systematic Biology. DOI: 10.1093/sysbio/syae032

Corominas M, Marquès-Bonet T, Arnedo MA, Bayés M, Belmonte J, Escrivà H, Fernández R, Gabaldón T, Garnatje T, Germain J, Niell M, Palero F, Pons J, Puigdomènech P, Initiative For The Earth BioGenome Project TC; Catalan initiative for the Earth BioGenome Project; Arroyo V, Cuevas-Caballé C, Obiol JF, Gut I, Gut M, Hidalgo O, Izquierdo-Arànega G, Pérez-Sorribes L, Righi E, Riutort M, Vallès J, Rozas J, Alioto T, Guigó R. 2024. The Catalan initiative for the Earth BioGenome Project: contributing local data to global biodiversity genomics. NAR Genomics and Bioinformatics, 6(3). DOI:10.1093/nargab/lqae075

Cruz J, Ureña E, Iñiguez LP, Irimia M, Franch-Marro X, Martín D. 2024. E93 controls adult differentiation by repressing broad in Drosophila. Proceedings of the National Academy of Sciences, 121(51):2017. DOI:10.1073/pnas.2403162121

D'Ercole J, Dapporto L, Opler P, Schmidt CB, Ho C, Menchetti M, Zakharov EV, Burns JM, Hebert PDN. 2024. A genetic atlas for the butterflies of continental Canada and United States. PLOS ONE, 19(4):e0300811. DOI:10.1371/journal.pone.0300811

Dapporto L, Menchetti M, Dincă V, Talavera G, Garcia-Berro A, D'Ercole J, Hebert PD, Vila R. 2024. The genetic legacy of the Quaternary ice ages for West Palearctic butterflies. Science Advances, 10(38):1-13. DOI:10.1126/sciadv.adm8596

Decroly T, Vila R, Lohse K, Mackintosh A. 2024. Rewinding the Ratchet: Rare Recombination Locally Rescues Neo-W Degeneration and Generates Plateaus of Sex-Chromosome Divergence. Molecular Biology and Evolution, 41(7):2024.01.20.576444. DOI:10.1093/molbev/msae124

Deulofeu-Capo O, Sebastián M, Auladell A, Cardelús C, Ferrera I, Sánchez O, Gasol JM. 2024. Growth rates of marine prokaryotes are extremely diverse, even among closely related taxa. ISME Communications, 4(1). DOI:10.1093/ismeco/ycae066

Diemar MG, Vinken M, Teunis M, Krul CAM, Busquet F, Zajac JD, Kandarova H, Corvi R, Rosso MZ, Kharina A, Bryndum LS, Santillo M, Bloch D, Kucheryavenko O, Panagiotakos D, Rogiers V, Beekhuijzen M, Giusti A, Najjar A, Courage C, Koenig T, Kolle S, Boonen H, Dhalluin S, Boberg J, Müller BP, Kukic P, Ritskes-Hoitinga M, Grasselli E, Zietek T, Stoddart G, Heusinkveld HJ, Castell JV, Benfenati E, Yang H, Perera S, Paini A, Kramer NI, Hartung T, Janssen M, Fritsche E, Jennen DGJ, Piumatti M, Rathman J, Marusczyk J, Milec L, Roggen EL. 2024. Report of the First ONTOX Stakeholder Network Meeting: Digging Under the Surface of ONTOX Together With the Stakeholders. Alternatives to Laboratory Animals, 52(2):117-131. DOI:10.1177/02611929231225730

Duran‐Nebreda S, Vidiella B, Spiridonov A, Eldredge N, O'Brien MJ, Bentley RA, Valverde S. 2024. The many ways toward punctuated evolution. Palaeontology, 67(5). DOI:10.1111/pala.12731

Duran-Nebreda S, Bentley RA, Vidiella B, Spiridonov A, Eldredge N, O’Brien, MJ, Valverde S. 2024. On the multiscale dynamics of punctuated evolution. Trends in Ecology & Evolution, 39(8):734-744. DOI:10.1016/j.tree.2024.05.003

Farrus N, Maestro JL, Piulachs MD. 2024. CHMP4B contributes to maintaining the follicular cells integrity in the panoistic ovary of the cockroach Blattella germanica. Biology of the Cell, 116(9):1-13. DOI:10.1111/boc.202400010

Fiore L, Arderiu J, Martí-Sarrias A, Turpín I, Pareja RI, Navarro A, Holubiec M, Bianchelli J, Falzone T, Spelzini G, Scicolone G, Acosta S. 2024. Early Unguided Human Brain Organoid Neurovascular Niche Modeling into the Permissive Chick Embryo Chorioallantoic Membrane. Journal of Visualized Experiments, 204:1-12. DOI:10.3791/65710

Fromont LA, Moldes M, Baudis M, Brookes AJ, Navarro A, Rambla J. 2024 Twelve quick tips for deploying a Beacon. PLOS Computational Biology, 20(3):e1011817. DOI:10.1371/journal.pcbi.1011817

Galindo LJ, Mathur V, Frost H, Torruella G, Richards TA, Irwin NAT. 2024. Transcriptomics of Diphyllatea (CRuMs)from South Pacific crater lakes confirm new cryptic clades. Journal of Eukaryotic Microbiology, (September):1-7. DOI:10.1111/jeu.13060

Gàlvez-Morante A, Guéguen L, Natsidis P, Telford MJ, Richter DJ. 2024. Dollo Parsimony Overestimates Ancestral Gene Content Reconstructions. Genome Biology and Evolution, 16(4). DOI:10.1093/gbe/evae062

Ghouri S, Reich MS, Lopez-Mañas R, Talavera G, Bowen GJ, Vila R, Talla VNK, Collins SC, Martins DJ, Bataille CP. 2024. A hydrogen isoscape for tracing the migration of herbivorous lepidopterans across the Afro‐Palearctic range. Rapid Communications in Mass Spectrometry, 38(3):1-23. DOI:10.1002/rcm.9675

Gunasekaram C, Battiston F, Sadekar O, Padilla-Iglesias C, van Noordwijk MA, Furrer R, Manica A, Bertranpetit J, Whiten A, van Schaik CP, Vinicius L, Migliano AB. 2024. Population connectivity shapes the distribution and complexity of chimpanzee cumulative culture. Science, 386(6724):920-925. DOI:10.1126/science.adk3381

Hake KH, West PT, McDonald K, Laundon D, Reyes-Rivera J, Garcia De Las Bayonas A, Feng C, Burkhardt P, Richter DJ, Banfield JF, King N. 2024. A large colonial choanoflagellate from Mono Lake harbors live bacteria. mBio, 1-11 . DOI:10.1128/mbio.01623-24

Hämmerle M, Guellil M, Trgovec-Greif L, Cheronet O, Sawyer S, Ruiz-Gartzia I, Lizano E, Rymbekova A, Gelabert P, Bernardi P, Han S, Rattei T, Schuenemann VJ, Marques-Bonet T, Guschanski K, Calvignac-Spencer S, Pinhasi R, Kuhlwilm M. 2024. Screening great ape museum specimens for DNA viruses. Scientific Reports, 14(1):29806. DOI:10.1038/s41598-024-80780-w

Han S, de Filippo C, Parra G, Meneu JR, Laurent R, Frandsen P, Hvilsom C, Gronau I, Marques-Bonet T, Kuhlwilm M, Andrés AM. 2024. Deep genetic substructure within bonobos. Current Biology, 1-8. DOI:10.1016/j.cub.2024.09.043

He R, Al-Tamimi J, Sánchez-Benavides G, Montaña-Valverde G, Domingo Gispert J, Grau-Rivera O, Suárez-Calvet M, Minguillon C, Fauria K, Navarro A, Hinzen W. 2024. Atypical cortical hierarchy in Aβ-positive older adults and its reflection in spontaneous speech. Brain Research, 1830:148806. DOI:10.1016/j.brainres.2024.148806

Hermosilla-Albala N, Silva FE, Cuadros-Espinoza S, Fontsere C, Valenzuela-Seba A, Pawar H, Gut M, Kelley JL, Ruibal-Puertas S, Alentorn-Moron P, Faella A, Lizano E, Farias I, Hrbek T, Valsecchi J, Gut IG, Rogers J, Farh KK, Kuderna LFK, Marques-Bonet T, Boubli JP. 2024. Whole genomes of Amazonian uakari monkeys reveal complex connectivity and fast differentiation driven by high environmental dynamism. Communications Biology, 7(1):1-14. DOI:10.1038/s42003-024-06901-3

Holt CC, del Campo J, Keeling PJ. 2024. Source and variation of the amazing live Sea-Monkey microbiome. PLOS ONE, 19(8):e0308763. DOI:10.1371/journal.pone.0308763

Hünemeier T. 2024. Biogeographic Perspectives on Our Species’ Genetic Diversification. Molecular Biology and Evolution, 41(3). DOI:10.1093/molbev/msae029

Indacochea A, Guitart T, Boada A, Peg V, Quer A, Laayouni H, Condal L, Espinosa P, Manzano JL, Gebauer F. 2024. CSDE1 Intracellular Distribution as a Biomarker of Melanoma Prognosis. International Journal of Molecular Sciences, 25(4):2319. DOI:10.3390/ijms25042319

James C, Trevisan-Herraz M, Juan D, Rico D. 2024. Evolutionary analysis of gene ages across TADs associates chromatin topology with whole-genome duplications. Cell Reports, 43(4):113895. DOI:10.1016/j.celrep.2024.113895

Juéry C, Auladell A, Füssy Z, Chevalier F, Yee DP, Pelletier E, Corre E, Allen AE, Richter DJ, Decelle J. 2024. Transportome remodeling of a symbiotic microalga inside a planktonic host. The ISME Journal, (March):1-18. DOI:10.1093/ismejo/wrae239

Karamperis K, Katz S, Melograna F, Ganau FP, Van Steen K, Patrinos GP, Lao O. 2024. Genetic ancestry in population pharmacogenomics unravels distinct geographical patterns related to drug toxicity. iScience, 27(10):110916. DOI:10.1016/j.isci.2024.110916

Kéfi S, Génin A, Garcia-Mayor A, Guirado E, Cabral JS, Berdugo M, Guerber J, Solé R, Maestre FT. 2024. Self-organization as a mechanism of resilience in dryland ecosystems. Proceedings of the National Academy of Sciences, 121(6):2017. DOI:10.1073/pnas.2305153121

Kelly M, Cuomo CA, Beukema W, Carranza S, Erens J, Foubert M, Li Z, Lötters S, Schulz V, Steinfartz S, Van Praet S, Veith M, Pasmans F, Martel A. 2024. High phenotypic diversity correlated with genomic variation across the European Batrachochytrium salamandrivorans epizootic. PLOS Pathogens, 20(10):e1012579. DOI:10.1371/journal.ppat.1012579

Kopp J, Rovai A, Ott M, Wedemeyer H, Tiede A, Böhmer HJ, Marques T, Langemeier J, Bohne J, Krooss SA. 2024. A transposable element prevents severe hemophilia B and provides insights into the evolution of new- and old world primates. PLOS ONE, 19(10):e0312303. DOI:10.1371/journal.pone.0312303

Larivière D, Abueg L, Brajuka N, Gallardo-Alba C, Grüning B, Ko BJ, Ostrovsky A, Palmada-Flores M, Pickett BD, Rabbani K, Antunes A, Balacco JR, Chaisson MJP, Cheng H, Collins J, Couture M, Denisova A, Fedrigo O, Gallo GR, Giani AM, Gooder GM, Horan K, Jain N, Johnson C, Kim H, Lee C, Marques-Bonet T, O'Toole B, Rhie A, Secomandi S, Sozzoni M, Tilley T, Uliano-Silva M, van den Beek M, Williams RW, Waterhouse RM, Phillippy AM, Jarvis ED, Schatz MC, Nekrutenko A, Formenti G. 2024. Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy. Nature Biotechnology, 5:10-13. DOI:10.1038/s41587-023-02100-3

Leger MM, Gawryluk RMR. 2024. Evolution: A gene-rich mitochondrial genome sheds light on the last eukaryotic common ancestor. Current Biology, 34(16):R776-R779. DOI:10.1016/j.cub.2024.06.067