2024 ISI PUBLICATIONS

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

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. DOI:10.1016/j.celrep.2024.113791

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. DOI:10.1111/jeu.13035

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

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

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. DOI:10.1177/02611929231225730

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. 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. 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

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

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

Hoedjes KM, Grath S, Posnien N, Ritchie MG, Schlötterer C, Abbott JK, Almudi I, Coronado-Zamora M, Durmaz Mitchell E, Flatt T, Fricke C, Glaser-Schmitt A, González J, Holman L, Kankare M, Lenhart B, Orengo DJ, Snook RR, Yılmaz VM, Yusuf L. 2024. From whole bodies to single cells: A guide to transcriptomic approaches for ecology and evolutionary biology. Molecular Ecology. DOI:10.1111/mec.17382

Hünemeier T. 2024. Biogeographic Perspectives on Our Species’ Genetic Diversification. Molecular Biology and Evolution. 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

Johnson MTJ, Arif I, Marchetti F, Munshi-South J, Ness RW, Szulkin M, Verrelli BC, Yauk CL, Anstett DN, Booth W, Caizergues AE, Carlen EJ, Dant A, González J, Lagos CG, Oman M, Phifer-Rixey M, Rennison DJ, Rosenberg MS, Winchell KM. 2024. Effects of urban-induced mutations on ecology, evolution and health. Nature Ecology & Evolution. DOI:10.1038/s41559-024-02401-z

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

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

Librado P, Tressières G, Chauvey L, Fages A, Khan N, Schiavinato S, Calvière-Tonasso L, Kusliy MA, Gaunitz C, Liu X, Wagner S, Der Sarkissian C, Seguin-Orlando A, Perdereau A, Aury JM, Southon J, Shapiro B, Bouchez O, Donnadieu C, Collin YRH, Gregersen KM, Jessen MD, Christensen K, Claudi-Hansen L, Pruvost M, Pucher E, Vulic H, Novak M, Rimpf A, Turk P, Reiter S, Brem G, Schwall C, Barrey É, Robert C, Degueurce C, Horwitz LK, Klassen L, Rasmussen U, Kveiborg J, Johannsen NN, Makowiecki D, Makarowicz P, Szeliga M, Ilchyshyn V, Rud V, Romaniszyn J, Mullin VE, Verdugo M, Bradley DG, Cardoso JL, Valente MJ, Antunes MT, Ameen C, Thomas R, Ludwig A, Marzullo M, Prato O, Gianni GB, Tecchiati U, Granado J, Schlumbaum A, Deschler-Erb S, Mráz MS, Boulbes N, Gardeisen A, Mayer C, Döhle HJ, Vicze M, Kosintsev PA, Kyselý R, Peške L, O'Connor T, Ananyevskaya E, Shevnina I, Logvin A, Kovalev AA, Iderkhangai TO, Sablin MV, Dashkovskiy PK, Graphodatsky AS, Merts I, Merts V, Kasparov AK, Pitulko VV, Onar V, Öztan A, Arbuckle BS, McColl H, Renaud G, Khaskhanov R, Demidenko S, Kadieva A, Atabiev B, Sundqvist M, Lindgren G, López-Cachero FJ, Albizuri S, Trbojević Vukičević T, Rapan Papeša A, Burić M, Rajić Šikanjić P, Weinstock J, Vilaró DA, Codina F, Dalmau CG, de Llorens JM, Pou J, de Prado G, Sanmartí J, Kallala N, Torres JR, Maraoui-Telmini B, Belarte Franco MC, Valenzuela-Lamas S, Zazzo A, Lepetz S, Duchesne S, Alexeev A, Bayarsaikhan J, Houle JL, Bayarkhuu N, Turbat T, Crubézy É, Shingiray I, Mashkour M, Berezina NY, Korobov DS, Belinskiy A, Kalmykov A, Demoule JP, Reinhold S, Hansen S, Wallner B, Roslyakova N, Kuznetsov PF, Tishkin AA, Wincker P, Kanne K, Outram A, Orlando L. 2024. Widespread horse-based mobility arose around 2,200 BCE in Eurasia. Nature. DOI:10.1038/s41586-024-07597-5

Long C, Deng J, Nguyen J, Liu YY, Alm EJ, Solé R, Saavedra S. 2024. Structured community transitions explain the switching capacity of microbial systems. Proceedings of the National Academy of Sciences, 121(6):1-9. DOI:10.1073/pnas.2312521121

Mantica F, Iñiguez LP, Marquez Y, Permanyer J, Torres-Mendez A, Cruz J, Franch-Marro X, Tulenko F, Burguera D, Bertrand S, Doyle T, Nouzova M, Currie PD, Noriega FG, Escriva H, Arnone MI, Albertin CB, Wotton KR, Almudi I, Martin D, Irimia M. 2024. Evolution of tissue-specific expression of ancestral genes across vertebrates and insects. Nature Ecology & Evolution. DOI:10.1038/s41559-024-02398-5

Marques V, Hinojosa JC, Dapporto L, Talavera G, Stefanescu C, Gutiérrez D, Vila R. 2024. The opposed forces of differentiation and admixture across glacial cycles in the butterfly Aglais urticae. Molecular Ecology. DOI:10.1111/mec.17304

Oehlert AM, Garza J, Nixon S, Frank L, Folkerts EJ, Stieglitz JD, Lu C, Heuer RM, Benetti DD, Del Campo J, Gomez FA, Grosell M. 2024. Implications of dietary carbon incorporation in fish carbonates for the global carbon cycle. Science of The Total Environment, 916:169895. DOI:10.1016/j.scitotenv.2024.169895

Rispo F, De Negri Atanasio G, Demori I, Costa G, Marchese E, Perera-Del-Rosario S, Serrano-Candelas E, Palomino-Schätzlein M, Perata E, Robino F, Ferrari PF, Ferrando S, Letasiova S, Markus J, Zanotti-Russo M, Grasselli E. 2024. An extensive review on phenolic compounds and their potential estrogenic properties on skin physiology. Frontiers in Cell and Developmental Biology, 11(January):1-16. DOI:10.3389/fcell.2023.1305835

Roca-Ayats N, Maceda I, Bruque CD, Martínez-Gil N, Garcia-Giralt N, Cozar M, Mellibovsky L, Van Hul W, Lao O, Grinberg D, Balcells S. 2024. Evolutionary and functional analyses of LRP5 in archaic and extant modern humans. Human Genomics, 18(1):53. DOI:10.1186/s40246-024-00616-6

Rodríguez-Fernández B, Sánchez-Benavides G, Genius P, Minguillon C, Fauria K, De Vivo I, Navarro A, Molinuevo JL, Gispert JD, Sala-Vila A, Vilor-Tejedor N, Crous-Bou M; ALFA study. 2024. Association between telomere length and cognitive function among cognitively unimpaired individuals at risk of Alzheimer’s disease. Neurobiology of Aging, 141(June):140-150. DOI:10.1016/j.neurobiolaging.2024.05.015

Rojo I, Escudero N, Fernández R, Fernández-Álvarez FÁ. 2024. First record of the alien land flatworm Marionfyfea adventor (Platyhelminthes: Geoplanidae) in the Iberian Peninsula. Zootaxa, 5397(2):291-294. DOI:10.11646/zootaxa.5397.2.10

Sardanyés J, Ivančić F, Vidiella B. 2024. Identifying regime shifts, transients and late warning signals for proactive ecosystem management. Biological Conservation, 290(January). DOI:10.1016/j.biocon.2023.110433

Sasso S, Saag L, Spros R, Beneker O, Molinaro L, Biagini SA, Lehouck A, Van De Vijver K, Hui R, D'Atanasio E, Kushniarevich A, Kabral H, Metspalu E, Guellil M, Ali MQA, Geypen J, Hoebreckx M, Berk B, De Winter N, Driesen P, Pijpelink A, Van Damme P, Scheib CL, Deschepper E, Deckers P, Snoeck C, Dewilde M, Ervynck A, Tambets K, Larmuseau MHD, Kivisild T. 2024. Capturing the fusion of two ancestries and kinship structures in Merovingian Flanders. Proceedings of the National Academy of Sciences, 121(27). DOI:10.1073/pnas.2406734121

Sinigaglia B, Escudero J, Biagini SA, Garcia-Calleja J, Moreno J, Dobon B, Acosta S, Mondal M, Walsh S, Aguileta G, Vallès M, Forrow S, Martin-Caballero J, Migliano AB, Bertranpetit J, Muñoz FJ, Bosch E. 2024. Exploring Adaptive Phenotypes for the Human Calcium-Sensing Receptor Polymorphism R990G. Molecular Biology and Evolution, 41(2):1-18. DOI:10.1093/molbev/msae015

Talavera A, Palmada-Flores M, Burriel-Carranza B, Valbuena-Ureña E, Mochales-Riaño G, Adams DC, Tejero-Cicuéndez H, Soler-Membrives A, Amat F, Guinart D, Carbonell F, Obon E, Marquès-Bonet T, Carranza S. 2024. Genomic insights into the Montseny brook newt (Calotriton arnoldi), a Critically Endangered glacial relict. iScience, 27(1):108665. DOI:10.1016/j.isci.2023.108665

Talavera A, Valbuena-Ureña E, Burriel-Carranza B, Mochales-Riaño G, Adams DC, Amat F, Carbonell F, Carranza S. 2024. Integrative systematic revision of the Montseny brook newt (Calotriton arnoldi), with the description of a new subspecies. PeerJ, 12:e17550. DOI:10.7717/peerj.17550

Toro-Delgado E, Vila R, Talavera G, Turner EC, Hayes MP, Horrocks NPC, Bladon AJ. 2024. Regional differences in thermoregulation between two European butterfly communities. Journal of Animal Ecology, 93(2):183-195. DOI:10.1111/1365-2656.14039

Vilà-Valls L, Abdeli A, Lucas-Sánchez M, Bekada A, Calafell F, Benhassine T, Comas D. 2024. Understanding the genomic heterogeneity of North African Imazighen: from broad to microgeographical perspectives. Scientific Reports, 14(1):9979. DOI:10.1038/s41598-024-60568-8

Villena-Alemany C, Mujakić I, Fecskeová LK, Woodhouse J, Auladell A, Dean J, Hanusová M, Socha M, Gazulla CR, Ruscheweyh HJ, Sunagawa S, Silva Kavagutti V, Andrei AŞ, Grossart HP, Ghai R, Koblížek M, Piwosz K. 2024. Phenology and ecological role of aerobic anoxygenic phototrophs in freshwaters. Microbiome, 12(1):65. DOI:10.1186/s40168-024-01786-0

Yee SW, Ferrández-Peral L, Alentorn-Moron P, Fontsere C, Ceylan M, Koleske ML, Handin N, Artegoitia VM, Lara G, Chien HC, Zhou X, Dainat J, Zalevsky A, Sali A, Brand CM, Wolfreys FD, Yang J, Gestwicki JE, Capra JA, Artursson P, Newman JW, Marquès-Bonet T, Giacomini KM. 2024. Illuminating the function of the orphan transporter, SLC22A10, in humans and other primates. Nature Communications, 15(1):4380. DOI:10.1038/s41467-024-48569-7

Zavadska D, Henry N, Auladell A, Berney C, Richter DJ. 2024. Diverse patterns of correspondence between protist metabarcodes and protist metagenome-assembled genomes. PLoS One. DOI:10.1371/journal.pone.0303697