• How genomics can help biodiversity conservation

  Theissinger, Kathrin; European Reference Genome Atlas Consortium (Elsevier, 2023)

  The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts by providing evidence for scientifically informed management decisions. Here we survey the main ...
• ​Comparative genomics of Balto, a famous historic dog, captures lost diversity of 1920s sled dogs

  Moon, Katherine L.; Huson, Heather J.; Morrill, Kathleen; Wang, Ming-Shan; Li, Xue; Srikanth, Krishnamoorthy; Zoonomia Consortium; Lindblad-Toh, Kerstin; Svenson, Gavin J.; Karlsson, Elinor K.; Shapiro, Beth (American Association for the Advancement of Science (AAAS), 2023)

  We reconstruct the phenotype of Balto, the heroic sled dog renowned for transporting diphtheria antitoxin to Nome, Alaska, in 1925, using evolutionary constraint estimates from the Zoonomia alignment of 240 mammals and 682 ...
• Evolutionary constraint and innovation across hundreds of placental mammals

  Christmas, Matthew J.; Valenzuela, Alejandro; Marquès i Bonet, Tomàs, 1975-; Navarro i Cuartiellas, Arcadi, 1969-; Karlsson, Elinor K. (American Association for the Advancement of Science (AAAS), 2023)

  Zoonomia is the largest comparative genomics resource for mammals produced to date. By aligning genomes for 240 species, we identify bases that, when mutated, are likely to affect fitness and alter disease risk. At least ...
• Widespread inter- and intra-domain horizontal gene transfer of d-amino acid metabolism enzymes in eukaryotes

  Naranjo-Ortíz, Miguel A.; Brock, Matthias; Brunke, Sascha; Hube, Bernhard; Marcet Houben, Marina; Gabaldón Estevan, Juan Antonio, 1973- (Frontiers, 2016)

  Analysis of the growing number of available fully-sequenced genomes has shown that Horizontal Gene Transfer (HGT) in eukaryotes is more common than previously thought. It has been proposed that genes with certain functions ...
• Dissecting the effect of genetic variation on the hepatic expression of drug disposition genes across the collaborative cross mouse strains

  Nachshon, Aharon; Abu-Toamih Atamni, Hanifa Jalal; Steuerman, Yael; Sheikh-Hamed, Roa'a; Dorman, Alexandra; Mott, Richard; Dohm, Juliana C.; Lehrach, Hans; Sultan, Marc; Shamir, Ron; Sauer, Sascha; Himmelbauer, Heinz; Iraqi, Fuad A.; Gat-Viks, Irit (Frontiers, 2016)

  A central challenge in pharmaceutical research is to investigate genetic variation in response to drugs. The Collaborative Cross (CC) mouse reference population is a promising model for pharmacogenomic studies because of ...
• ALS/FTD mutation-induced phase transition of FUS liquid droplets and reversible hydrogels into irreversible hydrogels impairs RNP granule function

  Murakami, Tetsuro; Gaetano Tartaglia, Gian; George-Hyslop, Peter St (Cell Press, 2015)

  The mechanisms by which mutations in FUS and other RNA binding proteins cause ALS and FTD remain controversial. We propose a model in which low-complexity (LC) domains of FUS drive its physiologically reversible assembly ...
• Profiling the secretome and extracellular proteome of the potato late blight pathogen phytophthora infestans

  Meijer, Harold J. G.; Mancuso, Francesco M.; Espadas, Guadalupe; Seidl, Michael F.; Chiva, Cristina; Govers, Francine; Sabidó Aguadé, Eduard, 1981- (American Society for Biochemistry and Molecular Biology (ASBMB), 2014)

  Oomycetes are filamentous organisms that cause notorious diseases, several of which have a high economic impact. Well known is Phytophthora infestans, the causal agent of potato late blight. Previously, in silico analyses ...
• The contribution of historical processes to contemporary extinction risk in placental mammals

  Wilder, Aryn P.; Supple, Megan A.; Subramanian, Ayshwarya; Mudide, Anish; Swofford, Ross; Serres-Armero, Aitor; Steiner, Cynthia; Koepfli, Klaus-Peter; Genereux, Diane P.; Karlsson, Elinor K.; Lindblad-Toh, Kerstin; Marquès i Bonet, Tomàs, 1975-; Muñoz-Fuentes, Violeta; Foley, Kathleen; Meyer, Wynn K.; Zoonomia Consortium; Ryder, Oliver A.; Shapiro, Beth (American Association for the Advancement of Science (AAAS), 2023)

  Species persistence can be influenced by the amount, type, and distribution of diversity across the genome, suggesting a potential relationship between historical demography and resilience. In this study, we surveyed genetic ...
• Relating enhancer genetic variation across mammals to complex phenotypes using machine learning

  Kaplow, Irene M.; Lawler, Alyssa J.; Schäffer, Daniel E.; Srinivasan, Chaitanya; Sestili, Heather H.; Wirthlin, Morgan E.; Phan, BaDoi N.; Prasad, Kavya; Brown, Ashley; Zhang, Xiaomeng; Foley, Kathleen; Genereux, Diane P.; Zoonomia Consortium; Karlsson, Elinor K.; Lindblad-Toh, Kerstin; Meyer, Wynn K.; Pfenning, Andreas R. (American Association for the Advancement of Science (AAAS), 2023)

  Protein-coding differences between species often fail to explain phenotypic diversity, suggesting the involvement of genomic elements that regulate gene expression such as enhancers. Identifying associations between enhancers ...
• Integrating gene annotation with orthology inference at scale

  Kirilenko, Bogdan M.; Munegowda, Chetan; Osipova, Ekaterina; Jebb, David; Sharma, Virag; Blumer, Moritz; Morales, Ariadna E.; Ahmed, Alexis-Walid; Kontopoulos, Dimitrios-Georgios; Hilgers, Leon; Lindblad-Toh, Kerstin; Karlsson, Elinor K.; Zoonomia Consortium; Hiller, Michael (American Association for the Advancement of Science (AAAS), 2023)

  Annotating coding genes and inferring orthologs are two classical challenges in genomics and evolutionary biology that have traditionally been approached separately, limiting scalability. We present TOGA (Tool to infer ...
• The functional and evolutionary impacts of human-specific deletions in conserved elements

  Xue, James R.; Mackay-Smith, Ava; Mouri, Kousuke; Fernandez Garcia, Meilin; Dong, Michael X.; Akers, Jared F.; Noble, Mark; Li, Xue; Zoonomia Consortium; Lindblad-Toh, Kerstin; Karlsson, Elinor K.; Noonan, James P.; Capellini, Terence D.; Brennand, Kristen J.; Tewhey, Ryan; Sabeti, Pardis C.; Reilly, Steven K. (American Association for the Advancement of Science (AAAS), 2023)

  Conserved genomic sequences disrupted in humans may underlie uniquely human phenotypic traits. We identified and characterized 10,032 human-specific conserved deletions (hCONDELs). These short (average 2.56 base pairs) ...
• Leveraging base-pair mammalian constraint to understand genetic variation and human disease

  Sullivan, Patrick F.; Zoonomia Consortium; Lindblad-Toh, Kerstin (American Association for the Advancement of Science (AAAS), 2023)

  Thousands of genomic regions have been associated with heritable human diseases, but attempts to elucidate biological mechanisms are impeded by an inability to discern which genomic positions are functionally important. ...
• N6-methyladenosine modification is not a general trait of viral RNA genomes

  Baquero Pérez, Belinda; Yonchev, Ivaylo D.; Delgado-Tejedor, Anna; Medina, Rebeca; Puig-Torrents, Mireia; Sudbery, Ian; Begik, Oguzhan; Wilson, Stuart A.; Novoa, Eva Maria; Díez Antón, Juana, 1962- (Nature Research, 2024)

  Despite the nuclear localization of the m6A machinery, the genomes of multiple exclusively-cytoplasmic RNA viruses, such as chikungunya (CHIKV) and dengue (DENV), are reported to be extensively m6A-modified. However, these ...
• An integrated precision medicine approach in major depressive disorder: a study protocol to create a new algorithm for the prediction of treatment response

  Baune, Bernhard T.; Domínguez Barragán, Jorge; Donlo, Chus; Martínez de Lagrán Cabredo, María; Mayer, Miguel Ángel, 1960-; Perera Bel, Júlia; Sierra, Cesar; Sanz, Ferran; Dierssen, Mara (Frontiers, 2024)

  Major depressive disorder (MDD) is the most common psychiatric disease worldwide with a huge socio-economic impact. Pharmacotherapy represents the most common option among the first-line treatment choice; however, only ...
• Asymptotics of the frequency spectrum for general Dirichlet Ξ-coalescents

  González-Casanova, Adrián; Miró Pina, Verónica; Schertzer, Emmanuel; Siri-Jégousse, Arno (Institute of Mathematical Statistics, 2024)

  In this work, we study general Dirichlet coalescents, which are a family of Ξ-coalecents constructed from i.i.d mass partitions, and are an extension of the symmetric coalescent. This class of models is motivated by ...
• Twelve quick tips for deploying a Beacon

  Fromont, Lauren A.; Moldes, Mauricio; Baudis, Michael; Brookes, Anthony J.; Navarro i Cuartiellas, Arcadi, 1969-; Rambla de Argila, Jordi (Public Library of Science (PLoS), 2024)
• Distinct roles of the polarity factors Boi1 and Boi2 in the control of exocytosis and abscission in budding yeast

  Masgrau Fortuny, Aina, 1986-; Battola, Andrea, 1987-; Sanmartín Olmo, Trinidad; Pryszcz, Leszek Piotr, 1985-; Gabaldón Estevan, Juan Antonio, 1973-; Mendoza, Manuel (Mendoza Palomares) (American Society for Cell Biology, 2017)

  Boi1 and Boi2 (Boi1/2) are budding yeast plasma membrane proteins that function in polarized growth, and in cytokinesis inhibition in response to chromosome bridges via the NoCut abscission checkpoint. How Boi1/2 act in ...
• The genome of the generalist plant pathogen fusarium avenaceum is enriched with genes involved in redox, signaling and secondary metabolism

  Lysøe, Erik; Harris, Linda J.; Walkowiak, Sean; Subramaniam, Rajagopal; Divon, Hege H.; Riiser, Even S.; Llorens, Carlos, 1968-; Gabaldón Estevan, Juan Antonio, 1973-; Kistler, H. Corby; Jonkers, Wilfried; Kolseth, Anna-Karin; Nielsen, Kristian F.; Thrane, Ulf; Frandsen, Rasmus J. N. (Public Library of Science (PLoS), 2014)

  Fusarium avenaceum is a fungus commonly isolated from soil and associated with a wide range of host plants. We present here three genome sequences of F. avenaceum, one isolated from barley in Finland and two from spring ...
• State of art of cancer pharmacogenomics in Latin American populations

  López-Cortés, Andrés; Guerrero, Santiago, 1957-; Redal, María Ana; Alvarado, Angel Tito; Quiñones, Luis (MDPI, 2017)

  Over the past decades, several studies have shown that tumor-related somatic and germline alterations predicts tumor prognosis, drug response and toxicity. Latin American populations present a vast geno-phenotypic diversity ...
• Distinct structural transitions of chromatin topological domains correlate with coordinated hormone-induced gene regulation

  Le Dily, François; Baù, Davide; Pohl, Andy, 1979-; Vicent, Guillermo Pablo; Serra, François; Soronellas, Daniel; Castellano, Giancarlo; Wright, Roni H.G.; Ballare, Cecilia Julia; Filion, Guillaume; Marti-Renom, Marc A.; Beato, Miguel (Cold Spring Harbor Laboratory Press (CSHL Press), 2014)

  The human genome is segmented into topologically associating domains (TADs), but the role of this conserved organization during transient changes in gene expression is not known. Here we describe the distribution of ...

Más