Publication List

@article{Blevins2019_2,
title = {Extensive post-transcriptional buffering of gene expression in the response to severe oxidative stress in baker's yeast},
author = {William R. Blevins, Teresa Tavella, Simone G. Moro, Bernat Blasco-Moreno, Adrià Closa-Mosquera, Juana Díez, Lucas B. Carey, M.Mar Albà},
url = {https://www.nature.com/articles/s41598-019-47424-w},
year = {2019},
date = {2019-07-29},
journal = {Scientific Reports},
volume = {9},
pages = {11005},
keywords = {oxidative stress, proteomics, ribosome profiling, RNA-Seq, translation regulation, yeast}
}

@article{Blevins2019b,
title = {Transcriptomics data of 11 species of yeast identically grown in rich media and oxidative stress conditions},
author = {William R. Blevins, Lucas B. Carey, M.Mar Albà},
url = {https://bmcresnotes.biomedcentral.com/articles/10.1186/s13104-019-4286-0},
year = {2019},
date = {2019-05-03},
journal = {BMC Research Notes},
volume = {12},
pages = {250},
keywords = {oxidative stress, RNA-Seq, transcriptomics, yeast}
}

@article{Blevins2019,
title = {Frequent birth of de novo genes in the compact yeast genome},
author = {William R. Blevins, Jorge Ruiz-Orera, Xavier Messeguer, Bernat Blasco-Moreno, José Luis Villanueva-Cañas, Lorena Espinar, Juana Díez, Lucas B. Carey, M. Mar Albà},
url = {https://doi.org/10.1101/575837 },
year = {2019},
date = {2019-03-13},
journal = {bioRxiv, March 13},
abstract = {Evidence has accumulated that some genes originate directly from previously non-genic sequences, or de novo, rather than by the duplication or fusion of existing genes. However, how de novo genes emerge and eventually become functional is largely unknown. Here we perform the first study on de novo genes that uses transcriptomics data from eleven different yeast species, all grown identically in both rich media and in oxidative stress conditions. The genomes of these species are densely-packed with functional elements, leaving little room for the co-option of genomic sequences into new transcribed loci. Despite this, we find that at least 213 transcripts (~5%) have arisen de novo in the past 20 million years of evolution of baker’s yeast-or approximately 10 new transcripts every million years. Nearly half of the total newly expressed sequences are generated from regions in which both DNA strands are used as templates for transcription, explaining the apparent contradiction between the limited ‘empty’ genomic space and high rate of de novo gene birth. In addition, we find that 40% of these de novo transcripts are actively translated and that at least a fraction of the encoded proteins are likely to be under purifying selection. This study shows that even in very highly compact genomes, de novo transcripts are continuously generated and can give rise to new functional protein-coding genes.},
keywords = {de novo gene, RNA-Seq, Saccharomyces cerevisiae, yeast}
}

@article{SL2018,
title = {Transcriptomics in the wild: Hibernation physiology in free-ranging dwarf lemurs.},
author = {Sheena L. Faherty S#*, José Luis Villanueva-Cañas#, Marina B. Blanco, M.Mar Albà*, Anne D. Yoder.},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/mec.14483},
year = {2018},
date = {2018-01-29},
journal = {Molecular Ecology},
volume = {27},
number = {3},
pages = {709-722},
abstract = {Hibernation is an adaptive strategy some mammals use to survive highly seasonal or unpredictable environments. We present the first investigation on the transcriptomics of hibernation in a natural population of primate hibernators: Crossley\'s dwarf lemurs (Cheirogaleus crossleyi). Using capture-mark-recapture techniques to track the same animals over a period of 7 months in Madagascar, we used RNA-seq to compare gene expression profiles in white adipose tissue (WAT) during three distinct physiological states. We focus on pathway analysis to assess the biological significance of transcriptional changes in dwarf lemur WAT and, by comparing and contrasting what is known in other model hibernating species, contribute to a broader understanding of genomic contributions of hibernation across Mammalia. The hibernation signature is characterized by a suppression of lipid biosynthesis, pyruvate metabolism and mitochondrial-associated functions, and an accumulation of transcripts encoding ribosomal components and iron-storage proteins. The data support a key role of pyruvate dehydrogenase kinase isoenzyme 4 (PDK4) in regulating the shift in fuel economy during periods of severe food deprivation. This pattern of PDK4 holds true across representative hibernating species from disparate mammalian groups, suggesting that the genetic underpinnings of hibernation may be ancestral to mammals.},
keywords = {hibernation, lemur, metabolism, RNA-Seq, torpor, transcriptomics}
}

@article{Faherty2016,
title = {Gene expression profiling in the hibernating primate, Cheirogaleus medius},
author = {Sheena L. Faherty, José Luis Villanueva-Cañas, Peter H. Klopfer, M. Mar Albà and Anne D. Yoder},
url = {http://gbe.oxfordjournals.org/content/early/2016/07/11/gbe.evw163.abstract},
year = {2016},
date = {2016-07-12},
journal = {Genome Biology and Evolution},
volume = {advance access (doi: 10.1093/gbe/evw163)},
keywords = {differential gene expression, hibernation, primate, RNA-Seq, transcriptomics}
}

@article{Ruiz-Orera2015b,
title = {Origins of de novo genes in human and chimpanzee},
author = {Ruiz-Orera, Jorge, Hernandez-Rodriguez, Jessica, Chiva, Cristina, Sabidó, Eduard, Kondova, Ivanela, Bontrop, Ronald, Marqués-Bonet, Tomàs, Albà, M.Mar},
url = {http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1005721},
year = {2015},
date = {2015-12-31},
journal = {Plos Genetics},
volume = {11},
number = {12},
pages = {e1005721},
keywords = {chimpanzee, de novo gene, Evolution, Humans, lncRNA, Promoter, proteomics, ribosome profiling, RNA-Seq, transcription factor binding site, transcriptomics}
}