Publication List

@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{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}
}

@article{vanD2015,
title = {Slow-growing cells within isogenic populations have increased RNA polymerase error rates and DNA damage},
author = {van Dijk, David, Dhar, Riddhiman, Missarova, Alsu M, Espinar, Lorena, Blevins, William R, Lehner, Ben, Carey, Lucas B},
url = {http://www.nature.com/ncomms/2015/150813/ncomms8972/full/ncomms8972.html},
isbn = {10.1038/ncomms8972},
year = {2015},
date = {2015-08-13},
journal = {Nature Communications},
volume = {6},
pages = {7972},
keywords = {RNA polymerase error rate, transcriptomics, yeast}
}

@article{Baldo2015,
title = {Gut Microbiota Dynamics during Dietary Shift in Eastern African Cichlid Fishes.},
author = {Baldo, Laura and Riera, Joan Lluís and Tooming-Klunderud, Ave and Albà, M Mar and Salzburger, Walter},
url = {http://www.ncbi.nlm.nih.gov/pubmed/25978452},
issn = {1932-6203},
year = {2015},
date = {2015-01-01},
journal = {PloS one},
volume = {10},
number = {5},
pages = {e0127462},
abstract = {The gut microbiota structure reflects both a host phylogenetic history and a signature of adaptation to the host ecological, mainly trophic niches. African cichlid fishes, with their array of closely related species that underwent a rapid dietary niche radiation, offer a particularly interesting system to explore the relative contribution of these two factors in nature. Here we surveyed the host intra- and interspecific natural variation of the gut microbiota of five cichlid species from the monophyletic tribe Perissodini of lake Tanganyika, whose members transitioned from being zooplanktivorous to feeding primarily on fish scales. The outgroup riverine species Astatotilapia burtoni, largely omnivorous, was also included in the study. Fusobacteria, Firmicutes and Proteobacteria represented the dominant components in the gut microbiota of all 30 specimens analysed according to two distinct 16S rRNA markers. All members of the Perissodini tribe showed a homogenous pattern of microbial alpha and beta diversities, with no significant qualitative differences, despite changes in diet. The recent diet shift between zooplantkon- and scale-eaters simply reflects on a significant enrichment of Clostridium taxa in scale-eaters where they might be involved in the scale metabolism. Comparison with the omnivorous species A. burtoni suggests that, with increased host phylogenetic distance and/or increasing herbivory, the gut microbiota begins differentiating also at qualitative level. The cichlids show presence of a large conserved core of taxa and a small set of core OTUs (average 13-15%), remarkably stable also in captivity, and putatively favoured by both restricted microbial transmission among related hosts (putatively enhanced by mouthbrooding behavior) and common host constraints. This study sets the basis for a future large-scale investigation of the gut microbiota of cichlids and its adaptation in the process of the host adaptive radiation.},
keywords = {cichlid fishes, diet, transcriptomics}
}