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MethFlowVM: a virtual machine for the integral analysis of bisulfite sequencing data [article]

Ricardo Lebron, Guillermo Barturen, Cristina Gomez-Martin, Jose L Oliver, Michael Hackenberg
2016 bioRxiv   pre-print
Lebrón 1,2 , Guillermo Barturen 3 , Cristina Gómez-Martín 1,2 , José L.  ...  V M : a v i r t u a l m a c h i n e f o r t h e i n t e g r a l a n a l y s i s o f b i s u l f i t e s e q u e n c i n g d a t a Ricardo  ... 
doi:10.1101/066795 fatcat:7yzvm4sskvc5na243xsvqjzoc4

NGSmethDB 2017: enhanced methylomes and differential methylation

Ricardo Lebrón, Cristina Gómez-Martín, Pedro Carpena, Pedro Bernaola-Galván, Guillermo Barturen, Michael Hackenberg, José L. Oliver
2016 Nucleic Acids Research  
Our most recent development is MethFlow (Lebrón et al.  ...  For the most recent genome assemblies, we used our improved methylation pipeline MethFlow (Lebrón et al.  ... 
doi:10.1093/nar/gkw996 pmid:27794041 pmcid:PMC5210667 fatcat:qa55agoltjgljh6bhotxum5sd4

miRNAgFree: prediction and profiling of novel microRNAs without genome assembly [article]

Ernesto L. Aparicio, Antonio Rueda, Bastian Fromm, Cristina Gómez-Martin, Ricardo Lebrón, Jose L Oliver, Juan A Marchal, Michail Kotsyfakis, Michael Hackenberg
2017 bioRxiv   pre-print
The prediction of novel miRNA genes generally requires the availability of genome sequences in order to assess important properties such as the characteristic hairpin-shaped secondary structure. However, although the sequencing costs have decreased over the last years, still many important species lack an assembled genome of certain quality. We implemented an algorithm which for the first time exploits characteristic biogenesis features like the 5' homogeneity that can be assessed without
more » ... sequences. We used a phylogenetically broad spectrum of well annotated animal genomes for benchmarking. We found that between 90-100% of the most expressed miRNA candidates (top quartile) corresponded to known miRNA sequences.
doi:10.1101/193094 fatcat:xj3iacpoabdq5c25eo42ldwavy

sRNAtoolbox: an integrated collection of small RNA research tools

Antonio Rueda, Guillermo Barturen, Ricardo Lebrón, Cristina Gómez-Martín, Ángel Alganza, José L. Oliver, Michael Hackenberg
2015 Nucleic Acids Research  
Small RNA research is a rapidly growing field. Apart from microRNAs, which are important regulators of gene expression, other types of functional small RNA molecules have been reported in animals and plants. MicroRNAs are important in host-microbe interactions and parasite microRNAs might modulate the innate immunity of the host. Furthermore, small RNAs can be detected in bodily fluids making them attractive non-invasive biomarker candidates. Given the general broad interest in small RNAs, and
more » ... n particular microRNAs, a large number of bioinformatics aided analysis types are needed by the scientific community. To facilitate integrated sRNA research, we developed sRNAtoolbox, a set of independent but interconnected tools for expression profiling from high-throughput sequencing data, consensus differential expression, target gene prediction, visual exploration in a genome context as a function of read length, gene list analysis and blast search of unmapped reads. All tools can be used independently or for the exploration and downstream analysis of sRNAbench results. Workflows like the prediction of consensus target genes of parasite mi-croRNAs in the host followed by the detection of enriched pathways can be easily established. The webinterface interconnecting all these tools is available at http://bioinfo5.ugr.es/srnatoolbox
doi:10.1093/nar/gkv555 pmid:26019179 pmcid:PMC4489306 fatcat:ff5jj7krwvb5xpm23xolo2f4nm

liqDB: a small-RNAseq knowledge discovery database for liquid biopsy studies

Ernesto Aparicio-Puerta, David Jáspez, Ricardo Lebrón, Danijela Koppers-Lalic, Juan A Marchal, Michael Hackenberg
2018 Nucleic Acids Research  
MiRNAs are important regulators of gene expression and are frequently deregulated under pathologic conditions. They are highly stable in bodily fluids which makes them feasible candidates to become minimally invasive biomarkers. In fact, several studies already proposed circulating miRNA-based biomarkers for different types of neoplastic, cardiovascular and degenerative diseases. However, many of these studies rely on small RNA sequencing experiments that are based on different RNA extraction
more » ... d processing protocols, rendering results incomparable. We generated liqDB, a database for liquid biopsy small RNA sequencing profiles that provides users with meaningful information to guide their small RNA liquid biopsy research and to overcome technical and conceptual problems. By means of a user-friendly web interface, miRNA expression profiles from 1607 manually annotated samples can be queried and explored at different levels. Result pages include downloadable expression matrices, differential expression analysis, most stably expressed miRNAs, cluster analysis and relevant visualizations by means of boxplots and heatmaps. We anticipate that liqDB will be a useful tool in liquid biopsy research as it provides a consistently annotated large compilation of experiments together with tools for reproducible analysis, comparison and hypothesis generation. LiqDB is available at http://bioinfo5.ugr.es/liqdb.
doi:10.1093/nar/gky981 pmid:30357370 pmcid:PMC6323997 fatcat:ioj24rgrajepla7wlqcarm7njm

Tracking evolutionary trends towards increasing complexity: a case study in Cyanobacteria [article]

Andres Moya, Jose L. Oliver, Miguel Verdu, Luis Delaye, Vicente Arnau, Pedro Bernaola-Galvan, Rebeca de la Fuente, Wladimiro Diaz, Cristina Gomez-Martin, Francisco M. Gonzalez, Amparo Latorre, Ricardo Lebron (+1 others)
2020 bioRxiv   pre-print
Progressive evolution, the tendency towards increasing complexity, is a controversial issue in Biology, whose resolution requires a proper measurement of complexity. Genomes are the best entities to address this challenge, as they record the history and information gaining of organisms in their ongoing biotic and environmental interactions. Using six metrics of genome complexity, none of which is primarily associated to biological function, we measure genome complexity in 91 genomes from the
more » ... lum Cyanobacteria. Several phylogenetic analyses reveal the existence of progressive evolution towards higher genome complexity: 1) all the metrics detect strong phylogenetic signals; 2) ridge regressions detect positive trends towards higher complexity; and 3) classical proofs for progressive evolution (the minimum, the ancestor-descendent and the sub-clade tests), show that some of these positive trends are driven, being mainly due to natural selection. These findings support the existence of progressive genome evolution in this ancient and diverse group of organisms.
doi:10.1101/2020.01.29.924464 fatcat:pb55lttskvam7kkvgg2qqwgbgm

Transcriptional Dynamics and Candidate Genes Involved in Pod Maturation of Common Bean (Phaseolus vulgaris L.)

Cristina Gómez-Martín, Carmen Capel, Ana M. González, Ricardo Lebrón, Fernando J. Yuste-Lisbona, Michael Hackenberg, José L. Oliver, Marta Santalla, Rafael Lozano
2020 Plants  
Pod maturation of common bean relies upon complex gene expression changes, which in turn are crucial for seed formation and dispersal. Hence, dissecting the transcriptional regulation of pod maturation would be of great significance for breeding programs. In this study, a comprehensive characterization of expression changes has been performed in two common bean cultivars (ancient and modern) by analyzing the transcriptomes of five developmental pod stages, from fruit setting to maturation.
more » ... eq analysis allowed for the identification of key genes shared by both accessions, which in turn were homologous to known Arabidopsis maturation genes and furthermore showed a similar expression pattern along the maturation process. Gene- expression changes suggested a role in promoting an accelerated breakdown of photosynthetic and ribosomal machinery associated with chlorophyll degradation and early activation of alpha-linolenic acid metabolism. A further study of transcription factors and their DNA binding sites revealed three candidate genes whose functions may play a dominant role in regulating pod maturation. Altogether, this research identifies the first maturation gene set reported in common bean so far and contributes to a better understanding of the dynamic mechanisms of pod maturation, providing potentially useful information for genomic-assisted breeding of common bean yield and pod quality attributes.
doi:10.3390/plants9040545 pmid:32331491 fatcat:ua45cax4wvdrlhojly4vp6z63e

Driven progressive evolution of genome sequence complexity in Cyanobacteria

Andrés Moya, José L. Oliver, Miguel Verdú, Luis Delaye, Vicente Arnau, Pedro Bernaola-Galván, Rebeca de la Fuente, Wladimiro Díaz, Cristina Gómez-Martín, Francisco M. González, Amparo Latorre, Ricardo Lebrón (+1 others)
2020 Scientific Reports  
Progressive evolution, or the tendency towards increasing complexity, is a controversial issue in biology, which resolution entails a proper measurement of complexity. Genomes are the best entities to address this challenge, as they encode the historical information of a species' biotic and environmental interactions. As a case study, we have measured genome sequence complexity in the ancient phylum Cyanobacteria. To arrive at an appropriate measure of genome sequence complexity, we have chosen
more » ... metrics that do not decipher biological functionality but that show strong phylogenetic signal. Using a ridge regression of those metrics against root-to-tip distance, we detected positive trends towards higher complexity in three of them. Lastly, we applied three standard tests to detect if progressive evolution is passive or driven—the minimum, ancestor–descendant, and sub-clade tests. These results provide evidence for driven progressive evolution at the genome-level in the phylum Cyanobacteria.
doi:10.1038/s41598-020-76014-4 pmid:33149190 fatcat:7xo5xpq6enfhvlh4bnhognhnqq

Functional characterization of the tomato HAIRPLUS gene reveals the implication of the epigenome in the control of glandular trichome formation

Rocío Fonseca, Carmen Capel, Fernando J Yuste-Lisbona, Jorge L Quispe, Cristina Gómez-Martín, Ricardo Lebrón, Michael Hackenberg, José L Oliver, Trinidad Angosto, Rafael Lozano, Juan Capel
2022 Horticulture Research  
Trichomes are specialised epidermal cells developed in the aerial surface of almost every terrestrial plant. These structures form physical barriers, which combined with their capability of synthesis of complex molecules, prevent plagues from spreading and confer trichomes a key role in the defence against herbivores. In this work, the tomato gene HAIRPLUS (HAP) that controls glandular trichome density in tomato plants was characterised. HAP belongs to a group of proteins involved in histone
more » ... l modifications although some also bind methylated DNA. HAP loss of function promotes epigenomic modifications in the tomato genome reflected in numerous differentially methylated cytosines and causes transcriptomic changes in hap mutant plants. Taken together, these findings demonstrate that HAP links epigenome remodelling with multicellular glandular trichome development and reveal that HAP is a valuable genomic tool for pest resistance in tomato breeding.
doi:10.1093/hr/uhab015 pmid:35039829 pmcid:PMC8795820 fatcat:5a7rh2cqqncybhskmcsi2r5zza

A Tomato EMS-Mutagenized Population Provides New Valuable Resources for Gene Discovery and Breeding of Developmental Traits

Rocío Fonseca, Carmen Capel, Roberto Nieto-Canseco, Ana Ortiz-Atienza, Sandra Bretones, Juan D. López-Fábregas, Abraham S. Quevedo-Colmena, Ricardo Lebrón, Teresa Barragán-Lozano, Víctor Villalobos-Ramírez, Fernando J. Yuste-Lisbona, Trinidad Angosto (+2 others)
2022 Plants  
Tomato (Solanum lycopersicum L.) is a major horticultural crop and a model species among eudicots, especially for traits related to reproductive development. Although considerable progress has been made since the tomato genome sequence project was completed, most of the genes identified remain predictions with an unknown or hypothetical function. This lack of functional characterization hampers the use of the huge amount of genomic information available to improve the quality and productivity
more » ... this crop. Reverse genetics strategies such as artificial mutagenesis and next-generation sequencing approaches build the perfect tandem for increasing knowledge on functional annotation of tomato genes. This work reports the phenotypic characterization of a tomato mutant collection generated from an EMS chemical mutagenesis program aimed to identify interesting agronomic mutants and novel gene functions. Tomato mutants were grouped into fourteen phenotypic classes, including vegetative and reproductive development traits, and the inheritance pattern of the identified mutations was studied. In addition, causal mutation of a selected mutant line was isolated through a mapping-by-sequencing approach as a proof of concept of this strategy's successful implementation. Results support tomato mutagenesis as an essential tool for functional genomics in this fleshy-fruited model species and a highly valuable resource for future breeding programs of this crop species aimed at the development of more productive and resilient new varieties under challenging climatic and production scenarios.
doi:10.3390/plants11192453 fatcat:tol7vgbegjdc7fbdfccgwnsm5i

Age-Related Metabolic Pathways Changes in Dental Follicles: A Pilot Study

Victor Coutinho Bastos, Jéssica Gardone Vitório, Roberta Rayra Martins-Chaves, Flávia Leite-Lima, Yuri Abner Rocha Lebron, Victor Rezende Moreira, Filipe Fideles Duarte-Andrade, Thaís dos Santos Fontes Pereira, Lucilaine Valéria de Souza Santos, Liséte Celina Lange, Adriana Nori de Macedo, Gisele André Baptista Canuto (+2 others)
2021 Frontiers in Oral Health  
Aging is not a matter of choice; it is our fate. The "time-dependent functional decline that affects most living organisms" is coupled with several alterations in cellular processes, such as cell senescence, epigenetic alterations, genomic instability, stem cell exhaustion, among others. Age-related morphological changes in dental follicles have been investigated for decades, mainly motivated by the fact that cysts and tumors may arise in association with unerupted and/or impacted teeth. The
more » ... e we understand the physiology of dental follicles, the more we are able to contextualize biological events that can be associated with the occurrence of odontogenic lesions, whose incidence increases with age. Thus, our objective was to assess age-related changes in metabolic pathways of dental follicles associated with unerupted/impacted mandibular third molars from young and adult individuals. For this purpose, a convenience sample of formalin-fixed paraffin-embedded (FFPE) dental follicles from young (<16 y.o., n = 13) and adult (>26 y.o., n = 7) individuals was selected. Samples were analyzed by high-performance liquid chromatography-mass spectrometry (HPLC-MS)-based untargeted metabolomics. Multivariate and univariate analyses were conducted, and the prediction of altered pathways was performed by mummichog and Gene Set Enrichment Analysis (GSEA) approaches. Dental follicles from young and older individuals showed differences in pathways related to C21-steroid hormone biosynthesis, bile acid biosynthesis, galactose metabolism, androgen and estrogen biosynthesis, starch and sucrose metabolism, and lipoate metabolism. We conclude that metabolic pathways differences related to aging were observed between dental follicles from young and adult individuals. Our findings support that similar to other human tissues, dental follicles associated with unerupted tooth show alterations at a metabolic level with aging, which can pave the way for further studies on oral pathology, oral biology, and physiology.
doi:10.3389/froh.2021.677731 pmid:35048024 pmcid:PMC8757705 fatcat:en35htwtl5bxzdlbler7odtglm

Wandering spleen presenting as recurrent pancreatitis

Ricardo Lebron, Michael Self, Alicia Mangram, Ernest Dunn
Journal of the Society of Laparoendoscopic Surgeons  
A wandering spleen occurs when there is a laxity of the ligaments that fix the spleen in its normal anatomical position. We present the case of a wandering spleen in a 20-year-old female who presented with recurrent pancreatitis and underwent a laparoscopic splenectomy. The presentation of a wandering spleen varies from an asymptomatic mass to splenic infarct with an acute abdomen. Its correct diagnosis relies mostly on imaging studies. Treatment consists of performing either splenectomy or
more » ... nopexy. The diagnosis of wandering spleen can often be difficult due to the intermittent nature of the torsion. Computed tomography studies for diagnosis and laparoscopic surgery have changed the management of this interesting disease.
pmid:18765060 pmcid:PMC3015861 fatcat:6ych2hhhubhexe4qp4rikzmngi

TAM volume 77 issue 4 Cover and Front matter

2020 The Americas: A Quarterly Review of Latin American History  
Edited by Yarimar Bonilla and Marisol LeBrón. Jorell Meléndez-Badillo PANAMA CANAL 652 Erased: The Untold Story of the Panama Canal. By Marixa Lasso. Robert C.  ...  Ricardo López-Pedreros. David Griffith REVIEWS BOOK REVIEWS AZTECS 633 Justyna Olko CONQUEST OF MEXICO 635 Conquistadoren und Azteken: Cortés und die Eroberung Mexikos. By Stefan Rinke.  ... 
doi:10.1017/tam.2020.103 fatcat:54xq444w7jea3eoyaelaqmncqa

"La Gran Vía" durante la dirección de Salvador Rueda (diciembre 1894-septiembre 1895), y la renovación poética finisecular: Índice de las composiciones poéticas

Marta Palenque
2001 Philología Hispalensis  
Sanmartín, Fernando Zaide, Miguel Lebrón, Federico Balart, Emilio del Palacio, Juan Pérez y Rodríguez, sin título [doble página].  ...  -Zacarías Carbó: «A una mujer»; Gabriel de Enciso, Rafael García Ormaechea, Miguel Lebrón, J. Orovetto, todas sin título. -Mi álbum.  ... 
doi:10.12795/ph.2001.v15.i01.16 fatcat:jzhev5rtjngb3pi5la7yz6ur7a

First record of Blankaartia sinnamaryi (Floch & Fauran, 1956) (Trombidiformes: Trombiculidae) parasitizing the striped owl in Northeastern Brazil

Ricardo Bassini-Silva, Fernando de Castro Jacinavicius, Matheus Huang-Bastos, Aksa Ingrid Vieira Batista, Nathália Caroline Souza da Silva, Thiago Ferreira Lopes Nery, Josivania Soares Pereira, Cal Welbourn, Ron Ochoa, Darci Moraes Barros-Battesti
2021 Revista Brasileira de Parasitologia Veterinária  
Acknowledgements To Gabrielle Ribeiro de Andrade and Maria Cristina Ferreira do Rosário for technical contribution, Debra Creel, Andrew Ulsamer (SEL-USDA), and Armando Rosario-Lebron (APHIS-USDA) for their  ... 
doi:10.1590/s1984-29612021042 pmid:34037190 fatcat:xrblsmdkcvdrje6doorzvhsynu
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