2025

Mármol-Sánchez E, Luigi-Sierra MG, Bardou P, Charlier C, Colli L, Cardoso TF, Crepaldi P, Bionda A, Milanesi M, Lazzari B, VarGoats Consortium, Tosser-Klopp G, Amills M. The variability of goat microRNA genes is strongly shaped by functional constraints. Under Review. https://doi.org/10.1101/2025.09.30.679575. Contribution: I am leading this project where I have planned all the implementation and performed all the data analyses. This project involves the analysis of potentially deleterious load within noncoding loci in the goat genome and across multiple breeds world-wide with different population sizes and inbreeding trajectories through time.

2024

Aslanzadeh M, Stanicek L, Tarbier M, Mármol-Sánchez E, Biryukova I, Friedländer MR. Malat1 affects transcription and splicing through distinct pathways in mouse embryonic stem cells. NAR Genomics & Bioinformatics 2024; 6(2):lqae045. https://doi.org/10.1093/nargab/lqae045. Contribution: I participated in co-supervising the main author of the paper as senior postdoctoral researcher in the team, as well as analyzing exon-intron splicing patterns using RNA-seq data.

Varela-Martínez E, Luigi-Sierra MG, Guan D, López-Béjar M, Casas E, Olvera S, Gardela J, Palomo MJ, Osuagwuh UI, Ohaneje UL, Mármol-Sánchez E, Amills M. The landscape of long non-coding RNA expression in the goat brain. Journal of Dairy Science 2024; 107(6):4075-4091. https://doi.org/10.3168/jds.2023-23966. Contribution: I participated in tissue sampling, manuscript writing and editing.

2023

Mármol-Sánchez E, Fromm B, Oskolkov N, Pochon Z, Kalogeropoulos P, Eriksson E, Biryukova I, Sekar V, Ersmark E, Andersson B, Dalén L, Friedländer MR. Historical RNA expression profiles from the extinct Tasmanian tiger. Genome Research 2023; 3(8):1299-1316. https://doi.org/10.1101/gr.277663.123. Contribution: I led the project performing all laboratory work, sequencing and data analysis. With this, I generated, for the first time, historic transcriptional profiles from the extinct Tasmanian tiger using skeletal muscle and skins preserved at room temperature in desiccation. It has been recognized as a significant scientific contribution of the year by the Gizmodo Science Fair 2024.

Sekar V, Mármol-Sánchez E, Kalogeropoulos P, Stanicek L, Sagredo EA, Widmark A, Doukoumopoulos E, Bonath F, Biryukova I, Friedländer MR. Detection of transcriptome-wide microRNA-target interactions in single cells with agoTRIBE. Nature Biotechnology 2023; 42(8):1296-1302. https://doi.org/10.1038/s41587-023-01951-0. Contribution: I co-supervised, revised and actively participated as senior postdoc in the development of the computational pipeline for the detection of TRIBE-derived editing signatures in miRNA targets using single cell and bulk RNA-seq.

Manaig YJY, Mármol-Sánchez E, Castelló A, Esteve-Codina A, Sandrini S, Savoini G, Agazzi A, Sánchez A, Folch JM. Exon-intron split analysis reveals post-transcriptional regulatory signals induced by high and low n-6/n-3 polyunsaturated fatty acid ratio diets in piglets. Journal of Animal Science 2023; 101:skad271. https://doi.org/10.1093/jas/skad271. Shared first co-authorship. Contribution: I performed all computational analyses for post-transcriptional signal modeling using bulk RNA-seq, as well as participating in data visualization, manuscript writing and editing.

Luigi-Sierra MG, Guan D, López-Béjar M, Casas E, Olvera S, Gardela J, Palomo MJ, Osuagwuh UI, Ohaneje UL, Mármol-Sánchez E, Amills M. A protein-coding gene expression atlas from the brain of pregnant and non-pregnant goats. Frontiers in Genetics 2023; 14:1114749. https://doi.org/10.3389. Contribution: I participated in tissue sample collection, advised on data analysis and visualization and contributed to manuscript writing and editing.

Mármol-Sánchez E, Heidemann PL, Gredal H, Cirera S. MicroRNA profiling of cerebrospinal fluid from dogs with steroid responsive meningitis-arteritis and meningoencephalitis of unknown origin. Frontiers in Veterinary Science 2023; 10:1144084. https://doi.org/10.3389/fvets.2023.1144084. Shared first co-authorship. Contribution: I performed all computational analyses of small RNA-seq and qPCR data, and contributed to data visualization, manuscript writing and editing.

Manaig YJY, Criado-Mesas L, Esteve-Codina A, Mármol-Sánchez E, Castelló A, Sánchez A, Folch JM. Identifying miRNA-mRNA regulatory networks on extreme n-6/n-3 polyunsaturated fatty acid ratio expression profiles in porcine skeletal muscle. PLoS One 2023; 18(5);e0283231. https://doi.org/10.1371/journal.pone.0283231. Contribution: I participated in RNA-seq and small RNA-seq data analysis, data visualization, manuscript writing and editing.

2022

Gòdia M, Brogaard L, Mármol-Sánchez E, Langhorn R, Nordang Kieler I, Jan Reezigt B, Nicolic Nielsen L, Rem Jessen L, Cirera S. Urinary microRNAome in healthy cats and cats with pyelonephritis or other urological conditions. PLoS One 2022; 17(7):e0270067. https://doi.org/10.1371/journal.pone.0270067. Shared second co-authorship. Contribution: I participated in qPCR data analysis, expression profiling and clustering, data visualization, manuscript writing and editing.

Mármol-Sánchez E, Cirera S, Zingaretti LM, Jacobsen MJ, Ramayo-Caldas Y, Jørgensen CB, Fredholm M, Cardoso TF, Quintanilla R, Amills M. Modeling microRNA-driven post-transcriptional regulation using exon-intron split analysis in pigs. Animal Genetics 2022; 53(5):613-626. https://doi.org/10.1111/age.13238. Contribution: I led the development of a publicly available pipeline for modelling post-transcriptional regulatory signals using bulk RNA-seq data (EISAcompR). With this, I run the pipeline to generate exon-intron split profiles using porcine RNA-seq data, and integrated it with small RNA-seq data from the same experiment jointly with qPCR validation.

Fromm B, Høye E, Domanska D, Zhong X, Aparicio-Puerta E, Ovchinnikov V, Umul SU, Chabot P, Kang W, Aslanzadeh M, Tarbier M, Mármol-Sánchez E, Urgese G, Johansen M, Hovig E, Hackenberg M, Friedländer MR, Peterson KJ. MirGeneDB 2.1: Toward a complete sampling of all major animal phyla. Nucleic Acids Research 2022; 50(D1):D204-D210. https://doi.org/10.1093/nar/gkab1101. Contribution: I contributed to modeling folding structures for microRNA sequences, data visualization and manuscript editing.

2021

Cardoso TF, Luigi-Sierra MG, Castelló A, Cabrera B, Noce A, Mármol-Sánchez E, García-González R, Fernández-Arias A, Alabart JL, López-Olvera JR, Mentaberre G, Granados-Torres JE, Cardells-Peris J, Molina A, Sánchez A, Clop A, Amills A. Assessing the levels of intraspecific admixture and interspecific hybridization in Iberian wild goats (Capra pyrenaica). Evolutionary Applications 2021; 14(11):2618-2634. https://doi.org/10.1111/eva.13299. Contribution: I performed SNP calling and data analysis on a wild goat dataset for cross-validation and contributed to manuscript writing and editing.

Mármol-Sánchez E, Quintanilla R, Luigi-Sierra MG, Amills M. An association analysis between a polymorphism in the SEC24A gene and lipid traits recorded in Duroc pigs. Italian Journal of Animal Science 2021; 20(1):1444-1451. https://doi.org/10.1080/1828051X.2021.1951129. Contribution: I analyzed all SNP sequencing data, phenotype-genotype association analyses and performed all laboratory work, data visualization, manuscript writing and editing.

Dussex N, Bergfeldt N, de Anca Prado V, Dehasque M, Díez-del-Molino D, Ersmark E, Kanellidou F, Larsson P, Lemež Š, Lord E, Mármol-Sánchez E, Meleg IN, Måsviken J, Naidoo T, Studerus J, Vicente M, von Seth J, Götherström A, Dalén L, Heintzman PD. Integrating multi-taxon palaeogenomes and sedimentary ancient DNA to study past ecosystem dynamics. Proceedings of the Royal Society B. Biological Sciences 2021; 288(1597):20211252. https://doi.org/10.1098/rspb.2021.1252. Contribution: I contributed in the writing of the manuscript regarding new integrative approaches for ancient DNA and environmental DNA data.

Rosengren E, Acatrinei A, Cruceru N, Dehasque M, Haliuc A, Lord E, Mircea CI, Rusu I, Mármol-Sánchez E, Kelemen BS, Meleg IN. Ancient faunal history revealed by interdisciplinary biomolecular approaches. Diversity 2021; 13(8):370. https://doi.org/10.3390/d13080370. Contribution: I contributed in the writing of the manuscript regarding novel transcriptional analyses for ancient RNA.

Mármol-Sánchez E, Luigi-Sierra MG, Castelló A, Guan D, Quintanilla R, Tonda R, Amills M. Variability in porcine microRNA genes and its association with mRNA expression and lipid phenotypes. Genetics Selection Evolution 2021; 53(1):43. https://doi.org/10.1186/s12711-021-00632-3. Contribution: I led this project where I performed all laboratory work and analyzed all genome-wide sequencing data for the characterization of polymorphic sites in microRNA loci across multiple pig breeds worldwide. I also performed phenotype-genotype association analyses using gene expression data and qPCR validation.

Reverter A, Ballester M, Alexandre PA, Mármol-Sánchez E, Dalmau T, Quintanilla R, Ramayo-Caldas Y. A gene co-association network regulating gut microbiotal communities in a Duroc pig population. Microbiome 2021; 9(1):52. https://doi.org/10.1186/s40168-020-00994-8. Contribution: I performed SNP-miRNA association analyses, modeling miRNA folding structures and contributed to manuscript writing and editing.

Mármol-Sánchez E, Artman JS, Fredholm M, Cirera S. Unraveling molecular mechanisms involved in the development of leptin resistance using the pig as a model. Animal Genetics 2021;52(1):55-56. https://doi.org/10.1111/age.13028. Contribution: I performed candidate gene selection, all computational analyses of qPCR data, data visualization, manuscript writing and editing.

Fromm B, Tarbier M, Smith O, Mármol-Sánchez E, Dalen L, Gilbert TP, Friedlander MR. Ancient microRNA profiles of a 14,300-year-old canid samples confirm taxonomic origin and give glimpses into tissue-specific gene regulation from the Pleistocene. RNA 2021;27(3):324-34. https://doi.org/10.1261/rna.078410.120. Contribution: I contributed performing RNA damage analyses, microRNA quantification, data visualization manuscript writing and editing.

2020

Luigi-Sierra MG, Landi V, Guan D, Delgado JV, Castelló A, Cabrera B, Mármol-Sánchez E, Fernández-Álvarez J, Gómez-Carpio M, Martínez A, Such X, Jordana J, Amills M. A genome-wide association analysis for body, udder and leg conformation traits recorded in Murciano-Granadina goats. Journal of Dairy Science 2020;103(12):11605-11617. https://doi.org/10.3168/jds.2020-18461. Contribution: I performed SNP calling and contributed data analysis on the domestic goat dataset and participated in manuscript writing and editing.

Mármol-Sánchez E, Amills M. Modulation of porcine production and molecular phenotypes by nutrition and genetics. 2020. https://ddd.uab.cat/record/240818. Contribution: This is the public document of my PhD thesis, led under the supervision of Dr. Marcel Amills at the Department of Animal Science in the Faculty of Veterinary Medicine of the Autonomous University of Barcelona (UAB) and the Center for Research in Agricultural Genomics (CRAG).

Luigi-Sierra MG, Mármol-Sánchez E, Amills M. Comparing the diversity of the casein genes in the Asian mouflon and domestic sheep. Animal Genetics 2020; 51(3):470-475. https://doi.org/10.1111/age.12937. Contribution: I performed SNP calling and contributed to data analysis on the domestic sheep dataset and participated in manuscript writing and editing.

Guan D, Landi V, Luigi-Sierra MG, Delgado JV, Such X, Castelló A, Cabrera B, Mármol-Sánchez E, Fernández-Álvarez J, Ruíz de la Torre JL, Martínez A, Jordana J, Amills M. Analyzing the genomic and transcriptomic architecture of milt traits in Murciano-Granadina goats. Journal of Animal Science and Biotechnology 2020; 11:35. https://doi.org/10.1186/s40104-020-00435-4. Contribution: I performed SNP calling and data analysis on the domestic goat dataset and participated in manuscript writing and editing.

Mármol-Sánchez E, Ramayo-Caldas Y, Quintanilla R, Cardoso TF, González-Prendes R, Tibau J, Amills M. Co-expression network analysis predicts a key role of microRNAs in the adaptation of the porcine skeletal muscle to nutrient supply. Journal of Animal Science and Biotechnology 2020; 11:10. https://doi.org/10.1186/s40104-019-0412-z. Contribution: I led this project where I analyzed all RNA-seq sequencing data, phenotype-genotype association analyses and performed all laboratory work, data visualization, manuscript writing and editing.

Mármol-Sánchez E, Luigi-Sierra MG, Quintanilla R, Amills M. Detection of homozygous genotypes for a putatively lethal recessive mutation in the porcine argininosuccinate synthase 1 (ASS1) gene. Animal Genetics 2020; 51(1):106-110. https://doi.org/10.1111/age.12877. Contribution: I analyzed all SNP sequencing data, phenotype-genotype association analyses and performed all laboratory work, data visualization, manuscript writing and editing.

Mármol-Sánchez E, Quintanilla R, Jordana J, Amills M. An association analysis for 14 porcine genes mapping to meat quality QTL reveals a close relationship between ATP1A2 genotype and muscle electric conductivity. Animal Genetics 2020; 51(1):95-100. https://doi.org/10.1111/age.12864. Contribution: I analyzed all SNP sequencing data, phenotype-genotype association analyses and performed all laboratory work, data visualization, manuscript writing and editing.

2019

Mármol-Sánchez E, Cirera S, Quintanilla R, Pla A, Amills M. Discovery and annotation of novel microRNAs in the porcine genome by using a semi-supervised learning approach. Genomics 2019; 112(3):2107-2118. https://doi.org/10.1016/j.ygeno.2019.12.005. Contribution: I led the development of a publicly available pipeline for novel microRNA prediction and miRNA-mRNA target prediction using small RNA-seq data (eMIRNA) and implemented it for predicting novel microRNA candidates in the pig genome, jointly with validation using qPCR, data visualization, manuscript writing and editing.

Ramayo-Caldas Y, Mármol-Sánchez E, Ballester M, Sánchez JP, González-Prendes R, Amills M, Quintanilla R. Integrating genome-wide co-association and gene expression to identify putative regulators and predictors of feed efficiency in pigs. Genetics Selection Evolution 2019; 51(1):48. https://doi.org/10.1186/s12711-019-0490-6. Contribution: I participated in laboratory work, sequencing data analysis, microarray and eQTL integration, data visualization, manuscript writing and editing.

González-Prendes R, Mármol-Sánchez E, Quintanilla R, Castelló A, Zidi A, Ramayo-Caldas Y, Cardoso TF, Manunza A, Cánovas Á, Amills M. About the existence of common determinants of gene expression in the porcine liver and skeletal muscle. BMC Genomics 2019; 20(1):518. https://doi.org/10.1186/s12864-019-5889-5. Shared first co-authorship. Contribution: I participated in laboratory work, sequencing data analysis, microarray and eQTL integration, data visualization, manuscript writing and editing.

Mármol-Sánchez E, Quintanilla R, Cardoso TF, Jordana Vidal J, Amills M. Polymorphism of the chryptochrome 2 and mitoguarding 2 genes are associated with the variation of lipid-related traits in Duroc pigs. Scientific Reports 2019; 9(1):9025. https://doi.org/10.1038/s41598-019-45108-z. Contribution: I analyzed all SNP sequencing data, performed phenotype-genotype association analyses and carried out all laboratory work, data visualization, manuscript writing and editing.

Guan D, Mármol-Sánchez E, Cardoso TF, Such X, Landi V, Tawari NR, Amills M. Genomic analysis of the origins of extant casein variation in goats. Journal of Dairy Science 2019; 102(6):5230-5241. https://doi.org/10.3168/jds.2018-15281. Contribution: I participated in laboratory work, sequencing data analysis, data visualization, manuscript writing and editing.

González-Prendes R, Quintanilla R, Mármol-Sánchez E, Pena RN, Ballester M, Cardoso TF, Manunza A, Casellas J, Cánovas Á, Díaz I, Noguera JL, Castelló A, Mercadé A, Amills M. Comparing the mRNA expression profile and the genetic determinism of intramuscular fat traits in the porcine gluteus medius and longissimus dorsi muscles. BMC Genomics 2019; 20(1):170. https://doi.org/10.1186/s12864-019-5557-9. Contribution: I participated in sequencing data analysis, manuscript writing and editing.

2018

Cardoso TF, Quintanilla R, Castelló A, Mármol-Sánchez E, Ballester M, Jordana J, Amills M. Analysing the expression of eight clock genes in five tissues from fasting and fed sows. Frontiers in Genetics 2018; 9:475. https://doi.org/10.3389/fgene.2018.00475. Contribution: I participated in laboratory work, sequencing data analysis, manuscript writing and editing.

Mármol-Sánchez E, Pla Planas A. Annotation of novel microRNA genes in the porcine genome using a Machine Learning approach. 2018. https://hdl.handle.net/10609/82085. Contribution: This is the public document of my Master thesis led under the supervision of Dr. Albert Pla Planas at the Universitat Oberta de Catalunya (UOC) and University of Barcelona (UB) within the Master of Bioinformatics and Biostatistics (UOC-UB).

2017

Cardoso TF, Quintanilla R, Tibau J, Gil M, Mármol-Sánchez E, González-Rodríguez O, González-Prendes R, Amills M. Nutrient supply affects the mRNA expression profile of the porcine skeletal muscle. BMC Genomics 2017; 18(1):603. https://doi.org/10.1186/s12864-017-3986-x. Contribution: I participated in laboratory work, sequencing data analysis, manuscript writing and editing.