Curriculum Vitae

Professional Experience

• Programming for bioinformatics subject (Python)
• Master Thesis Supervisor

• Project leader: Extensive experience leading bioinformatics projects (+50), coordinating team efforts, and ensuring successful project outcomes. Proficient in managing project scope, timelines, and resources.
• Single cell (sc) expert. Continuous evaluation of the newest literature to keep pipelines updated with the latest cutting- edge analytical tools. Development & implementation of comprehensive workflows and pipelines for production. Sample tag cell demultiplexing, trajectory analysis, cell-cell communication, co-expression network analysis (WGCNA), Transposable Elements (TEs) analysis, ... Advanced projects as integration of distinct technologies datasets or multi-modal approaches such as CITE-seq or single cell immune profiling (BCR/TCR). Single nuclei. Spatial transcriptomics and single cell integration. Internal and external training.
• Transcriptomics expert. Differential expression analysis. Complex experimental designs with multiple covariates and possible confounding variables. Integration with whole exome sequencing (WES) for allele specific expression (ASE) analyses. Expression analysis of interspersed repeats such as transposons.
• Orchestrated and drove complex bioinformatics projects with remarkable success: Integration of WES, bulk RNA-seq, ASE, scRNA-seq and methylome to analyse Klinefelter syndrome. Integrated analysis of RNA-seq and ChIP-seq.
• Constant contact with lab scientists and other non-bioinformaticians to tailor the analyses to the project needs. Development of interactive reports with R Markdown and Shiny apps to explore the results.
• Developer of a comprehensive and user-friendly web app facilitating transcriptomic analyses to non-bioinformaticians through the utilization of customized gene sets, aimed at evaluating specific agricultural traits.
• Emphasis on code documentation, version control and coding environments to ensure reproducibility.

• Leader of successful bioinformatics projects (proteomics, epigenomics, metagenomics & transcriptomics integration) in close contact with lab scientists whose outcomes resulted in scientific publications.

• Developer of first Sequentia Biotech scRNA-seq pipeline. Report to Scientific Director

• RNA-seq data analysis. Cufflinks. R
• Design and construction of a new heat-shock system (see patents)
• Laser Microdissection (Leica LMD7000) for RNA extraction. cDNA linear amplification. Automated PCR (Eppendorf epMotion 5070)
• TALENs & CRISPRs. Zebrafish transgenic lines generation
• Mentoring of undergraduates and graduate students

• Microarray data analysis. High-throughput functional annotation of novel sequence data.
• DNA and RNA extraction. cDNA synthesis. DNA cloning and sequencing
• PCR (Regular, Semi-quantitative, Real-time). RACE. DNA electrophoresis
• Radioimmunoassay (RIA) and ELISA. Circulating metabolite assays
• Monitoring of fish nutrition, health, and welfare of fish species of aquaculture interest
• Development and assessment of new fish feeds and feeding strategies

Education

Prices and awards

1. TECNIOspring PLUS fellowship. MSCA COFUND program H2020 (2019-2021).
2. Marie Sklodowska-Curie Actions Seal of Excellence – 2017. Proposal scored as a high-quality project (90.4) in a highly competitive evaluation process.
3. Marie Sklodowska-Curie Actions Seal of Excellence – 2016 (91.4 score).
4. Post-doctoral fellowship “Alfonso Martín Escudero” (2011-2013)
5. Post-doctoral fellowship “Juan de la Cierva” (2011-2014; rejected to accept number 5)
6. Extraordinary Doctorate Award (University of Valencia). PhD thesis rated among the top few that year in the University of Valencia.
7. Student Travel Award (7th Meeting of the Iberian Comparative Endocrinology Association)
8. Pre-doctoral fellowship “Diputación de Castellón” (2004-2008)

Patents

“Automated Scalable Heat-Shock Apparatus for Standard Aquatic Housing Systems”. Inventors: Kahana A, Saera-Vila A, Kish PE. U.S. Provisional Application 62/132.585. March 13, 2015 (See paper 29)

Publication list

1. Alsolami S, Chandrasekaran AP, Jin Y, Wang Y, Zhang L, Shakir IM, Zhang Y, Ramos-Mandujano G, Yuan B, Ayach M, Saera-Vila A, Siddique A, Izpisua Belmonte JC, Zhang J, Yu Y, Fan Z, Fu S, Zhang H, Xin S, AlDakhil K, Li M. 2026. A Single Small-Molecule-Based Human Embryo Model Reveals V-ATPase Requirement in Mammalian Blastocyst Cavitation. Cell Research, accepted.
2. Godino-Gimero A, Rocha A, Chivite M, Saera-Vila A, Rotlland J, Miguez JM, Cerdá-Reverter JM. 2024. Agouti-induced anxiety-like behaviour is mediated by central serotonergic pathways in zebrafish. J Neurosci 44 (32), e1970232024. doi:10.1523/JNEUROSCI.1970-23.2024.
3. Mangiavacchi A, Morelli G, Reppe S, Saera-Vila A, Liu P, Eggerschwiler B, Zhang H, Bensaddek D, Casanova EA, Medina Gomez C, Prijatelj V, Della Valle F, Atinbayeva N, Izpisua Belmonte JC, Rivadeneira F, Cinelli P, Morten Gautvik K, Orlando V. 2024. LINE-1 RNA triggers matrix formation in bone cells via a PKR-mediated inflammatory response. The EMBO Journal, 10.1038/s44318-024-00143-z.
4. Al-Amoodi AS, Kai J, Li Y, Malki JS, Alghamdi A, Al-Ghuneim A, Saera-Vila A, Habuchi S, Merzaban JS. 2024. α1,3-Fucosylation Treatment Improves Cord blood CD34 Negative HSC Navigation. iScience 27 (2). doi:10.1016/j.isci.2024.108882.
5. Alsolami S, Pandian Chandrasekaran A, Jin Y, Shakir IM, Zhang Y, Ramos-Mandujano G, Yuan B, Saera-Vila A, Izpisua Belmonte JC, Li M. 2024. DMSO derives Trophectoderm and Clonal Blastoid from Single Human Pluripotent Stem Cell. bioRxiv 2023.12.31.573770; doi:10.1101/2023.12.31.573770.
6. Boronat-Toscano A, Vañó I, Monfort-Ferré D, Menacho M, Valldosera G, Caro A, Espina B, Mañas MJ, Marti M, Espin E, Saera-Vila A, Serena C. 2023. Smoking Suppresses the Therapeutic Potential of Adipose Stem Cells in Crohn’s Disease Patients through Epigenetic Changes. Cells 12 (7), 1021. doi:https://doi.org/10.3390/cells12071021
7. Leal E, Angotzi AR, Godino-Gimeno A, Gregorio SF, Rotlland J, Saera-Vila A, Fuentes J, Cerdá-Reverter JM. 2022. Agouti overexpression in a transgenic model regulates integrity, permeability and electrogenic amino acid transport in zebrafish intestine. Frontiers in Marine Science 9. doi:https://doi.org/10.3389/fmars.2022.1011702
8. Boronat-Toscano A, Monfort-Ferré D, Menacho M, Caro A, Bosch R, Espina B, Algaba-Chueca F, Saera-Vila A, Moliné A, Marti M, Espin E, Millan M, Serena C. 2022. Anti-TNF Therapies Suppress Adipose Tissue Inflammation in Crohn’s Disease. International Journal of Molecular Sciences 23 (19), 11170. doi:https://doi.org/10.3390/ijms231911170
9. Della Valle F, Reddy P, Yamamoto M, Liu P, Saera-Vila A, Bensaddek D, Zhang H, Prieto Martinez J, Abassi L, Celii M, Ocampo A, Nuñez Delicado E, Mangiavacchi A, Aiese Cigliano R, Rodriguez Esteban C, Horvath S, Izpisua Belmonte JC, Orlando V. 2022. LINE-1 RNA causes heterochromatin erosion and is a target for amelioration of senescent phenotypes in progeroid syndromes. Science Translational Medicine 14 (657), eabl6057. doi:https://doi.org/10.1126/scitranslmed.abl6057
10. Astro V, Ramirez-Calderon G, Pennucci R, Caroli J, Saera-Vila A, Cardona-Londoño KJ, Forastieri C, Fiacco E, Maksoud F, Alowaysi M, Sogne E, Falqui A, Gonzàlez F, Montserrat N, Battaglioli E, Mattevi A, Adamo A. 2022. Fine-tuned KDM1A alternative splicing regulates human cardiomyogenesis through an enzymatic-independent mechanism. iScience 25 (7), 104665. doi:https://doi.org/10.1016/j.isci.2022.104665
11. Astro V, Alowaysi MT, Fiacco E, Saera-Vila A, Cardona-Londoño KJ, Aiese Cigliano R, Adamo A. 2021. Pseudoautosomal Region 1 Overdosage Affects the Global Transcriptome in iPSCs From Patients With Klinefelter Syndrome and High-Grade X Chromosome Aneuploidies. Frontiers in Cell and Developmental Biology 9: 801597. doi:10.3389/fcell.2021.801597
12. Calle García J, Guadagno A, Paytuvi-Gallart A, Saera-Vila A, Gianmaria Amoroso C, D’Esposito D, Andolfo G, Aiese Cigliano R, Sanseverino W, Ercolano MR. 2022. PRGdb 4.0: an updated database dedicated to genes involved in plant disease resistance process. Nucleic Acids Research 50 (D1): D1483–D1490. doi:10.1093/nar/gkab1087
13. Ang NB*, Saera-Vila A*, Walsh C, Hitchcock PF, Kahana A Thummel R, Nagashima M. 2020. Midkine-a functions as a universal regulator of proliferation during epimorphic regeneration in adult zebrafish. PLOS ONE 15(6): e0232308. (*, contributed equally). doi:10.1371/journal.pone.0232308
14. Serena C, Millan M, Ejarque M, Saera-Vila A, Maymo-Masip E, Nuñez-Roa C, Monfort-Ferre D, Terrón-Puig M, Bautista M, Menacho M, Martí M, Espin E, Vendrell J, Fernandez-Veledo S. 2020. Adipose stem cells from patients with Crohn’s disease show a distinctive DNA methylation pattern. Clinical Epigenetics volume 12 (1), Article number: 53. doi:10.1186/s13148-020-00843-3
15. Saera-Vila A, Kish PE, Kahana A. 2019. Autophagy in Zebrafish Extraocular Muscle Regeneration. In: Methods in molecular biology (Clifton, N.J.). Invited Chapter. Co-corresponding author. doi:10.1007/7651_2018_160
16. Saera-Vila A, Louie KL, Sha C, Kelly RM, Kish PE, Kahana A. 2018. Extraocular muscle regeneration in zebrafish requires late signals from Insulin-like growth factors. PLoS ONE 13(2): e0192214. Co-corresponding author. doi:10.1371/journal.pone.0192214
17. Louie KL*, Saera-Vila A*, Kahana A. 2017. Temporally Distinct Transcriptional Regulation of Myocyte Dedifferentiation and Myofiber Growth During Muscle Regeneration. BMC genomics 18, 854. (*, contributed equally). Co-corresponding author. doi:10.1186/s12864-017-4236-y
18. Kasprick DS, Kish PE, Rajaii F, Saera-Vila A, Kahana A. 2016. Retinoic Acid and T3 Induce CCL2 in Human Orbital Fibroblasts–A Model of Thyroid Eye Disease. Invest Ophthalmol Vis Sci 57, 5992.
19. Kahana A, Kish PE, Saera-Vila A. 2016. Differential expression analysis for early gene activation patterns in regenerating lateral rectus muscle. Invest Ophthalmol Vis Sci 57. 12.
20. Louie KL, Saera-Vila A, Chiari EF, Kish PE, Klionsky D, Kahana A. 2016. Regulation of extraocular muscle cell identity and dedifferentiation by epigenetic regulators of chromatin structure. Invest Ophthalmol Vis Sci 57, 4572.
21. Saera-Vila A, Kish PE, Klionsky D, Kahana A. 2016. Autophagy plays a key role in cellular reprograming of myocytes during EOM regeneration. Invest Ophthalmol Vis Sci 57, 4571.
22. Louie KL, Saera-Vila A, Kish PE, Kahana A. 2016. Zebrafish adult cell dedifferentiation as a noncancer model of cancer. Cancer Research 76, 2541.
23. Saera-Vila A, Kish PE, Louie KL, Grzegorski SJ, Klionsky D, Kahana A. 2016. Autophagy Regulates Cytoplasmic Remodeling During Cell Reprogramming in a Zebrafish Model of Muscle Regeneration. Autophagy 12, 1864-1875. doi:10.1080/15548627.2016.1207015
24. Saera-Vila A, Kish PE, Kahana A. 2016. Fgf regulates dedifferentiation during skeletal muscle regeneration in adult zebrafish. Cell Signalling 28, 1196-1204. doi:10.1016/j.cellsig.2016.06.001
25. Saera-Vila A, Kish PE, Kahana A. 2015. Automated Scalable Heat Shock Modification for Standard Aquatic Housing Systems. Zebrafish 12, 312-314. doi:10.1089/zeb.2015.1087
26. Saera-Vila A, Kasprick DS, Junttila TL, Grzegorski SJ, Louie KL, Chiari EF, Kish PE, Kahana A. 2015. Myocyte Dedifferentiation Drives Extraocular Muscle Regeneration in Adult Zebrafish. Invest Ophthalmol Vis Sci 56, 4977- 4993. doi:10.1167/iovs.14-16103
27. Saera-Vila A, Kahana A. 2015. Growth factors regulate early events in adult zebrafish extraocular muscle (EOM) regeneration. Invest Ophthalmol Vis Sci 56, 561.
28. Perez-Sanchez J, Borrel M, Bermejo-Nogales A, Benedito-Palos L, Saera-Vila A, Calduch-Giner JA, Kaushik, S. 2013. Dietary oils mediate cortisol kinetics and the hepatic mRNA expression profile of stress-responsive genes in gilthead sea bream (Sparus aurata) exposed to crowding stress. Implications on energy homeostasis and stress susceptibility. Comparative Biochemistry and Physiology 8D, 123-130. doi:10.1016/j.cbd.2013.02.001
29. Cruz-Garcia L, Sanchez-Gurmaches J, Bouraoui L, Saera-Vila A, Perez-Sanchez J, Gutierrez J, Navarro I. 2011. Changes in adipocyte cell size, gene expression of lipid metabolism markers, and lipolytic responses induced by dietary fish oil replacement in gilthead sea bream (Sparus aurata L.). Comparative Biochemistry and Physiology 158A, 391-399. doi:10.1016/j.cbpa.2010.11.024
30. Saera-Vila A, Calduch-Giner JA, Pérez-Sánchez J. 2011. Gilthead sea bream microarray analysis of alterations induced by essential fatty acid deficiencies in the adipose tissue gene expression profiling. Avances en Endocrinología Comparada V, 12-15.
31. Saera-Vila A, Benedito-Palos L, Sitjà-Bobadilla A, Nácher-Mestre J, Serrano R, Kaushik, S, Pérez-Sánchez J. 2011. Health and antioxidant trade-off in gilthead sea bream fed alternative diets. Avances en Endocrinología Comparada V, 137-141.
32. Calduch-Giner JA, Davey G, Saera-Vila A, Houeix B, Talbot A, Prunet P, Cairns MT, Pérez-Sánchez J. 2010. Use of microarray technology to assess the time course of liver stress response after confinement exposure in gilthead sea bream (Sparus aurata L.). BMC Genomics 11, 193. doi:10.1186/1471-2164-11-193
33. Saera-Vila A, Benedito-Palos L, Sitjà-Bobadilla A, Nácher-Mestre J, Serrano R, Kaushik, S, Pérez-Sánchez J. 2009. Assessment of the health and antioxidant trade-off in gilthead sea bream (Sparus aurata L.) fed alternative diets with low levels of contaminants. Aquaculture 296, 87-95. doi:10.1016/j.aquaculture.2009.07.028
34. Benedito-Palos L, Navarro JC, Bermejo-Nogales A, Saera-Vila A, Kaushik S, Pérez-Sánchez J. 2009. The time course of fish oil wash-out follows a simple dilution model in gilthead sea bream (Sparus aurata) fed shift levels in vegetable oils. Aquaculture 288, 98-105. doi:10.1016/j.aquaculture.2008.11.010
35. Saera-Vila A, Calduch-Giner JA, Prunnet P, Pérez-Sánchez J. 2009. Dynamics of liver GH/IGF axis and selected stress markers in juvenile gilthead sea bream (Sparus aurata) exposed to acute confinement. Differential stress response of growth hormone receptors. General and Comparative Endocrinology 154, 197-203.
36. Cruz-García L, Saera-Vila A, Calduch-Giner JA, Navarro I, Pérez-Sánchez J. 2009. Targets for TNFα-induced lipolysis in gilthead sea bream (Sparus aurata L.) adipocytes isolated from lean and fat juvenile fish. Journal of Experimental Biology 212, 2254-2260. doi:10.1242/jeb.029025
37. Cruz-García L, Saera-Vila A, Navarro I, Pérez-Sánchez J. 2008. Lipólisis basal e inducida en adipocitos aislados de juveniles de dorada (Sparus aurata L.). Variabilidad inter-individual. Avances en Endocrinología Comparada IV, 227- 230
38. Bermejo-Nogales A, Benedito-Palos L, Saera-Vila A, Calduch-Giner JA, Sitjà-Bobadillla A, Pérez-Sánchez J. 2008. Tissue-specific expression of GRP75/mortalin/MTHSP70/PB74/ HSPA9B in a Mediterranean perciform fish, gilthead sea bream (Sparus aurata L.). Confinement exposure up-regulates hepatic GRP75. Avances en Endocrinología Comparada IV, 195-198.
39. Saera-Vila A, Calduch-Giner JA, Pérez-Sánchez J. 2008. Stress-mediated effects on the liver GH/IGF axis of gilthead sea bream (Sparus aurata L.). Functional partitioning of GH receptors. Avances en Endocrinología Comparada IV, 91- 96.
40. Bermejo-Nogales A, Saera-Vila A, Benedito-Palos L, Calduch-Giner JA, Pérez-Sánchez J. 2008. Differential tissue expression of uncoupling proteins in gilthead sea bream (Sparus aurata L.): Lessons from UCP1 and UCP3 in fish. Comparative Biochemistry and Physiology 151A, S41.
41. Calduch-Giner JA, Saera-Vila A, Cairns M, Davey G, Prunet P, Pérez-Sánchez J. 2008. Time series analysis of sea bream (Sparus aurata L.) stress response after confinement exposure. Comparative Biochemistry and Physiology 151A, S41.
42. Sitjà-Bobadilla A, Calduch-Giner JA, Saera-Vila A, Palenzuela O, Álvarez-Pellitero P, Pérez-Sánchez J. 2008. Chronic exposure to the parasite Enteromyxum leei (Myxozoa: Myxosporea) modulates the immune response and the expression of growth, redox and immune relevant genes in gilthead sea bream, Sparus aurata L. Fish and Shellfish Immunology 24, 610-619. doi:10.1016/j.fsi.2008.01.014
43. Bermejo-Nogales A, Benedito-Palos L, Saera-Vila A, Calduch-Giner JA, Sitjà-Bobadilla A, Pérez-Sánchez J. 2008. Confinement exposure induces glucose regulated protein 75 (GRP75/mortalin/mtHsp70/PBP74/HSPA9B) in the hepatic tissue of gilthead sea bream (Sparus aurata L.). Comparative Biochemistry and Physiology 149B, 428-438. doi:10.1016/j.cbpb.2007.11.003
44. Saera-Vila A, Calduch-Giner JA, Pérez-Sánchez J. 2007. Caracterización molecular y regulación transcripcional de la lipoprotein lipasa de dorada. Avancos em Endocrinologia Comparativa III, 247-252.
45. Calduch-Giner JA, Saera-Vila A, Pérez-Sánchez J. 2007. Genomic duplication and evolutive divergence of fish growth hormone receptors. Physiological implications for growth hormone and somatolactin mediated effects. Avancos em Endocrinologia Comparativa III, 39-46.
46. Saera-Vila A, Calduch-Giner JA, Pérez-Sánchez J. 2007. Co-expression of IGFs and GH receptors (GHRs) in gilthead sea bream (Sparus aurata L.): sequence analysis of the GHR-flanking region. Journal of Endocrinology 194, 361-372. doi:10.1677/JOE-06-0229
47. Albalat A, Saera-Vila A, Capilla E, Gutiérrez J, Pérez-Sánchez J, Navarro I. 2007. Insulin regulation of lipoprotein lipase (LPL) activity and expression in gilthead sea bream (Sparus aurata). Comparative Biochemistry and Physiology 148B, 151-159. doi:10.1016/j.cbpb.2007.05.004
48. Bermejo-Nogales A, Saera-Vila A, Calduch-Giner JA, Navarro JC, Sitjà-Bobadilla A, Pérez-Sánchez J. 2007. Differential metabolic and gene expression profile of juvenile common dentex (Dentex dentex L.) and gilthead sea bream (Sparus aurata L.) in relation to redox homeostasis. Aquaculture 267, 213-224. doi:10.1016/j.aquaculture.2007.01.024
49. Benedito-Palos L, Saera-Vila A, Calduch-Giner JA, Kaushik S, Pérez-Sánchez J. 2007. Combined replacement of fish meal and oil in practical diets for fast growing juveniles of gilthead sea bream (Sparus aurata L.): networking of systemic and local components of GH/IGF axis. Aquaculture 267, 199-212. doi:10.1016/j.aquaculture.2007.01.011
50. Saera-Vila A, Calduch-Giner JA, Navarro I, Pérez-Sánchez J. 2007. Tumour necrosis factor (TNF)α as a regulator of fat tissue mass in the Mediterranean gilthead sea bream (Sparus aurata L.). Comparative Biochemistry and Physiology 146B, 338-345. doi:10.1016/j.cbpb.2006.11.003
51. Saera-Vila A, Calduch-Giner JA, Gómez-Requeni P, Médale F, Kaushik S, Pérez-Sánchez J. 2005. Molecular characterization of gilthead sea bream (Sparus aurata) lipoprotein lipase. Transcriptional regulation by season and nutritional condition in skeletal muscle and fat storage tissues. Comparative Biochemistry and Physiology. 142B, 224-232. doi:10.1016/j.cbpb.2005.07.009
52. Saera-Vila A, Calduch-Giner JA, Pérez-Sánchez J. 2005. Duplication of growth hormone receptor (GHR) in fish genome: gene organization and transcriptional regulation of GHR type I and II in gilthead sea bream (Sparus aurata). General and Comparative Endocrinology 142, 193-203. doi:10.1016/j.ygcen.2004.11.005
53. Pérez-Sánchez J, Calduch-Giner JA, Mingarro M, Vega-Rubín de Celis S, Gómez-Requeni P, Saera-Vila A, Astola A, Valdivia MM. 2004. Overview of fish growth hormone family. New insights in genomic organization and heterogeneity of fish growth hormone receptors. Fish Physiology and Biochemistry 27, 243-258. doi:10.1023/B:FISH.0000032729.72746.c8