Genome-resolved (meta)genomics, bioprospecting, and artificial intelligence for marine ecosystems and conservation.

Institutions:* J. Craig Venter InstitutePublications:* Everything between 2016 - 2024:* https://scholar.google.com/citations?user=r9y1tTQAAAAJ&hl=en

Institutions:* J. Craig Venter InstitutePublications:* Warshan D, Espinoza JL, Stuart RK, Richter RA, Kim SY, Shapiro N, Woyke T, C Kyrpides N, Barry K, Singan V, Lindquist E, Ansong C, Purvine SO, M Brewer H, Weyman PD, Dupont CL, Rasmussen U. Feathermoss and epiphytic Nostoc cooperate differently: expanding the spectrum of plant-cyanobacteria symbiosis. ISME J. 2017 Dec;11(12):2821-2833. doi: 10.1038/ismej.2017.134. Epub 2017 Aug 11. PubMed PMID: 28800136; PubMed Central PMCID: PMC5702739.

Institutions:* Department of Applied Sciences, Durban University of Technology, South Africa* J. Craig Venter InstituteDissertation:* https://github.com/jolespin/publications/blob/master/PDFs/Espinoza_2022__PhD-Dissertation-DUT.pdf(Co-)First Author Publications:* Espinoza JL+, Dupont CL+, O'Rourke A, Beyhan S, Morales P, Spoering A, Meyer KJ, Chan AP, Choi Y, Nierman WC, Lewis K, Nelson KE. Predicting antimicrobial mechanism-of-action from transcriptomes: A generalizable explainable artificial intelligence approach. PLoS Comput Biol. 2021 Mar 29;17(3):e1008857. doi: 10.1371/journal.pcbi.1008857. * Espinoza JL, Shah N, Singh S, Nelson KE, Dupont CL. Applications of weighted association networks applied to compositional data in biology. Environ Microbiol. 2020 May 20;. doi: 10.1111/1462-2920.15091. Review. PubMed PMID: 32436334. * Nabwera HM+, Espinoza JL+, Worwui A, Betts M, Okoi C, Sesay AK, Bancroft R, Agbla SC, Jarju S, Bradbury RS, Colley M, Jallow AT, Liu J, Houpt ER, Prentice AM, Antonio M, Bernstein RM, Dupont CL+, Kwambana-Adams BA+. Interactions between fecal gut microbiome, enteric pathogens, and energy regulating hormones among acutely malnourished rural Gambian children. EBioMedicine. 2021 Oct 22;73:103644. doi: 10.1016/j.ebiom.2021.103644. PMID: 34695658. * Espinoza JL, Dupont CL. VEBA: A modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes. BMC Bioinformatics. Accepted.* Espinoza JL, Torralba M, Leong P, Saffery R, Bockmann M, Kuelbs C, Singh S, Hughes T, Craig JM, Nelson KE, Dupont CL. Differential network analysis of oral microbiome metatranscriptomes identifies community scale metabolic restructuring in dental caries. PNAS Nexus. In Review.

Institutions:* Jack Baskin School of Engineering, iGEM. University of California, Santa CruzThesis: * https://github.com/jolespin/publications/blob/master/PDFs/Espinoza_2016__MSc-Thesis-UCSC.pdf

Institutions:* Department of Reproductive Medicine, University of California, San Diego Publications:* Domingo D, Nawaz U, Corbett M, Espinoza JL, Tatton-Brown K, Coman D, Wilkinson MF, Gecz J, Jolly LA. A synonymous UPF3B variant causing a speech disorder implicates NMD as a regulator of neurodevelopmental disorder gene networks. Hum Mol Genet. 2020 Aug 29;29(15):2568-2578. doi: 10.1093/hmg/ddaa151. PubMed PMID: 32667670.* Huang L, Shum EY, Jones SH, Lou CH, Dumdie J, Kim H, Roberts AJ, Jolly LA, Espinoza JL, Skarbrevik DM, Phan MH, Cook-Andersen H, Swerdlow NR, Gecz J, Wilkinson MF. A Upf3b-mutant mouse model with behavioral and neurogenesis defects. Mol Psychiatry. 2018 Aug;23(8):1773-1786. doi: 10.1038/mp.2017.173. Epub 2017 Sep 26. PubMed PMID: 28948974; PubMed Central PMCID: PMC5869067.

Institutions:* California Institute of Regenerative Medicine* University of California, San Diego* San Diego State UniversityAwards: * Dean's Award for Research Symposium PresentationPublications:* Shum EY, Jones SH, Shao A, Dumdie J, Krause MD, Chan WK, Lou CH, Espinoza JL, Song HW, Phan MH, Ramaiah M, Huang L, McCarrey JR, Peterson KJ, De Rooij DG, Cook-Andersen H, Wilkinson MF. The Antagonistic Gene Paralogs Upf3a and Upf3b Govern Nonsense-Mediated RNA Decay. Cell. 2016 Apr 7;165(2):382-95. doi: 10.1016/j.cell.2016.02.046. Epub 2016 Mar 31. PubMed PMID: 27040500; PubMed Central PMCID: PMC4826573.* Shum EY, Espinoza JL, Ramaiah M, Wilkinson MF. Identification of novel post-transcriptional features in olfactory receptor family mRNAs. Nucleic Acids Res. 2015 Oct 30;43(19):9314-26. doi: 10.1093/nar/gkv324. Epub 2015 Apr 23. PubMed PMID: 25908788; PubMed Central PMCID: PMC4627058.* Lou CH, Shao A, Shum EY, Espinoza JL, Huang L, Karam R, Wilkinson MF. Posttranscriptional control of the stem cell and neurogenic programs by the nonsense-mediated RNA decay pathway. Cell Rep. 2014 Feb 27;6(4):748-64. doi: 10.1016/j.celrep.2014.01.028. Epub 2014 Feb 13. PubMed PMID: 24529710; PubMed Central PMCID: PMC3962089.

Institutions:* California Institute of Regenerative Medicine* The Scripps Research Institute

Institutions:* San Diego State UniversityDescription:* Senior Theisis | Elizabeth Dinsdale | 01/2012 - 05/2012Computational Science Research Center | Department of Biology, San Diego State UniversityGenerating high-throughput programs to analyze metagenomic sequence data collected from various kelp beds along the San Diego coast and constructing phylogenetic trees based on 16S ribosomal RNA sequences. Operation of the Roche 454 Life Sciences pyrosequencing machine and all of the preliminary protocols involved in the sequencing process* Electron Microscopy Research | Steve Barlow | 08/2011 - 12/2011EM Facility, San Diego State UniversitySolo operation of the FEI Quanta 450 scanning electron microscope including: (i) coating samples in Platinum; (ii) preparing cells with osmium tetraoxide; and (iii) all aspects of operating the physical and virtual machinery of the scope. The primary goals for this research were to take accurate images/videos of objects at magnifications ranging from 100x – 200,000x and measure the composition of samples by analyzing x-ray emissions generated by atomic ionization. (Images available upon request)* Ornithology Research | Kevin Burns | 01/2011 - 12/2011Department of Biology, San Diego State UniversityDiscovering correlations between morphological characteristics and song complexity of Tanagers by using spectrographic software (Raven) developed by Cornell University.