Espinoza JL, Phillips A, Prentice MB, Tan GS, Kamath PL, Lloyd KG, Dupont CL. Unveiling the microbial realm with VEBA 2.0: a modular bioinformatics suite for end-to-end genome-resolved prokaryotic, (micro)eukaryotic and viral multi-omics from either short- or long-read sequencing. Nucleic Acids Res. 2024 Jun 22:gkae528. doi: 10.1093/nar/gkae528. PMID: 38909293. PDF
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. 2022 Oct 12;23(1):419. doi: 10.1186/s12859-022-04973-8. PMID: 36224545. PDF
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. PubMed PMID: 33780444. PDF
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, Volume 1, Issue 5, November 2022, pgac239, doi:10.1093/pnasnexus/pgac239. PDF
Espinoza JL, Harkins DM, Torralba M, Gomez A, Highlander SK, Jones MB, Leong P, Saffery R, Bockmann M, Kuelbs C, Inman JM, Hughes T, Craig JM, Nelson KE, Dupont CL. Supragingival Plaque Microbiome Ecology and Functional Potential in the Context of Health and Disease. MBio. 2018 Nov 27;9(6). pii: e01631-18. doi: 10.1128/mBio.01631-18. PubMed PMID: 30482830. PDF
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. PDF
Gomez A+, Espinoza JL+, Harkins DM, Leong P, Saffery R, Bockmann M, Torralba M, Kuelbs C, Kodukula R, Inman J, Hughes T, Craig JM, Highlander SK, Jones MB, Dupont CL, Nelson KE. Host Genetic Control of the Oral Microbiome in Health and Disease. Cell Host Microbe. 2017 Sep 13;22(3):269-278.e3. doi: 10.1016/j.chom.2017.08.013. PubMed PMID: 28910633; PubMed Central PMCID: PMC5733791. PDF
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. PDF
Walworth NG+, Espinoza JL+, Argyle PA, Hinners J, Levine NM, Doblin MA, Dupont CL, Collins S. Genus-Wide Transcriptional Landscapes Reveal Correlated Gene Networks Underlying Microevolutionary Divergence in Diatoms. Mol Biol Evol. 2023 Oct 4;40(10):msad218. doi: 10.1093/molbev/msad218. PMID: 37874344. PDF
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. PubMed PMID: 25908788; PubMed Central PMCID: PMC4627058. PDF
Imai Y, Meyer KJ, Iinishi A, Favre-Godal Q, Green R, Manuse S, Caboni M, Mori M, Niles S, Ghiglieri M, Honrao C, Ma X, Guo JJ, Makriyannis A, Linares-Otoya L, Böhringer N, Wuisan ZG, Kaur H, Wu R, Mateus A, Typas A, Savitski MM, Espinoza JL, O'Rourke A, Nelson KE, Hiller S, Noinaj N, Schäberle TF, D'Onofrio A, Lewis K. A new antibiotic selectively kills Gram-negative pathogens. Nature. 2019 Dec;576(7787):459-464. doi: 10.1038/s41586-019-1791-1. PMID: 31747680. PDF
Gambogi CW, Birchak GJ, Mer E, Brown DM, Yankson G, Kixmoeller K, Gavade JN, Espinoza JL, Kashyap P, Dupont CL, Logsdon GA, Heun P, Glass JI, Black BE. Efficient Formation of Single-copy Human Artificial Chromosomes. Science383,1344-1349(2024). doi:10.1126/science.adj3566. PDF. PDF-Perspective
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. PubMed PMID: 28800136; PubMed Central PMCID: PMC5702739. PDF
Santoro EP, Borges RM, Espinoza JL, Freire M, Messias CSMA, Villela HDM, Pereira LM, Vilela CLS, Rosado JG, Cardoso PM, Rosado PM, Assis JM, Duarte GAS, Perna G, Rosado AS, Macrae A, Dupont CL, Nelson KE, Sweet MJ, Voolstra CR, Peixoto RS. Coral microbiome manipulation elicits metabolic and genetic restructuring to mitigate heat stress and evade mortality. Sci Adv. 2021 Aug 13;7(33):eabg3088. doi: 10.1126/sciadv.abg3088. PMID: 34389536. PDF
Badrane, H., Cheng, S., Dupont, C. L., Hao, B., Driscoll, E., Morder, K., Liu, G., Newbrough, A., Fleres, G., Kaul, D., Espinoza, J. L., Clancy, C. J., & Nguyen, M. H. (2023). Genotypic diversity and unrecognized antifungal resistance among populations of Candida glabrata from positive blood cultures. Nature Communications, 14(1), 5918. doi: 10.1038/s41467-023-41509-x. PDF
Michaud JM, Thompson LR, Kaul D+, Espinoza JL+, Richter RA, Xu ZZ, Lee C, Pham KM, Beall CM, Malfatti F, Azam F, Knight R, Burkart MD, Dupont CL, Prather KA. Taxon-specific aerosolization of bacteria and viruses in an experimental ocean-atmosphere mesocosm. Nat Commun. 2018 May 22;9(1):2017. doi: 10.1038/s41467-018-04409-z. PubMed PMID: 29789621; PubMed Central PMCID: PMC5964107. PDF
Alqedari H, Altabtbaei K, Espinoza JL, Bin-Hasan S, Alghounaim M, Alawady A, Altabtabae A, AlJamaan S, Devarajan S, AlShammari T, Eid MB, Matsuoka M, Jang H, Dupont CL, Freire M. Host-Microbiome Associations in Saliva Predict COVID-19 Severity. PNAS Nexus. 2024 May 25. doi: 10.1093/pnasnexus/pgae126. PDF
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. PubMed PMID: 27040500; PubMed Central PMCID: PMC4826573. PDF
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. PubMed PMID: 24529710; PubMed Central PMCID: PMC3962089. PDF
Kumar M, Tibocha-Bonilla JD, Füssy Z, Lieng C, Schwenck SM, Levesque AV, Al-Bassam MM, Passi A, Neal M, Zuniga C, Kaiyom F, Espinoza JL, Lim H, Polson SW, Allen LZ, Zengler K. Mixotrophic growth of a ubiquitous marine diatom. Sci Adv. 2024 Jul 19;10(29):eado2623. doi: 10.1126/sciadv.ado2623. Epub 2024 Jul 17. PMID: 39018398; PMCID: PMC466952. PDF
Nakatsuji T, Brinton SL, Cavagnero KJ, O'Neill AM, Chen Y, Dokoshi T, Butcher AM, Osuoji OC, Shafiq F, Espinoza JL, Dupont CL, Hata TR, Gallo RL. Competition between skin antimicrobial peptides and commensal bacteria in type 2 inflammation enables survival of S. aureus. Cell Rep. 2023 May 10;42(5):112494. doi: 10.1016/j.celrep.2023.112494. PMID: 37167061. PDF
Shahsavari N, Wang B, Imai Y, Mori M, Son S, Liang L, Böhringer N, Manuse S, Gates MF, Morrissette M, Corsetti R, Espinoza JL, Dupont CL, Laub MT, Lewis K. A Silent Operon of Photorhabdus luminescens Encodes a Prodrug Mimic of GTP. mBio. 2022 May 16:e0070022. doi: 10.1128/mbio.00700-22. PMID: 35575547. PDF
Manck LE, Espinoza JL, Dupont CL, Barbeau KA. Transcriptomic Study of Substrate-Specific Transport Mechanisms for Iron and Carbon in the Marine Copiotroph Alteromonas macleodii. mSystems. 2020 Apr 28;5(2). doi: 10.1128/mSystems.00070-20. PubMed PMID: 32345736; PubMed Central PMCID: PMC7190382. PDF
O'Rourke A, Beyhan S, Choi Y, Morales P, Chan AP, Espinoza JL, Dupont CL, Meyer KJ, Spoering A, Lewis K, Nierman WC, Nelson KE. Mechanism-of-Action Classification of Antibiotics by Global Transcriptome Profiling. Antimicrob Agents Chemother. 2020 Feb 21;64(3). doi: 10.1128/AAC.01207-19. PubMed PMID: 31907190; PubMed Central PMCID: PMC7038283. PDF
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. PubMed PMID: 28948974; PubMed Central PMCID: PMC5869067. PDF
Garza EA, Bielinski VA, Espinoza JL, Orlandi K, Alfaro JR, Bolt TM, Beeri K, Weyman PD, Dupont CL. Validating a Promoter Library for Application in Plasmid-Based Diatom Genetic Engineering. ACS Synth Biol. 2023 Oct 19. doi: 10.1021/acssynbio.3c00163. PMID: 37857380. PDF
Diner RE, Noddings CM, Lian NC, Kang AK, McQuaid JB, Jablanovic J, Espinoza JL, Nguyen NA, Anzelmatti MA Jr, Jansson J, Bielinski VA, Karas BJ, Dupont CL, Allen AE, Weyman PD. Diatom centromeres suggest a mechanism for nuclear DNA acquisition. Proc Natl Acad Sci U S A. 2017 Jul 18;114(29):E6015-E6024. doi: 10.1073/pnas.1700764114. PubMed PMID: 28673987; PubMed Central PMCID: PMC5530661. PDF
Bartelme RP, Custer JM, Dupont CL, Espinoza JL, Torralba M, Khalili B, Carini P. Influence of Substrate Concentration on the Culturability of Heterotrophic Soil Microbes Isolated by High-Throughput Dilution-to-Extinction Cultivation. mSphere. 2020 Jan 29;5(1). doi: 10.1128/mSphere.00024-20. PubMed PMID: 31996418; PubMed Central PMCID: PMC6992367. PDF
Domingo D, Nawaz U, Corbett M, Espinoza JL, Tatton-Brown K, Coman D, Wilkinson MF, Gecz J, Jolly LA. UPF3B mutations including a novel synonymous variant associated with absent speech implicate nonsense mediated mRNA decay as a regulator of neurodevelopmental disorder gene networks. Hum Mol Genet. 2020 Jul 15:ddaa151. doi: 10.1093/hmg/ddaa151. PMID: 32667670. PDF
Weiss H, Hertzberg VS, Dupont C, Espinoza JL, Levy S, Nelson K, Norris S; FlyHealthy Research Team. The Airplane Cabin Microbiome. Microb Ecol. 2018 Jun 6. doi: 10.1007/s00248-018-1191-3. PubMed PMID: 29876609. PDF
Walker M. Federico E. Espinoza JL. Dupont CL. Unveiling Molecular Diversity in Cerebral Thrombi via Spatial Transcriptomics. Stroke. 2024. doi: 10.1161/STROKEAHA.124.04790 PDF
Emerick Larkin, Andrew Schuerger, Richard Barker, Jessica Audrey Lee, Natasha Haveman, Jayson F Enciso, Lee J Kerhof, Bruce M Link, Christian R Voolstra, Manual Aranda, Christopher Dupont, Josh L. Espinoza. Ground and Flight-Based Plant Microbial Interaction Research and Related Space Crop Production Applications. NASA. 2021 December 3. https://ntrs.nasa.gov/citations/20210023782. PDF
Human interpretable artificial intelligence applications for microbial-related diseases. Durban University of Technology. PhD in Biotechnology (2022). doi:10.51415/10321/4701. PDF
Fluxomic analysis-based approach for engineering an ethanologenic strain of Haloferax volcanii. University of California, Santa Cruz. Masters in Bioinformatics (2016). UCSC Source. PDF
+ Equal contribution
https://orcid.org/0000-0003-3447-3845