Espinoza JL - Search Results

1

Efficient formation of single-copy human artificial chromosomes.

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. Gambogi CW, et al. Among authors: espinoza jl. Science. 2024 Mar 22;383(6689):1344-1349. doi: 10.1126/science.adj3566. Epub 2024 Mar 21. Science. 2024. PMID: 38513017 Free PMC article.

2

Mechanism-of-Action Classification of Antibiotics by Global Transcriptome Profiling.

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. O'Rourke A, et al. Among authors: espinoza jl. Antimicrob Agents Chemother. 2020 Feb 21;64(3):e01207-19. doi: 10.1128/AAC.01207-19. Print 2020 Feb 21. Antimicrob Agents Chemother. 2020. PMID: 31907190 Free PMC article.

3

Applications of weighted association networks applied to compositional data in biology.

Espinoza JL, Shah N, Singh S, Nelson KE, Dupont CL. Espinoza JL, et al. Environ Microbiol. 2020 Aug;22(8):3020-3038. doi: 10.1111/1462-2920.15091. Epub 2020 Jun 22. Environ Microbiol. 2020. PMID: 32436334 Review.

4

Predicting antimicrobial mechanism-of-action from transcriptomes: A generalizable explainable artificial intelligence approach.

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. Espinoza JL, et al. PLoS Comput Biol. 2021 Mar 29;17(3):e1008857. doi: 10.1371/journal.pcbi.1008857. eCollection 2021 Mar. PLoS Comput Biol. 2021. PMID: 33780444 Free PMC article.

5

VEBA: a modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes.

Espinoza JL, Dupont CL. Espinoza JL, et al. BMC Bioinformatics. 2022 Oct 12;23(1):419. doi: 10.1186/s12859-022-04973-8. BMC Bioinformatics. 2022. PMID: 36224545 Free PMC article.

6

Differential network analysis of oral microbiome metatranscriptomes identifies community scale metabolic restructuring in dental caries.

Espinoza JL, Torralba M, Leong P, Saffery R, Bockmann M, Kuelbs C, Singh S, Hughes T, Craig JM, Nelson KE, Dupont CL. Espinoza JL, et al. PNAS Nexus. 2022 Oct 18;1(5):pgac239. doi: 10.1093/pnasnexus/pgac239. eCollection 2022 Nov. PNAS Nexus. 2022. PMID: 36712365 Free PMC article.

7

Genus-Wide Transcriptional Landscapes Reveal Correlated Gene Networks Underlying Microevolutionary Divergence in Diatoms.

Walworth NG, Espinoza JL, Argyle PA, Hinners J, Levine NM, Doblin MA, Dupont CL, Collins S. Walworth NG, et al. Among authors: espinoza jl. Mol Biol Evol. 2023 Oct 4;40(10):msad218. doi: 10.1093/molbev/msad218. Mol Biol Evol. 2023. PMID: 37874344 Free PMC article.

8

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.

Espinoza JL, Phillips A, Prentice MB, Tan GS, Kamath PL, Lloyd KG, Dupont CL. Espinoza JL, et al. Nucleic Acids Res. 2024 Aug 12;52(14):e63. doi: 10.1093/nar/gkae528. Nucleic Acids Res. 2024. PMID: 38909293 Free PMC article.

9

Host Genetic Control of the Oral Microbiome in Health and Disease.

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. Gomez A, et al. Among authors: espinoza jl. Cell Host Microbe. 2017 Sep 13;22(3):269-278.e3. doi: 10.1016/j.chom.2017.08.013. Cell Host Microbe. 2017. PMID: 28910633 Free PMC article.

10

The Airplane Cabin Microbiome.

Weiss H, Hertzberg VS, Dupont C, Espinoza JL, Levy S, Nelson K, Norris S; FlyHealthy Research Team. Weiss H, et al. Among authors: espinoza jl. Microb Ecol. 2019 Jan;77(1):87-95. doi: 10.1007/s00248-018-1191-3. Epub 2018 Jun 6. Microb Ecol. 2019. PMID: 29876609 Free PMC article.

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