Research output per year
Research output per year
- 1 - 50 out of 99 results
Search results
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2025
Deciphering age-related transcriptomic changes in the mouse retinal pigment epithelium
Dubey, S. K., Dubey, R., Jung, K., Hernandez, A. G. & Kleinman, M. E., 2025, In: Aging. 17, 3, p. 657-684 28 p.Research output: Contribution to journal › Article › peer-review
Open Access -
2024
Epigenetic disruptions in the offspring hypothalamus in response to maternal infection
Alsegehy, S., Southey, B. R., Hernandez, A. G., Rund, L. A., Antonson, A. M., Nowak, R. A., Johnson, R. W. & Rodriguez-Zas, S. L., Jun 5 2024, In: Gene. 910, 148329.Research output: Contribution to journal › Article › peer-review
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Genome sequences of nine Clostridium scindens strains isolated from human feces
Fernandez-Materan, F. V., Olivos-Caicedo, K. Y., Daniel, S. L., Walden, K. K. O., Fields, C. J., Hernandez, A. G., Alves, J. M. P. & Ridlon, J. M., Nov 2024, In: Microbiology Resource Announcements. 13, 11, e00848-24.Research output: Contribution to journal › Article › peer-review
Open Access -
High-quality genome assemblies for nine non-model North American insect species representing six orders (Insecta: Coleoptera, Diptera, Hemiptera, Hymenoptera, Lepidoptera, Neuroptera)
Walden, K. K. O., Cao, Y., Fields, C. J., Hernandez, A. G., Rendon, G. A., Robinson, G. E., Skinner, R. K., Stein, J. A. & Dietrich, C. H., Nov 2024, In: Molecular ecology resources. 24, 8, e14010.Research output: Contribution to journal › Article › peer-review
Open Access -
Histone deficiency and hypoacetylation in the aging retinal pigment epithelium
Dubey, S. K., Dubey, R., Prajapati, S. C., Jung, K., Mohan, K., Liu, X., Roney, J., Tian, W., Abney, J., Giarmarco, M. M., Hernandez, A. G., Liu, J. & Kleinman, M. E., May 2024, In: Aging Cell. 23, 5, e14108.Research output: Contribution to journal › Article › peer-review
Open Access -
Plastid genomics of wild grapevines (Vitis vinifera subsp. sylvestris) of Georgia the cradle of viticulture
Pipia, I., Ujmajuridze, L., Mamasakhlisashvili, L., Hernández, Á. & Tabidze, V., Sep 27 2024, In: Oeno One. 58, 4Research output: Contribution to journal › Article › peer-review
Open Access -
Use of a Candida albicans SC5314 PacBio HiFi reads dataset to close gaps in the reference genome assembly, reveal a subtelomeric gene family, and produce accurate phased allelic sequences
Hoyer, L. L., Freeman, B. A., Hogan, E. K. & Hernandez, A. G., 2024, In: Frontiers in Cellular and Infection Microbiology. 14, 1329438.Research output: Contribution to journal › Article › peer-review
Open Access -
2023
A Chromosome-Level Genome Assembly for Yamadazyma tenuis ATCC 10573
Hoyer, L. L., Hogan, E. K., Oh, S. H., Freeman, B. A., Walden, K. K. O. & Hernandez, A. G., Jun 2023, In: Microbiology Resource Announcements. 12, 6Research output: Contribution to journal › Article › peer-review
Open Access -
A Highly Contiguous and Annotated Genome Assembly of the Lesser Prairie-Chicken (Tympanuchus pallidicinctus)
Black, A. N., Bondo, K. J., Mularo, A., Hernandez, A., Yu, Y., Stein, C. M., Gregory, A., Fricke, K. A., Prendergast, J., Sullins, D., Haukos, D., Whitson, M., Grisham, B., Lowe, Z. & DeWoody, J. A., Apr 1 2023, In: Genome biology and evolution. 15, 4, evad043.Research output: Contribution to journal › Article › peer-review
Open Access -
Alzheimer’s disease pathogenetic progression is associated with changes in regulated retained introns and editing of circular RNAs
Arizaca Maquera, K. A., Welden, J. R., Margvelani, G., Miranda Sardón, S. C., Hart, S., Robil, N., Hernandez, A. G., de la Grange, P., Nelson, P. T. & Stamm, S., 2023, In: Frontiers in Molecular Neuroscience. 16, 1141079.Research output: Contribution to journal › Article › peer-review
Open Access -
An improved Lodderomyces elongisporus NRRL YB-4239 genome assembly substantiated by its electrophoretic karyotype
Hoyer, L. L., Hogan, E. K., Freeman, B. A., Walden, K. K. O. & Hernández, A. G., Oct 2023, In: Microbiology Resource Announcements. 12, 10Research output: Contribution to journal › Article › peer-review
Open Access -
Complete genome sequence of the archetype bile acid 7α-dehydroxylating bacterium, Clostridium scindens VPI12708, isolated from human feces, circa 1980
Caicedo, K. Y. O., Fernandez-Materan, F. V., Hernandez, A. G., Daniel, S. L., Alves, J. M. P. & Ridlon, J. M., Sep 2023, In: Microbiology Resource Announcements. 12, 9Research output: Contribution to journal › Article › peer-review
Open Access -
Draft genome assemblies of the avian louse Brueelia nebulosa and its associates using long-read sequencing from an individual specimen.
Sweet, A. D., Browne, D. R., Hernandez, A. G., Johnson, K. P. & Cameron, S. L., Apr 11 2023, In: G3: Genes, Genomes, Genetics. 13, 4, jkad030.Research output: Contribution to journal › Article › peer-review
Open Access -
First Draft Genome Assembly of Root-Lesion Nematode Pratylenchus scribneri Generated Using Long-Read Sequencing
Arora, D., Hernandez, A. G., Walden, K. K. O., Fields, C. J. & Yan, G., Apr 2023, In: International journal of molecular sciences. 24, 8, 7311.Research output: Contribution to journal › Article › peer-review
Open Access -
Genome sequence of Emydomyces testavorans type strain 16-2883 (ATCC TSD-145), an onygenalean fungus associated with freshwater aquatic turtle shell lesions
Hoyer, L. L., Hogan, E. K., Adamovicz, L., Allender, M. C., Terio, K. A. & Hernandez, A. G., Sep 2023, In: Microbiology Resource Announcements. 12, 9Research output: Contribution to journal › Article › peer-review
Open Access -
2022
Expanding the Molecular Alphabet of DNA-Based Data Storage Systems with Neural Network Nanopore Readout Processing
Tabatabaei, S. K., Pham, B., Pan, C., Liu, J., Chandak, S., Shorkey, S. A., Hernandez, A. G., Aksimentiev, A., Chen, M., Schroeder, C. M. & Milenkovic, O., Mar 9 2022, In: Nano letters. 22, 5, p. 1905-1914 10 p.Research output: Contribution to journal › Article › peer-review
Open Access -
Genomic regions associated with virulence in Setosphaeria turcica identified by linkage mapping in a biparental population
Singh, P., Huang, S. Y., Hernandez, A. G., Adhikari, P., Jamann, T. M. & Mideros, S. X., Apr 2022, In: Fungal Genetics and Biology. 159, 103655.Research output: Contribution to journal › Article › peer-review
Open Access -
Rat Spinal Cord Injury Associated with Spasticity Leads to Widespread Changes in the Regulation of Retained Introns
Hart, S. N., Patel, S. P., Michael, F. M., Stoilov, P., Leow, C. J., Hernandez, A. G., Jolly, A., De La Grange, P., Rabchevsky, A. G. & Stamm, S., Mar 1 2022, In: Neurotrauma Reports. 3, 1, p. 105-121 17 p.Research output: Contribution to journal › Article › peer-review
Open Access -
Rewritable two-dimensional DNA-based data storage with machine learning reconstruction
Pan, C., Tabatabaei, S. K., Tabatabaei Yazdi, S. M. H., Hernandez, A. G., Schroeder, C. M. & Milenkovic, O., Dec 2022, In: Nature communications. 13, 1, 2984.Research output: Contribution to journal › Article › peer-review
Open Access -
RNA editing of microtubule-associated protein tau circular RNAs promotes their translation and tau tangle formation
Welden, J. R., Margvelani, G., Arizaca Maquera, K. A., Gudlavalleti, B., Miranda Sardón, S. C., Campos, A. R., Robil, N., Lee, D. C., Hernandez, A. G., Wang, W. X., Di, J., De La Grange, P., Nelson, P. T. & Stamm, S., Dec 9 2022, In: Nucleic acids research. 50, 22, p. 12979-12996 18 p.Research output: Contribution to journal › Article › peer-review
Open Access -
Sulfate-reducing bacteria streamers and iron sulfides abruptly occlude porosity and increase hydraulic resistance in proppant-filled shale fractures
Fouke, B. W., Bhattacharjee, A. S., Fried, G. A., Sivaguru, M., Sanford, R. A., Zhou, L., Alcalde, R. E., Wunch, K., Stephenson, A., Ferrar, J. A., Hernandez, A. G., Wright, C., Fields, C. J., Todorov, L. G., Fouke, K. W., Bailey, C. M. & Werth, C. J., Jan 1 2022, In: AAPG Bulletin. 106, 1, p. 179-208 30 p.Research output: Contribution to journal › Article › peer-review
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2021
Interacting Impact of Maternal Inflammatory Response and Stress on the Amygdala Transcriptome of Pigs
Keever-Keigher, M. R., Zhang, P., Bolt, C. R., Rymut, H. E., Antonson, A. M., Corbett, M. P., Houser, A. K., Hernandez, A. G., Southey, B. R., Rund, L. A., Johnson, R. W. & Rodriguez-Zas, S. L., Aug 2021, In: G3 (Bethesda, Md.). 11, 8, jkab113.Research output: Contribution to journal › Article › peer-review
Open Access -
Pursuing Advances in DNA Sequencing Technology to Solve a Complex Genomic Jigsaw Puzzle: The Agglutinin-Like Sequence (ALS) Genes of Candida tropicalis
Oh, S. H., Isenhower, A., Rodriguez-Bobadilla, R., Smith, B., Jones, J., Hubka, V., Fields, C., Hernandez, A. & Hoyer, L. L., Jan 20 2021, In: Frontiers in Microbiology. 11, 594531.Research output: Contribution to journal › Article › peer-review
Open Access -
Three-dimensional microscale hanging drop arrays with geometric control for drug screening and live tissue imaging
Ganguli, A., Mostafa, A., Saavedra, C., Kim, Y., Le, P., Faramarzi, V., Feathers, R. W., Berger, J., Ramos-Cruz, K. P., Adeniba, O., Diaz, G. J. P., Drnevich, J., Wright, C. L., Hernandez, A. G., Lin, W., Smith, A. M., Kosari, F., Vasmatzis, G., Anastasiadis, P. Z. & Bashir, R., Apr 21 2021, In: Science Advances. 7, 17, eabc1323.Research output: Contribution to journal › Article › peer-review
Open Access -
Ultra-long DNA molecule isolation from plant nuclei for ultra-long read genome sequencing
Zerpa-Catanho, D., Zhang, X., Song, J., Hernandez, A. G. & Ming, R., Mar 19 2021, In: STAR Protocols. 2, 1, 100343.Research output: Contribution to journal › Article › peer-review
Open Access -
Using Genomics to Shape the Definition of the Agglutinin-Like Sequence (ALS) Family in the Saccharomycetales
Oh, S. H., Schliep, K., Isenhower, A., Rodriguez-Bobadilla, R., Vuong, V. M., Fields, C. J., Hernandez, A. G. & Hoyer, L. L., Dec 14 2021, In: Frontiers in Cellular and Infection Microbiology. 11, 794529.Research output: Contribution to journal › Article › peer-review
Open Access -
2020
Association of Common Genetic Variants in the CPSF7 and SDHAF2 Genes with Canine Idiopathic Pulmonary Fibrosis in the West Highland White Terrier
Piras, I. S., Bleul, C., Siniard, A., Wolfe, A. J., De Both, M. D., Hernandez, A. G. & Huentelman, M. J., Jun 2020, In: Genes. 11, 6, 609.Research output: Contribution to journal › Article › peer-review
Open Access -
A Staphylococcus pro-apoptotic peptide induces acute exacerbation of pulmonary fibrosis
D’alessandro-gabazza, C. N., Kobayashi, T., Yasuma, T., Toda, M., Kim, H., Fujimoto, H., Hataji, O., Takeshita, A., Nishihama, K., Okano, T., Okano, Y., Nishii, Y., Tomaru, A., Fujiwara, K., D’alessandro, V. F., Abdel-hamid, A. M., Ren, Y., Pereira, G. V., Wright, C. L. & Hernandez, A. & 15 others, , Dec 1 2020, In: Nature Communications. 11, 1, 1539.Research output: Contribution to journal › Article › peer-review
Open Access -
DNA punch cards for storing data on native DNA sequences via enzymatic nicking
Tabatabaei, S. K., Wang, B., Athreya, N. B. M., Enghiad, B., Hernandez, A. G., Fields, C. J., Leburton, J. P., Soloveichik, D., Zhao, H. & Milenkovic, O., Dec 1 2020, In: Nature communications. 11, 1, 1742.Research output: Contribution to journal › Article › peer-review
Open Access -
Lasting and Sex-Dependent Impact of Maternal Immune Activation on Molecular Pathways of the Amygdala
Keever, M. R., Zhang, P., Bolt, C. R., Antonson, A. M., Rymut, H. E., Caputo, M. P., Houser, A. K., Hernandez, A. G., Southey, B. R., Rund, L. A., Johnson, R. W. & Rodriguez-Zas, S. L., Aug 11 2020, In: Frontiers in Neuroscience. 14, 774.Research output: Contribution to journal › Article › peer-review
Open Access -
The ‘in vivo lifestyle’ of bile acid 7α-dehydroxylating bacteria: comparative genomics, metatranscriptomic, and bile acid metabolomics analysis of a defined microbial community in gnotobiotic mice
Ridlon, J. M., Devendran, S., Alves, J. M., Doden, H., Wolf, P. G., Pereira, G. V., Ly, L., Volland, A., Takei, H., Nittono, H., Murai, T., Kurosawa, T., Chlipala, G. E., Green, S. J., Hernandez, A. G., Fields, C. J., Wright, C. L., Kakiyama, G., Cann, I. & Kashyap, P. & 2 others, , May 3 2020, In: Gut Microbes. 11, 3, p. 381-404 24 p.Research output: Contribution to journal › Article › peer-review
Open Access -
2019
Agglutinin-Like Sequence (ALS) Genes in the Candida parapsilosis Species Complex: Blurring the Boundaries Between Gene Families That Encode Cell-Wall Proteins
Oh, S.-H., Smith, B., Miller, A. N., Staker, B., Fields, C., Hernandez, A. & Hoyer, L. L., 2019, In: Frontiers in Microbiology. 10, 781.Research output: Contribution to journal › Article › peer-review
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Characterization of the Candida orthopsilosis agglutinin-like sequence (ALS) genes
Lombardi, L., Zoppo, M., Rizzato, C., Bottai, D., Hernandez, A. G., Hoyer, L. L. & Tavanti, A., Apr 2019, In: PloS one. 14, 4, e0215912.Research output: Contribution to journal › Article › peer-review
Open Access -
Clostridium scindens ATCC 35704: Integration of nutritional requirements, the complete genome sequence, and global transcriptional responses to bile acids
Devendran, S., Shrestha, R., Alves, J. M. P., Wolf, P. G., Ly, L., Hernandez, A. G., Méndez-García, C., Inboden, A., Wiley, J., Paul, O., Allen, A., Springer, E., Wright, C. L., Fields, C. J., Daniel, S. L. & Ridlon, J. M., Apr 1 2019, In: Applied and environmental microbiology. 85, 7, e00052-19.Research output: Contribution to journal › Article › peer-review
Open Access -
Genome of ‘Charleston Gray’, the principal American watermelon cultivar, and genetic characterization of 1,365 accessions in the U.S. National Plant Germplasm System watermelon collection
Wu, S., Wang, X., Reddy, U., Sun, H., Bao, K., Gao, L., Mao, L., Patel, T., Ortiz, C., Abburi, V. L., Nimmakayala, P., Branham, S., Wechter, P., Massey, L., Ling, K. S., Kousik, C., Hammar, S. A., Tadmor, Y., Portnoy, V. & Gur, A. & 13 others, , Dec 1 2019, In: Plant Biotechnology Journal. 17, 12, p. 2246-2258 13 p.Research output: Contribution to journal › Article › peer-review
Open Access -
Physiology, Metabolism, and Fossilization of Hot-Spring Filamentous Microbial Mats
Dong, Y., Sanford, R. A., Inskeep, W. P., Srivastava, V., Bulone, V., Fields, C. J., Yau, P. M., Sivaguru, M., Ahrén, D., Fouke, K. W., Weber, J., Werth, C. R., Cann, I. K., Keating, K. M., Khetani, R. S., Hernandez, A. G., Wright, C., Band, M., Imai, B. S. & Fried, G. A. & 1 others, , Dec 2019, In: Astrobiology. 19, 12, p. 1442-1458 17 p.Research output: Contribution to journal › Article › peer-review
Open Access -
Sex-dependent dominance maintains migration supergene in rainbow trout
Pearse, D. E., Barson, N. J., Nome, T., Gao, G., Campbell, M. A., Abadía-Cardoso, A., Anderson, E. C., Rundio, D. E., Williams, T. H., Naish, K. A., Moen, T., Liu, S., Kent, M., Moser, M., Minkley, D. R., Rondeau, E. B., Brieuc, M. S. O., Sandve, S. R., Miller, M. R. & Cedillo, L. & 12 others, , Dec 1 2019, In: Nature Ecology and Evolution. 3, 12, p. 1731-1742 12 p.Research output: Contribution to journal › Article › peer-review
Open Access -
Transcriptome analysis of egg viability in rainbow trout, Oncorhynchus mykiss
Ma, H., Martin, K., Dixon, D., Hernandez, A. G. & Weber, G. M., Apr 27 2019, In: BMC genomics. 20, 1, 319.Research output: Contribution to journal › Article › peer-review
Open Access -
2018
Bile acid oxidation by Eggerthella lenta strains C592 and DSM 2243T
Harris, S. C., Devendran, S., Méndez- García, C., Mythen, S. M., Wright, C. L., Fields, C. J., Hernandez, A. G., Cann, I., Hylemon, P. B. & Ridlon, J. M., Nov 2 2018, In: Gut Microbes. 9, 6, p. 523-539 17 p.Research output: Contribution to journal › Article › peer-review
Open Access -
Expression of FLOWERING LOCUS C and a frameshift mutation of this gene on chromosome 20 differentiate a summer and winter annual biotype of Camelina sativa
Anderson, J. V., Horvath, D. P., Doğramaci, M., Dorn, K. M., Chao, W. S., Watkin, E. E., Hernandez, A. G., Marks, M. D. & Gesch, R., Jul 2018, In: Plant Direct. 2, 7, e00060.Research output: Contribution to journal › Article › peer-review
Open Access -
Gene network dysregulation in the trigeminal ganglia and nucleus accumbens of a model of chronic migraine-associated hyperalgesia
Jeong, H., Moye, L. S., Southey, B. R., Hernandez, A. G., Dripps, I., Romanova, E. V., Rubakhin, S. S., Sweedler, J. V., Pradhan, A. A. & Rodriguez-Zas, S. L., Dec 18 2018, In: Frontiers in Systems Neuroscience. 12, 63.Research output: Contribution to journal › Article › peer-review
Open Access -
Weed presence altered biotic stress and light signaling in maize even when weeds were removed early in the critical weed-free period
Horvath, D. P., Bruggeman, S., Moriles-Miller, J., Anderson, J. V., Dogramaci, M., Scheffler, B. E., Hernandez, A. G., Foley, M. E. & Clay, S., Apr 2018, In: Plant Direct. 2, 4, e00057.Research output: Contribution to journal › Article › peer-review
Open Access -
2017
Foliar glyphosate treatment alters transcript and hormone profiles in crown buds of leafy spurge and induces dwarfed and bushy phenotypes throughout its perennial lifecycle
Doğramaci, M., Anderson, J. V., Chao, W. S., Horvath, D. P., Hernandez, A. G., Mikel, M. A. & Foley, M. E., Nov 2017, In: Plant Genome. 10, 3Research output: Contribution to journal › Article › peer-review
Open Access -
Similar genetic architecture with shared and unique quantitative trait loci for bacterial cold water disease resistance in two rainbow trout breeding populations
Vallejo, R. L., Liu, S., Gao, G., Fragomeni, B. O., Hernandez, A. G., Leeds, T. D., Parsons, J. E., Martin, K. E., Evenhuis, J. P., Welch, T. J., Wiens, G. D. & Palti, Y., Oct 23 2017, In: Frontiers in Genetics. 8, OCT, 156.Research output: Contribution to journal › Article › peer-review
Open Access -
Whole genome comparative analysis of four Georgian grape cultivars
Tabidze, V., Pipia, I., Gogniashvili, M., Kunelauri, N., Ujmajuridze, L., Pirtskhalava, M., Vishnepolsky, B., Hernandez, A. G., Fields, C. J. & Beridze, T., Dec 1 2017, In: Molecular Genetics and Genomics. 292, 6, p. 1377-1389 13 p.Research output: Contribution to journal › Article › peer-review
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Wild emmer genome architecture and diversity elucidate wheat evolution and domestication
Avni, R., Nave, M., Barad, O., Baruch, K., Twardziok, S. O., Gundlach, H., Hale, I., Mascher, M., Spannagl, M., Wiebe, K., Jordan, K. W., Golan, G., Deek, J., Ben-Zvi, B., Ben-Zvi, G., Himmelbach, A., Maclachlan, R. P., Sharpe, A. G., Fritz, A. & Ben-David, R. & 28 others, , Jul 7 2017, In: Science. 357, 6346, p. 93-97 5 p.Research output: Contribution to journal › Article › peer-review
Open Access -
2016
Capturing one of the human gut microbiome's most wanted: Reconstructing the genome of a novel butyrate-producing, clostridial scavenger from metagenomic sequence data
Jeraldo, P., Hernandez, A., Nielsen, H. B., Chen, X., White, B. A., Goldenfeld, N., Nelson, H., Alhquist, D., Boardman, L. & Chia, N., 2016, In: Frontiers in Microbiology. 7, MAY, 783.Research output: Contribution to journal › Article › peer-review
Open Access -
Cerebellum transcriptome of mice bred for high voluntary activity offers insights into locomotor control and reward-dependent behaviors
Caetano-Anollés, K., Rhodes, J. S., Garland, T., Perez, S. D., Hernandez, A. G., Southey, B. R. & Rodriguez-Zas, S. L., Nov 2016, In: PloS one. 11, 11, e0167095.Research output: Contribution to journal › Article › peer-review
Open Access -
Differential transcriptome networks between IDO1-Knockout and wild-type mice in brain microglia and macrophages
Gonzalez-Pena, D., Nixon, S. E., Southey, B. R., Lawson, M. A., McCusker, R. H., Hernandez, A. G., Dantzer, R., Kelley, K. W. & Rodriguez-Zas, S. L., Jun 2016, In: PloS one. 11, 6, e0157727.Research output: Contribution to journal › Article › peer-review
Open Access -
Draft assembly of elite inbred line PH207 provides insights into genomic and transcriptome diversity in maize
Hirsch, C. N., Hirsch, C. D., Brohammer, A. B., Bowman, M. J., Soifer, I., Barad, O., Shem-Tov, D., Baruch, K., Lu, F., Hernandez, A. G., Fields, C. J., Wright, C. L., Koehler, K., Springer, N. M., Buckler, E., Buell, C. R., de Leon, N., Kaeppler, S. M., Childs, K. L. & Mikel, M. A., Nov 2016, In: Plant Cell. 28, 11, p. 2700-2714 15 p.Research output: Contribution to journal › Article › peer-review
Open Access