GenSAS Citations

Here are the researchers who have cited GenSAS:

2026 (9)

  1. Ko, J. T., Hoof, J. B., Meyer, A. S., & Santos, A. (2026). Graph data science in fungal biotechnology: Opportunities and applications. Biotechnology Advances, 108864.
  2. Malmberg, M. M., Suraweera, D. D., Baillie, R. C., Smith, K. F., & Cogan, N. O. I. (2026). Genomic resources for Australian alfalfa (Medicago sativa L.) genomics: reformatted reference genome, annotated variants, gene presence-absence and diversity analysis from genome re-sequencing. BMC Plant Biology, 26(1), 102.
  3. Rivarola, M., Conte, C. A., Berube, P., Chen, S. H., Giardini, M. C., Scannapieco, A. C., ... & Lanzavecchia, S. B. (2026). Chromosome‐scale genome assembly of the South American fruit fly, Anastrepha fraterculus sp. 1. Insect Science, 33(2), 640-664.
  4. Mohindra, V., Chowdhury, L. M., Mukhim, D. K. B., Sarma, K., Warbah, D. P., Sarma, D., & Jena, J. (2026). Genome sequencing and assembly of Neolissochilus pnar, the largest cavefish species of Mahseer. Scientific Data.
  5. Han, H., Oh, Y., Jang, Y. J., Chandra, S., Gill, U., Verma, S., ... & Lee, S. (2026). Genomic architecture of the resistance to Phytophthora cactorum 2 (RPc2) locus in strawberry (Fragaria× ananassa). The Plant Genome, 19(1), e70168.
  6. Dani, M., Beszteri, S., Castellanos, A. B., Schimani, K., Skibbe, O., Zimmermann, J., ... & Beszteri, B. (2026). Species delimitation within the Achnanthidium minutissimum complex (Bacillariophyta), based on morphological, molecular, and ecophysiological approaches. Journal of Phycology.
  7. Christinaki, A. C., Floudas, D., Myridakis, A. I., Gonou-Zagou, Z., & Kouvelis, V. N. (2026). Cladobotryum rhodochroum sp. nov.(Hypocreales, Ascomycota): A New Fungicolous Species Revealed by Morphology, Phylogeny, and Comparative Genomics. Journal of Fungi, 12(2), 117.
  8. Wang, W., Zong, L., He, J. W., Mao, C. Y., Dong, Z. W., Yang, P. P., ... & Ge, S. Q. (2026). Comparative genomics reveals evolutionary signatures of genes associated with jumping in beetles. Zoological Research, 47(1), 88.
  9. Ramzan, F., Vassiliou, L., & Tsaltas, D. (2026). Unveiling the diversity and mechanisms of plant growth-promoting bacteria in orchids: a comprehensive review. Frontiers in Microbiology, 17, 1697953.

2025 (29)

  1. Roshka, Y. A., Markelova, N. N., Mashkova, S. D., Malysheva, K. V., Georgieva, M. L., Levshin, I. B., ... & Sadykova, V. S. (2025). Antimicrobial potential of secalonic acids from Arctic-derived Penicillium chrysogenum INA 01369. Antibiotics, 14(1), 88.
  2. Jobe, T. O., Abdurakhmonov, I. Y., Ulloa, M., Fokar, M., Buriev, Z. T., Shermatov, S. E., ... & Ellis, M. L. (2025). Molecular Characterization of Fusarium Isolates from Upland Cotton Roots in Uzbekistan and Whole-Genome Comparison with Isolates from the United States. Phytopathology®, 115(1), 54-65.
  3. Medhi, U., Chaliha, C., Singh, A., Nath, B. K., & Kalita, E. (2025). Third generation sequencing transforming plant genome research: Current trends and challenges. Gene, 940, 149187.
  4. Poelzer, J., Han, S., Saha, S., Oler, E., Kruger, R., Berjanskii, M., ... & Wishart, D. S. (2025). BASys2: a next-generation bacterial genome annotation system. Nucleic Acids Research, 53(W1), W57-W67.
  5. Hessenauer, P., Feau, N., Heinzelmann, R., & Hamelin, R. C. (2025). Genomic exploration of climate-driven evolution and evolutionary convergence in forest pathogens. Genome Biology and Evolution, 17(5), evaf069.
  6. Suhre, T., Fabricio, M. F., Tischer, B., Ayub, M. A. Z., Evans, J. D., Frazzon, J., & Kothe, C. I. (2025). Fermentation of native Brazilian fruits with kombucha: A novel opportunity for producing low-alcohol beverages. Food Bioscience, 65, 106122.
  7. Han, H., Salinas, N., Barbey, C. R., Jang, Y. J., Fan, Z., Verma, S., ... & Lee, S. (2025). A telomere-to-telomere phased genome of an octoploid strawberry reveals a receptor kinase conferring anthracnose resistance. GigaScience, 14, giaf005.
  8. Han, H., Jang, Y. J., Han, K., Park, H. N., Kim, D. S., Lee, S., & Oh, Y. (2025). Chromosome-level genome assembly of cultivated strawberry ‘Seolhyang’(Fragaria× ananassa). Scientific Data, 12(1), 1002.
  9. Sampson, J. M., Morrissey, K. A., Mikolajova, K. J., Zimmerly, K. M., Gemmell, N. J., Gardner, M. G., ... & Miller, R. D. (2025). Squamate reptiles may have compensated for the lack of γδTCR with a duplication of the TRB locus. Frontiers in immunology, 15, 1524471.
  10. Krawczyk, K., Szablińska-Piernik, J., Paukszto, Ł., Maździarz, M., Sulima, P., Przyborowski, J. A., ... & Sawicki, J. (2025). Chromosome-scale telomere to telomere genome assembly of common crystalwort (Riccia sorocarpa Bisch.). Scientific Data, 12(1), 77.
  11. Liu, Y., Xiong, W., Wang, X., Liang, S., He, L., Lin, X., ... & Wang, K. (2025). Biochemical analyses of a new GH18 chitinase from Beauveria bassiana KW1 and its synergy with a commercial protease on silkworm exuviae hydrolysis. Applied and Environmental Microbiology, 91(10), e01285-25.
  12. Hospodářská, M., Mora, P., Voleníková, A. C., Al‐Rikabi, A., Altmanová, M., Simanovsky, S. A., ... & Sember, A. (2025). Multiple Origins of Sex Chromosomes in Nothobranchius Killifishes. Molecular Ecology, 34(16), e70029.
  13. Hall, N., Montgomery, J., Chen, J., Saski, C., Matzrafi, M., Westra, P., ... & Patterson, E. (2025). FHY3/FAR1 transposable elements generate adaptive genetic variation in the Bassia scoparia genome. Pest Management Science, 81(8), 4393-4402.
  14. He, T., Li, X., del Carmen Flores-Vallejo, R., Radu, A. M., van Dijl, J. M., & Haslinger, K. (2025). The endophytic fungus Cosmosporella sp. VM-42 from Vinca minor is a source of bioactive compounds with potent activity against drug-resistant bacteria. Current Research in Microbial Sciences, 8, 100390.
  15. Kim, J. H., Whitaker, V. M., & Lee, S. (2025). A haplotype-phased genome characterizes the genomic architecture and causal variants for RXf1 conferring resistance to Xanthomonas fragariae in strawberry (F.× ananassa). BMC genomics, 26(1), 453.
  16. Jeevalatha, A., Reddy, B., Eapen, S. J., Javed, M., Anandaraj, M., & Kumar, A. (2025). Pathogenomics insights into Phytophthora capsici and Phytophthora tropicalis-Sibling species causing black pepper foot rot: Genomic architecture, metabolic pathways, and effector diversity. Gene, 947, 149328.
  17. Louw, N. L., Eagan, J. L., Larlee, J., Kehler, M., Keller, N. P., & Wolfe, B. E. (2025). Long-term monitoring of a North American cheese cave reveals mechanisms and consequences of fungal adaptation. Current Biology, 35(20), 4909-4921.
  18. Serén, N., Pinho, C., Megía-Palma, R., Aguilar, P., Žagar, A., Andrade, P., & Carretero, M. A. (2025). Selection on the vascular-remodeling BMPER gene is associated with altitudinal adaptation in an insular lizard. Evolution letters, 9(1), 41-50.
  19. Maybery-Reupert, K., Giri, K., Hayden, M., Cogan, N., & Isenegger, D. (2025). Novel protocol for isolation and transient transformation of Rhodes grass (Chloris gayana) protoplasts: Maybery-Reupert et al. In Vitro Cellular & Developmental Biology-Plant, 61(2), 471-479.
  20. Maguvu, T. E., Frias, R. J., & Trouillas, F. P. (2025). Genome sequencing and analysis of isolates of Cytospora sorbicola and Cytospora plurivora associated with almond and peach canker. Plos one, 20(10), e0334178.
  21. Todd, O. E., Simpson, S., Scheffler, B., & Dorn, K. M. (2025). A fully phased, chromosome-scale genome of sugar beet line FC309 enables the discovery of Fusarium yellows resistance QTL. DNA Research, 32(1), dsae032.
  22. Sampson, J. M., Mikolajova, K. J., Zimmerly, K. M., & Miller, R. D. (2025). Marsupial Ig genomics revisited and the potential role of retroelements in the limited number of heavy chain isotypes. BMC biology, 23(1), 215.
  23. Basak, S., Saikia, K., Konwar, A. N., Hepat, R. P., Patra, A., Borah, R., ... & Thakur, D. (2025). Phenotypic and molecular insights into a cypovirus isolated from Antheraea assamensis Helfer (Lepidoptera: Saturniidae) and modelling of its polyhedrin protein structure. Journal of Biomolecular Structure and Dynamics, 1-15.
  24. Sampson, J. M., Mikolajova, K. J., Gardner, M. G., Bertozzi, T., & Miller, R. D. (2025). Immunoglobulin genetics of a model squamate reptile, Tiliqua rugosa. Immunogenetics, 77(1), 30.
  25. Silva, H. A. O. D., Nascimento, C. R. B., Anjos, R. S., & Mizubuti, E. S. (2025). Draft genomes of Diaporthe ueckeri and Diaporthe longicolla strains associated with the soybean pod and grain rot disease in Brazil. Microbiology Resource Announcements, 14(5), e01225-24.
  26. Hsiang, T. F., Yamane, H., Lin, Y. J., Sugimori, M., Nishiyama, S., Nagasaka, K., ... & Tao, R. (2025). The haplotype-phased genome assembly facilitated the deciphering of the bud dormancy-related QTLs in Prunus mume. DNA Research, 32(1), dsae034.
  27. Grossman, N. T., Fan, Y., Zimin, A. V., Wear, M. P., Jedlicka, A., Dziedzic, A., ... & Casadevall, A. (2025). Three annotated chromosome-level de novo genome assemblies of Lomentospora prolificans provide evidence for a chromosomal translocation event. G3: Genes, Genomes, Genetics, 15(6), jkaf091.
  28. Aguilera, P. M., & Grabiele, M. (2025). An Integrated Resource for Genetics and Breeding of Erva/Yerba Mate (Ilex paraguariensis). Brazilian Archives of Biology and Technology, 68, e25240954.
  29. Duarte, A., Sheng, H., Schroeder, B. K., & Murray, T. D. (2025). Genome Resource of Afrina sporoboliae for the Analyses of Gall-Forming Nematodes of the Family Anguinidae. PhytoFrontiers™, PHYTOFR-09.

2024 (28)

  1. Mpeyako, L. A., Hart, A. J., Bailey, N. P., Carlton, J. M., Henrissat, B., Sullivan, S. A., & Hirt, R. P. (2024). Comparative genomics between Trichomonas tenax and Trichomonas vaginalis: CAZymes and candidate virulence factors. Frontiers in microbiology, 15, 1437572.
  2. Kortsinoglou, A. M., Wood, M. J., Myridakis, A. I., Andrikopoulos, M., Roussis, A., Eastwood, D., ... & Kouvelis, V. N. (2024). Comparative genomics of Metarhizium brunneum strains V275 and ARSEF 4556: unraveling intraspecies diversity. G3: Genes, Genomes, Genetics, 14(10), jkae190.
  3. Rahmati-Holasoo, H., Marandi, A., Mousavi, H. E., Arabkhazaeli, F., Shokrpoor, S., & Ziafati Kafi, Z. (2024). Clinical, histopathological and phylogenetic analysis of Myxobolus lentisturalis (Myxozoa: Myxobolidae) infecting the musculature of farmed population of goldfish (Carassius auratus) in Iran: 2021–2022. BMC Veterinary Research, 20(1), 361.
  4. Liu, X., Liu, Y., Liu, J., Zhang, H., Shan, C., Guo, Y., ... & Tang, M. (2024). Correlation between the gut microbiome and neurodegenerative diseases: a review of metagenomics evidence. Neural Regeneration Research, 19(4), 833-845.
  5. Mora, P., Hospodářská, M., Voleníková, A. C., Koutecký, P., Štundlová, J., Dalíková, M., ... & Nguyen, P. (2024). Sex‐biased gene content is associated with sex chromosome turnover in Danaini butterflies. Molecular Ecology, 33(24), e17256.
  6. Haese-Hill, W., Crouch, K., & Otto, T. D. (2024). Annotation and visualization of parasite, fungi and arthropod genomes with Companion. Nucleic Acids Research, 52(W1), W39-W44.
  7. Bukhman, Y. V., Morin, P. A., Meyer, S., Chu, L. F., Jacobsen, J. K., Antosiewicz-Bourget, J., ... & Stewart, R. (2024). A high-quality blue whale genome, segmental duplications, and historical demography. Molecular Biology and Evolution, 41(3), msae036.
  8. Iacovelli, R., He, T., Allen, J. L., Hackl, T., & Haslinger, K. (2024). Genome sequencing and molecular networking analysis of the wild fungus Anthostomella pinea reveal its ability to produce a diverse range of secondary metabolites. Fungal Biology and Biotechnology, 11(1), 1.
  9. Iacovelli, R., Poon, F., & Haslinger, K. (2024). Identification and reconstitution of the first two enzymatic steps for the biosynthesis of bioactive meroterpenoids from Hericium erinaceus (Lion’s Mane Mushroom). Molecules, 29(23), 5576.
  10. Christinaki, A. C., Myridakis, A. I., & Kouvelis, V. N. (2024). Genomic insights into the evolution and adaptation of secondary metabolite gene clusters in fungicolous species Cladobotryum mycophilum ATHUM6906. G3: Genes, Genomes, Genetics, 14(4), jkae006.
  11. Chowdhury, L. M., Mohindra, V., Kumar, R., & Jena, J. (2024). Genome sequencing and assembly of Indian major carp, Cirrhinus mrigala (Hamilton, 1822). Scientific Data, 11(1), 898.
  12. Bartholomew, H. P., Gottschalk, C., Cooper, B., Bukowski, M. R., Yang, R., Gaskins, V. L., ... & Jurick, W. M. (2024). Omics-Based Comparison of Fungal Virulence Genes, Biosynthetic Gene Clusters, and Small Molecules in Penicillium expansum and Penicillium chrysogenum. Journal of Fungi, 11(1), 14.
  13. Mohindra, V., Chowdhury, L. M., Charan, R., Basheer, V. S., & Jena, J. (2024). Genome sequencing and assembly of near threatened Clarias dussumieri (Valenciennes, 1840), an endemic catfish of peninsular India. Scientific Data, 11(1), 1406.
  14. Luciano-Rosario, D., Jurick, W. M., & Gottschalk, C. (2024). The near-gapless Penicillium fuscoglaucum genome enables the discovery of lifestyle features as an emerging post-harvest phytopathogen. Journal of Fungi, 10(6), 430.
  15. Cossette, M. L., Stewart, D. T., & Shafer, A. B. (2024). Comparative Genomics of the World's Smallest Mammals Reveals Links to Echolocation, Metabolism, and Body Size Plasticity. Genome Biology and Evolution, 16(11), evae225.
  16. Ong, C. T., Mody, K. T., Cavallaro, A. S., Yan, Y., Nguyen, L. T., Shao, R., ... & Ross, E. M. (2024). Chromosome-Scale Genome Assembly of the Sheep-Biting Louse Bovicola ovis Using Nanopore Sequencing Data and Pore-C Analysis. International Journal of Molecular Sciences, 25(14), 7824.
  17. Maguvu, T. E., Raimi, A., Trouillas, F. P., Adeleke, R., & Bezuidenhout, C. C. (2024). Genome sequence of Colletotrichum karsti isolated from rose leaves exhibiting anthracnose symptoms in Potchefstroom, South Africa. Microbiology Resource Announcements, 13(10), e00275-24.
  18. Louw, N. L., Wolfe, B. E., & Uricchio, L. H. (2024). A phylogenomic perspective on interspecific competition. Ecology Letters, 27(2), e14359.
  19. Han, H., Jang, Y. J., Oh, Y., Marin, M. V., Huguet-Tapia, J., Peres, N. A., & Lee, S. (2024). Chromosome-Scale Genome Sequence Resource for Two Neopestalotiopsis spp. Isolates with Different Virulence in Strawberry (Fragaria× ananassa). PhytoFrontiers™, 4(3), 422-426.
  20. Cequeña, R. C. M., & Sumabat-Dacones, L. G. (2024). Presence of elsinochrome and other putative effectors in select genomes of the plant pathogen Elsinoë spp. based on in silico analysis. SciEnggJ, 17(1), 59-70.
  21. Chellappan, B. V. (2024). Comparative secretome analysis unveils species-specific virulence factors in Elsinoe perseae, the causative agent of the scab disease of avocado (Persea americana). AIMS microbiology, 10(4), 894.
  22. Balakrishnan, I. K., Debnath, R., KS, T. N., Moorthy, S. M., Ramesh, K. V., & Dubey, H. (2024). Genome-wide In-silico Identification of Microsatellites in Eri Silkworm, Samia ricini (Lepidoptera: Saturniidae). Ecology, Environment & Conservation (0971765X), 30(4).
  23. Vanitha, C., Balakrishnan1&2, I. K., Debnath, R., Lavanya, C., KS, T. N., Moorthy, S. M., ... & Dubey, H. (2024). Genome-wide In-silico Identification of Microsatellites in Eri Silkworm, Samia ricini (Lepidoptera: Saturniidae). ECOLOGY, ENVIRONMENT AND CONSERVATION, 30(04), 1888-1898.
  24. Ye, R., Biango-Daniels, M., Steenwyk, J. L., Rokas, A., Louw, N., Nardella, R., & Wolfe, B. E. (2024). Genomic, transcriptomic, and ecological diversity of Penicillium species in cheese rind microbiomes. Fungal Genetics and Biology, 103862.
  25. Cho, M., Lee, S. J., Choi, E., Kim, J., Choi, S., Lee, J. H., & Park, H. (2024). An Antarctic lichen isolate (Cladonia borealis) genome reveals potential adaptation to extreme environments. Scientific Reports, 14(1), 1342.
  26. Jobe, T. O., Ulloa, M., & Ellis, M. L. (2024). A high-quality whole-genome sequence, assembly, and gene annotation of Fusarium oxysporum f. sp. vasinfectum (Fov) race 1 from California. Microbiology Resource Announcements, 13(1), e00702-23.
    Cited By
  27. Li, Y., Wei, Z. Z., Sela, H., Govta, L., Klymiuk, V., Roychowdhury, R., ... & Fahima, T. (2024). Dissection of a rapidly evolving wheat resistance gene cluster by long-read genome sequencing accelerated the cloning of Pm69. Plant Communications, 5(1).
    Cited By
  28. Jobe, T. O., Ulloa, M., & Ellis, M. L. (2024). Two de novo genome assemblies from pathogenic Fusarium oxysporum f. sp. vasinfectum race 4 (FOV4) isolates from California. Microbiology Resource Announcements, 13(1), e00760-23. 
    Cited By

2023 (21)

  1. Sumner, J. T., Andrasz, C. L., Johnson, C. A., Wax, S., Anderson, P., Keeling, E. L., & Davidson, J. M. (2023). De novo genome assembly and comparative genomics for the colonial ascidian Botrylloides violaceus. G3: Genes, Genomes, Genetics, 13(10), jkad181.
  2. Ghosh Dasgupta, M., Senthilkumar, S., Muthulakshmi, E., & Balasubramanian, A. (2023). The draft genome reveals early duplication event in Pterocarpus santalinus: an endemic timber species. Planta, 258(2), 27.
  3. Gadagkar, S. R., Baeza, J. A., Buss, K., & Johnson, N. (2023). De-novo whole genome assembly of the orange jewelweed, Impatiens capensis Meerb.(Balsaminaceae) using nanopore long-read sequencing. PeerJ, 11, e16328.
  4. Rahmati-Holasoo, H., Ghalyanchilangeroudi, A., Kafi, Z. Z., Marandi, A., Shokrpoor, S., Imantalab, B., & Mousavi, H. E. (2023). Detection of lymphocystis disease virus (LCDV) from yellowbar angelfish (Pomacanthus maculosus Forsskål, 1775) in Iran: Histopathological and phylogenetic analysis. Aquaculture, 562, 738862. 
    Cited By
  5. Tateo, F., Bononi, M., Castorina, G., Colecchia, S. A., De Benedetti, S., Consonni, G., & Geuna, F. (2023). Whole-genome resequencing-based characterization of a durum wheat landrace showing similarity to ‘Senatore Cappelli’. Plos one, 18(9), e0291430.
  6. Han, H., Jang, Y. J., Oh, Y., Marin, M. V., Huguet-Tapia, J., Peres, N. A., & Lee, S. (2023). Chromosome-Scale Genome Resource for Two Neopestalotiopsis spp. Isolates with Different Virulence in Strawberry (Fragaria× ananassa). PhytoFrontiers, (ja).
  7. Spawton, K. A., Peever, T., & du Toit, L. J. (2023). Genome resource for Stemphylium beticola, one of the causal agents of Stemphylium leaf spot of spinach (Spinacia oleracea). PhytoFrontiers, (ja).
  8. Quade, A., Park, R. F., Stodart, B. J., Ding, Y., Zhang, P., Thang, M., ... & Ash, G. J. (2023). Phenotypic and genotypic diversity of Puccinia sorghi in Eastern Australia: implications for maize breeding programs. PhytoFrontiers™, PHYTOFR-12.
  9. Paguirigan, J. A. G., Kim, J. A., Hur, J. S., & Kim, W. (2023). Identification of a biosynthetic gene cluster for a red pigment cristazarin produced by a lichen-forming fungus Cladonia metacorallifera. Plos one, 18(6), e0287559.
  10. Cheng, F., Dennis, A. B., Osuoha, J. I., Canitz, J., Kirschbaum, F., & Tiedemann, R. (2023). A new genome assembly of an African weakly electric fish (Campylomormyrus compressirostris, Mormyridae) indicates rapid gene family evolution in Osteoglossomorpha. BMC genomics, 24(1), 129.  
    Cited By
  11. Alsubaie, B., Kharabian-Masouleh, A., Furtado, A., Al-Dossary, O., Al-Mssallem, I., & Henry, R. J. (2023). Highly sex specific gene expression in Jojoba. BMC Plant Biology, 23(1), 440. 
    Cited By
  12. Maguvu, T. E., Travadon, R., Cantu, D., & Trouillas, F. P. (2023). Whole genome sequencing and analysis of multiple isolates of Ceratocystis destructans, the causal agent of Ceratocystis canker of almond in California. Scientific Reports, 13(1), 14873.
  13. Moghaddam, S., Lotfollahzadeh, S., Salehi, T. Z., Hassanpour, A., Manesh, H. T., & Tamai, I. A. (2023). Molecular and sequencing study and identification of novel SeM-type in beta-hemolytic streptococci involving the upper respiratory tract in Iran. BMC Veterinary Research, 19(1), 210.
  14. Mongue, A. J., Martin, S. H., Manweiler, R. E., Scullion, H., Koehn, J. L., De Roode, J. C., & Walters, J. R. (2023). Genome sequence of Ophryocystis elektroscirrha, an apicomplexan parasite of monarch butterflies: cryptic diversity and response to host-sequestered plant chemicals. BMC genomics, 24(1), 278. 
    Cited By
  15. He, T., Li, X., Iacovelli, R., Hackl, T., & Haslinger, K. (2023). Genomic and Metabolomic Analysis of the Endophytic Fungus Fusarium sp. VM-40 Isolated from the Medicinal Plant Vinca minor. Journal of Fungi, 9(7), 704.
  16. Cossette, M. L., Stewart, D. T., Haghani, A., Zoller, J. A., Shafer, A. B., & Horvath, S. (2023). Epigenetics and island‐mainland divergence in an insectivorous small mammal. Molecular Ecology, 32(1), 152-166. 
    Cited By
  17. Caliskan, A., Dangwal, S., & Dandekar, T. (2023). Metadata integrity in bioinformatics: Bridging the gap between data and knowledge. Computational and Structural Biotechnology Journal.
  18. Hamese, S., Mugwanda, K., Takundwa, M., Prinsloo, E., & Thimiri Govinda Raj, D. B. (2023). Recent advances in genome annotation and synthetic biology for the development of microbial chassis. Journal of Genetic Engineering and Biotechnology, 21(1), 1-9.
  19. Li, Y., Wei, Z. Z., Sela, H., Govta, L., Klymiuk, V., Roychowdhury, R., ... & Fahima, T. (2023). Dissection of a rapidly evolving wheat resistance gene cluster by long-read genome sequencing accelerated the cloning of Pm69. Plant Communications. 
    Cited By
  20. Mikheenko, A., Saveliev, V., Hirsch, P., & Gurevich, A. (2023). WebQUAST: online evaluation of genome assemblies. Nucleic Acids Research, gkad406. 
    Cited By
  21. Jobe, T. O., Ulloa, M., & Ellis, M. L. (2023). Two de novo genome assemblies from pathogenic Fusarium oxysporum f. sp. vasinfectum race 4 (FOV4) isolates from California. Microbiology Resource Announcements, e00760-23.

2022 (11)

  1. Rico, Y., Lorenzana, G. P., Benítez-Pineda, C. A., & Olukolu, B. A. (2022). Development of Genomic Resources in Mexican Bursera (Section: Bullockia: Burseraceae): Genome Assembly, Annotation, and Marker Discovery for Three Copal Species. Genes, 13(10), 1741.
    Cited By
  2. Ogaji, Y. O., Lee, R. C., Sawbridge, T. I., Cocks, B. G., Daetwyler, H. D., & Kaur, S. (2022). De Novo Long-Read Whole-Genome Assemblies and the Comparative Pan-Genome Analysis of Ascochyta Blight Pathogens Affecting Field Pea. Journal of Fungi, 8(8), 884.
    Cited By
  3. Kafi, Z. Z., Najafi, H., Alishahi, M., Rahmati-Holasoo, H., Mouloki, A., & Ghalyanchilangeroudi, A. (2022). Detection and phylogenetic analysis of carp edema virus in common carp (Cyprinus Carpio) in Iran; 2020–2021. Aquaculture, 558, 738381.
    Cited By
  4. Nath, O., Fletcher, S. J., Hayward, A., Shaw, L. M., Masouleh, A. K., Furtado, A., ... & Mitter, N. (2022). A haplotype resolved chromosomal level avocado genome allows analysis of novel avocado genes. Horticulture Research, 9.
    Cited By
  5. Morrissey, K. A., Sampson, J. M., Rivera, M., Bu, L., Hansen, V. L., Gemmell, N. J., ... & Miller, R. D. (2022). Comparison of reptilian genomes reveals deletions associated with the natural loss of γδ T cells in squamates. The Journal of Immunology, 208(8), 1960-1967.
    Cited By
  6. Reddy, B., Mehta, S., Prakash, G., Sheoran, N., & Kumar, A. (2022). Structured framework and genome analysis of Magnaporthe grisea inciting pearl millet blast disease reveals versatile metabolic pathways, protein families, and virulence factors. Journal of Fungi, 8(6), 614.
    Cited By
  7. Widanagama, S. D., Freeland, J. R., Xu, X., & Shafer, A. B. (2022). Genome assembly, annotation, and comparative analysis of the cattail Typha latifolia. G3, 12(2), jkab401.
    Cited By
  8. Volenikova, A., Nguyen, P., Davey, P., Sehadova, H., Kludkiewicz, B., Koutecky, P., ... & Zurovec, M. (2022). Genome sequence and silkomics of the spindle ermine moth, Yponomeuta cagnagella, representing the early diverging lineage of the ditrysian Lepidoptera. Communications Biology, 5(1), 1281.
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  9. Peters, S. L., Borges, A. L., Giannone, R. J., Morowitz, M. J., Banfield, J. F., & Hettich, R. L. (2022). Experimental validation that human microbiome phages use alternative genetic coding. Nature Communications, 13(1), 5710.
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  10. De Panis, D., Dopazo, H., Bongcam-Rudloff, E., Conesa, A., & Hasson, E. (2022). Transcriptional responses are oriented towards different components of the rearing environment in two Drosophila sibling species. BMC genomics, 23(1), 515.
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  11. Mehla, S., Kumar, U., Kapoor, P., Singh, Y., Sihag, P., Sagwal, V., ... & Dhankher, O. P. (2022). Structural and functional insights into the candidate genes associated with different developmental stages of flag leaf in bread wheat (Triticum aestivum l.). Frontiers in Genetics, 13, 933560.
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2021 (17)

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  2. Gallardo-Escárate, C., Valenzuela-Muñoz, V., Nuñez-Acuña, G., Valenzuela-Miranda, D., Gonçalves, A. T., Escobar-Sepulveda, H., ... & Warren, W. (2021). Chromosome-scale genome assembly of the sea louse Caligus rogercresseyi by SMRT sequencing and Hi-C analysis. Scientific data, 8(1), 60.
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  3. Weng, Y. M., Francoeur, C. B., Currie, C. R., Kavanaugh, D. H., & Schoville, S. D. (2021). A high‐quality carabid genome assembly provides insights into beetle genome evolution and cold adaptation. Molecular Ecology Resources, 21(6), 2145-2165.
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  4. Kim, W., Jeong, M. H., Yun, S. H., & Hur, J. S. (2021). Transcriptome analysis identifies a gene cluster for the biosynthesis of biruloquinone, a rare phenanthraquinone, in a lichen-forming fungus Cladonia macilenta. Journal of Fungi, 7(5), 398.
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  5. Patturaj, M., Munusamy, A., Kannan, N., Kandasamy, U., & Ramasamy, Y. (2021). Chromosome-specific polymorphic SSR markers in tropical eucalypt species using low coverage whole genome sequences: systematic characterization and validation. Genomics & Informatics, 19(3).
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  6. Barrera-Redondo, J., Sanchez-de La Vega, G., Aguirre-Liguori, J. A., Castellanos-Morales, G., Gutiérrez-Guerrero, Y. T., Aguirre-Dugua, X., ... & Eguiarte, L. E. (2021). The domestication of Cucurbita argyrosperma as revealed by the genome of its wild relative. Horticulture research, 8.
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  7. Polonio, Á., Díaz-Martínez, L., Fernández-Ortuño, D., de Vicente, A., Romero, D., López-Ruiz, F. J., & Pérez-García, A. (2021). A hybrid genome assembly resource for Podosphaera xanthii, the main causal agent of powdery mildew disease in cucurbits. Molecular Plant-Microbe Interactions, 34(3), 319-324.
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  8. Saud, Z., Hitchings, M. D., & Butt, T. M. (2021). Nanopore sequencing and de novo assembly of a misidentified camelpox vaccine reveals putative epigenetic modifications and alternate protein signal peptides. Scientific Reports, 11(1), 17758.
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  9. Reddy, B., Kumar, A., Mehta, S., Sheoran, N., Chinnusamy, V., & Prakash, G. (2021). Hybrid de novo genome-reassembly reveals new insights on pathways and pathogenicity determinants in rice blast pathogen Magnaporthe oryzae RMg_Dl. Scientific Reports, 11(1), 22922.
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  10. Saud, Z., Kortsinoglou, A. M., Kouvelis, V. N., & Butt, T. M. (2021). Telomere length de novo assembly of all 7 chromosomes and mitogenome sequencing of the model entomopathogenic fungus, Metarhizium brunneum, by means of a novel assembly pipeline. BMC genomics, 22(1), 1-15.
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  11. Callahan, A. M., Zhebentyayeva, T. N., Humann, J. L., Saski, C. A., Galimba, K. D., Georgi, L. L., ... & Dardick, C. D. (2021). Defining the ‘HoneySweet’insertion event utilizing NextGen sequencing and a de novo genome assembly of plum (Prunus domestica). Horticulture research, 8.
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  12. Phan, I. Q., Rice, C. A., Craig, J., Noorai, R. E., McDonald, J. R., Subramanian, S., ... & Myler, P. J. (2021). The transcriptome of Balamuthia mandrillaris trophozoites for structure-guided drug design. Scientific Reports, 11(1), 21664.
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  13. Navarro-Escalante, L., Hernandez-Hernandez, E. M., Nuñez, J., Acevedo, F. E., Berrio, A., Constantino, L. M., ... & Benavides, P. (2021). A coffee berry borer (Hypothenemus hampei) genome assembly reveals a reduced chemosensory receptor gene repertoire and male-specific genome sequences. Scientific reports, 11(1), 4900.
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  14. Fernández, L., Olanda, R., Pérez, M., & Orduña, J. M. (2021). A Web-Based Tool for Automatic Detection and Visualization of DNA Differentially Methylated Regions. Electronics, 10(9), 1083.
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  15. Vlasova, A., Hermoso Pulido, T., Camara, F., Ponomarenko, J., & Guigó, R. (2021). FA-Nf: A functional annotation pipeline for proteins from non-model organisms implemented in nextflow. Genes, 12(10), 1645.
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  16. Wu, K., Cheng, Z. H., Williams, E., Turner, N. T., Ran, D., Li, H., ... & Long, H. (2021). Unexpected discovery of hypermutator phenotype sounds the alarm for quality control strains. Genome biology and evolution, 13(8), evab148.
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  17. Huang, Q., Wu, Z. H., Li, W. F., Guo, R., Xu, J. S., Dang, X. Q., ... & Evans, J. D. (2021). Genome and evolutionary analysis of Nosema ceranae: A microsporidian parasite of honey bees. Frontiers in Microbiology, 12, 645353.
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2020 (8)

  1. Ejigu, G. F., & Jung, J. (2020). Review on the computational genome annotation of sequences obtained by next-generation sequencing. Biology, 9(9), 295.
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  2. Braich, S., Baillie, R. C., Spangenberg, G. C., & Cogan, N. O. (2020). A new and improved genome sequence of Cannabis sativa. Gigabyte, 2020.
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  3. Montgomery, J. S., Giacomini, D., Waithaka, B., Lanz, C., Murphy, B. P., Campe, R., ... & Tranel, P. J. (2020). Draft Genomes of Amaranthus tuberculatus, Amaranthus hybridus, and Amaranthus palmeri. Genome biology and evolution, 12(11), 1988-1993.
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  4. Gañán, L., White III, R. A., Friesen, M. L., Peever, T. L., & Amiri, A. (2020). A genome resource for the apple powdery mildew pathogen Podosphaera leucotricha. Phytopathology®, 110(11), 1756-1758.
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  5. Pérez-Cobas, A. E., Gomez-Valero, L., & Buchrieser, C. (2020). Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses. Microbial genomics, 6(8).
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  6. Jeffress, S., Arun-Chinnappa, K., Stodart, B., Vaghefi, N., Tan, Y. P., & Ash, G. (2020). Genome mining of the citrus pathogen Elsinoë fawcettii; prediction and prioritisation of candidate effectors, cell wall degrading enzymes and secondary metabolite gene clusters. PLoS One, 15(5), e0227396.
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  7. Sargent, L., Liu, Y., Leung, W., Mortimer, N. T., Lopatto, D., Goecks, J., & Elgin, S. C. (2020). G-OnRamp: Generating genome browsers to facilitate undergraduate-driven collaborative genome annotation. PLoS computational biology, 16(6), e1007863.
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  8. Jung, H., Ventura, T., Chung, J. S., Kim, W. J., Nam, B. H., Kong, H. J., ... & Eyun, S. I. (2020). Twelve quick steps for genome assembly and annotation in the classroom. PLoS computational biology, 16(11), e1008325.
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2019 (7)

  1. Dasgupta, M. G., Ulaganathan, K., Dev, S. A., & Balakrishnan, S. (2019). Draft genome of Santalum album L. provides genomic resources for accelerated trait improvement. Tree Genetics & Genomes, 15, 1-15.
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  2. Million, C. R., Wijeratne, S., Cassone, B. J., Lee, S., Rouf Mian, M. A., McHale, L. K., & Dorrance, A. E. (2019). Hybrid genome assembly of a major quantitative disease resistance locus in soybean toward Fusarium graminearum. The Plant Genome, 12(2), 180102.
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  3. Bodinaku, I., Shaffer, J., Connors, A. B., Steenwyk, J. L., Biango-Daniels, M. N., Kastman, E. K., ... & Wolfe, B. E. (2019). Rapid phenotypic and metabolomic domestication of wild Penicillium molds on cheese. MBio, 10(5), 10-1128.
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  4. Dunn, N. A., Unni, D. R., Diesh, C., Munoz-Torres, M., Harris, N. L., Yao, E., ... & Lewis, S. E. (2019). Apollo: democratizing genome annotation. PLoS computational biology, 15(2), e1006790.
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  5. Weitemier, K., Straub, S. C., Fishbein, M., Bailey, C. D., Cronn, R. C., & Liston, A. (2019). A draft genome and transcriptome of common milkweed (Asclepias syriaca) as resources for evolutionary, ecological, and molecular studies in milkweeds and Apocynaceae. PeerJ, 7, e7649.
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  6. Patterson, E. L., Saski, C., Küpper, A., Beffa, R., & Gaines, T. A. (2019). Omics potential in herbicide-resistant weed management. Plants, 8(12), 607.
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  7. Udall, J. A., Long, E., Ramaraj, T., Conover, J. L., Yuan, D., Grover, C. E., ... & Wendel, J. F. (2019). The genome sequence of Gossypioides kirkii illustrates a descending dysploidy in plants. Frontiers in plant science, 10, 1541.
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2018 (3)

  1. Stamps, B. W., Andrade, O. C., Lyon, W. J., Floyd, J. G., Nunn, H. S., Bojanowski, C. L., ... & Stevenson, B. S. (2018). Genome sequence of a Byssochlamys sp. strain isolated from fouled B20 biodiesel. Genome announcements, 6(9), 10-1128.
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  2. Long, E., Evans, C., Chaston, J., & Udall, J. A. (2018). Genomic structural variations within five continental populations of Drosophila melanogaster. G3: Genes, Genomes, Genetics, 8(10), 3247-3253.
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  3. Gaire, R., & Wilde, H. D. (2018). Natural allelic variation in blueberry TERMINAL FLOWER 1. Plant Genetic Resources, 16(1), 59-67.
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2017 (2)

  1. Burrows, B. A., & McCubbin, A. G. (2017). Sequencing the genomic regions flanking S-linked PvGLO sequences confirms the presence of two GLO loci, one of which lies adjacent to the style-length determinant gene CYP734A50. Plant reproduction, 30, 53-67.
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  2. Kahodariya, J. H., Gajera, H. P., Golakiya, B. A., Kothari, V. V., Kheni, J. V., Sanghani, J. M., ... & Garaniya, N. H. (2017). Study of orthologous gene clusters among Aspergillus species. Bull. Env. Pharmacol. Life Sci, 6, 115-118.

2016 (1)

  1. Buels, R., Yao, E., Diesh, C. M., Hayes, R. D., Munoz-Torres, M., Helt, G., ... & Holmes, I. H. (2016). JBrowse: a dynamic web platform for genome visualization and analysis. Genome biology, 17(1), 1-12.
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2015 (1)

  1. Yu, J., & Main, D. (2015). Role of bioinformatic tools and databases in cotton research. Cotton, 57, 303-337.
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2014 (1)

  1. Jung, S., & Main, D. (2014). Genomics and bioinformatics resources for translational science in Rosaceae. Plant biotechnology reports, 8, 49-64.
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2012 (1)

  1. Wegrzyn, J. L., Main, D., Figueroa, B., Choi, M., Yu, J., Neale, D. B., ... & Abbott, A. G. (2012). Uniform standards for genome databases in forest and fruit trees. Tree genetics & genomes, 8, 549-557.
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2011 (2)

  1. Lee, T., Peace, C., Jung, S., Zheng, P., Main, D., & Cho, I. (2011, October). GenSAS—An online integrated genome sequence annotation pipeline. In 2011 4th International Conference on Biomedical Engineering and Informatics (BMEI) (Vol. 4, pp. 1967-1973). IEEE.
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  2. Lee, T., Cho, I., Peace, C., Jung, S., Zheng, P., & Main, D. (2011). Development Approach and Architecture of GenSAS: the Genome Sequence Annotation Server. In Proceedings of the International Conference on Bioinformatics & Computational Biology (BIOCOMP) (p. 1). The Steering Committee of The World Congress in Computer Science, Computer Engineering and Applied Computing (WorldComp).