Publications
2024
What is new in FungiDB: a web-based bioinformatics platform for omics-scale data analysis for fungal and oomycete species.
Basenko, E. Y., Shanmugasundram, A., Böhme, U., Starns, D., Wilkinson, P. A., Davison, H. R., . . . Jones, A. (2024). What is new in FungiDB: a web-based bioinformatics platform for omics-scale data analysis for fungal and oomycete species.. Genetics, iyae035. doi:10.1093/genetics/iyae035
2023
VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center in 2023.
Alvarez-Jarreta, J., Amos, B., Aurrecoechea, C., Bah, S., Barba, M., Barreto, A., . . . Zheng, J. (2023). VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center in 2023.. Nucleic acids research, gkad1003. doi:10.1093/nar/gkad1003
High-quality co-expression networks for accurate gene function predictions in the fungal cell factory<i>Aspergillus niger</i>and beyond
2022
VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center
Amos, B., Aurrecoechea, C., Barba, M., Barreto, A., Basenko, E. Y., Bazant, W., . . . Zheng, J. (2022). VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center. NUCLEIC ACIDS RESEARCH, 50(D1), D898-D911. doi:10.1093/nar/gkab929
2021
Versatile cell-based assay for measuring DNA alkylation damage and its repair
Li, Y., Mao, P., Basenko, E. Y., Lewis, Z., Smerdon, M. J., & Czaja, W. (2021). Versatile cell-based assay for measuring DNA alkylation damage and its repair. Scientific Reports, 11(1). doi:10.1038/s41598-021-97523-w
Versatile cell-based assay for measuring DNA alkylation damage and its repair
2020
Growing a circular economy with fungal biotechnology: a white paper.
Meyer, V., Basenko, E. Y., Benz, J. P., Braus, G. H., Caddick, M. X., Csukai, M., . . . Wösten, H. A. B. (2020). Growing a circular economy with fungal biotechnology: a white paper.. Fungal biology and biotechnology, 7, 5. doi:10.1186/s40694-020-00095-z
2018
Sharing mutants and experimental information prepublication using FgMutantDb (https://scabusa.org/FgMutantDb)
Baldwin, T. T., Basenko, E., Harb, O., Brown, N. A., Urban, M., Hammond-Kosack, K. E., & Bregitzer, P. P. (2018). Sharing mutants and experimental information prepublication using FgMutantDb (https://scabusa.org/FgMutantDb). FUNGAL GENETICS AND BIOLOGY, 115, 90-93. doi:10.1016/j.fgb.2018.01.002
FungiDB: An Integrated Bioinformatic Resource for Fungi and Oomycetes
Basenko, E. Y., Pulman, J. A., Shanmugasundram, A., Harb, O. S., Crouch, K., Starns, D., . . . Hertz-Fowler, C. (2018). FungiDB: An Integrated Bioinformatic Resource for Fungi and Oomycetes. JOURNAL OF FUNGI, 4(1). doi:10.3390/jof4010039
EuPathDB: The Eukaryotic Pathogen Genomics Database Resource.
Warrenfeltz, S., Basenko, E. Y., Crouch, K., Harb, O. S., Kissinger, J. C., Roos, D. S., . . . Silva-Franco, F. (2018). EuPathDB: The Eukaryotic Pathogen Genomics Database Resource.. In Unknown Book (Vol. 1757, pp. 69-113). doi:10.1007/978-1-4939-7737-6_5
2017
EuPathDB: the eukaryotic pathogen genomics database resource
Aurrecoechea, C., Barreto, A., Basenko, E. Y., Brestelli, J., Brunk, B. P., Cade, S., . . . Zheng, J. (2017). EuPathDB: the eukaryotic pathogen genomics database resource. NUCLEIC ACIDS RESEARCH, 45(D1), D581-D591. doi:10.1093/nar/gkw1105
2016
Histone H1 Limits DNA Methylation in <i>Neurospora crassa</i>
Seymour, M., Ji, L., Santos, A. M., Kamei, M., Sasaki, T., Basenko, E. Y., . . . Lewis, Z. A. (2016). Histone H1 Limits DNA Methylation in <i>Neurospora crassa</i>. G3-GENES GENOMES GENETICS, 6(7), 1879-1889. doi:10.1534/g3.116.028324
Histone H1 limits DNA methylation in<i>Neurospora crassa</i>
The LSH/DDM1 Homolog MUS-30 Is Required for Genome Stability, but Not for DNA Methylation in <i>Neurospora crassa</i>
Basenko, E. Y., Kamei, M., Ji, L., Schmitz, R. J., & Lewis, Z. A. (2016). The LSH/DDM1 Homolog MUS-30 Is Required for Genome Stability, but Not for DNA Methylation in <i>Neurospora crassa</i>. PLOS GENETICS, 12(1). doi:10.1371/journal.pgen.1005790
2015
Genome-wide redistribution of H3K27me3 is linked to genotoxic stress and defective growth
Basenko, E. Y., Sasaki, T., Ji, L., Prybol, C. J., Burckhardt, R. M., Schmitz, R. J., & Lewis, Z. A. (2015). Genome-wide redistribution of H3K27me3 is linked to genotoxic stress and defective growth. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 112(46), E6339-E6348. doi:10.1073/pnas.1511377112
2013
Telomeres are guardians of chromosomal integrity
Basenko, E. Y. (n.d.). Telomeres are guardians of chromosomal integrity. Postdoc Journal. doi:10.14304/surya.jpr.v1n1.9
2011
Recombination Can either Help Maintain Very Short Telomeres or Generate Longer Telomeres in Yeast Cells with Weak Telomerase Activity
Basenko, E., Topcu, Z., & McEachern, M. J. (2011). Recombination Can either Help Maintain Very Short Telomeres or Generate Longer Telomeres in Yeast Cells with Weak Telomerase Activity. EUKARYOTIC CELL, 10(8), 1131-1142. doi:10.1128/EC.05079-11
2010
Arabidopsis Genome Initiative
Katam, R., Panthee, D., Basenko, E., Bandopadhyay, R., Basha, S., Eswaran, K., & Kole, C. (2010). Arabidopsis Genome Initiative. In Principles and Practices of Plant Genomics, Volume 3 (pp. 175-204). Science Publishers. doi:10.1201/9781439845523-7
Whole Genome Sequencing
Parida, S., & Mohapatra, T. (2010). Whole Genome Sequencing. In Principles and Practices of Plant Genomics, Volume 3 (pp. 120-174). Science Publishers. doi:10.1201/9781439845523-6
2009
Telomeric circles are abundant in the <i>stn1-M1</i> mutant that maintains its telomeres through recombination
Basenko, E. Y., Cesare, A. J., Iyer, S., Griffith, J. D., & McEachern, M. J. (2010). Telomeric circles are abundant in the <i>stn1-M1</i> mutant that maintains its telomeres through recombination. NUCLEIC ACIDS RESEARCH, 38(1), 182-189. doi:10.1093/nar/gkp814
2006
Effects of S6-strain <i>Mycoplasma gallisepticum</i> inoculation at ten, twenty-two, or forty-five weeks of age on the blood characteristics of commercial egg-laying hens
Peebles, E. D., Basenko, E. Y., Branton, S. L., Whitmarsh, S. K., & Gerard, P. D. (2006). Effects of S6-strain <i>Mycoplasma gallisepticum</i> inoculation at ten, twenty-two, or forty-five weeks of age on the blood characteristics of commercial egg-laying hens. POULTRY SCIENCE, 85(11), 2012-2018. doi:10.1093/ps/85.11.2012
Effects of S6-strain <i>Mycoplasma gallisepticum</i> inoculation at ten, twenty-two, or forty-five weeks of age on the egg yolk composition of commercial egg-laying hens
Peebles, E. D., Basenko, E. Y., Branton, S. L., Whitmarsh, S. K., Maurice, D. V., & Gerard, P. D. (2006). Effects of S6-strain <i>Mycoplasma gallisepticum</i> inoculation at ten, twenty-two, or forty-five weeks of age on the egg yolk composition of commercial egg-laying hens. POULTRY SCIENCE, 85(8), 1502-1508. doi:10.1093/ps/85.8.1502
Effects of S6-strain <i>Mycoplasma gallisepticum</i> inoculation at 10, 22, or 45 weeks of age on the digestive and reproductive organ characteristics of commercial egg-laying hens
Peebles, E. D., Baseako, E. Y., Branton, S. L., Whitmarsh, S. K., & Gerard, P. D. (2006). Effects of S6-strain <i>Mycoplasma gallisepticum</i> inoculation at 10, 22, or 45 weeks of age on the digestive and reproductive organ characteristics of commercial egg-laying hens. POULTRY SCIENCE, 85(5), 825-830. doi:10.1093/ps/85.5.825
2005
Effects of S6-strain <i>Mycoplasma gallisepticum</i> inoculation at ten, twenty-two, or forty-five weeks of age on the performance characteristics of commercial egg laying hens
Basenko, E. Y., Peebles, E. D., Branton, S. L., Whitmarsh, S. K., & Gerard, P. D. (2005). Effects of S6-strain <i>Mycoplasma gallisepticum</i> inoculation at ten, twenty-two, or forty-five weeks of age on the performance characteristics of commercial egg laying hens. POULTRY SCIENCE, 84(11), 1663-1670. doi:10.1093/ps/84.11.1663