Publications | ES Bioinformatics & AI Lab

2025

bioRxiv

Balanced polymorphism in a floral transcription factor underlies an ancient rhythm of daily sex alternation in avocado

J. S. Groh, M. F. Santos, E. Dios, and 7 more authors

bioRxiv, 2025

@article{groh2025avocado,
  title = {Balanced polymorphism in a floral transcription factor underlies an ancient rhythm of daily sex alternation in avocado},
  author = {Groh, J. S. and Soares dos Santos, M. F. and Avila de Dios, E. and Ackerman, G. and Solares, E. and Focht, E. and Seymour, D. and Gaut, B. S. and Arpaia, M. L. and Coop, G.},
  journal = {bioRxiv},
  year = {2025},
  doi = {10.64898/2025.12.22.695989}
}

medRxiv

PvGAP: Development of a globally-applicable, highly-multiplexed microhaplotype amplicon panel for Plasmodium vivax

A. Hubbard, E. A. Solares, L. Bradley, and 6 more authors

medRxiv, 2025

DOI Bib

@article{hubbard2025pvgap,
  title = {PvGAP: Development of a globally-applicable, highly-multiplexed microhaplotype amplicon panel for Plasmodium vivax},
  author = {Hubbard, A. and Solares, E. A. and Bradley, L. and Jeang, B. and Yewhalaw, D. and Janies, D. and Lo, E. and Yan, G. and Hemming-Schroeder, E.},
  journal = {medRxiv},
  year = {2025},
  doi = {10.1101/2025.04.30.25326751}
}

2024

Nat. Commun.

AI-driven predictive diagnostics for antimicrobial resistance forecasting

Informuta Team

Nature Communications, 2024

Contributed as ML Engineer

Bib

@article{informuta2024amr,
  title = {AI-driven predictive diagnostics for antimicrobial resistance forecasting},
  author = {Team, Informuta},
  journal = {Nature Communications},
  year = {2024},
  note = {Contributed as ML Engineer}
}

2023

Genome Res.

miRNA-like secondary structures in maize (Zea mays) genes and transposable elements correlate with small RNAs, methylation, and expression

Galen T. Martin, Edwin A. Solares, Jeanelle Guardado-Mendez, and 3 more authors

Genome Research, 2023

DOI Bib

@article{martin2023maize,
  title = {miRNA-like secondary structures in maize (Zea mays) genes and transposable elements correlate with small RNAs, methylation, and expression},
  author = {Martin, Galen T. and Solares, Edwin A. and Guardado-Mendez, Jeanelle and Muyle, Aline and Bousios, Alexandros and Gaut, Brandon S.},
  journal = {Genome Research},
  year = {2023},
  doi = {10.1101/gr.277459.122},
}

Front. Mar. Sci.

Cycle of Heat Exposure Elevate Metabolic Enzyme Genes and Alters Digestion in Mussels

G. Chan, A. Y. Gracey, E. A. Solares, and 2 more authors

Frontiers in Marine Science, 2023

DOI Bib

@article{chan2023mussels,
  title = {Cycle of Heat Exposure Elevate Metabolic Enzyme Genes and Alters Digestion in Mussels},
  author = {Chan, G. and Gracey, A. Y. and Solares, E. A. and Wherle, B. and Connor, K. M.},
  journal = {Frontiers in Marine Science},
  year = {2023},
  doi = {10.3389/fmars.2023.1120695}
}

PNAS

Sex-linked gene traffic underlies the acquisition and loss of sexually dimorphic UV color vision in Heliconius butterflies

Mahul Chakraborty, A. Guadalupe Lara, A. Dang, and 9 more authors

Proceedings of the National Academy of Sciences, 2023

DOI Bib

@article{chakraborty2023butterfly,
  title = {Sex-linked gene traffic underlies the acquisition and loss of sexually dimorphic UV color vision in Heliconius butterflies},
  author = {Chakraborty, Mahul and Guadalupe Lara, A. and Dang, A. and McCulloch, K. J. and Rainbow, D. and Carter, D. and Solares, E. A. and Said, I. and Corbett-Detig, R. and Gilbert, L. E. and Emerson, J. J. and Briscoe, A. D.},
  journal = {Proceedings of the National Academy of Sciences},
  year = {2023},
  doi = {10.1073/pnas.2301411120},
}

Insights into the domestication of avocado and potential genetic contributors to heterodichogamy

Edwin A. Solares, Abraham Morales-Cruz, Rosa Figueroa Balderas, and 6 more authors

G3: Genes, Genomes, Genetics, 2023

DOI Bib

@article{solares2023avocado,
  title = {Insights into the domestication of avocado and potential genetic contributors to heterodichogamy},
  author = {Solares, Edwin A. and Morales-Cruz, Abraham and Figueroa Balderas, Rosa and Focht, Eric and Ashworth, Vanessa E. T. M. and Minio, Andrea and Cantu, Dario and Arpaia, Mary Lu and Gaut, Brandon S.},
  journal = {G3: Genes, Genomes, Genetics},
  volume = {13},
  number = {2},
  year = {2023},
  doi = {10.1093/g3journal/jkac323},
}

2021

BMC Bioinf.

HapSolo: An optimization approach for removing secondary haplotigs during diploid genome assembly

Edwin A. Solares, Y. Tao, A. D. Long, and 1 more author

BMC Bioinformatics, 2021

DOI Bib

@article{solares2021hapsolo,
  title = {HapSolo: An optimization approach for removing secondary haplotigs during diploid genome assembly},
  author = {Solares, Edwin A. and Tao, Y. and Long, A. D. and Gaut, Brandon S.},
  journal = {BMC Bioinformatics},
  volume = {22},
  pages = {9},
  year = {2021},
  doi = {10.1186/s12859-020-03939-y},
}

2019

Nat. Plants

The population genetics of structural variants in grapevine domestication

Yongfeng Zhou, Andrea Minio, Mélanie Massonnet, and 5 more authors

Nature Plants, 2019

DOI Bib

@article{zhou2019grapevine,
  title = {The population genetics of structural variants in grapevine domestication},
  author = {Zhou, Yongfeng and Minio, Andrea and Massonnet, Mélanie and Solares, Edwin A. and Lv, Yuanda and Beridze, Tengiz and Cantu, Dario and Gaut, Brandon S.},
  journal = {Nature Plants},
  volume = {5},
  pages = {965--979},
  year = {2019},
  doi = {10.1038/s41477-019-0507-8},
}

2018

Rapid Low-Cost Assembly of the Drosophila melanogaster Reference Genome Using Low-Coverage, Long-Read Sequencing

Edwin A. Solares, Mahul Chakraborty, Danny E. Miller, and 5 more authors

G3: Genes, Genomes, Genetics, 2018

DOI Bib

@article{solares2018drosophila,
  title = {Rapid Low-Cost Assembly of the Drosophila melanogaster Reference Genome Using Low-Coverage, Long-Read Sequencing},
  author = {Solares, Edwin A. and Chakraborty, Mahul and Miller, Danny E. and Kalsow, Shannon and Hall, Kate and Perera, Anoja G. and Emerson, J. J. and Hawley, R. Scott},
  journal = {G3: Genes, Genomes, Genetics},
  volume = {8},
  number = {10},
  pages = {3143--3154},
  year = {2018},
  doi = {10.1534/g3.118.200162},
}

2017

MBE

Rapid Functional and Sequence Differentiation of a Tandemly Repeated Species-Specific Multigene Family in Drosophila

Bryan D. Clifton, Pablo Librado, Shu-Dan Yeh, and 4 more authors

Molecular Biology and Evolution, 2017

DOI Bib

@article{clifton2017drosophila,
  title = {Rapid Functional and Sequence Differentiation of a Tandemly Repeated Species-Specific Multigene Family in Drosophila},
  author = {Clifton, Bryan D. and Librado, Pablo and Yeh, Shu-Dan and Solares, Edwin S. and Real, Darlene A. and Jayasekera, Sunetra U. and Ranz, José M.},
  journal = {Molecular Biology and Evolution},
  year = {2017},
  doi = {10.1093/molbev/msw212}
}