ES Bioinformatics & AI Lab

We develop and apply computational methods to address critical challenges in food security, species conservation, and climate resilience.

Our research combines machine learning, computer vision, and genomics to understand how organisms adapt to changing environments and to develop tools that enable sustainable agriculture.

Research Focus

AI for Aquaculture

Computer vision and genomic approaches for fish farming, including AI-assisted sex determination in sturgeon to improve sustainability and reduce costs.

Crop Genomics

Understanding the genetic basis of adaptation in economically important crops including maize, avocado, and grapevine to inform breeding programs.

RNA Biology

Discovering regulatory mechanisms controlling gene expression in plants, with implications for crop improvement and stress tolerance.

Antimicrobial Resistance

Deep learning approaches to predict and forecast antimicrobial resistance patterns from genomic data.

Funding

Our research is supported by:

USDA NIFA Western Regional Aquaculture Center
NSF ACCESS Computing Allocations

Join Us

We are recruiting graduate students, undergraduates, and postdocs interested in computational biology, machine learning, and agricultural genomics.

Learn more about opportunities

Contact

Email: esolares [at] ucsd [dot] edu

Location: CSE Building, UC San Diego, La Jolla, CA 92093

news

Apr 23, 2025	Our Sturgeon AI research featured in SDSC, ACCESS-CI, and SeafoodSource - “New AI Technology Aims to Revolutionize Fish Farming”
Oct 20, 2024	Joined Informuta, Inc. as Machine Learning Engineer, applying AI solutions to industry challenges alongside academic research.
Jun 15, 2024	Awarded ~$465,000 grant from USDA NIFA Western Regional Aquaculture Center as PI to develop AI technology for sturgeon aquaculture.
Feb 23, 2024	Maize RNA structures research featured in SDSC press release - “Supercomputing Simulations in Multiyear Study of Corn to Address Food Insecurity”
Jan 15, 2024	Expanded teaching role at Halicioglu Data Science Institute (HDSI) at UC San Diego, teaching graduate-level big data analytics and machine learning courses.

selected publications

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},
}

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},
}

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},
}

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},
}

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},
}