More Lab Members:

• Angel Montes: Undergraduate student (2023-Present)

• Dayton Klopman: Undergraduate student (2024-Present)

• Edwin Martinez: Undergraduate student (2025-Present)

• Melika Soltani: Undergraduate student (2025-Present)

• Destiny Canchola: Undergraduate student (2025-Present)

Alumni:

• Undergraduate students (2024-2025): Hend Ali, Ziyue Xue, Roxanna Ward

• Undergraduate students (2022-2023): Urta Berani, Eunkyu Bang, Jongbum Won

• Internship (2021-2023): Yunseol Park, Jeesu Park

Grants and Awards:

• National Institutes of Health (NIH)

  • Award Number: 1R16AI184350-01 (2024–2028)

  • Project Title: Surveillance of drug-resistant bacteria in resource-limited settings: a focus on cost-effective long-read sequencing of eyedrop-associated P. aeruginosa and locally sourced metagenomic samples

  • Principal Investigator: Dr. Hyunjin Shim

• American Society for Microbiology: Peggy Cotter Travel Award (2025)

• CSUF: Claude C. Laval Jr Award for Innovative Technology and Research (2024-2025)

• CSUF: Dean's Faculty Mini-Grant Funding (2023)

• CSUBIOTECH: Faculty Travel Grant Program (2023)

Selected Publications:

• H. Shim. Self-assembling T7 phage syringes with modular genomes for targeted delivery of penicillin against β-lactam-resistant Escherichia coli. BMC biotechnol 25:1, 63 (2025).

• B. Hunter, T. Cromwell, H. Shim. Nanopore sequencing from protozoa to phages: decoding biological information on a string of biochemical molecules into human-readable signals. Comput. Struct. Biotechnol. J. 27, 440-450 (2025).

• H. Shim. NAD: Noise-augmented direct sequencing of target nucleic acids by augmenting with noise and selective sampling. F1000Research, 14:423 (2025).

• J. Lee, B. Hunter, H. Shim. A pangenome analysis of ESKAPE bacteriophages: the underrepresentation may impact machine learning models. Front. Mol. Biosci. 11:1395450 (2024).

• Y. Park, J. Lee, H. Shim. Sequencing, fast and slow: profiling microbiomes in human samples with nanopore sequencing. Appl. Biosci. 2:3, 437-458 (2023).

• H. Park, J. Won, Y. Park, E. T. Anzaku, J. Vankerschaver, A. Van Messem, W. De Neve, H. Shim. CRISPR-Cas-Docker: Web-based in silico docking and machine learning-based classification for crRNAs and Cas proteins. BMC bioinformatics 24:1, 167 (2023). 

• H. Shim. Three innovations of next-generation antibiotics: evolvability, specificity, and non-immunogenicity. Antibiotics 12:2, 204 (2023).

• H. Park*, Y. Park*, U. Berani, E. Bang, J. Vankerschaver, A. Van Messem, W. De Neve, H. Shim. In silico optimization of RNA-protein interactions for CRISPR-Cas13-based antimicrobials. Biology Direct 17:1, 1-16 (2022). *authors contributed equally

• H. Shim. Investigating the genomic background of CRISPR-Cas genomes for CRISPR-based antimicrobials. Evol. Bioinform. 18, 11769343221103887 (2022). 

• H. Park, Y. Park, J. Vankerschaver, A. Van Messem, W. De Neve, H. Shim. Rethinking protein drug design with highly accurate structure prediction of anti-CRISPR proteins. Pharmaceuticals 15:3, 310 (2022).

• H. Shim, H. Shivram, S. Lei, J.A. Doudna, J.F. Banfield. Diverse ATPase proteins in mobilomes constitute a large potential sink for prokaryotic host ATP. Front. Microbiol. 12, 691847 (2021).

• H. Shim. Futuristic methods in virus genome evolution using the Third-Generation DNA sequencing and artificial neural networks (invited chapter in Global Virology volume III: Virology in the 21st Century, edited by Shapshak P.). Springer International Publishing (2019).

• H. Shim. Feature learning of virus genome evolution with the nucleotide skip-gram neural networks (invited paper for Special Collection: Algorithm Development for Evolutionary Biological Computation). Evol. Bioinform. 15, 1176934318821072 (2019).