Research

Research Interests

Coding DNA sequence (CDS) architecture <-> protein design

Evolutionary Systems Biology

Large-scale (Meta)genomics

Microbial symbionts

Microbial Metabolism (Methanotrophy)

Publications

  • Shrestha B, Romero MF, Villada JC, Plastid MAG Consortium, Blaby-Haas CE, & Schulz F (2026). Global metagenomics reveals plastid diversity and unexplored algal lineages. Nature Communications. Link

  • Ahrendt SR, Haridas S, Stong S, Salamov A, Steindorff A, LaButti K, Riley R, Shabalov I, Lukashin I, Dusheyko S, Schulz F, Romero MF, Villada JC, Grigoriev IV, & Mondo SJ (2026). Comparative mitogenomics of kingdom Fungi–evolutionary insights and metagenomic applications. Nucleic Acids Research. Link

  • Villada JC, Yumary M Vasquez, Gitta Szabo, Ewan Whittaker-Walker, Miguel F Romero, Sarina Qin, Neha Varghese, Emiley A Eloe-Fadrosh, Nikos C Kyrpides, SymGs data consortium, Axel Visel, Tanja Woyke, & Frederik Schulz (2026). A genomic catalog of Earth’s bacterial and archaeal symbionts. bioRxiv Link

  • Bushnell B, Villada JC (2026). Deployable high-fidelity metagenome binning at scale with QuickBin. bioRxiv Link

  • Bushnell B, Schulz F, Villada JC (2026). Rapid terabase-scale simulation of realistic metagenomes for experimental design and pathogen detection with RandomReadsMG. bioRxiv Link

  • Bowers RM, Bennett S, Riley R, Villada JC, Da Silva IR, Woyke T, & Frank AC (2025). Host species and geographic location shape microbial diversity and functional potential in the conifer needle microbiome. Microbiome, 13(1):222. Link

  • Dutkiewicz Z, Singleton CM, Sereika M, Villada JC, Mussig AJ, Chuvochina M, …, & Rinke C (2025). Proposal of Patescibacterium danicum gen. nov., sp. nov. in the ubiquitous bacterial phylum Patescibacteriota phyl. nov. ISME Communications. Link

  • Vasquez YM, Nardi T, Terasaki GM, Byl P, Bruna T, Villada JC, …, & Schulz F (2025). Genome-resolved expansion of Nucleocytoviricota and Mirusviricota reveals new diversity, functional potential, and biotechnological applications. bioRxiv. Link

  • Villada JC & Schulz F (2022). The endosymbiotic box of protective tricks. Nature Reviews Microbiology. Link

  • Villada JC, Duran MF, Lim CK & Lee PKH (2022). Integrative genome-scale metabolic modeling reveals versatile metabolic strategies for methane utilization in Methylomicrobium album BG8. mSystems. Link

  • Villada JC, Duran MF & Lee PKH (2020). Interplay between position-dependent codon usage bias and hydrogen bonding at the 5’ end of ORFeomes. mSystems. Link

  • Villada JC, Duran MF & Lee PKH (2019). Genomic evidence for simultaneous optimization of transcription and translation through codon variants in the pmoCAB operon of type Ia methanotrophs. mSystems. Link

  • Lim CK, Villada JC, Chalifour A, Duran MF, Lu H & Lee PKH (2019). Designing and engineering Methylorubrum extorquens AM1 for itaconic acid production. Frontiers in Microbiology. Link

  • Lu H, Villada JC & Lee PKH (2018). Modular metabolic engineering for biobased chemical production. Trends in Biotechnology. Link

  • Villada JC, Brustolini OJB & da Silveira WB (2017). Integrated analysis of individual codon contribution to protein biosynthesis reveals a new approach to improving the basis of rational gene design. DNA Research. Link

  • Diniz RHS, Villada JC, Alvim MCT, et al. (2017). Transcriptome analysis of the thermotolerant yeast Kluyveromyces marxianus CCT 7735 under ethanol stress. Applied Microbiology and Biotechnology. Link

Awards

(2024) Recognition of Excellence Award. Lawrence Berkeley National Laboratory. "Excellent delivery of IAC talk." Nominated by Kjiersten Fagnan. Berkeley, CA, USA

(2023) Recognition of Excellence Award. Lawrence Berkeley National Laboratory. "In recognition of exceptional and voluntary efforts toward development and writing of the new JGI Strategic Plan." Nominated by Axel Visel. Berkeley, CA, USA

(2018) Best of the Best Award, B4B Challenge Big Data for Business. Hong Kong Science & Technology Park. Hong Kong SAR

(2017) Chow Yei Ching School of Graduate Studies Entrance Scholarship. Research Grants Council. Hong Kong SAR

(2016) EMBL Corporate Partnership Programme Fellowship. European Molecular Biology Laboratory. Heidelberg, Germany

(2016) Hong Kong PhD Fellowship (HKPFS). Research Grants Council. Hong Kong SAR

(2013) Scholarship for MSc Studies in Brazil. Organization of American States. Washington, DC

(2012) Laureate Thesis Award (BSc). Universidad del Valle. Colombia

Education

PhD. Energy and Environment. (2021) City University of Hong Kong. Research: Genomics and Systems Biology of Aerobic Methanotrophs.

MSc. Agricultural Microbiology. (2016) Universidade Federal de Viçosa. Research: Individual Codon Contribution to Protein Biosynthesis in Yeast.

BSc. Agricultural Engineering. (2013) Universidad del Valle. Research: Comparative Genomics of Nitrogen Fixing Bacteria.

Contact

jvillada (AT) lbl (DOT) gov

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