Juan C. Villada, Ph.D.

• Villada JC, Vasquez YM, Szabó G, Whittaker-Walker E, Romero MF, Qin S, Varghese N, Eloe-Fadrosh EA, Kyrpides NC, SymGs data consortium, Visel A, Woyke T, & Schulz F (2026). A genomic catalog of Earth’s bacterial and archaeal symbionts.
  Nature Biotechnology. Link · Published online 31 August 2026.

• Related Research Briefing: Machine learning interprets genome sequences to map possible microbial symbionts.
  Nature Biotechnology. Link · Published online 2 September 2026.

• Bushnell B, Schulz F, Villada JC (2026). RandomReadsMG: Rapid, realistic metagenome simulation at terabase scale for benchmarking and experimental design.
  Cell Genomics. Link · 101384. Published online 5 October 2026.

• Bushnell B, Villada JC (2026). Deployable high-fidelity metagenome binning at scale with QuickBin.
  Communications Biology. Link · 9:1135.

• Vasquez YM, Nardi T, Terasaki GM, Byl P, Brůna T, Villada JC, Romero-Gutiérrez MF, Mock T, James TY, GVMAGs data consortium, Woyke T, & Schulz F (2026). Genomic catalogue of giant viruses reveals expanded diversity and functional potential.
  Nature Microbiology. Link · 11(9):2634–2646.

• 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 · 17:2194.

• 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 · 54(2):gkaf1419.

• 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. Link · 13(1):222.

• 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

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

• Villada JC, Duran MF, Lim CK, Stein LY & 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

Preprints

• Bushnell B, Bowers RM, Villada JC (2026). GradeBins: a comprehensive framework to augment metagenomic bin quality control.
  bioRxiv. Link · (preprint, posted 12 March 2026).