Petar Penev

About

I am a computational biologist from Bulgaria. I lead the bioinformatics team at Eligo Bioscience in Paris, which I joined in 2024 as a Senior Bioinformatics Scientist. Eligo is pioneering a novel class of medicines, targeting the human microbiome.

Before Eligo, I was a postdoctoral fellow in Jill Banfield's lab at UC Berkeley, where I studied phages, extrachromosomal elements and soil microbiomes through genome-resolved metagenomics. I earned my PhD in bioinformatics at the Georgia Institute of Technology as a Fulbright scholar, working on ribosome evolution with Loren Williams and Anton Petrov.

I got into bioinformatics because I noticed a cycle of information between the wet lab and the dry lab, and I still believe it pays to know both fields equally well.

Path so far

Hover over or tap a city or a step to see what I did there.

Research

Microbiome engineering

I joined Eligo Bioscience in 2024 as a Senior Bioinformatics Scientist and have led its bioinformatics team since 2026. Eligo is pioneering a novel class of medicines, targeting the human microbiome.

Phages, archaea and soil metagenomics

In the Banfield lab I studied how phages and extrachromosomal elements (plasmids, Borgs) handle genetic information, including phage stop-codon recoding, phage-encoded ribosomal proteins and elements of Methanoperedens archaea. I also used metagenomics-informed stable isotope probing to find which soil microbes are active across depth and seasons, and worked on the structure and processing of archaeal ribosomes.

Ribosome evolution

My PhD focused on how the ribosome evolved: supersized rRNA expansion segments in Asgard archaea, tools for comparing deep sequence alignments (TwinCons) and web servers for visualizing ribosomal proteins and RNAs (ProteoVision, RiboVision2).

Earlier work

In Eric Gaucher's lab I compared phylogenetic methods for ancestral protein reconstruction. In Dolf Weijers' lab in Wageningen I searched for new interactors of the Auxin Response Factor in Arabidopsis thaliana.

Code from my papers and projects is on GitHub.

Publications

Full and up-to-date list on Google Scholar and ORCID.

Preprints

  1. The origin and evolution of archaeal Borg extrachromosomal elements Shi L.-D., Penev P.I., Kolody B.C., Miloslavich L., Lei S., Sachdeva R., … Hug L.A., Banfield J.F. bioRxiv (2026)
  2. Microbial autotrophy is widespread across soils and most prevalent in deep and saturated environments Kuhn A.N., Jaffe A.L., Penev P.I., Creamer K.E., Kolody B.C., Tasoff P.M., Voutsinos M., Pett-Ridge J., Banfield J.F. bioRxiv (2026)
  3. Engineered orthogonal translation systems from metagenomic libraries expand the genetic code Seki K., Nguyen M.T.A., Penev P.I., Banfield J.F., Isaacs F.J., Jewett M.C. bioRxiv (2025)
  4. The active subset of grassland soil microbiomes changes with soil depth, water availability and prominently features predatory bacteria and episymbionts Penev P.I., Estera-Molina K., Allen G.M., Sachdeva R., Lei S., Law K.K., Hoff J., Blazewicz S.J., Pett-Ridge J., Banfield J.F. bioRxiv (2024)first author

Peer-reviewed articles

  1. Circularization of 23S rRNA but not 16S rRNA within archaeal ribosomes Shi L.-D., Penev P.I., Nissley A.J., Nayak D.D., Sachdeva R., Cate J.H.D., Banfield J.F. Genome Biology (2026)
  2. Structure of an archaeal ribosome reveals a divergent active site and hibernation factor Nissley A.J., Shulgina Y., Kivimae R.W., Downing B.E., Penev P.I., Banfield J.F., Nayak D.D., Cate J.H.D. Nature Microbiology (2025)
  3. RiboVision2: A web server for advanced visualization of ribosomal RNAs McCann H.M., Meade C.D., Banerjee B., Penev P.I., Williams L.D., Petrov A.S. J. Mol. Biol. (2024)
  4. Methanotrophic Methanoperedens archaea host diverse and interacting extrachromosomal elements Shi L.-D., West-Roberts J., Schoelmerich M.C., Penev P.I., Chen L., Amano Y., Lei S., Sachdeva R., Banfield J.F. Nature Microbiology (2024)
  5. Chapter 5: Major biological innovations in the history of life on Earth Bozdag G.O., Szeinbaum N., Conlin P.L., Chen K., Fos S.M., Garcia A., Penev P.I., Schaible G.A., Trubl G. Astrobiology (2024)
  6. Chapter 1: The Astrobiology Primer 3.0 Schaible M.J., Szeinbaum N., Bozdag G.O., … Penev P.I., … Young A. Astrobiology (2024)
  7. Rare ribosomal RNA sequences from archaea stabilize the bacterial ribosome Nissley A.J., Penev P.I., Watson Z.L., Banfield J.F., Cate J.H.D. Nucleic Acids Research (2023)
  8. A widespread group of large plasmids in methanotrophic Methanoperedens archaea Schoelmerich M.C., Ouboter H.T., Sachdeva R., Penev P.I., Amano Y., West-Roberts J., Welte C.U., Banfield J.F. Nature Communications (2022)
  9. AbGradCon 2021: lessons in digital meetings, international collaboration, and interdisciplinarity in astrobiology Jia T.Z., Johnson-Finn K.N., Alian O.M., Bonati I., Fujishima K., Grefenstette N., Heenatigala T., Li Y., Noda N., Penev P.I., Prondzinsky P., Smith H.B. Int. J. Astrobiology (2022)
  10. Widespread stop-codon recoding in bacteriophages may regulate translation of lytic genes Borges A.L., Lou Y.C., Sachdeva R., Al-Shayeb B., Penev P.I., Jaffe A.L., Lei S., Santini J.M., Banfield J.F. Nature Microbiology (2022)
  11. Phage-encoded ribosomal protein S21 expression is linked to late-stage phage replication Chen L.-X., Jaffe A.L., Borges A.L., Penev P.I., Nelson T.C., Warren L.A., Banfield J.F. ISME Communications (2022)
  12. TwinCons: Conservation score for uncovering deep sequence similarity and divergence Penev P.I., Alvarez-Carreño C., Smith E., Petrov A.S., Williams L.D. PLoS Comp. Biol. (2021)first author
  13. Fold evolution before LUCA: Common ancestry of SH3 domains and OB domains Alvarez-Carreño C., Penev P.I., Petrov A.S., Williams L.D. Mol. Biol. Evol. (2021)
  14. ProteoVision: web server for advanced visualization of ribosomal proteins Penev P.I., McCann H.M., Meade C.D., Maddala A., Bernier C.R., Chivukula V.L., Ahmad M., Gulen B., Sharma A., Alvarez-Carreño C., Williams L.D., Petrov A.S. Nucleic Acids Research (2021)first author
  15. Supersized ribosomal RNA expansion segments in Asgard archaea Penev P.I., Fakhretaha-Aval S., Patel V.J., Cannone J.J., Gutell R.R., Petrov A.S., Williams L.D., Glass J.B. Genome Biol. Evol. (2020)first author
  16. A blueprint for academic laboratories to produce SARS-CoV-2 quantitative RT-PCR test kits Mascuch S.J., Fakhretaha-Aval S., Bowman J.C., … Penev P.I., … Williams L.D., Lieberman R.L. J. Biol. Chem. (2020)
  17. Root of the tree: The significance, evolution, and origins of the ribosome Bowman J.C., Petrov A.S., Frenkel-Pinter M., Penev P.I., Williams L.D. Chemical Reviews (2020)
  18. Profusion of G-quadruplexes on both subunits of metazoan ribosomes Mestre-Fos S., Penev P.I., Richards J.C., Dean W.L., Gray R.D., Chaires J.B., Williams L.D. PLoS ONE (2019)
  19. G-quadruplexes in human ribosomal RNA Mestre-Fos S., Penev P.I., Suttapitugsakul S., Hu M., Ito C., Petrov A.S., Wartell R.M., Wu R., Williams L.D. J. Mol. Biol. (2019)
  20. Circular permutation obscures universality of a ribosomal protein Kovacs N.A., Penev P.I., Venapally A., Petrov A.S., Williams L.D. J. Mol. Evol. (2018)
  21. Translation: The universal structural core of life Bernier C.R., Petrov A.S., Kovacs N.A., Penev P.I., Williams L.D. Mol. Biol. Evol. (2018)

Contact

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