About me

I’m a Postdoctoral Associate in Feng Zhang’s Lab at the Broad Institute/MIT. I completed my PhD in the Baym Lab through the Harvard Systems Biology Graduate Program, where I studied mobile genetic elements in bacteria, at the intersection of method development, microbiology, and genomics.

My work spans both experimental and computational biology, with expertise in bioinformatics, including genomics, metagenomics, RNA and protein homology, and pipeline development in HPC environments. I’m particularly interested in integrating wet lab and computational methods to better understand and engineer biological systems. Across projects, my research has involved advanced methods in data analysis, machine learning, and data visualization.

Publications

2025

TIGR-Tas: A family of modular RNA-guided DNA-targeting systems in prokaryotes and their viruses
Guilhem Faure*, Makoto Saito*, Max E Wilkinson*, Natalia Quinones-Olvera, Peiyu Xu, Daniel Flam-Shepherd, Stephanie Kim, Nishith Reddy, Shiyou Zhu, Lilia Evgeniou, Eugene V Koonin, Rhiannon K Macrae, Feng Zhang
Science (2025)

Efficient and robust search of microbial genomes via phylogenetic compression
Karel Břinda, Leandro Lima, Simone Pignotti, Natalia Quinones-Olvera, Kamil Salikhov, Rayan Chikhi, Gregory Kucherov, Zamin Iqbal, Michael Baym
Nature Methods (2025)

Pitfalls of bacterial pan-genome analysis approaches: a case study of M. tuberculosis and two less clonal bacterial species
Maximillian G Marin, Natalia Quinones-Olvera, Christoph Wippel, Mahboobeh Behruznia, Brendan M Jeffrey, Michael Harris, Brendon C Mann, Alex Rosenthal, Karen R Jacobson, Robin M Warren, Heng Li, Conor J Meehan, Maha R Farhat
Bioinformatics (2025)

RNA-guided nucleases enable a gene drive of insertion sequences in plasmids
Kepler S Mears*, Fernando W Rossine*, Natalia Quinones-Olvera, Célia Souque, Michael Baym
bioRxiv (2025)

Phage DisCo: targeted discovery of bacteriophages by co-culture
Eleanor A Rand, Natalia Quinones-Olvera, Kesther DC Jean, Carmen Hernandez-Perez, Sian V Owen, Michael Baym
MSystems (2025)

Complete genome sequence of a virulent barcoded Mycobacterium tuberculosis str. Erdman commonly used for non-human primate infection studies
Maximillian G Marin, Michael R Chase, Natalia Quinones-Olvera, Shoko Wakabayashi, Douaa Mugahid, Sarah M Fortune, Maha R Farhat, Michael C Chao
Microbiology Resource Announcements (2025)

2024

Diverse and abundant phages exploit conjugative plasmids
Natalia Quinones-Olvera, Siân V Owen, Lucy M McCully, Maximillian G Marin, Eleanor A Rand, Alice C Fan, Oluremi J Martins Dosumu, Kay Paul, Cleotilde E Sanchez Castaño, Rachel Petherbridge, Jillian S Paull, Michael Baym
Nature Communications (2024)

(Thesis) New Methods to Explore Mobile Genetic Elements in Bacteria
Natalia Quinones-Olvera
Harvard University (2024)

2021

Prophages encode phage-defense systems with cognate self-immunity
Siân V Owen, Nicolas Wenner, Charles L Dulberger, Ella V Rodwell, Arthur Bowers-Barnard, Natalia Quinones-Olvera, Daniel J Rigden, Eric J Rubin, Ethan C Garner, Michael Baym, Jay CD Hinton
Cell Host & Microbe (2021)

2019

The fitness landscape of the African Salmonella Typhimurium ST313 strain D23580 reveals unique properties of the pBT1 plasmid
Rocío Canals, Roy R Chaudhuri, Rebecca E Steiner, Siân V Owen, Natalia Quinones-Olvera, Melita A Gordon, Michael Baym, Michael Ibba, Jay CD Hinton
PLoS Pathogens (2019)

2018

Non‐coding RNA analysis using the Rfam database
Ioanna Kalvari, Eric P Nawrocki, Joanna Argasinska, Natalia Quinones‐Olvera, Robert D Finn, Alex Bateman, Anton I Petrov
Current Protocols in Bioinformatics (2018)

Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families
Ioanna Kalvari, Joanna Argasinska, Natalia Quinones-Olvera, Eric P Nawrocki, Elena Rivas, Sean R Eddy, Alex Bateman, Robert D Finn, Anton I Petrov
Nucleic Acids Research (2018)

2016

(Thesis) Implicaciones evolutivas de la plasticidad del RNA
Natalia Quinones-Olvera
Universidad Nacional Autónoma de México (2016)

Training