Publications
Publication highlights
For a complete overview, check GoogleScholar.
Systematic dissection of Cas12a-mediated precision genome editing defines design principles for genome-scale variant engineering
Delhay A*, Batagui VS*, Nysten J, Troubleyn D, Vonesch SC
*these authors contributed equally
This study systematically maps the factors that determine successful Cas12a precision editing in yeast. It defines practical design rules and establishes a pooled, barcoded platform for genome-scale variant engineering and phenotyping.
From edits to insights: precision microbial engineering for systems biology
, ,
This review explores how emerging precision genome-editing approaches allow thousands of defined sequence variants to be tested systematically. We highlight how these technologies can deepen our understanding of genotype–phenotype relationships and accelerate microbial engineering.
The editable landscape of the yeast genome reveals hotspots of structural variant formation
Li S*, Vonesch SC*, Roy KR*, Szu Tu C, Steudle F, Nguyen M, Jann C, Steinmetz LM
*these authors contributed equally
By analyzing nearly 1,900 CRISPR-edited yeast genomes, this study maps where unintended structural variants are most likely to arise. It introduces SCORE, a predictive model that identifies editing-risk hotspots and helps guide safer genome engineering.
The rise and future of CRISPR-based approaches for high-throughput genomics
Vercauteren S*, Fiesack S*, Maroc L, Verstraeten N, Dewachter L, Michiels J, Vonesch SC
*equal contribution
In this review we survey CRISPR-based technologies for genome-wide functional screens, with a particular focus on CRISPR interference in microbes. We discuss their strengths, limitations, and expanding potential for dissecting complex microbial traits at scale.
An Efficient CRISPR/Cas12e System for Genome Editing in Sinorhizobium meliloti
Liu G, Wang H, Tong B, Cui Y, Vonesch SC, Dong H, Zhang D
This study develops an efficient Cas12e-based genome-editing toolkit for Sinorhizobium meliloti, a bacterium that is otherwise difficult to edit precisely. The optimized system enables more efficient engineering for both fundamental research and metabolic applications.
Fast and inexpensive whole genome sequencing library preparation from intact yeast cells
Vonesch SC#, Li S, Szu Tu C, Hennig BP, Dobrev N, Steinmetz LM#
#corresponding authors
This work introduces a scalable method for preparing whole-genome sequencing libraries directly from yeast cultures, bypassing conventional DNA extraction. The protocol reduces preparation time and cost while maintaining high-quality, unbiased sequencing data.
McQ – an open-source multiplexed SARS-CoV-2 quantification platform
Vonesch SC#, Bredikhin D, Dobrev N, Villacorta L, Kleinendorst R, Cacace E, Flock J, Frank M, Jung F, Kornienko J, Mitosch K, Osuna-Lopez M, Zimmermann J, Göttig S, Hamprecht A, Kräusslich HG, Knop M, Typas A, Steinmetz LM, Benes V#, Remans K#, Krebs AR#
#corresponding authors
Developed during the COVID-19 pandemic, McQ combines early sample barcoding with high-throughput sequencing to quantify SARS-CoV-2 across thousands of samples in parallel. The open-source approach was designed to enable scalable, low-cost testing while reducing dependence on commercial reagents.
Evolthon: A community endeavor to evolve lab evolution
Kaminski Strauss S, Schirman D, Jona G, Brooks AN, Kunjapur AM, Nguyen Ba AN, Flint A, Solt A, Mershin A, Dixit A, Yona AH, Csörgő B, Busby BP, Hennig BP, Pál C, Schraivogel D, Schultz D, Wernick DG, Agashe D, Levi D, Zabezhinsky D, Russ D, Sass E, Tamar E, Herz E, Levy ED, Church GM, Yelin I, Nachman I, Gerst JE, Georgeson JM, Adamala KP, Steinmetz LM, Rübsam M, Ralser M, Klutstein M, Desai MM, Walunjkar N, Yin N, Aharon Hefetz N, Jakimo N, Snitser O, Adini O, Kumar P, Soo Hoo Smith R, Zeidan R, Hazan R, Rak R, Kishony R, Johnson S, Nouriel S, Vonesch SC, Foster S, Dagan T, Wein T, Karydis T, Wannier TM, Stiles T, Olin-Sandoval V, Mueller WF, Bar-On YM, Dahan O, Pilpel Y
Evolthon brought together around 30 research teams worldwide to test different strategies for experimentally evolving yeast and bacteria towards improved growth at low temperature. The collaborative experiment revealed principles for effective laboratory evolution while showcasing a community-driven approach to experimental science.
Multiplexed precision genome editing with trackable genomic barcodes in yeast
Roy KR*, Smith JD*, Vonesch SC*, Lin G, Szu Tu C, Lederer AR, Chu A, Suresh S, Nguyen M, Horecka J, Tripathi A, Burnett WT, Morgan MA, Schulz J, Orsley KM, Wei W, Aiyar RS, Davis RW, Bankaitis VA, Haber JE, Salit ML, St.Onge RP, Steinmetz LM
*equal contribution
This study introduced MAGESTIC, a CRISPR-Cas9 platform that enables thousands of precisely defined genetic variants to be engineered and tracked in parallel in yeast. The technology links individual mutations to phenotypes at scale and laid the foundation for much of the lab’s current work in precision genome engineering.