About

Ido Golding is a Professor of Physics and an Affiliate Professor of Microbiology at the University of Illinois Urbana-Champaign. His research focuses on the biophysical aspects of microbiology, particularly involving bacteriophysics, which explores the physical principles underlying bacterial and viral behaviors. His work integrates physics and microbiology to better understand cellular processes and microbial interactions. Throughout his career, Professor Golding has contributed to the understanding of microbial dynamics through experimental and theoretical approaches. His lab has a history of collaboration with researchers from various institutions, including the Weizmann Institute of Science, Harvard University, and Baylor College of Medicine, among others. His research aims to elucidate the physical mechanisms that govern microbial life, with implications for microbiology, biophysics, and related fields.

Research topics

• Biology
• Genetics
• Artificial Intelligence
• Computer Science
• Algorithm
• Computational biology
• Biological system
• Mathematics
• Cell biology
• Cancer research
• Virology
• Statistics
• Immunology

Selected publications

• Single-phage profiling illuminates viral individuality during cell fate determination

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-02-20

  articleOpen accessSenior authorCorresponding

  SUMMARY The choice between cell death (lysis) and viral dormancy (lysogeny) following bacteriophage infection serves as a founding paradigm for the emergence of cellular heterogeneity in a genetically uniform population. The determination of host fate arises through the stochastic transcription from multiple viral genomes present within each cell, but this activity remains hidden from empirical interrogation, which typically stops at the whole-cell level. Here we use parallel sequential fluorescence in situ hybridization (par-seqFISH), followed by spatial clustering of phage-encoded transcripts within each cell, to profile the transcriptional activity of individual phages during synchronized infection of Escherichia coli ( E. coli ) by bacteriophage lambda. At the whole-cell level, transcription kinetics capture the developmental choice between lysis and lysogeny, and further demonstrate that viral replication is required for the emergence of diverging fate decisions. Zooming in to the single-phage level illuminates an individuality of viral activity during infection. We find that, while cells pursuing lysogeny display consensus activity of all in-habiting phages, lytic cells may contain phages that exhibit lysogenic activity. These findings support an earlier suggestion that consensus among coinfecting phages is required for cell dormancy. More broadly, our results highlight the need to identify how whole-cell behavior emerges from the activity of physically distinct copies of the same genetic circuit.

  PublisherOA PDFDOI

• Cell Growth and Division Shape mRNA–Protein Correlations

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-05-06

  articleOpen access

  1 Abstract Correlations between cellular variables, such as gene-expression levels, provide insights into regulatory mechanisms. We focus here on correlations between mRNA and protein levels and re-examine previously derived analytical predictions. We test this prediction on single-cell E. coli data and see substantial disagreement. We hypothesize that this discrepancy arises from the assumption of constant cell volume and develop a theoretical framework for mRNA–protein correlations in growing and dividing cells. Within this framework, we derive an analytical expression for mRNA– protein correlations and show that explicit incorporation of growth and division substantially alters these correlations. The resulting relation is invariant to upstream transcriptional dynamics, and we validate it using stochastic simulations across multiple gene-regulatory architectures. Finally, we show that the derived predictions are consistent with the E. coli data.

  PublisherOA PDFDOI

• Phage-encoded small RNA hijacks host replication machinery to support the phage lytic cycle

  Molecular Cell · 2025-12-01 · 6 citations

  articleOpen access

  Bacteriophages (phages) are major drivers of bacterial population dynamics, yet the significance of post-transcriptional regulation during infection remains largely unexplored. Central to this regulatory layer are small RNAs (sRNAs), which regulate target mRNAs via base-pairing, typically facilitated by RNA chaperones such as Hfq. Here, we applied RNA interaction by ligation and sequencing (RIL-seq) to comprehensively map the in vivo RNA-RNA interaction network in Escherichia coli during phage lambda infection. This analysis revealed extensive reprogramming of E. coli-E. coli interactions, phage-specific lambda-lambda interactions, and interkingdom interactions between phage and host RNAs. Among these, we identified a phage-encoded sRNA, phage replication enhancer sRNA (PreS), embedded within the early left operon. PreS regulates essential host genes, including dnaN, which encodes the DNA polymerase β sliding clamp. This regulation enhances DNA replication and fine-tunes the phage lytic cycle. These findings uncover an RNA-level regulatory layer in phage-host interactions and demonstrate how a phage-encoded sRNA can hijack host replication machinery to optimize infection.

  PublisherDOI

• Cytoplasmic localization of the mRNA encoding actin regulator, Serendipity-α, promotes adherens junction assembly and nuclear repositioning

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-07-31

  preprintOpen access

  embryos ~70% of mRNAs localize to specific sites in the cytoplasm, but the functional significance of this mRNA localization is largely unknown. During the process of embryo cellularization, mRNA encoding Serendipity-α (Sry-α), an actin filament (F-actin) binding protein, moves apically, concentrating near centrosomes. Transport is mediated by the Egl/BicD/Dynein complex and requires two stem loops in the 3'UTR of the mRNA, which serve as localization signals. mRNA localization is dispensable for Sry-α function at cleavage furrows in early cellularization but is necessary for repositioning nuclei in late cellularization. Sry-α protein promotes assembly of cortical F-actin and apical spot adherens junctions (AJs) in late cellularization, and these AJs contribute to nuclear repositioning. We suggest that mRNA localization restricts cytoskeletal functions in late cellularization to regulate nuclear repositioning in preparation for the tissue morphogenesis events that immediately follow.

  PublisherOA PDFDOI

• Reducing Cofilin dosage makes embryos resilient to heat stress

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-01-03 · 2 citations

  preprintOpen access

  Abstract In addition to regulating the actin cytoskeleton, Cofilin also senses and responds to environmental stress. Cofilin can promote cell survival or death depending on context. Yet, many aspects of Cofilin’s role in survival need clarification. Here, we show that exposing early Drosophila embryos to mild heat stress (32°C) induces a Cofilin-mediated Actin Stress Response and upregulation of heat- and ER-stress response genes. However, these responses do not alleviate the negative impacts of heat exposure. Instead, heat stressed embryos show downregulation of hundreds of developmental genes, including determinants of the embryonic body plan, and are less likely to hatch as larvae and adults. Remarkably, reducing Cofilin dosage blunts induction of all stress response pathways, mitigates downregulation of developmental genes, and completely rescues survival. Thus, Cofilin intersects with multiple stress response pathways, and modulates the transcriptomic response to heat stress. Strikingly, Cofilin knockdown emerges as a potent pro-survival manipulation for embryos.

  PublisherOA PDFDOI

• Measurement of bacteriophage infection kinetics in optically trapped, motile E. coli cells

  2024-10-02

  article

  We use a combination of optical trapping, microfluidics, and fluorescence microscopy to track individual, motile E. coli cells during infection by fluorescently labeled bacteriophages. Dual-trap optical tweezers immobilize swimming cells in a flow chamber, into which phages can be perfused. We measure the absorption of phages onto the cell surface with fluorescence imaging, while simultaneously monitoring the cell’s flagellar rotation with the optical traps. Utilizing the flagellar rotation frequency as a proxy for proton motive force, we examine phage-induced changes to E. coli’s membrane potential. These measurements reveal perturbations to host membrane integrity by phage attachment, followed by its recovery. This technique allows us to illuminate for the kinetics of viral infection of cells at the level of individual phages and bacteria.

  PublisherDOI

• Transcription–replication interactions reveal bacterial genome regulation

  Nature · 2024-01-24 · 47 citations

  articleOpen access
  PublisherOA PDFDOI

• Using bacterial population dynamics to count phages and their lysogens

  Nature Communications · 2024-09-06 · 31 citations

  articleOpen accessSenior author

  Traditional assays for counting bacteriophages and their lysogens are labor-intensive and perturbative to the host cells. Here, we present a high-throughput infection method in a microplate reader, where the growth dynamics of the infected culture is measured using the optical density (OD). We find that the OD at which the culture lyses scales linearly with the logarithm of the initial phage concentration, providing a way of measuring phage numbers over nine orders of magnitude and down to single-phage sensitivity. Interpreting the measured dynamics using a mathematical model allows us to infer the phage growth rate, which is a function of the phage-cell encounter rate, latent period, and burst size. Adding antibiotic selection provides the ability to measure the rate of host lysogenization. Using this method, we found that when E. coli growth slows down, the lytic growth rate of lambda phages decreases, and the propensity for lysogeny increases, demonstrating how host physiology influences the viral developmental program. Traditional assays for counting bacteriophages and their lysogens are labor-intensive and perturbative to the host cells. Here, the authors present a high-throughput method that can be used to estimate the number of phages in a sample, by measuring growth dynamics of the infected culture in a microplate reader.

  PublisherOA PDFDOI

• <i>Colloquium</i>: Gene expression in growing cells: A biophysical primer

  Reviews of Modern Physics · 2024-10-04 · 7 citations

  article1st authorCorresponding

  Gene expression, that is, the way in which genes encoded in the genome determine a cell's growth and biological function, is crucially influenced by growth-related processes, such as replication of the genome and the doubling of all cellular components. Historically, this interplay has been largely ignored. This Colloquium describes recent experiments designed to shed light on this important coupling and theoretical models that take it into account.

  PublisherDOI

• Single-virus transcriptomics of bacteriophage lambda

  Biophysical Journal · 2024-02-01

  articleSenior author
  PublisherDOI

Recent grants

• CAREER: Towards a quantitative picture of gene regulation in individual cells

  NSF · $932k · 2013–2019

• GENE REGULATION IN PHAGE LAMBDA: A REAL-TIME STUDY WITH SINGLE-EVENT RESOLUTION

  NIH · $4.0M · 2008–2021

• ILLUMINATING CELLULAR INDIVIDUALITY THROUGH BACTERIOPHAGE INFECTION

  NIH · $1.9M · 2021–2026

Frequent coauthors

• Heng Xu

  Sichuan University

  58 shared

• Samuel O. Skinner

  University of Queensland

  55 shared

• Thu Vu Phuc Nguyen

  38 shared

• Leonardo A. Sepúlveda

  Howard Hughes Medical Institute

  35 shared

• Seth Coleman

  Rice University

  32 shared

• Tianyou Yao

  University of Illinois Urbana-Champaign

  28 shared

• Mengyu Wang

  University of Illinois Urbana-Champaign

  24 shared

• Anna Marie Sokac

  University of Illinois Urbana-Champaign

  23 shared

Labs

• Golding LabPI