Saeed Tavazoie
Columbia University, NY·Genetics
Cells constantly face changing conditions, and some challenges are ones they have never met before. Some respond within hours, while others adapt over many generations of evolution.
- Fields
Genetics
Microbiology & Immunology
Computer Science
- Topics
systems biology
cellular adaptation
stochastic tuning
- Grants
- 3 known grants, through Mar 2031
What they work on
- Identify the protein and DNA effectors of stochastic tuning, in which yeast cells use random gene-expression noise to adapt, using CRISPR interference, reporter assays and chemical, genetic and optogenetic perturbations of single cells in microfluidic devices.
- Determine how conserved gut-colonization genes found by tree-of-life genotype-habitat association work, using functional genomics, and improve detection with deep learning and protein language models.
- Develop a platform that couples in vivo expressed proteins to their mRNAs, so that DNA sequencing can map all-against-all protein-protein and protein-DNA interactions within days.
- Discover RNA motifs bound by RNA-binding proteins across 25 TCGA cancer cohorts with information-theoretic algorithms, and find motif-defined gene modules that predict patient survival.
- Test which RNA-binding proteins cause tumor formation and metastasis using pooled CRISPR loss-of-function screens in mouse xenografts, then map their downstream genes with in vivo CRISPR epistasis.
- Define the cell state of rare E. coli persister cells that tolerate antibiotics using PETRI-seq single-cell RNA sequencing and global protein-DNA and RNA-RNA interaction maps.
- Measure how knocking down every E. coli gene with the CALM CRISPR interference platform changes persister fraction and kill rates, then validate key vulnerabilities in persistence.
More about the research
This research seeks the general rules by which cells reach adaptive patterns of gene activity, studying the whole system at once rather than one gene at a time. The work spans yeast, gut bacteria, E. coli that tolerate antibiotics, and human cancers. Because these questions often need measurements beyond the reach of existing tools, the lab also builds new technologies and computational methods.
Why it matters
Persister bacteria make chronic infections hard to clear, and non-mutational drug resistance is a major barrier to effective cancer therapy. This work could reveal vulnerable points for eliminating antibiotic-tolerant bacteria. It may also uncover RNA-binding protein pathways that improve cancer diagnosis, prognosis and treatment. In addition, it will give researchers new tools for mapping molecular interactions and engineering gut microbes.
Known grants
From NIH and NSF research grants. Labs often have other funding we can't see.
Systems-Level Principles and Mechanisms Underlying Cellular Adaptation
NIH · May 2026 – Mar 2031
Mapping the regulatory landscape of RNA binding proteins and their causal roles in tumorigenesis and patient survival
NIH · Feb 2021 – Jan 2027
Systems biological interrogation of bacterial persistence
NIH · Jun 2009 – Aug 2026
Closest labs
Allon Klein
Harvard University, MA·Biomedical Engineering
Optimize single-lineage RNA-Seq in CAGE capsules and produce a benchmark bacterial Perturb-seq dataset that knocks down every E. coli transcription factor using CRISPR interference.
Mehmet Orman
University of Houston, TX·Microbiology & Immunology·Early-career
Identify genes important for persister colonization using a high-throughput fluorescence-based screen combined with transposon mutagenesis and genomic sequencing.
Daniel Lim
University of California-San Francisco, CA·Neuroscience
Test whether the brain-specific lncRNA Pnky contains structural modules, such as a pseudoknot (a looped RNA fold), that are needed for its control of neuron production from neural stem cells.
The school
Columbia University: 89 labs on PI Pages, $1.4B a year on research, 625 research doctorates a year.
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