Saeed Tavazoie

The genetic landscape of antibiotic sensitivity in Staphylococcus aureus

This study identifies gene-drug and gene-gene interactions in Staphylococcus aureus using CRISPR-interference, revealing vulnerabilities for new drug targets and combination therapies.

Noise-driven morphogenesis independent of transcriptional regulatory programs

This paper proposes a new framework for development that emphasizes stochastic gene expression as a driving force rather than a noise, using reinforcement learning analogies to guide cell fates.

Multiscale regulation of nutrient stress responses in Escherichia coli from chromatin structure to small regulatory RNAs

The paper identifies nutrient stress response mechanisms in E. coli by integrating chromatin structure and small regulatory RNA data, revealing novel transcription factor-sRNA interactions.

Adaptation by stochastic tuning of gene expression in mammalian cells

The paper shows human cells adapt to methotrexate through stochastic tuning, a process similar to yeast, which is reversible and not mutation-driven.

Molecular topography of an entire nervous system

The paper provides a comprehensive gene expression profile of all 302 neurons in the C. elegans nervous system and identifies cis-regulatory elements and adhesion proteins involved in synaptic specificity.

Dynamic landscape of protein occupancy across the Escherichia coli chromosome

The paper uses IPOD-HR to globally map protein-DNA interactions in E. coli, revealing dynamic transcription factor occupancy and stable nucleoid factor domains, and develops computational models for transcription factor specificity.

An inducible CRISPR-interference library for genetic interrogation of Saccharomyces cerevisiae biology

The paper develops an inducible CRISPRi library for S. cerevisiae to systematically interrogate gene function with high precision and low false discovery rate.

Prokaryotic Single-Cell RNA Sequencing by In Situ Combinatorial Indexing

PETRI-seq enables single-cell RNA sequencing of prokaryotes by overcoming technical barriers, revealing growth phase-specific cell states and prophage induction in S. aureus.

A post-transcriptional regulatory code for mRNA stability during the zebrafish maternal-to-zygotic transition

The paper identifies cis-regulatory elements and trans-factors governing mRNA stability during zebrafish MZT and develops a model to predict mRNA stability.

Cellular Adaptation Through Fitness-Directed Transcriptional Tuning

The paper shows that yeast adapts to new environments through transcriptional tuning at gene promoters, influenced by chromatin modifications.