Srivatsan Raman

This study uses deep mutational scanning to analyze a phage tailspike protein, revealing structural constraints and adaptive flexibility that influence its function and host range.

This paper uses deep learning to design bacteriophage receptor binding proteins with multiobjective specificity, showing high tunability and success rates in targeting diverse strains.

The paper maps chromatin dysregulation caused by viral transcriptional regulators using PROD-ATAC, identifying vTRs that remodel chromatin and reveal shared host transcription factor networks.

This study investigates how energy and structure control multidrug transporter specificity by analyzing mutations across substrates and energy conditions.

This study systematically profiles 95 viral transcriptional regulators (vTRs) across multiple assays, revealing their diverse mechanisms of rewiring host pathways to promote viral replication and disease links.

This study introduces TOXGREEN sort-seq to measure transmembrane helix oligomerization in large libraries, validating twelve dimer interfaces in human single-pass membrane proteins.

This paper introduces Meta-SIFT, a method to discover functional sequence motifs in metagenomes to engineer bacteriophage activity, demonstrating its utility in creating variants with novel host specificity.

This study introduces PhageMaP, a high-throughput method to assess gene essentiality in bacteriophages across diverse hosts and uses it to engineer synthetic phages with enhanced infectivity.

The paper introduces PHAGEPACK, a CRISPR-based assay to systematically identify host genes affecting phage infectivity, revealing new pathways in both permissive and non-permissive E. coli.

This paper introduces Sensor-seq, a high-throughput platform to design and identify allosteric transcription factor biosensors for non-native ligands, demonstrating utility with novel biosensors for naltrexone and quinine.

This study examines T7 bacteriophage and E. coli interactions in microgravity, finding delayed initial phage activity but eventual success with mutations enhancing fitness and revealing differences in mutational preferences.

The paper introduces PROD-ATAC, a method to study chromatin effects of protein-coding variants, revealing common dysregulation mechanisms across oncofusions and cancers.

This study redesigns bacterial RNA polymerase promoter specificity using computational design and screening to create orthogonal sigma factors that recognize new promoter targets.

This study engineers a controllable infectivity switch in bacteriophage T7 using synthetic promoters and ribosome binding sites, showing tunable virulence and latency.

The paper uses deep mutational scanning to map the functional landscape of the T7 bacteriophage receptor binding domain, identifying host-specific functional residues and tradeoffs between activity and host range.

This paper presents a computational method to optimize split protein systems by guiding the evaluation of mutants to find an optimal functional window.

This paper designs a portable biosensor for detecting cyanuric acid using a hybrid promoter system in E. coli, enabling rapid and on-demand detection with fluorescent and colorimetric reporters.