Ahmad S. Khalil

The paper designs a new T-DNA vector for Arabidopsis thaliana that enables predictable, single-copy transgene integration with reduced genome instability and silencing.

This study shows that synthetic cell-cell adhesion in yeast allows large aggregates to grow as well as unicellular strains, suggesting benefits from nutrient sharing rather than diffusion limitations.

This study uses AneVO to show that cofeeding C1 substrates with CO or glucose enhances growth and acetate productivity in E. limosum.

This study shows that diploid yeast under selection for larger multicellular size rapidly undergoes spontaneous whole-genome duplication, which persists and facilitates adaptation through increased genetic variation.

The paper develops HT-recruit to measure transcriptional effector function across contexts and identifies context-dependent effectors for CRISPR-based transcription control.

This study shows that cooperative self-assembly of transcriptional regulators can improve regulatory specificity and long-term stability of synthetic gene circuits in yeast.

The paper shows that ORF57 from Human Herpesvirus 8 reduces TDP-43 aggregation and cell death by interacting with ISR components.

This paper uses deep neural networks to predict single-cell responses and probability landscapes, showing they can infer cell dynamics despite noise and stochasticity.

This study investigates epigenetic adaptation in fission yeast by inducing H3K9me redistribution, revealing slow kinetics and memory-like behavior in chromatin and transcriptional states during stress adaptation.

The paper integrates modeling and synthetic biology to show that transcriptional synergy depends on both kinetic regulation of the transcription cycle and TF binding.

This paper designs synthetic gene regulatory programs for human cells that can be controlled by FDA-approved drugs and demonstrate therapeutic applications in immune cells.

The paper develops drug-gated CAR circuits using NS3 protease domains and FDA-approved inhibitors to enhance CAR T cell therapy safety and specificity.

This paper designs and demonstrates synthetic receptors for tunable gene regulation in therapeutic cells, enabling customizable and clinical-ready gene control.

This paper introduces ACE, a platform for automated continuous evolution of proteins in vivo, showing it can achieve desired functions like drug resistance and improved enzyme activity through real-time feedback control.

The paper introduces eVOLVER, a scalable DIY framework for automated cell growth and laboratory evolution, demonstrating its versatility through yeast experiments and novel millifluidic modules.

The paper shows that Hsf1 phosphorylation creates cell-to-cell variation in Hsp90 levels, which enhances phenotypic plasticity in budding yeast.