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Ahmad S. Khalil

Inspire ·
Area of research
Molecular Biology · Genetics
Research interest
Research interests include CRISPR and Genetic Engineering, Gene Regulatory Network Analysis, Genomics and Chromatin Dynamics, and Evolution and Genetic Dynamics.
h-index
41
citations
8,902
works
151
NIH funding
primary concept
Biology
email

Recent publications

Genome duplication in a long-term multicellularity evolution experiment
Nature 2025cited by 14position: middledoi
Brainwide silencing of prion protein by AAV-mediated delivery of an engineered compact epigenetic editor
Science 2024cited by 98position: middledoi
Development of compact transcriptional effectors using high-throughput measurements in diverse contexts
Nature Biotechnology 2024cited by 37position: middledoi
Anti-CRISPR Anopheles mosquitoes inhibit gene drive spread under challenging behavioural conditions in large cages
Nature Communications 2024cited by 28position: middledoi
Structural Mapping of Protein Aggregates in Live Cells Modeling Huntington's Disease
Angewandte Chemie International Edition 2024cited by 10position: middledoi
Mapping the dynamics of epigenetic adaptation in S. pombe during heterochromatin misregulation
Developmental Cell 2024cited by 9position: middledoi
Unlocking the magic in mycelium: Using synthetic biology to optimize filamentous fungi for biomanufacturing and sustainability
Materials Today Bio 2023cited by 93position: middledoi
A Multiplex MoClo Toolkit for Extensive and Flexible Engineering of <i>Saccharomyces cerevisiae</i>
ACS Synthetic Biology 2023cited by 52position: middledoi
Cooperative assembly confers regulatory specificity and long-term genetic circuit stability
Cell 2023cited by 41position: lastdoi
Transcriptional kinetic synergy: A complex landscape revealed by integrating modeling and synthetic biology
Cell Systems 2023cited by 33position: middledoi
Effects of antibiotic interaction on antimicrobial resistance development in wastewater
Scientific Reports 2023cited by 18position: middledoi
The sound of silence: Transgene silencing in mammalian cell engineering
Cell Systems 2022cited by 192position: middledoi
Modular design of synthetic receptors for programmed gene regulation in cell therapies
Cell 2022cited by 189position: middledoi
Multidimensional control of therapeutic human cell function with synthetic gene circuits
Science 2022cited by 149position: lastdoi
In vivo hypermutation and continuous evolution
Nature Reviews Methods Primers 2022cited by 136position: middledoi
High-throughput continuous evolution of compact Cas9 variants targeting single-nucleotide-pyrimidine PAMs
Nature Biotechnology 2022cited by 107position: middledoi
High-performance multiplex drug-gated CAR circuits
Cancer Cell 2022cited by 97position: middledoi
In vivo hypermutation and continuous evolution
Nature Reviews Methods Primers 2022cited by 58position: middledoi
A Toolkit for Precise, Multigene Control in <i>Saccharomyces cerevisiae</i>
ACS Synthetic Biology 2022cited by 37position: lastdoi
Screening microbially produced Δ9-tetrahydrocannabinol using a yeast biosensor workflow
Nature Communications 2022cited by 25position: middledoi
Recent progress of gene circuit designs in immune cell therapies
Cell Systems 2022cited by 23position: middledoi
Enhancing nutritional niche and host defenses by modifying the gut microbiome
Molecular Systems Biology 2022cited by 16position: middledoi
A Code of Ethics for Gene Drive Research
The CRISPR Journal 2021cited by 42position: middledoi
Computational Model To Quantify the Growth of Antibiotic-Resistant Bacteria in Wastewater
mSystems 2021cited by 36position: middledoi
Protein assembly systems in natural and synthetic biology
BMC Biology 2020cited by 76position: lastdoi
Automated Continuous Evolution of Proteins <i>in Vivo</i>
ACS Synthetic Biology 2020cited by 70position: middledoi
Barcoded microbial system for high-resolution object provenance
Science 2020cited by 44position: middledoi
Colonization with heterologous bacteria reprograms a <i>Caenorhabditis elegans</i> nutritional phenotype
bioRxiv (Cold Spring Harbor Laboratory) 2020cited by 2position: middledoi
Functional genomics of the rapidly replicating bacterium Vibrio natriegens by CRISPRi
Nature Microbiology 2019cited by 235position: middledoi
Complex signal processing in synthetic gene circuits using cooperative regulatory assemblies
Science 2019cited by 149position: lastdoi

Grants

Collaborative Research: NSF/MCB: Kinetic Control of the Transcription Cycle Revealed by Synthetic Enhancers
NSF1713855$300,0002017–2020PIRePORTER
CAREER: Evolution and Engineering of Cellular Bet-hedging Devices
NSF1350949$760,0002013–2018PIRePORTER
Conference: 2012 Rustbelt RNA Meeting to be held October 19-20, 2012 at Crowne Plaza in Dayton, OH
NSF1205190$12,5002012–2013PIRePORTER

Frequent collaborators

James J. Collins · Broad Institute of MIT and Harvard10 papers (2012–2022)Nikit Patel · GLS University6 papers (2016–2023)Szilvia Kiriakov · Boston University6 papers (2014–2022)Brandon G. Wong · Boston University5 papers (2017–2022)Zachary Heins · Boston University5 papers (2021–2023)Caleb J. Bashor · Rice University5 papers (2012–2023)Christopher P. Mancuso · Massachusetts Institute of Technology5 papers (2017–2022)Albert J. Keung · North Carolina State University5 papers (2014–2018)J. Keith Joung · Harvard University4 papers (2012–2022)Ali Beyzavi · Boston University3 papers (2016–2019)Chang C. Liu · University of California System3 papers (2020–2022)Muhammad H. Zaman · Boston University3 papers (2018–2023)Minhee Park · Stanford University3 papers (2016–2023)Joanna Krakowiak · The University of Texas Health Science Center at Houston3 papers (2016–2018)David Pincus · University of Chicago3 papers (2016–2018)Xu Zheng · Nanchang University3 papers (2016–2018)Wilson W. Wong · Boston University3 papers (2022–2022)Nic M. Vega · Emory University3 papers (2012–2022)Timothy K. Lu · Massachusetts Institute of Technology3 papers (2012–2022)Eric G. Schwarz · Boston University2 papers (2014–2015)