Ahmad S. Khalil

Also affiliated with Boston University, Harvard University, Inspire

Biochemistry, Genetics and Molecular Biology

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 100%percentile

0Author DataRank

Indexed papers

0in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Papers

Driven by 42 papers. Top paper: “Environmental fluctuations reshape an unexpected diversity-disturbance relationship in a microbial community”.

Environmental fluctuations reshape an unexpected diversity-disturbance relationship in a microbial community

eLife(2021)10.7554/elife.67175

N/A

1.6DataRank · unranked

49 citations

Hyunseok Lee, Clare Abreu, Jeff Gore, Ahmad S. Khalil, Christopher P. Mancuso

High-throughput continuous evolution of compact Cas9 variants targeting single-nucleotide-pyrimidine PAMs

Nature Biotechnology(2022)10.1038/s41587-022-01410-2

N/A

0.710DataRank · unranked

113 citations

Zachary Heins, Shannon M. Miller, Brandon G. Wong, Pallavi A. Balivada, Tina Wang +3 more

In vivo hypermutation and continuous evolution

Nature Reviews Methods Primers(2022)10.1038/s43586-022-00130-w

N/A

0.612DataRank · unranked

58 citations

Gordon Rix, Amanuella A. Mengiste, Beatriz Álvarez, Daeje Seo, Haiqi Chen +16 more

Long-term evolution of proliferating cells using the eVOLVER platform

Open Biology(2023)10.1098/rsob.230118

N/A

0.344DataRank · unranked

8 citations

Akanksha Jain, Zachary Heins, Brandon G. Wong, Ezira Yimer Wolle, Ahmad S. Khalil +2 more

Environmental fluctuations reshape an unexpected diversity-disturbance relationship in a microbial community

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.07.28.225987

N/A

0DataRank · unranked

4 citations

Hyunseok Lee, Clare Abreu, Jeff Gore, Ahmad S. Khalil, Christopher P. Mancuso

Computational Model to Quantify the Growth of Antibiotic Resistant Bacteria in Wastewater

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.10.09.333575

N/A

0DataRank · unranked

4 citations

Carly Ching, Darash Desai, Mark P. Suprenant, Emma Briars, Zachary Heins +3 more

Automated continuous evolution of proteins in vivo

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.02.21.960328

N/A

0DataRank · unranked

2 citations

Brandon G. Wong, Arjun Ravikumar, Garri A. Arzumanyan, Ahmad S. Khalil, Chang C. Liu +1 more

Computational Model To Quantify the Growth of Antibiotic-Resistant Bacteria in Wastewater

mSystems(2021)10.1128/msystems.00360-21

N/A

0DataRank · unranked

38 citations

Carly Ching, Darash Desai, Mark P. Suprenant, Emma Briars, Zachary Heins +3 more

Clinically-driven design of synthetic gene regulatory programs in human cells

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.02.22.432371

N/A

0DataRank · unranked

24 citations

Hui-Shan Li, Keith A. Gagnon, Jeffry D. Sander, Kole T. Roybal, J. Keith Joung +3 more

Design and modular assembly of synthetic intramembrane proteolysis receptors for custom gene regulation in therapeutic cells

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.05.21.445218

N/A

0DataRank · unranked

13 citations

Raymond Liu, Axel Hyrenius‐Wittsten, Dan I. Piraner, Josef Alavi, Divya V. Israni +3 more

The sound of silence: Transgene silencing in mammalian cell engineering

Cell Systems(2022)10.1016/j.cels.2022.11.005

N/A

0DataRank · unranked

205 citations

Hailey I. Edelstein, Fokion Glykofrydis, Kasey S. Love, Sebastian Palacios, Josh Tycko +22 more

Modular design of synthetic receptors for programmed gene regulation in cell therapies

Cell(2022)10.1016/j.cell.2022.03.023

N/A

0DataRank · unranked

196 citations

Raymond Liu, Julie Garcia, Axel Hyrenius‐Wittsten, Dan I. Piraner, Josef Alavi +5 more

Multidimensional control of therapeutic human cell function with synthetic gene circuits

Science(2022)10.1126/science.ade0156

N/A

0DataRank · unranked

157 citations

Divya V. Israni, Keith A. Gagnon, Kok Ann Gan, Michael H. Raymond, Jeffry D. Sander +5 more

In vivo hypermutation and continuous evolution

Nature Reviews Methods Primers(2022)10.1038/s43586-022-00119-5

N/A

0DataRank · unranked

141 citations

Gordon Rix, Amanuella A. Mengiste, Beatriz Álvarez, Daeje Seo, Haiqi Chen +16 more

High-performance multiplex drug-gated CAR circuits

Cancer Cell(2022)10.1016/j.ccell.2022.08.008

N/A

0DataRank · unranked

102 citations

Nicole M. Wong, Elliot P. Tague, John T. Ngo, Ahmad S. Khalil, Wilson W. Wong +1 more

A Toolkit for Precise, Multigene Control in Saccharomyces cerevisiae

ACS Synthetic Biology(2022)10.1021/acssynbio.2c00423

N/A

0DataRank · unranked

38 citations

Szilvia Kiriakov, Ahmad S. Khalil, Adam Sanford

Recent progress of gene circuit designs in immune cell therapies

Cell Systems(2022)10.1016/j.cels.2022.09.006

N/A

0DataRank · unranked

24 citations

Ahmad S. Khalil, Wilson W. Wong, Seung‐Hee Lee

Cooperative assembly confers regulatory specificity and long-term genetic circuit stability

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.05.22.492993

N/A

0DataRank · unranked

3 citations

Nikit Patel, James Chuang, Ethan Levien, Caleb J. Bashor, Ahmad S. Khalil +1 more

Unlocking the magic in mycelium: Using synthetic biology to optimize filamentous fungi for biomanufacturing and sustainability

Materials Today Bio(2023)10.1016/j.mtbio.2023.100560

N/A

0DataRank · unranked

95 citations

Jing Zhang, Jenny M. Tam, George M. Church, Ahmad S. Khalil, Daniel Segrè +2 more

Cooperative assembly confers regulatory specificity and long-term genetic circuit stability

Cell(2023)10.1016/j.cell.2023.07.012

N/A

0DataRank · unranked

43 citations

Nikit Patel, James Chuang, Ethan Levien, Caleb J. Bashor, Ahmad S. Khalil +1 more

Transcriptional kinetic synergy: A complex landscape revealed by integrating modeling and synthetic biology

Cell Systems(2023)10.1016/j.cels.2023.02.003

N/A

0DataRank · unranked

33 citations

Minhee Park, Kelly M. Biette, Dhana Friedrich, Clarissa Scholes, Ahmad S. Khalil +3 more

Effects of antibiotic interaction on antimicrobial resistance development in wastewater

Scientific Reports(2023)10.1038/s41598-023-34935-w

N/A

0DataRank · unranked

18 citations

Carly Ching, Darash Desai, Zachary Heins, Ahmad S. Khalil, Muhammad H. Zaman +1 more

Human herpesvirus 8 ORF57 protein is able to reduce TDP-43 pathology: network analysis identifies interacting pathways

Human Molecular Genetics(2023)10.1093/hmg/ddad122

N/A

0DataRank · unranked

3 citations

Caroline N. Murphy, Alejandro N. Rondón-Ortiz, Sophie J. F. van der Spek, Elena X. Kelly, Noah M. Lampl +5 more

Long-term evolution of proliferating cells using the eVOLVER platform

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.03.28.534552

N/A

0DataRank · unranked

1 citations

Akanksha Jain, Zachary Heins, Brandon G. Wong, Ezira Yimer Wolle, Ahmad S. Khalil +2 more

Effects of Antibiotic Interaction on Antimicrobial Resistance Development in Wastewater

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.02.10.528009

N/A

0DataRank · unranked

0 citations

Carly Ching, Darash Desai, Zachary Heins, Ahmad S. Khalil, Muhammad H. Zaman +1 more

Human Herpesvirus 8 ORF57 protein is able to reduce TDP-43 pathology: Network analysis Identifies Interacting Pathways

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.05.18.540717

N/A

0DataRank · unranked

0 citations

Caroline N. Murphy, Alejandro N. Rondón-Ortiz, Sophie J. F. van der Spek, Elena X. Kelly, Noah M. Lampl +5 more

Deep neural networks for predicting single cell responses and probability landscapes

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.06.24.546373

N/A

0DataRank · unranked

0 citations

Jean‐Baptiste Lugagne, Ahmad S. Khalil, Mary J. Dunlop, Heidi E. Klumpe

Mapping the dynamics of epigenetic adaptation during heterochromatin misregulation

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.07.10.548368

N/A

0DataRank · unranked

0 citations

Colin Kunze, Melissa Seman, Alexander Levashkevich, Justin Curran, Dionysus Morris-Evans +4 more

eLife Assessment: Predicting the effect of CRISPR-Cas9-based epigenome editing

(2023)10.7554/elife.92991.1.sa2

N/A

0DataRank · unranked

0 citations

Ahmad S. Khalil

Brainwide silencing of prion protein by AAV-mediated delivery of an engineered compact epigenetic editor

Science(2024)10.1126/science.ado7082

N/A

0DataRank · unranked

106 citations

Tessa M. Bertozzi, Elaine Wu, Fiona E. Serack, John W. Harvey, Pamela P. Brauer +13 more

Development of compact transcriptional effectors using high-throughput measurements in diverse contexts

Nature Biotechnology(2024)10.1038/s41587-024-02442-6

N/A

0DataRank · unranked

39 citations

Mike V. Van, Aradhana, Nicole DelRosso, Haihong Ye, David Yao +21 more

Structural Mapping of Protein Aggregates in Live Cells Modeling Huntington's Disease

Angewandte Chemie International Edition(2024)10.1002/anie.202408163

N/A

0DataRank · unranked

10 citations

Giulio Chiesa, Jiaze Yin, Adam Sanford, Stefan Meier, Ahmad S. Khalil +2 more

Mapping the dynamics of epigenetic adaptation in S. pombe during heterochromatin misregulation

Developmental Cell(2024)10.1016/j.devcel.2024.07.006

N/A

0DataRank · unranked

9 citations

Colin Kunze, Melissa Seman, Alexander Levashkevich, Justin Curran, Dionysus Morris-Evans +4 more

Structural Mapping of Protein Aggregates in Live Cells Modeling Huntington's Disease

Angewandte Chemie(2024)10.1002/ange.202408163

N/A

0DataRank · unranked

3 citations

Giulio Chiesa, Jiaze Yin, Adam Sanford, Stefan Meier, Ahmad S. Khalil +2 more

eLife Assessment: Predicting the effect of CRISPR-Cas9-based epigenome editing

(2024)10.7554/elife.92991.2.sa3

N/A

0DataRank · unranked

0 citations

Ahmad S. Khalil

Exploring substrate cofeeding for enhanced acetogenic C1 bioconversion with AneVO, a low-cost anaerobic parallel bioreactor platform

Trends in biotechnology(2025)10.1016/j.tibtech.2025.11.012

N/A

0DataRank · unranked

1 citations

Guanyu Zhou, William Gasparrini, Patrick J. Sliter, Daniel J. Hart, Ahmad S. Khalil +2 more

Exploring C1 substrate cofeeding in Eubacterium limosum with AneVO, a low-cost anaerobic parallel bioreactor platform

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.05.02.651948

N/A

0DataRank · unranked

1 citations

Guanyu Zhou, William Gasparrini, Patrick J. Sliter, Daniel J. Hart, Ahmad S. Khalil +2 more

Protein assembly systems in natural and synthetic biology

BMC Biology(2020)10.1186/s12915-020-0751-4

N/A

0DataRank · unranked

77 citations

Szilvia Kiriakov, Ahmad S. Khalil, Giulio Chiesa

The next phase of mammalian synthetic biology: Trends and applications

Current Opinion in Biomedical Engineering(2025)10.1016/j.cobme.2025.100608

N/A

0DataRank · unranked

0 citations

Ahmad S. Khalil, Wilson W. Wong

Sphingomonas solaris sp. nov., isolated from a solar panel in Boston, Massachusetts

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY(2020)10.1099/ijsem.0.003977

N/A

0DataRank · unranked

13 citations

Christopher P. Mancuso, Juli Peretό, Ahmad S. Khalil, Cristina Vilanova, Javier Pascual +1 more

Transcriptional kinetic synergy: a complex landscape revealed by integrating modelling and synthetic biology

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.08.31.276261

N/A

0DataRank · unranked

7 citations

Minhee Park, Kelly M. Biette, Dhana Friedrich, Clarissa Scholes, Ahmad S. Khalil +3 more

Engineering clinically-approved drug gated CAR circuits

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.12.14.419812

N/A

0DataRank · unranked

5 citations

Nicole M. Wong, Elliot P. Tague, John T. Ngo, Ahmad S. Khalil, Wilson W. Wong +1 more