Podcast episodes
Rapid Detection of DNA and RNA Shrimp Viruses Using CRISPR-Based Diagnostics
- Samuel R Major, Matthew J Harke, Roberto Cruz-Flores, …, Arun K Dhar, Andrea G Bodnar, Shelly A Wanamaker
- Appl Environ Microbiol, 10.1128/aem.02151-22
Discovering small-molecule senolytics with deep neural networks
- Felix Wong, Satotaka Omori, Nina M Donghia, …, Nina M Donghia, Erica J Zheng, James J Collins
- Nat Aging, 10.1038/s43587-023-00415-z
Autocatalytic base editing for RNA-responsive translational control
- Raphaël V Gayet, Katherine Ilia, Shiva Razavi, …, Jonathan C Chen, Jose Vargas-Asencio, James J Collins
- Nat Commun, 10.1038/s41467-023-36851-z
Harnessing synthetic biology to enhance ocean health
- Peter Q Nguyen, Xiaoning Huang, Daniel S Collins, …, Daniel S Collins, James J Collins, Ting Lu
- Trends Biotechnol, 10.1016/j.tibtech.2022.12.015
The sound of silence: Transgene silencing in mammalian cell engineering
- Alan Cabera, Hailey I Edelstein, Fokion Glykofrydis, …, Lacramioara Bintu, Kate E Galloway, Tara L Deans
- Cell Syst, 10.1016/j.cels.2022.11.005
Multiplexed rapid antigen tests developed using multicolored nanoparticles and cross-reactive antibody pairs: Implications for pandemic preparedness
- Helena de Puig, Irene Bosch, Nol Salcedo, …, James J Collins, Kimberly Hamad-Schifferli, Lee Gehrke
- None, 10.1016/j.nantod.2022.101669
Reactive metabolic byproducts contribute to antibiotic lethality under anaerobic conditions
- Felix Wong, Jonathan M Stokes, Sarah C Bening, …, Charles Vidoudez, Sunia A Trauger, James J Collins
- Mol Cell, 10.1016/j.molcel.2022.07.009
A lab-on-a-chip for the concurrent electrochemical detection of SARS-CoV-2 RNA and anti-SARS-CoV-2 antibodies in saliva and plasma
- Devora Najjar, Joshua Rainbow, Sanjay Sharma Timilsina, …, Pedro Estrela, James J Collins, Donald E Ingber
- Nat Biomed Eng, 10.1038/s41551-022-00919-w
Nanozyme-catalysed CRISPR assay for preamplification-free detection of non-coding RNAs
- Marta Broto, Michael M Kaminski, Christopher Adrianus, …, Anand S Dighe, James J Collins, Molly M Stevens
- Nat Nanotechnol, 10.1038/s41565-022-01179-0
End-to-end design of wearable sensors
- H Ceren Ates, Peter Q Nguyen, Laura Gonzalez-Macia, …, Firat Güder, James J Collins, Can Dincer
- None, 10.1038/s41578-022-00460-x
SETDB1 acts as a topological accessory to Cohesin via an H3K9me3-independent, genomic shunt for regulating cell fates
- Tushar Warrier, Chadi El Farran, Yingying Zeng, …, Hu Li, Jian Xu, Yuin-Han Loh
- Nucleic Acids Res, 10.1093/nar/gkac531
Modulating the evolutionary trajectory of tolerance using antibiotics with different metabolic dependencies
- Erica J Zheng, Ian W Andrews, Alexandra T Grote, …, Miguel A Alcantar, Ashlee M Earl, James J Collins
- Nat Commun, 10.1038/s41467-022-30272-0
CellComm infers cellular crosstalk that drives haematopoietic stem and progenitor cell development
- Edroaldo Lummertz da Rocha, Caroline Kubaczka, Wade W Sugden, …, James J Collins, Trista E North, George Q Daley
- Nat Cell Biol, 10.1038/s41556-022-00884-1
An engineered live biotherapeutic for the prevention of antibiotic-induced dysbiosis
- Andrés Cubillos-Ruiz, Miguel A Alcantar, Nina M Donghia, …, Pablo Cárdenas, Julian Avila-Pacheco, James J Collins
- Nat Biomed Eng, 10.1038/s41551-022-00871-9
Field validation of the performance of paper-based tests for the detection of the Zika and chikungunya viruses in serum samples
- Margot Karlikow, Severino Jefferson Ribeiro da Silva, Yuxiu Guo, …, Constância Ayres, Lindomar Pena, Keith Pardee
- Nat Biomed Eng, 10.1038/s41551-022-00850-0
Intron mutations and early transcription termination in Duchenne and Becker muscular dystrophy
- Megan A Waldrop, Steven A Moore, Katherine D Mathews, …, Diane M Dunn, Robert B Weiss, Kevin M Flanigan
- Hum Mutat, 10.1002/humu.24343
RNA-responsive elements for eukaryotic translational control
- Evan M Zhao, Angelo S Mao, Helena de Puig, …, Eric S Zigon, Max A English, James J Collins
- Nat Biotechnol, 10.1038/s41587-021-01068-2
Engineering living therapeutics with synthetic biology
- Andres Cubillos-Ruiz, Tingxi Guo, Anna Sokolovska, …, James J Collins, Timothy K Lu, Jose M Lora
- Nat Rev Drug Discov, 10.1038/s41573-021-00285-3
Deep learning identifies synergistic drug combinations for treating COVID-19
- Wengong Jin, Jonathan M Stokes, Richard T Eastman, …, James J Collins, Tommi S Jaakkola, Regina Barzilay
- Proc Natl Acad Sci U S A, 10.1073/pnas.2105070118
Minimally instrumented SHERLOCK (miSHERLOCK) for CRISPR-based point-of-care diagnosis of SARS-CoV-2 and emerging variants
- Helena de Puig, Rose A Lee, Devora Najjar, …, Hani Sallum, James Niemi, James J Collins
- Sci Adv, 10.1126/sciadv.abh2944
Wearable materials with embedded synthetic biology sensors for biomolecule detection
- Peter Q Nguyen, Luis R Soenksen, Nina M Donghia, …, Evan M Zhao, James B Niemi, James J Collins
- Nat Biotechnol, 10.1038/s41587-021-00950-3
Cytoplasmic condensation induced by membrane damage is associated with antibiotic lethality
- Felix Wong, Jonathan M Stokes, Bernardo Cervantes, …, Jens Friedrichs, Lars D Renner, James J Collins
- Nat Commun, 10.1038/s41467-021-22485-6
Designing Biological Circuits: Synthetic Biology Within the Operon Model and Beyond
- Max A English, Raphaël V Gayet, James J Collins
- Annu Rev Biochem, 10.1146/annurev-biochem-013118-111914
Clinically relevant mutations in core metabolic genes confer antibiotic resistance
- Allison J Lopatkin, Sarah C Bening, Abigail L Manson, …, Nicole J Cheney, Jason H Yang, James J Collins
- Science, 10.1126/science.aba0862
Using deep learning for dermatologist-level detection of suspicious pigmented skin lesions from wide-field images
- Luis R Soenksen, Timothy Kassis, Susan T Conover, …, James J Collins, Regina Barzilay, Martha L Gray
- Sci Transl Med, 10.1126/scitranslmed.abb3652
Synthetic biology in the clinic: engineering vaccines, diagnostics, and therapeutics
- Xiao Tan, Justin H Letendre, James J Collins, Wilson W Wong
- Cell, 10.1016/j.cell.2021.01.017
Engineering advanced logic and distributed computing in human CAR immune cells
- Jang Hwan Cho, Atsushi Okuma, Katri Sofjan, Seunghee Lee, James J Collins, Wilson W Wong
- Nat Commun, 10.1038/s41467-021-21078-7
Evidence that coronavirus superspreading is fat-tailed
- Felix Wong, James J Collins
- Proc Natl Acad Sci U S A, 10.1073/pnas.2018490117
Deep-Learning Resources for Studying Glycan-Mediated Host-Microbe Interactions
- Daniel Bojar, Rani K Powers, Diogo M Camacho, James J Collins
- Cell Host Microbe, 10.1016/j.chom.2020.10.004
A deep learning approach to programmable RNA switches
- Nicolaas M Angenent-Mari, Alexander S Garruss, Luis R Soenksen, George Church, James J Collins
- Nat Commun, 10.1038/s41467-020-18677-1
Ultrasensitive CRISPR-based diagnostic for field-applicable detection of Plasmodium species in symptomatic and asymptomatic malaria
- Rose A Lee, Helena De Puig, Peter Q Nguyen, …, Catherine M Klapperich, Nira R Pollock, James J Collins
- Proc Natl Acad Sci U S A, 10.1073/pnas.2010196117
Diversification of reprogramming trajectories revealed by parallel single-cell transcriptome and chromatin accessibility sequencing
- Q R Xing, Chadi A El Farran, Pradeep Gautam, …, Hu Li, Li-Feng Zhang, Yuin-Han Loh
- Sci Adv, 10.1126/sciadv.aba1190
Eradicating Bacterial Persisters with Combinations of Strongly and Weakly Metabolism-Dependent Antibiotics
- Erica J Zheng, Jonathan M Stokes, James J Collins
- Cell Chem Biol, 10.1016/j.chembiol.2020.08.015
Continuous bioactivity-dependent evolution of an antibiotic biosynthetic pathway
- Chad W Johnston, Ahmed H Badran, James J Collins
- Nat Commun, 10.1038/s41467-020-18018-2
Creating CRISPR-responsive smart materials for diagnostics and programmable cargo release
- Raphael V Gayet, Helena de Puig, Max A English, …, Angelo S Mao, Nicolaas M Angenent-Mari, James J Collins
- Nat Protoc, 10.1038/s41596-020-0367-8
Parallel bimodal single-cell sequencing of transcriptome and chromatin accessibility
- Qiao Rui Xing, Chadi A El Farran, Ying Ying Zeng, …, Hu Li, Li-Feng Zhang, Yuin-Han Loh
- Genome Res, 10.1101/gr.257840.119
Cell-free biosensors for rapid detection of water contaminants
- Jaeyoung K Jung, Khalid K Alam, Matthew S Verosloff, …, David P Giedroc, James J Collins, Julius B Lucks
- Nat Biotechnol, 10.1038/s41587-020-0571-7
Point-of-Care Devices to Detect Zika and Other Emerging Viruses
- Helena de Puig, Irene Bosch, James J Collins, Lee Gehrke
- Annu Rev Biomed Eng, 10.1146/annurev-bioeng-060418-052240
Predictive biology: modelling, understanding and harnessing microbial complexity
- Allison J Lopatkin, James J Collins
- Nat Rev Microbiol, 10.1038/s41579-020-0372-5
A Deep Learning Approach to Antibiotic Discovery
- Jonathan M Stokes, Kevin Yang, Kyle Swanson, …, Tommi S Jaakkola, Regina Barzilay, James J Collins
- Cell, 10.1016/j.cell.2020.04.001
A CRISPR-based assay for the detection of opportunistic infections post-transplantation and for the monitoring of transplant rejection
- Michael M Kaminski, Miguel A Alcantar, Isadora T Lape, …, Enver Akalin, Leonardo V Riella, James J Collins
- Nat Biomed Eng, 10.1038/s41551-020-0546-5
De novo-designed translation-repressing riboregulators for multi-input cellular logic
- Jongmin Kim, Yu Zhou, Paul D Carlson, …, Julius B Lucks, Peng Yin, Alexander A Green
- Nat Chem Biol, 10.1038/s41589-019-0388-1
Engineering microbial peer pressure
- Chad W Johnston, James J Collins
- Science, 10.1126/science.aay3157