Collins, James J.

A Common Mechanism of Cellular Death Induced by Bactericidal Antibiotics

Kohanski, M. A., Dwyer, D. J., Hayete, B., Lawrence, C. A., & Collins, J. J. (2007) · Cell

Bacterial Genetics and BiotechnologyRedox biology and oxidative stress

Cited by 2,982

Highly efficient reprogramming to pluripotency and directed differentiation of human cells with synthetic modified mRNA

Warren, L., Manos, P. D., Ahfeldt, T., Loh, Y.-H., Li, H., Lau, F., Ebina, W., Mandal, P. K., Smith, Z. D., Meissner, A., et al. (2010) · Cell Stem Cell

Pluripotent Stem Cells ResearchCRISPR and Genetic Engineering

Cited by 2,662

A Deep Learning Approach to Antibiotic Discovery

Stokes, J. M., Yang, K., Swanson, K., Jin, W., Cubillos-Ruiz, A., Donghia, N. M., MacNair, C. R., French, S., Carfrae, L. A., Bloom-Ackermann, Z., et al. (2020) · Cell

Computational Drug Discovery MethodsMicrobial Natural Products and Biosynthesis

Cited by 2,463

The Immunological Genome Project: networks of gene expression in immune cells

The Immunological Genome Project Consortium, Heng, T. S. P., Painter, M. W., Elpek, K., Lukacs-Kornek, V., Mauermann, N., Turley, S. J., Koller, D., Kim, F. S., Wagers, A. J., et al. (2008) · Nature Immunology

Bioinformatics and Genomic NetworksGenomics and Chromatin Dynamics

Cited by 1,864

Wisdom of crowds for robust gene network inference

The DREAM5 Consortium, Marbach, D., Costello, J. C., Küffner, R., Vega, N. M., Prill, R. J., Camacho, D. M., Allison, K. R., Kellis, M., Collins, J. J., et al. (2012) · Nature Methods

Gene Regulatory Network AnalysisMicrobial Metabolic Engineering and Bioproduction

Cited by 1,667

Highly efficient Cas9-mediated transcriptional programming

Chavez, A., Scheiman, J., Vora, S., Pruitt, B. W., Tuttle, M., P R Iyer, E., Lin, S., Kiani, S., Guzman, C. D., Wiegand, D. J., et al. (2015) · Nature Methods

CRISPR and Genetic EngineeringPluripotent Stem Cells Research

Cited by 1,622

Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles

Faith, J. J., Hayete, B., Thaden, J. T., Mogno, I., Wierzbowski, J., Cottarel, G., Kasif, S., Collins, J. J., & Gardner, T. S. (2007) · PLoS Biology

Gene Regulatory Network AnalysisBacterial Genetics and Biotechnology

Cited by 1,563

Definitions and guidelines for research on antibiotic persistence

Balaban, N. Q., Helaine, S., Lewis, K., Ackermann, M., Aldridge, B., Andersson, D. I., Brynildsen, M. P., Bumann, D., Camilli, A., Collins, J. J., et al. (2019) · Nature Reviews Microbiology

Bacterial Genetics and BiotechnologyAntimicrobial Resistance in Staphylococcus

Cited by 1,313

End-to-end design of wearable sensors

Ates, H. C., Nguyen, P. Q., Gonzalez-Macia, L., Morales-Narváez, E., Güder, F., Collins, J. J., & Dincer, C. (2022) · Nature Reviews Materials

Advanced Sensor and Energy Harvesting MaterialsNon-Invasive Vital Sign Monitoring

Cited by 1,306

Inferring Genetic Networks and Identifying Compound Mode of Action via Expression Profiling

Gardner, T. S., di Bernardo, D., Lorenz, D., & Collins, J. J. (2003) · Science

Gene Regulatory Network AnalysisBacterial Genetics and Biotechnology

Cited by 1,117

Metabolite-enabled eradication of bacterial persisters by aminoglycosides

Allison, K. R., Brynildsen, M. P., & Collins, J. J. (2011) · Nature

Bacterial Genetics and BiotechnologyBacterial biofilms and quorum sensing

Cited by 1,025

Sublethal Antibiotic Treatment Leads to Multidrug Resistance via Radical-Induced Mutagenesis

Kohanski, M. A., DePristo, M. A., & Collins, J. J. (2010) · Molecular Cell

Bacterial Genetics and BiotechnologyAntibiotic Resistance in Bacteria

Cited by 985

Contributions of microbiome and mechanical deformation to intestinal bacterial overgrowth and inflammation in a human gut-on-a-chip

Kim, H. J., Li, H., Collins, J. J., & Ingber, D. E. (2016) · Proceedings of the National Academy of Sciences

Gut microbiota and healthGastrointestinal motility and disorders

Cited by 922

Dispersing biofilms with engineered enzymatic bacteriophage

Lu, T. K., & Collins, J. J. (2007) · Proceedings of the National Academy of Sciences

Bacteriophages and microbial interactionsBacterial biofilms and quorum sensing

Cited by 895

Antibiotics and the Gut Microbiota

Modi, S. R., Collins, J. J., & Relman, D. A. (2014) · Journal of Clinical Investigation

Gut microbiota and healthAntibiotic Use and Resistance

Cited by 667

Reverse engineering gene networks using singular value decomposition and robust regression

Yeung, M. K. S., Tegnér, J., & Collins, J. J. (2002) · Proceedings of the National Academy of Sciences

Gene Regulatory Network AnalysisGene expression and cancer classification

Cited by 667

Bacterial charity work leads to population-wide resistance

Lee, H. H., Molla, M. N., Cantor, C. R., & Collins, J. J. (2010) · Nature

Bacterial Genetics and BiotechnologyEvolution and Genetic Dynamics

Cited by 638

Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome

Modi, S. R., Lee, H. H., Spina, C. S., & Collins, J. J. (2013) · Nature

Bacteriophages and microbial interactionsEvolution and Genetic Dynamics

Cited by 542

Reverse engineering gene networks: integrating genetic perturbations with dynamical modeling

Tegnér, J., Yeung, M. K. S., Hasty, J., & Collins, J. J. (2003) · Proceedings of the National Academy of Sciences

Gene Regulatory Network AnalysisMicrobial Metabolic Engineering and Bioproduction

Cited by 433

Next-generation synthetic gene networks

Lu, T. K., Khalil, A. S., & Collins, J. J. (2009) · Nature Biotechnology

Gene Regulatory Network AnalysisMicrobial Metabolic Engineering and Bioproduction

Cited by 365

Oncogenic NRAS signaling differentially regulates survival and proliferation in melanoma

Kwong, L. N., Costello, J. C., Liu, H., Jiang, S., Helms, T. L., Langsdorf, A. E., Jakubosky, D., Genovese, G., Muller, F. L., Jeong, J. H., et al. (2012) · Nature Medicine

Melanoma and MAPK PathwaysProtein Kinase Regulation and GTPase Signaling

Cited by 358

Deconstructing transcriptional heterogeneity in pluripotent stem cells

Kumar, R. M., Cahan, P., Shalek, A. K., Satija, R., Jay DaleyKeyser, A., Li, H., Zhang, J., Pardee, K., Gennert, D., Trombetta, J. J., et al. (2014) · Nature

Pluripotent Stem Cells ResearchDevelopmental Biology and Gene Regulation

Cited by 356

Designing microbial consortia with defined social interactions

Kong, W., Meldgin, D. R., Collins, J. J., & Lu, T. (2018) · Nature Chemical Biology

Microbial Metabolic Engineering and BioproductionGene Regulatory Network Analysis

Cited by 327

Benchmarking AlphaFold‐enabled molecular docking predictions for antibiotic discovery

Wong, F., Krishnan, A., Zheng, E. J., Stärk, H., Manson, A. L., Earl, A. M., Jaakkola, T., & Collins, J. J. (2022) · Molecular Systems Biology

Computational Drug Discovery MethodsProtein Structure and Dynamics

Cited by 284