Arkin, Adam P.

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

Price, M. N., Dehal, P. S., & Arkin, A. P. (2010) · PLoS ONE

Genomics and Phylogenetic StudiesRNA and protein synthesis mechanisms

Cited by 14,894

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

Price, M. N., Dehal, P. S., & Arkin, A. P. (2009) · Molecular Biology and Evolution

Genomics and Phylogenetic StudiesRNA and protein synthesis mechanisms

Cited by 5,602

Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression

Qi, L. S., Larson, M. H., Gilbert, L. A., Doudna, J. A., Weissman, J. S., Arkin, A. P., & Lim, W. A. (2013) · Cell

CRISPR and Genetic EngineeringBacterial Genetics and Biotechnology

Cited by 5,016

Functional profiling of the Saccharomyces cerevisiae genome

Giaever, G., Chu, A. M., Ni, L., Connelly, C., Riles, L., Véronneau, S., Dow, S., Lucau-Danila, A., Anderson, K., André, B., et al. (2002) · Nature

Fungal and yeast genetics researchBioinformatics and Genomic Networks

Cited by 4,316

The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models

Hucka, M., Finney, A., Sauro, H. M., Bolouri, H., Doyle, J. C., Kitano, H., Arkin, A. P., Bornstein, B. J., Bray, D., Cornish-Bowden, A., et al. (2003) · Bioinformatics

Gene Regulatory Network AnalysisBioinformatics and Genomic Networks

Cited by 3,060

Control, exploitation and tolerance of intracellular noise

Rao, C. V., Wolf, D. M., & Arkin, A. P. (2002) · Nature

stochastic dynamics and bifurcationGene Regulatory Network Analysis

Cited by 1,006

Mutant phenotypes for thousands of bacterial genes of unknown function

Price, M. N., Wetmore, K. M., Waters, R. J., Callaghan, M., Ray, J., Liu, H., Kuehl, J. V., Melnyk, R. A., Lamson, J. S., Suh, Y., et al. (2018) · Nature

Genomics and Phylogenetic StudiesBacterial Genetics and Biotechnology

Cited by 576

RegPrecise 3.0–a resource for genome-scale exploration of transcriptional regulation in bacteria

Novichkov, P. S., Kazakov, A. E., Ravcheev, D. A., Leyn, S. A., Kovaleva, G. Y., Sutormin, R. A., Kazanov, M. D., Riehl, W., Arkin, A. P., Dubchak, I., et al. (2013) · BMC Genomics

Bacterial Genetics and BiotechnologyGene Regulatory Network Analysis

Cited by 451

Quantifying the local adaptive landscape of a nascent bacterial community

Ascensao, J. A., Wetmore, K. M., Good, B. H., Arkin, A. P., & Hallatschek, O. (2023) · Nature Communications

Evolution and Genetic DynamicsBacterial Genetics and Biotechnology

Cited by 447

Composability of regulatory sequences controlling transcription and translation in Escherichia coli

Kosuri, S., Goodman, D. B., Cambray, G., Mutalik, V. K., Gao, Y., Arkin, A. P., Endy, D., & Church, G. M. (2013) · Proceedings of the National Academy of Sciences

Microbial Metabolic Engineering and BioproductionGene Regulatory Network Analysis

Cited by 392

Motifs, modules and games in bacteria

Wolf, D. M., & Arkin, A. P. (2003) · Current Opinion in Microbiology

Gene Regulatory Network AnalysisBacterial Genetics and Biotechnology

Cited by 303

A test case of correlation metric construction of a reaction pathway from measurements

Arkin, A., Shen, P., & Ross, J. (1997) · Science

Gene Regulatory Network AnalysisMicrobial Metabolic Engineering and Bioproduction

Cited by 291

High-throughput mapping of the phage resistance landscape in E. coli

Mutalik, V. K., Adler, B. A., Rishi, H. S., Piya, D., Zhong, C., Koskella, B., Kutter, E. M., Calendar, R., Novichkov, P. S., Price, M. N., et al. (2020) · PLOS Biology

Bacteriophages and microbial interactionsBacterial Genetics and Biotechnology

Cited by 171

Towards synthetic biological approaches to resource utilization on space missions

Menezes, A. A., Cumbers, J., Hogan, J. A., & Arkin, A. P. (2015) · Journal of The Royal Society Interface

Space Science and Extraterrestrial LifeMicrobial Metabolic Engineering and Bioproduction

Cited by 147

Statistical construction of chemical reaction mechanisms from measured time-series

Arkin, A., & Ross, J. (1995) · The Journal of Physical Chemistry

Gene Regulatory Network AnalysisControl Systems and Identification

Cited by 143

The genetic basis of phage susceptibility, cross-resistance and host-range in Salmonella

Adler, B. A., Kazakov, A. E., Zhong, C., Liu, H., Kutter, E., Lui, L. M., Nielsen, T. N., Carion, H., Deutschbauer, A. M., Mutalik, V. K., et al. (2021) · Microbiology

Bacteriophages and microbial interactionsBacterial Genetics and Biotechnology

Cited by 65

A Phage Foundry Framework to Systematically Develop Viral Countermeasures to Combat Antibiotic-Resistant Bacterial Pathogens

Mutalik, V. K., & Arkin, A. P. (2022) · iScience

Bacteriophages and microbial interactionsCRISPR and Genetic Engineering

Cited by 32

Systematic and scalable genome-wide essentiality mapping to identify nonessential genes in phages

Piya, D., Nolan, N., Moore, M. L., Ramirez Hernandez, L. A., Cress, B. F., Young, R., Arkin, A. P., & Mutalik, V. K. (2023) · PLOS Biology

Bacteriophages and microbial interactionsCRISPR and Genetic Engineering

Cited by 31

Multicopy suppressor screens reveal convergent evolution of single-gene lysis proteins

Adler, B. A., Chamakura, K., Carion, H., Krog, J., Deutschbauer, A. M., Young, R., Mutalik, V. K., & Arkin, A. P. (2023) · Nature Chemical Biology

Bacteriophages and microbial interactionsBacterial Genetics and Biotechnology

Cited by 19

Phage therapy in oncology: opportunities for cancer prevention and treatment

Mutalik, V. K., Inman, J. L., Chang, H., Arkin, A., & Mao, J.-H. (2026) · Trends in Molecular Medicine

Bacteriophages and microbial interactionsBacterial Cancer Therapy

Cited by 7