The DOI matches its Crossref record; 149 of the 149 references it cites were found in a registry or an index.
A decade of advances in transposon-insertion sequencing
Open accessAbstract
It has been 10 years since the introduction of modern transposon-insertion sequencing (TIS) methods, which combine genome-wide transposon mutagenesis with high-throughput sequencing to estimate the fitness contribution or essentiality of each genetic component in a bacterial genome. Four TIS variations were published in 2009: transposon sequencing (Tn-Seq), transposon-directed insertion site sequencing (TraDIS), insertion sequencing (INSeq) and high-throughput insertion tracking by deep sequencing (HITS). TIS has since become an important tool for molecular microbiologists, being one of the few genome-wide techniques that directly links phenotype to genotype and ultimately can assign gene function. In this Review, we discuss the recent applications of TIS to answer overarching biological questions. We explore emerging and multidisciplinary methods that build on TIS, with an eye towards future applications. In this Review, several experts discuss progress in the decade since the development of transposon-based approaches for bacterial genetic screens. They describe how advances in both experimental technologies and analytical strategies are resulting in insights into diverse biological processes.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Structural absorption by barbule microstructures of super black bird of paradise feathers
McCoy, D. E., Feo, T., Harvey, T. A., & Prum, R. O. (2018) · Nature Communications · doi:10.1038/s41467-017-02088-w · Cited by 7,424
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 · doi:10.1016/j.cell.2013.02.022 · 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 · doi:10.1038/nature00935 · Cited by 4,316
Efficient generation of mouse models of human diseases via ABE- and BE-mediated base editing
Liu, Z., Lu, Z., Yang, G., Huang, S., Li, G., Feng, S., Liu, Y., Li, J., Yu, W., Zhang, Y., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-04768-7 · Cited by 2,074
Simultaneous Identification of Bacterial Virulence Genes by Negative Selection
Hensel, M., Shea, J. E., Gleeson, C., Jones, M. D., Dalton, E., & Holden, D. W. (1995) · Science · doi:10.1126/science.7618105 · Cited by 1,198
Mutants of Salmonella typhimurium that cannot survive within the macrophage are avirulent.
Fields, P. I., Swanson, R. V., Haidaris, C. G., & Heffron, F. (1986) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.83.14.5189 · Cited by 1,114
van Opijnen, T., Bodi, K. L., & Camilli, A. (2009) · Nature Methods · doi:10.1038/nmeth.1377 · Cited by 933
Self-citationZhang, M., Wang, C., Otto, T. D., Oberstaller, J., Liao, X., Adapa, S. R., Udenze, K., Bronner, I. F., Casandra, D., Mayho, M., et al. (2018) · Science · doi:10.1126/science.aap7847 · Cited by 922
Identifying Genetic Determinants Needed to Establish a Human Gut Symbiont in Its Habitat
Goodman, A. L., McNulty, N. P., Zhao, Y., Leip, D., Mitra, R. D., Lozupone, C. A., Knight, R., & Gordon, J. I. (2009) · Cell Host & Microbe · doi:10.1016/j.chom.2009.08.003 · Cited by 731
Self-citationA Comprehensive, CRISPR-based Functional Analysis of Essential Genes in Bacteria
Peters, J. M., Colavin, A., Shi, H., Czarny, T. L., Larson, M. H., Wong, S., Hawkins, J. S., Lu, C. H. S., Koo, B.-M., Marta, E., et al. (2016) · Cell · doi:10.1016/j.cell.2016.05.003 · Cited by 714
Cited by
Horizontal gene transfer and adaptive evolution in bacteria.
Arnold, B. J., Huang, I.-T., & Hanage, W. P. (2022) · Nature Reviews Microbiology · doi:10.1038/s41579-021-00650-4 · Cited by 869
Deciphering the quorum-sensing lexicon of the gut microbiota
Oliveira, R. A., Cabral, V., Torcato, I., & Xavier, K. B. (2023) · Cell Host & Microbe · doi:10.1016/j.chom.2023.03.015 · Cited by 74
Light and carbon: Synthetic biology toward new cyanobacteria-based living biomaterials
Goodchild-Michelman, I. M., Church, G. M., Schubert, M. G., & Tang, T.-C. (2023) · Materials Today Bio · doi:10.1016/j.mtbio.2023.100583 · Cited by 41
Luneau, J. S., Baudin, M., Quiroz Monnens, T., Carrère, S., Bouchez, O., Jardinaud, M., Gris, C., François, J., Ray, J., Torralba, B., et al. (2022) · New Phytologist · doi:10.1111/nph.18313 · Cited by 35
Gray, J., Torres, V. V. L., Goodall, E., McKeand, S. A., Scales, D., Collins, C., Wetherall, L., Lian, Z. J., Bryant, J. A., Milner, M. T., et al. (2024) · eLife · doi:10.7554/elife.88971.3 · Cited by 12
Metadata
- Authors
- Cain, A. K., Barquist, L., Goodman, A. L., Paulsen, I. T., Parkhill, J., & van Opijnen, T.
- Venue
- Nature Reviews Genetics
- Published
- 2020-06-12
- Volume
- 21
- Issue
- 9
- Pages
- 526-540
- ISSN
- 1471-0056 (ISSN-L)
- 1471-0064
- OpenAlex
- W3035131755
- Cited by
- 391
- References
- 149
- FWCI
- 7.60
- Type
- journal article
- Language
- en
- Open access
- hybrid
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: A decade of advances in transposon-insertion sequencing. https://app.cochat.ai/papers/10.1038/s41576-020-0244-x
- The paper
- Cain, A. K., Barquist, L., Goodman, A. L., Paulsen, I. T., Parkhill, J., & van Opijnen, T. (2020). A decade of advances in transposon-insertion sequencing. Nature Reviews Genetics. https://doi.org/10.1038/s41576-020-0244-x
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
