title: The design and analysis of transposon insertion sequencing experiments.
abstract: Transposon insertion sequencing (TIS) is a powerful approach that can be extensively applied to the genome-wide definition of loci that are required for bacterial growth under diverse conditions. However, experimental design choices and stochastic biological processes can heavily influence the results of TIS experiments and affect downstream statistical analysis. In this Opinion article, we discuss TIS experimental parameters and how these factors relate to the benefits and limitations of the various statistical frameworks that can be applied to the computational analysis of TIS data.
authors.affiliation: Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02115, USA; the Division of Infectious Disease, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA; and the Howard Hughes Medical Institute, Boston, Massachusetts 02115, USA.
authors.forename: Michael C
authors.initials: MC
authors.lastname: Chao
authors.affiliation: Department of Pharmacy, University of Tromsø, The Arctic University of Norway, 9019 Tromsø, Norway.
authors.forename: Sören
authors.initials: S
authors.lastname: Abel
authors.affiliation: Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02115, USA; the Division of Infectious Disease, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA; and the Howard Hughes Medical Institute, Boston, Massachusetts 02115, USA.
authors.forename: Brigid M
authors.initials: BM
authors.lastname: Davis
authors.affiliation: Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02115, USA; the Division of Infectious Disease, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA; and the Howard Hughes Medical Institute, Boston, Massachusetts 02115, USA.
authors.forename: Matthew K
authors.initials: MK
authors.lastname: Waldor
mesh_terms: D001419:Bacteria / Q000235:genetics* / Q000378:metabolism*; D004251:DNA Transposable Elements / Q000235:genetics*; D004269:DNA, Bacterial / Q000235:genetics*; D015964:Gene Expression Regulation, Bacterial / Q000502:physiology; D015723:Gene Library; D008954:Models, Biological; D015233:Models, Statistical; D016254:Mutagenesis, Insertional / Q000379:methods*
chemical_list: D004251:DNA Transposable Elements; D004269:DNA, Bacterial