Cargando…

TRANSIT - A Software Tool for Himar1 TnSeq Analysis

TnSeq has become a popular technique for determining the essentiality of genomic regions in bacterial organisms. Several methods have been developed to analyze the wealth of data that has been obtained through TnSeq experiments. We developed a tool for analyzing Himar1 TnSeq data called TRANSIT. TRA...

Descripción completa

Detalles Bibliográficos
Autores principales:	DeJesus, Michael A., Ambadipudi, Chaitra, Baker, Richard, Sassetti, Christopher, Ioerger, Thomas R.
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Public Library of Science 2015
Materias:	Research Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4598096/ https://www.ncbi.nlm.nih.gov/pubmed/26447887 http://dx.doi.org/10.1371/journal.pcbi.1004401

Ejemplares similares

Modeling Site-Specific Nucleotide Biases Affecting Himar1 Transposon Insertion Frequencies in TnSeq Data Sets
por: Choudhery, Sanjeevani, et al.
Publicado: (2021)

Statistical analysis of variability in TnSeq data across conditions using zero-inflated negative binomial regression
por: Subramaniyam, Siddharth, et al.
Publicado: (2019)

Statistical analysis of genetic interactions in Tn-Seq data
por: DeJesus, Michael A., et al.
Publicado: (2017)

TnSeq of Mycobacterium tuberculosis clinical isolates reveals strain-specific antibiotic liabilities
por: Carey, Allison F., et al.
Publicado: (2018)

Correction: TnSeq of Mycobacterium tuberculosis clinical isolates reveals strain-specific antibiotic liabilities
por: Carey, Allison F., et al.
Publicado: (2019)

Is amplification bias consequential in transposon sequencing (TnSeq) assays? A case study with a Staphylococcus aureus TnSeq library subjected to PCR-based and amplification-free enrichment methods
por: Alkam, Duah, et al.
Publicado: (2021)

Experimental and Analytical Approaches for Improving the Resolution of Randomly Barcoded Transposon Insertion Sequencing (RB-TnSeq) Studies
por: Borchert, Andrew J., et al.
Publicado: (2022)

Probing Differences in Gene Essentiality Between the Human and Animal Adapted Lineages of the Mycobacterium tuberculosis Complex Using TnSeq
por: Gibson, Amanda J., et al.
Publicado: (2021)

Bacterial Hypoxic Responses Revealed as Critical Determinants of the Host-Pathogen Outcome by TnSeq Analysis of Staphylococcus aureus Invasive Infection
por: Wilde, Aimee D., et al.
Publicado: (2015)

Himar1 Transposon for Efficient Random Mutagenesis in Aggregatibacter actinomycetemcomitans
por: Ding, Qinfeng, et al.
Publicado: (2017)

TnseqDiff: identification of conditionally essential genes in transposon sequencing studies
por: Zhao, Lili, et al.
Publicado: (2017)

Droplet Tn-Seq combines microfluidics with Tn-Seq for identifying complex single-cell phenotypes
por: Thibault, Derek, et al.
Publicado: (2019)

High-Resolution Phenotypic Profiling Defines Genes Essential for Mycobacterial Growth and Cholesterol Catabolism
por: Griffin, Jennifer E., et al.
Publicado: (2011)

An improved statistical method to identify chemical-genetic interactions by exploiting concentration-dependence
por: Dutta, Esha, et al.
Publicado: (2021)

Tn5Prime, a Tn5 based 5′ capture method for single cell RNA-seq
por: Cole, Charles, et al.
Publicado: (2018)

A Hidden Markov Model for identifying essential and growth-defect regions in bacterial genomes from transposon insertion sequencing data
por: DeJesus, Michael A, et al.
Publicado: (2013)

Tn-Seq Explorer: A Tool for Analysis of High-Throughput Sequencing Data of Transposon Mutant Libraries
por: Solaimanpour, Sina, et al.
Publicado: (2015)

A Simplified and Efficient Method for Himar-1 Transposon Sequencing in Bacteria, Demonstrated by Creation and Analysis of a Saturated Transposon-Mutant Library in Mycobacterium abscessus
por: Foreman, Mark, et al.
Publicado: (2020)

Distinct Bacterial Pathways Influence the Efficacy of Antibiotics against Mycobacterium tuberculosis
por: Bellerose, Michelle M., et al.
Publicado: (2020)

Genome-Scale Identification of Resistance Functions in Pseudomonas aeruginosa Using Tn-seq
por: Gallagher, Larry A., et al.
Publicado: (2011)

Identification by Tn‐seq of Dickeya dadantii genes required for survival in chicory plants
por: Royet, Kévin, et al.
Publicado: (2018)

Epigenetic Application of ATAC-Seq Based on Tn5 Transposase Purification Technology
por: Li, Wangchun, et al.
Publicado: (2022)

Tn-Seq reveals hidden complexity in the utilization of host-derived glutathione in Francisella tularensis
por: Ramsey, Kathryn M., et al.
Publicado: (2020)

RNA-seq and Tn-seq reveal fitness determinants of vancomycin-resistant Enterococcus faecium during growth in human serum
por: Zhang, Xinglin, et al.
Publicado: (2017)

Tn-seq; high-throughput parallel sequencing for fitness and genetic interaction studies in microorganisms
por: van Opijnen, Tim, et al.
Publicado: (2009)

Comprehensive identification of virulence factors required for respiratory melioidosis using Tn-seq mutagenesis
por: Gutierrez, Maria G., et al.
Publicado: (2015)

Multi-strain Tn-Seq reveals common daptomycin resistance determinants in Staphylococcus aureus
por: Coe, Kathryn A., et al.
Publicado: (2019)

Construction and characterization of a saturated Tn-seq library of Salmonella Typhimurium ATCC 14028
por: Trotereau, Jérôme, et al.
Publicado: (2023)

Targeting Tn-positive tumors with an afucosylated recombinant anti-Tn IgG
por: Matsumoto, Yasuyuki, et al.
Publicado: (2023)

Comprehensive Essentiality Analysis of the Mycobacterium tuberculosis Genome via Saturating Transposon Mutagenesis
por: DeJesus, Michael A., et al.
Publicado: (2017)

Identification of L-Valine-initiated-germination-active genes in Bacillus subtilis using Tn-seq
por: Sayer, Cameron V., et al.
Publicado: (2019)

Challenges in Antibody Development against Tn and Sialyl-Tn Antigens
por: Loureiro, Liliana R., et al.
Publicado: (2015)

A dose-response based model for statistical analysis of chemical genetic interactions in CRISPRi libraries
por: Choudhery, Sanjeevani, et al.
Publicado: (2023)

RNA-Seq differential expression analysis: An extended review and a software tool
por: Costa-Silva, Juliana, et al.
Publicado: (2017)

Insertion site preference of Mu, Tn5, and Tn7 transposons
por: Green, Brian, et al.
Publicado: (2012)

Tn-Seq Analysis Identifies Genes Important for Yersinia pestis Adherence during Primary Pneumonic Plague
por: Eichelberger, Kara R., et al.
Publicado: (2020)

Behavioral and transcriptomic profiling of mice null for Lphn3, a gene implicated in ADHD and addiction
por: Orsini, Caitlin A., et al.
Publicado: (2016)

Detection of Tn7-Like Transposons and Antibiotic Resistance in Enterobacterales From Animals Used for Food Production With Identification of Three Novel Transposons Tn6813, Tn6814, and Tn6765
por: He, Juan, et al.
Publicado: (2020)

Investigation of the prevalence of Tn916/Tn916-like elements in oral streptococci
por: Lunde, Tracy
Publicado: (2017)

Combining Shigella Tn-seq data with gold-standard E. coli gene deletion data suggests rare transitions between essential and non-essential gene functionality
por: Freed, Nikki E., et al.
Publicado: (2016)

Cannot write session to /tmp/vufind_sessions/sess_posa6i841v3vrv9b4m39fsin37