Methylation of rRNA as a host defense against rampant group II intron retrotransposition

Bacterial group II intron genomic neighborhoods reflect survival strategies: hiding and hijacking

(2020) Justin Waldern et al.   MOLECULAR BIOLOGY AND EVOLUTION

A group II intron-encoded protein interacts with the cellular replicative machinery through the β-sliding clamp

(2019) Fernando M García-Rodríguez et al.   NUCLEIC ACIDS RESEARCH

Group II Intron RNPs and Reverse Transcriptases: From Retroelements to Research Tools

(2019) Marlene Belfort et al.   Cold Spring Harbor Perspectives in Biology

Host–transposon interactions: conflict, cooperation, and cooption

(2019) Rachel L Cosby et al.   GENES & DEVELOPMENT

High-Resolution Ion Mobility Spectrometry-Mass Spectrometry of Isomeric/Isobaric Ribonucleotide Variants

(2019) T. Kenderdine et al.   JOURNAL OF MASS SPECTROMETRY

Evolutionary entanglement of mobile genetic elements and host defence systems: guns for hire

(2019) Eugene V. Koonin et al.   NATURE REVIEWS GENETICS

Structural accommodations accompanying splicing of a group II intron RNP

(2018) Xiaolong Dong et al.   NUCLEIC ACIDS RESEARCH

Positive-sense RNA viruses reveal the complexity and dynamics of the cellular and viral epitranscriptomes during infection

(2018) Will McIntyre et al.   NUCLEIC ACIDS RESEARCH

Group II intron inhibits conjugative relaxase expression in bacteria by mRNA targeting

(2018) Guosheng Qu et al.   eLife

Comprehensive Functional Analysis of the Enterococcus faecalis Core Genome Using an Ordered, Sequence-Defined Collection of Insertional Mutations in Strain OG1RF

(2018) Jennifer L. Dale et al.   mSystems

Cytoscape StringApp: Network Analysis and Visualization of Proteomics Data

(2018) Nadezhda T. Doncheva et al.   JOURNAL OF PROTEOME RESEARCH

Testing the retroelement invasion hypothesis for the emergence of the ancestral eukaryotic cell

(2018) Gloria Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mobile Group II Introns as Ancestral Eukaryotic Elements

(2017) Olga Novikova et al.   TRENDS IN GENETICS

Recent horizontal transfer, functional adaptation and dissemination of a bacterial group II intron

(2016) Félix LaRoche-Johnston et al.   BMC EVOLUTIONARY BIOLOGY

Global Epitranscriptomics Profiling of RNA Post-Transcriptional Modifications as an Effective Tool for Investigating the Epitranscriptomics of Stress Response

(2016) Rebecca E. Rose et al.   MOLECULAR & CELLULAR PROTEOMICS

Structure of a group II intron in complex with its reverse transcriptase

(2016) Guosheng Qu et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Structure of a group II intron in complex with its reverse transcriptase

(2016) Guosheng Qu et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Restricting retrotransposons: a review

(2016) John L. Goodier   Mobile DNA

What do we know about ribosomal RNA methylation in Escherichia coli?

(2015) O.V. Sergeeva et al.   BIOCHIMIE

Retrotransposition and Crystal Structure of an Alu RNP in the Ribosome-Stalling Conformation

(2015) Valentina Ahl et al.   MOLECULAR CELL

A 3′ Poly(A) Tract Is Required for LINE-1 Retrotransposition

(2015) Aurélien J. Doucet et al.   MOLECULAR CELL

Profiling ribonucleotide modifications at full-transcriptome level: a step toward MS-based epitranscriptomics

(2015) Rebecca E. Rose et al.   RNA

Evolution of group II introns

(2015) Steven Zimmerly et al.   Mobile DNA

Expanded microbial genome coverage and improved protein family annotation in the COG database

(2014) Michael Y. Galperin et al.   NUCLEIC ACIDS RESEARCH

STRING v10: protein–protein interaction networks, integrated over the tree of life

(2014) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Interaction between Conjugative and Retrotransposable Elements in Horizontal Gene Transfer

(2014) Olga Novikova et al.   PLoS Genetics

SGAtools: one-stop analysis and visualization of array-based genetic interaction screens

(2013) Omar Wagih et al.   NUCLEIC ACIDS RESEARCH

Group II intron-ribosome association protects intron RNA from degradation

(2013) L. M. Contreras et al.   RNA

NIH Image to ImageJ: 25 years of image analysis

(2012) Caroline A Schneider et al.   NATURE METHODS

Normalization, bias correction, and peak calling for ChIP-seq

(2012) Aaron Diaz et al.   Statistical Applications in Genetics and Molecular Biology

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Cytoscape 2.8: new features for data integration and network visualization

(2010) M. E. Smoot et al.   BIOINFORMATICS

The Delta Subunit of RNA Polymerase, RpoE, Is a Global Modulator of Streptococcus mutans Environmental Adaptation

(2010) X. Xue et al.   JOURNAL OF BACTERIOLOGY

Specificity and kinetics of 23S rRNA modification enzymes RlmH and RluD

(2010) R. Ero et al.   RNA

Group II Introns: Mobile Ribozymes that Invade DNA

(2010) A. M. Lambowitz et al.   Cold Spring Harbor Perspectives in Biology

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Global Regulators Orchestrate Group II Intron Retromobility

(2009) Colin J. Coros et al.   MOLECULAR CELL

The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants

(2009) Peter J. A. Cock et al.   NUCLEIC ACIDS RESEARCH

Genome-Wide Functional Divergence after the Symbiosis of Proteobacteria with Insects Unraveled through a Novel Computational Approach

(2009) Christina Toft et al.   PLoS Computational Biology

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

The Take and Give Between Retrotransposable Elements and their Hosts

(2008) Arthur Beauregard et al.   Annual Review of Genetics

A mutant screen reveals RNase E as a silencer of group II intron retromobility in Escherichia coli

(2008) C. J. Coros et al.   RNA

Identification of pseudouridine methyltransferase in Escherichia coli

(2008) R. Ero et al.   RNA

YbeA is the m3  methyltransferase RlmH that targets nucleotide 1915 in 23S rRNA

(2008) E. Purta et al.   RNA

Retrotransposition of the Ll.LtrB group II intron proceeds predominantly via reverse splicing into DNA targets

(2003) Kenji Ichiyanagi et al.   MOLECULAR MICROBIOLOGY