Position-dependent termination and widespread obligatory frameshifting in Euplotes translation

Genetic Codes with No Dedicated Stop Codon: Context-Dependent Translation Termination

(2016) Estienne Carl Swart et al.   CELL

Novel Ciliate Genetic Code Variants Including the Reassignment of All Three Stop Codons to Sense Codons inCondylostoma magnum

(2016) Stephen M. Heaphy et al.   MOLECULAR BIOLOGY AND EVOLUTION

High frequency of +1 programmed ribosomal frameshifting in Euplotes octocarinatus

(2016) Ruanlin Wang et al.   Scientific Reports

Augmented genetic decoding: global, local and temporal alterations of decoding processes and codon meaning

(2015) Pavel V. Baranov et al.   NATURE REVIEWS GENETICS

LC–MS Proteomics Analysis of the Insulin/IGF-1-Deficient Caenorhabditis elegans daf-2(e1370) Mutant Reveals Extensive Restructuring of Intermediary Metabolism

(2014) Geert Depuydt et al.   JOURNAL OF PROTEOME RESEARCH

Ribosome profiling: new views of translation, from single codons to genome scale

(2014) Nicholas T. Ingolia   NATURE REVIEWS GENETICS

MS-GF+ makes progress towards a universal database search tool for proteomics

(2014) Sangtae Kim et al.   Nature Communications

Reduced Insulin/Insulin-like Growth Factor-1 Signaling and Dietary Restriction Inhibit Translation but Preserve Muscle Mass inCaenorhabditis elegans

(2013) Geert Depuydt et al.   MOLECULAR & CELLULAR PROTEOMICS

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

The Oxytricha trifallax Macronuclear Genome: A Complex Eukaryotic Genome with 16,000 Tiny Chromosomes

(2013) Estienne C. Swart et al.   PLOS BIOLOGY

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

High-pH reversed-phase chromatography with fraction concatenation for 2D proteomic analysis

(2012) Feng Yang et al.   Expert Review of Proteomics

Genome-wide ribosome profiling reveals complex translational regulation in response to oxidative stress

(2012) M. V. Gerashchenko et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Act together—implications of symbioses in aquatic ciliates

(2012) Claudia Dziallas et al.   Frontiers in Microbiology

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

A Pilot Study of Bacterial Genes with Disrupted ORFs Reveals a Surprising Profusion of Protein Sequence Recoding Mediated by Ribosomal Frameshifting and Transcriptional Realignment

(2011) V. Sharma et al.   MOLECULAR BIOLOGY AND EVOLUTION

Fast Identification and Removal of Sequence Contamination from Genomic and Metagenomic Datasets

(2011) Robert Schmieder et al.   PLoS One

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

Molecular cold-adaptation of protein function and gene regulation: The case for comparative genomic analyses in marine ciliated protozoa

(2009) Sandra Pucciarelli et al.   Marine Genomics

DtaRefinery, a Software Tool for Elimination of Systematic Errors from Parent Ion Mass Measurements in Tandem Mass Spectra Data Sets

(2009) Vladislav A. Petyuk et al.   MOLECULAR & CELLULAR PROTEOMICS

Connection between stop codon reassignment and frequent use of shifty stop frameshifting

(2009) H. Vallabhaneni et al.   RNA

Genetic Code Supports Targeted Insertion of Two Amino Acids by One Codon

(2009) A. A. Turanov et al.   SCIENCE

Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling

(2009) N. T. Ingolia et al.   SCIENCE

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

DeconMSn: a software tool for accurate parent ion monoisotopic mass determination for tandem mass spectra

(2008) A. M. Mayampurath et al.   BIOINFORMATICS

Macronuclear genome structure of the ciliate Nyctotherus ovalis: Single-gene chromosomes and tiny introns

(2008) Guénola Ricard et al.   BMC GENOMICS

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Characterization of the Mouse Pancreatic Islet Proteome and Comparative Analysis with Other Mouse Tissues

(2008) Vladislav A. Petyuk et al.   JOURNAL OF PROTEOME RESEARCH

Frameshifting RNA pseudoknots: Structure and mechanism

(2008) David P. Giedroc et al.   VIRUS RESEARCH