LokiarchaeotaMarks the Transition between the Archaeal and Eukaryotic Selenocysteine Encoding Systems

Distribution and Features of the Six Classes of Peroxiredoxins

(2016)   MOLECULES AND CELLS

Archaeal ancestors of eukaryotes: not so elusive any more

(2015) Eugene V. Koonin   BMC BIOLOGY

Archaea

(2015) Laura Eme et al.   CURRENT BIOLOGY

Comparative Genomics Reveals New Candidate Genes Involved in Selenium Metabolism in Prokaryotes

(2015) Jie Lin et al.   Genome Biology and Evolution

Evolution of selenophosphate synthetases: emergence and relocation of function through independent duplications and recurrent subfunctionalization

(2015) Marco Mariotti et al.   GENOME RESEARCH

Complex archaea that bridge the gap between prokaryotes and eukaryotes

(2015) Anja Spang et al.   NATURE

The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Targeted deletion of Secisbp2 reduces, but does not abrogate, selenoprotein expression and leads to striatal interneuron loss

(2014) Sandra Seeher et al.   FREE RADICAL BIOLOGY AND MEDICINE

Selenoproteins: Molecular Pathways and Physiological Roles

(2014) Vyacheslav M. Labunskyy et al.   PHYSIOLOGICAL REVIEWS

Adjustments, extinction, and remains of selenocysteine incorporation machinery in the nematode lineage

(2014) L. Otero et al.   RNA

The SBP2 protein central to selenoprotein synthesis contacts the human ribosome at expansion segment 7L of the 28S rRNA

(2014) O. Kossinova et al.   RNA

Handling tRNA introns, archaeal way and eukaryotic way

(2014) Tohru Yoshihisa   Frontiers in Genetics

Infernal 1.1: 100-fold faster RNA homology searches

(2013) E. P. Nawrocki et al.   BIOINFORMATICS

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

SECISearch3 and Seblastian: new tools for prediction of SECIS elements and selenoproteins

(2013) Marco Mariotti et al.   NUCLEIC ACIDS RESEARCH

The molecular recognition of kink-turn structure by the L7Ae class of proteins

(2013) L. Huang et al.   RNA

Selenocysteine in Thiol/Disulfide-Like Exchange Reactions

(2012) Robert J. Hondal et al.   ANTIOXIDANTS & REDOX SIGNALING

Genome-wide analysis of putative peroxiredoxin in unicellular and filamentous cyanobacteria

(2012) Hongli Cui et al.   BMC EVOLUTIONARY BIOLOGY

Evolution of selenoproteins in the metazoan

(2012) Liang Jiang et al.   BMC GENOMICS

Composition and Evolution of the Vertebrate and Mammalian Selenoproteomes

(2012) Marco Mariotti et al.   PLoS One

ViennaRNA Package 2.0

(2011) Ronny Lorenz et al.   Algorithms for Molecular Biology

Comparative Genomics of Thiol Oxidoreductases Reveals Widespread and Essential Functions of Thiol-based Redox Control of Cellular Processes

(2011) Dmitri E. Fomenko et al.   ANTIOXIDANTS & REDOX SIGNALING

A 4-Selenocysteine, 2-Selenocysteine Insertion Sequence (SECIS) Element Methionine Sulfoxide Reductase fromMetridium senileReveals a Non-catalytic Function of Selenocysteines

(2011) Byung Cheon Lee et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

Differing views of the role of selenium in thioredoxin reductase

(2010) Robert J. Hondal et al.   AMINO ACIDS

Selenoprofiles: profile-based scanning of eukaryotic genome sequences for selenoprotein genes

(2010) M. Mariotti et al.   BIOINFORMATICS

ETE: a python Environment for Tree Exploration

(2010) Jaime Huerta-Cepas et al.   BMC BIOINFORMATICS

Structural Basis for the Major Role of O-Phosphoseryl-tRNA Kinase in the UGA-Specific Encoding of Selenocysteine

(2010) Shiho Chiba et al.   MOLECULAR CELL

PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions

(2010) J. Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

The origin and early evolution of eukaryotes in the light of phylogenomics

(2010) Eugene V Koonin   GENOME BIOLOGY

On the unique function of selenocysteine — Insights from the evolution of selenoproteins

(2009) Sergi Castellano   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

Selenoproteins in Archaea and Gram-positive bacteria

(2009) Tilmann Stock et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

Eukaryotic selenoproteins and selenoproteomes

(2009) Alexey V. Lobanov et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

The many levels of control on bacterial selenoprotein synthesis

(2009) Satoko Yoshizawa et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

SECISaln, a web-based tool for the creation of structure-based alignments of eukaryotic SECIS elements

(2009) Charles E. Chapple et al.   BIOINFORMATICS

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

Evolutionary history of selenocysteine incorporation from the perspective of SECIS binding proteins

(2009) Jesse Donovan et al.   BMC EVOLUTIONARY BIOLOGY

Novel structural determinants in human SECIS elements modulate the translational recoding of UGA as selenocysteine

(2009) Lynda Latrèche et al.   NUCLEIC ACIDS RESEARCH

GBParsy: A GenBank flatfile parser library with high speed

(2008) Tae-Ho Lee et al.   BMC BIOINFORMATICS

RNAalifold: improved consensus structure prediction for RNA alignments

(2008) Stephan H Bernhart et al.   BMC BIOINFORMATICS

Discovering Sequence Motifs with Arbitrary Insertions and Deletions

(2008) Martin C. Frith et al.   PLoS Computational Biology

Trends in Selenium Utilization in Marine Microbial World Revealed through the Analysis of the Global Ocean Sampling (GOS) Project

(2008) Yan Zhang et al.   PLoS Genetics

Reduced reliance on the trace element selenium during evolution of mammals

(2008) Alexey V Lobanov et al.   GENOME BIOLOGY