Structure Prediction and Analysis of DNA Transposon and LINE Retrotransposon Proteins

Turning gold into ‘junk’: transposable elements utilize central proteins of cellular networks

(2013) György Abrusán et al.   NUCLEIC ACIDS RESEARCH

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Intrinsically disordered proteins: a 10-year recap

(2012) Peter Tompa   TRENDS IN BIOCHEMICAL SCIENCES

Evolution and disorder

(2011) Celeste J Brown et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

The Proteome Folding Project: Proteome-scale prediction of structure and function

(2011) K. Drew et al.   GENOME RESEARCH

Self-Interaction, Nucleic Acid Binding, and Nucleic Acid Chaperone Activities Are Unexpectedly Retained in the Unique ORF1p of Zebrafish LINE

(2011) M. Nakamura et al.   MOLECULAR AND CELLULAR BIOLOGY

Location of disorder in coiled coilproteins is influenced by its biological role and subcellular localization: a GO-based study on human proteome

(2011) Meenakshi Anurag et al.   Molecular BioSystems

A high-resolution map of human evolutionary constraint using 29 mammals

(2011) Kerstin Lindblad-Toh et al.   NATURE

Microfossils of sulphur-metabolizing cells in 3.4-billion-year-old rocks of Western Australia

(2011) David Wacey et al.   Nature Geoscience

Trimeric structure and flexibility of the L1ORF1 protein in human L1 retrotransposition

(2011) Elena Khazina et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Polymerization and nucleic acid-binding properties of human L1 ORF1 protein

(2011) Kathryn E. Callahan et al.   NUCLEIC ACIDS RESEARCH

A hyperactive piggyBac transposase for mammalian applications

(2011) K. Yusa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Distributions of Transposable Elements Reveal Hazardous Zones in Mammalian Introns

(2011) Ying Zhang et al.   PLoS Computational Biology

Intrinsically disordered chaperones in plants and animalsThis paper is one of a selection of papers published in this special issue entitled “Canadian Society of Biochemistry, Molecular & Cellular Biology 52nd Annual Meeting — Protein Folding: Principles and Diseases” and has undergone the Journal's usual peer review process.

(2010) Peter Tompa et al.   Biochemistry and Cell Biology

How significant is a protein structure similarity with TM-score = 0.5?

(2010) Jinrui Xu et al.   BIOINFORMATICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Hidden Markov model speed heuristic and iterative HMM search procedure

(2010) L Steven Johnson et al.   BMC BIOINFORMATICS

A Universal Molecular Clock of Protein Folds and Its Power in Tracing the Early History of Aerobic Metabolism and Planet Oxygenation

(2010) Minglei Wang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Comparative Analysis of Transposable Element Vector Systems in Human Cells

(2010) Ivana Grabundzija et al.   MOLECULAR THERAPY

A role for host–parasite interactions in the horizontal transfer of transposons across phyla

(2010) Clément Gilbert et al.   NATURE

I-TASSER: a unified platform for automated protein structure and function prediction

(2010) Ambrish Roy et al.   Nature Protocols

Ongoing and future developments at the Universal Protein Resource

(2010)   NUCLEIC ACIDS RESEARCH

CDD: a Conserved Domain Database for the functional annotation of proteins

(2010) A. Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

History of biological metal utilization inferred through phylogenomic analysis of protein structures

(2010) C. L. Dupont et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Promiscuous DNA: horizontal transfer of transposable elements and why it matters for eukaryotic evolution

(2010) Sarah Schaack et al.   TRENDS IN ECOLOGY & EVOLUTION

The origin, evolution and structure of the protein world

(2009) Gustavo Caetano-Anollés et al.   BIOCHEMICAL JOURNAL

Evolutionary formation of new protein folds is linked to metallic cofactor recruitment

(2009) Hong-Fang Ji et al.   BIOESSAYS

Molecular evolution of a novel hyperactive Sleeping Beauty transposase enables robust stable gene transfer in vertebrates

(2009) Lajos Mátés et al.   NATURE GENETICS

The evolutionary consequences of erroneous protein synthesis

(2009) D. Allan Drummond et al.   NATURE REVIEWS GENETICS

Non-LTR retrotransposons encode noncanonical RRM domains in their first open reading frame

(2009) Elena Khazina et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bimodal protein solubility distribution revealed by an aggregation analysis of the entire ensemble of Escherichia coli proteins

(2009) T. Niwa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Macromolecular Modeling with Rosetta

(2008) Rhiju Das et al.   Annual Review of Biochemistry

I-TASSER server for protein 3D structure prediction

(2008) Yang Zhang   BMC BIOINFORMATICS

Mistranslation-Induced Protein Misfolding as a Dominant Constraint on Coding-Sequence Evolution

(2008) D. Allan Drummond et al.   CELL

Function and structure of inherently disordered proteins

(2008) A Keith Dunker et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Transposable elements and the evolution of regulatory networks

(2008) Cédric Feschotte   NATURE REVIEWS GENETICS

FIEFDom: a transparent domain boundary recognition system using a fuzzy mean operator

(2008) R. Bondugula et al.   NUCLEIC ACIDS RESEARCH

SUPERFAMILY—sophisticated comparative genomics, data mining, visualization and phylogeny

(2008) Derek Wilson et al.   NUCLEIC ACIDS RESEARCH

OCEANS: Elements and Evolution

(2008) A. D. Anbar   SCIENCE