Modular Organization of Residue-Level Contacts Shapes the Selection Pressure on Individual Amino Acid Sites of Ribosomal Proteins

Plastid–Nuclear Interaction and Accelerated Coevolution in Plastid Ribosomal Genes in Geraniaceae

(2016) Mao-Lun Weng et al.   Genome Biology and Evolution

Causes of evolutionary rate variation among protein sites

(2016) Julian Echave et al.   NATURE REVIEWS GENETICS

Structure, Dynamics, Assembly, and Evolution of Protein Complexes

(2015) Joseph A. Marsh et al.   Annual Review of Biochemistry

TCR affinity for thymoproteasome-dependent positively selecting peptides conditions antigen responsiveness in CD8+ T cells

(2015) Kensuke Takada et al.   NATURE IMMUNOLOGY

High-resolution structure of the Escherichia coli ribosome

(2015) Jonas Noeske et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Assembly constraints drive co-evolution among ribosomal constituents

(2015) S. Mallik et al.   NUCLEIC ACIDS RESEARCH

Contingency and entrenchment in protein evolution under purifying selection

(2015) Premal Shah et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-resolution structure of the Escherichia coli ribosome

(2015) Jonas Noeske et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Forces stabilizing proteins

(2014) C. Nick Pace et al.   FEBS LETTERS

Molecular interactions within the halophilic, thermophilic, and mesophilic prokaryotic ribosomal complexes: clues to environmental adaptation

(2014) Saurav Mallik et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Compensatory Mutations Occur Within the Electrostatic Interaction Range of Deleterious Mutations in Protein Structure

(2014) Amrita Bhattacherjee et al.   JOURNAL OF MOLECULAR EVOLUTION

Evolution of protein structures and interactions from the perspective of residue contact networks

(2013) Xiuwei Zhang et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Evolutionary Rate Heterogeneity of Core and Attachment Proteins in Yeast Protein Complexes

(2013) Sandip Chakraborty et al.   Genome Biology and Evolution

FUBAR: A Fast, Unconstrained Bayesian AppRoximation for Inferring Selection

(2013) B. Murrell et al.   MOLECULAR BIOLOGY AND EVOLUTION

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

(2013) Koichiro Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Enhancing Human Spermine Synthase Activity by Engineered Mutations

(2013) Zhe Zhang et al.   PLoS Computational Biology

Evidence for Compensatory Evolution of Ribosomal Proteins in Response to Rapid Divergence of Mitochondrial rRNA

(2012) F. S. Barreto et al.   MOLECULAR BIOLOGY AND EVOLUTION

Assembly of Bacterial Ribosomes

(2011) Zahra Shajani et al.   Annual Review of Biochemistry

Mitochondrial–Nuclear Interactions and Accelerated Compensatory Evolution: Evidence from the Primate Cytochrome c Oxidase Complex

(2011) Naoki Osada et al.   MOLECULAR BIOLOGY AND EVOLUTION

Structural Calibration of the Rates of Amino Acid Evolution in a Search for Darwin in Drifting Biological Systems

(2010) Christina Toft et al.   MOLECULAR BIOLOGY AND EVOLUTION

Missense suppressor mutations in 16S rRNA reveal the importance of helices h8 and h14 in aminoacyl-tRNA selection

(2010) S. P. McClory et al.   RNA

A minimized rRNA-binding site for ribosomal protein S4 and its implications for 30S assembly

(2009) Deepti L. Bellur et al.   NUCLEIC ACIDS RESEARCH

Optimized Null Model for Protein Structure Networks

(2009) Tijana Milenković et al.   PLoS One

Evolutionary rates and centrality in the yeast gene regulatory network

(2009) Richard Jovelin et al.   GENOME BIOLOGY

GraphCrunch: A tool for large network analyses

(2008) Tijana Milenković et al.   BMC BIOINFORMATICS

Cooperativity in macromolecular assembly

(2008) James R Williamson   Nature Chemical Biology

Revealing unique properties of the ribosome using a network based analysis

(2008) Hilda David-Eden et al.   NUCLEIC ACIDS RESEARCH

Protein Complex Evolution Does Not Involve Extensive Network Rewiring

(2008) Teunis J. P. van Dam et al.   PLoS Computational Biology