Evolution of a Novel Antiviral Immune-Signaling Interaction by Partial-Gene Duplication

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

The Innate Immune Sensor LGP2 Activates Antiviral Signaling by Regulating MDA5-RNA Interaction and Filament Assembly

(2014) Annie M. Bruns et al.   MOLECULAR CELL

Molecular Imprinting as a Signal-Activation Mechanism of the Viral RNA Sensor RIG-I

(2014) Bin Wu et al.   MOLECULAR CELL

Structural basis for ubiquitin-mediated antiviral signal activation by RIG-I

(2014) Alys Peisley et al.   NATURE

DOT2: Macromolecular docking with improved biophysical models

(2013) Victoria A. Roberts et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Performance of Standard and Stochastic Branch-Site Models for Detecting Positive Selection among Coding Sequences

(2013) A. Lu et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Branch-Site Test of Positive Selection Is Surprisingly Robust but Lacks Power under Synonymous Substitution Saturation and Variation in GC

(2013) Walid H. Gharib et al.   MOLECULAR BIOLOGY AND EVOLUTION

Ancient Origins of Vertebrate-Specific Innate Antiviral Immunity

(2013) Krishanu Mukherjee et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Docking, scoring, and affinity prediction in CAPRI

(2013) Marc F. Lensink et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

How good is automated protein docking?

(2013) Dima Kozakov et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Ubiquitin-Induced Oligomerization of the RNA Sensors RIG-I and MDA5 Activates Antiviral Innate Immune Response

(2012) Xiaomo Jiang et al.   IMMUNITY

The RCSB Protein Data Bank: new resources for research and education

(2012) Peter W. Rose et al.   NUCLEIC ACIDS RESEARCH

CDD: conserved domains and protein three-dimensional structure

(2012) Aron Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

Problems With Estimation of Ancestral Frequencies Under Stationary Models

(2012) Edward Susko et al.   SYSTEMATIC BIOLOGY

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

ProtTest 3: fast selection of best-fit models of protein evolution

(2011) Diego Darriba et al.   BIOINFORMATICS

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

Cytoscape 2.8: new features for data integration and network visualization

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

Robustness of Ancestral Sequence Reconstruction to Phylogenetic Uncertainty

(2010) Victor Hanson-Smith et al.   MOLECULAR BIOLOGY AND EVOLUTION

Statistical Properties of the Branch-Site Test of Positive Selection

(2010) Z. Yang et al.   MOLECULAR BIOLOGY AND EVOLUTION

LGP2 is a positive regulator of RIG-I- and MDA5-mediated antiviral responses

(2010) T. Satoh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Origin and evolution of the RIG-I like RNA helicase gene family

(2009) Jun Zou et al.   BMC EVOLUTIONARY BIOLOGY

The Power of the Methods for Detecting Interlocus Gene Conversion

(2009) S. P. Mansai et al.   GENETICS

Using Sequence Similarity Networks for Visualization of Relationships Across Diverse Protein Superfamilies

(2009) Holly J. Atkinson et al.   PLoS One

Ubiquitous internal gene duplication and intron creation in eukaryotes

(2009) X. Gao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reliabilities of identifying positive selection by the branch-site and the site-prediction methods

(2009) M. Nozawa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Determining kinetics and affinities of protein interactions using a parallel real-time label-free biosensor, the Octet

(2008) Yasmina Abdiche et al.   ANALYTICAL BIOCHEMISTRY

False-positive results obtained from the branch-site test of positive selection

(2008) Yoshiyuki Suzuki   GENES & GENETIC SYSTEMS

Innate immunity to virus infection

(2008) Osamu Takeuchi et al.   IMMUNOLOGICAL REVIEWS

Reconciliation with Non-Binary Species Trees

(2008) Benjamin Vernot et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

An Improved General Amino Acid Replacement Matrix

(2008) S. Q. Le et al.   MOLECULAR BIOLOGY AND EVOLUTION

The amphioxus genome and the evolution of the chordate karyotype

(2008) Nicholas H. Putnam et al.   NATURE

Broad phylogenomic sampling improves resolution of the animal tree of life

(2008) Casey W. Dunn et al.   NATURE

Evolution of MDA-5/RIG-I-dependent innate immunity: Independent evolution by domain grafting

(2008) D. Sarkar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Crystal structure of human IPS-1/MAVS/VISA/Cardif caspase activation recruitment domain

(2008) Jane A Potter et al.   BMC STRUCTURAL BIOLOGY