Evolution of PAS domains and PAS-containing genes in eukaryotes

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

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

Structural Properties of PAS Domains from the KCNH Potassium Channels

(2013) Ricardo Adaixo et al.   PLoS One

Light-Induced Subunit Dissociation by a Light–Oxygen–Voltage Domain Photoreceptor from Rhodobacter sphaeroides

(2012) Karen S. Conrad et al.   BIOCHEMISTRY

The β-Scaffold of the LOV Domain of the Brucella Light-Activated Histidine Kinase Is a Key Element for Signal Transduction

(2012) Jimena Rinaldi et al.   JOURNAL OF MOLECULAR BIOLOGY

LOV Domain-Containing F-Box Proteins: Light-Dependent Protein Degradation Modules in Arabidopsis

(2012) Shogo Ito et al.   Molecular Plant

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

Unwinding the differences of the mammalian PERIOD clock proteins from crystal structure to cellular function

(2012) N. Kucera et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Crystal Structure of the Heterodimeric CLOCK:BMAL1 Transcriptional Activator Complex

(2012) N. Huang et al.   SCIENCE

Crystal Structures of Aureochrome1 LOV Suggest New Design Strategies for Optogenetics

(2012) Devrani Mitra et al.   STRUCTURE

Climate of the Neoproterozoic

(2011) R.T. Pierrehumbert et al.   Annual Review of Earth and Planetary Sciences

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

(2011) Diego Darriba et al.   BIOINFORMATICS

Phytochrome structure and photochemistry: recent advances toward a complete molecular picture

(2011) Andrew T Ulijasz et al.   CURRENT OPINION IN PLANT BIOLOGY

Molecular cloning and functional analysis of one ZEITLUPE homolog GmZTL3 in soybean

(2011) Zheng-Gang Xue et al.   MOLECULAR BIOLOGY REPORTS

Dating the arthropod tree based on large-scale transcriptome data

(2011) Peter Rehm et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Function, structure and mechanism of bacterial photosensory LOV proteins

(2011) Julien Herrou et al.   NATURE REVIEWS MICROBIOLOGY

Structural basis of photosensitivity in a bacterial light-oxygen-voltage/helix-turn-helix (LOV-HTH) DNA-binding protein

(2011) A. I. Nash et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structure of a Light-Activated LOV Protein Dimer That Regulates Transcription

(2011) A. T. Vaidya et al.   Science Signaling

Ligand-Binding PAS Domains in a Genomic, Cellular, and Structural Context

(2010) Jonathan T. Henry et al.   Annual Review of Microbiology

Does the core circadian clock in the moss Physcomitrella patens (Bryophyta) comprise a single loop?

(2010) Karl Holm et al.   BMC PLANT BIOLOGY

Circadian Clock Gene Bmal1 Is Not Essential; Functional Replacement with its Paralog, Bmal2

(2010) Shuqun Shi et al.   CURRENT BIOLOGY

Circadian Input Kinases and Their Homologs in Cyanobacteria: Evolutionary Constraints Versus Architectural Diversification

(2010) Ivan Baca et al.   JOURNAL OF MOLECULAR EVOLUTION

ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids

(2010) H. Ashkenazy et al.   NUCLEIC ACIDS RESEARCH

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

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

Molecular Evolution and Functional Divergence of the Cytochrome P450 3 (CYP3) Family in Actinopterygii (Ray-Finned Fish)

(2010) Jun Yan et al.   PLoS One

Robustness and evolvability in the functional anatomy of a PER-ARNT-SIM (PAS) domain

(2010) A. F. Philip et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

(PS)2-v2: template-based protein structure prediction server

(2009) Chih-Chieh Chen et al.   BMC BIOINFORMATICS

Distribution and Phylogeny of Light-Oxygen-Voltage-Blue-Light-Signaling Proteins in the Three Kingdoms of Life

(2009) U. Krauss et al.   JOURNAL OF BACTERIOLOGY

Circadian clock in Ciona intestinalis revealed by microarray analysis and oxygen consumption

(2009) Toshifumi Minamoto et al.   JOURNAL OF BIOCHEMISTRY

Fungi evolved right on track

(2009) Robert Lücking et al.   MYCOLOGIA

Mechanism-based tuning of a LOV domain photoreceptor

(2009) Brian D Zoltowski et al.   Nature Chemical Biology

Protein structure homology modeling using SWISS-MODEL workspace

(2009) Lorenza Bordoli et al.   Nature Protocols

Structural and Functional Analyses of PAS Domain Interactions of the Clock Proteins Drosophila PERIOD and Mouse PERIOD2

(2009) Sven Hennig et al.   PLOS BIOLOGY

Decoding of Light Signals by Plant Phytochromes and Their Interacting Proteins

(2008) Gabyong Bae et al.   Annual Review of Plant Biology

Light Activation of the LOV Protein Vivid Generates a Rapidly Exchanging Dimer†‡

(2008) Brian D. Zoltowski et al.   BIOCHEMISTRY

Comparative genomic analysis of teleost fish bmal genes

(2008) Han Wang   GENETICA

The Fungal Phytochrome FphA fromAspergillus nidulans

(2008) Sonja Brandt et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Comparative Analysis of Period Genes in Teleost Fish Genomes

(2008) Han Wang   JOURNAL OF MOLECULAR EVOLUTION

Comparative analysis of teleost fish genomes reveals preservation of different ancient clock duplicates in different fishes

(2008) Han Wang   Marine Genomics

An Improved General Amino Acid Replacement Matrix

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

Duplicated Paralogous Genes Subject to Positive Selection in the Genome of Trypanosoma brucei

(2008) Richard D. Emes et al.   PLoS One

The Avalon Explosion: Evolution of Ediacara Morphospace

(2008) B. Shen et al.   SCIENCE

The phytochrome red/far-red photoreceptor superfamily

(2008) Robert A Sharrock   GENOME BIOLOGY