Novel insights into the origin and diversification of photosynthesis based on analyses of conserved indels in the core reaction center proteins

Orientations of Iron–Sulfur Clusters FA and FB in the Homodimeric Type-I Photosynthetic Reaction Center of Heliobacterium modesticaldum

(2016) Toru Kondo et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Molecular signatures that are distinctive characteristics of the vertebrates and chordates and supporting a grouping of vertebrates with the tunicates

(2016) Radhey S. Gupta   MOLECULAR PHYLOGENETICS AND EVOLUTION

GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters

(2015) Itamar Sela et al.   NUCLEIC ACIDS RESEARCH

Evidence for the presence of key chlorophyll-biosynthesis-related proteins in the genus Rubrobacter (Phylum Actinobacteria) and its implications for the evolution and origin of photosynthesis

(2015) Radhey S. Gupta et al.   PHOTOSYNTHESIS RESEARCH

A fresh look at the evolution and diversification of photochemical reaction centers

(2014) Tanai Cardona   PHOTOSYNTHESIS RESEARCH

Functional type 2 photosynthetic reaction centers found in the rare bacterial phylum Gemmatimonadetes

(2014) Y. Zeng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural and kinetic properties of Rhodobacter sphaeroides photosynthetic reaction centers containing exclusively Zn-coordinated bacteriochlorophyll as bacteriochlorin cofactors

(2013) Rafael G. Saer et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

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

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

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

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

The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks

(2013) Pelin Yilmaz et al.   NUCLEIC ACIDS RESEARCH

PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes

(2013) Nicola Segata et al.   Nature Communications

Evolutionary inaccuracy of pairwise structural alignments

(2012) M. I. Sadowski et al.   BIOINFORMATICS

Chlorophyll Biosynthesis Gene Evolution Indicates Photosystem Gene Duplication, Not Photosystem Merger, at the Origin of Oxygenic Photosynthesis

(2012) Filipa L. Sousa et al.   Genome Biology and Evolution

Origin and Spread of Photosynthesis Based upon Conserved Sequence Features in Key Bacteriochlorophyll Biosynthesis Proteins

(2012) Radhey S. Gupta   MOLECULAR BIOLOGY AND EVOLUTION

FastML: a web server for probabilistic reconstruction of ancestral sequences

(2012) H. Ashkenazy et al.   NUCLEIC ACIDS RESEARCH

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

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

Evolution of Photosynthesis

(2011) Martin F. Hohmann-Marriott et al.   Annual Review of Plant Biology

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

Mechanisms of protein oligomerization, the critical role of insertions and deletions in maintaining different oligomeric states

(2010) K. Hashimoto et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural analysis of polarizing indels: an emerging consensus on the root of the tree of life

(2009) Ruben E Valas et al.   Biology Direct

Conserved inserts in the Hsp60 (GroEL) and Hsp70 (DnaK) proteins are essential for cellular growth

(2009) Bhag Singh et al.   MOLECULAR GENETICS AND GENOMICS

A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea

(2009) Dongying Wu et al.   NATURE

A viewpoint: Why chlorophyll a?

(2009) Lars Olof Björn et al.   PHOTOSYNTHESIS RESEARCH

An Improved General Amino Acid Replacement Matrix

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

Built-in loops allow versatility in domain-domain interactions: Lessons from self-interacting domains

(2008) E. Akiva et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA