Gene Transfers Shaped the Evolution of De Novo NAD + Biosynthesis in Eukaryotes

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Horizontal gene acquisitions by eukaryotes as drivers of adaptive evolution

(2013) Gerald Schönknecht et al.   BIOESSAYS

Pan genome of the phytoplankton Emiliania underpins its global distribution

(2013) Betsy A. Read et al.   NATURE

Data, information, knowledge and principle: back to metabolism in KEGG

(2013) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

The First Symbiont-Free Genome Sequence of Marine Red Alga, Susabi-nori (Pyropia yezoensis)

(2013) Yoji Nakamura et al.   PLoS One

Genome structure and metabolic features in the red seaweed Chondrus crispus shed light on evolution of the Archaeplastida

(2013) J. Collen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gene Transfer from Bacteria and Archaea Facilitated Evolution of an Extremophilic Eukaryote

(2013) G. Schonknecht et al.   SCIENCE

Assessing the bacterial contribution to the plastid proteome

(2013) Huan Qiu et al.   TRENDS IN PLANT SCIENCE

Genome of the red alga Porphyridium purpureum

(2013) Debashish Bhattacharya et al.   Nature Communications

Phylogeny of Heterokonta: Incisomonas marina, a uniciliate gliding opalozoan related to Solenicola (Nanomonadea), and evidence that Actinophryida evolved from raphidophytes

(2012) Thomas Cavalier-Smith et al.   EUROPEAN JOURNAL OF PROTISTOLOGY

The evolution of three types of indoleamine 2,3 dioxygenases in fungi with distinct molecular and biochemical characteristics

(2012) Hajime J. Yuasa et al.   GENE

Re-evaluating the Green versus Red Signal in Eukaryotes with Secondary Plastid of Red Algal Origin

(2012) Fabien Burki et al.   Genome Biology and Evolution

Reevaluating the Green Contribution to Diatom Genomes

(2012) Philippe Deschamps et al.   Genome Biology and Evolution

Genomes of Stigonematalean Cyanobacteria (Subsection V) and the Evolution of Oxygenic Photosynthesis from Prokaryotes to Plastids

(2012) Tal Dagan et al.   Genome Biology and Evolution

Improving the Accuracy of Demographic and Molecular Clock Model Comparison While Accommodating Phylogenetic Uncertainty

(2012) Guy Baele et al.   MOLECULAR BIOLOGY AND EVOLUTION

Kynurenines in the mammalian brain: when physiology meets pathology

(2012) Robert Schwarcz et al.   NATURE REVIEWS NEUROSCIENCE

Gain and loss of multiple functionally related, horizontally transferred genes in the reduced genomes of two microsporidian parasites

(2012) J.-F. Pombert et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The evolutionary history of haptophytes and cryptophytes: phylogenomic evidence for separate origins

(2012) F. Burki et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Cyanophora paradoxa Genome Elucidates Origin of Photosynthesis in Algae and Plants

(2012) D. C. Price et al.   SCIENCE

Molecular evolution of bacterial indoleamine 2,3-dioxygenase

(2011) Hajime J. Yuasa et al.   GENE

Red and Problematic Green Phylogenetic Signals among Thousands of Nuclear Genes from the Photosynthetic and Apicomplexa-Related Chromera velia

(2011) Christian Woehle et al.   Genome Biology and Evolution

Evolution of Patchily Distributed Proteins Shared between Eukaryotes and Prokaryotes: Dictyostelium as a Case Study

(2011) Jan O. Andersson   JOURNAL OF MOLECULAR MICROBIOLOGY AND BIOTECHNOLOGY

Large-Scale Phylogenomic Analyses Indicate a Deep Origin of Primary Plastids within Cyanobacteria

(2011) Alexis Criscuolo et al.   MOLECULAR BIOLOGY AND EVOLUTION

T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension

(2011) P. Di Tommaso et al.   NUCLEIC ACIDS RESEARCH

Niche of harmful alga Aureococcus anophagefferens revealed through ecogenomics

(2011) C. J. Gobler et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Horizontal Transfer, Not Duplication, Drives the Expansion of Protein Families in Prokaryotes

(2011) Todd J. Treangen et al.   PLoS Genetics

Phylogenomic Evidence for Separate Acquisition of Plastids in Cryptophytes, Haptophytes, and Stramenopiles

(2010) D. Baurain et al.   MOLECULAR BIOLOGY AND EVOLUTION

Reconstruction and flux-balance analysis of the Plasmodium falciparum metabolic network

(2010) Germán Plata et al.   Molecular Systems Biology

The endosymbiotic origin, diversification and fate of plastids

(2010) P. J. Keeling   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A Molecular Genetic Timescale for the Diversification of Autotrophic Stramenopiles (Ochrophyta): Substantive Underestimation of Putative Fossil Ages

(2010) Joseph W. Brown et al.   PLoS One

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

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Synthesizing and Salvaging NAD+: Lessons Learned from Chlamydomonas reinhardtii

(2010) Huawen Lin et al.   PLoS Genetics

Functional replacement of a primary metabolic pathway via multiple independent eukaryote-to-eukaryote gene transfers and selective retention

(2009) A. M. NEDELCU et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Microbial NAD Metabolism: Lessons from Comparative Genomics

(2009) F. Gazzaniga et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Genomic Footprints of a Cryptic Plastid Endosymbiosis in Diatoms

(2009) A. Moustafa et al.   SCIENCE

The transferome of metabolic genes explored: analysis of the horizontal transfer of enzyme encoding genes in unicellular eukaryotes

(2009) John W Whitaker et al.   GENOME BIOLOGY

Identification of Formyl Kynurenine Formamidase and Kynurenine Aminotransferase fromSaccharomyces cerevisiaeUsing Crystallographic, Bioinformatic and Biochemical Evidence‡

(2008) Mark Wogulis et al.   BIOCHEMISTRY

NAD Biosynthesis Evolution in Bacteria: Lateral Gene Transfer of Kynurenine Pathway in Xanthomonadales and Flavobacteriales

(2008) W. C. Lima et al.   MOLECULAR BIOLOGY AND EVOLUTION

Horizontal gene transfer in eukaryotic evolution

(2008) Patrick J. Keeling et al.   NATURE REVIEWS GENETICS