Synergistic use of plant-prokaryote comparative genomics for functional annotations

A role for the universal Kae1/Qri7/YgjD (COG0533) family in tRNA modification

(2011) Basma El Yacoubi et al.   EMBO JOURNAL

Moonlighting Glutamate Formiminotransferases Can Functionally Replace 5-Formyltetrahydrofolate Cycloligase

(2010) Linda Jeanguenin et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana

(2010) Insuk Lee et al.   NATURE BIOTECHNOLOGY

The ribosome assembly factor Nep1 responsible for Bowen–Conradi syndrome is a pseudouridine-N1-specific methyltransferase

(2010) Jan Philip Wurm et al.   NUCLEIC ACIDS RESEARCH

A role for tetrahydrofolates in the metabolism of iron-sulfur clusters in all domains of life

(2010) J. C. Waller et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

‘Unknown’ proteins and ‘orphan’ enzymes: the missing half of the engineering parts list – and how to find it

(2009) Andrew D. Hanson et al.   BIOCHEMICAL JOURNAL

Molecular identification of ω-amidase, the enzyme that is functionally coupled with glutamine transaminases, as the putative tumor suppressor Nit2

(2009) Stéphane Jaisson et al.   BIOCHIMIE

Identification of the putative tumor suppressor Nit2 as ω-amidase, an enzyme metabolically linked to glutamine and asparagine transamination

(2009) Boris F. Krasnikov et al.   BIOCHIMIE

A subset of the diverse COG0523 family of putative metal chaperones is linked to zinc homeostasis in all kingdoms of life

(2009) Crysten E Haas et al.   BMC GENOMICS

Contributions of Zur-Controlled Ribosomal Proteins to Growth under Zinc Starvation Conditions

(2009) S. E. Gabriel et al.   JOURNAL OF BACTERIOLOGY

6-Pyruvoyltetrahydropterin Synthase Paralogs Replace the Folate Synthesis Enzyme Dihydroneopterin Aldolase in Diverse Bacteria

(2009) A. Pribat et al.   JOURNAL OF BACTERIOLOGY

Two d-2-Hydroxy-acid Dehydrogenases inArabidopsis thalianawith Catalytic Capacities to Participate in the Last Reactions of the Methylglyoxal and β-Oxidation Pathways

(2009) Martin Engqvist et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Arabidopsis OBG-Like GTPase (AtOBGL) Is Localized in Chloroplasts and Has an Essential Function in Embryo Development

(2009) Fatima Chigri et al.   Molecular Plant

Fine-tuning of the ribosomal decoding center by conserved methyl-modifications in the Escherichia coli 16S rRNA

(2009) Satoshi Kimura et al.   NUCLEIC ACIDS RESEARCH

The universal YrdC/Sua5 family is required for the formation of threonylcarbamoyladenosine in tRNA

(2009) B. El Yacoubi et al.   NUCLEIC ACIDS RESEARCH

CyanoBase: the cyanobacteria genome database update 2010

(2009) Mitsuteru Nakao et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database

(2009) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

The chloroplast protein BPG2 functions in brassinosteroid-mediated post-transcriptional accumulation of chloroplast rRNA

(2009) Tomoyuki Komatsu et al.   PLANT JOURNAL

Global Functional Atlas of Escherichia coli Encompassing Previously Uncharacterized Proteins

(2009) Pingzhao Hu et al.   PLOS BIOLOGY

Annotation Error in Public Databases: Misannotation of Molecular Function in Enzyme Superfamilies

(2009) Alexandra M. Schnoes et al.   PLoS Computational Biology

Improved annotation through genome-scale metabolic modeling of Aspergillus oryzae

(2008) Wanwipa Vongsangnak et al.   BMC GENOMICS

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS

Molecular Identification of Pseudouridine-metabolizing Enzymes

(2008) Alice Preumont et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The Structure of YqeH

(2008) Jawahar Sudhamsu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Turning a hobby into a job: How duplicated genes find new functions

(2008) Gavin C. Conant et al.   NATURE REVIEWS GENETICS

PPDB, the Plant Proteomics Database at Cornell

(2008) Qi Sun et al.   NUCLEIC ACIDS RESEARCH

Pseudomonas Genome Database: facilitating user-friendly, comprehensive comparisons of microbial genomes

(2008) G. L. Winsor et al.   NUCLEIC ACIDS RESEARCH

ATTED-II provides coexpressed gene networks for Arabidopsis

(2008) T. Obayashi et al.   NUCLEIC ACIDS RESEARCH

EcoCyc: A comprehensive view of Escherichia coli biology

(2008) I. M. Keseler et al.   NUCLEIC ACIDS RESEARCH

Phylogenomic and Functional Analysis of Pterin-4a-Carbinolamine Dehydratase Family (COG2154) Proteins in Plants and Microorganisms

(2008) V. Naponelli et al.   PLANT PHYSIOLOGY

Annotating Genes of Known and Unknown Function by Large-Scale Coexpression Analysis

(2008) K. Horan et al.   PLANT PHYSIOLOGY

Refinement of Light-Responsive Transcript Lists Using Rice Oligonucleotide Arrays: Evaluation of Gene-Redundancy

(2008) Ki-Hong Jung et al.   PLoS One

Plasmodium falciparum: a paradigm for alternative folate biosynthesis in diverse microorganisms?

(2008) John E. Hyde et al.   TRENDS IN PARASITOLOGY