Published in Res Microbiol on December 19, 2005
Giant viruses, giant chimeras: the multiple evolutionary histories of Mimivirus genes. BMC Evol Biol (2008) 1.87
Structural and evolutionary bioinformatics of the SPOUT superfamily of methyltransferases. BMC Bioinformatics (2007) 1.74
A tale of two oxidation states: bacterial colonization of arsenic-rich environments. PLoS Genet (2007) 1.59
Phylogenomic analysis of the GIY-YIG nuclease superfamily. BMC Genomics (2006) 1.56
The last universal common ancestor: emergence, constitution and genetic legacy of an elusive forerunner. Biol Direct (2008) 1.40
On the origin of cells and viruses: primordial virus world scenario. Ann N Y Acad Sci (2009) 1.29
Divergence and convergence in enzyme evolution: parallel evolution of paraoxonases from quorum-quenching lactonases. J Biol Chem (2011) 1.24
Evolution of the arginase fold and functional diversity. Cell Mol Life Sci (2008) 1.09
From essential to persistent genes: a functional approach to constructing synthetic life. Trends Genet (2012) 1.04
Reconstructing ancestral gene content by coevolution. Genome Res (2009) 1.04
Computational identification of obligatorily autocatalytic replicators embedded in metabolic networks. Genome Biol (2008) 1.03
The proteomic complexity and rise of the primordial ancestor of diversified life. BMC Evol Biol (2011) 1.00
Toward a systems biology perspective on enzyme evolution. J Biol Chem (2011) 0.96
Evolution of small prokaryotic genomes. Front Microbiol (2015) 0.91
Virtual genomes in flux: an interplay of neutrality and adaptability explains genome expansion and streamlining. Genome Biol Evol (2012) 0.87
Did the last common ancestor have a biological membrane? Biol Direct (2006) 0.86
The queuine micronutrient: charting a course from microbe to man. Nutrients (2015) 0.86
Decoding in Candidatus Riesia pediculicola, close to a minimal tRNA modification set? Trends Cell Mol Biol (2012) 0.82
Oxygen and hydrogen peroxide in the early evolution of life on earth: in silico comparative analysis of biochemical pathways. Astrobiology (2012) 0.81
Detection of genomic idiosyncrasies using fuzzy phylogenetic profiles. PLoS One (2013) 0.80
Efficient algorithms for reconstructing gene content by co-evolution. BMC Bioinformatics (2011) 0.79
The last universal common ancestor (LUCA) and the ancestors of archaea and bacteria were progenotes. J Mol Evol (2010) 0.78
One step beyond a ribosome: The ancient anaerobic core. Biochim Biophys Acta (2016) 0.78
A synergism between adaptive effects and evolvability drives whole genome duplication to fixation. PLoS Comput Biol (2014) 0.78
Primal eukaryogenesis: on the communal nature of precellular States, ancestral to modern life. Life (Basel) (2012) 0.78
The conflict between horizontal gene transfer and the safeguard of identity: origin of meiotic sexuality. J Mol Evol (2009) 0.78
The non-biological meaning of the term "prokaryote" and its implications. J Mol Evol (2014) 0.76
The TIM Barrel Architecture Facilitated the Early Evolution of Protein-Mediated Metabolism. J Mol Evol (2016) 0.76
Enzymatic Antioxidant Systems in Early Anaerobes: Theoretical Considerations. Astrobiology (2016) 0.76
The orphan protein bis-γ-glutamylcystine reductase joins the pyridine nucleotide disulfide reductase family. Biochemistry (2013) 0.76
Physiology, phylogeny, and LUCA. Microb Cell (2016) 0.75
Facilitating the Evolution of Esterase Activity from a Promiscuous Enzyme (Mhg) with Catalytic Functions of Amide Hydrolysis and Carboxylic Acid Perhydrolysis by Engineering the Substrate Entrance Tunnel. Appl Environ Microbiol (2016) 0.75
2011 William Allan Award: development and evolution. Am J Hum Genet (2012) 0.75
De novo active sites for resurrected Precambrian enzymes. Nat Commun (2017) 0.75
Discovery of a widespread prokaryotic 5-oxoprolinase that was hiding in plain sight. J Biol Chem (2017) 0.75
A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature (2009) 15.06
CRISPR--a widespread system that provides acquired resistance against phages in bacteria and archaea. Nat Rev Microbiol (2008) 8.91
Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature (2007) 7.42
Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Res (2005) 7.13
Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities. Nat Biotechnol (2006) 5.71
Experimental factors affecting PCR-based estimates of microbial species richness and evenness. ISME J (2010) 4.15
Construction, visualisation, and clustering of transcription networks from microarray expression data. PLoS Comput Biol (2007) 2.73
An experimental metagenome data management and analysis system. Bioinformatics (2006) 2.71
The net of life: reconstructing the microbial phylogenetic network. Genome Res (2005) 2.31
Protein families and TRIBES in genome sequence space. Nucleic Acids Res (2003) 2.27
A korarchaeal genome reveals insights into the evolution of the Archaea. Proc Natl Acad Sci U S A (2008) 2.16
Stereotyped B-cell receptors in one-third of chronic lymphocytic leukemia: a molecular classification with implications for targeted therapies. Blood (2012) 2.14
Comprehensive analysis of pseudogenes in prokaryotes: widespread gene decay and failure of putative horizontally transferred genes. Genome Biol (2004) 1.88
Genome analysis of the anaerobic thermohalophilic bacterium Halothermothrix orenii. PLoS One (2009) 1.83
COmplete GENome Tracking (COGENT): a flexible data environment for computational genomics. Bioinformatics (2003) 1.77
Measuring genome conservation across taxa: divided strains and united kingdoms. Nucleic Acids Res (2005) 1.61
Classification schemes for protein structure and function. Nat Rev Genet (2003) 1.52
Is there a role for antigen selection in mantle cell lymphoma? Immunogenetic support from a series of 807 cases. Blood (2011) 1.49
MagicMatch--cross-referencing sequence identifiers across databases. Bioinformatics (2005) 1.34
Genome coverage, literally speaking. The challenge of annotating 200 genomes with 4 million publications. EMBO Rep (2005) 1.25
Molecular subsets of mantle cell lymphoma defined by the IGHV mutational status and SOX11 expression have distinct biologic and clinical features. Cancer Res (2012) 1.24
Antigen selection in B-cell lymphomas--tracing the evidence. Semin Cancer Biol (2013) 1.16
The normal IGHV1-69-derived B-cell repertoire contains stereotypic patterns characteristic of unmutated CLL. Blood (2009) 1.15
Emergence, development and diversification of the TGF-beta signalling pathway within the animal kingdom. BMC Evol Biol (2009) 1.14
Evidence for the significant role of immunoglobulin light chains in antigen recognition and selection in chronic lymphocytic leukemia. Blood (2008) 1.09
Metatranscriptomic array analysis of 'Candidatus Accumulibacter phosphatis'-enriched enhanced biological phosphorus removal sludge. Environ Microbiol (2010) 1.07
Beyond 100 genomes. Genome Biol (2003) 1.06
TreeQ-VISTA: an interactive tree visualization tool with functional annotation query capabilities. Bioinformatics (2007) 0.98
Multiple evidence for the role of an Ovate-like gene in determining fruit shape in pepper. BMC Plant Biol (2011) 0.97
Relating tissue specialization to the differentiation of expression of singleton and duplicate mouse proteins. Genome Biol (2006) 0.91
Denoising inferred functional association networks obtained by gene fusion analysis. BMC Genomics (2007) 0.90
Analysis of xyloglucan endotransglycosylase/hydrolase (XTH) genes from allotetraploid (Gossypium hirsutum) cotton and its diploid progenitors expressed during fiber elongation. J Plant Physiol (2008) 0.90
CoGenT++: an extensive and extensible data environment for computational genomics. Bioinformatics (2005) 0.89
CORRIE: enzyme sequence annotation with confidence estimates. BMC Bioinformatics (2007) 0.87
Highly conserved motifs in non-coding regions of Sirevirus retrotransposons: the key for their pattern of distribution within and across plants? BMC Genomics (2010) 0.87
The turbulent life of Sirevirus retrotransposons and the evolution of the maize genome: more than ten thousand elements tell the story. Plant J (2011) 0.87
Effects of OTU clustering and PCR artifacts on microbial diversity estimates. Microb Ecol (2012) 0.86
Metabolic innovations towards the human lineage. BMC Evol Biol (2008) 0.85
IgG-switched CLL has a distinct immunogenetic signature from the common MD variant: ontogenetic implications. Clin Cancer Res (2013) 0.84
MASiVEdb: the Sirevirus Plant Retrotransposon Database. BMC Genomics (2012) 0.83
Immunoglobulin heavy variable (IGHV) genes and alleles: new entities, new names and implications for research and prognostication in chronic lymphocytic leukaemia. Immunogenetics (2014) 0.83
The study of a SPATULA-like bHLH transcription factor expressed during peach (Prunus persica) fruit development. Plant Physiol Biochem (2011) 0.80
Sirevirus LTR retrotransposons: phylogenetic misconceptions in the plant world. Mob DNA (2013) 0.79
Stratification of co-evolving genomic groups using ranked phylogenetic profiles. BMC Bioinformatics (2009) 0.78
Temporal dynamics of clonal evolution in chronic lymphocytic leukemia with stereotyped IGHV4-34/IGKV2-30 antigen receptors: longitudinal immunogenetic evidence. Mol Med (2013) 0.78
The study of the E-class SEPALLATA3-like MADS-box genes in wild-type and mutant flowers of cultivated saffron crocus (Crocus sativus L.) and its putative progenitors. J Plant Physiol (2011) 0.77
Science communication media for scientists and the public. EMBO Rep (2007) 0.75
Automation of amplicon-based library preparation for next generation sequencing by centrifugal microfluidics. Anal Chem (2020) 0.75
Coexistence of different types of biallelic immunoglobulin heavy variable gene replacement events in a case of pediatric B precursor acute lymphoblastic leukemia. Leuk Lymphoma (2010) 0.75
famRCA-RACE: a rolling circle amplification race for isolating a family of homologous cDNAs in one reaction and its application to obtain NAC genes transcription factors from crocus (Crocus sativus) flower. Prep Biochem Biotechnol (2010) 0.75