Yves Van de Peer

Yves Van de Peer's AcademicInfluence.com Rankings

Yves Van de Peer

Biology

#4040

World Rank

#6086

Historical Rank

Bioinformatics

#37

World Rank

#37

Historical Rank

Computational Biology

#48

World Rank

#48

Historical Rank

Evolutionary Biology

#85

World Rank

#100

Historical Rank

biology Degrees

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Biology

Yves Van de Peer's Degrees

PhD Bioinformatics Ghent University
Masters Bioinformatics Ghent University
Bachelors Biology Ghent University

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Yves Van de Peer's Published Works

Number of citations in a given year to any of this author's works

Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author

Published Works

The Genome of Black Cottonwood, Populus trichocarpa (Torr. & Gray) (2006) (4003)
PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences (2002) (3977)
The tomato genome sequence provides insights into fleshy fruit evolution (2012) (2615)
TREECON for Windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment (1994) (2378)
The genome of the domesticated apple (Malus × domestica Borkh.) (2010) (1794)
The Physcomitrella Genome Reveals Evolutionary Insights into the Conquest of Land by Plants (2008) (1736)
The Phaeodactylum genome reveals the evolutionary history of diatom genomes (2008) (1451)
The Norway spruce genome sequence and conifer genome evolution (2013) (1261)
The Medicago Genome Provides Insight into the Evolution of Rhizobial Symbioses (2011) (1131)
A High Quality Draft Consensus Sequence of the Genome of a Heterozygous Grapevine Variety (2007) (997)
Re-evaluating prokaryotic species (2005) (981)
The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis (2008) (966)
From 2R to 3R: evidence for a fish-specific genome duplication (FSGD). (2005) (954)
The evolutionary significance of ancient genome duplications (2009) (917)
The evolutionary significance of polyploidy (2017) (878)
The genome of Tetranychus urticae reveals herbivorous pest adaptations (2011) (874)
Genome duplication, a trait shared by 22000 species of ray-finned fish. (2003) (852)
Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features. (2006) (830)
Modeling gene and genome duplications in eukaryotes. (2005) (828)
The Arabidopsis lyrata genome sequence and the basis of rapid genome size change (2011) (807)
The Ectocarpus genome and the independent evolution of multicellularity in brown algae (2010) (803)
Draft Genome Sequence of the Sexually Transmitted Pathogen Trichomonas vaginalis (2007) (739)
zt: A Sofware Tool for Simple and Partial Mantel Tests (2002) (733)
The genome of Eucalyptus grandis (2014) (654)
Green Evolution and Dynamic Adaptations Revealed by Genomes of the Marine Picoeukaryotes Micromonas (2009) (618)
The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation (2007) (605)
Robust Feature Selection Using Ensemble Feature Selection Techniques (2008) (584)
Compilation of small ribosomal subunit RNA sequences. (1990) (555)
Plants with double genomes might have had a better chance to survive the Cretaceous–Tertiary extinction event (2009) (554)
Obligate biotrophy features unraveled by the genomic analysis of rust fungi (2011) (546)
Robust biomarker identification for cancer diagnosis with ensemble feature selection methods (2010) (536)
Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences (2004) (533)
Major events in the genome evolution of vertebrates: paranome age and size differ considerably between ray-finned fishes and land vertebrates. (2004) (532)
The hidden duplication past of Arabidopsis thaliana (2002) (529)
Genome-Wide Characterization of the Lignification Toolbox in Arabidopsis1[w] (2003) (510)
Comparative genomics provides evidence for an ancient genome duplication event in fish. (2001) (500)
Compilation of small ribosomal subunit RNA sequences. (1991) (488)
Genome duplication and the origin of angiosperms. (2005) (487)
Compilation of small ribosomal subunit RNA structures (1993) (487)
Detection of 91 potential conserved plant microRNAs in Arabidopsis thaliana and Oryza sativa identifies important target genes. (2004) (475)
Estimating the total number of phosphoproteins and phosphorylation sites in eukaryotic proteomes (2017) (466)
Genome sequence of the recombinant protein production host Pichia pastoris (2009) (463)
TREECON: a software package for the construction and drawing of evolutionary trees (1993) (427)
Pan genome of the phytoplankton Emiliania underpins its global distribution (2013) (418)
Database on the structure of large ribosomal subunit RNA (1994) (400)
Genome dynamics of the human embryonic kidney 293 lineage in response to cell biology manipulations (2014) (397)
Obligate Biotrophy Features Unraveled by the Genomic Analysis of the Rust Fungi, Melampsora larici-populina and Puccinia graminis f. sp. tritici (2011) (388)
The Mycobacterium tuberculosis regulatory network and hypoxia (2013) (380)
The gain and loss of genes during 600 million years of vertebrate evolution (2006) (363)
The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea (2016) (352)
The genome sequence of the orchid Phalaenopsis equestris (2014) (348)
Opinion: Re-evaluating prokaryotic species. (2005) (336)
Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous–Paleogene boundary (2014) (336)
PLAZA 4.0: an integrative resource for functional, evolutionary and comparative plant genomics (2017) (333)
A quantitative map of nucleotide substitution rates in bacterial rRNA. (1996) (331)
Targeted interactomics reveals a complex core cell cycle machinery in Arabidopsis thaliana (2010) (317)
PLAZA 3.0: an access point for plant comparative genomics (2014) (303)
Database on the structure of small ribosomal subunit RNA (1997) (302)
Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes (2006) (300)
Convergent gene loss following gene and genome duplications creates single-copy families in flowering plants (2013) (296)
Polyploidy and genome evolution in plants. (2015) (293)
Construction of evolutionary distance trees with TREECON for Windows: accounting for variation in nucleotide substitution rate among sites (1997) (289)
The Determination and Comparison of the 16S rRNA Gene Sequences of Species of the Genus Pseudomonas (sensu stricto and Estimation of the Natural Intrageneric Relationships (1996) (288)
The European ribosomal RNA database (2004) (286)
TAPIR, a web server for the prediction of plant microRNA targets, including target mimics (2010) (285)
PLAZA: A Comparative Genomics Resource to Study Gene and Genome Evolution in Plants[W] (2009) (281)
The Chara Genome: Secondary Complexity and Implications for Plant Terrestrialization (2018) (278)
The flowering world: a tale of duplications. (2009) (277)
Evolutionary Relationships Among the Eukaryotic Crown Taxa Taking into Account Site-to-Site Rate Variation in 18S rRNA (1997) (270)
The Membrane-Bound NAC Transcription Factor ANAC013 Functions in Mitochondrial Retrograde Regulation of the Oxidative Stress Response in Arabidopsis[C][W] (2013) (261)
Dissecting Plant Genomes with the PLAZA Comparative Genomics Platform1[W] (2011) (261)
Fern genomes elucidate land plant evolution and cyanobacterial symbioses (2018) (261)
The European database on small subunit ribosomal RNA (2002) (259)
The European Small Subunit Ribosomal RNA database (2000) (242)
Structural diversification and neo-functionalization during floral MADS-box gene evolution by C-terminal frameshift mutations. (2003) (237)
Unraveling Transcriptional Control in Arabidopsis Using cis-Regulatory Elements and Coexpression Networks1[C][W] (2009) (229)
The Apostasia genome and the evolution of orchids (2017) (217)
Choose your partners: dimerization in eukaryotic transcription factors. (2008) (217)
The Dendrobium catenatum Lindl. genome sequence provides insights into polysaccharide synthase, floral development and adaptive evolution (2016) (214)
Evidence That Rice and Other Cereals Are Ancient Aneuploids Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.014019. (2003) (211)
The Plant Genome Integrative Explorer Resource: PlantGenIE.org. (2015) (209)
Comparative analysis of more than 3000 sequences reveals the existence of two pseudoknots in area V4 of eukaryotic small subunit ribosomal RNA. (2000) (208)
Computational Approaches to Identify Promoters and cis-Regulatory Elements in Plant Genomes1 (2003) (200)
The European Large Subunit Ribosomal RNA Database (2001) (199)
Microsporidia: accumulating molecular evidence that a group of amitochondriate and suspectedly primitive eukaryotes are just curious fungi. (2000) (198)
The Ghost of Selection Past: Rates of Evolution and Functional Divergence of Anciently Duplicated Genes (2001) (196)
Generic eukaryotic core promoter prediction using structural features of DNA. (2008) (194)
And then there were many: MADS goes genomic. (2003) (183)
Towards a prokaryotic genomic taxonomy. (2005) (182)
A reservoir of ‘historical’ antibiotic resistance genes in remote pristine Antarctic soils (2018) (181)
Nonrandom divergence of gene expression following gene and genome duplications in the flowering plant Arabidopsis thaliana (2006) (180)
GOLVEN secretory peptides regulate auxin carrier turnover during plant gravitropic responses. (2012) (178)
An ancient genome duplication contributed to the abundance of metabolic genes in the moss Physcomitrella patens (2007) (178)
Genome duplication, divergent resolution and speciation. (2001) (177)
Gene duplication and biased functional retention of paralogs in bacterial genomes. (2004) (175)
The water lily genome and the early evolution of flowering plants (2019) (174)
Reannotation and extended community resources for the genome of the non-seed plant Physcomitrella patens provide insights into the evolution of plant gene structures and functions (2013) (169)
An early origin of plastids within the cyanobacterial divergence is suggested by evolutionary trees based on complete 16S rRNA sequences. (1995) (165)
i-ADHoRe 3.0—fast and sensitive detection of genomic homology in extremely large data sets (2011) (165)
ORCAE: online resource for community annotation of eukaryotes (2012) (165)
Polyploidy: an evolutionary and ecological force in stressful times (2020) (163)
Substitution rate calibration of small subunit ribosomal RNA identifies chlorarachniophyte endosymbionts as remnants of green algae. (1996) (163)
Gene Duplicability of Core Genes Is Highly Consistent across All Angiosperms[OPEN] (2016) (162)
Compilation of small ribosomal subunit RNA sequences. (1992) (161)
An Updated and Comprehensive rRNA Phylogeny of (Crown) Eukaryotes Based on Rate-Calibrated Evolutionary Distances (2000) (159)
Genome-Wide Identification of Potential Plant E2F Target Genes1[w] (2005) (159)
Computational approaches to unveiling ancient genome duplications (2004) (157)
Genome of wild olive and the evolution of oil biosynthesis (2017) (157)
The automatic detection of homologous regions (ADHoRe) and its application to microcolinearity between Arabidopsis and rice. (2002) (154)
Tangled up in two: a burst of genome duplications at the end of the Cretaceous and the consequences for plant evolution (2014) (150)
Distribution of substitution rates and location of insertion sites in the tertiary structure of ribosomal RNA. (2001) (148)
Global expression analysis of the brown alga Ectocarpus siliculosus (Phaeophyceae) reveals large-scale reprogramming of the transcriptome in response to abiotic stress (2009) (143)
Gene functionalities and genome structure in Bathycoccus prasinos reflect cellular specializations at the base of the green lineage (2012) (143)
EST data suggest that poplar is an ancient polyploid. (2005) (143)
Divergent members of the bacterial division Verrucomicrobiales in a temperate freshwater lake (1998) (142)
A comprehensive analysis of genes encoding small secreted proteins identifies candidate effectors in Melampsora larici-populina (poplar leaf rust). (2012) (137)
The hornwort genome and early land plant evolution (2020) (134)
GenomeView: a next-generation genome browser (2011) (134)
Java-ML: A Machine Learning Library (2009) (131)
How many genes are there in plants (... and why are they there)? (2007) (131)
Globins in nonvertebrate species: dispersal by horizontal gene transfer and evolution of the structure-function relationships. (1996) (128)
Inference of genome duplications from age distributions revisited. (2013) (128)
Hydrogen peroxide-induced gene expression across kingdoms: a comparative analysis. (2008) (126)
Genomewide Structural Annotation and Evolutionary Analysis of the Type I MADS-Box Genes in Plants (2003) (125)
A Haploid System of Sex Determination in the Brown Alga Ectocarpus sp. (2014) (123)
Gamma paleohexaploidy in the stem lineage of core eudicots: significance for MADS-box gene and species diversification. (2012) (122)
Contrasting Rates of Molecular Evolution and Patterns of Selection among Gymnosperms and Flowering Plants (2017) (121)
Canalization without flux sensors: a traveling-wave hypothesis. (2007) (119)
Deletions involving long-range conserved nongenic sequences upstream and downstream of FOXL2 as a novel disease-causing mechanism in blepharophimosis syndrome. (2005) (118)
Reciprocal Responses in the Interaction between Arabidopsis and the Cell-Content-Feeding Chelicerate Herbivore Spider Mite1[W][OPEN] (2013) (118)
A genome for gnetophytes and early evolution of seed plants (2018) (118)
The complete chloroplast and mitochondrial DNA sequence of Ostreococcus tauri: organelle genomes of the smallest eukaryote are examples of compaction. (2007) (117)
SpliceMachine: predicting splice sites from high-dimensional local context representations (2005) (117)
Database on the structure of large subunit ribosomal RNA (1999) (117)
Feature subset selection for splice site prediction (2002) (116)
Large-Scale Event Extraction from Literature with Multi-Level Gene Normalization (2013) (113)
Molecular genealogy of some nematode taxa as based on cytochrome c and globin amino acid sequences. (1994) (113)
Genome Annotation in Plants and Fungi: EuGene as a Model Platform (2008) (112)
Comparative genomics of the pathogenic ciliate Ichthyophthirius multifiliis, its free-living relatives and a host species provide insights into adoption of a parasitic lifestyle and prospects for disease control (2011) (112)
Database on the structure of large ribosomal subunit RNA. (1997) (110)
Moss transcriptome and beyond. (2002) (110)
A review of estimation of distribution algorithms in bioinformatics (2008) (109)
Comparative Network Analysis Reveals That Tissue Specificity and Gene Function Are Important Factors Influencing the Mode of Expression Evolution in Arabidopsis and Rice1[W] (2011) (108)
A Snapshot of the Emerging Tomato Genome Sequence (2009) (107)
Insights into the Evolution of Multicellularity from the Sea Lettuce Genome (2018) (106)
Large-scale structural analysis of the core promoter in mammalian and plant genomes (2005) (106)
Genome-Wide Mapping of Structural Variations Reveals a Copy Number Variant That Determines Reproductive Morphology in Cucumber (2015) (106)
Systematic Structural Characterization of Metabolites in Arabidopsis via Candidate Substrate-Product Pair Networks[C][W] (2014) (104)
Construction of evolutionary distance trees with TREECON for Windows: accounting for variation in nucleotide substitution rate among sites. (1997) (103)
Genomes of early-diverging streptophyte algae shed light on plant terrestrialization (2019) (103)
wgd—simple command line tools for the analysis of ancient whole-genome duplications (2018) (103)
Predicting protein-protein interactions in Arabidopsis thaliana through integration of orthology, gene ontology and co-expression (2009) (103)
TRAPID: an efficient online tool for the functional and comparative analysis of de novo RNA-Seq transcriptomes (2013) (100)
Database on the structure of small subunit ribosomal RNA (1999) (99)
The Nucleotide-sequence of the Small Ribosomal-subunit Rna of the Yeast Candida-albicans and the Evolutionary Position of the Fungi Among the Eukaryotes (1989) (99)
The draft genomes of five agriculturally important African orphan crops (2018) (95)
Redundancy and rewiring of genetic networks following genome-wide duplication events. (2012) (95)
Genome-wide analysis of the diatom cell cycle unveils a novel type of cyclins involved in environmental signaling (2010) (95)
The (r)evolution of gene regulatory networks controlling Arabidopsis plant reproduction: a two-decade history. (2014) (95)
Module networks revisited: computational assessment and prioritization of model predictions (2009) (94)
Are all fishes ancient polyploids? (2004) (93)
Evolutionary Relationships Among Higher Fungi Inferred From Small Ribosomal-subunit Rna Sequence-analysis (1993) (92)
Journey through the past: 150 million years of plant genome evolution. (2011) (92)
ProSOM: core promoter prediction based on unsupervised clustering of DNA physical profiles (2008) (90)
The biosynthetic gene cluster for sophorolipids: a biotechnological interesting biosurfactant produced by Starmerella bombicola (2013) (88)
Overview of tomato (Solanum lycopersicum) candidate pathogen recognition genes reveals important Solanum R locus dynamics. (2013) (86)
Database on the structure of small ribosomal subunit RNA (1996) (85)
The small RNA world of plants. (2006) (85)
Phylogenetic analysis of the SSU rRNA from members of the Chrysophyceae. (1999) (84)
Integrative Genomic Analysis Implicates Gain of PIK3CA at 3q26 and MYC at 8q24 in Chronic Lymphocytic Leukemia (2012) (84)
The evolution of stramenopiles and alveolates as derived by "substitution rate calibration" of small ribosomal subunit RNA. (1996) (84)
Toward a gold standard for promoter prediction evaluation (2009) (83)
CoExpNetViz: Comparative Co-Expression Networks Construction and Visualization Tool (2016) (82)
AGRONOMICS1: A New Resource for Arabidopsis Transcriptome Profiling1[W][OA] (2009) (80)
Angiosperm polyploids and their road to evolutionary success (2010) (80)
Extracting protein-protein interactions from text using rich feature vectors and feature selection (2008) (78)
Microarray analysis of E2Fa-DPa-overexpressing plants uncovers a cross-talking genetic network between DNA replication and nitrogen assimilation (2003) (78)
Polyploidy: A Biological Force From Cells to Ecosystems. (2020) (77)
TAXONOMIC STUDY OF MARINE OSCILLATORIACEAN STRAINS (CYANOBACTERIA) WITH NARROW TRICHOMES. II. NUCLEOTIDE SEQUENCE ANALYSIS OF THE 16S RIBOSOMAL RNA 1 (1992) (77)
Building genomic profiles for uncovering segmental homology in the twilight zone. (2004) (74)
Development and implementation of a highly-multiplexed SNP array for genetic mapping in maritime pine and comparative mapping with loblolly pine (2011) (73)
In situ analysis of cross-hybridisation on microarrays and the inference of expression correlation (2007) (73)
An improved genome of the model marine alga Ostreococcus tauri unfolds by assessing Illumina de novo assemblies (2014) (73)
The gene coding for small ribosomal subunit RNA in the basidiomycete Ustilago maydis contains a group I intron. (1992) (73)
Identification of novel regulatory modules in dicotyledonous plants using expression data and comparative genomics (2006) (73)
Arabidopsis Ensemble Reverse-Engineered Gene Regulatory Network Discloses Interconnected Transcription Factors in Oxidative Stress[W] (2014) (71)
Comparative analysis of module-based versus direct methods for reverse-engineering transcriptional regulatory networks (2009) (71)
Feature selection for splice site prediction: A new method using EDA-based feature ranking (2004) (71)
Fast feature selection using a simple estimation of distribution algorithm: a case study on splice site prediction (2003) (70)
Phylogenetic Relationships among Ascomycetes and Ascomycete-like Yeasts as Deduced from Small Ribosomal Subunit RNA Sequences (1992) (70)
Lack of GLYCOLATE OXIDASE1, but Not GLYCOLATE OXIDASE2, Attenuates the Photorespiratory Phenotype of CATALASE2-Deficient Arabidopsis1[OPEN] (2016) (68)
Reconstructing evolution from eukaryotic small-ribosomal-subunit RNA sequences: Calibration of the molecular clock (1993) (67)
Functional divergence of proteins through frameshift mutations. (2005) (67)
Decoding Plant and Animal Genome Plasticity from Differential Paleo-Evolutionary Patterns and Processes (2012) (67)
Novel insights into evolution of protistan polyketide synthases through phylogenomic analysis. (2008) (66)
Horsetails Are Ancient Polyploids: Evidence from Equisetum giganteum[OPEN] (2015) (66)
Genome-wide analysis of core cell cycle genes in the unicellular green alga Ostreococcus tauri. (2005) (65)
18S Ribosomal RNA genes of insects : primary structure of the genes and molecular phylogeny of the Holometabola (1996) (65)
Genome of Crucihimalaya himalaica, a close relative of Arabidopsis, shows ecological adaptation to high altitude (2019) (65)
Expanding the repertoire of secretory peptides controlling root development with comparative genome analysis and functional assays (2015) (65)
Metazoan Relationships on the Basis of 18S rRNA Sequences: A Few Years Later ' (1998) (64)
Module Network Inference from a Cancer Gene Expression Data Set Identifies MicroRNA Regulated Modules (2010) (64)
pico-PLAZA, a genome database of microbial photosynthetic eukaryotes. (2013) (64)
Posttranslational regulation impacts the fate of duplicated genes (2010) (64)
Dealing with saturation at the amino acid level: a case study based on anciently duplicated zebrafish genes. (2002) (63)
Detecting the undetectable: uncovering duplicated segments in Arabidopsis by comparison with rice. (2002) (63)
The Litsea genome and the evolution of the laurel family (2020) (62)
Investigating ancient duplication events in the Arabidopsis genome (2004) (62)
hfAIM: A reliable bioinformatics approach for in silico genome-wide identification of autophagy-associated Atg8-interacting motifs in various organisms (2016) (61)
The FTO Gene, Implicated in Human Obesity, Is Found Only in Vertebrates and Marine Algae (2007) (60)
The evolution of stramenopiles and alveolates as derived by “substitution rate calibration» of small ribosomal subunit RNA (1996) (60)
Construction of a variability map for eukaryotic large subunit ribosomal RNA. (1999) (60)
Revisiting recent challenges to the ancient fish-specific genome duplication hypothesis (2001) (60)
Re-annotation, improved large-scale assembly and establishment of a catalogue of noncoding loci for the genome of the model brown alga Ectocarpus. (2017) (59)
Single-Copy Genes as Molecular Markers for Phylogenomic Studies in Seed Plants (2017) (59)
Functional and evolutionary genomic inferences in Populus through genome and population sequencing of American and European aspen (2018) (59)
About the Order of Divergence of the Major Bacterial Taxa During Evolution (1994) (58)
Primary and secondary structure of the 18S ribosomal RNA of the bird spider Eurypelma californica and evolutionary relationships among eukaryotic phyla. (1988) (58)
Analysis of a Gibbs sampler method for model-based clustering of gene expression data (2008) (58)
Evaluation and Properties of the Budding Yeast Phosphoproteome* (2012) (58)
Whole-genome analysis reveals molecular innovations and evolutionary transitions in chromalveolate species (2008) (57)
Revisiting ancestral polyploidy in plants (2017) (57)
i-ADHoRe 2.0: an improved tool to detect degenerated genomic homology using genomic profiles (2008) (56)
Of dups and dinos: evolution at the K/Pg boundary. (2016) (55)
Validating module network learning algorithms using simulated data (2007) (55)
Evolution of Basidiomycetous Yeasts As Deduced From Small Ribosomal-subunit Rna Sequences (1992) (54)
AFLPinSilico, simulating AFLP fingerprints (2003) (54)
Genome-Wide Analysis Reveals Diverged Patterns of Codon Bias, Gene Expression, and Rates of Sequence Evolution in Picea Gene Families (2015) (54)
Distinct Expression and Methylation Patterns for Genes with Different Fates following a Single Whole-Genome Duplication in Flowering Plants (2020) (54)
Redundancy and rewiring of genetic networks following genome-wide duplication events. (2012) (52)
2R or not 2R is not the question anymore (2010) (52)
Reciprocally Retained Genes in the Angiosperm Lineage Show the Hallmarks of Dosage Balance Sensitivity (2017) (51)
Evolution according to large ribosomal subunit RNA. (1995) (51)
Pseudo-chromosome–length genome assembly of a double haploid “Bartlett” pear (Pyrus communis L.) (2019) (50)
A transgenic mouse marking live replicating cells reveals in vivo transcriptional program of proliferation. (2012) (50)
Translation initiation site prediction on a genomic scale: beauty in simplicity (2007) (50)
Chromosome-level genome assembly of a parent species of widely cultivated azaleas (2020) (50)
Molecular phylogeny of part of the env gene of HIV‐1 strains isolated in Côte d'lvoire (1994) (49)
In search of the small ones: improved prediction of short exons in vertebrates, plants, fungi and protists (2007) (49)
ForCon : a software tool for the conversion of sequence alignments (1999) (49)
Gene cluster conservation provides insight into cercosporin biosynthesis and extends production to the genus Colletotrichum (2018) (49)
The evolutionary position of the rhodophytePorphyra umbilicalis and the basidiomyceteLeucosporidium scottii among other eukaryotes as deduced from complete sequences of small ribosomal subunit RNA (1991) (48)
The genome of Prasinoderma coloniale unveils the existence of a third phylum within green plants (2020) (48)
EVEX in ST’13: Application of a large-scale text mining resource to event extraction and network construction (2013) (48)
Ancient duplication of cereal genomes. (2005) (47)
Tetraodon genome confirms Takifugu findings: most fish are ancient polyploids (2004) (47)
Exploring Biomolecular Literature with EVEX: Connecting Genes through Events, Homology, and Indirect Associations (2012) (47)
Comparative phenomics and targeted use of genomics reveals variation in carbon and nitrogen assimilation among different Brettanomyces bruxellensis strains (2015) (47)
EVEX: A PubMed-Scale Resource for Homology-Based Generalization of Text Mining Predictions (2011) (47)
Comparative Metagenomic Analysis Reveals Mechanisms for Stress Response in Hypoliths from Extreme Hyperarid Deserts (2016) (47)
Tetraodon genome confirms Takifugu findings: most fish are ancient polyploids (2004) (46)
Exploring the Plant Transcriptome through Phylogenetic Profiling1[w] (2005) (46)
Gene duplication, the evolution of novel gene functions, and detecting functional divergence of duplicates in silico. (2003) (46)
Promoter analysis of MADS-box genes in eudicots through phylogenetic footprinting. (2006) (46)
How molecules evolve in eubacteria. (2000) (46)
Phylogenetic analysis of five medically important Candida species as deduced on the basis of small ribosomal subunit RNA sequences. (1991) (45)
Exoproteome analysis of Starmerella bombicola results in the discovery of an esterase required for lactonization of sophorolipids. (2014) (45)
The honeysuckle genome provides insight into the molecular mechanism of carotenoid metabolism underlying dynamic flower coloration. (2020) (45)
Pelistega europaea gen. nov., sp. nov., a bacterium associated with respiratory disease in pigeons: taxonomic structure and phylogenetic allocation. (1998) (44)
A multi-omics analysis of the grapevine pathogen Lasiodiplodia theobromae reveals that temperature affects the expression of virulence- and pathogenicity-related genes (2019) (44)
Discriminative and informative features for biomolecular text mining with ensemble feature selection (2010) (44)
Phylogenetic analysis of ten black yeast species using nuclear small subunit rRNA gene sequences (1995) (43)
Differential gene retention as an evolutionary mechanism to generate biodiversity and adaptation in yeasts (2015) (43)
Phylogenetic relationships among algae based on complete large-subunit rRNA sequences. (2001) (43)
Wanda: a database of duplicated fish genes (2002) (43)
Inference of Ancient Whole-Genome Duplications and the Evolution of Gene Duplication and Loss Rates. (2019) (42)
The European Large Subunit Ribosomal RNA database (2000) (42)
Significance and Biological Consequences of Polyploidization in Land Plant Evolution (2013) (42)
Network-based integration of systems genetics data reveals pathways associated with lignocellulosic biomass accumulation and processing (2017) (41)
The phylogeny of the Hyphochytriomycota as deduced from ribosomal RNA sequences of Hyphochytrium catenoides. (1995) (41)
Structure of 16S and 23S Ribosomal RNA Genes in Campylobacter Species: Phylogenetic Analysis of the Genus Campylobacter and Presence of Internal Transcribed Spacers (1993) (41)
Evolution according to large ribosomal subunit RNA (1995) (40)
Evaluation of the impact of Illumina error correction tools on de novo genome assembly (2017) (40)
Evolution and taxonomic distribution of nonribosomal peptide and polyketide synthases. (2008) (39)
Meta Analysis of Gene Expression Data within and Across Species (2008) (39)
A mystery unveiled (2011) (39)
Complex Evolutionary Dynamics of Massively Expanded Chemosensory Receptor Families in an Extreme Generalist Chelicerate Herbivore (2016) (39)
Polyploid Arabidopsis species originated around recent glaciation maxima. (2018) (38)
Candida bombicola as a platform organism for the production of tailor‐made biomolecules (2013) (38)
Higher intron loss rate in Arabidopsis thaliana than A. lyrata is consistent with stronger selection for a smaller genome. (2012) (38)
Peakbin Selection in Mass Spectrometry Data Using a Consensus Approach with Estimation of Distribution Algorithms (2011) (37)
The Potential of Text Mining in Data Integration and Network Biology for Plant Research: A Case Study on Arabidopsis[C][W] (2013) (37)
The First Green Lineage cdc25 Dual-Specificity Phosphatase (2004) (37)
Deconstruction of the (Paleo)Polyploid Grapevine Genome Based on the Analysis of Transposition Events Involving NBS Resistance Genes (2012) (37)
The Cycas genome and the early evolution of seed plants (2022) (36)
Systems genetics reveals a transcriptional network associated with susceptibility in the maize–grey leaf spot pathosystem (2017) (36)
Analyzing text in search of bio-molecular events: a high-precision machine learning framework (2009) (36)
Prediction of a gene regulatory network linked to prostate cancer from gene expression, microRNA and clinical data (2010) (35)
The Eucalyptus grandis Genome Project: Genome and transcriptome resources for comparative analysis of woody plant biology (2011) (35)
The hidden duplication past of the plant pathogen Phytophthora and its consequences for infection (2010) (35)
Structure of the small ribosomal subunit RNA of the pulmonate snail, Limicolaria kambeul, and phylogenetic analysis of the Metazoa (1992) (35)
The Evolution of Gene Duplicates in Angiosperms and the Impact of Protein–Protein Interactions and the Mechanism of Duplication (2019) (35)
Diffany: an ontology-driven framework to infer, visualise and analyse differential molecular networks (2016) (34)
The Complex Intron Landscape and Massive Intron Invasion in a Picoeukaryote Provides Insights into Intron Evolution (2013) (33)
Coordinated Functional Divergence of Genes after Genome Duplication in Arabidopsis thaliana[OPEN] (2017) (33)
Evolution of eukaryotes as deduced from small ribosomal subunit RNA sequences (1993) (32)
Towards a prokaryotic genomic taxonomy q (2005) (32)
The emergence and evolution of intron-poor and intronless genes in intron-rich plant gene families. (2020) (32)
Sequencing and Analyzing the Transcriptomes of a Thousand Species Across the Tree of Life for Green Plants. (2019) (31)
The evolutionary origin and domestication history of goldfish (Carassius auratus) (2020) (31)
Recent developments in computational approaches for uncovering genomic homology. (2004) (30)
The gene expression landscape of pine seedling tissues (2017) (30)
Database on the structure of small ribosomal subunit RNA (1998) (30)
Phylogenetic relationships among algae based on complete large-subunit rRNA sequences. (2001) (30)
The 18S ribosomal RNA sequence of the sea anemone Ammonia sulcata and its evolutionary position among other eukaryotes (1990) (30)
Orthology Guided Assembly in highly heterozygous crops: creating a reference transcriptome to uncover genetic diversity in Lolium perenne. (2013) (29)
Analysis of the evolutionary relationships of HIV-1 and SIVcpz sequences using bayesian inference: implications for the origin of HIV-1. (2003) (29)
The phylogeny of the Hyphochytriomycota as deduced from ribosomal RNA sequences of Hyphochytrium catenoides. (1995) (29)
Draft genome of Cercospora zeina, Fusarium pininemorale, Hawksworthiomyces lignivorus, Huntiella decipiens and Ophiostoma ips (2017) (28)
A model-based approach to study nearest-neighbor influences reveals complex substitution patterns in non-coding sequences. (2008) (28)
Whole-genome microsynteny-based phylogeny of angiosperms (2020) (28)
Inferring Transcriptional Networks by Mining 'Omics' Data (2006) (28)
Conservation of Nonsense-Mediated mRNA Decay Complex Components Throughout Eukaryotic Evolution (2017) (28)
Network Modeling Unravels Mechanisms of Crosstalk between Ethylene and Salicylate Signaling in Potato1[OPEN] (2018) (28)
RNA-sequencing of Cercospora beticola DMI-sensitive and -resistant isolates after treatment with tetraconazole identifies common and contrasting pathway induction. (2016) (27)
The Welwitschia genome reveals a unique biology underpinning extreme longevity in deserts (2021) (27)
Genome sequence of Malania oleifera, a tree with great value for nervonic acid production (2019) (27)
Rapid protein evolution, organellar reductions, and invasive intronic elements in the marine aerobic parasite dinoflagellate Amoebophrya spp (2021) (27)
First draft genome assembly of the desert locust, Schistocerca gregaria. (2020) (27)
Evolutionary relationships among heterokont algae (the autotrophic stramenopiles) based on combined analyses of small and large subunit ribosomal RNA. (2002) (27)
Open-ended on-board Evolutionary Robotics for robot swarms (2009) (27)
A mystery unveiled (2011) (26)
Serendipitous Meta-Transcriptomics: The Fungal Community of Norway Spruce (Picea abies) (2015) (26)
Investigating ancient duplication events in the Arabidopsis genome. (2003) (26)
Phylogenetic inference based on distance methods : theory (2009) (26)
On Adaptive Self-Organization in Artificial Robot Organisms (2009) (26)
An improved statistical method for detecting heterotachy in nucleotide sequences. (2006) (26)
Duplicate retention after small- and large-scale duplications (2011) (25)
A greedy, graph-based algorithm for the alignment of multiple homologous gene lists (2011) (25)
Virus-host coexistence in phytoplankton through the genomic lens (2019) (25)
Draft Genome Assembly of the Poultry Red Mite, Dermanyssus gallinae (2018) (24)
Phylogenetic analyses suggest lateral gene transfer from the mitochondrion to the apicoplast. (2002) (24)
Exploration of alternative splicing events in ten different grapevine cultivars (2015) (24)
Evidence for an ancient whole genome duplication in the cycad lineage (2017) (24)
Cell line name recognition in support of the identification of synthetic lethality in cancer from text (2015) (24)
Comparative in silico analysis of EST-SSRs in angiosperm and gymnosperm tree genera (2014) (23)
BrownieAligner: accurate alignment of Illumina sequencing data to de Bruijn graphs (2018) (23)
Using digital organisms to study the evolutionary consequences of whole genome duplication and polyploidy (2019) (23)
Predicting Human Immunodeficiency Virus (HIV) Drug Resistance Using Recurrent Neural Networks (2006) (23)
Structural and functional organization of RNA regulons in the post-transcriptional regulatory network of yeast (2011) (23)
Scalable hardware accelerator for comparing DNA and protein sequences (2006) (23)
Draft Genomes of Two Artocarpus Plants, Jackfruit (A. heterophyllus) and Breadfruit (A. altilis) (2019) (22)
Transcriptional Profiling of Plasmodium falciparum Parasites from Patients with Severe Malaria Identifies Distinct Low vs. High Parasitemic Clusters (2012) (22)
Large-scale gene and ancient genome duplications (2005) (22)
SILAC-based proteome analysis of Starmerella bombicola sophorolipid production. (2013) (22)
Transcription regulatory networks in Caenorhabditis elegans inferred through reverse-engineering of gene expression profiles constitute biological hypotheses for metazoan development. (2009) (21)
The Neighborhood of the Spike Gene Is a Hotspot for Modular Intertypic Homologous and Nonhomologous Recombination in Coronavirus Genomes (2021) (21)
Semantically linking molecular entities in literature through entity relationships (2012) (21)
A Cytoscape app for motif enumeration with ISMAGS (2016) (21)
Evolution of green plants and their relationship with other photosynthetic eukaryotes as deduced from 5S ribosomal RNA sequences (1990) (20)
Applications of Next-Generation Sequencing Technologies and Computational Tools in Molecular Evolution and Aquatic Animals Conservation Studies: A Short Review (2019) (20)
Small ribosomal subunit RNA sequences, evolutionary relationships among different life forms, and mitochondrial origins (1990) (20)
Unique Regulation of the Calvin Cycle in the Ultrasmall Green Alga Ostreococcus (2007) (20)
Evolutionary relationships among heterokont algae (the autotrophic stramenopiles) based on combined analyses of small and large subunit ribosomal RNA. (2002) (20)
The ‘TranSeq’ 3′‐end sequencing method for high‐throughput transcriptomics and gene space refinement in plant genomes (2018) (20)
Modelling the ancestral sequence distribution and model frequencies in context-dependent models for primate non-coding sequences (2010) (20)
Dual RNA Sequencing of Vitis vinifera during Lasiodiplodia theobromae Infection Unveils Host–Pathogen Interactions (2019) (20)
CyClus3D: a Cytoscape plugin for clustering network motifs in integrated networks (2011) (19)
Small RNA profiling in Pinus pinaster reveals the transcriptome of developing seeds and highlights differences between zygotic and somatic embryos (2019) (19)
The Seagrass Methylome Is Associated With Variation in Photosynthetic Performance Among Clonal Shoots (2020) (19)
A novel approach to identifying regulatory motifs in distantly related genomes (2005) (19)
The Global Invertebrate Genomics Alliance (GIGA): developing community resources to study diverse invertebrate genomes. (2014) (19)
5S rRNA sequences of representatives of the genera Chlorobium, Prosthecochloris, Thermomicrobium, Cytophaga, Flavobacterium, Flexibacter and Saprospira and a discussion of the evolution of eubacteria in general. (1990) (19)
Phylogeny inference based on distance methods : theory (2003) (18)
Genome streamlining in a minute herbivore that manipulates its host plant (2020) (18)
Illumina error correction near highly repetitive DNA regions improves de novo genome assembly (2019) (18)
'Natural selection merely modified while redundancy created' – Susumu Ohno's idea of the evolutionary importance of gene and genome duplications (2004) (18)
Finding Evidence for Whole Genome Duplications: A Reappraisal. (2019) (18)
Enrichment and aggregation of topological motifs are independent organizational principles of integrated interaction networks. (2011) (18)
Lack of GLYCOLATE OXIDASE 1 , but Not GLYCOLATE OXIDASE 2 , Attenuates the Photorespiratory Phenotype of CATALASE 2-De fi cient Arabidopsis 1 [ OPEN ] (2016) (17)
Phylogenetic analysis of the env gene of HIV‐1 isolates taking into account individual nucleotide substitution rates (1996) (17)
CARD: a drawing tool for RNA secondary structure models. (1995) (17)
Using Non-Reversible Context-Dependent Evolutionary Models to Study Substitution Patterns in Primate Non-Coding Sequences (2010) (17)
Polyploidy breaks speciation barriers in Australian burrowing frogs Neobatrachus (2020) (17)
The Cymbidium genome reveals the evolution of unique morphological traits (2021) (17)
U-Compare bio-event meta-service: compatible BioNLP event extraction services (2011) (17)
Complete mitochondrial genome of the Verticillium-wilt causing plant pathogen Verticillium nonalfalfae (2016) (16)
PubMed-Scale Event Extraction for Post-Translational Modifications, Epigenetics and Protein Structural Relations (2012) (16)
The heterothallic sugarbeet pathogen Cercospora beticola contains exon fragments of both MAT genes that are homogenized by concerted evolution. (2014) (16)
5S ribosomal ribonucleic acid sequences in Bacteroides and Fusobacterium: evolutionary relationships within these genera and among eubacteria in general. (1989) (16)
Digging into Acceptor Splice Site Prediction: An Iterative Feature Selection Approach (2004) (16)
Evolutionary history and pan-genome dynamics of strawberry (Fragaria spp.) (2021) (16)
A chromosome-level Amaranthus cruentus genome assembly highlights gene family evolution and biosynthetic gene clusters that may underpin the nutritional value of this traditional crop. (2021) (16)
The Phylogenetic Handbook: Phylogenetic inference based on distance methods (2009) (16)
Haplotype-resolved genome assembly and allele-specific gene expression in cultivated ginger (2021) (15)
Database on the structure of large ribosomal subunit RNA. (1994) (15)
The 5S ribosomal RNA sequences of a red algal rhodoplast and a gymnosperm chloroplast. Implications for the evolution of plastids and cyanobacteria (2005) (15)
Towards robust feature selection techniques (2008) (15)
Phylogenetic study of Cyanobacteria on the basis of 16S ribosomal RNA sequences (1992) (15)
Characterizing regulatory path motifs in integrated networks using perturbational data (2010) (15)
Improved chromosome-level genome assembly and annotation of the seagrass, Zostera marina (eelgrass) (2021) (15)
Genome sequence and genetic diversity analysis of an under-domesticated orphan crop, white fonio (Digitaria exilis) (2021) (14)
Together we stand: genes cluster to coordinate regulation. (2008) (14)
Compilation of small ribosomal subunit RNA sequences. (1988) (14)
Wolfberry genomes and the evolution of Lycium (Solanaceae) (2021) (14)
Single‐Gene and Whole‐Genome Duplications and the Evolution of Protein–Protein Interaction Networks (2010) (14)
The Ectocarpus genome and brown algal genomics: the Ectocarpus Genome Consortium (2012) (14)
Helicoidal transfer matrix model for inhomogeneous DNA melting. (2005) (14)
Multi-proxy analyses of a mid-15th century Middle Iron Age Bantu-speaker palaeo-faecal specimen elucidates the configuration of the ‘ancestral’ sub-Saharan African intestinal microbiome (2019) (14)
A genomic analysis and transcriptomic atlas of gene expression in Psoroptes ovis reveals feeding- and stage-specific patterns of allergen expression (2019) (14)
MANTIS: a phylogenetic framework for multi-species genome comparisons (2008) (14)
OMSim: a simulator for optical map data (2017) (13)
IMA Genome-F 8 (2017) (13)
The evolutionary conundrum of whole‐genome duplication (2020) (13)
Integration of Static Relations to Enhance Event Extraction from Text (2010) (13)
Erratum: Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes (Proceedings of the National Academy of Sciences of the United States of America (2006) 103 (14959-14964) DOI: 10.1073/pnas.0603228103) (2006) (13)
Draft Genome Assembly of the Sheep Scab Mite, Psoroptes ovis (2018) (13)
Unravelling cis-Regulatory Elements in the Genome of the Smallest Photosynthetic Eukaryote: Phylogenetic Footprinting in Ostreococcus (2009) (13)
Genomes of leafy and leafless Platanthera orchids illuminate the evolution of mycoheterotrophy (2022) (13)
The Phaeodactylum genome reveals the dynamic nature and multi-lineage evolutionary history of diatom genomes (2011) (13)
Improving the Adaptability of Simulated Evolutionary Swarm Robots in Dynamically Changing Environments (2014) (13)
ASP-G: an ASP-based method for finding attractors in genetic regulatory networks (2014) (13)
Loss of Wood Formation Genes in Monocot Genomes (2019) (13)
Transcriptomic responses of a simplified soil microcosm to a plant pathogen and its biocontrol agent reveal a complex reaction to harsh habitat (2016) (12)
The quest for genomic homology (2004) (12)
Structural interpretation of the amino acid sequence of a second domain from the Artemia covalent polymer globin. (1990) (12)
The taxonomic position of Chlamydomyxa labyrinthuloides (1999) (12)
Phylogenetic analysis of a fish tapeworm, Proteocephalus exiguus, based on the small subunit rRNA gene. (1997) (12)
Genome-Wide Characterization of the Lignification Toolbox in Arabidopsis 1 [ w ] (2003) (12)
Multi-faceted analysis provides little evidence for recurrent whole-genome duplications during hexapod evolution (2020) (12)
miRNA profiling in leaf and cork tissues of Quercus suber reveals novel miRNAs and tissue-specific expression patterns (2014) (11)
Chromosome-scale assembly and evolution of the tetraploid Salvia splendens (Lamiaceae) genome (2021) (11)
First draft genome assembly of the Argane tree ( Argania spinosa) (2018) (11)
Highlights of the BioTM 2010 workshop on advances in bio text mining (2010) (11)
Genome evolution : gene and genome duplications and the origin of novel gene functions (2003) (11)
Computational approaches to unveiling ancient genome duplications. (2004) (11)
Multiple Independent Recruitment of Sodefrin Precursor-like Factors in Anuran Sexually Dimorphic Glands. (2019) (11)
Reshuffling of the ancestral core-eudicot genome shaped chromatin topology and epigenetic modification in Panax (2022) (10)
Germline copy number variation associated with Mendelian inheritance of CLL in two families (2012) (10)
The genome of the extremophile Artemia provides insight into strategies to cope with extreme environments (2021) (10)
ORCAE-AOCC: A Centralized Portal for the Annotation of African Orphan Crop Genomes (2019) (10)
Molecular phylogeny of the stress-70 protein family with reference to algal relationships (1997) (10)
Application of the EVEX resource to event extraction and network construction: Shared Task entry and result analysis (2015) (10)
Database on the structure of small ribosomal subunit RNA. (1994) (9)
The transcriptome of the moss Physcomitrella patens : comparative analysis reveals a rich source of new genes (2002) (9)
5S rRNA sequences of myxobacteria and radioresistant bacteria and implications for eubacterial evolution. (1990) (9)
Agulhas Current properties shape microbial community diversity and potential functionality (2018) (9)
Computational approaches to unveiling ancient genome duplications (2004) (9)
MorphDB: Prioritizing Genes for Specialized Metabolism Pathways and Gene Ontology Categories in Plants (2018) (9)
Mitochondrial genes from 18 angiosperms fill sampling gaps for phylogenomic inferences of the early diversification of flowering plants (2020) (9)
Corrigendum: The genome sequence of the orchid Phalaenopsis equestris (2015) (9)
The Larix kaempferi genome reveals new insights into wood properties. (2022) (9)
Nearby transposable elements impact plant stress gene regulatory networks: a meta-analysis in A. thaliana and S. lycopersicum (2022) (9)
The genome of homosporous maidenhair fern sheds light on the euphyllophyte evolution and defences (2022) (9)
Integrating Large-Scale Text Mining and Co-Expression Networks : Targeting NADP ( H ) Metabolism in E . coli with Event Extraction (2012) (9)
Insights Into the Mechanisms Implicated in Pinus pinaster Resistance to Pinewood Nematode (2021) (9)
Draft Genome Assembly of the False Spider Mite Brevipalpus yothersi (2019) (9)
Corrigendum: Differential gene retention as an evolutionary mechanism to generate biodiversity and adaptation in yeasts (2015) (8)
Taxus yunnanensis genome offers insights into gymnosperm phylogeny and taxol production (2021) (8)
Phages actively challenge niche communities in the Antarctic soils (2020) (8)
Genomic and Metabolomic Analyses of the Marine Fungus Emericellopsis cladophorae: Insights into Saltwater Adaptability Mechanisms and Its Biosynthetic Potential (2021) (8)
Secundary structure of the large ribosomal subunit RNA of the moss Funaria hygrometrica (1997) (8)
HIGH‐PRECISION BIO‐MOLECULAR EVENT EXTRACTION FROM TEXT USING PARALLEL BINARY CLASSIFIERS (2011) (8)
The KnownLeaf literature curation system captures knowledge about Arabidopsis leaf growth and development and facilitates integrated data mining (2015) (8)
Evolutionary Relationships Among the Eukaryotic Crown Taxa Taking into Account Site-to-Site Rate Variation in 18S rRNA (1997) (8)
Mining the Enriched Subgraphs for Specific Vertices in a Biological Graph (2019) (7)
The taxonomic position ofChlamydomyxa labyrinthuloides (1999) (7)
Detecting Entity Relations as a Supporting Task for Bio-Molecular Event Extraction (2011) (7)
Application of second-generation sequencing (SGS) and third generation sequencing (TGS) in aquaculture breeding program (2021) (7)
Genome-Wide Identiﬁcation of Potential Plant E2F Target Genes 1[w] (2005) (7)
Current status of the multinational Arabidopsis community (2020) (7)
First draft genome assembly of the desert locust, Schistocerca gregaria (2020) (7)
Efficient context-dependent model building based on clustering posterior distributions for non-coding sequences (2009) (7)
TREECON: a software package for the construction and drawing of evolutionary trees. (1993) (7)
Erratum to: Polyploidy: an evolutionary and ecological force in stressful times (2021) (7)
Genomes shed light on the evolution of Begonia, a mega‐diverse genus (2022) (7)
Transcriptomic analysis of the poultry red mite, Dermanyssus gallinae, across all stages of the lifecycle (2021) (7)
The genome of Corydalis reveals the evolution of benzylisoquinoline alkaloid biosynthesis in Ranunculales. (2022) (6)
Evolutionary divergence of duplicated genomes in newly described allotetraploid cottons (2022) (6)
From DNA- to NA-centrism and the conditions for gene-centrism revisited (2014) (6)
Feature Extraction Using Clustering of Protein (2006) (6)
The seagrass methylome memorizes heat stress and is associated with variation in stress performance among clonal shoots (2019) (6)
The sociobiology of genes: the gene’s eye view as a unifying behavioural-ecological framework for biological evolution (2018) (6)
Optimising orbit counting of arbitrary order by equation selection (2019) (6)
Methylation variation promotes phenotypic diversity and evolutionary potential in a millenium-old clonal seagrass meadow (2019) (6)
Reverse‐Engineering Transcriptional Modules from Gene Expression Data (2009) (6)
Evolutionary genetics: When duplicated genes don't stick to the rules (2006) (6)
Context-dependent codon partition models provide significant increases in model fit in atpB and rbcL protein-coding genes (2011) (6)
Globins in nonvertebrate species (1996) (6)
Compilation of Pseudomonad Sequences Present in a Database on the Structure of Ribosomal RNA (1996) (6)
Model-based detection of whole-genome duplications in a phylogeny (2020) (6)
The 18S rRNA from Odontophrynus americanus 2n and 4n (Amphibia, Anura) reveals unusual extra sequences in the variable region V2. (2004) (5)
A functionally conserved STORR gene fusion in Papaver species that diverged 16.8 million years ago (2021) (5)
De novo Assembly of Transcriptomes From a B73 Maize Line Introgressed With a QTL for Resistance to Gray Leaf Spot Disease Reveals a Candidate Allele of a Lectin Receptor-Like Kinase (2020) (5)
Genome and Metabolome MS-Based Mining of a Marine Strain of Aspergillus affinis (2021) (5)
Emergent adaptive behaviour of GRN-controlled simulated robots in a changing environment (2016) (5)
Phages Actively Challenge Niche Communities in Antarctic Soils (2020) (5)
Ribosomal RNA as a tool for studying evolution (1992) (5)
Feature Ranking Using an EDA-based Wrapper Approach (2006) (5)
The Potential for pathogenicity was present in the ancestor of the Ascomycete subphylum Pezizomycotina (2010) (5)
Genomic Resources to Guide Improvement of the Shea Tree (2021) (4)
Comparative in silico analysis of SSRs in coding regions of high confidence predicted genes in Norway spruce (Picea abies) and Loblolly pine (Pinus taeda) (2015) (4)
Selecting relevant features for gene structure prediction (2004) (4)
Divergence of a genomic island leads to the evolution of melanization in a halophyte root fungus (2021) (4)
Discovery of significantly enriched subgraphs associated with selected vertices in a single graph (2015) (4)
The Euscaphis japonica genome and the evolution of malvids (2021) (4)
First draft genome assembly of the Argane tree ( Argania spinosa). (2018) (4)
Novel phylogeny of angiosperms inferred from whole-genome microsynteny analysis (2020) (4)
Investigation of fungal phylogeny on the basis of small ribosomal subunit RNA sequences (1995) (4)
Adaptive self-organizing organisms using a bio-inspired gene regulatory network controller: for the aggregation of evolutionary robots under a changing environment (2016) (4)
Evolution of NLR Resistance Genes in Magnoliids: Dramatic Expansions of CNLs and Multiple Losses of TNLs (2021) (3)
Size does matter (2011) (3)
Ancient duplication and horizontal transfer of a toxin gene cluster reveals novel mechanisms in the cercosporin biosynthesis pathway (2017) (3)
Genome‐wide analysis of butterfly bush (Buddleja alternifolia) in three uplands provides insights into biogeography, demography and speciation (2021) (3)
Benchmarking machine learning techniques for the extraction of protein-protein interactions from text (2008) (3)
Simulating Biological Complexity through Artificial Evolution (2017) (3)
Generation of open-source genomics resources for African orphan tree crops by African Orphan Crops Consortium (AOCC), a public-private partnership for promoting food and nutritional security in Africa (2020) (3)
The Challenges of Interpreting Phosphoproteomics Data: A Critical View Through the Bioinformatics Lens (2015) (3)
Genome analysis of the world's smallest free-living eukaryote Ostreococcus tauri unveils unique genome heterogeneity (2005) (3)
Annual Machine Learning Conference of Belgium and The Netherlands (2006) (3)
Gene expression Analysis of a Gibbs sampler method for model-based clustering of gene expression data (2008) (3)
MicroRNA-mediated post-transcriptional regulation of Pinus pinaster response and resistance to pinewood nematode (2022) (3)
The genome of wild olive and the evolution of oil biosynthesis The wild olive genome and oil biosynthesis (2017) (3)
Bioinformatics Unraveling Transcriptional Control in Arabidopsis Using cis-Regulatory Elements and Coexpression Networks 1 [ C ] [ W ] (2009) (3)
Correction: The Cymbidium genome reveals the evolution of unique morphological traits (2021) (3)
Cultivated hawthorn (Crataegus pinnatifida var. major) genome sheds light on the evolution of Maleae (apple tribe). (2022) (3)
Draft Genome Sequences of Two Unclassified Bacteria, Sphingomonas sp. Strains IBVSS1 and IBVSS2, Isolated from Environmental Samples (2017) (3)
Analysis of nucleotide sequences using TREECON (2003) (3)
O19-3Genome dynamics of the human embryonic kidney 293 (HEK293) lineage in response to cell biology manipulations (2014) (3)
Ancient duplication and horizontal transfer of a toxin gene cluster reveals novel mechanisms in the cercosporin biosynthesis pathway (2017) (3)
Standing genetic variation fuels rapid evolution of herbicide resistance in blackgrass (2021) (3)
Divergence of regulatory sequences in duplicated fish genes. (2007) (3)
CyEVEX : Literature-scale network integration and visualization through Cytoscape (2012) (3)
Ancient whole genome duplications and the evolution of the gene duplication and loss rate (2019) (2)
Erratum to: An ancient genome duplication contributed to the abundance of metabolic genes in the moss Physcomitrella patens (2016) (2)
Application of the EVEX resource to event extraction and network construction: Shared Task entry and result analysis (2015) (2)
The genome of Hibiscus hamabo reveals its adaptation to saline and waterlogged habitat (2022) (2)
TREECON for Windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment. (1994) (2)
Ocean currents drive the worldwide colonization of the most widespread marine plant, eelgrass (Zostera marina) (2022) (2)
Evaluating Large-scale Text Mining Applications Beyond the Traditional Numeric Performance Measures (2013) (2)
Breakthrough Technologies AGRONOMICS 1 : A New Resource for Arabidopsis Transcriptome Profiling 1 (2010) (2)
Phylogeny branches out (2001) (2)
Evolutionary genetics: When duplicated genes don't stick to the rules (2006) (2)
Chromosome‐scale assembly of the Moringa oleifera Lam. genome uncovers polyploid history and evolution of secondary metabolism pathways through tandem duplication (2022) (2)
'Horizontal' plant biology on the rise (2004) (2)
Nymphaea colorata (Blue-Petal Water Lily). (2020) (2)
Life’s Dual Nature: A Way Out of the Impasse of the Gene-Centred ‘Versus’ Complex Systems Controversy on Life (2015) (2)
A non-duplicated magnoliid genome (2021) (2)
Draft Genome Sequences of Two Unclassified Chitinophagaceae Bacteria, IBVUCB1 and IBVUCB2, Isolated from Environmental Samples (2017) (2)
The future for plants and plants for the future (2007) (2)
Substitution rate calibration of nucleotide sequence alignments and application to phylogenetic tree construction (1996) (2)
Network modelling unravels mechanisms of crosstalk between ethylene and salicylate signalling in potato (2017) (2)
The hornwort genome and early land plant evolution (2020) (2)
Selecting Relevant Features for Splice Site Prediction by Estimation of Distribution Algorithms. (2002) (2)
"Winter Is Coming": How did Polyploid Plants Survive? (2020) (2)
with stronger selection for a smaller genome (2011) (1)
syntenet: an R/Bioconductor package for the inference and analysis of synteny networks (2022) (1)
The future for plants and plants for the future. (2007) (1)
Characterizing transcriptional modules in Escherichia coli inferred from gene expression data (2009) (1)
A bio-inspired agent-based system for controlling robot behaviour (2011) (1)
Whole-genome microsynteny-based phylogeny of angiosperms 1 2 (2020) (1)
Gene duplicates in vibrio genomes (2006) (1)
Inferring Eubacterial Phylogeny from SS Ribosomal RNA Structure Analysis (1988) (1)
Genomes: the truth is in there (2011) (1)
A reservoir of ‘historical’ antibiotic resistance genes in remote pristine Antarctic soils (2018) (1)
Using digital organisms to investigate the effect of whole genome duplication in (artificial) evolution (2019) (1)
Studying Whole-Genome Duplication Using Experimental Evolution of Spirodela polyrhiza. (2023) (1)
The genome of the king protea, Protea cynaroides (2022) (1)
Study of invertebrate and plant globins : templates and evolutionary trees (1992) (1)
Cutaneous transcriptomic profiling and candidate pigment genes in the wild discus (Symphysodon spp.) (2023) (1)
TRAPID: an efficient online tool for the functional and comparative analysis of de novoRNA-Seq transcriptomes (2013) (1)
An improved genome of the model marine alga Ostreococcus tauri unfolds by assessing Illumina de novo assemblies (2014) (1)
Chinese fir genome and the evolution of gymnosperms (2022) (1)
Agulhas Current properties shape microbial community diversity and potential functionality (2018) (1)
Genome annotation of the flat mite Brevipalpus yothersi Baker (Tenuipalpidae). (2016) (1)
Corrigendum: The genome sequence of the orchid Phalaenopsis equestris (2015) (1)
FunSiP: a modular and extensible classifier for the prediction of functional sites in DNA (2008) (1)
Erratum for Orr et al., “Draft Genome Sequences of Two Unclassified Bacteria, Sphingomonas sp. Strains IBVSS1 and IBVSS2, Isolated from Environmental Samples” (2017) (1)
Revisiting Ancient Polyploidy in Leptosporangiate Ferns (2022) (1)
A two-type branching process model of gene family evolution (2021) (1)
Author Correction: The genome of Prasinoderma coloniale unveils the existence of a third phylum within green plants (2020) (1)
Jabba: hybrid error correction for long sequencing reads (2016) (1)
Erratum for Navia et al., “Draft Genome Assembly of the False Spider Mite Brevipalpus yothersi” (2019) (1)
Whole genome duplication potentiates inter-specific hybridisation and niche shifts in Australian burrowing frogs Neobatrachus (2019) (1)
Editorial overview: Genome studies and molecular genetics: Of plant genes, genomes, and genomics. (2016) (1)
Evolution according to large tribosomal subunit RNA (2004) (1)
Draft Genome Sequences of Two Unclassified Bacteria, Hydrogenophaga sp. Strains IBVHS1 and IBVHS2, Isolated from Environmental Samples (2017) (1)
Detecting microcolinearity between Arabidopsis and Rice (2002) (1)
Erratum for Orr et al., “Draft Genome Sequences of Two Unclassified Chitinophagaceae Bacteria, IBVUCB1 and IBVUCB2, Isolated from Environmental Samples” (2017) (1)
Lawrence Berkeley National Laboratory Recent Work Title A reservoir of ' historical ' antibiotic resistance genes in remote pristine Antarctic soils Permalink (2018) (1)
Conservation of a gene cluster reveals novel cercosporin biosynthetic mechanisms and extends production to the genus Colletotrichum (2017) (1)
1.11 Integrative Genomic Analysis Implicates PIK3CA and MYC in Chronic Lymphocytic Leukemia (2011) (1)
The evolution of secondary xylem in angiosperms and its loss in monocots (2017) (1)
Author Correction to: Rapid protein evolution, organellar reductions, and invasive intronic elements in the marine aerobic parasite dinoflagellate Amoebophrya spp (2021) (1)
Evaluation of the impact of Illumina error correction tools on de novo genome assembly (2017) (1)
Inference of Ancient Polyploidy Using Transcriptome Data. (2023) (0)
Nature, nurture and the structure of macroalgal genomes (2011) (0)
Author response: Genome streamlining in a minute herbivore that manipulates its host plant (2020) (0)
Semantically linking molecular entities in literature through entity relationships (2012) (0)
Most Cited Authors... Most Cited Authors... (2007) (0)
Nucleic Acids Research (2009) (0)
Ensemble optimisation of cis-regulatory element discovery : in planta benchmark and discovery in Eucalyptus (2012) (0)
Seagrass genomes reveal a hexaploid ancestry facilitating adaptation to the marine environment (2023) (0)
Cercospora zeina 0 Fusarium pininemorale 0 Hawksworthiomyces lignivorus , Huntiella decipiens and Ophiostoma ips (2019) (0)
The sociobiology of genes: the gene’s eye view as a unifying behavioural-ecological framework for biological evolution (2017) (0)
Optimising orbit counting of arbitrary order by equation selection (2019) (0)
Transcriptomic analysis of the poultry red mite, Dermanyssus gallinae, across all stages of the lifecycle (2021) (0)
Using novel bio-inspired principles to improve adaptability of evolutionary robots in dynamically changing environments (2013) (0)
Wolfberry genomes and the evolution of Lycium (Solanaceae) (2021) (0)
Genome sequence and genetic diversity analysis of an under-domesticated orphan crop, white fonio (2021) (0)
Software regulatory path motifs in integrated networks using perturbational data (2010) (0)
Adaptive Self-Organizing Organisms Using a Bio-Inspired Gene Regulatory Network Controller (2019) (0)
Faculty Opinions recommendation of Polyploids exhibit higher potassium uptake and salinity tolerance in Arabidopsis. (2013) (0)
Multi-proxy analyses of a mid-15th century Middle Iron Age Bantu-speaker palaeo-faecal specimen elucidates the configuration of the ‘ancestral’ sub-Saharan African intestinal microbiome (2020) (0)
Genomic resources and databases for plant research community (2016) (0)
A genomic analysis and transcriptomic atlas of gene expression in Psoroptes ovis reveals feeding- and stage-specific patterns of allergen expression (2019) (0)
Genomes of early-diverging streptophyte algae shed light on plant terrestrialization (2019) (0)
A genome for gnetophytes and early evolution of seed plants (2018) (0)
Predicting long term behavior of genetic regulatory networks with answer set programming (2012) (0)
Correction: The Cymbidium genome reveals the evolution of unique morphological traits (2021) (0)
The role of non-linear DNA structures in transcription (2004) (0)
Bioinformatics Exploring the Plant Transcriptome through Phylogenetic Profiling 1 [ w ] (2004) (0)
The Saururus chinensis genome provides insights into the evolution of pollination strategies and herbaceousness in magnoliids. (2023) (0)
Enhancing Coding Potential Prediction for Short Sequences Using Complementary Sequence Features and Feature Selection (2006) (0)
Detection of heterotachy and its influence on phylogenetic inference within Eukaryotes (2005) (0)
Author Correction to: Rapid protein evolution, organellar reductions, and invasive intronic elements in the marine aerobic parasite dinoflagellate Amoebophrya spp (2021) (0)
SNP Detection in Pinus pinaster Transcriptome and Association with Resistance to Pinewood Nematode (2022) (0)
Modeling context-dependent evolution: the influence of the immediate flanking bases (2007) (0)
Convergent Gene Loss Following Gene and Genome Duplications Creates Single-Copy Families: A Case Study On Flowering Plants (2013) (0)
Rapid protein evolution, organellar reductions, and invasive intronic elements in the marine aerobic parasite dinoflagellate Amoebophrya spp (2021) (0)
The sequence of 5-S rRNA of Deinococcus radiodurans and the evolutionary position of the radioresistant bacteria (1988) (0)
Divergence of Active Site Motifs among Different Classes of Populus Glutaredoxins Results in Substrate Switches. (2022) (0)
BIOINFORMATICS Robust biomarker identiﬁcation for cancer diagnosis with ensemble feature selection methods (2010) (0)
Identifying prokaryotic consortia that live in close interactions with algae (2015) (0)
Splice site prediction in eukaryote genome sequences : the algorithmic issues (2004) (0)
Correction: Divergence of a genomic island leads to the evolution of melanization in a halophyte root fungus (2021) (0)
The immediate effects of polyploidization of Spirodela polyrhiza change in a strain-specific way along environmental gradients (2023) (0)
Faculty Opinions recommendation of Whole-genome duplications spurred the functional diversification of the globin gene superfamily in vertebrates. (2011) (0)
Neutral processes underlying the macro eco-evolutionary dynamics of mixed-ploidy systems (2023) (0)
Size does matter (2018) (0)
ON THE NATURE OF THINGS: ESSAYS (2020) (0)
Transposition mediated deconstruction of a (paoleo)polyploid genome (2011) (0)
Gene functionalities and genome structure in Bathycoccus prasinos reflect cellular specializations at the base of the green lineage (2012) (0)
Reannotation and extended community resources for the genome of the non-seed plant Physcomitrella patens provide insights into the evolution of plant gene structures and functions (2013) (0)
TRANSCRIPTOME ANALYSIS OF COMPATIBLE AND INCOMPATIBLE INTERACTIONS OF ECTOCARPUS WITH EURYCHASMA DICKSONII USING RNA-SEQUENCING (2017) (0)
Erratum for Orr et al., “Draft Genome Sequences of Two Unclassified Bacteria, Hydrogenophaga sp. Strains IBVHS1 and IBVHS2, Isolated from Environmental Samples” (2017) (0)
Extensive RNA editing in tomato nuclear genes (2022) (0)
The genome of the extremophile Artemia provides insight into strategies to cope with extreme environments (2021) (0)
Assessing the quality of comparative genomics data and results with the cogeqc R/Bioconductor package (2023) (0)
Size does matter (2018) (0)
Haplotype-resolved genome assembly and allele-specific gene expression in cultivated ginger (2021) (0)
Evolution of isoform-level gene expression patterns across tissues during lotus species divergence. (2022) (0)
Fern genomes elucidate land plant evolution and cyanobacterial symbioses (2018) (0)
'Horizontal' plant biology on the rise (2004) (0)
Comparative in silico analysis of SSRs in coding regions of high confidence predicted genes in Norway spruce (Picea abies) and Loblolly pine (Pinus taeda) (2015) (0)
Diffany: an ontology-driven framework to infer, visualise and analyse differential molecular networks (2016) (0)
Author Correction: The Apostasia genome and the evolution of orchids (2020) (0)
Feature subset selection for splice site prediction by estimation of distribution algorithms (2002) (0)
Title Comparative genomics of the pathogenic ciliate Ichthyophthirius multifiliis , its free-living relatives and a host species provide insights into adoption of a parasitic lifestyle and prospects for disease control Permalink (2012) (0)
Correction: Divergence of a genomic island leads to the evolution of melanization in a halophyte root fungus (2021) (0)
Draft genome of an African isolate of the maize fungal pathogen, Cercospora zeina (2017) (0)
Illumina error correction near highly repetitive DNA regions improves de novo genome assembly (2019) (0)
Editorial overview: Genome studies and molecular genetics: Treasure troves of evolution. (2018) (0)
Nearby transposable elements impact plant stress gene regulatory networks: a meta-analysis in A. thaliana and S. lycopersicum (2022) (0)
From DNA- to NA-centrism and the conditions for gene-centrism revisited (2013) (0)
The duplication of genomes and gene regulatory networks and its potential for evolutionary adaptation and survival (2023) (0)
1KP: Sequencing and analyzing the transcriptomes for a thousand species representing the diversity of green plants (2019) (0)
A Cytoscape app for motif enumeration with ISMAGS. (2016) (0)
Comparative phenomics and targeted use of genomics reveals variation in carbon and nitrogen assimilation among different Brettanomyces bruxellensis strains (2015) (0)
Author Correction: A functionally conserved STORR gene fusion in Papaver species that diverged 16.8 million years ago (2022) (0)
Studying Whole-Genome Duplication Using Experimental Evolution of Chlamydomonas. (2023) (0)
Pyrus Communis chromosome scale assembly (2019) (0)
Principles of Systems Biology, No. 14. (2017) (0)
Phylogeny branches out (2001) (0)
An ASP-based simulation method for finding all synchronous and asynchronous attractors in genetic regulatory networks (2012) (0)
A novel approach to modelling site dependencies: biological realism and computational complexity (2006) (0)
Conservation of Nonsense-Mediated mRNA Decay Complex Components Throughout Eukaryotic Evolution (2017) (0)
Splice Site Prediction in Eukaryote Genome Sequences (2004) (0)
The annotation and analysis of the genome of Arabidopsis lyrata (2007) (0)
The study of polyploidy dates back more than 100 years to the work of biologists (2019) (0)
ProSOM: core promoter identification in the human genome (2008) (0)
Transcriptomic analysis of soil microorganisms in presence of a plant pathogen and its biocontrol agent (2014) (0)
Statistical methods for detecting heterotachy (2005) (0)
termination in the Brown Alga Ectocarpus sp . (2014) (0)
IXth International Fungal Biology Conference & (2006) (0)
The Cymbidium genome reveals the evolution of unique morphological traits (2021) (0)
Faculty Opinions recommendation of Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.). (2013) (0)
Whole-genome duplications and the long-term evolution of gene regulatory networks in angiosperms (2023) (0)
Towards system level modeling of functional modules and regulatory pathways using genome-scale data (2010) (0)
ORCAE, a wiki style genome annotation portal for eukaryotic genomes (2014) (0)
Characterization of transcriptional modules in Escherichia coli (2008) (0)
A Scalable Hardware Accelerator for Comparing Protein Sequences (2006) (0)
Molecular evolution and the incorporation of site-to-site rate variation in distance tree construction methods (1999) (0)
ArticleDraft Genomes of two Artocarpus plants (2019) (0)
Chapter 19 Single-Gene and Whole-Genome Duplications and the Evolution of Protein – Protein Interaction Networks (2009) (0)
Retrieving DNA sequence information from mass spectra of nucleic acids: application to the detection and identification of SNPs (2002) (0)
Analyses of a chromosome-scale genome assembly reveal the origin and evolution of cultivated chrysanthemum (2023) (0)
Database on the structure of large ribosomal subunit RNA. (1996) (0)
Comparative in silicoanalysis of EST-SSRs in angiosperm and gymnosperm tree genera (2014) (0)
Combining signal processing and machine learning techniques for coding potential prediction (2006) (0)
Short communication Phylogenetic analysis of a fish tapeworm, Proteocephalus exiguus, based on the small subunit rRNA gene 1 (1997) (0)
Transcriptomic responses of a simplified soil microcosm to a plant pathogen and its biocontrol agent reveal a complex reaction to harsh habitat (2016) (0)
Genomes: the truth is in there (2011) (0)
Multi-faceted analysis provides little evidence for recurrent whole-genome duplications during hexapod evolution (2020) (0)
Quantifying expression divergence of duplicated genes with microarrays (2015) (0)
miRNA profiling in leaf and cork tissues of Quercus suber reveals novel miRNAs and tissue-specific expression patterns (2014) (0)
BrownieAligner: accurate alignment of Illumina sequencing data to de Bruijn graphs (2018) (0)
Erratum for Orr et al., "Draft Genome Sequences of Two Unclassified Bacteria, sp. Strains IBVHS1 and IBVHS2, Isolated from Environmental Samples". (2017) (0)
Erratum to: An ancient genome duplication contributed to the abundance of metabolic genes in the moss Physcomitrella patens (2016) (0)
Phylogenetic analysis of a fish tapeworm Proteocephalus exiguus, based on the small subunit of the ribosomal RNA gene (1997) (0)
The improved assembly of the European Pear (2018) (0)
Lawrence Berkeley National Laboratory Recent Work Title Pan Genome of the Phytoplankton Emiliania Underpins its Global Distribution Permalink (2013) (0)
Faculty Opinions recommendation of Ancestral polyploidy in seed plants and angiosperms. (2011) (0)
The Litsea genome and the evolution of the laurel family (2020) (0)
Principles of systems biology, no. 14 : [...] Network analysis of woody biomass (2017) (0)
Getting up to speed. (2012) (0)
An improved genome of the model marine alga [ i ] Ostreococcus tauri [ / i ] unfolds by assessing Illumina (2018) (0)
5 Phylogenetic inference based on distance methods THEORY (2011) (0)
Event based text mining for integrated network construction (2009) (0)
Special issue: Plant synthetic biology (2020) (0)
Improved core promoter prediction using ensembles of Support Vector Machines (2006) (0)
ELIXIR Belgium: tools and services (2018) (0)
Exploration of alternative splicing events in ten different grapevine cultivars (2015) (0)
Evolution of multicellularity in the heterokont lineage : analysis of the Ectocarpus siliculosus genome sequence (2009) (0)

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