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The coffee genome provides insight into the convergent evolution of caffeine biosynthesis
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Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1002/(sici)1097-0010(20000515)80:7<1033::aid-jsfa595>3.0.co;2-topenalex-snapshot
Chlorogenic acids and other cinnamates - nature, occurrence, dietary burden, absorption and metabolism
inferredcites →https://doi.org/10.1002/0471250953.bi0410s25openalex-snapshot
Using RepeatMasker to Identify Repetitive Elements in Genomic Sequences
inferredcites →https://doi.org/10.1002/0471250953.bi1003s00openalex-snapshot
Using MUMmer to Identify Similar Regions in Large Sequence Sets
inferredcites →https://doi.org/10.1002/biot.200700184openalex-snapshot
Biotechnology of flavonoids and other phenylpropanoid‐derived natural products. Part II: Reconstruction of multienzyme pathways in plants and microbes
inferredcites →https://doi.org/10.1002/fsn3.35openalex-snapshot
Changes in sensory quality characteristics of coffee during storage
inferredcites →https://doi.org/10.1007/978-3-642-86659-3openalex-snapshot
Evolution by Gene Duplication
inferredcites →https://doi.org/10.1007/bf00033781openalex-snapshot
Doubled haploids of Coffea canephora: development, fertility and agronomic characteristics
inferredcites →https://doi.org/10.1007/s00122-003-1310-4openalex-snapshot
Genetic mapping of a caffeoyl-coenzyme A 3-O-methyltransferase gene in coffee trees. Impact on chlorogenic acid content
inferredcites →https://doi.org/10.1007/s00122-005-0112-2openalex-snapshot
Coffee and tomato share common gene repertoires as revealed by deep sequencing of seed and cherry transcripts
inferredcites →https://doi.org/10.1007/s00122-014-2293-zopenalex-snapshot
The Tvv1 retrotransposon family is conserved between plant genomes separated by over 100 million years
inferredcites →https://doi.org/10.1007/s001220051114openalex-snapshot
Relations between and inheritance of chlorogenic acid contents in an interspecific cross between Coffea pseudozanguebariae and Coffea liberica var ‘dewevrei’
inferredcites →https://doi.org/10.1007/s00239-004-2597-8openalex-snapshot
A Maximum Likelihood Method for Detecting Functional Divergence at Individual Codon Sites, with Application to Gene Family Evolution
inferredcites →https://doi.org/10.1007/s00299-006-0152-3openalex-snapshot
Isolation and genetic mapping of a Coffea canephora phenylalanine ammonia-lyase gene (CcPAL1) and its involvement in the accumulation of caffeoyl quinic acids
inferredcites →https://doi.org/10.1007/s00425-012-1613-2openalex-snapshot
Characterization, high-resolution mapping and differential expression of three homologous PAL genes in Coffea canephora Pierre (Rubiaceae)
inferredcites →https://doi.org/10.1007/s00438-005-0070-zopenalex-snapshot
Substrate specificity of N-methyltransferase involved in purine alkaloids synthesis is dependent upon one amino acid residue of the enzyme
inferredcites →https://doi.org/10.1007/s00438-008-0355-0openalex-snapshot
Recent duplications dominate NBS-encoding gene expansion in two woody species
inferredcites →https://doi.org/10.1007/s00438-009-0434-xopenalex-snapshot
Genome-wide analysis of Carica papaya reveals a small NBS resistance gene family
inferredcites →https://doi.org/10.1007/s004380050965openalex-snapshot
Molecular characterisation and origin of the Coffea arabica L. genome
inferredcites →https://doi.org/10.1007/s11103-007-9141-3openalex-snapshot
Functional characterization of two p-coumaroyl ester 3′-hydroxylase genes from coffee tree: evidence of a candidate for chlorogenic acid biosynthesis
inferredcites →https://doi.org/10.1007/s11103-008-9293-9openalex-snapshot
Genome-wide identification of NBS resistance genes in Populus trichocarpa
inferredcites →https://doi.org/10.1007/s11103-013-0077-5openalex-snapshot
BAC-end sequences analysis provides first insights into coffee (Coffea canephora P.) genome composition and evolution
inferredcites →https://doi.org/10.1007/s11295-010-0272-3openalex-snapshot
High resolution synteny maps allowing direct comparisons between the coffee and tomato genomes
inferredcites →https://doi.org/10.1007/s12042-008-9017-yopenalex-snapshot
The Value of Nonmodel Genomes and an Example Using SynMap Within CoGe to Dissect the Hexaploidy that Predates the Rosids
inferredcites →https://doi.org/10.1016/j.foodchem.2007.05.053openalex-snapshot
Profiling the chlorogenic acids of sweet potato (Ipomoea batatas) from China
inferredcites →https://doi.org/10.1016/j.gde.2007.08.014openalex-snapshot
The evolution of resistance genes in multi-protein plant resistance systems
inferredcites →https://doi.org/10.1016/j.lwt.2012.08.007openalex-snapshot
Changes in triacylglycerols and free fatty acids composition during storage of roasted coffee
inferredcites →https://doi.org/10.1016/j.pbi.2006.03.016openalex-snapshot
Acyltransferases in plants: a good time to be BAHD
inferredcites →https://doi.org/10.1016/j.phytochem.2006.02.016openalex-snapshot
Caffeine biosynthesis and adenine metabolism in transgenic Coffea canephora plants with reduced expression of N-methyltransferase genes
inferredcites →https://doi.org/10.1016/j.phytochem.2007.10.029openalex-snapshot
Caffeine and related purine alkaloids: Biosynthesis, catabolism, function and genetic engineering
inferredcites →https://doi.org/10.1016/j.phytochem.2008.04.024openalex-snapshot
Modulation of chlorogenic acid biosynthesis in Solanum lycopersicum; consequences for phenolic accumulation and UV-tolerance
inferredcites →https://doi.org/10.1016/j.phytochem.2008.09.021openalex-snapshot
Effectiveness of the fatty acid and sterol composition of seeds for the chemotaxonomy of Coffea subgenus Coffea
inferredcites →https://doi.org/10.1016/j.plantsci.2003.07.002openalex-snapshot
Chlorogenic acid content swap during fruit maturation in Coffea pseudozanguebariae
inferredcites →https://doi.org/10.1016/j.plantsci.2007.02.004openalex-snapshot
Chlorogenic acid synthesis in coffee: An analysis of CGA content and real-time RT-PCR expression of HCT, HQT, C3H1, and CCoAOMT1 genes during grain development in C. canephora
inferredcites →https://doi.org/10.1016/j.tplants.2009.08.001openalex-snapshot
NB-LRRs work a “bait and switch” on pathogens
inferredcites →https://doi.org/10.1016/j.tree.2010.06.001openalex-snapshot
Promiscuous DNA: horizontal transfer of transposable elements and why it matters for eukaryotic evolution
inferredcites →https://doi.org/10.1016/s0026-895x(25)09385-xopenalex-snapshot
Dicaffeoylquinic acid inhibitors of human immunodeficiency virus integrase: inhibition of the core catalytic domain of human immunodeficiency virus integrase.
inferredcites →https://doi.org/10.1016/s0304-4165(96)00151-1openalex-snapshot
Antioxidant activity of polyphenolics in diets
inferredcites →https://doi.org/10.1016/s0308-8146(01)00204-7openalex-snapshot
Caffeine, trigonelline, chlorogenic acids and sucrose diversity in wild Coffea arabica L. and C. canephora P. accessions
inferredcites →https://doi.org/10.1016/s0378-4290(97)00026-9openalex-snapshot
Peas (Pisum sativum L.)
inferredcites →https://doi.org/10.1021/jf011702qopenalex-snapshot
Effect of Roasting on the Antioxidant Activity of Coffee Brews
inferredcites →https://doi.org/10.1021/jf0341767openalex-snapshot
Real-Time Monitoring of 4-Vinylguaiacol, Guaiacol, and Phenol during Coffee Roasting by Resonant Laser Ionization Time-of-Flight Mass Spectrometry
inferredcites →https://doi.org/10.1021/jf048701topenalex-snapshot
Effect of Roasting on the Formation of Chlorogenic Acid Lactones in Coffee
inferredcites →https://doi.org/10.1021/jf0518305openalex-snapshot
Chlorogenic Acids and Lactones in Regular and Water-Decaffeinated Arabica Coffees
inferredcites →https://doi.org/10.1021/jf071052bopenalex-snapshot
Insecticidal Activity of Caffeine Aqueous Solutions and Caffeine Oleate Emulsions against Drosophila melanogaster and Hypothenemus hampei
inferredcites →https://doi.org/10.1021/jf102590popenalex-snapshot
Inhibition of Pro-inflammatory Responses and Antioxidant Capacity of Mexican Blackberry (Rubus spp.) Extracts
inferredcites →https://doi.org/10.1021/jf902441nopenalex-snapshot
Genotypic and Environmental Effects on Coffee (Coffea arabicaL.) Bean Fatty Acid Profile: Impact on Variety and Origin Chemometric Determination
inferredcites →https://doi.org/10.1023/a:1003097913349openalex-snapshot
Identification of RAPD markers for resistance to coffee berry disease, Colletotrichum kahawae, in arabica coffee
inferredcites →https://doi.org/10.1034/j.1399-3054.2001.1120406.xopenalex-snapshot
Tolerance of coffee (Coffea spp.) seeds to ultra‐low temperature exposure in relation to calorimetric properties of tissue water, lipid composition, and cooling procedure
inferredcites →https://doi.org/10.1038/35023072openalex-snapshot
Caffeine synthase gene from tea leaves
inferredcites →https://doi.org/10.1038/35048692openalex-snapshot
Analysis of the genome sequence of the flowering plant Arabidopsis thaliana
inferredcites →https://doi.org/10.1038/35080508openalex-snapshot
The arms race is ancient history in Arabidopsis, the wildflower
inferredcites →https://doi.org/10.1038/45471openalex-snapshot
Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana
inferredcites →https://doi.org/10.1038/47076openalex-snapshot
Mitochondrial DNA repairs double-strand breaks in yeast chromosomes
inferredcites →https://doi.org/10.1038/hdy.2013.51openalex-snapshot
Analysis of plastid and mitochondrial DNA insertions in the nucleus (NUPTs and NUMTs) of six plant species: size, relative age and chromosomal localization
inferredcites →https://doi.org/10.1038/nature03895openalex-snapshot
The map-based sequence of the rice genome
inferredcites →https://doi.org/10.1038/nature06148openalex-snapshot
The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla
inferredcites →https://doi.org/10.1038/nature11119openalex-snapshot
The tomato genome sequence provides insights into fleshy fruit evolution
inferredcites →https://doi.org/10.1038/nature11241openalex-snapshot
The banana (Musa acuminata) genome and the evolution of monocotyledonous plants
inferredcites →https://doi.org/10.1038/nature12132openalex-snapshot
Architecture and evolution of a minute plant genome
inferredcites →https://doi.org/10.1038/nbt966openalex-snapshot
Engineering plants with increased levels of the antioxidant chlorogenic acid
inferredcites →https://doi.org/10.1038/ng.2470openalex-snapshot
The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions
inferredcites →https://doi.org/10.1038/ng.2472openalex-snapshot
The draft genome of sweet orange (Citrus sinensis)
inferredcites →https://doi.org/10.1038/nrg2165openalex-snapshot
A unified classification system for eukaryotic transposable elements
inferredcites →https://doi.org/10.1046/j.1365-313x.1999.00606.xopenalex-snapshot
Plant disease resistance genes encode members of an ancient and diverse protein family within the nucleotide-binding superfamily
inferredcites →https://doi.org/10.1073/pnas.091110398openalex-snapshot
Complex mtDNA constitutes an approximate 620-kb insertion on Arabidopsis thaliana chromosome 2: Implication of potential sequencing errors caused by large-unit repeats
inferredcites →https://doi.org/10.1073/pnas.1109273108openalex-snapshot
Formation of plant metabolic gene clusters within dynamic chromosomal regions
inferredcites →https://doi.org/10.1073/pnas.1400975111openalex-snapshot
Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization
inferredcites →https://doi.org/10.1073/pnas.93.13.6326openalex-snapshot
Inhibitors of HIV-1 replication that inhibit HIV integrase.
inferredcites →https://doi.org/10.1074/jbc.m009480200openalex-snapshot
7-Methylxanthine Methyltransferase of Coffee Plants
inferredcites →https://doi.org/10.1074/jbc.m209362200openalex-snapshot
Purification, Cloning, and Properties of an Acyltransferase Controlling Shikimate and Quinate Ester Intermediates in Phenylpropanoid Metabolism
inferredcites →https://doi.org/10.1093/aob/mcg183openalex-snapshot
Genome Size Variations in Diploid African Coffea Species
inferredcites →https://doi.org/10.1093/aob/mcm257openalex-snapshot
Towards a Phylogeny for Coffea (Rubiaceae): Identifying Well-supported Lineages Based on Nuclear and Plastid DNA Sequences
inferredcites →https://doi.org/10.1093/bioinformatics/13.4.477openalex-snapshot
EST_GENOME: a program to align spliced DNA sequences to unspliced genomic DNA
inferredcites →https://doi.org/10.1093/bioinformatics/13.5.555openalex-snapshot
PAML: a program package for phylogenetic analysis by maximum likelihood
inferredcites →https://doi.org/10.1093/bioinformatics/bti1018openalex-snapshot
De novo identification of repeat families in large genomes
inferredcites →https://doi.org/10.1093/bioinformatics/bti610openalex-snapshot
Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research
inferredcites →https://doi.org/10.1093/bioinformatics/btl097openalex-snapshot
CAFE: a computational tool for the study of gene family evolution
inferredcites →https://doi.org/10.1093/bioinformatics/btl334openalex-snapshot
Additional Gene Ontology structure for improved biological reasoning
inferredcites →https://doi.org/10.1093/bioinformatics/btp324openalex-snapshot
Fast and accurate short read alignment with Burrows–Wheeler transform
inferredcites →https://doi.org/10.1093/bioinformatics/btp336openalex-snapshot
SOAP2: an improved ultrafast tool for short read alignment
inferredcites →https://doi.org/10.1093/bioinformatics/btr623openalex-snapshot
BadiRate: estimating family turnover rates by likelihood-based methods
inferredcites →https://doi.org/10.1093/bioinformatics/bts392openalex-snapshot
Fractionation, rearrangement and subgenome dominance
inferredcites →https://doi.org/10.1093/bioinformatics/bts565openalex-snapshot
CD-HIT: accelerated for clustering the next-generation sequencing data
inferredcites →https://doi.org/10.1093/gbe/evq032openalex-snapshot
Genome-Wide Phylogenetic Comparative Analysis of Plant Transcriptional Regulation: A Timeline of Loss, Gain, Expansion, and Correlation with Complexity
inferredcites →https://doi.org/10.1093/genetics/166.2.935openalex-snapshot
Genomic Duplication, Fractionation and the Origin of Regulatory Novelty
inferredcites →https://doi.org/10.1093/jhered/est025openalex-snapshot
Differences in Evolution Rates among Eudicotyledon Species Observed by Analysis of Protein Divergence
inferredcites →https://doi.org/10.1093/jxb/erp304openalex-snapshot
Phytochrome functions in Arabidopsis development
inferredcites →https://doi.org/10.1093/molbev/msh110openalex-snapshot
NUMTs in Sequenced Eukaryotic Genomes
inferredcites →https://doi.org/10.1093/molbev/msi097openalex-snapshot
Bayes Empirical Bayes Inference of Amino Acid Sites Under Positive Selection
inferredcites →https://doi.org/10.1093/molbev/msi237openalex-snapshot
Evaluation of an Improved Branch-Site Likelihood Method for Detecting Positive Selection at the Molecular Level
inferredcites →https://doi.org/10.1093/molbev/msi242openalex-snapshot
Selectionism and Neutralism in Molecular Evolution
inferredcites →https://doi.org/10.1093/molbev/msm092openalex-snapshot
MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0
inferredcites →https://doi.org/10.1093/nar/25.17.3389openalex-snapshot
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
inferredcites →https://doi.org/10.1093/nar/27.2.573openalex-snapshot
Tandem repeats finder: a program to analyze DNA sequences
inferredcites →https://doi.org/10.1093/nar/30.1.276openalex-snapshot
The Pfam Protein Families Database
inferredcites →https://doi.org/10.1093/nar/gkh340openalex-snapshot
MUSCLE: multiple sequence alignment with high accuracy and high throughput
inferredcites →https://doi.org/10.1093/nar/gkh454openalex-snapshot
CD-Search: protein domain annotations on the fly
inferredcites →https://doi.org/10.1093/nar/gki198openalex-snapshot
MAFFT version 5: improvement in accuracy of multiple sequence alignment
inferredcites →https://doi.org/10.1093/nar/gkm960openalex-snapshot
The Pfam protein families database
inferredcites →https://doi.org/10.1093/nar/gkn845openalex-snapshot
CDD: specific functional annotation with the Conserved Domain Database
inferredcites →https://doi.org/10.1093/nar/gkq1189openalex-snapshot
CDD: a Conserved Domain Database for the functional annotation of proteins
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a003971openalex-snapshot
The Human Genome Project Reveals a Continuous Transfer of Large Mitochondrial Fragments to the Nucleus
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a004148openalex-snapshot
Codon-Substitution Models for Detecting Molecular Adaptation at Individual Sites Along Specific Lineages
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a025957openalex-snapshot
Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040153openalex-snapshot
A codon-based model of nucleotide substitution for protein-coding DNA sequences.
inferredcites →https://doi.org/10.1093/pcp/pcp175openalex-snapshot
Towards a Systems Approach for Lignin Biosynthesis in Populus trichocarpa: Transcript Abundance and Specificity of the Monolignol Biosynthetic Genes
inferredcites →https://doi.org/10.1101/gr.097261.109openalex-snapshot
De novo assembly of human genomes with massively parallel short read sequencing
inferredcites →https://doi.org/10.1101/gr.1224503openalex-snapshot
OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes
inferredcites →https://doi.org/10.1101/gr.149502openalex-snapshot
GAZE: A Generic Framework for the Integration of Gene-Prediction Data by Dynamic Programming
inferredcites →https://doi.org/10.1101/gr.164400.113openalex-snapshot
Widespread and frequent horizontal transfers of transposable elements in plants
inferredcites →https://doi.org/10.1101/gr.229202openalex-snapshot
BLAT —The BLAST -Like Alignment Tool
inferredcites →https://doi.org/10.1104/pp.105.073510openalex-snapshot
Mutations in the NB-ARC Domain of I-2 That Impair ATP Hydrolysis Cause Autoactivation
inferredcites →https://doi.org/10.1104/pp.106.094854openalex-snapshot
The Structure of Two N-Methyltransferases from the Caffeine Biosynthetic Pathway
inferredcites →https://doi.org/10.1104/pp.109.150144openalex-snapshot
Novel Hydroxycinnamoyl-Coenzyme A Quinate Transferase Genes from Artichoke Are Involved in the Synthesis of Chlorogenic Acid
inferredcites →https://doi.org/10.1104/pp.110.162438openalex-snapshot
A High-Throughput Data Mining of Single Nucleotide Polymorphisms inCoffeaSpecies Expressed Sequence Tags Suggests Differential Homeologous Gene Expression in the AllotetraploidCoffea arabica
inferredcites →https://doi.org/10.1105/tpc.005793openalex-snapshot
The Tomato R Gene Products I-2 and Mi-1 Are Functional ATP Binding Proteins with ATPase Activity
inferredcites →https://doi.org/10.1105/tpc.009308openalex-snapshot
Genome-Wide Analysis of NBS-LRR–Encoding Genes in Arabidopsis[W]
inferredcites →https://doi.org/10.1105/tpc.020297openalex-snapshot
Silencing of Hydroxycinnamoyl-Coenzyme A Shikimate/Quinate Hydroxycinnamoyltransferase Affects Phenylpropanoid Biosynthesis[W]
inferredcites →https://doi.org/10.1105/tpc.104.027706openalex-snapshot
The Rice Nuclear Genome Continuously Integrates, Shuffles, and Eliminates the Chloroplast Genome to Cause Chloroplast–Nuclear DNA Flux
inferredcites →https://doi.org/10.1105/tpc.11.3.495openalex-snapshot
Identification of Regions in Alleles of the Flax Rust Resistance Gene L That Determine Differences in Gene-for-Gene Specificity
inferredcites →https://doi.org/10.1105/tpc.110.082784openalex-snapshot
Evolution and Functional Diversification of MIRNA Genes
inferredcites →https://doi.org/10.1105/tpc.12.8.1367openalex-snapshot
Regions outside of the Leucine-Rich Repeats of Flax Rust Resistance Proteins Play a Role in Specificity Determination
inferredcites →https://doi.org/10.1111/j.1365-2621.2008.01800.xopenalex-snapshot
Antioxidant activity and phenolic content of lentils (Lens culinaris), chickpeas (Cicer arietinum L.), peas (Pisum sativum L.) and soybeans (Glycine max), and their quantitative changes during processing
inferredcites →https://doi.org/10.1111/j.1365-313x.2007.03326.xopenalex-snapshot
How to usefully compare homologous plant genes and chromosomes as DNA sequences
inferredcites →https://doi.org/10.1111/j.1469-1809.1943.tb02321.xopenalex-snapshot
THE ESTIMATION OF MAP DISTANCES FROM RECOMBINATION VALUES
inferredcites →https://doi.org/10.1111/j.1469-8137.2006.01798.xopenalex-snapshot
Genome‐wide analysis of the structural genes regulating defense phenylpropanoid metabolism in Populus
inferredcites →https://doi.org/10.1111/j.1469-8137.2008.02742.xopenalex-snapshot
Metabolic pathways in tropical dicotyledonous albuminous seeds: Coffea arabica as a case study
inferredcites →https://doi.org/10.1111/j.1742-4658.2005.04945.xopenalex-snapshot
Protein database searches using compositionally adjusted substitution matrices
inferredcites →https://doi.org/10.1111/j.2517-6161.1995.tb02031.xopenalex-snapshot
Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing
inferredcites →https://doi.org/10.1126/science.1083523openalex-snapshot
In-Depth View of Structure, Activity, and Evolution of Rice Chromosome 10
inferredcites →https://doi.org/10.1126/science.1128691openalex-snapshot
The Genome of Black Cottonwood, Populus trichocarpa (Torr. & Gray)
inferredcites →https://doi.org/10.1126/science.1154990openalex-snapshot
Metabolic Diversification—Independent Assembly of Operon-Like Gene Clusters in Different Plants
inferredcites →https://doi.org/10.1126/science.1174095openalex-snapshot
Evolution of a Novel Phenolic Pathway for Pollen Development
inferredcites →https://doi.org/10.1126/science.6207592openalex-snapshot
Caffeine and Related Methylxanthines: Possible Naturally Occurring Pesticides
inferredcites →https://doi.org/10.1128/aac.42.1.140openalex-snapshot
Dicaffeoylquinic and Dicaffeoyltartaric Acids Are Selective Inhibitors of Human Immunodeficiency Virus Type 1 Integrase
inferredcites →https://doi.org/10.1146/annurev-arplant-042110-103814openalex-snapshot
Convergent Evolution in Plant Specialized Metabolism
inferredcites →https://doi.org/10.1146/annurev-arplant-042809-112235openalex-snapshot
Insights from the Comparison of Plant Genome Sequences
inferredcites →https://doi.org/10.1146/annurev.arplant.54.031902.135035openalex-snapshot
Understanding the Functions of Plant Disease Resistance Proteins
inferredcites →https://doi.org/10.1146/annurev.phyto.39.1.285openalex-snapshot
R ESISTANCE G ENE C OMPLEXES : Evolution and Utilization
inferredcites →https://doi.org/10.1159/000084979openalex-snapshot
Repbase Update, a database of eukaryotic repetitive elements
inferredcites →https://doi.org/10.1177/117693430600200029openalex-snapshot
Modelling Prokaryote Gene Content
inferredcites →https://doi.org/10.1186/1471-2105-13-s14-s8openalex-snapshot
GapFiller: a de novo assembly approach to fill the gap within paired reads
inferredcites →https://doi.org/10.1186/1471-2105-13-s19-s8openalex-snapshot
A consolidation algorithm for genomes fractionated after higher order polyploidization
inferredcites →https://doi.org/10.1186/1471-2105-9-21openalex-snapshot
LeARN: a platform for detecting, clustering and annotating non-coding RNAs
inferredcites →https://doi.org/10.1186/1471-2148-9-58openalex-snapshot
Whole genome surveys of rice, maize and sorghum reveal multiple horizontal transfers of the LTR-retrotransposon Route66 in Poaceae
inferredcites →https://doi.org/10.1186/1471-2164-12-240openalex-snapshot
Organization and molecular evolution of a disease-resistance gene cluster in coffee trees
inferredcites →https://doi.org/10.1186/1471-2164-13-103openalex-snapshot
Ancestral synteny shared between distantly-related plant species from the asterid (Coffea canephora and Solanum Sp.) and rosid (Vitis vinifera) clades
inferredcites →https://doi.org/10.1186/1471-2164-14-109openalex-snapshot
Genome-wide analysis of NBS-encoding disease resistance genes in Cucumis sativusand phylogenetic study of NBS-encoding genes in Cucurbitaceae crops
inferredcites →https://doi.org/10.1186/1471-2164-9-603openalex-snapshot
High quality draft sequences for prokaryotic genomes using a mix of new sequencing technologies
inferredcites →https://doi.org/10.1186/1471-2229-9-22openalex-snapshot
Microcollinearity in an ethylene receptor coding gene region of the Coffea canephora genome is extensively conserved with Vitis vinifera and other distant dicotyledonous sequenced genomes
inferredcites →https://doi.org/10.1186/gb-2006-7-4-212openalex-snapshot
Plant NBS-LRR proteins: adaptable guards.
inferredcites →https://doi.org/10.1186/gb-2006-7-s1-s10openalex-snapshot
Automatic annotation of eukaryotic genes, pseudogenes and promoters
inferredcites →https://doi.org/10.1186/gb-2008-9-12-r175openalex-snapshot
Annotating genomes with massive-scale RNA sequencing
inferredcites →https://doi.org/10.1186/gb-2010-11-10-r106openalex-snapshot
Differential expression analysis for sequence count data
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What points at this work
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The sage genome provides insight into the evolutionary dynamics of diterpene biosynthesis gene cluster in plants
inferred← citeshttps://doi.org/10.1016/j.celrep.2024.114902openalex-snapshot
The tetraploid Camellia oleifera genome provides insights into evolution, agronomic traits, and genetic architecture of oil Camellia plants
inferred← citeshttps://doi.org/10.1016/j.chmed.2024.11.003openalex-snapshot
Metabolome and transcriptome association study reveals biosynthesis of specialized benzylisoquinoline alkaloids in Phellodendron amurense
inferred← citeshttps://doi.org/10.1016/j.chmed.2025.11.007openalex-snapshot
Genome-wide identification and characterization of methyltransferase involved in benzylisoquinoline alkaloids biosynthesis from Menispermum dauricum
inferred← citeshttps://doi.org/10.1016/j.cpb.2016.12.002openalex-snapshot
The South Green portal: a comprehensive resource for tropical and Mediterranean crop genomics
inferred← citeshttps://doi.org/10.1016/j.cpb.2026.100683openalex-snapshot
Expanding plant model systems: Classical references, emerging species, and a trait‑centric framework for modern plant science
inferred← citeshttps://doi.org/10.1016/j.crbiot.2020.02.001openalex-snapshot
Temporal shotgun metagenomics of an Ecuadorian coffee fermentation process highlights the predominance of lactic acid bacteria
inferred← citeshttps://doi.org/10.1016/j.csbj.2023.11.034openalex-snapshot
Genome mining of metabolic gene clusters in the Rubiaceae family
inferred← citeshttps://doi.org/10.1016/j.csbj.2024.02.028openalex-snapshot
Multi-omics analysis reveals promiscuous O -glycosyltransferases involved in the diversity of flavonoid glycosides in Periploca forrestii (Apocynaceae)
inferred← citeshttps://doi.org/10.1016/j.ejbt.2018.08.005openalex-snapshot
Cloning of the Coffea canephora SERK1 promoter and its molecular analysis during the cell-to-embryo transition
inferred← citeshttps://doi.org/10.1016/j.eng.2025.11.022openalex-snapshot
The Haplotype-Resolved Pentaploid Gynostemma pentaphyllum Genome Provides Insights into Chromosomal Evolution and the Convergent Evolution of Protopanaxadiol Synthases
inferred← citeshttps://doi.org/10.1016/j.envexpbot.2017.12.004openalex-snapshot
Transcriptional memory contributes to drought tolerance in coffee (Coffea canephora) plants
inferred← citeshttps://doi.org/10.1016/j.envexpbot.2019.103856openalex-snapshot
Lipid profile adjustments may contribute to warming acclimation and to heat impact mitigation by elevated [CO2] in Coffea spp
inferred← citeshttps://doi.org/10.1016/j.envexpbot.2020.104247openalex-snapshot
iTRAQ-based proteomic technique provides insights into salt stress responsive proteins in Apocyni Veneti Folium (Apocynum venetum L.)
inferred← citeshttps://doi.org/10.1016/j.envexpbot.2024.105983openalex-snapshot
Heterologous expression of coffee HB12 confers tolerance to water deficit in transgenic plants through an ABA-independent route
inferred← citeshttps://doi.org/10.1016/j.foodchem.2015.12.051openalex-snapshot
Interaction of coffee compounds with serum albumins. Part II: Diterpenes
inferred← citeshttps://doi.org/10.1016/j.foodcont.2018.01.014openalex-snapshot
Development of a rapid and efficient DNA-based method to detect and quantify adulterations in coffee (Arabica versus Robusta)
inferred← citeshttps://doi.org/10.1016/j.gce.2020.11.008openalex-snapshot
Accurate, automatic annotation of peptidases with hotpep-protease
inferred← citeshttps://doi.org/10.1016/j.heliyon.2024.e35513openalex-snapshot
Triumphs of genomic-assisted breeding in crop improvement
inferred← citeshttps://doi.org/10.1016/j.heliyon.2025.e43015openalex-snapshot
A bibliometric analysis of computational and mathematical techniques in the cocoa sustainable food value chain
inferred← citeshttps://doi.org/10.1016/j.ijbiomac.2023.128727openalex-snapshot
From genomics to metabolomics: Deciphering sanguinarine biosynthesis in Dicranostigma leptopodum
inferred← citeshttps://doi.org/10.1016/j.ijbiomac.2025.143103openalex-snapshot
Revealing the molecular mechanism of biosynthesis and transcriptional regulation of PAs, caffeine and linalool globally under simulative stress in coffee plants
inferred← citeshttps://doi.org/10.1016/j.indcrop.2021.114438openalex-snapshot
O-methyltransferases catalyze the last step of geniposide biosynthesis in Gardenia jasminoides
inferred← citeshttps://doi.org/10.1016/j.indcrop.2026.122951openalex-snapshot
The genome of the allotetrapolyploid Morinda citrifolia (Noni) provides insights into its evolution and antioxidant function
inferred← citeshttps://doi.org/10.1016/j.isci.2022.105026openalex-snapshot
Multifaceted roles of GRAS transcription factors in growth and stress responses in plants
inferred← citeshttps://doi.org/10.1016/j.jinorgbio.2017.07.032openalex-snapshot
Relationship between aluminum stress and caffeine biosynthesis in suspension cells of Coffea arabica L
inferred← citeshttps://doi.org/10.1016/j.jplph.2022.153788openalex-snapshot
High-resolution shotgun proteomics reveals that increased air [CO2] amplifies the acclimation response of Coffea species to drought regarding antioxidative, energy, sugar, and lipid dynamics
inferred← citeshttps://doi.org/10.1016/j.margen.2016.04.012openalex-snapshot
Next-generation biology: Sequencing and data analysis approaches for non-model organisms
inferred← citeshttps://doi.org/10.1016/j.microc.2024.110021openalex-snapshot
Uv–Vis molecular spectral resolution of multi-level mixture design-fingerprints of yerba mate leaves by chemometric methods
inferred← citeshttps://doi.org/10.1016/j.molp.2017.04.002openalex-snapshot
The Tea Tree Genome Provides Insights into Tea Flavor and Independent Evolution of Caffeine Biosynthesis
inferred← citeshttps://doi.org/10.1016/j.molp.2020.04.010openalex-snapshot
The Reference Genome of Tea Plant and Resequencing of 81 Diverse Accessions Provide Insights into Its Genome Evolution and Adaptation
inferred← citeshttps://doi.org/10.1016/j.molp.2022.05.013openalex-snapshot
Allele-aware chromosome-level genome assembly of Artemisia annua reveals the correlation between ADS expansion and artemisinin yield
inferred← citeshttps://doi.org/10.1016/j.molp.2022.07.007openalex-snapshot
Comparative genomics of orobanchaceous species with different parasitic lifestyles reveals the origin and stepwise evolution of plant parasitism
inferred← citeshttps://doi.org/10.1016/j.mseb.2021.115473openalex-snapshot
A surface-modified silicon carbide nanoparticles based electrochemical sensor for free interferences determination of caffeine in tea and coffee
inferred← citeshttps://doi.org/10.1016/j.pbi.2015.02.002openalex-snapshot
Progress, challenges and the future of crop genomes
inferred← citeshttps://doi.org/10.1016/j.pbi.2016.02.005openalex-snapshot
Ancestors of modern plant crops
inferred← citeshttps://doi.org/10.1016/j.pbi.2019.03.005openalex-snapshot
Tip of the trichome: evolution of acylsugar metabolic diversity in Solanaceae
inferred← citeshttps://doi.org/10.1016/j.pbi.2020.01.007openalex-snapshot
Computational approaches to unravel the pathways and evolution of specialized metabolism
inferred← citeshttps://doi.org/10.1016/j.pbi.2020.03.005openalex-snapshot
Gene and genome duplications in the evolution of chemodiversity: perspectives from studies of Lamiaceae
inferred← citeshttps://doi.org/10.1016/j.pbi.2026.102894openalex-snapshot
Revisiting tandem duplication in plant genomes: Technical challenges and pangenome solutions
inferred← citeshttps://doi.org/10.1016/j.pbiomolbio.2018.12.002openalex-snapshot
Decoding systems biology of plant stress for sustainable agriculture development and optimized food production
inferred← citeshttps://doi.org/10.1016/j.plantsci.2021.111018openalex-snapshot
Genomic and transcriptomic inventory of membrane transporters in coffee: Exploring molecular mechanisms of metabolite accumulation
inferred← citeshttps://doi.org/10.1016/j.plantsci.2022.111479openalex-snapshot
Expression of coffee florigen CaFT1 reveals a sustained floral induction window associated with asynchronous flowering in tropical perennials
inferred← citeshttps://doi.org/10.1016/j.plaphy.2015.07.024openalex-snapshot
Aquaporins in Coffea arabica L.: Identification, expression, and impacts on plant water relations and hydraulics
inferred← citeshttps://doi.org/10.1016/j.plaphy.2015.12.020openalex-snapshot
Natural allelic variations of TCS1 play a crucial role in caffeine biosynthesis of tea plant and its related species
inferred← citeshttps://doi.org/10.1016/j.plaphy.2016.12.004openalex-snapshot
Diterpenes biochemical profile and transcriptional analysis of cytochrome P450s genes in leaves, roots, flowers, and during Coffea arabica L. fruit development
inferred← citeshttps://doi.org/10.1016/j.plaphy.2025.110771openalex-snapshot
Gene coexpression network analysis of galactomannan biosynthesis and endosperm maturation in species of the genus Coffea
inferred← citeshttps://doi.org/10.1016/j.pld.2021.11.005openalex-snapshot
Transcriptome and carotenoid profiling of different varieties of Coffea arabica provides insights into fruit color formation
inferred← citeshttps://doi.org/10.1016/j.plgene.2015.09.002openalex-snapshot
Salicylic acid and methyljasmonate restore the transcription of caffeine biosynthetic N-methyltransferases from a transcription inhibition noticed during late endosperm maturation in coffee
inferred← citeshttps://doi.org/10.1016/j.plgene.2020.100263openalex-snapshot
The oleosin gene family in coffee: Analysis of oleosomes, oleosins and lipid-related gene expression during germination of Coffea arabica seeds
inferred← citeshttps://doi.org/10.1016/j.plgene.2021.100314openalex-snapshot
Large-scale prospection of genes on caffeine-free Coffea arabica plants – Discovery of novel markers associated with development and secondary metabolism
inferred← citeshttps://doi.org/10.1016/j.pmpp.2017.09.001openalex-snapshot
Early responses of coffee immunity-related genes to root-knot nematode infection
inferred← citeshttps://doi.org/10.1016/j.pmpp.2024.102539openalex-snapshot
Transcriptomic analyses reveal the involvement of miraculin family genes in the incompatible interaction between Meloidogyne incognita and coffee (Coffea arabica L.)
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