Published in BMC Bioinformatics on October 23, 2006
MetaCrop: a detailed database of crop plant metabolism. Nucleic Acids Res (2007) 1.53
Flux balance analysis of barley seeds: a computational approach to study systemic properties of central metabolism. Plant Physiol (2008) 1.43
Reconstruction and analysis of genome-scale metabolic model of a photosynthetic bacterium. BMC Syst Biol (2010) 1.23
MetaCrop 2.0: managing and exploring information about crop plant metabolism. Nucleic Acids Res (2011) 0.94
METANNOGEN: compiling features of biochemical reactions needed for the reconstruction of metabolic networks. BMC Syst Biol (2007) 0.91
Barley genomics: An overview. Int J Plant Genomics (2008) 0.86
Generation and Evaluation of a Genome-Scale Metabolic Network Model of Synechococcus elongatus PCC7942. Metabolites (2014) 0.79
From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res (2006) 44.35
Database resources of the National Center for Biotechnology Information. Nucleic Acids Res (2000) 34.79
The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics (2003) 32.92
Reactome: a knowledgebase of biological pathways. Nucleic Acids Res (2005) 20.05
BRENDA, the enzyme database: updates and major new developments. Nucleic Acids Res (2004) 8.21
VANTED: a system for advanced data analysis and visualization in the context of biological networks. BMC Bioinformatics (2006) 4.38
GEPASI: a software package for modelling the dynamics, steady states and control of biochemical and other systems. Comput Appl Biosci (1993) 3.67
The aMAZE LightBench: a web interface to a relational database of cellular processes. Nucleic Acids Res (2004) 3.39
MetaCyc and AraCyc. Metabolic pathway databases for plant research. Plant Physiol (2005) 3.00
The Molecular Biology Database Collection: 2006 update. Nucleic Acids Res (2006) 2.61
The University of Minnesota Biocatalysis/Biodegradation Database: the first decade. Nucleic Acids Res (2006) 2.52
The Plant Ontology Consortium and plant ontologies. Comp Funct Genomics (2002) 2.50
Addressing the problems with life-science databases for traditional uses and systems biology. Nat Rev Genet (2006) 1.97
Regulation of sucrose to starch conversion in growing potato tubers. J Exp Bot (2003) 1.36
Analysis and comparison of metabolic pathway databases. Brief Bioinform (2001) 1.26
The Systems Biology Graphical Notation. Nat Biotechnol (2009) 8.53
VANTED: a system for advanced data analysis and visualization in the context of biological networks. BMC Bioinformatics (2006) 4.38
Unlocking the barley genome by chromosomal and comparative genomics. Plant Cell (2011) 3.03
A 1,000-loci transcript map of the barley genome: new anchoring points for integrative grass genomics. Theor Appl Genet (2007) 2.44
Functional microRNA targets in protein coding sequences. Bioinformatics (2012) 2.40
Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ). Plant J (2013) 2.02
HTPheno: an image analysis pipeline for high-throughput plant phenotyping. BMC Bioinformatics (2011) 1.98
Frequent gene movement and pseudogene evolution is common to the large and complex genomes of wheat, barley, and their relatives. Plant Cell (2011) 1.98
The ability to detoxify the mycotoxin deoxynivalenol colocalizes with a major quantitative trait locus for Fusarium head blight resistance in wheat. Mol Plant Microbe Interact (2005) 1.94
Exploration of biological network centralities with CentiBiN. BMC Bioinformatics (2006) 1.78
miRGen 2.0: a database of microRNA genomic information and regulation. Nucleic Acids Res (2009) 1.78
Dynamic exploration and editing of KEGG pathway diagrams. Bioinformatics (2006) 1.75
Barley grain maturation and germination: metabolic pathway and regulatory network commonalities and differences highlighted by new MapMan/PageMan profiling tools. Plant Physiol (2008) 1.73
Editing, validating and translating of SBGN maps. Bioinformatics (2010) 1.71
Software support for SBGN maps: SBGN-ML and LibSBGN. Bioinformatics (2012) 1.69
De novo 454 sequencing of barcoded BAC pools for comprehensive gene survey and genome analysis in the complex genome of barley. BMC Genomics (2009) 1.61
Gene content and virtual gene order of barley chromosome 1H. Plant Physiol (2009) 1.53
MetaCrop: a detailed database of crop plant metabolism. Nucleic Acids Res (2007) 1.53
Apomictic and sexual ovules of Boechera display heterochronic global gene expression patterns. Plant Cell (2010) 1.52
SNP2CAPS: a SNP and INDEL analysis tool for CAPS marker development. Nucleic Acids Res (2004) 1.52
Phosphate systemically inhibits development of arbuscular mycorrhiza in Petunia hybrida and represses genes involved in mycorrhizal functioning. Plant J (2010) 1.50
VANTED v2: a framework for systems biology applications. BMC Syst Biol (2012) 1.49
Genes driving potato tuber initiation and growth: identification based on transcriptional changes using the POCI array. Funct Integr Genomics (2008) 1.44
Flux balance analysis of barley seeds: a computational approach to study systemic properties of central metabolism. Plant Physiol (2008) 1.43
Large-scale analysis of the barley transcriptome based on expressed sequence tags. Plant J (2004) 1.41
A transcriptomic hourglass in plant embryogenesis. Nature (2012) 1.40
Systems analysis of a maize leaf developmental gradient redefines the current C4 model and provides candidates for regulation. Plant Cell (2011) 1.38
Selfish supernumerary chromosome reveals its origin as a mosaic of host genome and organellar sequences. Proc Natl Acad Sci U S A (2012) 1.37
From RNA-seq to large-scale genotyping - genomics resources for rye (Secale cereale L.). BMC Plant Biol (2011) 1.35
Barley whole exome capture: a tool for genomic research in the genus Hordeum and beyond. Plant J (2013) 1.34
Application of Petri net theory for modelling and validation of the sucrose breakdown pathway in the potato tuber. Bioinformatics (2004) 1.31
Path2Models: large-scale generation of computational models from biochemical pathway maps. BMC Syst Biol (2013) 1.29
Applications of recursive segmentation to the analysis of DNA sequences. Comput Chem (2002) 1.25
Toward the identification and regulation of the Arabidopsis thaliana ABI3 regulon. Nucleic Acids Res (2012) 1.25
Manipulation of plant innate immunity and gibberellin as factor of compatibility in the mutualistic association of barley roots with Piriformospora indica. Plant J (2009) 1.23
Transcriptional dynamics of two seed compartments with opposing roles in Arabidopsis seed germination. Plant Physiol (2013) 1.23
Kavosh: a new algorithm for finding network motifs. BMC Bioinformatics (2009) 1.21
Evidence and evolutionary analysis of ancient whole-genome duplication in barley predating the divergence from rice. BMC Evol Biol (2009) 1.19
A general approach for discriminative de novo motif discovery from high-throughput data. Nucleic Acids Res (2013) 1.18
Centrality analysis methods for biological networks and their application to gene regulatory networks. Gene Regul Syst Bio (2008) 1.17
A sequence-ready physical map of barley anchored genetically by two million single-nucleotide polymorphisms. Plant Physiol (2013) 1.17
Simulating plant metabolic pathways with enzyme-kinetic models. Plant Physiol (2010) 1.16
ABA biosynthesis and degradation contributing to ABA homeostasis during barley seed development under control and terminal drought-stress conditions. J Exp Bot (2011) 1.14
Integration of -omics data and networks for biomedical research with VANTED. J Integr Bioinform (2010) 1.12
De-novo discovery of differentially abundant transcription factor binding sites including their positional preference. PLoS Comput Biol (2011) 1.11
Calculation of the biological effects of ion beams based on the microscopic spatial damage distribution pattern. Int J Radiat Biol (2011) 1.11
Dynamic ¹³C/¹ H NMR imaging uncovers sugar allocation in the living seed. Plant Biotechnol J (2011) 1.10
Distribution, functional impact, and origin mechanisms of copy number variation in the barley genome. Genome Biol (2013) 1.10
How to identify essential genes from molecular networks? BMC Syst Biol (2009) 1.09
Combined noninvasive imaging and modeling approaches reveal metabolic compartmentation in the barley endosperm. Plant Cell (2011) 1.06
Systematic analysis of RBE and related quantities using a database of cell survival experiments with ion beam irradiation. J Radiat Res (2012) 1.06
Multiscale metabolic modeling: dynamic flux balance analysis on a whole-plant scale. Plant Physiol (2013) 1.04
Barley grain development toward an integrative view. Int Rev Cell Mol Biol (2010) 1.04
MODA: an efficient algorithm for network motif discovery in biological networks. Genes Genet Syst (2009) 1.03
e!DAL--a framework to store, share and publish research data. BMC Bioinformatics (2014) 1.02
Transcriptome analysis of mlo-mediated resistance in the epidermis of barley. Mol Plant Pathol (2005) 1.01
Natural variation of transcriptional auxin response networks in Arabidopsis thaliana. Plant Cell (2010) 1.01
Maize source leaf adaptation to nitrogen deficiency affects not only nitrogen and carbon metabolism but also control of phosphate homeostasis. Plant Physiol (2012) 1.00
Reticulate evolution of the rye genome. Plant Cell (2013) 1.00
Mapping-by-sequencing accelerates forward genetics in barley. Genome Biol (2014) 0.99
An engineer's view on regulation of seed development. Trends Plant Sci (2010) 0.99
Analysis of sequence, map position, and gene expression reveals conserved essential genes for iron uptake in Arabidopsis and tomato. Plant Physiol (2004) 0.99
Asexual genome evolution in the apomictic Ranunculus auricomus complex: examining the effects of hybridization and mutation accumulation. Mol Ecol (2013) 0.98
Fractionally integrated process with power-law correlations in variables and magnitudes. Phys Rev E Stat Nonlin Soft Matter Phys (2005) 0.98
The LAILAPS search engine: relevance ranking in life science databases. J Integr Bioinform (2010) 0.97
Evidence of a key role for photosynthetic oxygen release in oil storage in developing soybean seeds. New Phytol (2005) 0.97
Hypothesis-driven approach to predict transcriptional units from gene expression data. Bioinformatics (2004) 0.96
Modularization of biochemical networks based on classification of Petri net t-invariants. BMC Bioinformatics (2008) 0.96
FBA-SimVis: interactive visualization of constraint-based metabolic models. Bioinformatics (2009) 0.95
The differential transcription network between embryo and endosperm in the early developing maize seed. Plant Physiol (2013) 0.95
Creating interactive, web-based and data-enriched maps with the Systems Biology Graphical Notation. Nat Protoc (2012) 0.95
Repeats and correlations in human DNA sequences. Phys Rev E Stat Nonlin Soft Matter Phys (2003) 0.94
MetaCrop 2.0: managing and exploring information about crop plant metabolism. Nucleic Acids Res (2011) 0.94
Integrating data from biological experiments into metabolic networks with the DBE information system. In Silico Biol (2005) 0.93
Sequencing of BAC pools by different next generation sequencing platforms and strategies. BMC Res Notes (2011) 0.92
454 Transcriptome sequencing suggests a role for two-component signalling in cellularization and differentiation of barley endosperm transfer cells. PLoS One (2012) 0.91
Adaptation of maize source leaf metabolism to stress related disturbances in carbon, nitrogen and phosphorus balance. BMC Genomics (2013) 0.91
Controllability in cancer metabolic networks according to drug targets as driver nodes. PLoS One (2013) 0.91
Antisense inhibition of the plastidial glucose-6-phosphate/phosphate translocator in Vicia seeds shifts cellular differentiation and promotes protein storage. Plant J (2007) 0.90
Bioinformatics strategies for the analysis of lipids. Methods Mol Biol (2009) 0.90