相关参考文献
注意:仅列出部分参考文献,下载原文获取全部文献信息。Plant Regulomics: a data-driven interface for retrieving upstream regulators from plant multi-omics data
Xiaojuan Ran et al.
PLANT JOURNAL (2020)
Integrated analysis of the transcriptome and metabolome in young and mature leaves of Ginkgo biloba L.
Jing Guo et al.
INDUSTRIAL CROPS AND PRODUCTS (2020)
PANOMICS meets germplasm
Wolfram Weckwerth et al.
PLANT BIOTECHNOLOGY JOURNAL (2020)
Assessment of weighted topological overlap (wTO) to improve fidelity of gene co-expression networks
Andre Voigt et al.
BMC BIOINFORMATICS (2019)
Robust predictions of specialized metabolism genes through machine learning
Bethany M. Moore et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)
Modeling Protein Destiny in Developing Fruit
Isma Belouah et al.
PLANT PHYSIOLOGY (2019)
Machine learning approaches and their current application in plant molecular biology: A systematic review
Jose Cleydson F. Silva et al.
PLANT SCIENCE (2019)
Systems Biology and Multi-Omics Integration: Viewpoints from the Metabolomics Research Community
Farhana R. Pinu et al.
METABOLITES (2019)
Reconstructing functional networks in the human intestinal tract using synthetic microbiomes
Sudarshan A. Shetty et al.
CURRENT OPINION IN BIOTECHNOLOGY (2019)
Integration of proteomics and metabolomics data of early and middle season Hass avocados under heat treatment
Virgilio Gavicho Uarrota et al.
FOOD CHEMISTRY (2019)
Methyl jasmonate-induced compositional changes of volatile organic compounds in Polygonum minus leaves
Reyhaneh Rahnamaie-Tajadod et al.
JOURNAL OF PLANT PHYSIOLOGY (2019)
Protein replenishment in pitcher fluids of Nepenthes x ventrata revealed by quantitative proteomics (SWATH-MS) informed by transcriptomics
Wan Nor Adibah Wan Zakaria et al.
JOURNAL OF PLANT RESEARCH (2019)
Investigation and development of maize fused network analysis with multi-omics
Jing Jiang et al.
PLANT PHYSIOLOGY AND BIOCHEMISTRY (2019)
Knowledge Base Commons (KBCommons) v1.1: a universal framework for multi-omics data integration and biological discoveries
Shuai Zeng et al.
BMC GENOMICS (2019)
Outsmarting and outmuscling cancer cells with synthetic and systems immunology
Laurence C. Chen et al.
CURRENT OPINION IN BIOTECHNOLOGY (2019)
MapMan4: A Refined Protein Classification and Annotation Framework Applicable to Multi-Omics Data Analysis
Rainer Schwacke et al.
MOLECULAR PLANT (2019)
Toward a Unification of System-Theoretical Principles in Biology and Ecology-The Stochastic Lyapunov Matrix Equation and Its Inverse Application
Wolfram Weckwerth
FRONTIERS IN APPLIED MATHEMATICS AND STATISTICS (2019)
Progress Toward Rice Seed OMICS in Low-Level Gamma Radiation Environment in Iitate Village, Fukushima
Randeep Rakwal et al.
JOURNAL OF HEREDITY (2018)
A multi-omics approach reveals function of Secretory Carrier-Associated Membrane Proteins in wood formation of Populus trees
Ogonna Obudulu et al.
BMC GENOMICS (2018)
The coupling of transcriptome and proteome adaptation during development and heat stress response of tomato pollen
Mario Keller et al.
BMC GENOMICS (2018)
Transcriptomic and metabolomic analyses reveal that bacteria promote plant defense during infection of soybean cyst nematode in soybean
Wenshu Kang et al.
BMC PLANT BIOLOGY (2018)
Integration of proteomic and transcriptomic profiles reveals multiple levels of genetic regulation of salt tolerance in cotton
Zhen Peng et al.
BMC PLANT BIOLOGY (2018)
Plant genome-scale reconstruction: from single cell to multi-tissue modelling and omics analyses
Cristiana Gomes de Oliveira Dal'Molin et al.
CURRENT OPINION IN BIOTECHNOLOGY (2018)
PaintOmics 3: a web resource for the pathway analysis and visualization of multi-omics data
Rafael Hernandez-de-Diego et al.
NUCLEIC ACIDS RESEARCH (2018)
Unraveling lipid metabolism in maize with time-resolved multi-omics data
Francisco de Abreu e Lima et al.
PLANT JOURNAL (2018)
PlantSEED enables automated annotation and reconstruction of plant primary metabolism with improved compartmentalization and comparative consistency
Samuel M. D. Seaver et al.
PLANT JOURNAL (2018)
Multi-Omics Driven Assembly and Annotation of the Sandalwood (Santalum album) Genome
Hirehally Basavarajegowda Mahesh et al.
PLANT PHYSIOLOGY (2018)
Metabolomics analysis of developing Garcinia mangostana eseed reveals modulated levels of sugars, organic acids and phenylpropanoid compounds
Othman Mazlan et al.
SCIENTIA HORTICULTURAE (2018)
Improving wood properties for wood utilization through multi-omics integration in lignin biosynthesis
Jack P. Wang et al.
NATURE COMMUNICATIONS (2018)
SolCyc: a database hub at the Sol Genomics Network (SGN) for the manual curation of metabolic networks in Solanum and Nicotiana specific databases
Hartmut Foerster et al.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION (2018)
Homeolog expression analysis in an allotriploid non-model crop via integration of transcriptomics and proteomics
Jelle van Wesemael et al.
SCIENTIFIC REPORTS (2018)
Integration of large-scale data for extraction of integrated Arabidopsis root cell-type specific models
Michael Scheunemann et al.
SCIENTIFIC REPORTS (2018)
Constraint-Based Modeling Highlights Cell Energy, Redox Status and alpha-Ketoglutarate Availability as Metabolic Drivers for Anthocyanin Accumulation in Grape Cells Under Nitrogen Limitation
Eric Soubeyrand et al.
FRONTIERS IN PLANT SCIENCE (2018)
A Multi-Omics Analysis Pipeline for the Metabolic Pathway Reconstruction in the Orphan Species Quercus ilex
Cristina Lopez-Hidalgo et al.
FRONTIERS IN PLANT SCIENCE (2018)
Integrated transcriptomic and metabolomic analyses of a wax deficient citrus mutant exhibiting jasmonic acid-mediated defense against fungal pathogens
Yizhong He et al.
HORTICULTURE RESEARCH (2018)
Review: The application of omics to rumen microbiota function
S. E. Denman et al.
ANIMAL (2018)
Metabolomics analysis of mangosteen (Garcinia mangostana Linn.) fruit pericarp using different extraction methods and GC-MS
Siti Farah Mamat et al.
Plant Omics (2018)
Proteomics (SWATH-MS) informed by transcriptomics approach of tropical herb Persicaria minor leaves upon methyl jasmonate elicitation
Wan Mohd Aizat et al.
PEERJ (2018)
OnPLS-Based Multi-Block Data Integration: A Multivariate Approach to Interrogating Biological Interactions in Asthma
Stacey N. Reinke et al.
ANALYTICAL CHEMISTRY (2018)
Integrating omics datasets with the OmicsPLS package
Said el Bouhaddani et al.
BMC BIOINFORMATICS (2018)
Ethylene Receptors, CTRs and EIN2 Target Protein Identification and Quantification Through Parallel Reaction Monitoring During Tomato Fruit Ripening
Clara Mata et al.
FRONTIERS IN PLANT SCIENCE (2018)
Metabolomics Analysis of Soybean Hypocotyls in Response to Phytophthora sojae Infection
Longming Zhu et al.
FRONTIERS IN PLANT SCIENCE (2018)
The multi-omics promise in context: from sequence to microbial isolate
Johanna Gutleben et al.
CRITICAL REVIEWS IN MICROBIOLOGY (2018)
Metabolite-Centric Reporter Pathway and Tripartite Network Analysis of Arabidopsis Under Cold Stress
Ibrahim Koc et al.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY (2018)
Pathview Web: user friendly pathway visualization and data integration
Weijun Luo et al.
NUCLEIC ACIDS RESEARCH (2017)
Integrated omics analyses of retrograde signaling mutant delineate interrelated stress-response strata
Marta Bjornson et al.
PLANT JOURNAL (2017)
Integrated omics analysis of specialized metabolism in medicinal plants
Amit Rai et al.
PLANT JOURNAL (2017)
Metabolite profiling and associated gene expression reveal two metabolic shifts during the seed-to-seedling transition in Arabidopsis thaliana
Anderson Tadeu Silva et al.
PLANT MOLECULAR BIOLOGY (2017)
The best models of metabolism
Eberhard O. Voit
WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE (2017)
mixOmics: An R package for 'omics feature selection and multiple data integration
Florian Rohart et al.
PLOS COMPUTATIONAL BIOLOGY (2017)
Metabolic Pathway Assignment of Plant Genes based on Phylogenetic Profiling-A Feasibility Study
Sandra Weissenborn et al.
FRONTIERS IN PLANT SCIENCE (2017)
Differential Gene Expression Analysis in Polygonum minus Leaf upon 24 h of Methyl Jasmonate Elicitation
Reyhaneh Rahnamaie-Tajadod et al.
FRONTIERS IN PLANT SCIENCE (2017)
A Concise Review on Multi-Omics Data Integration for Terroir Analysis in Vitis vinifera
Pastor Jullian Fabres et al.
FRONTIERS IN PLANT SCIENCE (2017)
System-Level and Granger Network Analysis of Integrated Proteomic and Metabolomic Dynamics Identifies Key Points of Grape Berry Development at the Interface of Primary and Secondary Metabolism
Lei Wang et al.
FRONTIERS IN PLANT SCIENCE (2017)
Multi-Omics and Integrated Network Analyses Reveal New Insights into the Systems Relationships between Metabolites, Structural Genes, and Transcriptional Regulators in Developing Grape Berries (Vitis vinifera L.) Exposed to Water Deficit
Stefania Savoi et al.
FRONTIERS IN PLANT SCIENCE (2017)
Combination of iTRAQ proteomics and RNA-seq transcriptomics reveals multiple levels of regulation in phytoplasma-infected Ziziphus jujuba Mill
Xia Ye et al.
HORTICULTURE RESEARCH (2017)
Transcriptomic and metabolomic data integration
Rachel Cavill et al.
BRIEFINGS IN BIOINFORMATICS (2016)
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
Ron Caspi et al.
NUCLEIC ACIDS RESEARCH (2016)
Integration of multi-omics data for prediction of phenotypic traits using random forest
Animesh Acharjee et al.
BMC BIOINFORMATICS (2016)
Transcriptome and metabolite profiling reveals that prolonged drought modulates the phenylpropanoid and terpenoid pathway in white grapes (Vitis vinifera L.)
Stefania Savoi et al.
BMC PLANT BIOLOGY (2016)
Quantifying plant phenotypes with isotopic labeling & metabolic flux analysis
Doug K. Allen
CURRENT OPINION IN BIOTECHNOLOGY (2016)
More effort - more results: recent advances in integrative 'omics' data analysis
Dhivyaa Rajasundaram et al.
CURRENT OPINION IN PLANT BIOLOGY (2016)
Approaches to Sample Size Determination for Multivariate Data: Applications to PCA and PLS-DA of Omics Data
Edoardo Saccenti et al.
JOURNAL OF PROTEOME RESEARCH (2016)
System level analysis of cacao seed ripening reveals a sequential interplay of primary and secondary metabolism leading to polyphenol accumulation and preparation of stress resistance
Lei Wang et al.
PLANT JOURNAL (2016)
Multiscale Metabolic Modeling of C4 Plants: Connecting Nonlinear Genome-Scale Models to Leaf-Scale Metabolism in Developing Maize Leaves
Eli Bogart et al.
PLOS ONE (2016)
Integration of omic networks in a developmental atlas of maize
Justin W. Walley et al.
SCIENCE (2016)
Quantitative phosphoproteomics reveals the role of the AMPK plant ortholog SnRK1 as a metabolic master regulator under energy deprivation
Ella Nukarinen et al.
SCIENTIFIC REPORTS (2016)
Metabolic Reconstruction of Setaria italica: A Systems Biology Approach for Integrating Tissue-Specific Omics and Pathway Analysis of Bioenergy Grasses
Cristiana G. de Oliveira Dal'Molin et al.
Frontiers in Plant Science (2016)
An integrated multi-omics analysis of the NK603 Roundup-tolerant GM maize reveals metabolism disturbances caused by the transformation process
Robin Mesnage et al.
SCIENTIFIC REPORTS (2016)
A systems biology approach toward understanding seed composition in soybean
Ling Li et al.
BMC GENOMICS (2015)
Systems Biology Tools for Integrated Omics Analysis
Mark Hughes
Genetic Engineering & Biotechnology News (2015)
Multi -omics and metabolic modelling pipelines: Challenges and tools for systems microbiology
Marco Fondi et al.
MICROBIOLOGICAL RESEARCH (2015)
PathVisio 3: An Extendable Pathway Analysis Toolbox
Martina Kutmon et al.
PLOS COMPUTATIONAL BIOLOGY (2015)
The quest for tolerant varieties: the importance of integrating omics techniques to phenotyping
Michel Zivy et al.
FRONTIERS IN PLANT SCIENCE (2015)
Genomic, Proteomic, and Metabolomic Data Integration Strategies
Wanjeera Wanichthanarak et al.
BIOMARKER INSIGHTS (2015)
A multivariate approach to the integration of multi-omics datasets
Chen Meng et al.
BMC BIOINFORMATICS (2014)
Poly-Omic Prediction of Complex Traits: OmicKriging
Heather E. Wheeler et al.
GENETIC EPIDEMIOLOGY (2014)
Integrated enrichment analysis and pathway-centered visualization of metabolomics, proteomics, transcriptomics, and genomics data by using the InCroMAP software
Johannes Eichner et al.
JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES (2014)
Omics technologies and their applications to evaluate metal toxicity in mice M. spretus as a bioindicator
Miguel Angel Garcia-Sevillano et al.
JOURNAL OF PROTEOMICS (2014)
Machine learning for Big Data analytics in plants
Chuang Ma et al.
TRENDS IN PLANT SCIENCE (2014)
Integration of a constraint-based metabolic model of Brassica napus developing seeds with 13C-metabolic flux analysis
Jordan O. Hay et al.
FRONTIERS IN PLANT SCIENCE (2014)
Integrated network analysis and effective tools in plant systems biology
Atsushi Fukushima et al.
FRONTIERS IN PLANT SCIENCE (2014)
GIM3E: condition-specific models of cellular metabolism developed from metabolomics and expression data
Brian J. Schmidt et al.
BIOINFORMATICS (2013)
Plant genome-scale metabolic reconstruction and modelling
Cristiana Gomes de Oliveira Dal'Molin et al.
CURRENT OPINION IN BIOTECHNOLOGY (2013)
COVAIN: a toolbox for uni- and multivariate statistics, time-series and correlation network analysis and inverse estimation of the differential Jacobian from metabolomics covariance data
Xiaoliang Sun et al.
METABOLOMICS (2012)
Paintomics: a web based tool for the joint visualization of transcriptomics and metabolomics data
Fernando Garcia-Alcalde et al.
BIOINFORMATICS (2011)
Integrated pathway-level analysis of transcriptomics and metabolomics data with IMPaLA
Atanas Kamburov et al.
BIOINFORMATICS (2011)
Green systems biology - From single genomes, proteomes and metabolomes to ecosystems research and biotechnology
Wolfram Weckwerth
JOURNAL OF PROTEOMICS (2011)
KaPPA-View4: a metabolic pathway database for representation and analysis of correlation networks of gene co-expression and metabolite co-accumulation and omics data
Nozomu Sakurai et al.
NUCLEIC ACIDS RESEARCH (2011)
OmicsAnalyzer: a Cytoscape plug-in suite for modeling omics data
Tian Xia et al.
BIOINFORMATICS (2010)
What is flux balance analysis?
Jeffrey D. Orth et al.
NATURE BIOTECHNOLOGY (2010)
The challenges of integrating multi-omic data sets
Bernhard Palsson et al.
NATURE CHEMICAL BIOLOGY (2010)
A protocol for generating a high-quality genome-scale metabolic reconstruction
Ines Thiele et al.
NATURE PROTOCOLS (2010)
C4GEM, a Genome-Scale Metabolic Model to Study C4 Plant Metabolism
Cristiana Gomes de Oliveira Dal'Molin et al.
PLANT PHYSIOLOGY (2010)
Integrated omics approaches in plant systems biology
Atsushi Fukushima et al.
CURRENT OPINION IN CHEMICAL BIOLOGY (2009)
Co-expression tools for plant biology: opportunities for hypothesis generation and caveats
Bjoern Usadel et al.
PLANT CELL AND ENVIRONMENT (2009)
Protein-protein interactions more conserved within species than across species
Sven Mika et al.
PLOS COMPUTATIONAL BIOLOGY (2006)