Toward a systems-level understanding of gene regulatory, protein interaction, and metabolic networks in cyanobacteria

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Toward a systems-level understanding of gene regulatory, protein interaction, and metabolic networks in cyanobacteria is …
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scholarly articleQ13442814

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P356DOI10.3389/FGENE.2014.00191
P3181OpenCitations bibliographic resource ID1897491
P932PMC publication ID4079066
P698PubMed publication ID25071821
P5875ResearchGate publication ID264393790

P50authorMatthias FutschikQ37376165
Miguel A Hernández-PrietoQ42323450
P2093author name stringTrudi A Semeniuk
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Differential transcriptional analysis of the cyanobacterium Cyanothece sp. strain ATCC 51142 during light-dark and continuous-light growthQ36672928
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Coastal strains of marine Synechococcus species exhibit increased tolerance to copper shock and a distinctive transcriptional response relative to those of open-ocean strainsQ37301767
Caveat emptor: limitations of the automated reconstruction of metabolic pathways in PlasmodiumQ37318419
Proteomic responses of oceanic Synechococcus WH8102 to phosphate and zinc scarcity and cadmium additionsQ37397517
Current trends in high throughput proteomics in cyanobacteriaQ37432778
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Light history influences the response of the marine cyanobacterium Synechococcus sp. WH7803 to oxidative stress.Q38334368
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An assessment of recently published gene expression data analyses: reporting experimental design and statistical factorsQ30477677
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Global transcriptomic analysis of Cyanothece 51142 reveals robust diurnal oscillation of central metabolic processesQ30481752
Unraveling the genomic mosaic of a ubiquitous genus of marine cyanobacteria.Q30482490
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Impacts of atmospheric anthropogenic nitrogen on the open oceanQ34779284
Flux balance analysis of cyanobacterial metabolism: the metabolic network of Synechocystis sp. PCC 6803.Q34811786
The genome of Cyanothece 51142, a unicellular diazotrophic cyanobacterium important in the marine nitrogen cycleQ34835279
Genomic taxonomy of the genus prochlorococcus.Q34959599
Metatranscriptomics reveals unique microbial small RNAs in the ocean's water columnQ34981167
Review of biological network data and its applicationsQ35086178
A novel clade of Prochlorococcus found in high nutrient low chlorophyll waters in the South and Equatorial Pacific Ocean.Q35092536
A high resolution map of a cyanobacterial transcriptome.Q35561165
Cyanobacterial postgenomic research and systems biologyQ35565922
Predictive ability of DNA microarrays for cancer outcomes and correlates: an empirical assessmentQ35577543
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Detailing the optimality of photosynthesis in cyanobacteria through systems biology analysisQ35786863
Comparative quantitative proteomics of prochlorococcus ecotypes to a decrease in environmental phosphate concentrations.Q35951038
Low genomic diversity in tropical oceanic N2-fixing cyanobacteriaQ36140821
Application of synthetic biology in cyanobacteria and algaeQ36246966
Metagenomics and industrial applicationsQ33216319
Temporal patterns of nitrogenase gene (nifH) expression in the oligotrophic North Pacific OceanQ33223028
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Localization of the small CAB-like proteins in photosystem II.Q33263611
SynechoNET: integrated protein-protein interaction database of a model cyanobacterium Synechocystis sp. PCC 6803Q33322209
Applications of cyanobacteria in biotechnologyQ33405407
Choreography of the transcriptome, photophysiology, and cell cycle of a minimal photoautotroph, prochlorococcusQ33427883
Distinct, ecotype-specific genome and proteome signatures in the marine cyanobacteria ProchlorococcusQ33530539
CyanoBase: the cyanobacteria genome database update 2010.Q33600527
Ultraviolet stress delays chromosome replication in light/dark synchronized cells of the marine cyanobacterium Prochlorococcus marinus PCC9511.Q33644902
Integrative analysis of large scale expression profiles reveals core transcriptional response and coordination between multiple cellular processes in a cyanobacteriumQ33647384
Characterization ofProchlorococcusclades from iron-depleted oceanic regionsQ33669961
Comparative proteomic profiles of the marine cyanobacterium Trichodesmium erythraeum IMS101 under different nitrogen regimes.Q33804098
Diurnal rhythms result in significant changes in the cellular protein complement in the cyanobacterium Cyanothece 51142.Q33834112
Strengthening insights into host responses to mastitis infection in ruminants by combining heterogeneous microarray data sources.Q33898550
Directional RNA deep sequencing sheds new light on the transcriptional response of Anabaena sp. strain PCC 7120 to combined-nitrogen deprivation.Q33944890
The tricarboxylic acid cycle in cyanobacteria.Q34029850
Dynamic proteomic profiling of a unicellular cyanobacterium Cyanothece ATCC51142 across light-dark diurnal cyclesQ34088548
Complete genomic sequence of the filamentous nitrogen-fixing cyanobacterium Anabaena sp. strain PCC 7120.Q34106809
Cytoscape Web: an interactive web-based network browserQ34110503
LIL3, a light-harvesting-like protein, plays an essential role in chlorophyll and tocopherol biosynthesisQ34151722
MINT, the molecular interaction database: 2012 updateQ34233947
iAK692: a genome-scale metabolic model of Spirulina platensis C1.Q34306483
Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencingQ34320216
BioLingua: a programmable knowledge environment for biologistsQ34340789
Unicellular, aerobic nitrogen-fixing cyanobacteria of the genus CyanotheceQ34361240
RNA-Seq analysis and targeted mutagenesis for improved free fatty acid production in an engineered cyanobacteriumQ34362128
CINPER: an interactive web system for pathway prediction for prokaryotesQ34510805
How deep is deep enough for RNA-Seq profiling of bacterial transcriptomes?Q34523883
New cyclic peptides with cytotoxic activity from the ascidian Lissoclinum patella.Q34528910
An experimentally anchored map of transcriptional start sites in the model cyanobacterium Synechocystis sp. PCC6803.Q34549972
Reconstruction of phyletic trees by global alignment of multiple metabolic networksQ34569325
Ecogenomic perspectives on domains of unknown function: correlation-based exploration of marine metagenomesQ34629267
Autotrophic picoplankton in the tropical oceanQ39177075
Ecology of uncultured Prochlorococcus clades revealed through single-cell genomics and biogeographic analysisQ39208679
Physiology and molecular phylogeny of coexisting Prochlorococcus ecotypesQ39265944
A model of cyclic transcriptomic behavior in the cyanobacterium Cyanothece sp. ATCC 51142.Q39519702
Globally distributed uncultivated oceanic N2-fixing cyanobacteria lack oxygenic photosystem II.Q39623745
Differential gene expression in response to hydrogen peroxide and the putative PerR regulon of Synechocystis sp. strain PCC 6803.Q40883478
A marine natural product, patellamide D, reverses multidrug resistance in a human leukemic cell lineQ41540847
Abundances and distributions of the dominant nifH phylotypes in the Northern Atlantic OceanQ41826233
Circadian gating of the cell cycle revealed in single cyanobacterial cellsQ41849818
Recent applications of metabolomics toward cyanobacteriaQ41889805
Comparative transcriptomics of two environmentally relevant cyanobacteria reveals unexpected transcriptome diversityQ41955064
CyanoEXpress: A web database for exploration and visualisation of the integrated transcriptome of cyanobacterium Synechocystis sp. PCC6803.Q41966104
OpenFLUX: efficient modelling software for 13C-based metabolic flux analysisQ41973085
Iron deprivation in Synechocystis: inference of pathways, non-coding RNAs, and regulatory elements from comprehensive expression profilingQ42395262
Coastal Synechococcus metagenome reveals major roles for horizontal gene transfer and plasmids in population diversityQ42611416
Detection of an L-amino acid dehydrogenase activity in Synechocystis sp. PCC 6803.Q43167303
Cold-regulated genes under control of the cold sensor Hik33 in Synechocystis.Q43572135
Consensus and Meta-analysis regulatory networks for combining multiple microarray gene expression datasetsQ43920791
Comparative analysis of 126 cyanobacterial genomes reveals evidence of functional diversity among homologs of the redox-regulated CP12 proteinQ43996200
Automated genome annotation and metabolic model reconstruction in the SEED and Model SEED.Q44669931
Subunit composition of NDH-1 complexes of Synechocystis sp. PCC 6803: identification of two new ndh gene products with nuclear-encoded homologues in the chloroplast Ndh complexQ44854754
Genomic island variability facilitates Prochlorococcus-virus coexistenceQ45365312
The mechanism of iron homeostasis in the unicellular cyanobacterium synechocystis sp. PCC 6803 and its relationship to oxidative stressQ45733366
Flux coupling and transcriptional regulation within the metabolic network of the photosynthetic bacterium Synechocystis sp. PCC6803.Q46085522
Occurrence of phosphate acquisition genes in Prochlorococcus cells from different ocean regionsQ46109476
Metabolic flux analysis of Cyanothece sp. ATCC 51142 under mixotrophic conditionsQ46134614
The metabolic network of Synechocystis sp. PCC 6803: systemic properties of autotrophic growthQ46403337
Flux balance analysis of photoautotrophic metabolismQ46830137
SHARP: genome-scale identification of gene-protein-reaction associations in cyanobacteriaQ47705537
InteroPORC: automated inference of highly conserved protein interaction networksQ48341318
Closely related Prochlorococcus genotypes show remarkably different depth distributions in two oceanic regions as revealed by in situ hybridization using 16S rRNA-targeted oligonucleotidesQ48356241
Gene inactivation in the cyanobacterium Synechococcus sp. PCC 7002 and the green sulfur bacterium Chlorobium tepidum using in vitro-made DNA constructs and natural transformation.Q50802570
Niche partitioning among Prochlorococcus ecotypes along ocean-scale environmental gradients.Q51242132
Transcriptomic responses of Synechocystis sp. PCC 6803 encapsulated in silica gel.Q51554883
Ocean Science: The power of plankton.Q51569869
Network inference, analysis, and modeling in systems biology.Q53556135
DNA microarray analysis of cyanobacterial gene expression during acclimation to high light.Q53894778
Synthetic biology in cyanobacteria engineering and analyzing novel functions.Q54360949
A novel free-living prochlorophyte abundant in the oceanic euphotic zoneQ55966586
Estimates of global cyanobacterial biomass and its distributionQ56083040
Microarray analysis of phosphate regulation in the marine cyanobacterium Synechococcus sp. WH8102Q57007246
Integration of carbon and nitrogen metabolism with energy production is crucial to light acclimation in the cyanobacterium SynechocystisQ58293459
Physiology and molecular phylogeny of coexisting Prochlorococcus ecotypesQ59069640
Repression by Fur is not the main mechanism controlling the iron-inducible isiAB operon in the cyanobacterium Synechocystis sp. PCC 6803Q79236690
A strategy for meta-analysis of short time series microarray datasetsQ83453140
P4510describes a project that usesCytoscapeQ3699942
P407language of work or nameEnglishQ1860
P921main subjectCyanobacteriaQ93315
metabolic networkQ2263094
P304page(s)191
P577publication date2014-07-02
P1433published inFrontiers in GeneticsQ2499875
P1476titleToward a systems-level understanding of gene regulatory, protein interaction, and metabolic networks in cyanobacteria
P478volume5

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