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The genome portal of the Department of Energy Joint Genome Institute: 2014 updates

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1038/nature08656openalex-snapshot
A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea
inferredcites →https://doi.org/10.1093/nar/gkh073openalex-snapshot
Database resources of the National Center for Biotechnology Information: update
inferredcites →https://doi.org/10.1093/nar/gkr1044openalex-snapshot
IMG: the integrated microbial genomes database and comparative analysis system
inferredcites →https://doi.org/10.1093/nar/gkr944openalex-snapshot
Phytozome: a comparative platform for green plant genomics
inferredcites →https://doi.org/10.1093/nar/gkr947openalex-snapshot
The Genome Portal of the Department of Energy Joint Genome Institute
inferredcites →https://doi.org/10.1093/nar/gkr975openalex-snapshot
IMG/M: the integrated metagenome data management and comparative analysis system
inferredcites →https://doi.org/10.1093/nar/gks1189openalex-snapshot
Database resources of the National Center for Biotechnology Information
inferredcites →https://doi.org/10.1109/sc.2005.72openalex-snapshot
The Globus Striped GridFTP Framework and Server

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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inferred← citeshttps://doi.org/10.1016/j.fgb.2020.103416openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.fgb.2020.103456openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.fgb.2022.103689openalex-snapshot
Marker-free CRISPR-Cas9 based genetic engineering of the phytopathogenic fungus, Penicillium expansum
inferred← citeshttps://doi.org/10.1016/j.fgb.2022.103712openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.funbio.2024.07.005openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.funbio.2025.101713openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.funeco.2020.101002openalex-snapshot
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OGRP: A comprehensive bioinformatics platform for the efficient empowerment of Oleaceae genomics research
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inferred← citeshttps://doi.org/10.1016/j.jbiotec.2017.12.004openalex-snapshot
Complete genome sequence of the highly Mn(II) tolerant Staphylococcus sp. AntiMn-1 isolated from deep-sea sediment in the Clarion-Clipperton Zone
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Impact assessment of ephemeral discharge of contamination downstream of two legacy base metal mines using environmental DNA
inferred← citeshttps://doi.org/10.1016/j.jmb.2014.12.024openalex-snapshot
Structure and Evolution of N-domains in AAA Metalloproteases
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Label-free quantitative proteomic analysis of pre-flowering PMeV-infected Carica papaya L.
inferred← citeshttps://doi.org/10.1016/j.jsb.2016.02.021openalex-snapshot
Molecular cloning and functional analysis of chitinases in the fresh water snail, Lymnaea stagnalis
inferred← citeshttps://doi.org/10.1016/j.margen.2015.06.010openalex-snapshot
The upstream regulatory sequence of the light harvesting complex Lhcf2 gene of the marine diatom Phaeodactylum tricornutum enhances transcription in an orientation- and distance-independent fashion
inferred← citeshttps://doi.org/10.1016/j.margen.2015.07.002openalex-snapshot
Actin, actin-related proteins and profilin in diatoms: A comparative genomic analysis
inferred← citeshttps://doi.org/10.1016/j.margen.2017.10.001openalex-snapshot
Novel subfamilies of actin-regulating proteins
inferred← citeshttps://doi.org/10.1016/j.mec.2023.e00221openalex-snapshot
Engineered production of isoprene from the model green microalga Chlamydomonas reinhardtii
inferred← citeshttps://doi.org/10.1016/j.micres.2023.127507openalex-snapshot
Degradation of polypropylene by fungi Coniochaeta hoffmannii and Pleurostoma richardsiae
inferred← citeshttps://doi.org/10.1016/j.micres.2023.127592openalex-snapshot
Response of Bacillus velezensis 83 to interaction with Colletotrichum gloeosporioides resembles a Greek phalanx-style formation: A stress resistant phenotype with antibiosis capacity
inferred← citeshttps://doi.org/10.1016/j.molp.2018.05.003openalex-snapshot
Genome Analysis of the Ancient Tracheophyte Selaginella tamariscina Reveals Evolutionary Features Relevant to the Acquisition of Desiccation Tolerance
inferred← citeshttps://doi.org/10.1016/j.molp.2024.07.006openalex-snapshot
Hordedane diterpenoid phytoalexins restrict Fusarium graminearum infection but enhance Bipolaris sorokiniana colonization of barley roots
inferred← citeshttps://doi.org/10.1016/j.molp.2026.05.014openalex-snapshot
Exploring the oasis of plant genomes: From genetic variations to function and beyond
inferred← citeshttps://doi.org/10.1016/j.myc.2018.10.002openalex-snapshot
Monitoring of in planta gene expression for xylan degradation and assimilation in the maize pathogen Bipolaris maydis
inferred← citeshttps://doi.org/10.1016/j.nbt.2015.08.004openalex-snapshot
Expression of the mammalian peptide hormone obestatin in Trichoderma reesei
inferred← citeshttps://doi.org/10.1016/j.parco.2017.09.002openalex-snapshot
Reprint of “A parallel connectivity algorithm for de Bruijn graphs in metagenomic applications”
inferred← citeshttps://doi.org/10.1016/j.pestbp.2026.107209openalex-snapshot
Transcriptomics analysis elucidates the growth inhibitory mechanisms of volatile fungistatic compound 3-ethylbenzaldehyde to Pseudocryphonectria elaeocarpicola
inferred← citeshttps://doi.org/10.1016/j.plantsci.2017.10.014openalex-snapshot
Raising orphans from a metadata morass: A researcher's guide to re-use of public ’omics data
inferred← citeshttps://doi.org/10.1016/j.plantsci.2024.112371openalex-snapshot
Genome-wide identification and analysis of autophagy-related (ATG) genes in Lycium ruthenicum Murray reveals their crucial roles in salt stress tolerance
inferred← citeshttps://doi.org/10.1016/j.plgene.2020.100262openalex-snapshot
Identification, evolutionary and expression analysis of the galactinol synthase (GolS) genes in Panicum virgatum L. and Panicum hallii : An in silico approach
inferred← citeshttps://doi.org/10.1016/j.pmpp.2021.101676openalex-snapshot
Expression analysis of the NEP-1 and cell-wall degrading genes of Gilbertella persicaria during pathogenesis in papaya (Carica papaya L.) fruits
inferred← citeshttps://doi.org/10.1016/j.pmpp.2021.101758openalex-snapshot
A rapid fungal DNA extraction method suitable for PCR screening fungal mutants, infected plant tissue and spore trap samples
inferred← citeshttps://doi.org/10.1016/j.pmpp.2023.102101openalex-snapshot
Avirulence (Avr) genes in fungal pathogen Venturia inaequalis, a causal agent of scab disease on apple trees
inferred← citeshttps://doi.org/10.1016/j.protis.2023.125994openalex-snapshot
A three-genome ultraconserved element phylogeny of Cryptophytes
inferred← citeshttps://doi.org/10.1016/j.resmic.2015.02.004openalex-snapshot
Osmotic swelling activates a novel anionic current with VRAC-like properties in a cytoplasmic droplet membrane from Phycomyces blakesleeanus sporangiophores
inferred← citeshttps://doi.org/10.1016/j.sajb.2023.01.019openalex-snapshot
The genome of Lignosus tigris: Uncovering its hidden nutraceutical potential
inferred← citeshttps://doi.org/10.1016/j.sbi.2025.102985openalex-snapshot
Advancing protein structure prediction beyond AlphaFold2
inferred← citeshttps://doi.org/10.1016/j.scitotenv.2017.02.184openalex-snapshot
Towards a competitive solid state fermentation: Cellulases production from coffee husk by sequential batch operation and role of microbial diversity
inferred← citeshttps://doi.org/10.1016/j.scitotenv.2020.138431openalex-snapshot
A comprehensive framework for the production of mycelium-based lignocellulosic composites
inferred← citeshttps://doi.org/10.1016/j.simyco.2018.10.005openalex-snapshot
Inside Plectosphaerellaceae
inferred← citeshttps://doi.org/10.1016/j.sjbs.2019.06.004openalex-snapshot
Analysis of genomic tRNA revealed presence of novel genomic features in cyanobacterial tRNA
inferred← citeshttps://doi.org/10.1016/j.soilbio.2026.110208openalex-snapshot
Rapid changes in transcription during a feast-famine event
inferred← citeshttps://doi.org/10.1016/j.str.2025.03.002openalex-snapshot
A mesophilic Argonaute from Clostridium formicaceticum with efficient DNA cleavage activity guided by small DNA
inferred← citeshttps://doi.org/10.1016/j.str.2026.06.002openalex-snapshot
Identification and structure determination of a type III-Bv CRISPR complex that post-translationally modifies an associated toxin
inferred← citeshttps://doi.org/10.1016/j.syapm.2016.09.004openalex-snapshot
Phylogenomic re-assessment of the thermophilic genus Geobacillus
inferred← citeshttps://doi.org/10.1016/j.tibtech.2018.09.003openalex-snapshot
Strategies for Engineering Natural Product Biosynthesis in Fungi
inferred← citeshttps://doi.org/10.1016/j.tim.2017.12.008openalex-snapshot
Evolutionary Transition of GAL Regulatory Circuit from Generalist to Specialist Function in Ascomycetes
inferred← citeshttps://doi.org/10.1016/j.tim.2024.11.001openalex-snapshot
Current advancements in fungal engineering technologies for Sustainable Development Goals
inferred← citeshttps://doi.org/10.1016/j.wasman.2017.10.048openalex-snapshot
A comparison between biostimulation and bioaugmentation in a solid treatment of anaerobic sludge: Drug content and microbial evaluation
inferred← citeshttps://doi.org/10.1016/j.ygcen.2014.12.001openalex-snapshot
Influence of temperature on thyroid hormone signaling and endocrine disruptor action in Rana (Lithobates) catesbeiana tadpoles
inferred← citeshttps://doi.org/10.1016/j.ygcen.2017.12.006openalex-snapshot
Changes in steroid profiles of the blue mussel Mytilus trossulus as a function of season, stage of gametogenesis, sex, tissue and mussel bed depth
inferred← citeshttps://doi.org/10.1016/j.ygeno.2019.03.012openalex-snapshot
Genome Annotator Light (GAL): A Docker-based package for genome analysis and visualization
inferred← citeshttps://doi.org/10.1016/j.ygeno.2021.05.020openalex-snapshot
Genome assembly of Scorias spongiosa and comparative genomics provide insights into ecological adaptation of honeydew-dependent sooty mould fungi
inferred← citeshttps://doi.org/10.1016/j.ympev.2015.08.019openalex-snapshot
Phylogenomic analysis reveals ancient segmental duplications in the human genome
inferred← citeshttps://doi.org/10.1016/j.ympev.2016.03.031openalex-snapshot
The evolutionary origin of CIPK16: A gene involved in enhanced salt tolerance
inferred← citeshttps://doi.org/10.1016/j.ympev.2017.02.015openalex-snapshot
An insight into the evolutionary history of human MHC paralogon
inferred← citeshttps://doi.org/10.1016/j.ympev.2021.107068openalex-snapshot
Phylogenomics of Gesneriaceae using targeted capture of nuclear genes
inferred← citeshttps://doi.org/10.1017/9781108776387.013openalex-snapshot
Development and Morphogenesis
inferred← citeshttps://doi.org/10.1021/acs.est.2c09010openalex-snapshot
Identifying Eukaryotes and Factors Influencing Their Biogeography in Drinking Water Metagenomes
inferred← citeshttps://doi.org/10.1021/acs.jafc.3c03240openalex-snapshot
Assessing the Biosynthetic Inventory of the Biocontrol Fungus Trichoderma afroharzianum T22
inferred← citeshttps://doi.org/10.1021/acs.jcim.6b00087openalex-snapshot
Discovery and Characterization of the Highly Active Fungal Immunomodulatory Protein Fip-vvo82
inferred← citeshttps://doi.org/10.1021/acs.jnatprod.3c00148openalex-snapshot
Metabolomics-Guided Discovery, Isolation, Structure Elucidation, and Bioactivity of Myropeptins C–E from Myrothecium inundatum
inferred← citeshttps://doi.org/10.1021/acs.jnatprod.6c00702openalex-snapshot
Genome Mining of the Biocontrol Fungus Trichoderma afroharzianum T22 Led to the Discovery of Dehydrobutyrine-Containing Lipopeptides
inferred← citeshttps://doi.org/10.1021/acs.jproteome.6b00636openalex-snapshot
Analysis of the Biotechnological Potential of a Lentinus crinitus Isolate in the Light of Its Secretome
inferred← citeshttps://doi.org/10.1021/acs.orglett.1c03792openalex-snapshot
Biosynthesis of Calipyridone A Represents a Fungal 2-Pyridone Formation without Ring Expansion in Aspergillus californicus
inferred← citeshttps://doi.org/10.1021/acs.orglett.3c01924openalex-snapshot
Biochemical and Genetic Basis of Guanacastane Diterpene Biosynthesis in Basidiomycete Fungi
inferred← citeshttps://doi.org/10.1021/acschembio.4c00678openalex-snapshot
Strategic Acyl Carrier Protein Engineering Enables Functional Type II Polyketide Synthase Reconstitution In Vitro
inferred← citeshttps://doi.org/10.1021/acsinfecdis.3c00475openalex-snapshot
A Family of Antibiotics That Evades Resistance by Binding Polyprenyl Phosphates
inferred← citeshttps://doi.org/10.1021/acsomega.0c06078openalex-snapshot
Computational Screening of Potential Inhibitors of Desulfobacter postgatei for Pyrite Scale Prevention in Oil and Gas Wells
inferred← citeshttps://doi.org/10.1021/acsomega.6c02253openalex-snapshot
Novel Cell-Type-Specific Drought-Responsive Proteins in Root Tips of Field-Grown Perennial Switchgrass
inferred← citeshttps://doi.org/10.1021/acssuschemeng.5c03763openalex-snapshot
Thermostable Enzyme Variants in the Lower Mevalonate Pathway Improve Isoprenoid Production by Cell-Free Biocatalysis
inferred← citeshttps://doi.org/10.1021/acssynbio.2c00116openalex-snapshot
High-Titer Production of the Fungal Anhydrotetracycline, TAN-1612, in Engineered Yeasts
inferred← citeshttps://doi.org/10.1021/jacs.1c03988openalex-snapshot
Harzianic Acid from Trichoderma afroharzianum Is a Natural Product Inhibitor of Acetohydroxyacid Synthase
inferred← citeshttps://doi.org/10.1021/jacs.2c11170openalex-snapshot
Generation of Alternate Indole Diterpene Architectures in Two Species of Aspergilli
inferred← citeshttps://doi.org/10.1021/jacs.4c18232openalex-snapshot
Non-Canonical Type II Terpene Cyclases Deliver Rare Terpenoid Architectures
inferred← citeshttps://doi.org/10.1021/pr500385yopenalex-snapshot
Study of Phanerochaete chrysosporium Secretome Revealed Protein Glycosylation as a Substrate-Dependent Post-Translational Modification
inferred← citeshttps://doi.org/10.1029/2024jg008470openalex-snapshot
Harnessing the Power of Machine Learning and Omics to Identify Environmental Regulation on Microbial Functional Composition for Soil C, N, and P Cycling
inferred← citeshttps://doi.org/10.1038/nature23314openalex-snapshot
Cryo-EM structure of the protein-conducting ERAD channel Hrd1 in complex with Hrd3
inferred← citeshttps://doi.org/10.1038/s41396-018-0270-2openalex-snapshot
Soil exchange rates of COS and CO18O differ with the diversity of microbial communities and their carbonic anhydrase enzymes
inferred← citeshttps://doi.org/10.1038/s41396-018-0288-5openalex-snapshot
Modeling microbial communities from atrazine contaminated soils promotes the development of biostimulation solutions
inferred← citeshttps://doi.org/10.1038/s41396-020-00746-4openalex-snapshot
Presence of toxin-antitoxin systems in picocyanobacteria and their ecological implications
inferred← citeshttps://doi.org/10.1038/s41396-021-01077-8openalex-snapshot
The coral symbiont Candidatus Aquarickettsia is variably abundant in threatened Caribbean acroporids and transmitted horizontally
inferred← citeshttps://doi.org/10.1038/s41396-023-01407-yopenalex-snapshot
Metabolic influence of core ciliates within the rumen microbiome
inferred← citeshttps://doi.org/10.1038/s41396-023-01414-zopenalex-snapshot
Unexplored diversity and ecological functions of transposable phages
inferred← citeshttps://doi.org/10.1038/s41437-018-0181-zopenalex-snapshot
Single-cell expression noise and gene-body methylation in Arabidopsis thaliana
inferred← citeshttps://doi.org/10.1038/s41438-020-0268-6openalex-snapshot
The chromosome-scale assembly of the willow genome provides insight into Salicaceae genome evolution
inferred← citeshttps://doi.org/10.1038/s41467-019-12112-wopenalex-snapshot
EMS1 and BRI1 control separate biological processes via extracellular domain diversity and intracellular domain conservation
inferred← citeshttps://doi.org/10.1038/s41467-020-17615-5openalex-snapshot
Lipo-chitooligosaccharides as regulatory signals of fungal growth and development
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