Reference health

Maize GO Annotation - Methods, Evaluation, and Review (maize-GAMER)

https://doi.org/10.1101/222836
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1 of 27 checkable references need attention · checked 2026-07-22

At the dated check, the references listed below either did not resolve in Crossref or DataCite, or carried a retraction notice. Each one is shown with the registry record that put it there.

4 without a DOI — not checked. A reference deposited without a DOI is never matched by title or guessed at; it stays outside the checked set, and this line discloses that.

References needing attention

does not resolve to a known work10.1006/jmbi.1990.9999
The 26 checked references that resolve
resolves10.1186/1471-2105-8-284
Exploring inconsistencies in genome-wide protein function annotations: a machine learning approach
resolves10.1093/nar/gkv1007
MaizeGDB update: new tools, data and interface for the maize model organism database
resolves10.1002/dvg.22877
The arabidopsis information resource: Making and mining the “gold standard” annotated reference plant genome
resolves10.1093/bioinformatics/btp536
QuickGO: a web-based tool for Gene Ontology searching
resolves10.1002/prot.23029
Analysis of protein function and its prediction from amino acid sequence
resolves10.1093/bioinformatics/btt228
Information-theoretic evaluation of predicted ontological annotations
resolves10.1155/2008/619832
Blast2GO: A Comprehensive Suite for Functional Analysis in Plant Genomics
resolves10.1186/1471-2105-12-431
AIGO: Towards a unified framework for the Analysis and the Inter-comparison of GO functional annotations
resolves10.1093/nar/gkr367
HMMER web server: interactive sequence similarity searching
resolves10.1093/nar/gkw1107
InterPro in 2017—beyond protein family and domain annotations
resolves10.1093/nar/gkr944
Phytozome: a comparative platform for green plant genomics
resolves10.1093/nar/gkh036
The Gene Ontology (GO) database and informatics resource
resolves10.1073/pnas.1108359108
Brassinosteroid control of sex determination in maize
resolves10.1093/database/baw053
Ensembl comparative genomics resources
resolves10.1105/tpc.16.00353
Draft Assembly of Elite Inbred Line PH207 Provides Insights into Genomic and Transcriptome Diversity in Maize
resolves10.1093/nar/gkn785
InterPro: the integrative protein signature database
resolves10.1186/s13059-016-1037-6
An expanded evaluation of protein function prediction methods shows an improvement in accuracy
resolves10.1038/nature22971
Improved maize reference genome with single-molecule technologies
resolves10.1093/bioinformatics/btu031
InterProScan 5: genome-scale protein function classification
resolves10.1093/bioinformatics/btu851
PANNZER: high-throughput functional annotation of uncharacterized proteins in an error-prone environment
resolves10.1093/nar/gkh011
MaizeGDB, the community database for maize genetics and genomics
resolves10.1093/bioinformatics/btm585
Choosing BLAST options for better detection of orthologs as reciprocal best hits
resolves10.1038/nmeth.2340
A large-scale evaluation of computational protein function prediction
resolves10.1126/science.1178534
The B73 Maize Genome: Complexity, Diversity, and Dynamics
resolves10.1093/nar/gkv1179
Gramene 2016: comparative plant genomics and pathway resources
resolves10.1093/nar/gku989
UniProt: a hub for protein information
The 4 references without a DOI — listed, not checked
no DOI — not checkedArgot2: a large scale function prediction tool relying on semantic similarity of weighted Gene Ontology terms
no DOI — not checkedMaizeGDB: The maize model organism database for basic, translational, and applied research
no DOI — not checkedMaize Metabolic Network Construction and Transcriptome Analysis
no DOI — not checkedSen, T.Z. , Andorf, C.M. , Schaeffer, M.L. , Harper, L.C. , Sparks, M.E. , Duvick, J. , Brendel, V.P. , Cannon, E. , Campbell, D.A. , and Lawrence, C.J. (2009). MaizeGDB becomes “sequence-centric”. Database (Oxford)2009, bap020.
What this badge says. CiteStamped means the CHECKABLE references of this work were clean at the dated check: each resolved to a known work in a public registry, and none carried a retraction notice at that time. It says nothing about the quality, findings, or importance of the work itself, and nothing about references deposited without a DOI.

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