Paper Citation Record · LEDGER

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers

As of 18 August 2026, this Paper Citation Record lists 80 of 80 outbound references and 2 inbound Pith citation observations for arXiv:2412.12688.

A citation records a reference. It does not transfer a finding from one paper to another.

pith.paper-citation-record.v1
2412.12688 v1

Coverage vector

measured 80 of 80 reference resolution

Typed states for the displayed outbound observations.

Source: paper_references, paper_reference_links, observed 2026-08-11T13:52:45.303600Z

measured 82 of 82 standing notices

One-hop event checks from named stored sources.

Source: scholarly_work_events, retraction_status_cache, observed 2026-08-18T06:34:40.430872+00:00

measured 2 of 2 inbound itemization

Pith citing papers itemized under the disclosed page cap.

Source: paper_references, paper_reference_links, observed 2026-08-10T22:18:57.244213Z

measured 0 of 1 external citation measurements

A source-named dated measurement, never combined with another source.

Source: pith, observed 2026-08-10T22:18:57.369397Z

Reference resolution

80 of 80 outbound references displayed

verified exact1
verified fuzzy69
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External citation measurements

No source-named external measurement is stored.

Outbound references

Observation 823cbf4e-fe28-4d2c-a03b-d72fb520911d · outbound

This paper cites Gene ontology: tool for the unification of biology.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers Gene ontology: tool for the unification of biology

Reference 1

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T13:52:47.710793Z

Source-reported events for the cited work

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Observation 8f3fe0a7-d924-4f7a-8a2b-d8ddbefe0edf · outbound

This paper cites An ontology for cell types.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers An ontology for cell types

Reference 2

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T13:52:47.690310Z

Source-reported events for the cited work

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Observation d9d502a0-1627-4b47-943c-e8d3839f69a9 · outbound

This paper cites A single-cell transcriptomic map of the human and mouse pancreas reveals inter-and intra-cell population structure.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers A single-cell transcriptomic map of the human and mouse pancreas reveals inter-and intra-cell population structure

Reference 3

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T13:52:47.663230Z

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Observation a558e0be-b15f-40c9-b8eb-e4d67c5a4840 · outbound

This paper cites Ncbi geo: archive for functional genomics data sets—update.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers Ncbi geo: archive for functional genomics data sets—update

Reference 4

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T13:52:47.636223Z

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Observation 430c25bd-ce7b-4efb-9de9-e86d9a6f50fd · outbound

This paper cites an unresolved cited work.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers Unresolved cited work

Reference 5

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Source-reported events for the cited work

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Observation 0138b8b0-109f-468f-87b0-c47edad0670e · outbound

This paper cites Predictprotein-predicting protein structure and function for 29 years.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers Predictprotein-predicting protein structure and function for 29 years

Reference 6

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T13:52:47.576122Z

Source-reported events for the cited work

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Observation 3a43f925-fcec-488a-8d73-d204dd9d6a7a · outbound

This paper cites Enrichr: interactive and collaborative html5 gene list enrichment analysis tool.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers Enrichr: interactive and collaborative html5 gene list enrichment analysis tool

Reference 7

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T13:52:47.536797Z

Source-reported events for the cited work

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Observation 560c2df6-d3ca-4872-9025-c80df8672653 · outbound

This paper cites Transformer for one stop interpretable cell type annotation.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers Transformer for one stop interpretable cell type annotation

Reference 8

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T13:52:47.504242Z

Source-reported events for the cited work

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Observation 4b1c3e39-7402-40ba-a685-4a39d8e92ff0 · outbound

This paper cites Genept: A simple but hard-to-beat foundation model for genes and cells built from chatgpt.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers Genept: A simple but hard-to-beat foundation model for genes and cells built from chatgpt

Reference 9

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T13:52:47.439204Z

Source-reported events for the cited work

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Observation 58bc7956-c957-4229-b930-52f412f09e8e · outbound

This paper cites The gene ontology (go) database and informatics resource.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers The gene ontology (go) database and informatics resource

Reference 10

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T13:52:47.402653Z

Source-reported events for the cited work

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Observation 9e92e478-2d8b-4b30-9b1b-5255e8bb3903 · outbound

This paper cites The gene ontology resource: 20 years and still going strong.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers The gene ontology resource: 20 years and still going strong

Reference 11

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T13:52:47.368605Z

Source-reported events for the cited work

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Observation 99c0e953-7b70-4831-b39a-6804d6260730 · outbound

This paper cites Uniprot: a worldwide hub of protein knowledge.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers Uniprot: a worldwide hub of protein knowledge

Reference 12

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T13:52:47.324896Z

Source-reported events for the cited work

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Observation e75a0b02-bb08-4030-9050-05d3b631c862 · outbound

This paper cites Chebi: a database and ontology for chemical entities of biological interest.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers Chebi: a database and ontology for chemical entities of biological interest

Reference 13

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T13:52:47.278836Z

Source-reported events for the cited work

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Observation 93c5d56f-ba1a-41e1-b4e7-4381fc15cb26 · outbound

This paper cites Advancing genome editing with artificial intelligence: opportunities, challenges, and future directions.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers Advancing genome editing with artificial intelligence: opportunities, challenges, and future directions

Reference 14

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T13:52:47.252434Z

Source-reported events for the cited work

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Observation 8aa4e744-3535-48bd-9c1e-89e338b546a7 · outbound

This paper cites Gene2vec: distributed representation of genes based on co-expression.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers Gene2vec: distributed representation of genes based on co-expression

Reference 15

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T13:52:47.212953Z

Source-reported events for the cited work

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Observation b7d67551-4399-4fc3-9fb6-3a8be134d2df · outbound

This paper cites Transcriptome-wide gene-gene interaction associations elucidate pathways and functional enrichment of complex traits.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers Transcriptome-wide gene-gene interaction associations elucidate pathways and functional enrichment of complex traits

Reference 16

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T13:52:47.186233Z

Source-reported events for the cited work

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Observation d28da09f-6e88-40b2-99e3-beecc200a084 · outbound

This paper cites Controllable protein design with language models.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers Controllable protein design with language models

Reference 17

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T13:52:47.162849Z

Source-reported events for the cited work

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Observation 72910136-81fb-4fe0-bcca-b17fa8cfe10f · outbound

This paper cites Native mass spectrometry-directed drug discovery: Recent advances in investigating protein function and modulation.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers Native mass spectrometry-directed drug discovery: Recent advances in investigating protein function and modulation

Reference 18

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T13:52:47.121628Z

Source-reported events for the cited work

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Observation 47ff45af-bcd6-40fd-9fd8-95714b93db1e · outbound

This paper cites What is a gene, post-ENCODE ? history and updated definition.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers What is a gene, post-ENCODE ? history and updated definition

Reference 19

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T13:52:47.090377Z

Source-reported events for the cited work

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Observation d360ad70-dbc3-40f3-8c55-9e73a985a1b7 · outbound

This paper cites Structure-based protein function prediction using graph convolutional networks.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers Structure-based protein function prediction using graph convolutional networks

Reference 20

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T13:52:47.054112Z

Source-reported events for the cited work

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Observation 482cfdcb-1def-48d5-9299-fb5e2be34294 · outbound

This paper cites Systematic and integrative analysis of large gene lists using david bioinformatics resources.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers Systematic and integrative analysis of large gene lists using david bioinformatics resources

Reference 21

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T13:52:47.027834Z

Source-reported events for the cited work

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Observation 01948ba9-6aa6-4c45-84f0-556fe1c56e40 · outbound

This paper cites Genomic language model predicts protein co-regulation and function.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers Genomic language model predicts protein co-regulation and function

Reference 22

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T13:52:47.003557Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation e3d94b1a-819e-4ef3-b6fd-3c7601872afb · outbound

This paper cites Dnabert: pre-trained bidirectional encoder representations from transformers model for dna-language in genome.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers Dnabert: pre-trained bidirectional encoder representations from transformers model for dna-language in genome

Reference 23

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Source-reported events for the cited work

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This paper cites Molecular biology of the cell.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers Molecular biology of the cell

Reference 24

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T13:52:46.946044Z

Source-reported events for the cited work

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Observation adb55d0e-b24e-4228-aab6-db2a2bb6fce2 · outbound

This paper cites Reactome: a knowledgebase of biological pathways.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers Reactome: a knowledgebase of biological pathways

Reference 25

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T13:52:46.912873Z

Source-reported events for the cited work

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Observation 7687bb65-8fbf-4a1c-a61a-97b2fba2d550 · outbound

This paper cites Expansion of the human phenotype ontology (hpo) knowledge base and resources.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers Expansion of the human phenotype ontology (hpo) knowledge base and resources

Reference 26

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Source-reported events for the cited work

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Observation c2f21ccc-2e20-4d09-b53f-582121b90223 · outbound

This paper cites Single-cell transcriptomes identify human islet cell signatures and reveal cell-type--specific expression changes in type 2 diabetes.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers Single-cell transcriptomes identify human islet cell signatures and reveal cell-type--specific expression changes in type 2 diabetes

Reference 27

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T13:52:46.863139Z

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No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation 4419bf0a-da82-4215-92ad-f9f8a4af7c8f · outbound

This paper cites Open source strikes bread - new fluffy embeddings model, 2024.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers Open source strikes bread - new fluffy embeddings model, 2024

Reference 28

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T13:52:46.839150Z

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Observation 144fbe4d-6a17-4d19-8ead-5ff8db89c774 · outbound

This paper cites AnglE-optimized Text Embeddings.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers AnglE-optimized Text Embeddings

Reference 29

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Observation 1e1f7e46-ee11-4c57-aef0-6aa447815882 · outbound

This paper cites Molecular signatures database (msigdb) 3.0.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers Molecular signatures database (msigdb) 3.0

Reference 30

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T13:52:46.803163Z

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Observation 9ad46dee-3c0c-4801-b22f-18bee10ce209 · outbound

This paper cites Molecular cell biology.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers Molecular cell biology

Reference 31

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T13:52:46.776425Z

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Observation 0270071e-c73e-45ba-be48-cce8f7d08e68 · outbound

This paper cites Progressive computational approaches to facilitate decryption of allosteric mechanism and drug discovery.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers Progressive computational approaches to facilitate decryption of allosteric mechanism and drug discovery

Reference 32

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T13:52:46.752301Z

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Observation c5c87af1-82a1-4d30-94fa-2a469004d1f0 · outbound

This paper cites u ttner, Kridsadakorn Chaichoompu, Anna Danese, Marta Interlandi, Michaela F M \.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers u ttner, Kridsadakorn Chaichoompu, Anna Danese, Marta Interlandi, Michaela F M \

Reference 33

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T13:52:46.727470Z

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Observation 302ee5c8-4fbc-4a25-a9f1-2bc4a925bd31 · outbound

This paper cites Learning Unknown from Correlations: Graph Neural Network for Inter-novel-protein Interaction Prediction.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers Learning Unknown from Correlations: Graph Neural Network for Inter-novel-protein Interaction Prediction

Reference 34

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Observation 0909c817-4f94-4468-90ca-05203e9c7a7a · outbound

This paper cites Entrez gene: gene-centered information at ncbi.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers Entrez gene: gene-centered information at ncbi

Reference 35

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T13:52:46.697050Z

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Observation d77333ed-e840-452d-a3f2-efbfbd634d29 · outbound

This paper cites Ensembl 2023.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers Ensembl 2023

Reference 36

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T13:52:46.644667Z

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Observation d0f86ba6-152a-414c-82c6-dc473d4394dd · outbound

This paper cites Multi-modal self-supervised pre-training for large-scale genome data.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers Multi-modal self-supervised pre-training for large-scale genome data

Reference 37

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T13:52:46.616788Z

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Observation f631a542-280e-4289-8237-a4c2add8433d · outbound

This paper cites Uberon, an integrative multi-species anatomy ontology.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers Uberon, an integrative multi-species anatomy ontology

Reference 38

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T13:52:46.585548Z

Source-reported events for the cited work

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Observation bee56ea8-a39b-492e-ba8a-f9ec44b95e8e · outbound

This paper cites A single-cell transcriptome atlas of the human pancreas.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers A single-cell transcriptome atlas of the human pancreas

Reference 39

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T13:52:46.555966Z

Source-reported events for the cited work

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Observation 8d5afb77-3056-4d10-901d-ee37a69329f7 · outbound

This paper cites The protein ontology: a structured representation of protein forms and complexes.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers The protein ontology: a structured representation of protein forms and complexes

Reference 40

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T13:52:46.530341Z

Source-reported events for the cited work

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Observation b69af0ac-0e12-4270-a63c-9c54c28bfa06 · outbound

This paper cites Reference sequence (refseq) database at ncbi: current status, taxonomic expansion, and functional annotation.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers Reference sequence (refseq) database at ncbi: current status, taxonomic expansion, and functional annotation

Reference 41

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T13:52:46.506505Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation 99315550-0c51-49c0-acd3-c1893aeead66 · outbound

This paper cites Ncbi reference sequences (refseq): a curated non-redundant sequence database of genomes, transcripts and proteins.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers Ncbi reference sequences (refseq): a curated non-redundant sequence database of genomes, transcripts and proteins

Reference 42

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T13:52:46.481113Z

Source-reported events for the cited work

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Observation b6ad1e5d-8281-4968-aa1b-9cd056c11b10 · outbound

This paper cites Ai-powered therapeutic target discovery.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers Ai-powered therapeutic target discovery

Reference 43

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T13:52:46.455700Z

Source-reported events for the cited work

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Observation 88c27c87-40ce-41c6-837e-ad8cffd4de1b · outbound

This paper cites The rise of ai language pathologists: Exploring two-level prompt learning for few-shot weakly-supervised whole slide image classification.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers The rise of ai language pathologists: Exploring two-level prompt learning for few-shot weakly-supervised whole slide image classification

Reference 44

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T13:52:46.427248Z

Source-reported events for the cited work

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Observation 691ce8c5-56c0-4552-b2db-b14ee82a48f1 · outbound

This paper cites Evaluating protein transfer learning with tape.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers Evaluating protein transfer learning with tape

Reference 45

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Source-reported events for the cited work

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Observation 90b8d92c-91ce-4f74-964c-702a9154f026 · outbound

This paper cites Pathway Commons 2019 Update: integration, analysis and exploration of pathway data.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers Pathway Commons 2019 Update: integration, analysis and exploration of pathway data

Reference 46

Resolution: unresolved; no resolver link, observed 2026-08-11T13:52:44.970944Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation d62be53b-be24-4246-9081-ac4e647bf465 · outbound

This paper cites GeneMask: Fast Pretraining of Gene Sequences to Enable Few-Shot Learning.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers GeneMask: Fast Pretraining of Gene Sequences to Enable Few-Shot Learning

Reference 47

Resolution: verified exact; local_arxiv, observed 2026-08-11T13:52:45.408873Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation 481bcbb7-efae-4e29-a404-6322683525d4 · outbound

This paper cites Ncbi taxonomy: a comprehensive update on curation, resources and tools.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers Ncbi taxonomy: a comprehensive update on curation, resources and tools

Reference 48

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T13:52:46.354890Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation 1e7cba40-2550-4f30-8c7c-d8eb3e20fa91 · outbound

This paper cites Single-cell transcriptome profiling of human pancreatic islets in health and type 2 diabetes.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers Single-cell transcriptome profiling of human pancreatic islets in health and type 2 diabetes

Reference 49

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T13:52:46.318557Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation 436490a5-7854-41e4-9638-5abfa7f0d6a9 · outbound

This paper cites Ontofact: Unveiling fantastic fact-skeleton of llms via ontology-driven reinforcement learning.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers Ontofact: Unveiling fantastic fact-skeleton of llms via ontology-driven reinforcement learning

Reference 50

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T13:52:46.297273Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation f4640159-55cc-4800-8f71-c59dedf255c8 · outbound

This paper cites Predictonco: a web tool supporting decision-making in precision oncology by extending the bioinformatics predictions with advanced computing and machine learning.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers Predictonco: a web tool supporting decision-making in precision oncology by extending the bioinformatics predictions with advanced computing and machine learning

Reference 51

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T13:52:46.267542Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation 37023f78-4f2b-4c89-9141-1e9dd5a14af8 · outbound

This paper cites Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles

Reference 52

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T13:52:46.237784Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation 97ccf1dd-422c-4d5c-a74b-1d5396e6910a · outbound

This paper cites String v11: protein--protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers String v11: protein--protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets

Reference 53

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T13:52:46.211789Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation 9e325d17-613b-4352-9a7e-5d75ea68f0d5 · outbound

This paper cites Science forum: Author-sourced capture of pathway knowledge in computable form using biofactoid.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers Science forum: Author-sourced capture of pathway knowledge in computable form using biofactoid

Reference 54

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T13:52:46.185191Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation 42d8e3f1-2209-47e5-9b78-67d4bd31cdff · outbound

This paper cites Rna sequencing of single human islet cells reveals type 2 diabetes genes.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers Rna sequencing of single human islet cells reveals type 2 diabetes genes

Reference 55

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T13:52:46.154700Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation af88f9c4-90e5-4c2b-9f9c-33c062aa71f9 · outbound

This paper cites scbert as a large-scale pretrained deep language model for cell type annotation of single-cell rna-seq data.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers scbert as a large-scale pretrained deep language model for cell type annotation of single-cell rna-seq data

Reference 56

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T13:52:46.127889Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation 94c84bab-fc01-42ba-82e1-8721ddf34db1 · outbound

This paper cites Integrating convolution and self-attention improves language model of human genome for interpreting non-coding regions at base-resolution.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers Integrating convolution and self-attention improves language model of human genome for interpreting non-coding regions at base-resolution

Reference 57

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T13:52:46.094396Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation d201d191-e705-4205-a6ab-6e87339f72e6 · outbound

This paper cites OntoProtein: Protein Pretraining With Gene Ontology Embedding.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers OntoProtein: Protein Pretraining With Gene Ontology Embedding

Reference 58

Resolution: unresolved; no resolver link, observed 2026-08-11T13:52:45.067994Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation a50ccf77-13e3-4710-9b08-21fdb000acaa · outbound

This paper cites Massively parallel digital transcriptional profiling of single cells.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers Massively parallel digital transcriptional profiling of single cells

Reference 59

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T13:52:46.068987Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation 187725fa-635b-40c5-a341-59f222fb4afd · outbound

This paper cites Dnabert-2: Efficient foundation model and benchmark for multi-species genome, 2023.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers Dnabert-2: Efficient foundation model and benchmark for multi-species genome, 2023

Reference 60

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T13:52:46.044370Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation 30de60bb-ae93-4fb6-a71c-f61e30349c22 · outbound

This paper cites Nucleic acids research, 49 0 (D1): 0 D212--D220, 2021.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers Nucleic acids research, 49 0 (D1): 0 D212--D220, 2021

Reference 61

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T13:52:46.003917Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation 32903006-2552-41bc-8389-2472e5cea731 · outbound

This paper cites Flybase: establishing a gene group resource for drosophila melanogaster.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers Flybase: establishing a gene group resource for drosophila melanogaster

Reference 62

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T13:52:45.979922Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation aa1a862f-e7d5-4f94-8ccf-cf37e1b30085 · outbound

This paper cites Giardiadb and trichdb: integrated genomic resources for the eukaryotic protist pathogens giardia lamblia and trichomonas vaginalis.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers Giardiadb and trichdb: integrated genomic resources for the eukaryotic protist pathogens giardia lamblia and trichomonas vaginalis

Reference 63

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T13:52:45.950212Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation 5f2172b0-2b5b-4e53-abd6-bc88f3e54f68 · outbound

This paper cites Plasmodb: a functional genomic database for malaria parasites.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers Plasmodb: a functional genomic database for malaria parasites

Reference 64

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T13:52:45.920581Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation 0c52595a-2854-4ba8-961e-39ee2b4e03dd · outbound

This paper cites Amoebadb and microsporidiadb: functional genomic resources for amoebozoa and microsporidia species.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers Amoebadb and microsporidiadb: functional genomic resources for amoebozoa and microsporidia species

Reference 65

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T13:52:45.887270Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation 4d22a5b2-cc4d-45f9-8540-9013aa54d895 · outbound

This paper cites What is new in fungidb: a web-based bioinformatics platform for omics-scale data analysis for fungal and oomycete species.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers What is new in fungidb: a web-based bioinformatics platform for omics-scale data analysis for fungal and oomycete species

Reference 66

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T13:52:45.859379Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation dd2ffe90-a5a2-4158-94d9-2ec05a2e102c · outbound

This paper cites Dictybase 2013: integrating multiple dictyostelid species.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers Dictybase 2013: integrating multiple dictyostelid species

Reference 67

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T13:52:45.836917Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation 3061867b-63aa-4a45-9fbe-d3ed0d57aa2f · outbound

This paper cites gold standard.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers gold standard

Reference 68

Resolution: unresolved; no resolver link, observed 2026-08-11T13:52:45.154799Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation a73f8a2d-00a4-4454-af2b-8161ca57f821 · outbound

This paper cites Mouse genome database (mgd) 2019.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers Mouse genome database (mgd) 2019

Reference 69

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T13:52:45.793842Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation 2a42e282-9168-46d3-bf3c-42ecfef373ae · outbound

This paper cites Saccharomyces genome database: the genomics resource of budding yeast.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers Saccharomyces genome database: the genomics resource of budding yeast

Reference 70

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T13:52:45.758325Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation 02689ff6-e067-4d11-8706-46f0c1e7e6a7 · outbound

This paper cites Uniprot: a worldwide hub of protein knowledge.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers Uniprot: a worldwide hub of protein knowledge

Reference 71

Resolution: unresolved; no resolver link, observed 2026-08-11T13:52:45.179840Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation d464fbf3-b0ff-4045-9146-1208dc25eb4f · outbound

This paper cites Toxodb: the functional genomic resource for toxoplasma and related organisms.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers Toxodb: the functional genomic resource for toxoplasma and related organisms

Reference 72

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T13:52:45.719700Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation 3b32dd72-3eaa-4167-90c3-ff15cd393c6b · outbound

This paper cites Cryptodb: a cryptosporidium bioinformatics resource update.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers Cryptodb: a cryptosporidium bioinformatics resource update

Reference 73

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T13:52:45.695575Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation 1c1b6e75-3d61-4e54-9a24-7ef41af6699e · outbound

This paper cites Zfin, the zebrafish model organism database: increased support for mutants and transgenics.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers Zfin, the zebrafish model organism database: increased support for mutants and transgenics

Reference 74

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T13:52:45.656186Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation 243067d7-14d4-448b-bd48-674a97b6f8e4 · outbound

This paper cites Xenbase: a genomic, epigenomic and transcriptomic model organism database.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers Xenbase: a genomic, epigenomic and transcriptomic model organism database

Reference 75

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T13:52:45.624496Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation f71c835e-4c6b-4880-ad48-57a8abd59ac9 · outbound

This paper cites Japonicusdb: rapid deployment of a model organism database for an emerging model species.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers Japonicusdb: rapid deployment of a model organism database for an emerging model species

Reference 76

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T13:52:45.600024Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation 62661ea4-da90-4db5-bdbf-016b914977ec · outbound

This paper cites Tritrypdb: An integrated functional genomics resource for kinetoplastida.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers Tritrypdb: An integrated functional genomics resource for kinetoplastida

Reference 77

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T13:52:45.577560Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation 518925a1-a245-4397-816d-66ff769ded08 · outbound

This paper cites The candida genome database (cgd): incorporation of assembly 22, systematic identifiers and visualization of high throughput sequencing data.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers The candida genome database (cgd): incorporation of assembly 22, systematic identifiers and visualization of high throughput sequencing data

Reference 78

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T13:52:45.545104Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation 9ec33286-ac94-415e-a6fe-8bf4d788145b · outbound

This paper cites Enhanced annotations and features for comparing thousands of pseudomonas genomes in the pseudomonas genome database.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers Enhanced annotations and features for comparing thousands of pseudomonas genomes in the pseudomonas genome database

Reference 79

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T13:52:45.509701Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation 5dd60a8f-4915-4ce2-ac10-47c14ae4ab7f · outbound

This paper cites u rg B \.

UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers u rg B \

Reference 80

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T13:52:45.486462Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Pith citing papers

Observation 4f6fba7c-4413-47cf-847e-409c1990aee4 · inbound

GoBERT: Gene Ontology Graph Informed BERT for Universal Gene Function Prediction cites this paper.

GoBERT: Gene Ontology Graph Informed BERT for Universal Gene Function Prediction UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers

Reference 22

Resolution: verified exact; local_arxiv, observed 2026-08-10T22:18:57.381729Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation 9dcbb9e6-675e-464d-93c7-39e6abf3a0e3 · inbound

LLMBDC: Language Model for Biological Domains Oriented Clustering of Gene Ontology cites this paper.

LLMBDC: Language Model for Biological Domains Oriented Clustering of Gene Ontology UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers

Reference 16

Resolution: unresolved; no resolver link, observed 2026-08-04T01:24:24.954743Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.