Paper Citation Record · LEDGER

DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome

As of 13 August 2026, this Paper Citation Record lists 0 of 0 outbound references and 42 inbound Pith citation observations for arXiv:2306.15006.

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

pith.paper-citation-record.v1
2306.15006 v2

Coverage vector

measured 0 of 0 reference resolution

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Source: paper_references, paper_reference_links

measured 42 of 42 standing notices

One-hop event checks from named stored sources.

Source: scholarly_work_events, retraction_status_cache, observed 2026-08-13T06:32:02.005865+00:00

measured 42 of 42 inbound itemization

Pith citing papers itemized under the disclosed page cap.

Source: paper_references, paper_reference_links, observed 2026-08-12T13:07:04.442804Z

measured 0 of 1 external citation measurements

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

Source: arxiv_reference, observed 2026-07-03T03:57:38.576237Z

Reference resolution

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External citation measurements

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Outbound references

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Pith citing papers

Observation 08a27a26-d261-4102-a522-af5be2970db8 · inbound

Fundamental Limits of Prompt Tuning Transformers: Universality, Capacity and Efficiency cites this paper.

Fundamental Limits of Prompt Tuning Transformers: Universality, Capacity and Efficiency DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome

Reference 72

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Observation 7101b6ef-0d9b-4fe6-9e0b-d27f9b1888e6 · inbound

LLaMA-Gene: A General-purpose Gene Task Large Language Model Based on Instruction Fine-tuning cites this paper.

LLaMA-Gene: A General-purpose Gene Task Large Language Model Based on Instruction Fine-tuning DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome

Reference 2

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Observation d6b939cb-b9d7-44fa-9315-e8516135f1ef · inbound

Does your model understand genes? A benchmark of gene properties for biological and text models cites this paper.

Does your model understand genes? A benchmark of gene properties for biological and text models DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome

Reference 52

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Observation 17ce30a7-0ab6-40a5-bd80-e4baf7767b93 · inbound

Can linguists better understand DNA? cites this paper.

Can linguists better understand DNA? DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome

Reference 13

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Observation af3c0a34-bc07-4912-940f-f415675a6342 · inbound

COMET: Benchmark for Comprehensive Biological Multi-omics Evaluation Tasks and Language Models cites this paper.

COMET: Benchmark for Comprehensive Biological Multi-omics Evaluation Tasks and Language Models DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome

Reference 17

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Observation e81aa89e-5659-42cf-a812-c4baf618271d · inbound

BarcodeMamba: State Space Models for Biodiversity Analysis cites this paper.

BarcodeMamba: State Space Models for Biodiversity Analysis DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome

Reference 24

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Observation a053cc48-3d4f-4380-bb47-2574e3b41884 · inbound

Model Decides How to Tokenize: Adaptive DNA Sequence Tokenization with MxDNA cites this paper.

Model Decides How to Tokenize: Adaptive DNA Sequence Tokenization with MxDNA DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome

Reference 5

Resolution: unresolved; no resolver link, observed 2026-08-11T12:55:40.362299Z

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Observation bf422c40-c57a-488e-b81f-08cbbf5de4ad · inbound

VirusT5: Harnessing Large Language Models to Predicting SARS-CoV-2 Evolution cites this paper.

VirusT5: Harnessing Large Language Models to Predicting SARS-CoV-2 Evolution DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome

Reference 18

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Observation 3934f65c-3186-4ce1-a459-9daab215778a · inbound

PhyloGen: Language Model-Enhanced Phylogenetic Inference via Graph Structure Generation cites this paper.

PhyloGen: Language Model-Enhanced Phylogenetic Inference via Graph Structure Generation DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome

Reference 49

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Observation 669663b6-613f-4628-8f21-53f10a18f8e8 · inbound

METAGENE-1: Metagenomic Foundation Model for Pandemic Monitoring cites this paper.

METAGENE-1: Metagenomic Foundation Model for Pandemic Monitoring DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome

Reference 28

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Observation 4c3316a7-7913-41a6-ada5-7d19ad341730 · inbound

Scaling Up ESM2 Architectures for Long Protein Sequences Analysis: Long and Quantized Approaches cites this paper.

Scaling Up ESM2 Architectures for Long Protein Sequences Analysis: Long and Quantized Approaches DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome

Reference 28

Resolution: unresolved; no resolver link, observed 2026-08-10T20:38:59.571770Z

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Observation 5a620154-94cc-45cb-bb4c-728563d2707c · inbound

Human Genome Book: Words, Sentences and Paragraphs cites this paper.

Human Genome Book: Words, Sentences and Paragraphs DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome

Reference 16

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Observation fbf27ed7-a175-4a62-9cde-4feea7ad5018 · inbound

TFBS-Finder: Deep Learning-based Model with DNABERT and Convolutional Networks to Predict Transcription Factor Binding Sites cites this paper.

TFBS-Finder: Deep Learning-based Model with DNABERT and Convolutional Networks to Predict Transcription Factor Binding Sites DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome

Reference 37

Resolution: unresolved; no resolver link, observed 2026-08-09T15:44:41.753306Z

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Observation d75c0912-fecb-4add-ad52-d63807033712 · inbound

Omni-DNA: A Unified Genomic Foundation Model for Cross-Modal and Multi-Task Learning cites this paper.

Omni-DNA: A Unified Genomic Foundation Model for Cross-Modal and Multi-Task Learning DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome

Reference 53

Resolution: unresolved; no resolver link, observed 2026-08-09T10:16:49.313150Z

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Observation 3c572736-a75f-4926-922d-9de34d8471ce · inbound

Find Central Dogma Again: Leveraging Multilingual Transfer in Large Language Models cites this paper.

Find Central Dogma Again: Leveraging Multilingual Transfer in Large Language Models DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome

Reference 12

Resolution: unresolved; no resolver link, observed 2026-08-08T16:17:55.128254Z

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Observation 8db58757-dc8f-4cff-8697-db40984be141 · inbound

Nature Language Model: Deciphering the Language of Nature for Scientific Discovery cites this paper.

Nature Language Model: Deciphering the Language of Nature for Scientific Discovery DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome

Reference 96

Resolution: unresolved; no resolver link, observed 2026-08-08T12:31:52.298340Z

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Observation 6da71cb3-f4aa-4b62-901a-ac15323f4a1d · inbound

OmniGenBench: A Modular Platform for Reproducible Genomic Foundation Models Benchmarking cites this paper.

OmniGenBench: A Modular Platform for Reproducible Genomic Foundation Models Benchmarking DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome

Reference 11

Resolution: unresolved; no resolver link, observed 2026-08-07T15:39:02.491956Z

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Observation 700e4e8a-caf4-45ef-bfb2-347f4c249a7d · inbound

Minimalist Softmax Attention Provably Learns Constrained Boolean Functions cites this paper.

Minimalist Softmax Attention Provably Learns Constrained Boolean Functions DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome

Reference 26

Resolution: unresolved; no resolver link, observed 2026-08-07T14:21:01.955998Z

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Observation 23d35700-a73e-4104-8252-f38eb3b3bf17 · inbound

HAD: Hybrid Architecture Distillation Outperforms Teacher in Genomic Sequence Modeling cites this paper.

HAD: Hybrid Architecture Distillation Outperforms Teacher in Genomic Sequence Modeling DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome

Reference 4

Resolution: unresolved; no resolver link, observed 2026-08-07T13:53:40.729297Z

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Observation 8862244a-006e-4a9d-a184-d59a348ab690 · inbound

GeneBreaker: Jailbreak Attacks against DNA Language Models with Pathogenicity Guidance cites this paper.

GeneBreaker: Jailbreak Attacks against DNA Language Models with Pathogenicity Guidance DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome

Reference 81

Resolution: unresolved; no resolver link, observed 2026-08-07T13:15:24.749565Z

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Observation d72606d8-f719-4b34-8f87-030383e8a8b6 · inbound

Leveraging Natural Language Processing to Unravel the Mystery of Life: A Review of NLP Approaches in Genomics, Transcriptomics, and Proteomics cites this paper.

Leveraging Natural Language Processing to Unravel the Mystery of Life: A Review of NLP Approaches in Genomics, Transcriptomics, and Proteomics DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome

Reference 26

Resolution: unresolved; no resolver link, observed 2026-08-07T11:31:19.045431Z

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Observation 7b0a3283-ed0b-4b25-a95b-460161addb09 · inbound

Evaluating DNA function understanding in genomic language models using evolutionarily implausible sequences cites this paper.

Evaluating DNA function understanding in genomic language models using evolutionarily implausible sequences DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome

Reference 32

Resolution: unresolved; no resolver link, observed 2026-08-07T04:36:21.667026Z

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Observation 0a639e47-ef46-44d1-955f-1ae710012c0a · inbound

BMFM-DNA: A SNP-aware DNA foundation model to capture variant effects cites this paper.

BMFM-DNA: A SNP-aware DNA foundation model to capture variant effects DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome

Reference 13

Resolution: unresolved; no resolver link, observed 2026-08-06T22:36:02.166688Z

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Observation bb3b5c4d-0897-4e4f-a23c-b0455a1cef72 · inbound

Evaluation of Coding Schemes for Transformer-based Gene Sequence Modeling cites this paper.

Evaluation of Coding Schemes for Transformer-based Gene Sequence Modeling DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome

Reference 2015

Resolution: unresolved; no resolver link, observed 2026-08-06T15:47:06.344749Z

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Observation 1b3ad77e-0132-4532-86e3-98db3743104e · inbound

Fast and Scalable Gene Embedding Search: A Comparative Study of FAISS and ScaNN cites this paper.

Fast and Scalable Gene Embedding Search: A Comparative Study of FAISS and ScaNN DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome

Reference 23

Resolution: unresolved; no resolver link, observed 2026-08-06T15:05:25.176787Z

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Observation edd983a4-cc16-4e81-849e-bd03cee932df · inbound

EnTao-GPM: DNA Foundation Model for Predicting the Germline Pathogenic Mutations cites this paper.

EnTao-GPM: DNA Foundation Model for Predicting the Germline Pathogenic Mutations DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome

Reference 6

Resolution: unresolved; no resolver link, observed 2026-08-06T12:34:03.697041Z

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Observation 1b0fc6c4-36c4-4b13-9102-e6a29e814b30 · inbound

NucEL: Single-Nucleotide ELECTRA-Style Genomic Pre-training for Efficient and Interpretable Representations cites this paper.

NucEL: Single-Nucleotide ELECTRA-Style Genomic Pre-training for Efficient and Interpretable Representations DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome

Reference 22

Resolution: unresolved; no resolver link, observed 2026-08-05T20:00:19.244272Z

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Observation 388a6010-4f5a-4a0d-a732-03dd31d965a9 · inbound

Generative Artificial Intelligence in Bioinformatics: A Systematic Review of Models, Applications, and Methodological Advances cites this paper.

Generative Artificial Intelligence in Bioinformatics: A Systematic Review of Models, Applications, and Methodological Advances DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome

Reference 19

Resolution: unresolved; no resolver link, observed 2026-08-03T23:59:54.514934Z

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Observation e49a4bf5-7ed9-41ef-ac17-9f32135b0ca4 · inbound

BioArc: Discovering Optimal Neural Architectures for Biological Foundation Models cites this paper.

BioArc: Discovering Optimal Neural Architectures for Biological Foundation Models DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome

Reference 4054

Resolution: unresolved; no resolver link, observed 2026-08-03T19:32:01.164181Z

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Observation da62046b-d94c-4010-ae79-4ccd9afd3665 · inbound

Rethinking Genomic Modeling Through Optical Character Recognition cites this paper.

Rethinking Genomic Modeling Through Optical Character Recognition DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome

Reference 51

Resolution: unresolved; no resolver link, observed 2026-08-03T05:34:18.210942Z

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Observation 1246c614-d824-4f69-8608-a946486481ed · inbound

JEPA-DNA: Grounding Genomic Foundation Models through Joint-Embedding Predictive Architectures cites this paper.

JEPA-DNA: Grounding Genomic Foundation Models through Joint-Embedding Predictive Architectures DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome

Reference 25

Resolution: unresolved; no resolver link, observed 2026-08-02T22:21:33.203727Z

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Observation 8641dfd4-aebe-4672-9c04-a3bbe9a42a5d · inbound

In Search of Lost DNA Sequence Pretraining cites this paper.

In Search of Lost DNA Sequence Pretraining DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome

Reference 40

Resolution: metadata mismatch; arxiv_id, observed 2026-05-10T08:53:03.604418Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-13T06:32:02.005865+00:00.

Observation 781154fb-33c9-4fd7-900a-a6948c520d5a · inbound

Evaluating Post-hoc Explanations of the Transformer-based Genome Language Model DNABERT-2 cites this paper.

Evaluating Post-hoc Explanations of the Transformer-based Genome Language Model DNABERT-2 DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome

Reference 31

Resolution: metadata mismatch; arxiv_id, observed 2026-05-09T22:34:07.319885Z

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No event found in the named queried sources as of 2026-08-13T06:32:02.005865+00:00.

Observation 0f381a55-dcf4-4edd-ac8f-038565affa18 · inbound

Set-Aggregated Genome Embeddings for Microbiome Abundance Prediction cites this paper.

Set-Aggregated Genome Embeddings for Microbiome Abundance Prediction DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome

Reference 16

Resolution: metadata mismatch; arxiv_id, observed 2026-05-13T03:07:08.655044Z

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Observation 386ea257-d437-4f4b-8fba-85e2d3dbe1a1 · inbound

GGBound: A Genome-Grounded Agent for Microbial Life-Boundary Prediction cites this paper.

GGBound: A Genome-Grounded Agent for Microbial Life-Boundary Prediction DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome

Reference 15

Resolution: verified exact; arxiv_id, observed 2026-05-15T02:13:30.434972Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-13T06:32:02.005865+00:00.

Observation b5085feb-692b-4a27-802c-75ff4919adbd · inbound

TadA-Bench: A Million-Variant Benchmark for Future-Round Discovery Toward Agentic Protein Engineering cites this paper.

TadA-Bench: A Million-Variant Benchmark for Future-Round Discovery Toward Agentic Protein Engineering DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome

Reference 99

Resolution: metadata mismatch; arxiv_id, observed 2026-06-28T20:12:37.859641Z

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No event found in the named queried sources as of 2026-08-13T06:32:02.005865+00:00.

Observation a931e25b-137b-4173-a238-d0e42cceefdd · inbound

Biological Reasoning-Informed Regression for Interpretable Regulatory DNA Activity Prediction cites this paper.

Biological Reasoning-Informed Regression for Interpretable Regulatory DNA Activity Prediction DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome

Reference 44

Resolution: verified exact; arxiv_id, observed 2026-07-02T22:17:26.272078Z

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No event found in the named queried sources as of 2026-08-13T06:32:02.005865+00:00.

Observation f9619132-339f-4b0b-bdb6-0131eb2f648e · inbound

Flexible Flows for Biological Sequence Design cites this paper.

Flexible Flows for Biological Sequence Design DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome

Reference 9

Resolution: metadata mismatch; arxiv_id, observed 2026-07-03T03:57:38.577658Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-13T06:32:02.005865+00:00.

Observation 2eeb9d5a-7574-4dad-b1c5-9b1cef876972 · inbound

How Post-Training Shapes Biological Reasoning Models cites this paper.

How Post-Training Shapes Biological Reasoning Models DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome

Reference 36

Resolution: verified exact; arxiv_id, observed 2026-07-01T07:55:31.056974Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-13T06:32:02.005865+00:00.

Observation 5fbac5d3-2744-45d5-b53c-3d21a2c7644f · inbound

DNA Language Models: An Assessment of Pre-Training for Fine-Tuning Tasks cites this paper.

DNA Language Models: An Assessment of Pre-Training for Fine-Tuning Tasks DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome

Reference 13

Resolution: verified exact; arxiv_id, observed 2026-06-30T03:34:13.167209Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-13T06:32:02.005865+00:00.

Observation 5f819af3-be52-41d5-af98-ccd4d3ec50e6 · inbound

Deep and Probabilistic Models for Gene Regulatory Network Inference cites this paper.

Deep and Probabilistic Models for Gene Regulatory Network Inference DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome

Reference 160

Resolution: unresolved; no resolver link, observed 2026-08-01T21:34:24.389119Z

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Observation 7c860de4-861a-441c-a1d0-47819840e889 · inbound

Frozen but Not Always Accessible: A Representation Analysis of Genomic Language Models cites this paper.

Frozen but Not Always Accessible: A Representation Analysis of Genomic Language Models DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome

Reference 55

Resolution: unresolved; no resolver link, observed 2026-08-08T15:15:00.033761Z

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