Paper Citation Record · LEDGER

Learning Genomic Structure from $k$-mers

As of 15 August 2026, this Paper Citation Record lists 37 of 37 outbound references and 0 inbound Pith citation observations for arXiv:2505.16680.

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

pith.paper-citation-record.v1
2505.16680 v1

Coverage vector

measured 37 of 37 reference resolution

Typed states for the displayed outbound observations.

Source: paper_references, paper_reference_links, observed 2026-08-07T15:00:52.195424Z

measured 37 of 37 standing notices

One-hop event checks from named stored sources.

Source: scholarly_work_events, retraction_status_cache, observed 2026-08-15T06:32:42.880941+00:00

measured 0 of 0 inbound itemization

Pith citing papers itemized under the disclosed page cap.

Source: paper_references, paper_reference_links

measured 0 of 1 external citation measurements

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

Source: cited_works

Reference resolution

37 of 37 outbound references displayed

verified exact10
verified fuzzy20
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External citation measurements

No source-named external measurement is stored.

Outbound references

Observation 2e1a7d1e-4972-4697-b002-3a8bda9ed068 · outbound

This paper cites an unresolved cited work.

Learning Genomic Structure from $k$-mers Unresolved cited work

Reference 1

Resolution: verified exact; doi, observed 2026-08-07T15:00:54.006304Z

Source-reported events for the cited work

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Observation 63b0ef61-e0c7-4dfc-9b99-6e4adab09b12 · outbound

This paper cites Singer, Brunilda Balliu, David Koslicki, Pavel Skums, Alex Zelikovsky, Can Alkan, Onur Mutlu, and Serghei Mangul.

Learning Genomic Structure from $k$-mers Singer, Brunilda Balliu, David Koslicki, Pavel Skums, Alex Zelikovsky, Can Alkan, Onur Mutlu, and Serghei Mangul

Reference 2

Resolution: unresolved; no resolver link, observed 2026-08-07T15:00:47.581048Z

Source-reported events for the cited work

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Observation 94d97e70-5904-448f-a2c6-29ce85c73f9b · outbound

This paper cites Logsdon, Mitchell R.

Learning Genomic Structure from $k$-mers Logsdon, Mitchell R

Reference 3

Resolution: verified exact; doi, observed 2026-08-07T15:00:53.727458Z

Source-reported events for the cited work

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Observation f5aac4dd-a411-4b77-be7e-b2794639f133 · outbound

This paper cites McPherson, and W.

Learning Genomic Structure from $k$-mers McPherson, and W

Reference 4

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Source-reported events for the cited work

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Observation 418d9c03-18e8-4156-84d8-2123a7942b86 · outbound

This paper cites Method of the year: long-read sequencing.

Learning Genomic Structure from $k$-mers Method of the year: long-read sequencing

Reference 5

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Source-reported events for the cited work

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Observation 94e2e1e9-8e5f-4fb1-b291-4575aa185e5a · outbound

This paper cites Read length dominates phylogenetic placement accuracy of ancient DNA reads.

Learning Genomic Structure from $k$-mers Read length dominates phylogenetic placement accuracy of ancient DNA reads

Reference 6

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T15:00:58.866193Z

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Observation 217b6b97-77a6-415e-b176-ec919c3b3a77 · outbound

This paper cites Briggs, Udo Stenzel, Philip L.

Learning Genomic Structure from $k$-mers Briggs, Udo Stenzel, Philip L

Reference 7

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Source-reported events for the cited work

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Observation 4adc59a9-0ad6-4413-938c-0ed0b4c3a121 · outbound

This paper cites BetaAlign: a deep learning approach for multiple sequence alignment.

Learning Genomic Structure from $k$-mers BetaAlign: a deep learning approach for multiple sequence alignment

Reference 8

Resolution: verified exact; doi, observed 2026-08-07T15:00:53.183254Z

Source-reported events for the cited work

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Observation 3239af69-8e91-4a9e-b9cc-080423597d1f · outbound

This paper cites Deep reinforcement learning-based pairwise DNA sequence alignment method compatible with embedded edge devices.

Learning Genomic Structure from $k$-mers Deep reinforcement learning-based pairwise DNA sequence alignment method compatible with embedded edge devices

Reference 9

Resolution: verified exact; doi, observed 2026-08-07T15:00:52.963278Z

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Observation 673f9524-58b1-45a0-b905-f103b6c334bd · outbound

This paper cites Hill, and Lila Kari.

Learning Genomic Structure from $k$-mers Hill, and Lila Kari

Reference 10

Resolution: verified exact; doi, observed 2026-08-07T15:00:52.826138Z

Source-reported events for the cited work

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Observation 4c688f62-cee3-4af4-b2d3-33ee080f1d5f · outbound

This paper cites A deep learning approach to pattern recognition for short DNA sequences.

Learning Genomic Structure from $k$-mers A deep learning approach to pattern recognition for short DNA sequences

Reference 11

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T15:00:58.613454Z

Source-reported events for the cited work

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Observation 565bdf57-ac8d-4e3b-a939-0c7a459e36ed · outbound

This paper cites Read alignment using deep neural networks.

Learning Genomic Structure from $k$-mers Read alignment using deep neural networks

Reference 12

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T15:00:58.393393Z

Source-reported events for the cited work

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Observation 720d0aeb-22e8-47af-ae69-9a9cae1cda4d · outbound

This paper cites FaceNet: A unified embedding for face recognition and clustering.

Learning Genomic Structure from $k$-mers FaceNet: A unified embedding for face recognition and clustering

Reference 13

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Source-reported events for the cited work

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Observation 19d88381-603f-4a04-8853-0fe70fd791d0 · outbound

This paper cites A simple framework for contrastive learning of visual representations.

Learning Genomic Structure from $k$-mers A simple framework for contrastive learning of visual representations

Reference 14

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Source-reported events for the cited work

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Observation c3df0f3f-df1d-477f-ac0d-03c4a0005751 · outbound

This paper cites Improved deep metric learning with multi-class N-pair loss objec- tive.

Learning Genomic Structure from $k$-mers Improved deep metric learning with multi-class N-pair loss objec- tive

Reference 15

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T15:00:57.987421Z

Source-reported events for the cited work

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Observation 6c5c5c4f-a85f-492c-b4ad-872d3eea0363 · outbound

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Learning Genomic Structure from $k$-mers Unresolved cited work

Reference 16

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Source-reported events for the cited work

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Observation 741775e0-4c41-44d6-a854-f7572aac663d · outbound

This paper cites Supervised contrastive learning.

Learning Genomic Structure from $k$-mers Supervised contrastive learning

Reference 17

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T15:00:57.788997Z

Source-reported events for the cited work

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Observation ab347529-0ff0-4b3d-b0cf-0ec27e03b008 · outbound

This paper cites A ConvNet for the 2020s.

Learning Genomic Structure from $k$-mers A ConvNet for the 2020s

Reference 18

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T15:00:57.542223Z

Source-reported events for the cited work

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Observation 1234a14f-1c07-489c-9fe8-d74f0af1f105 · outbound

This paper cites Analog Bits: Generating Discrete Data using Diffusion Models with Self-Conditioning.

Learning Genomic Structure from $k$-mers Analog Bits: Generating Discrete Data using Diffusion Models with Self-Conditioning

Reference 19

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Source-reported events for the cited work

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Observation 07390bad-ca9f-49ce-a0d8-e01482f8734f · outbound

This paper cites Improving language understanding by generative pre-training, 2018.

Learning Genomic Structure from $k$-mers Improving language understanding by generative pre-training, 2018

Reference 20

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Source-reported events for the cited work

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Observation 63b35fc7-3a95-462f-9376-86bf5e95df96 · outbound

This paper cites Escherichia coli str.

Learning Genomic Structure from $k$-mers Escherichia coli str

Reference 21

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Source-reported events for the cited work

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Observation 74509a51-2117-418b-beb6-019b60ad1d48 · outbound

This paper cites gargammel: a sequence simulator for ancient DNA.Bioinformatics, 33(4):577–579, 11 2016.

Learning Genomic Structure from $k$-mers gargammel: a sequence simulator for ancient DNA.Bioinformatics, 33(4):577–579, 11 2016

Reference 22

Resolution: verified exact; doi, observed 2026-08-07T15:00:52.607384Z

Source-reported events for the cited work

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Observation 21cbd0bb-33f5-450f-97ca-dd2874be20ec · outbound

This paper cites Myers, and Gabor T.

Learning Genomic Structure from $k$-mers Myers, and Gabor T

Reference 23

Resolution: verified exact; doi, observed 2026-08-07T15:00:52.426847Z

Source-reported events for the cited work

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Observation 83f617bb-d874-41af-b353-34fca7352d84 · outbound

This paper cites Additional evaluations show that specific BW A-aln settings still outperform BW A-mem for ancient DNA data alignment.

Learning Genomic Structure from $k$-mers Additional evaluations show that specific BW A-aln settings still outperform BW A-mem for ancient DNA data alignment

Reference 24

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Observation a63ce251-ffdf-470d-88d1-d77836843971 · outbound

This paper cites Ultrafast and memory- efficient alignment of short DNA sequences to the human genome.

Learning Genomic Structure from $k$-mers Ultrafast and memory- efficient alignment of short DNA sequences to the human genome

Reference 25

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Source-reported events for the cited work

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Observation 6eeeff2d-8e3f-4eda-be36-f90a52fe47dc · outbound

This paper cites Systematic benchmark of ancient DNA read mapping.

Learning Genomic Structure from $k$-mers Systematic benchmark of ancient DNA read mapping

Reference 26

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Source-reported events for the cited work

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Observation 5a29d291-c1d9-499b-a9de-5a355668b3f1 · outbound

This paper cites CuPy: A NumPy-compatible library for NVIDIA GPU calculations.

Learning Genomic Structure from $k$-mers CuPy: A NumPy-compatible library for NVIDIA GPU calculations

Reference 27

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T15:00:55.866119Z

Source-reported events for the cited work

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Observation d790a294-6a91-48bd-9897-236ebaae432d · outbound

This paper cites UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction.

Learning Genomic Structure from $k$-mers UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction

Reference 28

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Source-reported events for the cited work

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Observation 68d9dec0-b198-498f-851c-672cae2c9e48 · outbound

This paper cites Thousands of missed genes found in bacterial genomes and their analysis with COMBREX.

Learning Genomic Structure from $k$-mers Thousands of missed genes found in bacterial genomes and their analysis with COMBREX

Reference 29

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T15:00:55.625082Z

Source-reported events for the cited work

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Observation eff36a6b-c9aa-498d-9cce-2b3e2fca1dbf · outbound

This paper cites Lintner, Qiong Ding, Zou Wang, Jiang Hu, Depeng Wang, Feng Wang, Lin Wang, Gholson J.

Learning Genomic Structure from $k$-mers Lintner, Qiong Ding, Zou Wang, Jiang Hu, Depeng Wang, Feng Wang, Lin Wang, Gholson J

Reference 30

Resolution: verified exact; doi, observed 2026-08-07T15:00:55.351512Z

Source-reported events for the cited work

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Observation 8e8a70d3-e4d4-484f-b46f-f9efd0b53f52 · outbound

This paper cites De novo assembly of two swedish genomes reveals missing segments from the human GRCh38 reference and improves variant calling of Population-Scale sequencing data.

Learning Genomic Structure from $k$-mers De novo assembly of two swedish genomes reveals missing segments from the human GRCh38 reference and improves variant calling of Population-Scale sequencing data

Reference 31

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T15:00:55.120122Z

Source-reported events for the cited work

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Observation 2f9402ac-fd51-4d68-a3dd-746c9ebe3d5c · outbound

This paper cites Human pangenome analysis of sequences missing from the reference genome reveals their widespread evolutionary, phenotypic, and functional roles.

Learning Genomic Structure from $k$-mers Human pangenome analysis of sequences missing from the reference genome reveals their widespread evolutionary, phenotypic, and functional roles

Reference 32

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T15:00:54.882725Z

Source-reported events for the cited work

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Observation f0378ad6-9aec-4e01-b1fa-b08bc68240e1 · outbound

This paper cites The presence and impact of reference bias on population genomic studies of prehistoric human populations.

Learning Genomic Structure from $k$-mers The presence and impact of reference bias on population genomic studies of prehistoric human populations

Reference 33

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T15:00:54.700433Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

Observation e478825b-4af9-4c54-9cde-f5881066579f · outbound

This paper cites an unresolved cited work.

Learning Genomic Structure from $k$-mers Unresolved cited work

Reference 34

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Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 1f0b10de-8839-49b1-9a33-ccab442d2f92 · outbound

This paper cites Fast and accurate short read alignment with Burrows-Wheeler transform.

Learning Genomic Structure from $k$-mers Fast and accurate short read alignment with Burrows-Wheeler transform

Reference 35

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T15:00:54.496548Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

Observation bf1e2055-d3ef-4799-8787-7f9b7916d29f · outbound

This paper cites GenBank acces- sion: NC_000913.3.

Learning Genomic Structure from $k$-mers GenBank acces- sion: NC_000913.3

Reference 2022

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T15:00:56.749315Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

Observation 23a1f0a1-52e9-4c33-b6eb-203645032a48 · outbound

This paper cites doi: 10.1038/s41592-022-01730-w.

Learning Genomic Structure from $k$-mers doi: 10.1038/s41592-022-01730-w

Reference 2023

Resolution: verified exact; doi, observed 2026-08-07T15:00:53.497139Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

Pith citing papers

No inbound Pith citation observations are available.