Paper Citation Record · LEDGER

inMOTIFin: a lightweight end-to-end simulation software for regulatory sequences

As of 10 August 2026, this Paper Citation Record lists 29 of 29 outbound references and 0 inbound Pith citation observations for arXiv:2506.20769.

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

pith.paper-citation-record.v1
2506.20769 v1

Coverage vector

measured 29 of 29 reference resolution

Typed states for the displayed outbound observations.

Source: paper_references, paper_reference_links, observed 2026-08-06T22:47:07.140072Z

measured 29 of 29 standing notices

One-hop event checks from named stored sources.

Source: scholarly_work_events, retraction_status_cache, observed 2026-08-10T06:31:04.303077+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

29 of 29 outbound references displayed

verified exact0
verified fuzzy26
unresolved2
parse uncertain0
malformed identifier1
metadata mismatch0

External citation measurements

No source-named external measurement is stored.

Outbound references

Observation 574eb2f9-88be-44fe-9553-ce43d35e286b · outbound

This paper cites Access to ground truth at unconstrained size makes simulated data as indispensable as experimental data for bioinformatics methods development and benchmarking.

inMOTIFin: a lightweight end-to-end simulation software for regulatory sequences Access to ground truth at unconstrained size makes simulated data as indispensable as experimental data for bioinformatics methods development and benchmarking

Reference 1

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T22:47:07.616864Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

Observation 5e211dbf-17ea-44fd-96b2-f4993417beac · outbound

This paper cites Perspective on recent developments and challenges in regulatory and systems genomics.

inMOTIFin: a lightweight end-to-end simulation software for regulatory sequences Perspective on recent developments and challenges in regulatory and systems genomics

Reference 2

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T22:47:07.606776Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

Observation 4bc7dcdb-d788-43a3-a0cc-31d3bd6d47a6 · outbound

This paper cites Van Helden, B.

inMOTIFin: a lightweight end-to-end simulation software for regulatory sequences Van Helden, B

Reference 3

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T22:47:07.596327Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

Observation 7e8996d1-bcc0-4934-a75c-9ec12c422488 · outbound

This paper cites Identification of transcription factor co-binding patterns with non-negative matrix factorization.

inMOTIFin: a lightweight end-to-end simulation software for regulatory sequences Identification of transcription factor co-binding patterns with non-negative matrix factorization

Reference 4

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T22:47:07.585223Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

Observation 0212bbaf-2462-476b-8b10-ec45d1b7f474 · outbound

This paper cites Unlocking gene regulation with sequence-to-function models.

inMOTIFin: a lightweight end-to-end simulation software for regulatory sequences Unlocking gene regulation with sequence-to-function models

Reference 5

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T22:47:07.554159Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

Observation 61344f42-454b-464c-9235-0854062b2659 · outbound

This paper cites Assessing computational tools for the discovery of transcription factor binding sites.

inMOTIFin: a lightweight end-to-end simulation software for regulatory sequences Assessing computational tools for the discovery of transcription factor binding sites

Reference 6

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T22:47:07.521160Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

Observation 076fc664-eeb5-4082-a61a-508b87a76c4d · outbound

This paper cites Quantifying similarity between motifs.

inMOTIFin: a lightweight end-to-end simulation software for regulatory sequences Quantifying similarity between motifs

Reference 7

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T22:47:07.486975Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

Observation 5177cede-9563-4249-b6d8-a610f8a829e3 · outbound

This paper cites Price, and Donald Geman.

inMOTIFin: a lightweight end-to-end simulation software for regulatory sequences Price, and Donald Geman

Reference 8

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T22:47:07.446940Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

Observation 4f988c9f-1342-4fdf-988e-16367e8b4591 · outbound

This paper cites Learning Important Features Through Propagating Activation Differences.

inMOTIFin: a lightweight end-to-end simulation software for regulatory sequences Learning Important Features Through Propagating Activation Differences

Reference 9

Resolution: unresolved; no resolver link, observed 2026-08-06T22:47:07.056227Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation c227891c-747b-4ca3-8cd4-2c13ce65e406 · outbound

This paper cites Prakash, Avanti Shrikumar, and Anshul Kundaje.

inMOTIFin: a lightweight end-to-end simulation software for regulatory sequences Prakash, Avanti Shrikumar, and Anshul Kundaje

Reference 10

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T22:47:07.413703Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

Observation b95590df-062b-4f3c-a047-7fddbc0125d6 · outbound

This paper cites Al Hajj, Johan Pensar, and Geir K.

inMOTIFin: a lightweight end-to-end simulation software for regulatory sequences Al Hajj, Johan Pensar, and Geir K

Reference 11

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T22:47:07.399851Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

Observation 37d01824-af6c-4236-b59b-736a50095710 · outbound

This paper cites RSAT 2022: regulatory sequence analysis tools.

inMOTIFin: a lightweight end-to-end simulation software for regulatory sequences RSAT 2022: regulatory sequence analysis tools

Reference 12

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T22:47:07.389497Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

Observation c733cade-c886-4d41-9154-304954ba1abd · outbound

This paper cites Absence of a simple code: how transcription factors read the genome.

inMOTIFin: a lightweight end-to-end simulation software for regulatory sequences Absence of a simple code: how transcription factors read the genome

Reference 13

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T22:47:07.377741Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

Observation 2718b22f-8348-48a4-b432-f995f189565b · outbound

This paper cites Frith, James Johnson, and Timothy L.

inMOTIFin: a lightweight end-to-end simulation software for regulatory sequences Frith, James Johnson, and Timothy L

Reference 14

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T22:47:07.365852Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

Observation 594a6eca-b185-4fb0-aee7-11baca8c50e1 · outbound

This paper cites A review of deep learning applications in human genomics using next-generation sequencing data.

inMOTIFin: a lightweight end-to-end simulation software for regulatory sequences A review of deep learning applications in human genomics using next-generation sequencing data

Reference 15

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T22:47:07.353550Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

Observation 5571e51a-10f2-44b3-9946-0ac824b7b9b8 · outbound

This paper cites Predicting gene expression from DNA sequence using deep learning models.

inMOTIFin: a lightweight end-to-end simulation software for regulatory sequences Predicting gene expression from DNA sequence using deep learning models

Reference 16

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T22:47:07.339466Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

Observation c5c3a0ef-30e8-4e80-830f-af527d3787f0 · outbound

This paper cites Exploring explainability and transparency in deep neural networks: A comparative approach.

inMOTIFin: a lightweight end-to-end simulation software for regulatory sequences Exploring explainability and transparency in deep neural networks: A comparative approach

Reference 17

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T22:47:07.328031Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

Observation 214f5587-b0c7-41c6-b0eb-a37e915977c4 · outbound

This paper cites Perturbation-based methods for explaining deep neural networks: A survey.

inMOTIFin: a lightweight end-to-end simulation software for regulatory sequences Perturbation-based methods for explaining deep neural networks: A survey

Reference 18

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T22:47:07.316902Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

Observation 17735df8-ef7e-4fc9-9f75-044b8e40e178 · outbound

This paper cites tangermeme: Tutorial a4: Seqlets.

inMOTIFin: a lightweight end-to-end simulation software for regulatory sequences tangermeme: Tutorial a4: Seqlets

Reference 19

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T22:47:07.305457Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

Observation f708c964-c753-4140-b7ab-7417ad041e41 · outbound

This paper cites Ishak, James Johnson, Nicolas J.

inMOTIFin: a lightweight end-to-end simulation software for regulatory sequences Ishak, James Johnson, Nicolas J

Reference 20

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T22:47:07.292871Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

Observation e20ac252-c608-498f-9ff7-0224a8174572 · outbound

This paper cites Beyond authorship: attribution, contribution, collaboration, and credit.

inMOTIFin: a lightweight end-to-end simulation software for regulatory sequences Beyond authorship: attribution, contribution, collaboration, and credit

Reference 21

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T22:47:07.280297Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

Observation d79d65c6-9da9-4f8f-885d-e87c4c3e7ca8 · outbound

This paper cites write newline.

inMOTIFin: a lightweight end-to-end simulation software for regulatory sequences write newline

Reference 22

Resolution: malformed identifier; no resolver link, observed 2026-08-06T22:47:07.108710Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation f85da5e2-1407-4b02-9532-acb1c5dbca52 · outbound

This paper cites JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles.

inMOTIFin: a lightweight end-to-end simulation software for regulatory sequences JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles

Reference 23

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T22:47:07.260442Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

Observation e7004645-8192-4ae0-9027-1b9f9132c296 · outbound

This paper cites pyJASPAR : a Pythonic interface to JASPAR transcription factor motifs, February 2021.

inMOTIFin: a lightweight end-to-end simulation software for regulatory sequences pyJASPAR : a Pythonic interface to JASPAR transcription factor motifs, February 2021

Reference 24

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T22:47:07.247137Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

Observation ca32834c-ade7-46ab-ad2b-2856fa0c93b9 · outbound

This paper cites universalmotif: An R package for biological motifanalysis.

inMOTIFin: a lightweight end-to-end simulation software for regulatory sequences universalmotif: An R package for biological motifanalysis

Reference 25

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T22:47:07.234911Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

Observation 1cb67d13-a3e6-4ab7-a86e-6557f0e2e344 · outbound

This paper cites Base-resolution models of transcription-factor binding reveal soft motif syntax.

inMOTIFin: a lightweight end-to-end simulation software for regulatory sequences Base-resolution models of transcription-factor binding reveal soft motif syntax

Reference 26

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T22:47:07.221354Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

Observation b7c0f3b5-9d39-4a93-bb57-d9e4db242910 · outbound

This paper cites rMotifGen : random motif generator for DNA and protein sequences.

inMOTIFin: a lightweight end-to-end simulation software for regulatory sequences rMotifGen : random motif generator for DNA and protein sequences

Reference 27

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T22:47:07.209996Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

Observation 91081c87-1978-45b4-9b04-3d8d97594550 · outbound

This paper cites Intervene: a tool for intersection and visualization of multiple gene or genomic region sets.

inMOTIFin: a lightweight end-to-end simulation software for regulatory sequences Intervene: a tool for intersection and visualization of multiple gene or genomic region sets

Reference 28

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T22:47:07.197423Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

Observation ab42c167-3b3e-42b8-8276-4e84827c9eef · outbound

This paper cites A Unified Approach to Interpreting Model Predictions.

inMOTIFin: a lightweight end-to-end simulation software for regulatory sequences A Unified Approach to Interpreting Model Predictions

Reference 29

Resolution: unresolved; no resolver link, observed 2026-08-06T22:47:07.140072Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Pith citing papers

No inbound Pith citation observations are available.