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Paper Citation Record · LEDGER

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics

As of 18 August 2026, this Paper Citation Record lists 100 of 103 outbound references and 1 inbound Pith citation observation for arXiv:2507.20122.

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

pith.paper-citation-record.v1
2507.20122 v2

Coverage vector

measured 100 of 103 reference resolution

Typed states for the displayed outbound observations.

Source: paper_references, paper_reference_links, observed 2026-08-15T17:52:52.737802Z

measured 101 of 101 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 1 of 1 inbound itemization

Pith citing papers itemized under the disclosed page cap.

Source: paper_references, paper_reference_links, observed 2026-07-15T13:53:02.803305Z

measured 0 of 1 external citation measurements

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

Source: cited_works

Reference resolution

100 of 103 outbound references displayed

  • verified exact7
  • verified fuzzy31
  • unresolved61
  • parse uncertain0
  • malformed identifier1
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External citation measurements

No source-named external measurement is stored.

Outbound references

Observation 37c14ca8-5fac-4c4c-9c31-c247e16b1bdf · outbound

This paper cites an unresolved cited work.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Unresolved cited work

Reference 1

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Observation 3aa0d3f6-7a84-49c6-a418-b2d28428d9e3 · outbound

This paper cites Cohen-Boulakia, K.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Cohen-Boulakia, K

Reference 2

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Observation e43b161b-1db1-4e94-bab4-8f4b13d5576a · outbound

This paper cites S¨ anger, N.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics S¨ anger, N

Reference 3

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Observation 2094020a-1ab5-4bf4-8a1f-cb70829e5dd6 · outbound

This paper cites Wratten, A.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Wratten, A

Reference 4

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Observation e64f90fa-6334-409e-95a5-4204ea94efe0 · outbound

This paper cites Goodwin, J.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Goodwin, J

Reference 5

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Observation ee8b05d1-e125-4ad6-a443-2ad0c3955dd8 · outbound

This paper cites an unresolved cited work.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Unresolved cited work

Reference 6

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Observation 6b1527bb-4853-4a2e-81a4-6efb693d994b · outbound

This paper cites an unresolved cited work.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Unresolved cited work

Reference 7

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Source-reported events for the cited work

Unavailable: canonical work link unavailable.

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Observation 6143fdbb-577d-4e6e-9e1f-b0148bd3d8fa · outbound

This paper cites Goecks, A.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Goecks, A

Reference 8

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Source-reported events for the cited work

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Observation dfe65ccd-915f-4a85-82f9-693d57ef9d13 · outbound

This paper cites Di Tommaso, M.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Di Tommaso, M

Reference 9

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Observation 0a390f24-fe27-4dfe-a8a2-a4bf87cf3b35 · outbound

This paper cites K¨ oster, S.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics K¨ oster, S

Reference 10

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Observation b9cdfa4f-f19d-4a7b-955b-fd316d816854 · outbound

This paper cites Harenslak, et al., Data pipelines with apache airflow, Simon and Schuster, 2021.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Harenslak, et al., Data pipelines with apache airflow, Simon and Schuster, 2021

Reference 11

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Unavailable: canonical work link unavailable.

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Observation 0f40040d-4737-4d2a-88fb-b0323fedc0e2 · outbound

This paper cites Deelman, K.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Deelman, K

Reference 12

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Observation cc73a8d0-66cb-40f1-81e8-44e5c006a5b7 · outbound

This paper cites Goodstadt, Ruffus: a lightweight python library for computational pipelines, Bioinfor- matics 26 (21) (2010) 2778–2779.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Goodstadt, Ruffus: a lightweight python library for computational pipelines, Bioinfor- matics 26 (21) (2010) 2778–2779

Reference 13

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Unavailable: canonical work link unavailable.

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Observation 5b696a15-1aff-46bf-9054-8820f1fc2d06 · outbound

This paper cites Khodak, B.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Khodak, B

Reference 14

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Unavailable: canonical work link unavailable.

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Observation 788c7dfb-b7c0-4ee1-9b20-f0fe7e81082c · outbound

This paper cites Kumar, H.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Kumar, H

Reference 15

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Observation 46170667-32b5-4acc-a344-e97c8d95fbfc · outbound

This paper cites an unresolved cited work.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Unresolved cited work

Reference 16

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Observation 054eb5df-6730-49e3-8e1c-3757c9c5a00a · outbound

This paper cites Ferreira da Silva, D.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Ferreira da Silva, D

Reference 17

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Observation 1a1d7ed2-087c-428e-9a6b-6c562c05c00c · outbound

This paper cites Menaka, K.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Menaka, K

Reference 18

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Observation 0bed4e5a-5d22-4fed-b43d-afc1f536cc2d · outbound

This paper cites Deelman, T.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Deelman, T

Reference 19

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Observation 0fa84b00-6ce8-4ffd-bb92-01acf03a1b4e · outbound

This paper cites an unresolved cited work.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Unresolved cited work

Reference 20

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Observation 3874d2f2-46dd-418f-be5c-6e7f2fe0f3b1 · outbound

This paper cites De Roure, C.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics De Roure, C

Reference 21

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Source-reported events for the cited work

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Observation 7dd55696-cb57-4bde-ad3a-1707685ef65c · outbound

This paper cites Cohen-Boulakia, U.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Cohen-Boulakia, U

Reference 22

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Source-reported events for the cited work

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Observation 31d5cfed-e335-482a-8646-017cdf5531bb · outbound

This paper cites GPT-4o System Card.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics GPT-4o System Card

Reference 23

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Observation f9b6ac9a-46aa-43c3-a953-546eb38ffb69 · outbound

This paper cites Gemini 2.5: Pushing the Frontier with Advanced Reasoning, Multimodality, Long Context, and Next Generation Agentic Capabilities.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Gemini 2.5: Pushing the Frontier with Advanced Reasoning, Multimodality, Long Context, and Next Generation Agentic Capabilities

Reference 24

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Observation 4a97bfbd-1f4d-42b6-b182-cae159f9aafb · outbound

This paper cites DeepSeek-V3 Technical Report.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics DeepSeek-V3 Technical Report

Reference 25

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Observation 3c032d82-af34-4d65-8be7-5c181400e7f9 · outbound

This paper cites An Empirical Study of the Non-determinism of ChatGPT in Code Generation.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics An Empirical Study of the Non-determinism of ChatGPT in Code Generation

Reference 26

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Observation 0d7ab744-c430-4d6c-9b8b-75c8d03b3234 · outbound

This paper cites an unresolved cited work.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Unresolved cited work

Reference 27

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Source-reported events for the cited work

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Observation c8468289-b5dd-4062-9c05-d08ec39a1953 · outbound

This paper cites Ekin, Prompt engineering for chatgpt: a quick guide to techniques, tips, and best practices, Authorea Preprints (2023).

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Ekin, Prompt engineering for chatgpt: a quick guide to techniques, tips, and best practices, Authorea Preprints (2023)

Reference 28

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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.

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Observation aa4a1f1d-65ff-40d5-b700-7c0b637dac20 · outbound

This paper cites Arora, A.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Arora, A

Reference 29

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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.

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Observation 115fd476-c7ff-4729-9ce6-5c707e9787e5 · outbound

This paper cites Reynolds, K.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Reynolds, K

Reference 30

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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.

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Observation 1491c839-b1e8-4dba-aa12-c2128e8bfb45 · outbound

This paper cites an unresolved cited work.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Unresolved cited work

Reference 31

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raw_fallback, observed 2026-08-15T17:52:53.745227Z

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.

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Observation d4c4cf39-9d88-4e7c-a0bb-b02c76df1770 · outbound

This paper cites Large Language Models Are Human-Level Prompt Engineers.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Large Language Models Are Human-Level Prompt Engineers

Reference 32

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unresolved
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Source-reported events for the cited work

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Observation 98748bce-8cd0-4dde-a78c-90602d5da83c · outbound

This paper cites Marvin, N.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Marvin, N

Reference 33

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verified fuzzy
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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.

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Observation b104b758-3a55-43f7-ab18-8ee65a8d4fd7 · outbound

This paper cites Lin, How to write effective prompts for large language models, Nature Human Be- haviour 8 (4) (2024) 611–615.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Lin, How to write effective prompts for large language models, Nature Human Be- haviour 8 (4) (2024) 611–615

Reference 34

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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.

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Observation 3673d1ab-6438-4813-b89a-dee816f5b8a6 · outbound

This paper cites Hiltemann, et al., Galaxy training: A powerful framework for teaching!, PLoS compu- tational biology 19 (1) (2023) e1010752.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Hiltemann, et al., Galaxy training: A powerful framework for teaching!, PLoS compu- tational biology 19 (1) (2023) e1010752

Reference 35

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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.

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Observation 131ba8fa-0016-4a16-916b-8c4a3ac09abe · outbound

This paper cites an unresolved cited work.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Unresolved cited work

Reference 36

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raw_fallback, observed 2026-08-15T17:52:53.696980Z

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.

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Observation 91e526c5-02bc-4462-945d-0542c3df9015 · outbound

This paper cites Barker, J.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Barker, J

Reference 37

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raw_fallback, observed 2026-08-15T17:52:53.684487Z

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.

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Observation d053fefb-dbd4-4fe0-9a6f-8da01f8fea50 · outbound

This paper cites Lud¨ ascher, M.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Lud¨ ascher, M

Reference 38

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verified fuzzy
raw_fallback, observed 2026-08-15T17:52:53.671871Z

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.

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Observation 26cebf2a-34c6-4552-b7d9-63b3ca16f1ac · outbound

This paper cites an unresolved cited work.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Unresolved cited work

Reference 39

Resolution
unresolved
raw_fallback, observed 2026-08-15T17:52:53.660007Z

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.

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Observation ee614c23-a1df-4075-b0fb-214a90a95c3c · outbound

This paper cites an unresolved cited work.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Unresolved cited work

Reference 40

Resolution
unresolved
raw_fallback, observed 2026-08-15T17:52:53.648192Z

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.

source=pdf_text observed=2026-08-15T17:52:52.500301Z digest=sha256:c5bc980ff963100701d484e15a8497b5d84a5619fb81edf2b26ad88d1ed40285

Observation da3462f9-9854-409e-8e49-ad161f0c3fe0 · outbound

This paper cites an unresolved cited work.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Unresolved cited work

Reference 41

Resolution
unresolved
raw_fallback, observed 2026-08-15T17:52:53.635752Z

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.

source=pdf_text observed=2026-08-15T17:52:52.504156Z digest=sha256:c62d73aebffb161c6fbc5abde6f6c9a1e44383af471b1e2dde63e9e88c9655b0

Observation 5957c80b-2e90-4198-a0fb-bada37371f6c · outbound

This paper cites Vaswani, Attention is all you need, Advances in Neural Information Processing Systems (2017).

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Vaswani, Attention is all you need, Advances in Neural Information Processing Systems (2017)

Reference 42

Resolution
verified fuzzy
raw_fallback, observed 2026-08-15T17:52:53.622562Z

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.

source=pdf_text observed=2026-08-15T17:52:52.507886Z digest=sha256:448f652fdd3ab4a08028dafe08af5fb39ce31142a4a5dc89c81ab8b893c530c4

Observation 6fd8df88-4cc4-48e3-a325-8cd950939177 · outbound

This paper cites A Survey of Large Language Models.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics A Survey of Large Language Models

Reference 43

Resolution
unresolved
no resolver link, observed 2026-08-15T17:52:52.512029Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

source=pdf_text observed=2026-08-15T17:52:52.512029Z digest=sha256:3969dc4026e43c10854c472cc6b90a61bcb4ba526370441d91f424ed4f449302

Observation bedbabb2-0809-4c31-9158-7e11f627a0eb · outbound

This paper cites an unresolved cited work.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Unresolved cited work

Reference 44

Resolution
unresolved
raw_fallback, observed 2026-08-15T17:52:53.609798Z

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.

source=pdf_text observed=2026-08-15T17:52:52.516042Z digest=sha256:4e30968af18fbf1cae460eeb2bebf095732666bd1af04246a37fafc1b9aac8b0

Observation 0c607a70-ecfa-4ef8-9d81-5ad5354609ef · outbound

This paper cites An Insight into Security Code Review with LLMs: Capabilities, Obstacles, and Influential Factors.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics An Insight into Security Code Review with LLMs: Capabilities, Obstacles, and Influential Factors

Reference 45

Resolution
unresolved
no resolver link, observed 2026-08-15T17:52:52.519756Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

source=pdf_text observed=2026-08-15T17:52:52.519756Z digest=sha256:15cbe85716d2594d637ae6126703aa16984c901028f8d28411c3d240775a7ce7

Observation c6320c31-8e98-451d-98d8-6e33c4936d53 · outbound

This paper cites an unresolved cited work.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Unresolved cited work

Reference 46

Resolution
unresolved
raw_fallback, observed 2026-08-15T17:52:53.596874Z

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.

source=pdf_text observed=2026-08-15T17:52:52.523718Z digest=sha256:c714ebb972b2a71d905cf961c957334c2089dc1f6647a3197f98823e2e2956a5

Observation 358677b9-2354-433e-be9b-f6786f481604 · outbound

This paper cites an unresolved cited work.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Unresolved cited work

Reference 47

Resolution
unresolved
raw_fallback, observed 2026-08-15T17:52:53.583571Z

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.

source=pdf_text observed=2026-08-15T17:52:52.527169Z digest=sha256:a83c8df92a6f6bacd146efd38d8ab54648f8884277ee7bce04025a808043b677

Observation 30dfe176-26f8-4aa0-b5c2-d5b1bf3bfb86 · outbound

This paper cites Lost in Translation: A Study of Bugs Introduced by Large Language Models while Translating Code.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Lost in Translation: A Study of Bugs Introduced by Large Language Models while Translating Code

Reference 48

Resolution
unresolved
no resolver link, observed 2026-08-15T17:52:52.530491Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

source=pdf_text observed=2026-08-15T17:52:52.530491Z digest=sha256:941ecab56762e3ebe736c07dde66d679884c76ec5cda6fb93a392afa18609bf8

Observation 8d45bcaf-3b8e-4db0-8a6b-d3afb1f03ac3 · outbound

This paper cites an unresolved cited work.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Unresolved cited work

Reference 49

Resolution
unresolved
raw_fallback, observed 2026-08-15T17:52:53.571294Z

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.

source=pdf_text observed=2026-08-15T17:52:52.533993Z digest=sha256:51c51c4b13898435156c4f6b8b8c0aff85fe200072105378a510e1a8a9ce0409

Observation 98b25b45-95ac-4983-a667-f5f93395270b · outbound

This paper cites an unresolved cited work.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Unresolved cited work

Reference 50

Resolution
unresolved
raw_fallback, observed 2026-08-15T17:52:53.558534Z

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.

source=pdf_text observed=2026-08-15T17:52:52.537394Z digest=sha256:bd00b81ef4186e3dbbe9b6675af659fb44b092f2f81444729d263944407d40f6

Observation cc7991a1-562d-4552-bfaf-df0abd436384 · outbound

This paper cites SelfCheckGPT: Zero-Resource Black-Box Hallucination Detection for Generative Large Language Models.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics SelfCheckGPT: Zero-Resource Black-Box Hallucination Detection for Generative Large Language Models

Reference 51

Resolution
unresolved
no resolver link, observed 2026-08-15T17:52:52.541383Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

source=pdf_text observed=2026-08-15T17:52:52.541383Z digest=sha256:fe61404d0c645d4384ee2c4e9c25115a6462be641ceae5375900fe4155a973e0

Observation 0cd32c14-641f-485a-b7ec-f7f022b440ae · outbound

This paper cites Check Your Facts and Try Again: Improving Large Language Models with External Knowledge and Automated Feedback.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Check Your Facts and Try Again: Improving Large Language Models with External Knowledge and Automated Feedback

Reference 52

Resolution
unresolved
no resolver link, observed 2026-08-15T17:52:52.545077Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

source=pdf_text observed=2026-08-15T17:52:52.545077Z digest=sha256:42311f71f79f850f16c889df9776181fe230af62486d051b3b7bc05d0f07a0b3

Observation ff91266b-9847-45db-8962-c8e07eb3e92f · outbound

This paper cites Ugare, et al., Improving llm code generation with grammar augmentation, arXiv e- prints (2024) arXiv–2403.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Ugare, et al., Improving llm code generation with grammar augmentation, arXiv e- prints (2024) arXiv–2403

Reference 53

Resolution
verified fuzzy
raw_fallback, observed 2026-08-15T17:52:53.546468Z

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.

source=pdf_text observed=2026-08-15T17:52:52.548684Z digest=sha256:d840355ae57cb0411f3db42da36b05bc96212e4cc216619baec755f64818f184

Observation dfc756c9-a7b8-4357-9204-77979253f3eb · outbound

This paper cites Gu, Llm-based code generation method for golang compiler testing, in: Proceedings of the 31st ACM Joint European Software Engineering Conference and Symposium on the FSE, 2023, pp.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Gu, Llm-based code generation method for golang compiler testing, in: Proceedings of the 31st ACM Joint European Software Engineering Conference and Symposium on the FSE, 2023, pp

Reference 54

Resolution
verified fuzzy
raw_fallback, observed 2026-08-15T17:52:53.534966Z

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.

source=pdf_text observed=2026-08-15T17:52:52.552629Z digest=sha256:8f526aac487e00a401862ccfe779d7b8e3e84a6418fc92068d2ccebc8a32dd71

Observation 8c8fcb67-2e34-4ea2-9bdc-c981bbb77fec · outbound

This paper cites an unresolved cited work.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Unresolved cited work

Reference 55

Resolution
unresolved
raw_fallback, observed 2026-08-15T17:52:53.522667Z

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.

source=pdf_text observed=2026-08-15T17:52:52.556439Z digest=sha256:c234b95bbc2fc616e3a508af7c12b3f1e96bd876c6769ba88d1639d3a46942c0

Observation 0f600ab7-cb6d-42f1-9066-37f6c765e35e · outbound

This paper cites Jiang, E.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Jiang, E

Reference 56

Resolution
verified fuzzy
raw_fallback, observed 2026-08-15T17:52:53.510621Z

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.

source=pdf_text observed=2026-08-15T17:52:52.560506Z digest=sha256:45e68371dd7e4441db9d9ff79c5b259d92c403f4b755051d5760d571523dfd4e

Observation 61d57ee2-3dd1-473a-a251-6cb78c77ed85 · outbound

This paper cites Vaithilingam, et al., Expectation vs.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Vaithilingam, et al., Expectation vs

Reference 57

Resolution
verified fuzzy
raw_fallback, observed 2026-08-15T17:52:53.498284Z

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.

source=pdf_text observed=2026-08-15T17:52:52.564504Z digest=sha256:846702d2389fa8d09ee92f7b9bb96a6df19c59f3e28c0af804144a4f1a396781

Observation db2bd706-8e68-41f5-bb91-4fd40009a33a · outbound

This paper cites Evaluating the Code Quality of AI-Assisted Code Generation Tools: An Empirical Study on GitHub Copilot, Amazon CodeWhisperer, and ChatGPT.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Evaluating the Code Quality of AI-Assisted Code Generation Tools: An Empirical Study on GitHub Copilot, Amazon CodeWhisperer, and ChatGPT

Reference 58

Resolution
unresolved
no resolver link, observed 2026-08-15T17:52:52.568593Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

source=pdf_text observed=2026-08-15T17:52:52.568593Z digest=sha256:2d6b4ba66cc82ec569e169df0aa0a88d99e1a11f0e8dfa4aa8220671504bf10b

Observation 68ba5c99-97e0-4f83-b010-81e134bf7708 · outbound

This paper cites Kazemitabaar, J.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Kazemitabaar, J

Reference 59

Resolution
verified fuzzy
raw_fallback, observed 2026-08-15T17:52:53.485458Z

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.

source=pdf_text observed=2026-08-15T17:52:52.573238Z digest=sha256:4adbe65ade5bd4e1b9c171de186007b3c5f7843acc8f10c5d2db561e73160c60

Observation 43419545-e053-4b7f-b784-d6c2dd584eeb · outbound

This paper cites what it wants me to say.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics what it wants me to say

Reference 60

Resolution
verified fuzzy
raw_fallback, observed 2026-08-15T17:52:53.472875Z

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.

source=pdf_text observed=2026-08-15T17:52:52.577348Z digest=sha256:71bcd922e5f91e319d6e3b9bdc01385da875509a20713cef63229e73a4d50347

Observation 7752cfeb-0956-45db-a8c2-ac36fd894234 · outbound

This paper cites an unresolved cited work.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Unresolved cited work

Reference 61

Resolution
unresolved
raw_fallback, observed 2026-08-15T17:52:53.459832Z

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.

source=pdf_text observed=2026-08-15T17:52:52.581332Z digest=sha256:1d66eafaf44b61cb698f3452428d7c85e9e4f129fe3c539cb6d5cce30d499bcf

Observation 00f31cb7-6804-4862-8259-e333c0761a40 · outbound

This paper cites Brandes, D.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Brandes, D

Reference 62

Resolution
verified fuzzy
raw_fallback, observed 2026-08-15T17:52:53.445928Z

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.

source=pdf_text observed=2026-08-15T17:52:52.585330Z digest=sha256:4b383d7b21f0b31d9c09b0a65cd1626cd48ef7dcc02b5cfeb61a38abc101ec2c

Observation 2134e2fb-7dfe-4833-8842-328c3873b9c2 · outbound

This paper cites DNAGPT: A Generalized Pre-trained Tool for Versatile DNA Sequence Analysis Tasks.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics DNAGPT: A Generalized Pre-trained Tool for Versatile DNA Sequence Analysis Tasks

Reference 63

Resolution
unresolved
no resolver link, observed 2026-08-15T17:52:52.589301Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

source=pdf_text observed=2026-08-15T17:52:52.589301Z digest=sha256:6dd0e8f18ddccd39b2f27762a851a2739c8b5ea7e9f8a7a1910bc1e5489c7f94

Observation 8ef5e8db-cfc4-40b8-8378-969bbc2f2d02 · outbound

This paper cites Ferruz, S.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Ferruz, S

Reference 64

Resolution
verified fuzzy
raw_fallback, observed 2026-08-15T17:52:53.433234Z

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.

source=pdf_text observed=2026-08-15T17:52:52.593437Z digest=sha256:c2911d85e5df314cdd96a7b8dc934c6b0347f8c1569dd2bb70c01202f98ef028

Observation 7aec8edf-c704-468e-b50f-c9fdf9c5f178 · outbound

This paper cites Oppenlaender, A taxonomy of prompt modifiers for text-to-image generation, Be- haviour & Information Technology (2023) 1–14.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Oppenlaender, A taxonomy of prompt modifiers for text-to-image generation, Be- haviour & Information Technology (2023) 1–14

Reference 65

Resolution
verified fuzzy
raw_fallback, observed 2026-08-15T17:52:53.420186Z

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.

source=pdf_text observed=2026-08-15T17:52:52.597275Z digest=sha256:e8f078ef0d4e4fcf7cccb8e68670405dd0c548e5ad10154b2040579fdfbe6237

Observation dd0d59cf-7a5a-4988-a349-832f9854bcc2 · outbound

This paper cites A Prompt Pattern Catalog to Enhance Prompt Engineering with ChatGPT.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics A Prompt Pattern Catalog to Enhance Prompt Engineering with ChatGPT

Reference 66

Resolution
unresolved
no resolver link, observed 2026-08-15T17:52:52.601178Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

source=pdf_text observed=2026-08-15T17:52:52.601178Z digest=sha256:0d3182bf95d4a3de2f4991af98f71ff27151437d8ed4d1a1d2e34e997c03c2ae

Observation 3120e8f8-50f9-4ba4-8f2a-68540c8c1c6c · outbound

This paper cites Jailbreaking ChatGPT via Prompt Engineering: An Empirical Study.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Jailbreaking ChatGPT via Prompt Engineering: An Empirical Study

Reference 67

Resolution
unresolved
no resolver link, observed 2026-08-15T17:52:52.605670Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

source=pdf_text observed=2026-08-15T17:52:52.605670Z digest=sha256:481a0e3a322baf03bc2aff4e1715b2a1e260a6dbcc86057ecd73459224ee6d44

Observation 9b275eea-a464-4124-8cc4-2e2db8625a8d · outbound

This paper cites an unresolved cited work.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Unresolved cited work

Reference 68

Resolution
unresolved
raw_fallback, observed 2026-08-15T17:52:53.407334Z

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.

source=pdf_text observed=2026-08-15T17:52:52.609666Z digest=sha256:eed3c3c91aed46038d4e65e61273d25946b3bfb2c180d374681c443a6a362f05

Observation 97d1a3a0-835e-4e9c-9d9e-612d77285e1e · outbound

This paper cites A Systematic Survey of Prompt Engineering in Large Language Models: Techniques and Applications.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics A Systematic Survey of Prompt Engineering in Large Language Models: Techniques and Applications

Reference 69

Resolution
unresolved
no resolver link, observed 2026-08-15T17:52:52.613702Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

source=pdf_text observed=2026-08-15T17:52:52.613702Z digest=sha256:19a0dc0b3f0216ddc9bbf23a4339b613962908a7943604ab166ae390c69b06ee

Observation efaac122-da3e-4583-a962-40f6e11a9e7c · outbound

This paper cites Unleashing the potential of prompt engineering for large language models.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Unleashing the potential of prompt engineering for large language models

Reference 70

Resolution
unresolved
no resolver link, observed 2026-08-15T17:52:52.617842Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

source=pdf_text observed=2026-08-15T17:52:52.617842Z digest=sha256:c710394e21b42acd29b02ec7c5e76060af7abe6abd3d895ae5b0fc89a7aad3b4

Observation 4a5388aa-3958-4849-87be-966b943b300a · outbound

This paper cites Revisiting Prompt Engineering via Declarative Crowdsourcing.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Revisiting Prompt Engineering via Declarative Crowdsourcing

Reference 71

Resolution
unresolved
no resolver link, observed 2026-08-15T17:52:52.622028Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

source=pdf_text observed=2026-08-15T17:52:52.622028Z digest=sha256:3e52a88799763f10c190cdb49c76c7ebd8526187444dad61a0c2408933c3d152

Observation c68d5f4d-b04c-45ca-b5d7-08151b64ca09 · outbound

This paper cites A Survey of Prompt Engineering Methods in Large Language Models for Different NLP Tasks.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics A Survey of Prompt Engineering Methods in Large Language Models for Different NLP Tasks

Reference 72

Resolution
unresolved
no resolver link, observed 2026-08-15T17:52:52.626247Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

source=pdf_text observed=2026-08-15T17:52:52.626247Z digest=sha256:18cade911554c1b26f5a24655d9b5cded126f162a2c0d588ecd6e0a85ef00d39

Observation 0b0cf264-8650-45b2-93dd-1e6ee636dfb2 · outbound

This paper cites Shah, From prompt engineering to prompt science with humans in the loop, Commu- nications of the ACM 68 (6) (2025) 54–61.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Shah, From prompt engineering to prompt science with humans in the loop, Commu- nications of the ACM 68 (6) (2025) 54–61

Reference 73

Resolution
verified fuzzy
raw_fallback, observed 2026-08-15T17:52:53.395735Z

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.

source=pdf_text observed=2026-08-15T17:52:52.630611Z digest=sha256:86ec1727faefd72bf22a8119b69f24201adbde9b45e22af2a0d8c22ab6961fd3

Observation 82b25295-3765-4ffa-a646-ea307d2cb6db · outbound

This paper cites Smith, J.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Smith, J

Reference 74

Resolution
unresolved
no resolver link, observed 2026-08-15T17:52:52.634472Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

source=pdf_text observed=2026-08-15T17:52:52.634472Z digest=sha256:6b7eb8dc8f8bda892f3763c33f339357a8d2a61ac8783732b4c98e25d2629535

Observation 96681c34-39ec-4f52-b394-d883c30003d2 · outbound

This paper cites an unresolved cited work.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Unresolved cited work

Reference 75

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Observation 27b1973b-a970-44d6-a5eb-3724b55d5cc2 · outbound

This paper cites Progressive Prompts: Continual Learning for Language Models.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Progressive Prompts: Continual Learning for Language Models

Reference 76

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Source-reported events for the cited work

Unavailable: canonical work link unavailable.

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Observation ba292b82-ae7d-4227-98a5-62133d0923d8 · outbound

This paper cites Knoth, A.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Knoth, A

Reference 77

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Observation c52ea686-9f58-486a-9e10-0dea137b1fee · outbound

This paper cites an unresolved cited work.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Unresolved cited work

Reference 78

Resolution
unresolved
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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.

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Observation a8164a85-afcf-455f-8c21-a7ae3c8d4ed5 · outbound

This paper cites an unresolved cited work.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Unresolved cited work

Reference 79

Resolution
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Source-reported events for the cited work

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Observation 30b4fab0-2785-488b-b841-367a59684942 · outbound

This paper cites Hiltemann, H.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Hiltemann, H

Reference 80

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Source-reported events for the cited work

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Observation 8e0df1c8-9688-4a84-98ad-daec2ef4539b · outbound

This paper cites Hiltemann, et al., Galaxy basics for genomics (2024).

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Hiltemann, et al., Galaxy basics for genomics (2024)

Reference 81

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Observation 6ec5bb3d-bfc9-43a4-8b5a-6729d284a5a1 · outbound

This paper cites Pajon, C.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Pajon, C

Reference 82

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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.

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Observation c3e932f7-4752-43db-a40b-fd1db310b241 · outbound

This paper cites Clements, C.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Clements, C

Reference 83

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Source-reported events for the cited work

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Observation df8aea6b-874a-420f-b690-5ddbf98e275a · outbound

This paper cites Batut, M.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Batut, M

Reference 84

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verified fuzzy
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Source-reported events for the cited work

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Observation 96372f82-c48a-40c6-a774-cc3c0615171e · outbound

This paper cites Batut, Bacterial genome annotation (2024).

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Batut, Bacterial genome annotation (2024)

Reference 85

Resolution
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Observation 237cbbb7-653a-44b6-af63-b0dba11d65cc · outbound

This paper cites Hakkaart, M.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Hakkaart, M

Reference 86

Resolution
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Source-reported events for the cited work

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Observation 6f805f69-7808-4db5-961b-cff1ea804ba1 · outbound

This paper cites Patel, M.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Patel, M

Reference 87

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verified exact
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Source-reported events for the cited work

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Observation 80d7d4cf-7ba7-4117-8d83-75702e2368bb · outbound

This paper cites Ewels, Sateesh Peri, P.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Ewels, Sateesh Peri, P

Reference 88

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verified exact
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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.

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Observation 53f85157-4edb-4a79-a4cd-392362fd508b · outbound

This paper cites Patel, P.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Patel, P

Reference 89

Resolution
verified exact
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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.

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Observation 0daa7c65-7339-4529-8540-22dc5035feaf · outbound

This paper cites Lundin, nf-core bot, J.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Lundin, nf-core bot, J

Reference 90

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verified exact
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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.

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Observation be3248ae-9467-4c0a-8a4d-dc2942555d09 · outbound

This paper cites Efficient Prompting Methods for Large Language Models: A Survey.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Efficient Prompting Methods for Large Language Models: A Survey

Reference 91

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Source-reported events for the cited work

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Observation e6284fa1-bbad-43c6-9162-7c39fd72eac0 · outbound

This paper cites Liu, et al., Pre-train, prompt, and predict: A systematic survey of prompting methods in natural language processing, ACM Computing Surveys 55 (9) (2023) 1–35.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Liu, et al., Pre-train, prompt, and predict: A systematic survey of prompting methods in natural language processing, ACM Computing Surveys 55 (9) (2023) 1–35

Reference 92

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Source-reported events for the cited work

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Observation 8010deab-0bfb-4c73-9d59-2e26c3521133 · outbound

This paper cites Alam, From prompt to pipeline: Large language models for scientific workflow devel- opment in bioinformatics (Jul.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Alam, From prompt to pipeline: Large language models for scientific workflow devel- opment in bioinformatics (Jul

Reference 93

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

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Observation 2a8df1cd-2652-491a-bf4f-78d7cfc31fa1 · outbound

This paper cites Wohlin, P.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Wohlin, P

Reference 94

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Observation 1fdd229c-8ae6-49cc-a886-7e871fd67f45 · outbound

This paper cites Palmblad, et al., Automated workflow composition in mass spectrometry-based pro- teomics, Bioinformatics 35 (4) (2019) 656–664.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Palmblad, et al., Automated workflow composition in mass spectrometry-based pro- teomics, Bioinformatics 35 (4) (2019) 656–664

Reference 95

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Source-reported events for the cited work

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Observation 0f0b30bb-41ba-4fd9-9219-00da10c907e7 · outbound

This paper cites DiBernardo, et al., Semi-automatic web service composition for the life sciences using the biomoby semantic web framework, Journal of biomedical informatics 41 (5) (2008) 837–847.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics DiBernardo, et al., Semi-automatic web service composition for the life sciences using the biomoby semantic web framework, Journal of biomedical informatics 41 (5) (2008) 837–847

Reference 96

Resolution
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Source-reported events for the cited work

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Observation 558c177d-5897-40f1-b6f0-4380f9ede266 · outbound

This paper cites Koop, et al., Viscomplete: Automating suggestions for visualization pipelines, IEEE Transactions on Visualization and Computer Graphics 14 (6) (2008) 1691–1698.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Koop, et al., Viscomplete: Automating suggestions for visualization pipelines, IEEE Transactions on Visualization and Computer Graphics 14 (6) (2008) 1691–1698

Reference 97

Resolution
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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.

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Observation 614fe036-e24f-446e-8dc0-b89c03763a71 · outbound

This paper cites Kumar, B.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Kumar, B

Reference 98

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verified fuzzy
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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.

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Observation 3121c6ad-789d-4718-9c1f-42ab70026d73 · outbound

This paper cites Language Model Powered Digital Biology with BRAD.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics Language Model Powered Digital Biology with BRAD

Reference 99

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Source-reported events for the cited work

Unavailable: canonical work link unavailable.

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Observation 3ea58610-cdb9-41fc-abd6-dc96139cce60 · outbound

This paper cites OLAF: An Open Life Science Analysis Framework for Conversational Bioinformatics Powered by Large Language Models.

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics OLAF: An Open Life Science Analysis Framework for Conversational Bioinformatics Powered by Large Language Models

Reference 100

Resolution
verified exact
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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.

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Pith citing papers

Observation da7a0d49-9c7b-44cf-ad13-3fb82b07194c · inbound

Long-range machine-learning potentials with environment-dependent charges enable predicting LO-TO splitting and dielectric constants cites this paper.

Long-range machine-learning potentials with environment-dependent charges enable predicting LO-TO splitting and dielectric constants From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics

Reference 36

Resolution
unresolved
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Source-reported events for the cited work

Unavailable: canonical work link unavailable.

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