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References

  1. (PDF) ChatGPT as a bioinformatic partner — ResearchGate, accessed March 28, 2025, https://www.researchgate.net/publication/383369099_ChatGPT_as_a_bioinformatic_partner

  2. Large Language Models in Official Statistics — UNECE, accessed March 28, 2025, https://unece.org/sites/default/files/2023-12/HLGMOS%20LLM%20Paper_Preprint_1.pdf

  3. What Should Data Science Education Do With Large Language Models?, accessed March 28, 2025, https://hdsr.mitpress.mit.edu/pub/pqiufdew

  4. arxiv.org, accessed March 28, 2025, https://arxiv.org/html/2502.17814v1#:~:text=In%20fields%20such%20as%20medical,modeling%20in%20high%2Dstakes%20applications.

  5. From statistics to deep learning: Using large language models in psychiatric research — PMC, accessed March 28, 2025, https://pmc.ncbi.nlm.nih.gov/articles/PMC11707704/

  6. pmc.ncbi.nlm.nih.gov, accessed March 28, 2025, https://pmc.ncbi.nlm.nih.gov/articles/PMC10802675/#:~:text=Applications%20of%20large%20language%20models%20in%20bioinformatics%20include%20applications%20in,discovery%20and%20single%2Dcell%20analysis.

  7. Large language models and their applications in bioinformatics — PubMed, accessed March 28, 2025, https://pubmed.ncbi.nlm.nih.gov/39435343/

  8. Advancing bioinformatics with large language models: components, applications and perspectives — PMC, accessed March 28, 2025, https://pmc.ncbi.nlm.nih.gov/articles/PMC10802675/

  9. Large Language Models in Bioinformatics: A New Era of Discovery ..., accessed March 28, 2025, https://omicstutorials.com/large-language-models-in-bioinformatics-a-new-era-of-discovery/

  10. LLM Use Cases: For Data Science and ML Workflows, accessed March 28, 2025, https://labelyourdata.com/articles/llm-use-cases

  11. LLM Prompt Engineering Techniques and Best Practices | by Ali Shafique | Medium, accessed March 28, 2025, https://medium.com/@alishafique3/llm-prompt-engineering-techniques-and-best-practices-7cc0f46467e9

  12. Prompt Engineering in Bioinformatics — Omics tutorials, accessed March 28, 2025, https://omicstutorials.com/prompt-engineering-in-bioinformatics/

  13. AI prompt for writing code from scratch | by Drashti Shah | Bioinformatics with Rust | Medium, accessed March 28, 2025, https://medium.com/bioinformatics-with-rust/gpt-4-prompt-for-writing-code-from-scratch-4e9ad067c1c7

  14. Why coding with LLMs can be harder than you think — Niraj Chauhan, accessed March 28, 2025, https://www.niraj.life/blog/why-coding-with-llms-can-be-harder-than-you-think/

  15. Context is king: tools for feeding your code and website to LLMs — WorkOS, accessed March 28, 2025, https://workos.com/blog/context-is-king-tools-for-feeding-your-code-and-website-to-llms

  16. Large Language Models for Code Generation | FabricHQ, accessed March 28, 2025, https://blog.fabrichq.ai/large-language-models-for-code-generation-f95f93fe7de4

  17. Code Generation and Documentation Search using Large Language Model | Sage, accessed March 28, 2025, https://sagecontinuum.org/science/recent/llm-generation

  18. “Prompt it”, not “Google it” : Prompt Engineering for Statistical Programmers and Biostatisticians — PharmaSUG, accessed March 28, 2025, https://pharmasug.org/proceedings/2024/SD/PharmaSUG-2024-SD-141.pdf

  19. Prompt templates — LLM — Datasette, accessed March 28, 2025, https://llm.datasette.io/en/stable/templates.html

  20. How to build your own LLM applications with RAG, Prompt templates, Vector databases?, accessed March 28, 2025, https://blog.getbind.co/2024/01/07/what-is-a-large-language-model-llm/

  21. LLM Prompting Techniques for Developers — Pedro Alonso, accessed March 28, 2025, https://www.pedroalonso.net/blog/llm-prompting-techniques-developers/

  22. Prompt Engineering Guide: Techniques & Management Tips for LLMs — Portkey, accessed March 28, 2025, https://portkey.ai/blog/the-complete-guide-to-prompt-engineering

  23. A collection of prompts for generating high quality code... : r/ChatGPTCoding — Reddit, accessed March 28, 2025, https://www.reddit.com/r/ChatGPTCoding/comments/1f51y8s/a_collection_of_prompts_for_generating_high/

  24. Using LLMs in Life Sciences: Building a Bioinformatics Assistant — Genestack, accessed March 28, 2025, https://genestack.com/news/blog/using-llms-in-life-sciences/

  25. How to Use ChatGPT Code Interpreter: Complete Workflow for Data Analysis — Tilburg.ai, accessed March 28, 2025, https://tilburg.ai/2024/07/how-to-use-chatgpt-code-interpreter-complete-workflow-for-data-analysis/

  26. AI Prompts for Data Analysis — AnalyticsHacker, accessed March 28, 2025, https://www.analyticshacker.com/analytics-resources/ai-prompts-for-data-analysis

  27. ChatGPT for Univariate Statistics: Validation of AI-Assisted Data Analysis in Healthcare Research — PMC, accessed March 28, 2025, https://pmc.ncbi.nlm.nih.gov/articles/PMC11845875/

  28. LLM Evaluation: Comparing Four Methods to Automatically Detect Errors | Label Studio, accessed March 28, 2025, https://labelstud.io/blog/llm-evaluation-comparing-four-methods-to-automatically-detect-errors/

  29. A Deep Dive Into Large Language Model Code Generation Mistakes: What and Why?, accessed March 28, 2025, https://arxiv.org/html/2411.01414v1

  30. [Literature Review] A Deep Dive Into Large Language Model Code Generation Mistakes: What and Why? — Moonlight, accessed March 28, 2025, https://www.themoonlight.io/review/a-deep-dive-into-large-language-model-code-generation-mistakes-what-and-why

  31. Can large language models identify and correct their mistakes? — Google Research, accessed March 28, 2025, https://research.google/blog/can-large-language-models-identify-and-correct-their-mistakes/

  32. Using LLMs for Code Generation: A Guide to Improving Accuracy and Addressing Common Issues | by Dan Cleary | Medium, accessed March 28, 2025, https://medium.com/@dan_43009/using-llms-for-code-generation-a-guide-to-improving-accuracy-and-addressing-common-issues-566d68a149fc

  33. How to analyze MEDICAL DATA in minutes with ChatGPT Code Interpreter. — YouTube, accessed March 28, 2025, https://www.youtube.com/watch?v=e8bX48tx66Q

  34. Refining LLMs Outputs with Iterative Consensus Ensemble (ICE) — medRxiv, accessed March 28, 2025, https://www.medrxiv.org/content/10.1101/2024.12.25.24319629v1.full-text

  35. Refining LLMs Outputs with Iterative Consensus Ensemble (ICE) — medRxiv, accessed March 28, 2025, https://www.medrxiv.org/content/10.1101/2024.12.25.24319629v1

  36. Iterative Refinement with Self-Feedback — OpenReview, accessed March 28, 2025, https://openreview.net/pdf?id=S37hOerQLB

  37. NeurIPS Poster LeDex: Training LLMs to Better Self-Debug and Explain Code, accessed March 28, 2025, https://neurips.cc/virtual/2024/poster/94367

  38. IMPROVE: Iterative Model Pipeline Refinement and Optimization Leveraging LLM Agents, accessed March 28, 2025, https://arxiv.org/html/2502.18530v1

  39. Ten quick tips for harnessing the power of ChatGPT in computational biology — PMC, accessed March 28, 2025, https://pmc.ncbi.nlm.nih.gov/articles/PMC10414555/

  40. How I use ChatGPT as a Bioinformatics Scientist — YouTube, accessed March 28, 2025, https://m.youtube.com/watch?v=Kxy_G7CtRPY&pp=ygUHI2Jpb2dwdA%3D%3D

  41. When to Use ChatGPT for Bioinformatics (And When NOT To) — YouTube, accessed March 28, 2025, https://www.youtube.com/watch?v=FIuBd20UNvo

  42. Steering veridical large language model analyses by correcting and enriching generated database queries: first steps toward ChatGPT bioinformatics — Oxford Academic, accessed March 28, 2025, https://academic.oup.com/bib/article/doi/10.1093/bib/bbaf045/8002976

  43. Empowering Beginners in Bioinformatics with ChatGPT — PMC, accessed March 28, 2025, https://pmc.ncbi.nlm.nih.gov/articles/PMC10028953/

  44. Courses for Prompt Engineering for Data Science — Track 1 — Skillsoft, accessed March 28, 2025, https://www.skillsoft.com/journey/prompt-engineering-for-data-science-0c63d71b-2e95-4a07-a0d6-49eb01e69e12

  45. travistangvh/ChatGPT-Data-Science-Prompts — GitHub, accessed March 28, 2025, https://github.com/travistangvh/ChatGPT-Data-Science-Prompts

  46. What does prompt engineering entail in a Data Scientist role? : r/datascience — Reddit, accessed March 28, 2025, https://www.reddit.com/r/datascience/comments/1ijfjh6/what_does_prompt_engineering_entail_in_a_data/

  47. 35 Must-Try ChatGPT Prompts for Data Science Enthusiasts — Kanaries Docs, accessed March 28, 2025, https://docs.kanaries.net/articles/chatgpt-prompt-data-scientist

  48. Creating Effective Prompts: Best Practices, Prompt Engineering, and How to Get the Most Out of Your LLM — Visible Thread, accessed March 28, 2025, https://www.visiblethread.com/blog/creating-effective-prompts-best-practices-prompt-engineering-and-how-to-get-the-most-out-of-your-llm/

  49. 8 best practices for effective prompt engineering — KNIME, accessed March 28, 2025, https://www.knime.com/blog/prompt-engineering

  50. Prompt Engineering 1: Top 10 Best Prompting Practices for LLMs | by WAITS Software, accessed March 28, 2025, https://medium.com/waits-on-prompt-engineering/prompt-engineering-1-top-10-best-prompting-practices-for-llms-4ffa0449c005

  51. Mastering Coding with LLMs. Learn to choose the right model, refine… — Leon Nicholls, accessed March 28, 2025, https://leonnicholls.medium.com/mastering-coding-with-llms-a16af588b169

  52. Here's how I use LLMs to help me write code — Simon Willison's Weblog, accessed March 28, 2025, https://simonwillison.net/2025/Mar/11/using-llms-for-code/

  53. Expert in the Loop: Ensuring Safe and Effective LLM Integration in Code Development — Perle AI, accessed March 28, 2025, https://www.perle.ai/resources/expert-in-the-loop-ensuring-safe-and-effective-llm-integration-in-code-development

  54. My LLM codegen workflow atm | Harper Reed's Blog, accessed March 28, 2025, https://harper.blog/2025/02/16/my-llm-codegen-workflow-atm/

  55. Best Practices for Using LLM for Code Generation: Tips from Experts, accessed March 28, 2025, https://examples.tely.ai/best-practices-for-using-llm-for-code-generation-tips-from-experts/

  56. LLM's for handling recursion and complex loops in code generation : r/deeplearning — Reddit, accessed March 28, 2025, https://www.reddit.com/r/deeplearning/comments/1hi2um5/llms_for_handling_recursion_and_complex_loops_in/

  57. How LLMs Know When to Stop Talking? — Louis-François Bouchard, aka What's AI, accessed March 28, 2025, https://www.louisbouchard.ai/how-llms-know-when-to-stop/

  58. Know When To Stop: A Study of Semantic Drift in Text Generation | by Ema Ilic | Medium, accessed March 28, 2025, https://medium.com/@ema.ilic9/know-when-to-stop-77e03a4517df

  59. Controllable LLM Debugging: Knowing when to Stop Matters — CS191, accessed March 28, 2025, https://cs191w.stanford.edu/projects/Gulati,%20Aryan_NLP%20191W.pdf

  60. how do llms know when to stop outputting new tokens? : r/learnmachinelearning — Reddit, accessed March 28, 2025, https://www.reddit.com/r/learnmachinelearning/comments/1ibe27u/how_do_llms_know_when_to_stop_outputting_new/

  61. Analysis of Code and Test-Code generated by Large Language Models — arXiv, accessed March 28, 2025, https://arxiv.org/html/2408.16601v1

  62. Llm Evaluation Techniques In Code | Restackio, accessed March 28, 2025, https://www.restack.io/p/llm-evaluation-answer-techniques-in-code-cat-ai

  63. Top 3 Benchmarks to Evaluate LLMs for Code Generation — Athina AI Hub, accessed March 28, 2025, https://hub.athina.ai/top-benchmarks-to-evaluate-llms-for-code-generation/

  64. Sandboxed Evaluations of LLM-Generated Code — Promptfoo, accessed March 28, 2025, https://www.promptfoo.dev/docs/guides/sandboxed-code-evals/

  65. Evaluating LLM Code Generation for Specialized Libraries Like Spark SQL — CloudThat, accessed March 28, 2025, https://www.cloudthat.com/resources/blog/evaluating-llm-code-generation-for-specialized-libraries-like-spark-sql

  66. Fine-Tuning LLMs: A Guide With Examples — DataCamp, accessed March 28, 2025, https://www.datacamp.com/tutorial/fine-tuning-large-language-models

  67. Fine-tuning large language models (LLMs) in 2025 — SuperAnnotate, accessed March 28, 2025, https://www.superannotate.com/blog/llm-fine-tuning

  68. LLM Fine-Tuning—Overview with Code Example — Nexla, accessed March 28, 2025, https://nexla.com/enterprise-ai/llm-fine-tuning/

  69. Fine Tune Large Language Model (LLM) on a Custom Dataset with QLoRA | by Suman Das, accessed March 28, 2025, https://dassum.medium.com/fine-tune-large-language-model-llm-on-a-custom-dataset-with-qlora-fb60abdeba07

  70. Customizing and fine-tuning LLMs: What you need to know — The GitHub Blog, accessed March 28, 2025, https://github.blog/ai-and-ml/llms/customizing-and-fine-tuning-llms-what-you-need-to-know/

  71. Large language models can help with biostatistics and coding needed in radiology research, accessed March 28, 2025, https://pubmed.ncbi.nlm.nih.gov/39406582/

  72. An Empirical Study on the Potential of LLMs in Automated Software Refactoring — arXiv, accessed March 28, 2025, https://arxiv.org/html/2411.04444v1

  73. Next-Generation Refactoring: Combining LLM Insights and IDE Capabilities for Extract Method — Danny Dig, accessed March 28, 2025, https://danny.cs.colorado.edu/papers/EM-Assist.pdf

  74. LARGE LANGUAGE MODELS ON SOFTWARE REFACTORING — Trepo, accessed March 28, 2025, https://trepo.tuni.fi/bitstream/10024/160496/2/MetsolaMikko.pdf

  75. Why are many SWEs salty about LLM use for coding? : r/LocalLLaMA — Reddit, accessed March 28, 2025, https://www.reddit.com/r/LocalLLaMA/comments/1ikjhn7/why_are_many_swes_salty_about_llm_use_for_coding/

  76. 10 Best AI Tools for Bioinformatics — Wbcom Designs, accessed March 28, 2025, https://wbcomdesigns.com/10-best-ai-tools-for-bioinformatics/

  77. CodeBio — Superbio.ai, accessed March 28, 2025, https://app.superbio.ai/apps/652fdf059c811c2ce387c22a

  78. 10 Best AI Tools for Bioinformatics | GeeksforGeeks, accessed March 28, 2025, https://www.geeksforgeeks.org/ai-tools-for-bioinformatics/

  79. Chapter 21 AI for Bioinformatics | AI for Efficient Programming, accessed March 28, 2025, https://hutchdatascience.org/AI_for_Efficient_Programming/ai-for-bioinformatics.html

  80. Here's my one-line review of all the AI programming tools I tried : r/webdev — Reddit, accessed March 28, 2025, https://www.reddit.com/r/webdev/comments/1ihikux/heres_my_oneline_review_of_all_the_ai_programming/

  81. Helpful 201+ Best ChatGPT Prompts for Coding [List UPDATED] — LearnPrompt.org, accessed March 28, 2025, https://www.learnprompt.org/chat-gpt-prompts-for-coding/

  82. ChatGPT — Prompts for Coding Best Practices or Principles — DEV Community, accessed March 28, 2025, https://dev.to/techiesdiary/chatgpt-prompts-for-coding-best-practices-or-principles-33m

  83. Custom Instructions to make GPT-4o concise — Prompting — OpenAI Developer Community, accessed March 28, 2025, https://community.openai.com/t/custom-instructions-to-make-gpt-4o-concise/905595

  84. PickleBoxer/dev-chatgpt-prompts — GitHub, accessed March 28, 2025, https://github.com/PickleBoxer/dev-chatgpt-prompts

  85. How can I format code properly in a ChatGPT prompt? — Web Applications Stack Exchange, accessed March 28, 2025, https://webapps.stackexchange.com/questions/169461/how-can-i-format-code-properly-in-a-chatgpt-prompt

  86. Build a simple LLM application with chat models and prompt templates | 🦜️ LangChain, accessed March 28, 2025, https://python.langchain.com/docs/tutorials/llm_chain/

  87. Template-filling task with LLMs — usage — Prodigy Support, accessed March 28, 2025, https://support.prodi.gy/t/template-filling-task-with-llms/7118

  88. LLMs For Structured Data — Neptune.ai, accessed March 28, 2025, https://neptune.ai/blog/llm-for-structured-data

  89. Can Large Language Models Replace Data Scientists in Clinical Research? — arXiv, accessed March 28, 2025, https://arxiv.org/html/2410.21591v1

  90. Evaluation Framework of Large Language Models in Medical Documentation: Development and Usability Study, accessed March 28, 2025, https://www.jmir.org/2024/1/e58329/

  91. NHANES-GPT: Large Language Models (LLMs) and the Future of Biostatistics — medRxiv, accessed March 28, 2025, https://www.medrxiv.org/content/10.1101/2023.12.13.23299830v1.full.pdf

  92. Top 10 AI Tools for Biotech and Bioinformatics: AI Innovations You Need to Know, accessed March 28, 2025, https://datascienceforbio.com/ai-tools-for-biotech-and-bioinformatics/

  93. AutoXAI4Omics: an automated explainable AI tool for omics and tabular data | Briefings in Bioinformatics | Oxford Academic, accessed March 28, 2025, https://academic.oup.com/bib/article/26/1/bbae593/7906915

  94. AI-Driven Personalized Data Dictionaries — Kythera Labs, accessed March 28, 2025, https://www.kytheralabs.com/news/ai-driven-personalized-data-dictionaries

  95. 35 Must-Try ChatGPT Prompts for Data Science Enthusiasts — UVA Teaching Hub, accessed March 28, 2025, https://teaching.virginia.edu/collections/chatgpt-in-technical-courses/241

  96. Data-science-ML-and-DL-Resources/Chatgpt Prompts/README.md at main — GitHub, accessed March 28, 2025, https://github.com/chethanhn29/Data-science-ML-and-DL-Resources/blob/main/Chatgpt%20Prompts/README.md

  97. 20 Essential ChatGPT Prompts for Data Scientists | by Oluwafemidiakhoa — Medium, accessed March 28, 2025, https://oluwafemidiakhoa.medium.com/20-essential-chatgpt-prompts-for-data-scientists-36a055ef7ab7

  98. Readme Generator Streamlit App using ChatGPT — YouTube, accessed March 28, 2025, https://www.youtube.com/watch?v=3XFdq9RDz6A

  99. Best practices with large language models (LLMs) | Generative AI — Google Cloud, accessed March 28, 2025, https://cloud.google.com/vertex-ai/generative-ai/docs/learn/prompt-best-practices

  100. Evaluating an LLM code documentation generation application | by Aaron Zhao — Medium, accessed March 28, 2025, https://medium.com/gft-engineering/evaluating-an-llm-code-documentation-generation-application-719b57f801e5

  101. Ask HN: Recommendation for LLM-based "documentation interaction" — Hacker News, accessed March 28, 2025, https://news.ycombinator.com/item?id=41847966