10 Claude prompts I use weekly for paper writing

Why Prompt Structure Matters More Than the Model

The single biggest lesson from using LLMs on real manuscripts is that an unstructured prompt produces fluent, confident, and frequently wrong output. Models are very good at reproducing the shape of scientific writing — the cadence of a Methods section, the hedging of a Discussion — without any commitment to whether the underlying claims are true. Left open-ended, they will happily invent a trial name, a statistic, or a citation to fill a gap. The prompts below exist to remove that freedom: each one constrains the model to organize facts I supply rather than generate facts of its own.

When I sit down to write, I don't want magic. I want reliability. I've tested dozens of tools, and most fail when subjected to the rigors of peer review. I use my own workflows to ensure that the data I present is accurate, verifiable, and free of hallucinations.

Why I Use Structured Prompts

I spent far too long tweaking prompts to get a usable output. I finally sat down and codified the exact prompts I use for clinical research writing, and I keep them in a dedicated Claude Project so they are one paste away on every paper. The payoff is less time staring at a blank page and far fewer factual errors to catch later. I found that strict constraints are the only way to get clinical relevance out of an LLM.

The IMRaD Constraints

I always break my prompts down by section. I never ask the model to write an entire paper. I prompt specifically for the Introduction, Methods, Results, and Discussion. I provide the exact data points. I explicitly forbid the model from hallucinating specific trial names, authors, or DOIs. I learned this lesson the hard way, which I wrote about in /blog/citation-hallucination-ai-writing.

My Favorite Prompt

One of my most reliable prompts is for structural editing. I feed the model my raw, messy draft and ask it to enforce a specific logical flow without changing any facts. I tell it to flag any claims that lack a citation. I demand that it maintain my academic register. I use a variation of this prompt to critique my methodology, asking the model to act as a hostile Reviewer 2. I have packaged these and more advanced workflows into my Paper Structuring Prompt Pack, available at gumroad.com.

Connecting the Workflow

I use these prompts in conjunction with my overall tool stack, which I outline in /blog/ai-research-stack-5-tools-that-save-time. I also combine this with my Zotero workflow, detailed in /blog/zotero-claude-literature-synthesis. I treat the LLM as a Junior Analyst who is eager to please but prone to making things up. I manage it with strict instructions and rigid verification.