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Holubar Lab

Research Toolkit

Journal Acceptance·Literature RAG·Surgical Outcomes

Tools

Lab tools require a one-time email sign-in. Browse freely here; opening any tool prompts a one-time code sent to your Cleveland Clinic (@ccf.org) email. Use the Sign in button at the top to authenticate first.

Featured · LIVE
CORS RAG — CCF Colorectal Literature Search
Retrieval-augmented search across 866 CCF colorectal-surgery papers from 28 staff surgeons (2020–2025). Hybrid keyword + semantic retrieval with PMID-grounded citations. The lab's first-stop tool for prior-art screening, pre-submission lit review, and faculty productivity reporting.
Search Type a question or phrase → ranked CORS papers with abstract excerpts, PMIDs, and authors. Fast keyword + BGE semantic hybrid.
Ask Ask a synthesis question → Sonnet-grade answer grounded in the CORS corpus with PMID-badged citations back to source papers.
Open CORS RAG CCF email sign-in — @ccf.org only.
Featured · v1 beta
Pre-submission Check
Upload a manuscript draft and receive a pre-submission review by the Holubar Lab custom Odin retrieval system, reviewed and approved by Stefan Holubar, MD before release. Three deliverables per submission: aggressive critical review in SDH's voice, P(accept) speedometers ranked across 32 candidate journals, and the top 10 topically-similar papers among all PubMed journals — first author, year, journal, impact factor.
Stage 1 · Upload Drop your .docx. Title + abstract extracted in your browser — file never stored on the server.
Stage 2 · Critical Review (live) Opus 4.8 streams a SDH-voiced PI critique in real time. ~30–90 seconds end-to-end.
Stage 3 · Top 10 across PubMed Live PubMed search returns the 10 most topically-similar recent papers — first author, year, journal.
Submit a manuscript CCF email sign-in (one-time code). Download the whole report as .docx when done.

IRB & Research SOP · 4 tools

CORS Research SOP
Standard operating procedures for research in the CORS group — data access, IRB pathway, manuscript pipeline, authorship norms.
CCF IRB Templates
Cleveland Clinic IRB Office templates & guidance — protocol template, consent forms, FAQ, registry-data guide.
Research Methods & Epidemiology
19 methods PDFs — propensity scores, cluster RCTs, registry trials, EHR re-use, statistical methods. Browse or upload new references.
R Cheatsheets
12 RStudio one-page reference cards — tidyverse, lubridate, purrr, shiny, plumber. Useful for legacy code; lab default for new work is Python.
Python Biostats Cheatsheet · lab default
Python is the lab default over R for new analyses — LLM-assisted vibe-coding works dramatically better. Pandas / statsmodels / lifelines / pingouin / tableone with SDH idioms baked in.
Vibe Coding Primer
A working definition + the lab's 5-step loop for letting LLMs write your analysis code while keeping your fingerprints on every result. Pitfalls + do/don't.

Journals & Submissions · author guidelines · reference managers

Journal Cheat Sheet
Quick reference for the lab's target journals — scope, impact factor, acceptance bands, submission tips.
Authors Guidelines
34 journal author-instruction PDFs — word limits, structure, abstract format, figure specs for the journals the lab targets.
Which Reference Manager?
Side-by-side comparison — Zotero vs. Mendeley vs. EndNote — for fellows choosing a citation tool. Lab default is Zotero.
 Resource list ↗
awesome-zotero
Lab Zotero workflow: per-project profiles (one Zotero library per manuscript, scaffolded via the zot command on Studio — see .claude/rules/zotero-profiles.md). Replaces the retired ZotPilot semantic-search RAG; native Zotero search handles the smaller per-project libraries. This card links to the curated GitHub list of Zotero plugins (Better BibTeX, citation-key automation, AI integrations) for fellows building their own profile.

Pipelines · reusable analysis scaffolding

CEA Pipeline
Cost-effectiveness analysis scaffolding — Markov, decision tree, Drummond 2015 + CHEERS 2022. 3 active pilots.
IPAA QoL Pipeline
Reusable QoL analysis pipeline for IPAA outcome studies — Cleveland Pouch Survey → CGQLI scoring → AMA-styled tables + waterfall/CONSORT figures.

Posters & Art

Fellow Poster Archive
Upload a poster from a prior conference (DDW, ASCRS, ACG, etc.). Saved to the lab archive with consistent naming.
CCF Illustrations
98 ©Cleveland Clinic surgical illustrations in 17 categories — IPAA, stomas, hernias, anastomosis, anatomy. Browse by subfolder.

External sites · third-party tools we like

Sister site ↗
Pouchology.org
Provider-facing IPAA literature RAG with full-text, scoring, and decision-tier filtering. Opens in a new tab.
 AI tool ↗
Elicit.com
AI research assistant for evidence synthesis across PubMed + Semantic Scholar. Strong for SR screening, abstract triage, and data-extraction across hundreds of papers at once.
 AI tool ↗
OpenEvidence
Clinical-evidence search engine with AI-generated summaries grounded in peer-reviewed sources. Free for verified clinicians.
 AI tool ↗
Consensus.app
AI search across 200M+ scientific papers. Surfaces yes/no/possibly consensus across studies for a given claim.

About the Lab

Stefan D. Holubar, MD, MS, FACS, FASCRS

The Holubar Lab is the research arm of Stefan D. Holubar, MD, MS, FACS, FASCRS — Professor of Surgery at Cleveland Clinic and Director of Research, Department of Colon & Rectal Surgery. The lab focuses on IBD surgery, ileal pouch outcomes, surgical quality improvement, and clinical AI tools.

This site is the lab's research toolkit — hosted versions of the analysis and decision-support tools we build in-house: journal-acceptance recommendation, literature RAG search across our curated corpora, and cost-effectiveness analysis scaffolding. Fellows, collaborators, and select colleagues are welcome to use them.

For broader context: holubarconsulting.com (full bio + consulting), iPouch Consortium, Pouchology.org, Pouchy.org, and NSQIP IBD Collaborative.

300+ peer-reviewed publications
225+ IBD-focused articles
4 patient/provider RAG platforms
ACS NSQIP IBD Collaborative
ASCRS IBD Committee

Get in Touch

For toolkit access, manuscript submissions, fellow inquiries, or research collaboration — reach out directly. We respond personally.