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Benjamin Neely on Muck Rack

Benjamin Neely

Charleston
As seen in: The Proteomics Show, Nature, heart, MDPI, ACS Publications, BioRxiv
Analytical biochemist attempting molecular cartography across the tree of life, powered by MS-based proteomics. Opinions expressed are solely my own. he/him
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Articles

Agentic AI-Assisted Coding Offers a Unique Opportunity to Instill Epistemic Grounding during Software Development Click to copy article link Article link copied!

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By Magnus Palmblad, Jared Ragland, Benjamin Neely
| ACS Publications
Introduction Click to copy section linkSection link copied! Since Open AI’s ChatGPT LLM was publicly released in November 2022, frontier models (Claude, Gemini, Llama, Nemotron) have accelerated a paradigm shift: scientists now routinely use agent scaffolds (e.g., Claude Code, Codex, Copilot, Cursor, Windsurf, etc .) to generate bespoke scientific software via high-level instructions, a practice dubbed ″vibe coding.″ For proteomics scientists specifically, this means one-off bespoke software...
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Serum proteome of the Egyptian rousette bat ( Rousettus aegyptiacus ) reveals signatures of immunity, proteostasis, and metabolism

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By Brooke N. Genovese, Nistara Randhawa, Benjamin Neely, Gabriela Grigorean, Amy J. Schuh, Brian R Amman, Jessica A. Elbert, Simon J. Anthony, Jonna Mazet, Jonathan S. Towner, Brian Bird
| Nature Verified
Abstract Bats are increasingly studied for their ability to coexist with diverse viruses of human health importance. While this focus has yielded insights into host–pathogen dynamics, baseline physiological data from healthy bats remain limited, constraining comparative and mechanistic understanding. Serum proteomics offers a direct window into circulating proteins that underpin immune regulation, cellular maintenance, and metabolism.
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Quality Control in the Mass Spectrometry Proteomics Core: A Practical Primer

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By Benjamin Neely, Yasset Perez-Riverol, Magnus Palmblad
The past decade has seen widespread advances in quality control (QC) materials and software tools focused specifically on mass spectrometry–based proteomics, yet the rate of adoption is inconsistent. Despite the fundamental importance of QC, it typically falls behind learning new techniques, instruments, or software.
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