Jake Vogel (@_JakeVogel_) header
Jake Vogel (@_JakeVogel_) profile picture

Neuroimaging guy, Philadelphia sports fan, beer, open science.

Philadelphia, PA
Joined February 2019
Excited to share our new work now out in Nature Neuroscience!! We use a whole-brain framework to show that aging and Alzhiemer's disease affect the brain's functional organization along completely separate axes. Paper and thread below 👇
The first paper from my PhD is out in @NatureNeuro! Aging and Alzheimer's disease both reshape how the brain communicates. But not in the same way: aging vs AD related alterations follow two distinct axes of brain organization Paper → nature.com/articles/s41593-0… 🧵⬇️
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Jake Vogel retweeted
✨ 🔇 My lab has an opening for a full-time Research Assistant to support research projects focused on brain #aging & #AlzheimersDisease across the lifespan. If interested, pls email me a CV and a list of three references. Pls share! 🙏 @OhLabBrown @BrownPsychiatry @BrownCoPsy
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‼️ Preprint alert ‼️ How do we get more out of single-cell RNA findings besides just .. gene lists. 🤔 We built a reproducible model of the brain's multicellular response to AD—a potential reference for testing perturbations and treatments. doi.org/10.64898/2026.10.19.… A 🧵 1/16
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Two major axes emerged: a broad pattern linked to AD pathology, and a more focused pattern linked to sex. A compact summary of a very complicated cellular landscape! Most importantly: both axes reproduced very cleanly in the SEA-AD dataset!
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In the preprint, we delve into the biology underlying this signature. Big shout out to PhD student Gabi Vilkaite for leading this work, to our co-authors @anlijuncn @xiaoyucaly @ines_hristovska @consiglio_cr @NiklasMattsson4 and other non tweeps, and to ROSMAP and SEA-AD!
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Very happy to be involved in this super cool study, which examines mediators of inflammation on neurodegeneration and strattles both human and cell/animal model AD data!
Finally able to share my PhD work! I can’t thank my mentors and co-authors enough. Out now in #PNAS! 🧬 We uncover a mechanism by which SYK-mediated mTORC1 activation modulates microglial metabolism, responses to amyloid-β, and ultimately, cell survival. pnas.org/doi/10.1073/pnas.26…
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🚨 New preprint! 🧵 Brain regions 🧠 integrate information over different timescales ⏱️: short in sensorimotor cortex, long in association cortex. But do regions change their timescales when we engage in a task? And how does that flexibility develop? 👇 biorxiv.org/content/10.64898…
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Excited that this paper, "Highly replicable multisite patterns of adolescent white matter maturation", has now been published in Neuron! It may be found at cell.com/neuron/fulltext/S08…. To freely access the paper for the next 50 days, please use this link: authors.elsevier.com/c/1nxdd…
Diffusion MRI (dMRI) is a powerful tool to study white matter maturation. In our new preprint, we process and distribute a new resource of >24,000 ABCD dMRI scans using open source tools! We then evaluate how methods shape inferences about development. 🔗 bit.ly/3QMLG0K
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Interested in functional neuroimaging and looking for a PhD in a collaborative environment? We have a new position at LCBC on a projhect using longutidinal fMRI to track memory changes in development and aging. @LCBC_UiO jobbnorge.no/en/available-jo…
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Jake Vogel retweeted
The first paper from my PhD is out in @NatureNeuro! Aging and Alzheimer's disease both reshape how the brain communicates. But not in the same way: aging vs AD related alterations follow two distinct axes of brain organization Paper → nature.com/articles/s41593-0… 🧵⬇️
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Spatial organization of AQP4 water channel expression in the human brain | doi.org/10.1126/sciadv.aeg81… Aquaporins are a key component of the glymphatic system. How are they distributed + how do they relate to brain function and dysfunction? @ScienceAdvances ⤵️
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MIT published a brutally honest report on what AI is doing to students. A committee of professors and students spent five months studying how AI changed learning on campus, and the findings read like a warning to every university on the planet. Study groups are disappearing. Office hours are emptying out. Problem sets and take-home exams no longer prove anything, because AI can produce credible solutions to almost any written assignment in the undergraduate curriculum. Students who lean on chatbots lose mastery and confidence, and some slip into what the report calls cognitive surrender, reaching for AI at the first hint of struggle. The numbers are rough. 46 percent of surveyed MIT undergrads use LLMs daily. 90 percent worry about their own overreliance. Undergrads who feel AI makes them replaceable now outnumber those who feel it makes them capable. The committee's answer surprised me. They refused to fight AI with surveillance. The report calls AI detectors unreliable, says lockdown browsers feel like spying, and warns that policing students builds a classroom atmosphere of mutual distrust. Instead, MIT wants to rebuild education around the things AI can't replace. That means oral exams, semester portfolios, in-person project work, and a required social component in every subject. The report even floats the idea of rethinking grades entirely, since without a GPA to optimize, much of the incentive to cheat with AI evaporates. The committee warns professors against replacing undergrad research assistants with AI agents just because they're cheaper, because a university exists to grow people, not output. The most famous tech school on earth admitted the machines broke its way of teaching. Its answer is more humans, not more software.
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We’ve seen a lot of data leakage in proteomics studies—and it matters. Even simple mistakes can produce AUCs >0.7 from pure noise, while making models generalize worse. We built tools to help researchers avoid this. Please share so we can start reporting trustworthy models! <3
🧵 Struggling to replicate a proteomics biomarker study? Our new preprint quantifies one common cause: data leakage. With NO true signal, some runs with data leakage still reached AUCs near 0.8. w/ @_JakeVogel_, Caitlin Finney, Artur Shvetcov & @_neuroproteome
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I’m on the faculty market this fall! NIH K99/R00 awardee using birdsong to study how brains learn complex skills across molecules, synapses, circuits, behavior & computation. Know a faculty search where I might fit? Send it my way + share! drewschreiner.github.io/ #neuroscience
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Jake Vogel retweeted
Combining data to study lifespan brain aging is tempting: more data and wider age range! But mixing data across scanners/protocols without proper harmonization can bias age effects, including studies using high-quality HCP data. Imaging Neuroscience 🔔doi.org/10.1162/IMAG.a.1338
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🎉Congrats to PhD student Amaryllis Tsiknia on her new paper in Brain! 🧠We evaluated longitudinal cortical thinning in older adults from HABS-HD with and without type 2 diabetes. Check out a summary of our findings below ⬇️ 💻Read our paper here: bit.ly/46nPiLc
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Check out awesome new work from the lab, led by @ahmadbeyh!!! 👏🤘
⚠️ Preprint alert ⚠️ How does the brain's fixed anatomy support flexible function? We explore this using recurrent neural networks with increasing levels of brain-like constraints, comparing them to empirical fMRI activity. (1/8) biorxiv.org/content/10.64898…
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🚨 Only a few days left to apply! Don’t miss this opportunity!
‼️ DEADLINE EXTENDED ‼️ Good news! One more month to apply! If you’re a student or postdoc looking to connect with fellow trainees and get involved in the OHBM community, we’d love to hear from you. 👉 Apply here: forms.gle/nTem5UmsvbcfKU5J6 ⏰ Applications close: 29 August 2026
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