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Jake Vogel

@jwvogel.bsky.social

19 Posts241 Follower 165 Folgt

@biofinder.bsky.social · 3mo ago

New paper in Nature Aging led by PhD student Lina Lu! We mapped how APOE ε4 and APOE ε2 shape molecular changes in blood and cerebrospinal fluid across Alzheimer’s disease. www.nature.com/articles/s43...

Proteomic signatures of the APOE ε4 and APOE ε2 genetic variants and Alzheimer’s disease - Nature Aging

Apolipoprotein E (APOE) is the strongest genetic influence in Alzheimer’s disease (AD). Compared to the most frequent allele, ε3, the ε4 allele increases AD risk, and the ε2 allele is protective. Here...

nature.com

@biofinder.bsky.social · 4mo ago

New publication out in Brain! 📢We developed a data-driven multimodal biomarker framework to characterize a memory clinic cohort based on the presence, extent, and sequence of common pathologies. This framework may support diagnosis and trial selection. 🔗https://doi.org/10.1093/brain/awaf411

Jake Vogel @jwvogel.bsky.social · 4mo ago

Incredibly excited that the lab's first papers is now published! We use AI to simultaneously predict multiple neurodegenerative disease diagnoses from plasma proteomics. Congrats @anlijuncn.bsky.social ! #MedSky #neuroskyence #neurosky #alzsky #compneuro #ai #datascience #bioinformatics #neurology

Lijun An@anlijuncn.bsky.social · 4mo ago

Our work is now out in @natmed.nature.com www.nature.com/articles/s41... We developed a state-of-the-art AI-proteomics model for diagnosing multiple neurodegenerative diseases from blood plasma. ProtAIDe-Dx now outperformed both classic machine learning models and even foundation models like TabPFN!

Jake Vogel @jwvogel.bsky.social · 5mo ago

Going to ADPD? Come see our work! We would love to share it with you and chat about it if you are interested. See below for a schedule of our sessions, which cover fMRI, proteomics, transcriptomics and AI, led by brilliant lab members @anlijuncn.bsky.social @jorittmo.bsky.social and others

Toomas Erik Anijärv @teanijarv.bsky.social · 5mo ago

I couldn't find a tool to plot different #neuroimaging data in one consistent style, so I made one! Meet yabplot (yet another brain plot) - a #Python package for (sub)cortex & tracts.🧠 - Simple API - Built-in atlases - Custom atlas support 🔗 github.com/teanijarv/ya... (drop a ⭐️!)

Jake Vogel @jwvogel.bsky.social · 6mo ago

#MedSky #neuroskyence #neurosky #alzsky #compneuro #datascience #neurology

Post nicht verfügbar.

Mark A. Hanson @hansonmark.bsky.social · 9mo ago

We wrote the Strain on scientific publishing to highlight the problems of time & trust. With a fantastic group of co-authors, we present The Drain of Scientific Publishing: a 🧵 1/n Drain: arxiv.org/abs/2511.04820 Strain: direct.mit.edu/qss/article/... Oligopoly: direct.mit.edu/qss/article/...

A table showing profit margins of major publishers. A snippet of text related to this table is below.

1. The four-fold drain
1.1 Money
Currently, academic publishing is dominated by profit-oriented, multinational companies for
whom scientific knowledge is a commodity to be sold back to the academic community who
created it. The dominant four are Elsevier, Springer Nature, Wiley and Taylor & Francis,
which collectively generated over US$7.1 billion in revenue from journal publishing in 2024
alone, and over US$12 billion in profits between 2019 and 2024 (Table 1A). Their profit
margins have always been over 30% in the last five years, and for the largest publisher
(Elsevier) always over 37%.
Against many comparators, across many sectors, scientific publishing is one of the most
consistently profitable industries (Table S1). These financial arrangements make a substantial
difference to science budgets. In 2024, 46% of Elsevier revenues and 53% of Taylor &
Francis revenues were generated in North America, meaning that North American
researchers were charged over US$2.27 billion by just two for-profit publishers. The
Canadian research councils and the US National Science Foundation were allocated US$9.3
billion in that year.

A figure detailing the drain on researcher time.

1. The four-fold drain

1.2 Time
The number of papers published each year is growing faster than the scientific workforce,
with the number of papers per researcher almost doubling between 1996 and 2022 (Figure
1A). This reflects the fact that publishers’ commercial desire to publish (sell) more material
has aligned well with the competitive prestige culture in which publications help secure jobs,
grants, promotions, and awards. To the extent that this growth is driven by a pressure for
profit, rather than scholarly imperatives, it distorts the way researchers spend their time.
The publishing system depends on unpaid reviewer labour, estimated to be over 130 million
unpaid hours annually in 2020 alone (9). Researchers have complained about the demands of
peer-review for decades, but the scale of the problem is now worse, with editors reporting
widespread difficulties recruiting reviewers. The growth in publications involves not only the
authors’ time, but that of academic editors and reviewers who are dealing with so many
review demands.
Even more seriously, the imperative to produce ever more articles reshapes the nature of
scientific inquiry. Evidence across multiple fields shows that more papers result in
‘ossification’, not new ideas (10). It may seem paradoxical that more papers can slow
progress until one considers how it affects researchers’ time. While rewards remain tied to
volume, prestige, and impact of publications, researchers will be nudged away from riskier,
local, interdisciplinary, and long-term work. The result is a treadmill of constant activity with
limited progress whereas core scholarly practices – such as reading, reflecting and engaging
with others’ contributions – is de-prioritized. What looks like productivity often masks
intellectual exhaustion built on a demoralizing, narrowing scientific vision.

A table of profit margins across industries. The section of text related to this table is below:

1. The four-fold drain
1.1 Money
Currently, academic publishing is dominated by profit-oriented, multinational companies for
whom scientific knowledge is a commodity to be sold back to the academic community who
created it. The dominant four are Elsevier, Springer Nature, Wiley and Taylor & Francis,
which collectively generated over US$7.1 billion in revenue from journal publishing in 2024
alone, and over US$12 billion in profits between 2019 and 2024 (Table 1A). Their profit
margins have always been over 30% in the last five years, and for the largest publisher
(Elsevier) always over 37%.
Against many comparators, across many sectors, scientific publishing is one of the most
consistently profitable industries (Table S1). These financial arrangements make a substantial
difference to science budgets. In 2024, 46% of Elsevier revenues and 53% of Taylor &
Francis revenues were generated in North America, meaning that North American
researchers were charged over US$2.27 billion by just two for-profit publishers. The
Canadian research councils and the US National Science Foundation were allocated US$9.3
billion in that year.

The costs of inaction are plain: wasted public funds, lost researcher time, compromised
scientific integrity and eroded public trust. Today, the system rewards commercial publishers
first, and science second. Without bold action from the funders we risk continuing to pour
resources into a system that prioritizes profit over the advancement of scientific knowledge.

Anders Eklund @wandedob.bsky.social · 10mo ago

@biofinder.bsky.social · 11mo ago

🚨New paper alert! Our study led by @teanijarv.bsky.social investigated why some individuals with Alzheimer’s disease (AD) develop hemispheric asymmetry in tau pathology and what drives this phenomenon. Out now in Nature Communications! 🔗Full article: doi.org/10.1038/s414... A thread🧵👇

Hemispheric asymmetry of tau pathology is related to asymmetric amyloid deposition in Alzheimer’s Disease - Nature Communications

Asymmetrical distribution of tau pathology in Alzheimer’s disease is linked to asymmetrical amyloid-beta deposition, not reduced brain connectivity, suggesting regional vulnerability plays a key role ...

doi.org

Jake Vogel @jwvogel.bsky.social · 10mo ago

Really compelling evidence in humans for network propagation hypothesis of tau spread: individualized connectivity helps resolve individualized tau patterns. #MedSky #neuroskyence #neurosky #alzsky #compneuro #ai #datascience #bioinformatics #neurology

harry h behjat@aitchbi.bsky.social · 10mo ago

does brain connectivity drive spread of pathological proteins in Alzheimer’s disease? ✨ preprint: www.biorxiv.org/content/10.1... if the question intrigues you, please read on 🧵⤵️

Adrian Liston @labliston.bsky.social · 11mo ago

🧵How to write and manage your first research budgets The point of funding is to convert it into quality research. A well-spent research budget should fund the idea it was raised on, plus revision experiments, plus preliminary data for the next grant. So you need to spend, while avoiding waste.

Colleen Steckel @colleensteckel.bsky.social · last yr.

We need higher resolution brain scans for people with #MyalgicEncephalomyelitis. This is an exciting development that could lead to better clinical understanding for many of us. #Neuroskyence #medsky

Jake Vogel@jwvogel.bsky.social · last yr.

‼️NEW PREPRINT‼️ What if you could take a normal 3T T1w MRI and make it look like it was acquired from a 7T scanner? That's exactly what we do using AI in our new preprint! Link: arxiv.org/abs/2507.13782 #neuroskyence #neurosky #compneuro #AI #datascience #neurology #mrisky #neuroimaging

David H Friedel Jr @davidhfriedeljr.bsky.social · last yr.

If clinically validated, it could democratize access to advanced imaging, improve neuro-diagnostic precision, and streamline both research and patient care without requiring costly hardware upgrades. A win for everyone

Jake Vogel@jwvogel.bsky.social · last yr.

Jake Vogel @jwvogel.bsky.social · last yr.

Incredibly excited for this new work from our lab. We test the potential of AI-based neurodegenerative disease diagnostics using plasma proteomics data from n>17,000 people, led by the brilliant and indefatigable @anlijuncn.bsky.social Check it out!👇

Lijun An@anlijuncn.bsky.social · last yr.

Can AI reveal risk & co-pathology of multiple neurodegenerative diseases from a single blood sample? We explored AI-based diagnostic power on high rank plasma proteomics (N=17,170). www.medrxiv.org/content/10.1... #neuroskyence #neurosky #Alzheimer #compneuro #AI #datascience #neurology

Alex Fornito @alexfornito.bsky.social · last yr.

Have recent changes led to uncertainty in your future scientific career? Wonder it's like in Australia? Good news! Monash's is seeking to hire talented EMCRs from other countries. Come join a wonderful community of brain mappers & modellers! www.monash.edu/research/eme...

EMERGE

monash.edu

Jake Vogel @jwvogel.bsky.social · last yr.

‼️Preprint alert‼️ Star PhD student @jorittmo.bsky.social uses functional gradients as a framework to study longitudinal brain functional reorganization in aging and AD. Check out the thread 👇🏼 #MedSky #neuroskyence #neurosky #alzsky #compneuro #MRI #neuroimaging #neurology

Jonathan Rittmo@jorittmo.bsky.social · last yr.

How does the brain reorganize in the context of age and AD? Are functional changes in age and AD similar? Are these changes dynamic across the age/AD spectrum? We unpack these questions in a sample of N=973 with AD biomarkers Preprint: tinyurl.com/ymv8s7h8 ⬇️🧵 1/

Benjamin Kay @benjaminkay.bsky.social · last yr.

My med school textbook says stimulants like Ritalin treat hyperactivity by “stimulating” the brain’s attention and cognitive control systems. We studied children taking stimulants in the ABCD Study, and the largest differences were actually in arousal and reward networks! Check out our preprint!

Étienne Vachon-Presseau @evp82.bsky.social · last yr.

Our new @NatureComms paper: We used UK Biobank data (n≈193K) to build ML models predicting tinnitus presence (driven by hearing health) and severity (influenced by mood, neuroticism & sleep). A simple 6-item POST questionnaire forecasts 9-yr outcomes. shorturl.at/4AF4P

Tinnitus risk factors and its evolution over time - Nature Communications

Improving tinnitus prevention and clinical management by identifying key associated risk factors is crucial. Here, the authors use machine learning in a large cohort to identify key predictors of tinn...

shorturl.at

Linden Parkes @lindenmp.bsky.social · last yr.

Excited to share the first major piece of work and preprint from my lab! Led by Jason Kim! 🥳🎉🤘 www.biorxiv.org/content/10.1...

a man applauds with the words so proud of my team above him

ALT: a man applauds with the words so proud of my team above him

media.tenor.com

@biofinder.bsky.social · last yr.

‼️New preprint! We are happy to share our latest work led by @teanijarv.bsky.social investigating why tau pathology in AD often accumulates more in one hemisphere of the brain than the other. Check out 🔗https://biorxiv.org/content/10.1101/2025.04.15.648728v1 or dive into the details below👇

@biofinder.bsky.social · last yr.

🧠Exciting new findings from a great collaboration between the BioFINDER study and the talented @xiaoyucaly.bsky.social from @jwvogel.bsky.social group!! In their preprint, they show that tau presence and tau load are guided by unique brain mechanisms. Dive into the details here 👇

Yu Xiao (肖燏)@xiaoyucaly.bsky.social · last yr.

🧠New preprint! What drives tau, the pathological protein in AD, to spread? We found that WHERE tau appears and HOW MUCH accumulates are governed by different mechanisms. Check it out: www.biorxiv.org/content/10.1...  #MedSky #neuroskyence #neurosky #alzsky #compneuro #MRI #neuroimaging #neurology

Jake Vogel @jwvogel.bsky.social · last yr.

I am so very proud announce my lab's first preprint!! @xiaoyucaly.bsky.social delves into the mechanisms driving tau distribution: * Tau sequence driven by connectivity dynamics * Tau load driven by local factors Check out her thread below

Yu Xiao (肖燏)@xiaoyucaly.bsky.social · last yr.