A new comparative single-cell multi-omic study of two neurodegenerative disorders, Alzheimer's disease and Pick's disease. A long time in the making and finally published last week!! 🥳

Zechuan Shi@zechuanshi.bsky.social · 11mo ago

🚨 Our new paper is out on Science Advances @science.org! We mapped single-cell regulatory landscapes in Alzheimer’s (AD) and Pick’s disease (PiD) to uncover how distinct enhancer and TF programs shape disease-specific vulnerability. www.science.org/doi/10.1126/... #ScienceAdvances

🗞️ Genetic diversity has a profound impact on genomic annotations, and there is currently a massive European bias in widespread annotations like GRCh38 🤯 This paper is the result of the hard work and passion of @pclavell.bsky.social and @fairlie.bsky.social, congrats to the authors!

Melé Lab@melelab.bsky.social · 2y ago

Do you work in 💫human genetics💫? Have you ever worried about what’s inside your gene annotation GTF⁉️ WELL, YOU SHOULD! 😱 Especially when studying a genetically diverse 🌍 cohort! 🔴We discover that gene annotations are European-biased 👉 impacting downstream analyses! Don't miss this thread🧵⬇️ 1/13

Long-read transcriptomics of a diverse human cohort reveals widespread ancestry bias in gene annotation https://www.biorxiv.org/content/10.1101/2025.03.14.643250v1

I got laid off today, with the rest of 18F. 18F was an elite federal software shop. We made gov't websites work better, more efficiently for the American people. We saved taxpayers from getting screwed over by contractors. And were fired for it. We made this website to tell our story: 18f.org

“Assume that what you write will be read by malign foreign actors and tailor your response accordingly.”

Marisa Kabas@marisakabas.bsky.social · 2y ago

New — HHS just got another email with guidance stating that they aren’t required to respond to the 5 bullets email, but if they do they should follow specific guidelines including: “Assume that what you write will be read by malign foreign actors and tailor your response accordingly.”

As a result of Trump’s slashes to research funding, dozens of graduate programs have announced reductions and cancellations of graduate admissions slots. If you are an impacted applicant, please fill out this survey: docs.google.com/forms/d/e/1F... 🧪🧠🧬🔬🥼👩🏼‍🔬🧑‍🔬

Grad Admission Impacts Survey

It is grad admissions season and many postbacs are feeling the chilling impacts of the Trump administration's recent executive orders freezing and slashing extramural research funding. Dozens of gradu...

docs.google.com

🌟Great News: CNAG is now on BlueSky! 🚀From Barcelona to the world, we’re bringing you the latest in genomics! Stay tuned for breaking news, cutting-edge technologies, groundbreaking research, and upcoming events 🔗https://www.cnag.eu #Genomics #Innovation #Research #BlueSky #CNAG

a blue sky with a butterfly and the word bluesky on it

ALT: a blue sky with a butterfly and the word bluesky on it

media.tenor.com

Pretty sad. Just got the email that CZI is canceling the second round of Diversity Leadership Awards. Private industry will definitely not fill the hole that NIH and NSF are leaving. 😢💔

I was just told that I have to remove “climate” from the title of an ongoing grant if I want to keep it. And publications from that grant cannot include “climate” and other forbidden words. I can’t believe I’m writing this from the United States of America. #AcademicSky

Alessandro Rigolon@alerigolon.bsky.social · 2y ago

Just received an email saying that it's not advisable to include the following words in future applications for research funding to the US DOT. Here we are.

The National Institutes of Health plans to severely cut the percentage of its grant money that can be used for overhead costs rather than research.

NIH slashes overhead payments for research, sparking outrage

Move to cut indirect cost rate to 15% could cost universities billions of dollars

scim.ag

1. Today the NIH director issued a new directive slashing overhead rates to 15%. I want to provide some context on what that means and why it matters. grants.nih.gov/grants/guide...

Inspired by @charlesgaba.com's Herculean effort to post all Wayback URLs from the CDC website (including pages that have recently been deleted), I built this GitHub repo to share Wayback links to all CDC website pages, and will add more websites when I get a chance github.com/Niema-Lab/Go...

GitHub - Niema-Lab/Government-Wayback: Unofficial repository storing links to Wayback Machine for government pages

Unofficial repository storing links to Wayback Machine for government pages - Niema-Lab/Government-Wayback

github.com

Charles Ghoul-ba 🎃 ✡️@charlesgaba.com · 2y ago

Update: Here's the 2nd batch. Again, there's 500 per page, ~7,200 total. This batch includes everything from the "Bring Your Brave" campaign to educate younger women about breast cancer through the clinical overview of Long COVID: acasignups.net/25/02/02/lin...

📢 SUPER EXCITED to share our latest preprint: Decoding the immune response in leptomeningeal disease through single-cell sequencing of cerebrospinal fluid Incredible work and collaboration from @jcnietos.bsky.social @piazeiner.bsky.social @hoheyn.bsky.social and others. biorxiv.org/content/10.110…

All NIH study sections canceled indefinitely. This will halt science and devastate research budgets in universities.

Overjoyed to share that I was selected for the EMBO #postdoc fellowship for my proposal titled "Charting immune cell signatures to tackle non-response to immunotherapy in colorectal cancer". Excited to work on this project over the next few years in #Barcelona! #EMBOFellows

3 reviews on planning, execution, & validation of transcriptomic experiments in neuroscience published in @natureportfolio.bsky.social #NatureNeuroscience. A MUST READ if you're doing transcriptomics. 3 reviews, an amazing editorial, a beautiful cover – this is the issue of the year! (mini thread)

So excited that our work on predicting gene expression from histone modifications using deep learning is out in NAR today. Brilliant to work with lead author @al-murphy.bsky.social and collaborators Aydan Askarova, @borislenhard.bsky.social and Nathan Skene 🧬⭐️🙏 academic.oup.com/nar/advance-...

Predicting gene expression from histone marks using chromatin deep learning models depends on histone mark function, regulatory distance and cellular states

Abstract. To understand the complex relationship between histone mark activity and gene expression, recent advances have used in silico predictions based o

academic.oup.com

A really nice summary on Alzforum of my recent paper where we used #SingleCell and #spatial #omics to investigate molecular and cellular abnormalities in the brains of individuals with Alzheimer's in Down Syndrome (DSAD). www.alzforum.org/news/researc...

Big day for single cell and neuroscience. Trio of single cell perspective pieces discussing applications, opportunities, challenges, and validation of single cell and spatial genomics in neuroscience are out now in Nature Neuroscience. Links in thread below.👇 1/n

A little piece that's been in the works with former MSc, now PhD student, Jiayi Wang & @markrobinsonca.bsky.social in the multi-sample/-condition/-subpopulation theme: ...

bioRxiv Bioinfo@biorxiv-bioinfo.bsky.social · 2y ago

Disentangling cell type and state transcriptional programs https://www.biorxiv.org/content/10.1101/2024.11.29.626057v1

Hi all! I'm a computational biologist studying the impact of variation on the functional genome at @bsc-cns.bsky.social. Consortium alumnus (ENCODE, LRGASP, IGVF @igvfconsortium.bsky.social); @ucirvine.bsky.social PhD; @ucsandiego.bsky.social BS; and recent transplant from California to Barcelona.

Our comparative spatial & single-nuc study of Alzheimer's, Down Syndrome in AD, and a genetic mouse model, just published in Nature Genetics. Massive effort of the 2nd half of my PhD, and a pleasure to work with co-first author Emily, my advisor Vivek, & many others at UC Irvine 🧠 🧬

Spatial and single-nucleus transcriptomic analysis of genetic and sporadic forms of Alzheimer’s disease - Nature Genetics

Spatial and single-nucleus analyses in human postmortem Alzheimer’s disease (AD) brain tissues at early and late stages from individuals with and without Down syndrome, as well as in AD mouse models, ...

nature.com

STAMPing single cell like never before…at a ~0.25c/cell single cell-imaging is the new single cell-sequencing. www.biorxiv.org/content/10.1...

STAMP: Single-Cell Transcriptomics Analysis and Multimodal Profiling through Imaging

We introduce Single-Cell Transcriptomics Analysis and Multimodal Profiling (STAMP), a scalable profiling approach of individual cells. Leveraging transcriptomics and proteomics imaging platforms, STAM...

biorxiv.org

👀 Working on a #StarterPack for early career researchers (PhD students & Postdocs) in #genomics & #bioinformatics 🧬🖥️ Please share! Happy to add those working in this area so please suggest. Seeing a lot of PIs on here but would love to see more students 🎓🚀

Amazing new study led by my labmate Inés Sentís, leveraging #SingleCell 🖥️🧬 technologies to study the effects of #immunotherapy in #pediatric #cancer. Emphasis on #Tcell dynamics throughout treatment and comparing circulating vs. tumor-resident immune cells 🩸💪

Spatio-temporal T cell tracking for personalized TCR-T designs in childhood cancer

Immune checkpoint inhibition (ICI) has revolutionized oncology, offering extended survival and long-term remission in previously incurable cancers. While highly effective in tumors with high mutationa...

biorxiv.org

Has anybody made a starter pack specifically for trainees #phd students & #postdocs in #genomics or #bioinformatics 👀 🖥️ 🧬

"Single-cell atlas of the human immune system reveals sex-specific dynamics of immunosenescence" Interesting pre-print on immune cells dynamics throughout aging, from Marta Mele's group at Bacelona Supercomputing Center. www.biorxiv.org/content/10.1... #singlecell #immunology #aging

Single-cell atlas of the human immune system reveals sex-specific dynamics of immunosenescence

Immunosenescence, the gradual deterioration of the immune system with age, leads to an increased susceptibility to a range of diseases associated with immune dysfunction. Notably, sex is an important ...

biorxiv.org

Hi BlueSky! I am a computational biologist 🖥️🧬 using -omics to study human diseases like cancer & Alzheimer's 🧠 Originally from southern #California, now in #Barcelona as a postdoc in the #singlecell #genomics group at the Centre Nacional d'Anàlisi Genòmica (CNAG). Happy to connect w/ others on here!