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Sam Morabito

@sam-morabito.bsky.social

250 followers 300 following 22 posts

🌴 Californian scientist in #Barcelona ☀️ 🧬 EMBO postdoc @ cnag.eu 🧠 Systems Bio PhD from UC Irvine #singlecell • #immunology • #cancer • #neuro • #bioinformatics • #genomics https://smorabit.github.io/

smorabit.github.io

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Sam Morabito @sam-morabito.bsky.social · Nov 25

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, ...

www.nature.com

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Sam Morabito @sam-morabito.bsky.social · May 9

Reminds me of this tool TooManyCells

www.nature.com/articles/s41...

TooManyCells identifies and visualizes relationships of single-cell clades - Nature Methods

The TooManyCells approach to scRNA-seq data facilitates efficient and unbiased identification and visualization of cell clades and rare subpopulations. Application of TooManyCells to drug-resistant le...

www.nature.com

Sam Morabito @sam-morabito.bsky.social · Mar 20

🗞️ 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 · Mar 20

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🧵⬇️
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Long-read transcriptomics of a diverse human cohort reveals widespread ancestry bias in gene annotation

Accurate gene annotations are fundamental for interpreting genetic variation, cellular function, and disease mechanisms. However, current human gene annotations are largely derived from transcriptomic...

www.biorxiv.org

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Reposted by Sam Morabito

bioRxiv Genomics @biorxiv-genomic.bsky.social · Mar 17

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

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Reposted by Sam Morabito

John Skiles Skinner @skiles.blue · Mar 1

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

We're not done yet | 18F

18f.org

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Reposted by Sam Morabito

Chenxin Li, PhD @chenxinli2.bsky.social · Feb 25

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

Marisa Kabas @marisakabas.bsky.social · Feb 24

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.”

Subject: Proposed Response to HHS Employees

HHS Employees -

On Saturday, you received an email from OPM entitled "What did you do last week." The directive stated employees were to submit five bullets detailing their accomplishments in the past week.
In discussions with OPM Officials yesterday and today OPM has now rescinded that mandatory requirement.

There is no HHS expectation that HHS employees respond to OPM and there is no impact to your employment with the agency if you choose not to respond.

That said, if you choose to respond, here are the guidelines you should follow:
Respond to the email by the deadline established (today @ 11:59 P.M.).
Keep your response at a high level of generality and describe your work in a manner to protect sensitive data, personally identifiable information, and applicable privileges to the extent possible. Do not (1) identify, by name or title, any other HHS employees with whom you have been working; (2) identify, by case name or otherwise, matters you are working on, or (3) identify any specific grants or contracts, or any specific grantees or contractors.
If you are engaged in scientific research or reviews, do not identify by name any drugs, devices, biologics, therapeutics, or similar items in your response. If you are engaged in any scientific experiments, research, or reviews, do not provide Information that could allow anyone to identify the precise nature of your work.
Respond by replying to the OPM HR email as instructed, with a cc: to your supervisor.
Assume that what you write will be read by malign foreign actors and tailor your response accordingly.

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Reposted by Sam Morabito

Rosa Lafer-Sousa @rosalafersousa.bsky.social · Feb 24

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

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Reposted by Sam Morabito

CNAG @cnag-eu.bsky.social · Feb 19

🌟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

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Reposted by Sam Morabito

Crystal Rogers, PhD @rogerslabucd.bsky.social · Feb 19

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. 😢💔

Thank you for submitting your Letter of Intent (LOI) to CZI. We appreciate your interest in our work.

CZI has decided not to continue with the second round of its Science Diversity Leadership Awards. We are committed to supporting groundbreaking research that advances the frontiers of scientific knowledge in pursuit of our mission to cure, prevent, or manage all diseases by the end of the century. We will provide information on future funding opportunities.

We look forward to staying in touch.

Bil Clemons, Program Officer, CZI

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Reposted by Sam Morabito

Alessandro Rigolon @alerigolon.bsky.social · Feb 10

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 · Feb 6

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.

1. Climate change
2. Greenhouse gas emissions
3. Emissions
4. Racial equity
5. Gender identity
6. Diversity, equity and inclusion
7. Environmental justice
8. Justice40 initiative

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Reposted by Sam Morabito

Science Magazine @science.org · Feb 8

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

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Reposted by Sam Morabito

Carl T. Bergstrom @carlbergstrom.com · Feb 8

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...

NOT-OD-25-068: Supplemental Guidance to the 2024 NIH Grants Policy Statement: Indirect Cost Rates

NIH Funding Opportunities and Notices in the NIH Guide for Grants and Contracts: Supplemental Guidance to the 2024 NIH Grants Policy Statement: Indirect Cost Rates NOT-OD-25-068. OD

grants.nih.gov

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Sam Morabito @sam-morabito.bsky.social · Feb 6

This seems like an interesting tool to empower biomedical research 💪

However, it does not seem like this manuscript has a Methods section, or information about the peer review, even though the paper discusses "transparency standards required for reproducible research". Am I missing something?

Reposted by Sam Morabito

Niema Moshiri @niema.net · Feb 4

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...

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Reposted by Sam Morabito

Paula Nieto @paulanietog.bsky.social · Jan 29

📢 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…

https://biorxiv.org/content/10.110…

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Sam Morabito @sam-morabito.bsky.social · Jan 23

Added 😊

Reposted by Sam Morabito

Jane Liebschutz, MD MPH (she/her) @liebschutz.bsky.social · Jan 22

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

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Sam Morabito @sam-morabito.bsky.social · Dec 12

Very grateful 🙏 for all who helped throughout the process, my current advisor Holger Heyn, my PhD advisor Vivek Swarup, all of my labmates in the #SingleCell #Genomics team at CNAG.

Sam Morabito @sam-morabito.bsky.social · Dec 12

This year I wrote 5 applications for postdoc fellowships, most of which were rejected ☠️ so this feels like an early xmas present and some much needed encouragement to hit the ground running 🏃‍♂️ in 2025 💪

Sam Morabito @sam-morabito.bsky.social · Dec 12

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

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Reposted by Sam Morabito

Shane Liddelow @liddelowsa.bsky.social · Dec 11

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)

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Reposted by Sam Morabito

Sarah Marzi @sj-marzi.bsky.social · Dec 11

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

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Sam Morabito @sam-morabito.bsky.social · Dec 11

Link to the full paper:

www.nature.com/articles/s41...

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

www.nature.com

Sam Morabito @sam-morabito.bsky.social · Dec 11

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...

In Alzheimer’s Due to Down’s, Spatial Omics Spots Signs of Trouble | ALZFORUM

www.alzforum.org

Reposted by Sam Morabito

Samuel Marsh Ph.D. @samuelmarsh.bsky.social · Dec 3

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

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Reposted by Sam Morabito

Helena Lucia Crowell @helucro.bsky.social · Dec 4

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 · Dec 4

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

Single-cell omics approaches profile molecular constituents of individual cells. Replicated multi-co

www.biorxiv.org

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