Luay Almassalha
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almassalha.bsky.social
Luay Almassalha
@almassalha.bsky.social
84 followers 100 following 180 posts
Physician-Scientist studying and applying the rules of the physical genome in development, aging, cancer, and inflammation
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almassalha.bsky.social
Pretty neat paper:
www.biorxiv.org/content/10.1...
www.biorxiv.org
November 14, 2025 at 1:37 PM
Reposted by Luay Almassalha
physgencenter.bsky.social
Friday, Nov. 21 @ 12pm CT, Wendy Bickmore, PhD presents the Monthly Seminar on Physical Genomics live on Zoom: "Chromatin Folding And Gene Activation: From The Nucleosome To Transcription Hubs"

Registration is free. Join us!

tinyurl.com/f9njvnyu

#chromatin #genomics #northwestern #biology #dna
November 11, 2025 at 6:55 PM
Reposted by Luay Almassalha
hansonmark.bsky.social
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.
November 11, 2025 at 11:52 AM
almassalha.bsky.social
umm... was there an update to ChatGPT that turned it belligerent?
a man wearing a hat and glasses has the word rude on his chest
ALT: a man wearing a hat and glasses has the word rude on his chest
media.tenor.com
November 4, 2025 at 4:58 PM
Reposted by Luay Almassalha
kordinglab.bsky.social
A reminder:
kordinglab.bsky.social Konrad Kording @kordinglab.bsky.social · Nov 11
NSF makes you say who you got conflicts (coauthored) with. We (really just Jordan Matelsky) just built you a tool for that. Literally one click: bib.experiments.kordinglab.com/nsf-coa
NSF COA | Jordan Matelsky
bib.experiments.kordinglab.com
November 4, 2025 at 12:07 PM
Reposted by Luay Almassalha
kordinglab.bsky.social
Still beta-testing the app that helps people plan science, make it super clear, design their todos, and write a first version of the paper. Feeling overwhelmed by the countless aspects of doing science? Try this (for free): planyourscience.com
Scientific Paper Planner - AI-Powered Research Planning
Structure your scientific research with AI-powered guidance. From hypothesis to methodology, plan your research paper with intelligent mentoring.
planyourscience.com
October 29, 2025 at 10:06 PM
Reposted by Luay Almassalha
physgencenter.bsky.social
New CPGE research in Advanced Science describes a language hidden in the genome, beyond the DNA sequence. The geometric code may help cells “remember” how to create and preserve memories, functioning like a network of living computers.

#chromatin #dna

www.mccormick.northwestern.edu/news/article...
From Sequence to Shape: Scientists Discover the Possible Geometric Blueprint of Complex Life
New research from Professors Vadim Backman and Igal Szleifer reveals the language that stores cell memory -- written in the shape of the genome itself.
www.mccormick.northwestern.edu
October 29, 2025 at 6:15 PM
almassalha.bsky.social
Geometrically Encoded Positioning of Introns, Intergenic Segments, and Exons in the Human Genome - Almassalha - Advanced Science - Wiley Online Library advanced.onlinelibrary.wiley.com/doi/10.1002/...
Geometrically Encoded Positioning of Introns, Intergenic Segments, and Exons in the Human Genome
This study introduces a new hypothesis: exons, introns, and intergenic segments are non-random projections of the functional layers of 3D structure of chromatin packing domains. Evidence is presented...
advanced.onlinelibrary.wiley.com
October 27, 2025 at 9:19 PM
almassalha.bsky.social
Generative AI sometimes acts as a moving mirror - it reflects my thoughts back to me from different angles to flesh out a picture I've stared at for a long time
October 27, 2025 at 1:07 PM
Reposted by Luay Almassalha
irate-physicist.bsky.social
Excited to share our paper on dynamics of microcompartments during M-to-G1 is now published in @natsmb.nature.com www.nature.com/articles/s41...

Compared to biorxiv, published includes new analysis from James Jusuf and Viraat Goel (from @andersshansen.bsky.social lab) on transcriptional spiking
October 17, 2025 at 2:58 PM
Reposted by Luay Almassalha
neongrey.bsky.social
all discourse aside, there is one machine with consciousness. it's printers. they are alive and conscious and they hate you and they'd take your arm clean off if you let them. never trust a printer.
October 6, 2025 at 7:36 PM
Reposted by Luay Almassalha
greally.bsky.social
What an amazing assay.

DAF-seq, the evolution of Fiber-seq from the Andrew Stergachis group, using the @pacbio.bsky.social platform:
www.biorxiv.org/content/10.1...

This will revolutionise our understanding of transcriptional regulation and functional non-coding variants.
Deaminase-assisted single-molecule and single-cell chromatin fiber sequencing
Gene regulation is mediated by the co-occupancy of numerous proteins along individual chromatin fibers. However, our tools for deeply profiling how proteins co-occupy individual fibers, especially at ...
www.biorxiv.org
October 4, 2025 at 12:06 PM
almassalha.bsky.social
Christopher Nolan movies live rent free in my head
October 2, 2025 at 2:28 PM
almassalha.bsky.social
Everytime the chart says Billroth all I think about is LoTR
a demon with horns is surrounded by a group of people in a dark room .
ALT: a demon with horns is surrounded by a group of people in a dark room .
media.tenor.com
September 28, 2025 at 2:52 AM
Reposted by Luay Almassalha
jobdekker.bsky.social
New work from my lab with the Brown lab on how genome folding changes during motor neuron maturation, and how this process goes awry in ALS motor neurons. Led by Dr. Ozgun Uyan.
www.biorxiv.org/content/10.1...
Dynamic changes in chromosome and nuclear architecture during maturation of normal and ALS C9orf72 motor neurons
We have investigated changes in chromosome conformation, nuclear organization, and transcription during differentiation and maturation of control and mutant motor neurons harboring hexanucleotide expa...
www.biorxiv.org
September 23, 2025 at 9:13 PM
almassalha.bsky.social
I don't really encounter transposable elements (or Arabidopsis) in my clinical day-to-day, but this is awesome: www.science.org/doi/10.1126/...
Transposable elements are vectors of recurrent transgenerational epigenetic inheritance
DNA methylation loss at transposable elements (TEs) can affect neighboring genes and be epigenetically inherited in plants, yet the determinants and significance of this additional system of inheritan...
www.science.org
September 19, 2025 at 1:56 PM
Reposted by Luay Almassalha
richardsever.bsky.social
"AI has generated a genome for the first time" eu.36kr.com/en/p/3472136...

www.biorxiv.org/content/10.1...
World's First AI Genome Born: 3.5 Billion Years of Life Code Reprogrammed, Biology Enters "ChatGPT Moment"
Stanford AI Achieves First - Time Phage Genome Generation: 16 Phages Effectively Target Drug - Resistant Bacteria
eu.36kr.com
September 18, 2025 at 6:19 PM
Reposted by Luay Almassalha
lammerdinglab.bsky.social
How do LMNA mutations cause dilated cardiomyopathy (DCM) and other #laminopathies? In our latest preprint (doi.org/10.1101/2024...), led by the amazing Noam Zuela-Sopilniak and Julien Morival, we show that cardiomyocyte-specific lamin A/C depletion causes severe DCM, consistent with other studies.
September 18, 2025 at 6:12 PM
Reposted by Luay Almassalha
ewanbirney.bsky.social
Bioinformaticians / computational biologists take note - know where you should take your OS tool chain from and do not introduce backdoors.
jbonfield.bsky.social James Bonfield @jbonfield.bsky.social · Sep 15
Heads up: ignore samtools dot org, similarly minimap2 dot com and likely others. It's owned by a known phishing site and while the binaries they offer look valid currently (but note they may be serving us different binaries to others), that could change.

Ie: it's not us (Samtools team)! Be warned
September 15, 2025 at 8:44 AM
Reposted by Luay Almassalha
carmeloferrai.bsky.social
EpiSci - Hi there! Our review “Mechanotransduction in stem cells” is finally published. With @carstenschulte4.bsky.social we provided a comprehensive picture, that aims to cover the whole mechanotransductive pathway from the cell microenvironment to the nucleus. 1/3 pubmed.ncbi.nlm.nih.gov/38729084/
May 13, 2024 at 12:22 PM
almassalha.bsky.social
paper revisions irl
a man in a blue shirt and tie is pointing at a bulletin board with a lot of papers on it .
ALT: a man in a blue shirt and tie is pointing at a bulletin board with a lot of papers on it .
media.tenor.com
September 5, 2025 at 9:04 PM
almassalha.bsky.social
the drosophila genome is weird
September 5, 2025 at 5:31 PM
Reposted by Luay Almassalha
jorgeferreira.bsky.social
New preprint from the lab! Please check it out. 🚨
Have you ever wondered how cells decide when it’s time to divide? So did we!
www.biorxiv.org/content/10.1...
Chromosome condensation mechanically primes the nucleus for mitosis
Timely and accurate transition into mitosis is essential to preserve genome integrity and avoid chromosome segregation errors. This transition depends on spatial and temporal activity patterns of the ...
www.biorxiv.org
September 3, 2025 at 10:07 AM
Reposted by Luay Almassalha
kazu-maeshima.bsky.social
🧩 Also highly relevant: a modeling study from Bin Zhang group predicts condensed euchromatin domains with active protrusions. Perfectly complementary to our findings! 3
www.biorxiv.org/content/10.1...
August 28, 2025 at 4:18 AM