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Samir Amin

@samiramin.com
296 followers 144 following 61 posts

Comparative Genomics #glioma; #aneuploidy #evolution 🧑‍💻 🧬 | ❤️ 😋 🥘🧑‍🍳 📷 | @yaleschoolofmed.bsky.social | Views = own | ❤️ 🔄 ≠ endorsement | sbamin.com/about 📍 BDL | Prev. HOU, BOS, BDQ

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Samir Amin @samiramin.com · 10/09/2026
💎 Building a genomic language model using first principles of evolutionary biology
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Samir Amin @samiramin.com · 23/06/2026
Good one! Mix of technical (OOP, blockchain, database) but more importantly, on how to go after a problem. About: en.wikipedia.org/wiki/Barbara... podcasts.apple.com/us/podcast/e...
podcasts.apple.com
Barbara Liskov (MIT) - Finding the Great Problems
Podcast Episode · Entrepreneurial Thought Leaders (ETL) · October 23, 2019 · 44m
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Samir Amin @samiramin.com · 15/06/2026
Without getting in too much details, one of the most simple and useful intro to how agentic AI works. @hadley.nz tidydesign.substack.com/p/what-is-an...
tidydesign.substack.com
What is an agent?
Conversations, turns, rounds, tools, agents and more!
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Scripps National Spelling Bee @scrippsbee.bsky.social · 29/05/2026
"You are pure joy." — Head Judge Mary Brooks on #Speller213 Logan Bailey, who has won hearts here at the Bee! He started spelling before he could speak, and he hasn't stopped since. As the only Finalist debuting at the Bee and at just 12 years old, he's sure to make a BEEturn next year. #spellingbee
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Tami Gjorgjieva @tamigj.bsky.social · 18/05/2026
Hi Genetics/Comp-Bio community 👋 Interested in mentoring a comp-bio research student in East Africa over the summer? Do you have any experience in bioinformatics, biostats, genome/RNA-seq analyses, ML, or metagenomics? We'd love to have you as a mentor in our new program! 🧵 (1/n)
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Samir Amin @samiramin.com · 18/05/2026
a few good pointers @hadley.nz open.substack.com/pub/tidydesi...
open.substack.com
Returning to life!
Welcome back to the tidy design principles substack.
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Samir Amin @samiramin.com · 01/04/2026
It's GO 🚀 Godspeed NASA and Artemis II 😊https://www.youtube.com/watch?v=m3kR2KK8TEs
youtube.com
NASA's Artemis II Live Mission Coverage (Official Broadcast)
YouTube video by NASA
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Carolyn Bertozzi @carolynbertozzi.bskyverified.social · 26/03/2026
We found a new brain shuttle! Mucins on brain endothelium mediate transcytosis of cargo linked to mucin-binding “C domain”. Congratulations Sophia Shi, now a Roland Fellow @harvard.edu, and longtime collaborator Tony Wyss-Coray @stanfordmedicine.bsky.social www.biorxiv.org/content/10.6...
biorxiv.org
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Science Magazine @science.org · 19/03/2026
Wild rice is a perennial, creeping plant. The secret to its perennial growth habit lies in a developmental reversal directed by small RNAs. This image illustrates how combining perennial genes with prostrate growth genes allows cultivated rice to mimic wild rice. Learn more: scim.ag/40GOjDb
This image illustrates how combining perennial genes with prostrate growth genes allows cultivated rice to mimic wild rice.
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Yahaya Yabo @yahayayabo.bsky.social · 19/03/2026
🧵 1/8 Hot off the press! 🔥 link.springer.com/article/10.1... CAR-T cells show promising results in preclinical glioblastoma models, yet clinical benefit in patients has been limited. To understand why, we used a human brain slice model that preserves the native human GBM tumor microenvironment. 🧠
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Samir Amin @samiramin.com · 13/03/2026
comprehensive guide with background, approach and tools to design an antibody from scratch www.asimov.press/p/antibody-d...
asimov.press
How to Design Antibodies
A step-by-step guide to making de novo binders.
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Samir Amin @samiramin.com · 11/03/2026
Interesting and impactful 👏 💎
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Samir Amin @samiramin.com · 07/03/2026
Good concept but 🙅 and would rather prefer in-built global and project specific memory files. code.claude.com/docs/en/memory For detailed history, safer to grep/rg ~/.claude/ over exposing unwarranted APIs. Worth noting potential security risks (C1, C2). github.com/thedotmack/c...
code.claude.com
How Claude remembers your project - Claude Code Docs
Give Claude persistent instructions with CLAUDE.md files, and let Claude accumulate learnings automatically with auto memory.
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Samir Amin @samiramin.com · 22/02/2026
Claude 101: An excellent primer and best practices doing agentic (and NOT vibe) coding I have seen around. via @rendle.dev www.youtube.com/watch?v=pey9...
youtube.com
How I Tamed Claude - Emmz Rendle - NDC London 2026
YouTube video by NDC Conferences
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Samir Amin @samiramin.com · 17/02/2026
Worth a read
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Samir Amin @samiramin.com · 27/01/2026
Join @eunhee-yi.bsky.social lab if curious about ecDNA in cancer evolution and doing impactful science with cordial PI 🚀🫰
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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 20/01/2026
Ep 23 - So what actually IS CellPainting anyway? You may have heard of it if you're say, a fan of the @drannecarpenter.bsky.social - @shantanu-singh.cc lab (and who isn't????), but what, you know, is it? Let @erinweisbart.bsky.social break it down for you! youtu.be/9-d6DoHtgUY
youtu.be
Introduction to the Cell Painting Assay - AskErinDearBeth Episode 23
YouTube video by Ask Erin, Dear Beth
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Josh Persi @joshpersi.bsky.social · 21/01/2026
Come learn about deep learning with us! The Data Science Learning Community just started reading the free third edition of Deep Learning with Python. Meetings are Tuesday at 3 pm CST. DSLC: dslc.io Book: deeplearningwithpython.io #rstats #pydata
deeplearningwithpython.io
Deep Learning with Python, Third Edition
Deep Learning with Python is written for anyone who wishes to explore deep learning from scratch. This new edition adds comprehensive coverage of generative AI and modern deep learning frameworks. It ...
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Samir Amin @samiramin.com · 21/12/2025
last but not least one on in vivo base editing in mice models of prion (PRNP) disease achieved 50% reduction in PrP protein and 52% increase in lifespan. www.nature.com/articles/s41...
nature.com
In vivo base editing extends lifespan of a humanized mouse model of prion disease - Nature Medicine
An in vivo base editing approach targeting the PRNP gene led to a 52% increase in the lifespan of mouse models inoculated with the most common sporadic and genetic types of human pathogenic prion isol...
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Samir Amin @samiramin.com · 21/12/2025
www.cell.com/cell/fulltex... On how ~neutrally evolving CAG repeats over the lifespan eventually exerts neurodegenerative phenotype in Huntington’s disease.
cell.com
Long somatic DNA-repeat expansion drives neurodegeneration in Huntington’s disease
Single-cell measurement of the Huntington’s disease-causing CAG repeat reveals that somatic expansion of this repeat drives pathological changes in neurons, providing insights into disease progression...
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Samir Amin @samiramin.com · 21/12/2025
pubmed.ncbi.nlm.nih.gov/40044858/ On early origin and maintenance of WGD despite (instability driven) fitness cost an organism has to endure.
pubmed.ncbi.nlm.nih.gov
Genome duplication in a long-term multicellularity evolution experiment - PubMed
Whole-genome duplication (WGD) is widespread across eukaryotes and can promote adaptive evolution<sup>1-4</sup>. However, given the instability of newly formed polyploid genomes<sup>5-7</sup>, understanding how WGDs arise in a population, persist, and underpin adaptations remains a challenge. Here, …
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Dmitri Petrov @petrovadmitri.bsky.social · 21/12/2025
All right it’s time for the annual “please tell us about one (or a few if you are ambitious) paper from 2025 that really impressed you and why we should all read it“! Go! If you tell us how it changed your view of the world and what makes it so powerful and consequential It would be excellent.
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Traver Hart @traver.bsky.social · 21/12/2025
Merry Christmas, genetic interaction nerds: www.biorxiv.org/content/10.6...
biorxiv.org
Functional modules predict cancer-relevant genetic interactions in mammalian cells
Genetic interactions can reveal gene function and identify cancer-relevant synthetic lethals, but systematic mapping in human cells is constrained by inefficient reagents, vast combinatorial search sp...
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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 27/10/2025
Episode 17 - perhaps my favorite yet. How do you write a forum.image.sc post that will get you the answers you need without revealing information you don't want to tell? @erinweisbart.bsky.social and I go through what the experts need to know to help you. Post your sci q's today on forum.image.sc !
youtu.be
How to Write a Great Post on the Image.sc Forum - AskErinDearBeth Episode 17
YouTube video by Ask Erin, Dear Beth
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Samir Amin @samiramin.com · 23/10/2025
👏 @broadinstitute.org "in mice AND humans"
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Nature Methods @natmethods.nature.com · 16/10/2025
gReLU advances deep learning based modeling and analysis of DNA sequences with comprehensive toolsets and versatile applications. @avantikalal.bsky.social @gokcen.bsky.social www.nature.com/articles/s41...
nature.com
gReLU: a comprehensive framework for DNA sequence modeling and design - Nature Methods
gReLU advances deep-learning-based modeling and analysis of DNA sequences with comprehensive toolsets and versatile applications.
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Samir Amin @samiramin.com · 19/10/2025
तमसो मा ज्योतिर्गमय From darkness, lead me to the light. Focus on the good and let the year be an act of random kindness. Happy Diwali 🪔
Diwali - festival of lights Clay, Photograph by Nah Ting Feng, Dreamstime.

From https://kids.nationalgeographic.com/pages/article/diwali: lamps symbolize the inner light that protects each household from spiritual darkness.
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Samir Amin @samiramin.com · 16/10/2025
podcasts.apple.com/us/podcast/l... @florisbarthel.bsky.social and team on liquid biopsy for brain tumors 💪
podcasts.apple.com
Liquid Biopsy TGT September
Podcast Episode · TGen Talks · 09/30/2025 · 26m
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Floris Barthel @florisbarthel.bsky.social · 14/10/2025
This 7-year journey has reached a first milestone! 🥳 Excited to share our preprint (3rd of 2025) on the 3D telomeric interactome, a project that started with a K99 in 2018. Thanks to Yi-An Chen, first postdoc in our lab and first author who worked tirelessly to realize this dream. bit.ly/3W3wuMk
bit.ly
Mapping the Telomeric 3D Interactome with Telomere-C Reveals Repetitive Element Hubs Associated with Telomere Maintenance
Telomeres are essential for genome integrity, but the accurate, high-resolution mapping of their three-dimensional (3D) chromatin interactions, a process thought to mediate gene regulation and telomer...
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bioRxiv Cancer Bio @biorxiv-cancer.bsky.social · 04/10/2025
Characterising cancer-stroma interactions through high-content phenotyping from microscopy time-lapses www.biorxiv.org/content/10.1101/202…
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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 23/09/2025
Halfway to I2K is BACK, friends of all kinds! Last year, 650 people attended 30+ TOTALLY FREE image analysis workshops of all kinds, across many timezones. If you make image analysis software and want to teach it, workshop submissions are open now! We'd love to have your tool highlighted.
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Trevor Graham @trevorgraham.bsky.social · 10/09/2025
Studying cancer evolution needs multi-region or single cell seq for phylogenetics, right? Amazingly (I think!) we found single-sample bulk methylation suffices, via analysis of "fluctuating methylation". In @nature.com today led by brilliant @calumgabbutt.bsky.social www.nature.com/articles/s41...
nature.com
Fluctuating DNA methylation tracks cancer evolution at clinical scale - Nature
Cancer evolutionary dynamics are quantitatively inferred using a method, EVOFLUx, applied to fluctuating DNA methylation.
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Samir Amin @samiramin.com · 10/09/2025
@jeffgenome.bsky.social from ❤️ @jacksonlab.bsky.social at YaleMed grand rounds
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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 05/08/2025
Episode 11 - In which @erinweisbart.bsky.social and I talk about just how much we love ilastik (@ilastik-team.bsky.social) and how it's great for so many problems! Also, that you should use a small brush.
youtu.be
Intro to Pixel Classification in ilastik - AskErinDearBeth Episode 11
YouTube video by Ask Erin, Dear Beth
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The Jackson Laboratory @jax.org · 23/07/2025
New research, published today in @natureportfolio.nature.com, decodes the most elusive, difficult-to-sequence regions of the genome from populations around the world, rewriting knowledge of human biology and setting a new benchmark for precision medicine. 🧪🧬🔬
jax.org
The most complete view of the human genome yet sets new standard for use in precision medicine
What if scientists unlocked the most hidden, hardest-to-read regions of our DNA?
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Samir Amin @samiramin.com · 04/07/2025
👏 "...lineage tracing and conditional p53 mouse models to dissect how genetic alterations, cell state transitions, and microenvironmental remodeling converge to drive early PDAC progression."
biorxiv.org
Oncogenic and tumor-suppressive forces converge on a progenitor-orchestrated niche to shape early tumorigenesis
The transition from benign to malignant growth is a pivotal yet poorly understood step in cancer progression that marks the shift from a pathologically inert condition to a clinically lethal disease. ...
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Samir Amin @samiramin.com · 10/06/2025
❤️
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Ash Jogalekar @ashjogalekar.bsky.social · 22/05/2025
New post: On the failure of rescoring in virtual screening. Or why automated virtual screening and docking remains hard and why expertise remains essential. medchemash.substack.com/p/on-the-fai...
medchemash.substack.com
On the failure of rescoring in virtual screening
Why automated virtual screening and docking remains hard and why expertise remains essential
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Kadir Akdemir @kcakdemir.bsky.social · 22/05/2025
Excited to share our latest manuscript www.biorxiv.org/content/10.1... This was a great collaboration with Drs. Huse, Lang, @jesserdixon.bsky.social
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Samir Amin @samiramin.com · 22/05/2025
@s-j-aitken.bsky.social on how genetic background shapes cancer evolution. 💎
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Samir Amin @samiramin.com · 18/05/2025
The story of Python 😍 www.youtube.com/watch?v=pqBq...
youtube.com
Python: The Documentary [OFFICIAL TRAILER]
YouTube video by CultRepo (formerly Honeypot)
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Samir Amin @samiramin.com · 06/05/2025
landscape of CRISPR-Cas9 genome-wide double-standed breaks and underlying determinants of cut & repair process. www.nature.com/articles/s41...
nature.com
Linking CRISPR–Cas9 double-strand break profiles to gene editing precision with BreakTag - Nature Biotechnology
The genome-wide landscape of Cas-induced double-strand breaks and end structures is profiled at nucleotide resolution.
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Samir Amin @samiramin.com · 03/05/2025
Estimating de novo mutation rate over four generations from total 28 individuals. 👏
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Zachary Compton @zacharytcompton.bsky.social · 24/04/2025
Is cancer suppression in and of itself an adaptation? The full version of our The Elephant & the Spandrel is now online. academic.oup.com/emph/article...
academic.oup.com
The Elephant and the Spandrel
Abstract. Comparative oncology has made great strides in identifying patterns of cancer prevalence and risk across the tree of life. Such studies have ofte
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Thibaut Brunet @thibautbrunet.bsky.social · 22/04/2025
A dream come true: the first expansion microscopy images of C. flexa 🤩 Generated by Mylan & Uzuki who learned from the best (@hiralshah.bsky.social @gautamdey.bsky.social @dudinlab.bsky.social). We will learn so much from these!
Expansion microscopy micrograph of the choanoflagellate Choanoeca flexa, vaguely evocative of a cactus. Red = tubulin, green = actin, blue = DNASame with yellow = lipids (BODIPY)
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Samir Amin @samiramin.com · 24/04/2025
a tale of phage-bacteria co-evolution 💎 by Bonnie Bassler
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Samir Amin @samiramin.com · 15/04/2025
Targeting PDGFRA in pediatric high-grade glioma 👏 www.cell.com/cancer-cell/...
cell.com
Effective targeting of PDGFRA-altered high-grade glioma with avapritinib
PDGFRA is commonly altered in pediatric HGG. Mayr et al. report that the PDGFRA/KIT inhibitor avapritinib demonstrates on-target activity, brain penetrance, and survival benefit in pre-clinical H3K27M...
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Samir Amin @samiramin.com · 12/04/2025
From PCAWG resource to validation 👏: Cancer cells undo amplification of BRD4 region by introducing (and selecting for cells with) recurrent breakpoints in BRD4 locus to maintain goldilocks non-toxic state of BRD4 expression.
cell.com
Recurrent breakpoints in the BRD4 locus reduce toxicity associated with gene amplification
Wala et al. identify recurrent focal BRD4 deletions in tumors harboring larger amplifications, suggesting that these deletions may serve to limit toxic BRD4 overexpression. A CRISPR-Cas9 cell line mod...
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Sarah Aitken @s-j-aitken.bsky.social · 02/04/2025
🧩DNA Lesions Piece Together Impossible Trees🧩 This was a fun piece to write (and illustrate!) with Dr Claudia Arnedo Pac about @mikespencerchapman.bsky.social and co’s recent @nature.com paper. Thank you for the invitation, Maria @cp-trendsgenetics.bsky.social authors.elsevier.com/sd/article/S...
A person made up of jigsaw pieces representing the millions and millions of unique cells with unique genomes, which build a picture of our lifetime of cellular experiences. 
Four panels, anticlockwise from top left, highlight key findings. (i) Phylogeny-violating variants (PVVs) caused by persistent DNA lesions explain otherwise ‘impossible’ trees. (ii) An estimate (in chronological time) of when lesions were acquired and for how long they persist. (iii) Demonstration in vivo that individual DNA lesions can give rise to both single nucleotide variants (SNVs) and small insertions or deletions (indels) in different cell cycles; this is a form of multiallelic variation, which more commonly relates to two alternate SNVs at the same site. (iv) Identification of lesion segregation of APOBEC mutagenesis, implicating that genome-wide mutagenesis occurred within a single cell cycle and that lesion segregation could explain the strand coordination of clustered APOBEC mutations commonly seen in cancer genomes.
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Samir Amin @samiramin.com · 31/03/2025
Primer on blood brain barrier and CSF flow through ventricles: www.quantamagazine.org/how-the-brai...
quantamagazine.org
How the Brain Protects Itself From Blood-Borne Threats | Quanta Magazine
To buffer the brain against menaces in the blood, a dynamic, multi-tiered system of protection is built into the brain’s blood vessels.
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