Samir Amin
@samiramin.com
Comparative Genomics #glioma; #aneuploidy #evolution 🧑💻 🧬 | ❤️ 😋 🥘🧑🍳 📷 | @yaleschoolofmed.bsky.social | Views = own | ❤️ 🔄 ≠ endorsement | sbamin.com/about
📍 BDL | Prev. HOU, BOS, BDQ
📍 BDL | Prev. HOU, BOS, BDQ
Reposted by Samir Amin
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 !
October 27, 2025 at 6:20 PM
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 !
👏 @broadinstitute.org "in mice AND humans"
A new drug candidate for a difficult-to-treat type of lung cancer, developed by scientists in the Broad-Bayer oncology research alliance, targets HER2 mutations in lung cancer and shrinks tumors in mice and humans.
Broad-Bayer collaboration leads to drug candidate for a hard-to-treat type of lung cancer
The compound, now under priority review at FDA, targets HER2 mutations in lung cancer and shrinks tumors in mice and humans.
www.broadinstitute.org
October 23, 2025 at 3:23 PM
👏 @broadinstitute.org "in mice AND humans"
Reposted by Samir Amin
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...
www.nature.com/articles/s41...
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.
www.nature.com
October 16, 2025 at 3:26 PM
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...
www.nature.com/articles/s41...
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 🪔
Focus on the good and let the year be an act of random kindness.
Happy Diwali 🪔
October 19, 2025 at 2:30 PM
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 🪔
Focus on the good and let the year be an act of random kindness.
Happy Diwali 🪔
podcasts.apple.com/us/podcast/l...
@florisbarthel.bsky.social and team on liquid biopsy for brain tumors 💪
@florisbarthel.bsky.social and team on liquid biopsy for brain tumors 💪
Liquid Biopsy TGT September
Podcast Episode · TGen Talks · 09/30/2025 · 26m
podcasts.apple.com
October 16, 2025 at 8:14 PM
podcasts.apple.com/us/podcast/l...
@florisbarthel.bsky.social and team on liquid biopsy for brain tumors 💪
@florisbarthel.bsky.social and team on liquid biopsy for brain tumors 💪
Reposted by Samir Amin
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
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...
bit.ly
October 13, 2025 at 11:21 PM
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
Reposted by Samir Amin
Characterising cancer-stroma interactions through high-content phenotyping from microscopy time-lapses https://www.biorxiv.org/content/10.1101/2025.10.02.680037v1
October 4, 2025 at 5:48 AM
Characterising cancer-stroma interactions through high-content phenotyping from microscopy time-lapses https://www.biorxiv.org/content/10.1101/2025.10.02.680037v1
Reposted by Samir Amin
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.
If you make image analysis software and want to teach it, workshop submissions are open now! We'd love to have your tool highlighted.
#HappyFluorescenceFriday!
#microscopycommunity- want to learn open source image analysis or share your knowledge to help others? We’ve got a FREE virtual workshop Nov 17-19! Now accepting workshop session applications!
Learn more & sign up: buff.ly/esGIotD
#microscopycommunity- want to learn open source image analysis or share your knowledge to help others? We’ve got a FREE virtual workshop Nov 17-19! Now accepting workshop session applications!
Learn more & sign up: buff.ly/esGIotD
September 23, 2025 at 3:48 PM
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.
If you make image analysis software and want to teach it, workshop submissions are open now! We'd love to have your tool highlighted.
Reposted by Samir Amin
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...
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.
www.nature.com
September 10, 2025 at 3:21 PM
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...
@jeffgenome.bsky.social from ❤️ @jacksonlab.bsky.social at YaleMed grand rounds
September 10, 2025 at 1:53 AM
@jeffgenome.bsky.social from ❤️ @jacksonlab.bsky.social at YaleMed grand rounds
Reposted by Samir Amin
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.
August 5, 2025 at 12:38 PM
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.
Reposted by Samir Amin
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. 🧪🧬🔬
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?
www.jax.org
July 23, 2025 at 9:04 PM
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. 🧪🧬🔬
👏 "...lineage tracing and conditional p53 mouse models to dissect how genetic alterations, cell state transitions, and microenvironmental remodeling converge to drive early PDAC progression."
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. ...
www.biorxiv.org
July 4, 2025 at 3:27 PM
👏 "...lineage tracing and conditional p53 mouse models to dissect how genetic alterations, cell state transitions, and microenvironmental remodeling converge to drive early PDAC progression."
❤️
ggplot2 is turning 18! 🎂
For nearly two decades, it’s helped data scientists turn complex data into clear, beautiful insights.
We’re throwing a birthday party at Data+AI Summit, with treats and limited-edition swag. Come celebrate with us and @hadley.nz!
📍 Posit Lounge (402)
📅 June 10, 6–8pm
For nearly two decades, it’s helped data scientists turn complex data into clear, beautiful insights.
We’re throwing a birthday party at Data+AI Summit, with treats and limited-edition swag. Come celebrate with us and @hadley.nz!
📍 Posit Lounge (402)
📅 June 10, 6–8pm
June 10, 2025 at 2:00 AM
❤️
Reposted by Samir Amin
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...
Or why automated virtual screening and docking remains hard and why expertise remains essential. medchemash.substack.com/p/on-the-fai...
On the failure of rescoring in virtual screening
Why automated virtual screening and docking remains hard and why expertise remains essential
medchemash.substack.com
May 22, 2025 at 7:39 PM
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...
Or why automated virtual screening and docking remains hard and why expertise remains essential. medchemash.substack.com/p/on-the-fai...
Reposted by Samir Amin
Excited to share our latest manuscript www.biorxiv.org/content/10.1...
This was a great collaboration with Drs. Huse, Lang, @jesserdixon.bsky.social
This was a great collaboration with Drs. Huse, Lang, @jesserdixon.bsky.social
May 22, 2025 at 5:37 PM
Excited to share our latest manuscript www.biorxiv.org/content/10.1...
This was a great collaboration with Drs. Huse, Lang, @jesserdixon.bsky.social
This was a great collaboration with Drs. Huse, Lang, @jesserdixon.bsky.social
@s-j-aitken.bsky.social on how genetic background shapes cancer evolution. 💎
May 22, 2025 at 6:09 PM
@s-j-aitken.bsky.social on how genetic background shapes cancer evolution. 💎
The story of Python 😍 www.youtube.com/watch?v=pqBq...
Python: The Documentary [OFFICIAL TRAILER]
YouTube video by CultRepo (formerly Honeypot)
www.youtube.com
May 18, 2025 at 10:37 PM
The story of Python 😍 www.youtube.com/watch?v=pqBq...
landscape of CRISPR-Cas9 genome-wide double-standed breaks and underlying determinants of cut & repair process. www.nature.com/articles/s41...
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.
www.nature.com
May 6, 2025 at 2:18 AM
landscape of CRISPR-Cas9 genome-wide double-standed breaks and underlying determinants of cut & repair process. www.nature.com/articles/s41...
Estimating de novo mutation rate over four generations from total 28 individuals. 👏
Human de novo mutation rates from a four-generation pedigree reference www.nature.com/articles/s41... 🧬🖥️🧪
May 3, 2025 at 2:11 AM
Estimating de novo mutation rate over four generations from total 28 individuals. 👏
Reposted by Samir Amin
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...
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
academic.oup.com
April 24, 2025 at 5:16 PM
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...
Reposted by Samir Amin
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!
April 22, 2025 at 4:36 PM
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!
a tale of phage-bacteria co-evolution 💎 by Bonnie Bassler
April 24, 2025 at 8:44 PM
a tale of phage-bacteria co-evolution 💎 by Bonnie Bassler
Targeting PDGFRA in pediatric high-grade glioma 👏 www.cell.com/cancer-cell/...
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...
www.cell.com
April 14, 2025 at 11:44 PM
Targeting PDGFRA in pediatric high-grade glioma 👏 www.cell.com/cancer-cell/...
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.
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...
www.cell.com
April 12, 2025 at 8:39 PM
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.