Shaun Mahony
@shaunmahony.bsky.social
Studying gene regulation and transcription factor binding with machine learning. Assoc Prof at Penn State. 🇮🇪
Pinned
Shaun Mahony
@shaunmahony.bsky.social
· Nov 14
Next, if you're looking for your daily hit of posts that focus on gene regulation, here's a relevant feed:
bsky.app/profile/shau...
The way the feed works is that it searches for posts containing #GeneReg or a set of keywords (see next post).
bsky.app/profile/shau...
The way the feed works is that it searches for posts containing #GeneReg or a set of keywords (see next post).
Reposted by Shaun Mahony
One like = one scene from "AI, Claudius", the epic story of a stammering Markov model who survived corruption, lies, and intrigue to become LLM-peror of Ancient Rome
November 17, 2025 at 6:05 PM
One like = one scene from "AI, Claudius", the epic story of a stammering Markov model who survived corruption, lies, and intrigue to become LLM-peror of Ancient Rome
Reposted by Shaun Mahony
I'm very pleased to announce the official publication of our lab's paper "DNA mutagenesis driven by transcription factor competition with mismatch repair" in today's issue of Cell! www.cell.com/cell/abstrac...
DNA mutagenesis driven by transcription factor competition with mismatch repair
Competition between transcription factors and mismatch repair machinery drives localized
hypermutation at regulatory elements, with implications for cancer and genome evolution.
www.cell.com
October 2, 2025 at 11:37 PM
I'm very pleased to announce the official publication of our lab's paper "DNA mutagenesis driven by transcription factor competition with mismatch repair" in today's issue of Cell! www.cell.com/cell/abstrac...
Reposted by Shaun Mahony
A fundamental lesson of modern AI is that scale is essential: training bigger models on bigger datasets unlocks new capabilities. A fundamental lesson of AI engineering is that scaling up isn't trivial: it is not just a matter of spending more money and resources.
September 22, 2025 at 12:15 PM
A fundamental lesson of modern AI is that scale is essential: training bigger models on bigger datasets unlocks new capabilities. A fundamental lesson of AI engineering is that scaling up isn't trivial: it is not just a matter of spending more money and resources.
Reposted by Shaun Mahony
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
Ie: it's not us (Samtools team)! Be warned
September 15, 2025 at 8:40 AM
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
Ie: it's not us (Samtools team)! Be warned
Within 24hrs, our board of trustees closed the local NPR station because transferring to new owners would have cost too much ($17M over 5 yrs) AND they increased the President's pay (total >$20M over next 7 yrs). How does this further PSU's land grant mission to extend knowledge to the public?
September 12, 2025 at 7:51 PM
Within 24hrs, our board of trustees closed the local NPR station because transferring to new owners would have cost too much ($17M over 5 yrs) AND they increased the President's pay (total >$20M over next 7 yrs). How does this further PSU's land grant mission to extend knowledge to the public?
New preprint from Alan Brown in our lab, who is co-advised by @llinaslab.bsky.social. In this study, Alan studied chromatin state dynamics during the asexual intraerythrocytic development cycle (IDC) of the human malaria parasite, Plasmodium falciparum.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
September 7, 2025 at 3:10 PM
New preprint from Alan Brown in our lab, who is co-advised by @llinaslab.bsky.social. In this study, Alan studied chromatin state dynamics during the asexual intraerythrocytic development cycle (IDC) of the human malaria parasite, Plasmodium falciparum.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
New preprint from the lab: Dr. Daniela James led an effort to improve the ChIP-exo protocol for high-res protein-DNA interactions. Particularly focused on optimizing for use in mammalian cells and making the protocol compatible with newer Illumina sequencers.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Optimized ChIP-exo for mammalian cells and patterned sequencing flow cells
By combining chromatin immunoprecipitation (ChIP) with an exonuclease digestion of protein-bound DNA fragments, ChIP-exo characterizes genome-wide protein-DNA interactions at near base-pair resolution...
www.biorxiv.org
August 23, 2025 at 7:16 PM
New preprint from the lab: Dr. Daniela James led an effort to improve the ChIP-exo protocol for high-res protein-DNA interactions. Particularly focused on optimizing for use in mammalian cells and making the protocol compatible with newer Illumina sequencers.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Shaun Mahony
Reposted by Shaun Mahony
@jengreitz.bsky.social l & my lab want to co-hire a computational biologist/biostatistician with project management expertise to help map the regulatory code of the human genome and discover genetic mechanisms of disease.
Details below
careersearch.stanford.edu/jobs/computa...
Plz RT
Details below
careersearch.stanford.edu/jobs/computa...
Plz RT
August 19, 2025 at 12:29 AM
@jengreitz.bsky.social l & my lab want to co-hire a computational biologist/biostatistician with project management expertise to help map the regulatory code of the human genome and discover genetic mechanisms of disease.
Details below
careersearch.stanford.edu/jobs/computa...
Plz RT
Details below
careersearch.stanford.edu/jobs/computa...
Plz RT
Reposted by Shaun Mahony
"I want to vibe code the genome"
—the illustrious @casey.greenelab.com
as quoted by @jperkel.bsky.social @nature.com 🧬🖥️ #MLSky www.nature.com/articles/d41...
—the illustrious @casey.greenelab.com
as quoted by @jperkel.bsky.social @nature.com 🧬🖥️ #MLSky www.nature.com/articles/d41...
Beyond AlphaFold: how AI is decoding the grammar of the genome
Scientists are seeking to decipher the role of non-coding DNA in the human genome, helped by a suite of artificial-intelligence tools.
www.nature.com
August 18, 2025 at 9:42 PM
"I want to vibe code the genome"
—the illustrious @casey.greenelab.com
as quoted by @jperkel.bsky.social @nature.com 🧬🖥️ #MLSky www.nature.com/articles/d41...
—the illustrious @casey.greenelab.com
as quoted by @jperkel.bsky.social @nature.com 🧬🖥️ #MLSky www.nature.com/articles/d41...
Reposted by Shaun Mahony
The #RegSys @iscb-regsys.bsky.social track is gonna be outstanding again this year with a great selection of talks and keynotes @verapancaldi.bsky.social, Mafalda Dias, Roser Vento-Tormo, and @lucapinello.bsky.social !
www.iscb.org/ismbeccb2025...
www.iscb.org/ismbeccb2025...
RegSys
ISCB - International Society for Computational Biology
www.iscb.org
July 21, 2025 at 8:02 AM
The #RegSys @iscb-regsys.bsky.social track is gonna be outstanding again this year with a great selection of talks and keynotes @verapancaldi.bsky.social, Mafalda Dias, Roser Vento-Tormo, and @lucapinello.bsky.social !
www.iscb.org/ismbeccb2025...
www.iscb.org/ismbeccb2025...
Reposted by Shaun Mahony
Paper alert! I am really pleased to share the final version of the work led by Irène Amblard in the team on a regulatory switch controlling Cdx2 expression during posterior body development! #regulatorylogic #devbio @mrc-lms.bsky.social @imperialmed.bsky.social
June 27, 2025 at 3:07 PM
Paper alert! I am really pleased to share the final version of the work led by Irène Amblard in the team on a regulatory switch controlling Cdx2 expression during posterior body development! #regulatorylogic #devbio @mrc-lms.bsky.social @imperialmed.bsky.social
Reposted by Shaun Mahony
This a really exciting leap forward for genomic sequence to activity gene regulation models. It is a genuine improvement over pretty much all SOTA models spanning a wide range of regulatory, transcriptional and post-transcriptional processes. 1/
Excited to launch our AlphaGenome API goo.gle/3ZPUeFX along with the preprint goo.gle/45AkUyc describing and evaluating our latest DNA sequence model powering the API. Looking forward to seeing how scientists use it! @googledeepmind
June 25, 2025 at 4:18 PM
This a really exciting leap forward for genomic sequence to activity gene regulation models. It is a genuine improvement over pretty much all SOTA models spanning a wide range of regulatory, transcriptional and post-transcriptional processes. 1/
This has been a wild story to follow. Someone is leading a campaign of pure harassment against @devoevomed.bsky.social 1/
bsky.app/profile/devo...
bsky.app/profile/devo...
June 23, 2025 at 11:27 PM
This has been a wild story to follow. Someone is leading a campaign of pure harassment against @devoevomed.bsky.social 1/
bsky.app/profile/devo...
bsky.app/profile/devo...
Reposted by Shaun Mahony
@saramostafavi.bsky.social (@Genentech) & I (@Stanford) r excited to announce co-advised postdoc positions for candidates with deep expertise in ML for bio (especially sequence to function models, causal perturbational models & single cell models). See details below. Pls RT 1/
June 19, 2025 at 8:55 PM
@saramostafavi.bsky.social (@Genentech) & I (@Stanford) r excited to announce co-advised postdoc positions for candidates with deep expertise in ML for bio (especially sequence to function models, causal perturbational models & single cell models). See details below. Pls RT 1/
Reposted by Shaun Mahony
Much more important things going on in the world, but wanted to share this new work on parent-of-origin effects & “non-canonical” genomic imprinting in developmental plasticity of honey bees, out now in Genome Biology 🧪🧬🔄 link.springer.com/article/10.1...
Intragenomic conflict associated with extreme phenotypic plasticity in queen-worker caste determination in honey bees (Apis mellifera) - Genome Biology
Background Caste determination of honey bees (Apis mellifera) exemplifies developmental plasticity, where differences in larval diet result in identical genotypes yielding either long-lived, reproduct...
link.springer.com
June 18, 2025 at 3:30 PM
Much more important things going on in the world, but wanted to share this new work on parent-of-origin effects & “non-canonical” genomic imprinting in developmental plasticity of honey bees, out now in Genome Biology 🧪🧬🔄 link.springer.com/article/10.1...
Reposted by Shaun Mahony
A very special first post on Bluesky: I’m excited to share that I’ll be starting my lab at Penn State this coming January in the Dept of Biochemistry & Molecular Biology! I’ll be hiring at all levels soon. Check out updates, thoughts, and positions on the lab account: @hanna-lab.bsky.social
May 28, 2025 at 1:25 PM
A very special first post on Bluesky: I’m excited to share that I’ll be starting my lab at Penn State this coming January in the Dept of Biochemistry & Molecular Biology! I’ll be hiring at all levels soon. Check out updates, thoughts, and positions on the lab account: @hanna-lab.bsky.social
Reposted by Shaun Mahony
Free in-person registration is open for #MLCB2025! Sept 10-11 at @nygenome.org and online at youtube.com/@mlcbconf. Paper/abstract deadline is June 1, more deets including our fantastic invited speaker lineup at mlcb.org! Please RP.
Machine Learning in Computational Biology
Youtube channel for the Machine Learning in Computational Biology conference: https://mlcb.github.io/
youtube.com
May 15, 2025 at 12:24 AM
Free in-person registration is open for #MLCB2025! Sept 10-11 at @nygenome.org and online at youtube.com/@mlcbconf. Paper/abstract deadline is June 1, more deets including our fantastic invited speaker lineup at mlcb.org! Please RP.
Reposted by Shaun Mahony
🧬 Just out in Bioinformatics Advances: "Perspective on recent developments and challenges in regulatory and systems genomics"
Find the full paper here: https://doi.org/10.1093/bioadv/vbaf106
Find the full paper here: https://doi.org/10.1093/bioadv/vbaf106
May 14, 2025 at 10:02 AM
🧬 Just out in Bioinformatics Advances: "Perspective on recent developments and challenges in regulatory and systems genomics"
Find the full paper here: https://doi.org/10.1093/bioadv/vbaf106
Find the full paper here: https://doi.org/10.1093/bioadv/vbaf106
Reposted by Shaun Mahony
Our New perspective explores breakthroughs & challenges in regulatory & systems genomics: from cis-regulatory code & 3D chromatin to spatial omics & AI models.
🔗 doi.org/10.1093/bioa...
#Genomics #Bioinformatics #RegulatoryGenomics
🔗 doi.org/10.1093/bioa...
#Genomics #Bioinformatics #RegulatoryGenomics
Perspective on recent developments and challenges in regulatory and systems genomics
Abstract. Predicting how genetic variation affects phenotypic outcomes at the organismal, cellular, and molecular levels requires deciphering the cis-regul
doi.org
May 13, 2025 at 4:59 PM
Our New perspective explores breakthroughs & challenges in regulatory & systems genomics: from cis-regulatory code & 3D chromatin to spatial omics & AI models.
🔗 doi.org/10.1093/bioa...
#Genomics #Bioinformatics #RegulatoryGenomics
🔗 doi.org/10.1093/bioa...
#Genomics #Bioinformatics #RegulatoryGenomics
Reposted by Shaun Mahony
ai.stanford.edu/postdoctoral...
Postdoc candidates with strong expertise in AI for bio should apply for this new Stanford SAIL fellowship. We encourage applicants who would like to work with multiple SAIL faculty (we are part of SAIL as well). Come join us
Postdoc candidates with strong expertise in AI for bio should apply for this new Stanford SAIL fellowship. We encourage applicants who would like to work with multiple SAIL faculty (we are part of SAIL as well). Come join us
SAIL Postdoctoral Fellows – Stanford Artificial Intelligence Laboratory
ai.stanford.edu
April 18, 2025 at 5:39 PM
ai.stanford.edu/postdoctoral...
Postdoc candidates with strong expertise in AI for bio should apply for this new Stanford SAIL fellowship. We encourage applicants who would like to work with multiple SAIL faculty (we are part of SAIL as well). Come join us
Postdoc candidates with strong expertise in AI for bio should apply for this new Stanford SAIL fellowship. We encourage applicants who would like to work with multiple SAIL faculty (we are part of SAIL as well). Come join us
Reposted by Shaun Mahony
our work on the molecular differences between transcription factor isoforms is out now in Molecular Cell!
key point: 2/3rds of TF isos differ in properties like DNA binding & transcriptional activity
many are "negative regulators" & misexpressed in cancer
www.sciencedirect.com/science/arti...
key point: 2/3rds of TF isos differ in properties like DNA binding & transcriptional activity
many are "negative regulators" & misexpressed in cancer
www.sciencedirect.com/science/arti...
March 26, 2025 at 5:11 PM
our work on the molecular differences between transcription factor isoforms is out now in Molecular Cell!
key point: 2/3rds of TF isos differ in properties like DNA binding & transcriptional activity
many are "negative regulators" & misexpressed in cancer
www.sciencedirect.com/science/arti...
key point: 2/3rds of TF isos differ in properties like DNA binding & transcriptional activity
many are "negative regulators" & misexpressed in cancer
www.sciencedirect.com/science/arti...
Reposted by Shaun Mahony
Why AI won’t replace scientists capable of making disruptive conceptual breakthroughs - they pose questions that challenge, rather than align with, the training data set
thomwolf.io/blog/scienti...
thomwolf.io/blog/scienti...
🔭 The Einstein AI model
I shared a controversial take the other day at an event and I decided to write it down in a longer format: I’m afraid AI won't give us a compressed 21st century.
thomwolf.io
March 22, 2025 at 4:06 PM
Why AI won’t replace scientists capable of making disruptive conceptual breakthroughs - they pose questions that challenge, rather than align with, the training data set
thomwolf.io/blog/scienti...
thomwolf.io/blog/scienti...
Reposted by Shaun Mahony
@austintwang.bsky.social is a fantastic grad student in the lab who will be completing his PhD in the Fall & is looking for research position in AI for bio in industry.
www.austintwang.com 1/
www.austintwang.com 1/
Austin T. Wang
www.austintwang.com
March 5, 2025 at 10:11 PM
@austintwang.bsky.social is a fantastic grad student in the lab who will be completing his PhD in the Fall & is looking for research position in AI for bio in industry.
www.austintwang.com 1/
www.austintwang.com 1/
Reposted by Shaun Mahony
By crushing cancer research, what are Elon & Trump making more efficient?
Their NIH funding cuts are illegal—so instead, they're suffocating the grant approval process for cancer researchers with so much red tape that labs & clinical trials will be forced to shut down.
Their NIH funding cuts are illegal—so instead, they're suffocating the grant approval process for cancer researchers with so much red tape that labs & clinical trials will be forced to shut down.
February 24, 2025 at 9:16 PM
By crushing cancer research, what are Elon & Trump making more efficient?
Their NIH funding cuts are illegal—so instead, they're suffocating the grant approval process for cancer researchers with so much red tape that labs & clinical trials will be forced to shut down.
Their NIH funding cuts are illegal—so instead, they're suffocating the grant approval process for cancer researchers with so much red tape that labs & clinical trials will be forced to shut down.