Jacob Schreiber
@jmschreiber91.bsky.social
Studying genomics, machine learning, and fruit. My code is like our genomes -- most of it is junk.
Assistant Professor UMass Chan, Board of Directors NumFOCUS
Previously IMP Vienna, Stanford Genetics, UW CSE.
Assistant Professor UMass Chan, Board of Directors NumFOCUS
Previously IMP Vienna, Stanford Genetics, UW CSE.
Pinned
As a field, I believe we must move towards COMIC SANS logo plots immediately.
nbviewer.org/github/saket...
nbviewer.org/github/saket...
Reposted by Jacob Schreiber
Tune in for a great MIA talk on ML for regulatory genomics by @jmschreiber91.bsky.social and Gregory Andrews now! 🧪
broad.io/mia
(Will also be available online on our YouTube playlist later: www.youtube.com/watch?v=sMTO...)
broad.io/mia
(Will also be available online on our YouTube playlist later: www.youtube.com/watch?v=sMTO...)
October 29, 2025 at 1:00 PM
Tune in for a great MIA talk on ML for regulatory genomics by @jmschreiber91.bsky.social and Gregory Andrews now! 🧪
broad.io/mia
(Will also be available online on our YouTube playlist later: www.youtube.com/watch?v=sMTO...)
broad.io/mia
(Will also be available online on our YouTube playlist later: www.youtube.com/watch?v=sMTO...)
Reposted by Jacob Schreiber
I'm happy to share that our gReLU package is now published in Nature Methods!
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 15, 2025 at 9:21 PM
I'm happy to share that our gReLU package is now published in Nature Methods!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
had to land in a nor'eastern storm in boston and i'm ready to move back to the west coast forever
October 13, 2025 at 9:37 PM
had to land in a nor'eastern storm in boston and i'm ready to move back to the west coast forever
Reposted by Jacob Schreiber
Now that I'm settled in at @umasschan.bsky.social, I'm hiring at all levels: grad students, post-docs, and software engineers/bioinformaticians!
The goal of my lab is to understand the regulatory role of every nucleotide in our genomes and how this changes across every cell in our bodies.
The goal of my lab is to understand the regulatory role of every nucleotide in our genomes and how this changes across every cell in our bodies.
October 7, 2025 at 3:24 PM
Now that I'm settled in at @umasschan.bsky.social, I'm hiring at all levels: grad students, post-docs, and software engineers/bioinformaticians!
The goal of my lab is to understand the regulatory role of every nucleotide in our genomes and how this changes across every cell in our bodies.
The goal of my lab is to understand the regulatory role of every nucleotide in our genomes and how this changes across every cell in our bodies.
Now that I'm settled in at @umasschan.bsky.social, I'm hiring at all levels: grad students, post-docs, and software engineers/bioinformaticians!
The goal of my lab is to understand the regulatory role of every nucleotide in our genomes and how this changes across every cell in our bodies.
The goal of my lab is to understand the regulatory role of every nucleotide in our genomes and how this changes across every cell in our bodies.
October 7, 2025 at 3:24 PM
Now that I'm settled in at @umasschan.bsky.social, I'm hiring at all levels: grad students, post-docs, and software engineers/bioinformaticians!
The goal of my lab is to understand the regulatory role of every nucleotide in our genomes and how this changes across every cell in our bodies.
The goal of my lab is to understand the regulatory role of every nucleotide in our genomes and how this changes across every cell in our bodies.
is it a good idea to wear a "join, or die!" hat to a big talk in europe? please say yes
September 30, 2025 at 6:15 PM
is it a good idea to wear a "join, or die!" hat to a big talk in europe? please say yes
the greatest productivity hack is having a grant deadline. there's so much other stuff you can do when you're supposed to be working on a grant.
September 22, 2025 at 2:05 PM
the greatest productivity hack is having a grant deadline. there's so much other stuff you can do when you're supposed to be working on a grant.
I was delighted to have the unexpected opportunity to give a keynote at MLCB 2025 in NYC last week. I used it to explain how I view deep learning models in genomics not as "uninterpretable black boxes" but as indispensable tools for understanding genomics + designing the next gen of synthetic DNA.
September 19, 2025 at 1:59 PM
I was delighted to have the unexpected opportunity to give a keynote at MLCB 2025 in NYC last week. I used it to explain how I view deep learning models in genomics not as "uninterpretable black boxes" but as indispensable tools for understanding genomics + designing the next gen of synthetic DNA.
for some reason i thought being a professor would involve more mentoring and research and less filling out disclosures concerning whether plants and seeds were used in my computational study
September 9, 2025 at 7:24 PM
for some reason i thought being a professor would involve more mentoring and research and less filling out disclosures concerning whether plants and seeds were used in my computational study
stocking up the new apartment with essentials
September 3, 2025 at 2:24 PM
stocking up the new apartment with essentials
Reposted by Jacob Schreiber
In the genomics community, we have focused pretty heavily on achieving state-of-the-art predictive performance.
While undoubtedly important, how we *use* these models after training is potentially even more important.
tangermeme v1.0.0 is out now. Hope you find it useful!
While undoubtedly important, how we *use* these models after training is potentially even more important.
tangermeme v1.0.0 is out now. Hope you find it useful!
August 27, 2025 at 4:20 PM
In the genomics community, we have focused pretty heavily on achieving state-of-the-art predictive performance.
While undoubtedly important, how we *use* these models after training is potentially even more important.
tangermeme v1.0.0 is out now. Hope you find it useful!
While undoubtedly important, how we *use* these models after training is potentially even more important.
tangermeme v1.0.0 is out now. Hope you find it useful!
For some reason, hitting "comment" on GitHub is significantly more responsive than a month ago and it freaks me out. Surely there are some important calculations that need to be done before letting my thoughts into the wild?
August 27, 2025 at 9:43 PM
For some reason, hitting "comment" on GitHub is significantly more responsive than a month ago and it freaks me out. Surely there are some important calculations that need to be done before letting my thoughts into the wild?
In the genomics community, we have focused pretty heavily on achieving state-of-the-art predictive performance.
While undoubtedly important, how we *use* these models after training is potentially even more important.
tangermeme v1.0.0 is out now. Hope you find it useful!
While undoubtedly important, how we *use* these models after training is potentially even more important.
tangermeme v1.0.0 is out now. Hope you find it useful!
August 27, 2025 at 4:20 PM
In the genomics community, we have focused pretty heavily on achieving state-of-the-art predictive performance.
While undoubtedly important, how we *use* these models after training is potentially even more important.
tangermeme v1.0.0 is out now. Hope you find it useful!
While undoubtedly important, how we *use* these models after training is potentially even more important.
tangermeme v1.0.0 is out now. Hope you find it useful!
An excellent post about the receptive range of convolution models.
"You might reasonably ask: "If I have 100 layers with W=1000W=1000, that's a theoretical receptive field of 100,000 tokens. Doesn't that matter?"
The answer is no, and here's why:"
guangxuanx.com/blog/stackin...
"You might reasonably ask: "If I have 100 layers with W=1000W=1000, that's a theoretical receptive field of 100,000 tokens. Doesn't that matter?"
The answer is no, and here's why:"
guangxuanx.com/blog/stackin...
Why Stacking Sliding Windows Can't See Very Far
Modern LLMs use sliding window attention for efficiency, but why can't stacking sliding windows see as far as theory suggests? A mathematical exploration of information dilution and the exponential ba...
guangxuanx.com
August 26, 2025 at 6:32 PM
An excellent post about the receptive range of convolution models.
"You might reasonably ask: "If I have 100 layers with W=1000W=1000, that's a theoretical receptive field of 100,000 tokens. Doesn't that matter?"
The answer is no, and here's why:"
guangxuanx.com/blog/stackin...
"You might reasonably ask: "If I have 100 layers with W=1000W=1000, that's a theoretical receptive field of 100,000 tokens. Doesn't that matter?"
The answer is no, and here's why:"
guangxuanx.com/blog/stackin...
First week as a faculty was successful: one grant submitted, one paper submitted, and revision requests back on one paper.
If we extrapolate, by the time I'm up for tenure I'll have 260 grants submitted (none awarded) and 260 papers submitted/reviewed (none accepted). `
lgtm
If we extrapolate, by the time I'm up for tenure I'll have 260 grants submitted (none awarded) and 260 papers submitted/reviewed (none accepted). `
lgtm
August 25, 2025 at 2:42 PM
First week as a faculty was successful: one grant submitted, one paper submitted, and revision requests back on one paper.
If we extrapolate, by the time I'm up for tenure I'll have 260 grants submitted (none awarded) and 260 papers submitted/reviewed (none accepted). `
lgtm
If we extrapolate, by the time I'm up for tenure I'll have 260 grants submitted (none awarded) and 260 papers submitted/reviewed (none accepted). `
lgtm
Almost a year ago I submitted a NIH grant and federal funding collapsed. Continuing on that success, I'm proud to announce that I've just submitted a local grant...
August 20, 2025 at 7:52 PM
Almost a year ago I submitted a NIH grant and federal funding collapsed. Continuing on that success, I'm proud to announce that I've just submitted a local grant...
now i get to be happy, right?
August 20, 2025 at 12:25 PM
now i get to be happy, right?
I'm glad that I had a chance to contribute to this wide-ranging article discussing the myriad ways ML is being used in genomics: 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 19, 2025 at 6:26 PM
I'm glad that I had a chance to contribute to this wide-ranging article discussing the myriad ways ML is being used in genomics: www.nature.com/articles/d41...
sitting across the train from a very polite customer
August 14, 2025 at 1:15 PM
sitting across the train from a very polite customer
Reposted by Jacob Schreiber
I’m also excited to be presenting Oxbow as part of my talk on composability at the #SciPy2025 Conference on Wednesday! Hope to see some of you there.
cfp.scipy.org/scipy2025/ta...
cfp.scipy.org/scipy2025/ta...
Breaking the silo: composable bioinformatics through cross-disciplinary open standards SciPy 2025
The practice of data science in genomics and computational biology is fraught with friction. This is in large part because bioinformatic tools tend to be tightly coupled to file input/output. As a res...
cfp.scipy.org
July 7, 2025 at 9:22 PM
I’m also excited to be presenting Oxbow as part of my talk on composability at the #SciPy2025 Conference on Wednesday! Hope to see some of you there.
cfp.scipy.org/scipy2025/ta...
cfp.scipy.org/scipy2025/ta...
medium demand expected
July 2, 2025 at 11:03 AM
medium demand expected
Reposted by Jacob Schreiber
Today marks the end of en-JUNE-eering, the month where I focused mostly on the nitty gritty of improving genomics ML infrastructure.
Here are some of the highlights:
Here are some of the highlights:
June 30, 2025 at 6:34 PM
Today marks the end of en-JUNE-eering, the month where I focused mostly on the nitty gritty of improving genomics ML infrastructure.
Here are some of the highlights:
Here are some of the highlights:
Today marks the end of en-JUNE-eering, the month where I focused mostly on the nitty gritty of improving genomics ML infrastructure.
Here are some of the highlights:
Here are some of the highlights:
June 30, 2025 at 6:34 PM
Today marks the end of en-JUNE-eering, the month where I focused mostly on the nitty gritty of improving genomics ML infrastructure.
Here are some of the highlights:
Here are some of the highlights:
Thank you, Google Flights, for recommending this 10 hour layover in Athens first by "convenience" when trying to find a Frankfurt -> Vienna flight.
June 30, 2025 at 5:54 PM
Thank you, Google Flights, for recommending this 10 hour layover in Athens first by "convenience" when trying to find a Frankfurt -> Vienna flight.