Jeff Wintersinger
@jwintersinger.bsky.social
Senior Research Scientist in comp bio at @deepgenomics. Did PhD work on cancer evolution. My three favourite things are bananas, riding my bike very fast, and vim.
Reposted by Jeff Wintersinger
Nature Reviews Methods Primers: Uniform manifold approximation and projection (UMAP) www.nature.com/articles/s43... 🧬🖥️🧪 read free: rdcu.be/d0YZT
May 21, 2025 at 3:31 PM
Nature Reviews Methods Primers: Uniform manifold approximation and projection (UMAP) www.nature.com/articles/s43... 🧬🖥️🧪 read free: rdcu.be/d0YZT
Reposted by Jeff Wintersinger
Published in today's issue! OPEN ACCESS article, FREE massive dataset, FREE code, FREE pre-trained AI/ML model. #OpenScience was a mountain of work to make this happen: check it out if you haven't already 😉
Massively parallel characterization of transcriptional regulatory elements - Nature
Lentivirus-based reporter assays for 680,000 regulatory sequences from three cell lines coupled to machine-learning models lead to insights into the grammar of cis-regulatory elements.
www.nature.com
March 13, 2025 at 7:32 PM
Published in today's issue! OPEN ACCESS article, FREE massive dataset, FREE code, FREE pre-trained AI/ML model. #OpenScience was a mountain of work to make this happen: check it out if you haven't already 😉
Reposted by Jeff Wintersinger
1. Imagine we land a space probe on one of Jupiters’ moons, take up a sample of material, and find it is full of organic molecules. How can we tell whether those molecules are just randomly assembled goo or the outcome of some evolutionary process taking place there? 🧪
October 13, 2023 at 4:13 AM
1. Imagine we land a space probe on one of Jupiters’ moons, take up a sample of material, and find it is full of organic molecules. How can we tell whether those molecules are just randomly assembled goo or the outcome of some evolutionary process taking place there? 🧪
Reposted by Jeff Wintersinger
Hey #BikeTO! @cycletoronto.bsky.social has launched a campaign shaming Stantec Consulting Ltd for being retained to do work associated with Doug Ford's bike lane removal efforts. Please sign & spread the word. #TOpoli #ONpoli #VoteFordOut www.cycleto.ca/shame_on_you...
Shame on you, Stantec
www.cycleto.ca
January 29, 2025 at 10:35 PM
Hey #BikeTO! @cycletoronto.bsky.social has launched a campaign shaming Stantec Consulting Ltd for being retained to do work associated with Doug Ford's bike lane removal efforts. Please sign & spread the word. #TOpoli #ONpoli #VoteFordOut www.cycleto.ca/shame_on_you...
Reposted by Jeff Wintersinger
I wanted to write briefly about a very pleasant experience we recently had coordinating and collaborating closely on competing publications with 2 other teams. 1/
January 24, 2025 at 7:36 PM
I wanted to write briefly about a very pleasant experience we recently had coordinating and collaborating closely on competing publications with 2 other teams. 1/
Reposted by Jeff Wintersinger
Some thoughts about what I am looking forward this year from my vantage point of computational molecular biology. One mega-trend for me; we will definitely see more AI methods of all sorts emerge.
January 3, 2025 at 6:46 PM
Some thoughts about what I am looking forward this year from my vantage point of computational molecular biology. One mega-trend for me; we will definitely see more AI methods of all sorts emerge.
This looks like a wonderful gift to start 2025 off right 🤗
A generative framework for enhanced cell-type specificity in rationally designed mRNAs https://www.biorxiv.org/content/10.1101/2024.12.31.630783v1
December 31, 2024 at 4:07 PM
This looks like a wonderful gift to start 2025 off right 🤗
A Scottish study of 83k individuals over 17 years found commuting by bike halves the risk of early death: bmjpublichealth.bmj.com/content/2/1/.... The one outlier hazard ratio for people on bikes casts a harsh light on the Ford government's quest to destroy safe infrastructure in Toronto. #BikeTO
December 18, 2024 at 12:35 PM
A Scottish study of 83k individuals over 17 years found commuting by bike halves the risk of early death: bmjpublichealth.bmj.com/content/2/1/.... The one outlier hazard ratio for people on bikes casts a harsh light on the Ford government's quest to destroy safe infrastructure in Toronto. #BikeTO
Reposted by Jeff Wintersinger
Finally out! We present EXTRA-seq, a new EXTended Reporter Assay to quantify endogenous enhancer-promoter communication at kb scale!
www.biorxiv.org/content/10.1...
A 🧵about what it can do:
#SynBio #DeepLearning #GeneRegulation
www.biorxiv.org/content/10.1...
A 🧵about what it can do:
#SynBio #DeepLearning #GeneRegulation
EXTRA-seq: a genome-integrated extended massively parallel reporter assay to quantify enhancer-promoter communication
Precise control of gene expression is essential for cellular function, but the mechanisms by which enhancers communicate with promoters to coordinate this process are not fully understood. While seque...
biorxiv.org
December 16, 2024 at 2:39 PM
Finally out! We present EXTRA-seq, a new EXTended Reporter Assay to quantify endogenous enhancer-promoter communication at kb scale!
www.biorxiv.org/content/10.1...
A 🧵about what it can do:
#SynBio #DeepLearning #GeneRegulation
www.biorxiv.org/content/10.1...
A 🧵about what it can do:
#SynBio #DeepLearning #GeneRegulation
Reposted by Jeff Wintersinger
(1/10) Excited to announce our latest work! @arpita-s.bsky.social, @amanpatel100.bsky.social , and I will be presenting DART-Eval, a rigorous suite of evals for DNA Language Models on transcriptional regulatory DNA at #NeurIPS2024. Check it out! arxiv.org/abs/2412.05430
DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA
Recent advances in self-supervised models for natural language, vision, and protein sequences have inspired the development of large genomic DNA language models (DNALMs). These models aim to learn gen...
arxiv.org
December 11, 2024 at 2:30 AM
(1/10) Excited to announce our latest work! @arpita-s.bsky.social, @amanpatel100.bsky.social , and I will be presenting DART-Eval, a rigorous suite of evals for DNA Language Models on transcriptional regulatory DNA at #NeurIPS2024. Check it out! arxiv.org/abs/2412.05430
Reposted by Jeff Wintersinger
What's gayer than spandex? #bicycling #PattieGonia
December 7, 2024 at 9:18 PM
What's gayer than spandex? #bicycling #PattieGonia
Reposted by Jeff Wintersinger
So excited for this! The fight will be waged on all fronts.
Support @cycletoronto:
www.cycleto.ca/donate?utm_c...
Support @cycletoronto:
www.cycleto.ca/donate?utm_c...
December 3, 2024 at 6:25 PM
So excited for this! The fight will be waged on all fronts.
Support @cycletoronto:
www.cycleto.ca/donate?utm_c...
Support @cycletoronto:
www.cycleto.ca/donate?utm_c...
Reposted by Jeff Wintersinger
In response to last Monday's passing of Bill 212, @joelharden.bsky.social launched a new petition to repeal the legislation and "immediately stop the government’s attack against life-saving active transportation infrastructure." #BikeTO #ottbike #TOpoli #ONpoli www.joelhardenmpp.ca/stay_in_your...
Premier Ford: Stay In Your Lane
MPP / Député, Ottawa Centre
www.joelhardenmpp.ca
December 4, 2024 at 1:32 AM
In response to last Monday's passing of Bill 212, @joelharden.bsky.social launched a new petition to repeal the legislation and "immediately stop the government’s attack against life-saving active transportation infrastructure." #BikeTO #ottbike #TOpoli #ONpoli www.joelhardenmpp.ca/stay_in_your...
Reposted by Jeff Wintersinger
Reposted by Jeff Wintersinger
A pair of graphs I think about a lot. On the topic of pooled CRISPR screens, the left is "replicate correlation" when simply examining the abundance of guide RNAs, i.e. log-normalized read counts. On the right is taking those same data and subtracting from a common starting point, i.e. pDNA.
November 26, 2024 at 3:31 PM
A pair of graphs I think about a lot. On the topic of pooled CRISPR screens, the left is "replicate correlation" when simply examining the abundance of guide RNAs, i.e. log-normalized read counts. On the right is taking those same data and subtracting from a common starting point, i.e. pDNA.
Reposted by Jeff Wintersinger
Since it is inefficient to attempt to educate every reviewer individually, I am yeeting into your feed this clear paper from Gelman, Hill, and Yajima on how Bayesians can do even better than correcting for multiple comparisons. arxiv.org/abs/0907.2478
Why we (usually) don't have to worry about multiple comparisons
Applied researchers often find themselves making statistical inferences in settings that would seem to require multiple comparisons adjustments. We challenge the Type I error paradigm that underlies t...
arxiv.org
November 26, 2024 at 9:11 AM
Since it is inefficient to attempt to educate every reviewer individually, I am yeeting into your feed this clear paper from Gelman, Hill, and Yajima on how Bayesians can do even better than correcting for multiple comparisons. arxiv.org/abs/0907.2478
Reposted by Jeff Wintersinger
My deep learning course at the University of Geneva is available on-line. 1000+ slides, ~20h of screen-casts. Full of examples in PyTorch.
fleuret.org/dlc/
And my "Little Book of Deep Learning" is available as a phone-formatted pdf (nearing 700k downloads!)
fleuret.org/lbdl/
fleuret.org/dlc/
And my "Little Book of Deep Learning" is available as a phone-formatted pdf (nearing 700k downloads!)
fleuret.org/lbdl/
November 26, 2024 at 6:15 AM
My deep learning course at the University of Geneva is available on-line. 1000+ slides, ~20h of screen-casts. Full of examples in PyTorch.
fleuret.org/dlc/
And my "Little Book of Deep Learning" is available as a phone-formatted pdf (nearing 700k downloads!)
fleuret.org/lbdl/
fleuret.org/dlc/
And my "Little Book of Deep Learning" is available as a phone-formatted pdf (nearing 700k downloads!)
fleuret.org/lbdl/
Reposted by Jeff Wintersinger
A person on a bicycle is by far the most energy-efficient among animals and machines per distance traveled relative to body weight. The bicycle is magic.
www.jstor.org/stable/24923...
www.jstor.org/stable/24923...
November 24, 2024 at 11:12 PM
A person on a bicycle is by far the most energy-efficient among animals and machines per distance traveled relative to body weight. The bicycle is magic.
www.jstor.org/stable/24923...
www.jstor.org/stable/24923...
I don't understand why Santa had to close down all of University for his little parade today. He should just take the side streets. #biketo
November 24, 2024 at 7:33 PM
I don't understand why Santa had to close down all of University for his little parade today. He should just take the side streets. #biketo
Reposted by Jeff Wintersinger
Resharing here a recent X post. In this preprint, we introduce an improved version of NanoSeq, a duplex sequencing protocol with <5 errors per billion bp in single DNA molecules, and use it to study the somatic mutation landscape of oral epithelium in >1000 people. 1/ www.medrxiv.org/content/10.1...
Somatic mutation and selection at epidemiological scale
As we age, many tissues become colonised by microscopic clones carrying somatic driver mutations ([1][1]–[10][2]. Some of these clones represent a first step towards cancer whereas others may contribu...
www.medrxiv.org
November 20, 2024 at 2:28 PM
Resharing here a recent X post. In this preprint, we introduce an improved version of NanoSeq, a duplex sequencing protocol with <5 errors per billion bp in single DNA molecules, and use it to study the somatic mutation landscape of oral epithelium in >1000 people. 1/ www.medrxiv.org/content/10.1...
Reposted by Jeff Wintersinger
Reposted by Jeff Wintersinger
Such an interesting read from @math-rachel.bsky.social who has a remarkable gift for making complex topics (like AI ∩ immunology) accessible as well as engaging -> rachel.fast.ai/posts/2024-0... #biosky #medsky
Rachel Thomas, PhD - AI’s Quest to Predict T Cell Binding– The Holy Grail of Immunology
an AI researcher going back to school for immunology
rachel.fast.ai
November 20, 2024 at 1:39 AM
Such an interesting read from @math-rachel.bsky.social who has a remarkable gift for making complex topics (like AI ∩ immunology) accessible as well as engaging -> rachel.fast.ai/posts/2024-0... #biosky #medsky
Wow! I had no idea that Colonel Sanders lived close to Toronto for his final years. I'm honoured ☺️🐔☺️ That gives me one more fun fact to tell visitors, right after I show them the insulin exhibit in the MaRS entrance.
"MaRS is fine." is going to make me chuckle every time I walk past MaRS.
mishaglouberman.substack.com/p/stop-prete...
mishaglouberman.substack.com/p/stop-prete...
November 19, 2024 at 1:31 PM
Wow! I had no idea that Colonel Sanders lived close to Toronto for his final years. I'm honoured ☺️🐔☺️ That gives me one more fun fact to tell visitors, right after I show them the insulin exhibit in the MaRS entrance.