Jacob Ulirsch, PhD retweetledi
Jacob Ulirsch, PhD
594 posts
Jacob Ulirsch, PhD
@julirsch
Genetics person at @Illumina. Previously @BBS_Harvard, @broadinstitute, Patch Bio, and @NCSSM. he/him. Black lives still matter.
Cambridge, MA Katılım Şubat 2014
1K Takip Edilen761 Takipçiler
Jacob Ulirsch, PhD retweetledi
@CalebLareau is doing some of the most compelling work on viral contributions to human disease.
Here showing herpesvirus reactivation in Alzheimer’s disease.
x.com/CalebLareau/st…
Caleb Lareau@CalebLareau
A history of viral encephalitis is one of the strongest risk factors for developing dementia. With @JacobJacobog02, Yifan Chen, @RNA_Life, and @RyanDhindsa, we refine this link by describing a neuronal cell type that can reactivate HSV-1 in humans 1/n biorxiv.org/content/10.648…
English
Jacob Ulirsch, PhD retweetledi
We’re unwrapping a new method today @MSKCancerCenter!
Led by @SydneyBlattman, @NabihMaslah, @AustinAVarela, Ronan Chaligne and @dana_peer, plus colleagues at @10xGenomics, we’re delighted to share Genotyping In Fixed Transcriptomes (GIFT):
biorxiv.org/content/10.648…
1/n
English
Jacob Ulirsch, PhD retweetledi
As someone who has covered cancer drug development for 25 years, one of the few things I am sure of is that the odds of technology folks thinking they understand biology are much higher than the odds they actually do.
Egan Peltan@EganPeltan
This is totally out of control: There’s 0 - I repeat 0 - evidence any of the LLM work did anything meaningful for Rosie’s cancer I’m sorry to rain on the parade here. I know we want to believe. But, it’s possible to do a lot of things and have nothing happen @paul_conyngham co-administered α-PD-1 (conventional immunotherapy) with a TKI and the mRNA. It’s probably the most effective cancer immunotherapy of all time. This isn’t a small detail! There’s no evidence his process (beyond FDA approved doggie α-PD-1) had any impact on disease progression. The most parsimonious explanation is a partial response to α-PD-1 I get it. The chat bots make for a great story (although checking multiple LLMs isn’t validation), but it’s really just a neat story. It’s fundraising copy. Before he starts selling the “custom neoantigen mRNA vax” story to consumers, he should provide some evidence it did anything! That’s responsible citizen science This is just storytelling for the AGI true believers. Specifically, a story in search of venture money
English
Jacob Ulirsch, PhD retweetledi
Pinpointing the exact noncoding variants behind disease associations is challenging. Using MPRA, @LaylaSiraj, @julirsch, @ReillyLikesIt, @r_tewhey et al tested >220K variants in 5 cell types, resolving >13K & revealing mechanisms behind many disease traits broad.io/MPRA-news
English
Jacob Ulirsch, PhD retweetledi
⚠️ If you’re reading this, you’ve been infected* ⚠️
*~95% the human population has been infected by the Epstein-Barr Virus (EBV).
Today in @Nature with @nyeo_sherry, @EMC22381830, @RyanDhindsa @SlavePetrovski, we shed some light on what happens next.
nature.com/articles/s4158…
English
Jacob Ulirsch, PhD retweetledi
Ever wondered how to choose weights for rare variant burden/SKAT tests? @jschwart37 and I did too! Check out our (@illumina) straightforward new approach that improves discovery by ~50% or more than STAAR, Regenie, and DeepRVAT!
Jeremy Schwartzentruber@jschwart37
Let’s talk about rare variant association tests - we have a new method that helps you discover more with the same data! It’s called FlexRV to signal our approach: Flexibly modeling rare variant pathogenicity improves gene discovery for complex traits. biorxiv.org/content/10.110…
English
Jacob Ulirsch, PhD retweetledi
I am a strong believer that depth of data can be just as powerful as scale of data. Deep analysis of small groups of humans, and even individuals, can lead to novel biological insights and principles.
Today I am the guinea pig. In my own blood, @CalebLareau finds strong evidence that a synonymous genetic variant (no amino acid change in the protein) can impact T cell function via altered codon syntax.
pnas.org/doi/10.1073/pn…
English
Jacob Ulirsch, PhD retweetledi
Excited to share my first contribution here at Illumina! We developed PromoterAI, a deep neural network that accurately identifies non-coding promoter variants that disrupt gene expression.🧵 (1/)
English
Jacob Ulirsch, PhD retweetledi
We're thrilled to introduce PromoterAI — a tool for accurately identifying promoter variants that impact gene expression. 🧵 (1/)
English
@SashaGusevPosts The spicy chicken sandwich and the iced coffee are bops. And the best fast food fries for decades
English
Educated elite here, and I think McDonald's is delicious, eat there regularly (had the McRib this week b/c I'm a sucker for limited offers), enjoy seeing the old-timers and regulars, and am looking forward to a conference in Chicago so I can finally tour Hamburger University.
@ijbailey@ijbailey
This is the sum total of evidence in the piece for this sweeping claim: “They [the highly-educated] alone, as a group, seem to have moral issues with McDonald’s…” In other words, typical FP. No evidence required.
English
📣Big news! Our tag-team effort on common variants in rare neurodevelopmental conditions is now out in @Nature! 📣
Co-first authoring with the brilliant @qinqin_huang🌟—proof that teamwork does make the dream work. 💪 nature.com/articles/s4158…
GIF
English
Jacob Ulirsch, PhD retweetledi
Though the coarse tree topologies may appear similar between versions, the relative placement of cells (color bar) in the two trees is ~random! We therefore disagree that ReDeeM is “robust and reliable” between versions as edge variants in -1 remains a large driving signal. 5/n
English
Jacob Ulirsch, PhD retweetledi
In addition to the technical points raised by @CalebLareau, several biological questions remain after this preprint. We would appreciate your thoughts as these were not addressed @chenweng1991, @jswlab, @bloodgenes. 1/n
Caleb Lareau@CalebLareau
Thank you @chenweng1991, @jswlab, @bloodgenes for the feedback on our work. @LeifLudwig and I agree that the “-2” filtering method that mitigates edge bias is a critical development for ReDeeM. Nevertheless, we stand by our original preprint, noting the following: 1/n
English
my hot take is that nothing inspired by mexican food is bad. even the worst food at taco bell is good. real mexican food is better and homemade authentic mexican food is off the charts. but even this thing in a bag will taste good.
Christopher Ingraham🦗@_cingraham
This is probably what he's talking about, btw. They put ground beef and cheddar and maybe iceberg lettuce in a Doritos bag. They call it "taco in a bag" and it should be illegal.
English
@mike_feigin Mustard or mustard powder obliterates any cheese u use into velvety goodness. Just don't use too much or the tangy flavor is noticeable
English
Jacob Ulirsch, PhD retweetledi
Tools that predict the causal genes in GWAS loci are too complex! Many use XGBoost models with >45 features (i.e. L2G, Ei).
CALDERA achieves better performance despite using LASSO regression and only 12 features. This makes it much easier to understand why a gene was chosen.
medRxiv@medrxivpreprint
Simplifying causal gene identification in GWAS loci medrxiv.org/cgi/content/sh… #medRxiv
English
Jacob Ulirsch, PhD retweetledi
Any white hats out there want to make a virus that gets famous scientists to tweet about my recent papers? Unrelated, I just got a new MacBook for cheap ask me how.
English