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Jacob Ulirsch, PhD Profile
Jacob Ulirsch, PhD

@julirsch

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766
Following
2K
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589

Genetics person at @Illumina. Previously @BBS_Harvard, @broadinstitute, Patch Bio, and @NCSSM. he/him. Black lives still matter.

Cambridge, MA
Joined February 2014
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@Satpathology
Ansu Satpathy
3 months
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
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@NovakovskyG
Gherman Novakovsky (слава Україні! 🇺🇦)
5 months
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/)
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@kjaganatha
Kishore Jaganathan
5 months
We're thrilled to introduce PromoterAI — a tool for accurately identifying promoter variants that impact gene expression. 🧵 (1/)
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@CalebLareau
Caleb Lareau
1 year
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
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@LeifLudwig
LeifLudwig
1 year
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
@CalebLareau
Caleb Lareau
1 year
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
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@karlheilbron
Karl Heilbron
1 year
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.
@medrxivpreprint
medRxiv
1 year
Simplifying causal gene identification in GWAS loci https://t.co/3cGfDEIESW #medRxiv
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@Tyler_A_Harper
Tyler Austin Harper
1 year
California
@em_Lazzy
Lazzyyyyyy
1 year
What are you convinced people are pretending to enjoy?
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@julirsch
Jacob Ulirsch, PhD
1 year
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.
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@LeifLudwig
LeifLudwig
1 year
Hello Berlin students, we are looking for a motivated student assistant to support our research team at @berlinnovation and @BIMSB_MDC: https://t.co/4mnSJuUYKz. Please apply by July 20! What we do: https://t.co/6twsZ2hCms and https://t.co/uD1ZdHwF99 Retweets welcome 🙂
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@pnatarajanmd
Pradeep Natarajan
1 year
Huge congrats to 🌟@broadinstitute postdoc @ZhiYu_ACGT for starting as an Investigator & faculty member @MGH_CTEU @MGHMedicine @harvardmed on Sep 1!
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@tuuliel_lab
Lappalainen Lab
1 year
The Leena Peltonen Prize of 2024 goes to @SashaGusevPosts 🎉! I was honored to announce this and introduce Sasha just minutes ago at #ESHG24. Huge congrats!
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@yun_s_song
Yun S. Song
1 year
An independent benchmarking study comparing 84 variant effect predictors ranked our method, CPT, at the top for DMS data, beating AlphaMissense. Many thanks to @jmarshlab for conducting this study! Marsh lab paper: https://t.co/a2zsZD5N3T Our CPT paper: https://t.co/Sop1kUF8u6
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@julirsch
Jacob Ulirsch, PhD
1 year
There's no Teams in team
@beryl_bbc
Beryl Cummings
1 year
If you've ever wondered what it's like to try to build a company (#MyOneHillToDieOn)
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@LaylaSiraj
Layla Siraj, Ph.D.
1 year
Could not be more delighted to present our work investigating how over 220,000 complex and molecular trait-associated genetic variants affect transcriptional regulation using massively parallel reporter assays! https://t.co/1eoN4OxAvd See below for a 🧵. 1/n
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biorxiv.org
Identifying the causal variants and mechanisms that drive complex traits and diseases remains a core problem in human genetics. The majority of these variants have individually weak effects and lie...
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@voidshapes
stacy 🌤
2 years
Reminder that we're back at it again tonight with a talk from @julirsch (Illumina AI) on gene variant ID + interpretation. So so excited to have cool genomics content in our lineup 🥰 Register for location or watch via Zoom (link inside) 👋
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luma.com
[IN PERSON EVENT IN BERKELEY] Join us for the 11th seminar from the BioML group in Machine Learning at Berkeley, sponsored by Pillar VC. We're hosting Jacob…
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@mfgrp
Michael Fischbach
2 years
1) Spend more time on problem choice. In science and (non-software) engineering, a typical project for a grad student might involve 1-2 weeks of planning and 2-5 years of execution. That is way out of balance, especially considering that… 4/53
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@CalebLareau
Caleb Lareau
2 years
What a PERFFect day to share our new preprint! With @tsion_abay #BobStickels @MerilTakizawa @ChaligneRonan and @Satpathology, we introduce PERFF-seq, a new experimental approach to studying rare cells with scRNA-seq via transcript-specific enrichment. https://t.co/woKvdEdOf0 1/n
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biorxiv.org
Single-cell genomics technologies have accelerated our understanding of cell-state heterogeneity in diverse contexts. Although single-cell RNA sequencing (scRNA-seq) identifies many rare populations...
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@JorgeCondeBio
Jorge Conde
2 years
Congratulations to JB Michel, Uri Laserson & the brilliant team at Patch Biosciences on their acquisition by @Ginkgo Excited to bring Patch together with @jrkelly & Team Ginkgo to use AI to develop more effective, specific & durable genetic medicines. https://t.co/ag0PgXDIXI
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