@vyao

assistant prof of CS @RiceUniversity computational biology, disease genomics, data visualization https://xitter.cf/t.co/rrmgfgO9DC

 Rice University
cs.rice.edu/~vy/
Joined November 2008
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🚨 Faculty position alert! 🚨 @Rice_BIOE is now accepting applications for a tenure-track faculty position: apply.interfolio.com/152536 Please direct questions to me or search co-chair @veiseho Join a collegial faculty located in the biggest medical center in the world!
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Announcing the Sept. 11th invited speakers for the #AIHealthConference, Drs. Josiah Hester @ProfJosiah (Georgia Tech), Abria Magee (CPRIT), and Vicky Yao @vyao (Rice University)! Learn more about their sessions and the rest of Wednesday's lineup at aihealthconference.com.
Invited speakers for Wednesday, September 11th of the AI in Health Conference: Josiah Hester, PhD, Abria Magee

ALT Invited speakers for Wednesday, September 11th of the AI in Health Conference: Josiah Hester, PhD, Abria Magee

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Thanks @cziscience! Excited for this project 😄
Rice University Computer Science@RiceCompSci8 Aug 2024
Rice CS' Vicky Yao has been awarded a Data Insights award from the @ChanZuckerberg Initiative to characterize single-cell RNA-sequencing tools and track trends of their use across biomedical literature. bit.ly/3YHIRAl @vyao
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Had the pleasure of sharing my work in ontology-aware DNA methylation prediction at #ISMB2024!
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Anyone who’s interested come and visit poster 168 so that we can discuss everything there! It’s 7-10 pm tonight at Biondi Hall of #BoG24!
Vicky Yao@vyao9 May 2024
Replying to @vyao
One of the important factors that helped me stop procrastinating writing this thread is that @QiliangLai is at #BoG24 presenting this work later tonight! If you’re around and curious, catch him at poster 186 from 7pm-10pm! n=9
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Been behind on tweeting (x’ing?) about recent work, but wanted to highlight a new preprint: seismic, a framework that connects complex traits and diseases to cell types!🌋 This work was a collaboration between my group (@QiliangLai, @dnflsr) and @JP_Roussarie at @BUMedicine. 1/n
Flowchart of the seismic framework. "seismic allows for a flexible set of cell type labels or granularities, ranging from broader cell classes to specifically defined cell types, before calculating a novel gene specificity score for each of the corresponding cell characterizations. Within the selected granularity, seismic calculates the statistical significance of a cell type-trait association using a regression-based framework with the gene specificity scores and MAGMA z-scores. Unlike existing methods, individual gene contributions to the cell type-trait association can be quantified via influential gene analysis and can pinpoint the genes and underlying biological processes that drive significant associations."

ALT Flowchart of the seismic framework. "seismic allows for a flexible set of cell type labels or granularities, ranging from broader cell classes to specifically defined cell types, before calculating a novel gene specificity score for each of the corresponding cell characterizations. Within the selected granularity, seismic calculates the statistical significance of a cell type-trait association using a regression-based framework with the gene specificity scores and MAGMA z-scores. Unlike existing methods, individual gene contributions to the cell type-trait association can be quantified via influential gene analysis and can pinpoint the genes and underlying biological processes that drive significant associations."

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Here's the preprint: biorxiv.org/content/10.1101/… And we've also built seismic into a fast, easy to use R package! github.com/ylaboratory/seism… 8/n

Disentangling associations between complex traits and cell types with seismic

Integrating single-cell RNA sequencing (scRNA-seq) with Genome-Wide Association Studies (GWAS) can help reveal GWAS-associated cell types, furthering our understanding of the cell-type-specific...

biorxiv.org
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One of the important factors that helped me stop procrastinating writing this thread is that @QiliangLai is at #BoG24 presenting this work later tonight! If you’re around and curious, catch him at poster 186 from 7pm-10pm! n=9
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Another fun collab!
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Rice University's @traingene and @vyao will be hosting the 2nd annual #RADGenomics Workshop at the #AIHealthConference on October 9, 2023. "Reading, Assembling, Analyzing & Designing Genomic Data." View details at aihealthconference.com/works….
RAD Genomics Workshop | October 9, 2023

ALT RAD Genomics Workshop | October 9, 2023

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Now out! academic.oup.com/bioinformat…

Joint embedding of biological networks for cross-species functional alignment

AbstractMotivation. Model organisms are widely used to better understand the molecular causes of human disease. While sequence similarity greatly aids this

academic.oup.com
Vicky Yao@vyao23 Jan 2022
It’s a preprint! A new approach for network embedding & alignment, called ETNA: this work was the result of a fruitful collaboration between my group (@lli_rice, @dnflsr, Nathaniel Hejduk) and Santiago Segarra’s (w/ Yu Zhu) in @RiceECE. 1/n biorxiv.org/content/10.1101/…

Joint embedding of biological networks for cross-species functional alignment

Model organisms are widely used to better understand the molecular causes of human disease. While sequence similarity greatly aids this transfer, sequence similarity does not imply functional...

biorxiv.org
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So glad this cool collab is out w/ @danaorange ! Always impressed at how she can bring a story involving so many moving parts + labs together😀
Dana Orange@danaorange22 Feb 2023
I’m pleased to share our new paper showing how “leaky gums” can contribute to disease activity in rheumatoid arthritis. #rheumatoidarthritis #dentistry science.org/doi/10.1126/scit…

Oral mucosal breaks trigger anti-citrullinated bacterial and human protein antibody responses in...

Rheumatoid arthritis autoantibodies target oral bacteria detected in flare-associated bacteremias that activate inflammatory monocytes.

science.org
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Join us on November 7th for a free RAD #Genomics Workshop on Reading, Assembling, Analyzing, & Designing Genomic Data led by Todd Treangen & Vicky Yao from @RiceUniversity. #AIHealthConference bit.ly/3wi8qc9
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⏰The submission deadline for the Visualization in Biomedical AI workshop is approaching (Aug 17, AoE). Here are some exciting updates about the keynote and the panel discussion! (1/4)
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