Jeremy Gygi

Senior ML Scientist @AbbVie 💻 PhD Comp. Biology @YaleCBB 2024 🧬 BS Bioinformatics @BYU 🦾 Fascinated by ML applied to multi-omics data

[Jeremy Gygi @JeremyGygi]

Today, I’m thrilled to share a preprint of our work describing SPEAR, a sparse supervised #Bayesian factor model for #multiomic integration:

https://t.co/Z6dLUihVMx

Follow along this #tweetorial to learn about SPEAR!
@YaleCBB
(1/🧵)

[Cole Maguire @colemag9]

I’m excited to announce that our paper on viral molecular mimicry just came out! Molecular mimicry occurs when pathogens “mimic” host protein structure. Here, we explore mimicry across the human virome and its connection to autoimmunity. @MelamedEsther

https://t.co/4du8m59PbB

[Leying (Lexi) Guan @LeyingGuan]

Excited to share our latest #IMPACC study on patient subtype discovery using longitudinal multi-omics! We identified 5 subtypes among 1,000+ hospitalized #COVID19 patients, highlighting the link between distinct immune responses in those with similar respiratory status to various acute complications and #LongCOVID risk. https://t.co/8bBSb01txj
This work is co-led by wonderful students Kexin, Yutong, @colemag9, collaborators @VirusesImmunity, @JoannDArce, Lauren, and the #IMPACC consortium team.

[bpeters @bpeters]

We are excited to announce that the 3rd (Public) CMI-PB Challenge is officially underway! Test out your modeling skills to predict immune responses to B. pertussis #whoopingcough booster vaccination using multi-omics datasets for a chance to win. #bioinformatics #immunology (1/5)

[HIPC @hipcProject]

Our collaborators plot an "immune health metric" that that can be applied widely. Authors include @TsangLab @skleinstein
@NatureMedicine
The IHM
- recognizes marked #aging in healthy adults
- measures age-dependent #antibody responses to #vaccines
https://t.co/JzrriTg3Mf

[Dr. Anna Konstorum @a_konstorum]

I'm thrilled to share our new #Bioconductor package, nipalsMCIA, which performs multi-omic dimensionality reduction using the NIPALS algorithm. It is fast (especially for large datasets), and user friendly. Give it a try!
https://t.co/1wBpq016vQ (1/4)

[Kenneth Hoehn @hoehnousk]

Honored for our paper on heavy + light chain B cell tree building with Dowser to be picked as a #JI_TopRead!

[HIPC @hipcProject]

Our collaborators develop modeling that helps identify multi-omic #immune #signatures
#bioinformatics @LeyingGuan @skleinstein @JeremyGygi @a_konstorum + others
https://t.co/B1zOvFJiW9

[Journal of Clinical Investigation @jclinicalinvest]

#ClinicalMedicine:
Integrated longitudinal multiomics study identifies immune programs associated with acute #COVID_19 severity and mortality: https://t.co/tmTJ1F1EpT

@LeyingGuan @YaleMed
#Immunology

[Joann Arce, PhD @JoannDArce]

Congratulations to our #IMPACC team members @LeyingGuan @JeremyGygi @colemag9 @sciRPatel for our newly published COVID-19 multiomics paper in JCI! Grateful to be working with all of you for the past few years!

[Jeremy Gygi @JeremyGygi]

Our recent #IMPACC #COVID19 #multiomics study published in @jclinicalinvest is featured in @yalemed! Read about it:
"COVID-19: New ‘Omics’ Models Show Why Some People Are at Greater Risk of Severe Disease, Death"
https://t.co/cA99907m7Z
@LeyingGuan @colemag9 @sciRPatel

[Leying (Lexi) Guan @LeyingGuan]

I am excited to share that our #IMPACC paper - Integrated longitudinal multi-omics study identifies immune programs associated with acute COVID-19 severity and mortality - was recently published in @jclinicalinvest. https://t.co/uxzRhq3yLL #SystemsBiology #Bioinformatics [1/5]

[Waggoner Lab @LabWaggoner]

Integrated longitudinal multiomics study identifies immune programs associated with acute COVID-19 severity and mortality @jclinicalinvest @LeyingGuan
https://t.co/OwdCY8Sau5

[Hoang Van Phan @HoangVanPhan2]

Excited to share my latest research on #COVID19 and #aging, together with @ATsitsiklis and @colemag9, that just came out on @ScienceTM!
https://t.co/KfxCe4AWic

[antisense. @razoralign]

SPEAR: A supervised bayesian factor model for the identification of multi-omics signatures https://t.co/PxRaoyCuhX

[Jeremy Gygi @JeremyGygi]

So happy to have had the chance to present our work on SPEAR with @LeyingGuan and @skleinstein at the @hipcProject annual meeting! Grateful for all the valuable insight and interest.

[bpeters @bpeters]

I am excited to announce our paper predicting #immune responses after B. pertussis (#whoopingcough) booster vaccination based on the pre-vaccination immune state is coming out in the March 25th issue on @CellRepMethods https://t.co/tpc1qgxGFA #SystemsBiology #Bioinformatics (1/8)

[HIPC @hipcProject]

How can models "overfit" and fail to predict in #immunology? Our collaborators @skleinstein @LeyingGuan + @JeremyGygi explain in new paper.

https://t.co/nKo7eBQ73i

[Jeremy Gygi @JeremyGygi]

If you are working with any type of “omics” data and have a desire to find predictive analytes for a response of interest, we offer SPEAR as a free publicly available R-package. Feel free to reach out with any questions you may have.

https://t.co/Z6dLUihVMx

Thank you!

(13/13)

[Jeremy Gygi @JeremyGygi]

Today, I’m thrilled to share a preprint of our work describing SPEAR, a sparse supervised #Bayesian factor model for #multiomic integration:

https://t.co/Z6dLUihVMx

Follow along this #tweetorial to learn about SPEAR!
@YaleCBB
(1/🧵)

[Jeremy Gygi @JeremyGygi]

On both the TCGA and COVID-19 datasets, we demonstrate that SPEAR is able to construct biologically significant multi-omic factors, finding key pathways and insights that are backed by literature.

(12/13)