Todd Bartkowiak

Immunologist interested in glioblastoma research, tumor immunology, immunotherapy, cytometry, and computational biology

[Janet Markle @JanetMarkle]

We've also recently published on the clinical and immunological impacts of a novel CTLA4 mutation in a large kindred. Led by @jimmy_maiarana, our multi-talented R38 resident https://t.co/wZMU6RFUK5

[Laura Geben @laura_geben]

Thrilled to be defending my dissertation next week to be receiving my PhD from @VUmedicine! It's been a great 5 years in the @IhrieLab and @VandyPharm and I'm excited to share some of my work with the community. 🧪🧠🐭 Zoom link available if you're interested. @BiomedVandy

[Bo Wang @BoWang87]

🎉Exciting Update of scGPT 🎉: After receiving significant attention from the community since our April release, we're thrilled to announce the first major update for scGPT - a foundation model for single-cell multi-omic data.

This update integrates community feedback and leverages the latest data release from @cellxgene. It boasts larger pretraining data, and more robust models, and expands the range of application tasks.

Pre-print (V2) available: https://t.co/4aB2c4ZgJy
Access our open-source code and models here: https://t.co/13n0bJvgT2
Detailed tutorials: https://t.co/enNqXqXkdY

Highlights of this update include:

🔬 Introducing the first GPT-style foundation model for single-cell multi-omic data, pretrained on over 33M human cell atlas data.

💡 Our generalist approach enables one model to accomplish multiple tasks in single-cell analysis, including multi-omic integrative analysis and perturbation prediction.

🧬 Discovering gene-gene interactions specific to various conditions using learned attention weights and gene embeddings.

🚀 Uncovered a scaling law showcasing continuous model performance enhancement as data volume increases.

🐾 scGPT model zoo (see github) now offers multiple pre-trained foundation models for various solid organs and a comprehensive pan-cancer model. Begin exploring your data with the most fitting foundation model.

We welcome your thoughts on specialist vs generalist approaches in single-cell studies. Many thanks for the following technical analyses of scGPT:
1. Excellent twittorial by @simocristea: https://t.co/ICq3V78oxG
2. Comprehensive review on LLM in cell biology by @s_batzoglou: https://t.co/xtl5WCXijC
3. Insightful blog by @SalvatoreRaieli: https://t.co/7v8PRv9NNc

Kudos to Haotian (@HAOTIANCUI1) & Chloe (@chloexwang1) for their exemplary work on this project. @VectorInst @pmcc_ai @UHNAIHUB @bradwouters @drbarryrubin @UofT_TCAIREM @UofT_LMP @UofTCompSci @uoftmedicine

[JCI insight @JCI_insight]

Lateral ventricle-contacting glioblastomas have a distinct immunosuppressive microenvironment: https://t.co/GKHANOZ2HK
@jonathanirish @IhrieLab @lolachambless @toddbart001 @VUMChealth
#Immunology #Oncology

[Todd Bartkowiak @toddbart001]

What a great opportunity to share our work on IEI and the effect of IL-6 on immunometabolism in patients with STAT1-GOF mutations! @ImmunologyAAI

[The Journal of Immunology @J_Immunol]

What great talks from our @J_Immunol & @ImmunoHorizons authors at
#AAI2023 #Societypublisher
@DrNityaJain, @toddbart001, @taylor_tct, @ObarLab, @ZhichaoFan & @vanessa771987 . Thanks to cochairs @DJC5651 & @EugeneOltz

[Sylvester Comprehensive Cancer Center @SylvesterCancer]

.@DionysiosWatson and @d_bayik, researchers and co-first authors of a groundbreaking, preclinical study, identified how #glioblastoma cells obtain fuel to become aggressive and new ideas on how to target the deadly #BrainCancer. Learn more: https://t.co/f8AMXJ3uVZ

[The Journal of Immunology @J_Immunol]

Spotlight on AAI Journals (Sat. @ 10:15 Rm 202B) panelists: @DrNityaJain @toddbart001 @taylor_tct, @ObarLab @ZhichaoFan & @vanessa771987 | highlight papers recently published in @J_Immunol & @ImmunoHorizons #societypublisher #AAI2023

[SITC Early Career Scientist Committee @sitcancerECS]

Register for the free SITC-@theNCI Comp IO 2023 webinar series. Led by experts in the field, this 8 webinar series will help individual research labs embrace the computational challenges of analyzing and integrating diverse data across the spectrum of IO. https://t.co/9QYXZ3d1v8

[Vanderbilt Cell and Developmental Biology @VanderbiltCDB]

🔬 Nice publication from the @IhrieLab @scbiolab lab "Learning cell identity in immunology, neuroscience, and cancer." https://t.co/bH8PnqOGXd
@VUBasicSciences

[Vanderbilt Cell and Developmental Biology @VanderbiltCDB]

🎯 preprint highly collaborative publication @IhrieLab @scbiolab @marychalkley @laura_geben "Dephosphorylation of 4EBP1/2 Induces Prenatal Neural Stem Cell Quiescence" https://t.co/OgRtayZMSl
@VUBasicSciences

[Emily Baker, Ph.D. @enarner]

Interested in how metabolism of immune cells within the TME can drive tumor progression? Check out our new review in ⁦@Cancer_Cell⁩! ⁦⁦@JeffRathmell⁩ https://t.co/ZIyjhyipJD

[Laura Geben @laura_geben]

Excited to share my work in the
@IhrieLab detailing a new potential regulatory mechanism of the quiescence entry that preserves neural stem cells in the embryo for the adult brain. @VUBasicSciences

[Todd Bartkowiak @toddbart001]

Hot off the presses! Our mxIHC analysis pipeline. Great teamwork including @IhrieLab @jonathanirish @christine_lovly @coussens_lisa Alignment, segmentation and neighborhood analysis in cyclic immunohistochemistry data using CASSATT https://t.co/GGNZL9X5r2

[SNO @NeuroOnc]

Novel Murine Glioblastoma Models That Reflect the Immunotherapy Resistance Profile of Human Disease https://t.co/VKNXDJ7t4S

[Jeff Rathmell @JeffRathmell]

Great work by Andrew Patterson to show IEI & IEM share more than previously known--a CRISPR resource for new immunometabolic genes

Functional Overlap of Inborn Errors of Immunity and Metabolism Genes Define T Cell Immunometabolic Vulnerabilities https://t.co/7EdsoOOkfO

[Ruben Martinez Barricarte @RMBarricarte]

Check out our latest article!!

[Casey Ager @caseyager]

Ager Lab postdoc position currently open! More to come. Please share! Also feel free to DM if interested.

https://t.co/sGrX7mLp26

[Denis Mogilenko @denis_mogilenko]

Our lab is hiring! We are looking for a Research Assistant interested in studying how obesity reprograms the immune system and leads to inflammatory diseases. Please apply to join the fantastic @VUMC_VCI research community! ⬇️
https://t.co/1dNLyO33lu or DM

[Brendan Horton @blhorton]

Everyone at #SITC22 should come to the @sitcancerECS networking event tonight at the Omni at 9 PM! Fun party, great colleagues, free food and drinks!

[Dr. Josephine Giles @facts___matter]

So excited to share our work out in @NatImmunol !!! We analyzed antigen-specific CD8 T cells differentiating down effector/memory vs exhaustion (Exh) lineages using scRNAseq/scATACseq. Major findings 👇
@EJohnWherry @PennMedicine

https://t.co/ufRymESObz