Alexander

Computational Biologist @HiCinNYC

[Varvara Paraskevopoulou @VarvaraParask]

Respiratory failure is a leading cause of death in AML.
It begins when leukemia infiltrates the lung. Almost nothing was known about what happens locally.
We looked.
🧵 @NatImmunol
🔗 https://t.co/OkhyRTRN4F

[Effie Apostolou @efapostolou29]

Check it out and register for free! Always incredibly fun and impactful science and an amazing panel of speakers! Very glad to participate as an organizer this year #chromatin #cancer #4DNucleome

[UkJin Lee @6jinLee]

Cohesin is essential for maintaining structural loops but less so for regulatory loops and transcription. Is cohesin actually required for the establishment of loops and transcriptional activation?🧵https://t.co/HuJGghT0ZQ

[Dafne Campigli Di Giammartino @DafneDiGiammart]

🚀🚀🚀 Feeling beyond grateful and thrilled to share that our lab has been awarded the FIS grant from the Italian Ministry of Education!

📢 To all chromatin lovers: our lab will soon be opening up several positions! Contact me directly if interested!

https://t.co/CNGIheACL8

[Franco Izzo @FrancoIzzo85]

GoT-ChA!

I am thrilled to announce that our paper "Mapping Genotypes to Chromatin Accessibility Profiles in Single Cells" is now out in @Nature !!

👩‍🔬👨‍🔬🧬If you want to link somatic mutations to epigenetic changes directly in patient samples:

https://t.co/M9Y3wEvpuW
👇🧵

[Alexander @AlexPPolyzos]

@djmurph93 @SalataAda Cheat sheet:
i. Yes, 1toMany
ii. High co-regulation in 3D hubs
iii. Yes
iv. 3D-HiChAT model which predicts impactful enhancers & hubs.

Bonus cheat: 3D HiChAT survived the tests in multiple Mouse and Human cell lines and generated similar scores.

[Alexander @AlexPPolyzos]

Excited for our latest work https://t.co/sGY8XxJm4C with @efapostolou29 & @artsinyc. We study the role of 3D hubs & enhancer rewiring in early developmental lineages & introduce 3D-HiChAT machine learning approach to nominate impactful enhancers for gene regulation.

[Alexander @AlexPPolyzos]

@djmurph93 @SalataAda i. Multi-connectivity and gene expression: A 1-to-many relationship?
ii. Gene co-regulation in and out of the 3D hubs.
iii. Can enhancer rewiring dictate cell type specificity?
iv. What happens if we code all these questions in a ML?

Bonus question: How applicable is this ML?

[Iannis Aifantis @iannisaifantis1]

Happy to see our own @VarvaraParask representing blood cancer at @Fusion_Conf "Animal Models of Cancer"! Dont forget: Leukemia is a cancer and it has it's microenvironment 😀! Thanks @KevinHaigisLab & @SageJulien for inviting Varvara! #AifantisLab @NYUGSOM_Path #CancerResearch

[Aristotelis Tsirigos @artsinyc]

C.Origami, a machine learning model for cell type-specific chromatin architecture prediction and discovery of putative regulatory elements! Developed by our student @tan_jimin in collaboration with @BoXia7. @NatureBiotech @4DNucleome @EpigenChromatin @epigen_papers

[Jimin Tan @tan_jimin]

Our C.Origami paper is accepted at Nature Biotechnology. Special thanks to @BoXia7, @artsinyc and all my collaborators for their invaluable guidance and support along the way. It has been an amazing journey!

[Stelios Kosmidis @stelioskosmidis]

Slavi et al. @NeuroCellPress CyclinD2-mediated regulation of neurogenic output from the retinal cil... https://t.co/fgGo1SIFRL. Extremely proud to have worked in this seminal study led by Nefeli Slavi. Congratulations to all the participants. #AcademicTwitter

[Dafne Campigli Di Giammartino @DafneDiGiammart]

#postdoc position available in my lab!
Exciting opportunity to work on the role of #ncRNAs and #ChromatinArchitecture in #StemCells @IIT.
This position is fully supported by the ECF fellowship from the @HumanTechnopole and will be based in Genova (Italy). https://t.co/Bb3QMXb2Of

[Akis Papantonis @AkisPapantonis]

New preprint from the lab!
Led by @IMPRS_GS PhD students Shu Zhang and Nadine Ubelmesser and supported by @dr_barbieri_mar for modeling, we found selective dependency of enhancer-promoter loops on RNAPII using #MicroC. Our work assigns RNAPs with a clear role in #3Dgenome folding

[Jimin Tan @tan_jimin]

Our new study: C.Origami predicts cell type-specific 3D chromatin structures 🧬 and enables genome wide screening for crucial factors. It has been an honor working with @BoXia7 and @artsinyc in this exciting project!
Check out our website and a live demo!
https://t.co/cO5vzqO5O5

[Aristotelis Tsirigos @artsinyc]

Very excited to present our latest work with @tan_jimin and @BoXia7: using machine learning to predict cell type-specific chromatin architecture and enable in silico perturbation studies! @nyugrossman @Perlmutter_CC https://t.co/KODP799j7b

[Aristotelis Tsirigos @artsinyc]

NSD2 E1099K drives relapse in pediatric acute lymphoblastic leukemia by disrupting 3D chromatin organization @nyugrossman https://t.co/BwpxEsuA4a

[Stelios Kosmidis @stelioskosmidis]

A wonderful paper from the twitter-less Nefeli Slavi @LadyGlaucoma and the @drcarolmason lab, linking gene expression in the CMZ with the establishment of the binocular circuit and depth perception.
https://t.co/PUz4W2jVGy