Irem

PhD candidate, engineer, and a lifelong learner. | @Saar_Uni | @EpigenomeI | @ibgunduz.bsky.social

[Irem @_igunduz]

Our preprint is out! 🎉

methylTFR quantifies transcription factor activity from DNA methylation data, yielding an interpretable TF activity profile for each sample or cell.

📄 https://t.co/0SA5NzenCn
#SingleCell #DNAmethylation #Bioconductor #Epigenomics #Bioinformatics
🧵👇

[Anshul Kundaje @anshulkundaje]

Just a few quick things.

1. Nice rigorous study of the importance of being careful with performance metrics and taking into account data issues.

2. This should be done BEFOFE one fits big models & make lots of big claims. Nevertheless better late than never. 2/

[Irem @_igunduz]

The R package and hg38/mm10 annotations (on AnnotationHub) are in review at Bioconductor:
💻 https://t.co/MK8n1bZhsr

[Irem @_igunduz]

Our preprint is out! 🎉

methylTFR quantifies transcription factor activity from DNA methylation data, yielding an interpretable TF activity profile for each sample or cell.

📄 https://t.co/0SA5NzenCn
#SingleCell #DNAmethylation #Bioconductor #Epigenomics #Bioinformatics
🧵👇

[Irem @_igunduz]

🔬Across 147 human immune cell methylomes, methylTFR identified cell-type-specific regulators, including CEBP and ETS family activity in myeloid cells.
🔬It also works on sparse single-cell methylomes.

[Eric Topol @EricTopol]

How infections epigenetically edit and reshape our immune system
https://t.co/TJRtEpnzXE
https://t.co/cBudPemetV
@NatureGenet @JoeEcker @salkinstitute

[Salk Institute @salkinstitute]

How do nature and nurture shape our immune cells?

Salk scientists debut an epigenetic catalog revealing the distinct effects nature (genetic inheritance) and nurture (life experience) have on immune cells. The new cell type-specific database helps explain individual differences in immune responses and may serve as the foundation for more effective and personalized therapeutics.

Read more: https://t.co/8fo5uXWXy9

#immunecells #genetics #immunology #naturenurture

[William J. Greenleaf @WJGreenleaf]

Congrats to @juliaschaepe and @marklundem on the recent publication of their work linking the binding behaviors of TFs in vitro and in vivo! Out in Cell now: https://t.co/pF3H6EIX9b

[bioRxiv Bioinfo @biorxiv_bioinfo]

Dissecting the epigenome dynamics in human immune cells upon viral and chemical exposure by multimodal single-cell profiling https://t.co/84NoTsgUN1 #biorxiv_bioinfo

[William J. Greenleaf @WJGreenleaf]

Our single-cell, pan-cancer analysis of open chromatin in human cancers, done in collaboration with TCGA and the Chang and Corces labs (among others including Illumina), is out in Science today. Congrats to Laksshman Sundaram and all authors! https://t.co/4whYsPvqyN

[Kavya Gupta @kavyagupta05]

@KanubalaD will be presenting our work "Fairness Beyond Binary Decisions: A Case Study on German Credit" with @iValeraM at @EWAFWorkshop. Our work argues for a paradigm shift in Credit approval.
See in you in Mainz.
#fairness #societycenteredai #germancredit #EWAF24.

[Altuna Akalin @AltunaAkalin]

🚀 Onconaut AI gets an upgrade!!🚀 Now we provide tailored treatment recommendations based on the input patient profile and guidelines. For this, we make use of all relevant clinical variables in the query not just biomarkers

Check out the video to see how this works 🎥👩‍⚕️👨‍⚕️

[Melike Dönertaş @melikedonertas]

🚨 #PhDposition available for international applicants @LeibnizFLI

Multiple groups (incl. ours 😉) seeking applications!

Please RT

⏰ Deadline: May 12th

More info about our group & application form: https://t.co/VnamuNIbai

#aging #bioinformatics #microbiome

[EpigenomeInformatics @EpigenomeI]

Excited about the upcoming Functional Epigenomics Conference (May 27-28)
Excellent speakers and great science. Register here:
https://t.co/itqppej50w

[William J. Greenleaf @WJGreenleaf]

Our work using single-molecule chromatin configurations to link TF binding to gene expression is now out on bioRxiv! Amazing effort from @bgrdoughty, @MichaelaThinks, and @juliaschaepe, and an immensely rewarding collaboration with the @BintuLab: https://t.co/u9aNQV4Ub9 [1/n]

[Wenliang Wang @wenliang272]

We are thrilled to release our manuscript titled "Human Immune Cells Epigenomic Signatures in Response to Infectious Diseases and Chemical Exposures", which was led by my colleague @h_manoj and me. https://t.co/lE5yzHdfjg

[William J. Greenleaf @WJGreenleaf]

The Greenleaf Lab is looking for graduate students and postdocs interested in perturbing transcription factors and chromatin remodelers in human organoid systems with an aim of quantitatively understanding drivers of normal human development.

[Nature Neuroscience @NatureNeuro]

Single-cell transcriptomic landscape of the mid-gestation developing human spinal cord

New from @Sergiu_P_Pasca and colleagues

https://t.co/zSRW7KTFHw

[Irem @_igunduz]

@yjyang027 @RECOMBconf @EpigenomeI @tanmayee_n @KazwiniNour @ccastignani6 Thank you Yongjian, it was nice meeting you!

[Irem @_igunduz]

I had a great time attending #Recomb2023 to present the poster of our latest work! We had amazing keynotes, highlights, and posters. Special thanks to the organizers and volunteers who rocked 😎 Hope to see you soon again!