dad x 2, husband, son, brother, computational biologist, genome scientist, associate professor at la jolla institute https://xitter.cf/t.co/QmMDBcEu24
San Diego, CA
Joined November 2009
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We have several rotation projects open for UCSD graduate and undergraduate students as part of the BISB program. Shoot an email if interested: bioinformatics.ucsd.edu/node…
Ferhat Ay retweeted
In the latest issue! Nuclear speckles enable processing of RNA from GC-rich isochores dlvr.it/TRsgf9
To accommodate decision timelines from RECOMB main conference and ISMB, we have now extended the submission deadline with RECOMB-RSG to March 13th, there will be no more extensions. Looking forward to have you join us in Greece!
Thanks to @ferhatay and Aly Khan, we’re excited to announce a new chapter for RECOMB-RSG 2026. After years with ISCB/DREAM, we are transitioning to an official RECOMB satellite meeting (May 25 in Thessaloniki). recomb-rsg.github.io
Ferhat Ay retweeted
2 PhD candidates in my group: Michal and Lisa led this work. We are very thankful to Ay lab @ferhatay and Alev lab @alevlab, who helped make our story more complete. This work was funded by @dfg_public in the framework of @spp2202_dfg
Ferhat Ay retweeted
Analysis of the evolution of this gene architecture and the presence of GC-rich isochores revealed that these features are specific to amniotes. By using the pA-RNA signal as a proxy for speckles we show the speckles are present in amniotes and absent in fish and invertebrates.
Ferhat Ay retweeted
Our most recent work on the “function and evolution” of #nuclear_speckles is now online at Cell @CellCellPress
cell.com/cell/fulltext/S0092…
Read the thread 👇for the highlights of our findings.
Ferhat Ay retweeted
Thanks to @ferhatay and Aly Khan, we’re excited to announce a new chapter for RECOMB-RSG 2026. After years with ISCB/DREAM, we are transitioning to an official RECOMB satellite meeting (May 25 in Thessaloniki). recomb-rsg.github.io
Ferhat Ay retweeted
Dual dysregulation of TNF/interferon signaling and classical monocytes are implicated in Reactive Infectious Mucocutaneous Eruptions @JCI_insight @UCSanDiego @ferhatay
insight.jci.org/articles/vie…
But I realized I have no patience to deal with breaking my post into pieces because of character limits so go to Linkedn if you like to see what they are about: linkedin.com/posts/ferhat-ay…
ready to enjoy the rich scientific program at #ISMBECCB2025 in Liverpool. This is also the first year of our new COSI in Computational and System Immunology (CSI) happening on Tuesday. And of course looking forward RegSys, as usual with fantastic organizers.
For CSI COSI, I am very thankful to my co-chair @jishnu1729 and steering committee @YuriPritykin , @haticeulku, Aly Azeem Khan. And everyone who submitted their for consideration for this session iscb.org/ismbeccb2025/progra…
Ferhat Ay retweeted
🧬 Just out in Bioinformatics Advances: "Perspective on recent developments and challenges in regulatory and systems genomics"
Find the full paper here: doi.org/10.1093/bioadv/vbaf1…
Authors include: @JuliaZeitlinger, @sroyyors, @ferhatay, @AMathelier, @AleMedinaRivera, @mahonylab, @jernst98
Ferhat Ay retweeted
Perspective on recent developments and challenges in regulatory and systems genomics academic.oup.com/bioinformat… is out, amazing to think about this with @JuliaZeitlinger, @ferhatay, @mahonylab, @AMathelier, @AleMedinaRivera, @jernst98!
Ferhat Ay retweeted
Please also check out two other papers using HiChIP and Hi-C to detect genetic associations with chromatin looping by Ferhat Ay's and Gisela Orozco's labs, which were submitted in parallel to ours and provide complementary insights:
nature.com/articles/s41467-0…
Ferhat Ay retweeted
Our new paper is finally out, showing that the same enhancer sequences - and likely the same transcription factors recruited to them - affect the activity of distal enhancers and their looping over to target gene promoters.
nature.com/articles/s41467-0…
Ferhat Ay retweeted
Comparison of CD30L and OX40L Reveals CD30L as a Promising Therapeutic Target in Atopic Dermatitis. First author: Rinkesh K. Gupta; corresponding author: Michael Croft
Read the article here: doi.org/10.1111/all.16412
This study investigated whether targeting the T cell costimulatory molecule, CD30L (TNFSF8), might be a possible treatment option in atopic dermatitis (AD). Single-cell RNA-seq analysis from AD skin lesions showed upregulated expression of CD30 transcripts in CD4 T cells, which partially coincided with expression of CD30L, as well as with OX40 and OX40L transcripts, and effector cytokines IL13 and IL22. CD30L blockade attenuated AD-like skin inflammation in mice similar to OX40L or IL-13 blockade.
#Allergy_journal
Read more articles published in #Allergy on #atopicdermatitis here: journalallergy.com/Atopic_De…
Happy to share Dante Bolzan’s delicious new preprint-Soffritto. He developed a deep learning model that accurately predicts high-resolution replication timing data (16-fraction) using commonly available data types Creative name by Dante but i stopped him from forcing an acronym😂
Soffritto: a deep-learning model for predicting high-resolution replication timing biorxiv.org/cgi/content/shor… #biorxiv_bioinfo