If you are interested in learning computational biology techniques with a focus on their applications to immunology research this can be a good opportunity to get started.. Happy to serve as the director for Part I that is online and requires no prior expertise.. @aai.org

The American Association of Immunologists@aai.org · last wk.

Ready to bridge the gap between bench work and data science? Dr. Ferhat Ay and Dr. Dan Beiting share how the AAI Introduction to Computational Immunology course equips researchers at all career stages. Read the full interview & join us this fall: https://ow.ly/xSCh50ZQgtL. #AAIcourses

We've kicked off the 2026 LEAD Day program! This afternoon features a panel with: 👉 Eric Topol, MD, Scripps Research VP @erictopol.bsky.social 👉 LJI Associate Prof. Ferhat Ay, Ph.D. @ferhatay.bsky.social 👉 Global Autoimmune Disease Assistant Prof. Sam Myers, Ph.D. @samyers-lab.bsky.social 1/🧵

#ISMB2026 is off to a great start with recognition of Philip Bourne’s service and Richard Durbin’s award reception. If you are around, checkout the Comp Immunology COSI tomorrow. Two fantastic keynotes: www.iscb.org/ismb2026/sci...

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! recomb-rsg.github.io

Thanks to @ferhatay.bsky.social 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

2 PhD candidates in my group: Michal @malszycki.bsky.social and Lisa led this work. We are very thankful to Ay lab ( @ferhatay.bsky.social ) and Alev lab (ASHBi, Kyoto), who helped make our story more complete. This work was funded by @dfg.de in the framework of @spp2202.bsky.social

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.

The short & GC-rich introns emerged in amniotes and were once long and GC-poor (in fish). The emergence of this gene architecture coincides with the expansion of SON’s IDRs. IDRs of SON are necessary and sufficient to form functional speckles.

Problems in splicing, due to SF3 complex dispersal, cause changes in gene expression, but only a small set of exons-introns are sensitive to speckles loss. These genes have introns with short & GC-rich architecture and are found in GC-rich isochores.

Differential gene expression analysis upon speckles loss reveals only genes within high GC chromatin domains are susceptible. The distance of the chromosomes 18 (lowest GC content) and 19 (highest GC content) from the speckles also indicate their speckle dependency.

Speckles take a large space in the human cell nucleus and form viscoelastic boundaries that restrict random chromatin movements. Upon speckles loss, the chromatin mobility increases and active(A) and inactive(B) chromatin compartments mix as shown by the Pore-C analysis by @ferhatay.bsky.social lab

Nuclear speckles are protein and RNA rich condensates that are proximal to GC-rich regions of the human genome. We dissolved speckles by rapidly depleting the 2 core proteins; SON & SRRM2 and investigated the role of speckles in: 1. 3D genome folding 2. transcription & splicing.

Our most recent work on the “function and evolution” of #nuclear-speckles is now online at Cell @cp-cell.bsky.social doi.org/10.1016/j.ce... Read the thread👇 for the highlights of our findings.

Thanks to @ferhatay.bsky.social 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

From RIME to reason In this Research Letter by Hal M. Hoffman @ferhatay.bsky.social & team, scRNA-seq analysis before & after treatment of recurrent infectious mucocutaneous eruption (RIME) reveals dysregulation of TNF/IFN signaling & classical monocytes: doi.org/10.1172/jci....

10th year anniversary of Ay lab at LJI! What a journey so far! Thank you to all lab members, collaborators, LJI family, who made this enjoyable and exciting. Here is a photo that summarizes how my lab sees me now 😂😂😢😢

Happy to see this out @insight.jci.org The first paper of hopefully many with Reid Oldenburg, Croker lab and others at UCSD utilizing BD Rhapsody platform for single-cell profiling of patient samples for severe conditions such as RIME.

Waggoner Lab@labwaggoner.bsky.social · 10mo ago

Dual dysregulation of TNF/interferon signaling and classical monocytes are implicated in Reactive Infectious Mucocutaneous Eruptions @insight.jci.org @ucsandiego.bsky.social @ferhatay.bsky.social insight.jci.org/articles/vie...

Our latest paper on comparative analysis of HiChIP data is now online! HiChIP is one of the most useful/practical assays to profile 3D genome organization and chromatin loops but has its challenges in the data analysis especially when it comes to comparative analysis.

Important well-explained summary: “NIH has awarded nearly 3,000 fewer research project grants than it did the previous year”.

NIH pulled off a ‘near miracle.’ Scientists say there’s still a problem.

The National Institutes of Health is on track to give away all of its grant money to labs, but research on cancer, aging and diabetes is still being left behind.

washingtonpost.com

I have NIGMS R35, impact score 12 NIHGRI R21, 4th percentile NHGRI R01, 7th percentile (co-I) and it seems like none will be funded. 0/3. PO (who has been very helpful) said "Unfortunately, I do not expect this application will be selected for funding in FY25." 😭

Funding policy for 2025 from NCI. Was just released: 4 percentile…maybe! www.cancer.gov/grants-train...

RegSys Day 2! Starting the day with a keynote by Roser Vento-Tormo on the cellular components of the placenta and uterus interaction #ismbeccb2025

Today marks the start of the #RegSys @iscb-regsys.bsky.social track at ##ISMBECCB2025! Very much looking forward to listening to the exciting science that will be presented. Join us in room 11BC today and tomorrow.

#RegSys is starting with the keynote from @verapancaldi.bsky.social who talks about the changes of chromatin structure and the epigenome in cancer patients #ismbeccb2025

Laura Hinojosa talks about TFs that regulate replication timing #RegSys #ismbeccb2025 @ferhatay.bsky.social

Using ISMB 2025 as an opportunity, I like to announce three papers that came out from our lab in the past month in Bioinformatics, EMBO Journal and Genome Biology. Two of these will be talks at RegSys COSI today (Laura Hinojosa, short talk) and tomorrow (Dante Bolzan, Proceedings talk).

CSI COSI just started with a full room of audience and Julio-Saez Rodriguez’s @juliosaezrod.bsky.social talk on use of multiomic and spatial data alongside biological knowledge to model gene regulatory and signalling networks. Those of you who are at #ISMB2025, we are in room 4A if you like to join

After a long trip and a long sleep, i am 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

AP story about the Bethesda Declaration is now up... apnews.com/article/nih-...

NIH scientists publish declaration criticizing Trump's deep cuts in public health research

Scores of National Institutes of Health researchers and staffers have come forward to send their Trump-appointed leader a letter challenging policies they say undermine the NIH mission.

apnews.com

I'm going to use this clip the next time I explain to my students why they shouldn't use AI to write papers...

Aaron Rupar@atrupar.com · last yr.

Q: A NOTUS investigation found the MAHA commission report cites studies that appear to not exist. Does the WH have confidence in the info coming from HHS? LEAVITT: Yes. I understand there were some formatting issues but it does not negate the substance Q: Did they use AI? L: I can't speak to that

🧬 Just out in Bioinformatics Advances: "Perspective on recent developments and challenges in regulatory and systems genomics" Find the full paper here: https://doi.org/10.1093/bioadv/vbaf106