iiinova — where your digital self keeps evolving

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

aai.org

The American Association of Immunologists - Computational Immunology

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La Jolla Institute for Immunology (LJI) @lji.org · 15/09/2026

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/🧵

Photo of a conference room with people looking at a speaker at a lecturn

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Ferhat Ay @ferhatay.bsky.social · 13/07/2026

#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...

iscb.org

CSI

ISCB - International Society for Computational Biology

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Ferhat Ay @ferhatay.bsky.social · 02/03/2026

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

recomb-rsg.github.io

RECOMB-RSG 2026 | Regulatory Genomics Satellite

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Tugce Aktas @aktast.bsky.social · 25/02/2026

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

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Tugce Aktas @aktast.bsky.social · 25/02/2026

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.

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Tugce Aktas @aktast.bsky.social · 25/02/2026

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.

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Tugce Aktas @aktast.bsky.social · 25/02/2026

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.

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Tugce Aktas @aktast.bsky.social · 25/02/2026

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.

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Tugce Aktas @aktast.bsky.social · 25/02/2026

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

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Tugce Aktas @aktast.bsky.social · 25/02/2026

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.

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Tugce Aktas @aktast.bsky.social · 25/02/2026

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.

doi.org

Redirecting

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Sushmita Roy @sroyyors.bsky.social · 27/01/2026

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

recomb-rsg.github.io

RECOMB-RSG 2026 | Regulatory Genomics Satellite

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JCI insight @insight.jci.org · 14/01/2026

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....

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Ferhat Ay @ferhatay.bsky.social · 06/01/2026

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 😂😂😢😢

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Ferhat Ay @ferhatay.bsky.social · 25/11/2025

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.

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Ferhat Ay @ferhatay.bsky.social · 04/11/2025

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.

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Anders Sejr Hansen @andersshansen.bsky.social · 20/08/2025

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." 😭

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Alejandra Medina-Rivera @alemedinarivera.bsky.social · 24/07/2025

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

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Anthony Mathelier @amathelier.bsky.social · 23/07/2025

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.

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Marcel Schulz @themarcelschulz.bsky.social · 23/07/2025

#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

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Marcel Schulz @themarcelschulz.bsky.social · 23/07/2025

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

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Ferhat Ay @ferhatay.bsky.social · 23/07/2025

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).

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Ferhat Ay @ferhatay.bsky.social · 22/07/2025

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

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Ferhat Ay @ferhatay.bsky.social · 21/07/2025

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

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Shobita Parthasarathy @shobitap.org · 29/05/2025

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

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Bioinformatics Advances @bioinfoadv.bsky.social · 14/05/2025

🧬 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/vbaf106

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Ferhat Ay @ferhatay.bsky.social · 13/05/2025

Our perspective article is now out

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Ferhat Ay @ferhatay.bsky.social · 04/05/2025

(1/n) We will be announcing this tomorrow at #IMMUNOLOGY2025 #AAI2025 here in Honolulu but excited to share that AAI @aai.org will be starting a Computational Immunology Course this Fall. www.aai.org/Education/Co... Happy to be serving as a Developer & Director alongside Dan Beiting (U Penn),

aai.org

The American Association of Immunologists - Computational Immunology

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bioRxivpreprint @biorxivpreprint.bsky.social · 19/03/2025

Genomic Language Model for Predicting Enhancers and Their Allele-Specific Activity in the Human Genome www.biorxiv.org/content/10.1101/202…

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Vaughn Smider, MD, PhD @vvsmider.bsky.social · 17/03/2025

I’m a biomedical researcher who lost his wife to cancer. Finding cures is personal to me. What’s happening at the NIH is devastating. Here’s my editorial in my hometown newspaper. www.vindy.com/opinion/edit...

vindy.com

DOGE ends America’s golden age of biomedical research

Biomedical research impacts all of us. I became curious about how drugs work after my mom was diagnosed with rheumatoid arthritis when I was a small boy. She received “gold shots” as treatment, which ...

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Stand Up for Science! @standupforscience.net · 06/03/2025

STAND UP FOR SCIENCE SPEAKER ANNOUNCEMENT! ☀️ Dr. Francis Collins will be speaking at Stand Up for Science in D.C. on March 7th! More speaker announcements coming soon, stay tuned! 👀☀️

Image of Francis Collins, with text at the top of the image that says Speaker Announcement and at the bottom that says Stand Up for Science, March 7th, 2025 and a link to standupforscience2025.org.

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Ferhat Ay @ferhatay.bsky.social · 06/03/2025

Is eRA Commons down again? I am assuming there were a record number of grants submitted for this Mar 5th deadline but not sure if that explains it

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‘stina is a shiny special one 💥 @stinapag.bsky.social · 05/03/2025

I watched a Bluey episode with my three year old this morning about keeping promises. It's fundamental to a functioning society.

Text of the transcript of a Bluey episode:

Chilli: "You can't use promises to trick each other."
Bandit, Bluey: "Ohh!"
Chilli: "The whole point of promises is to build trust. If there's no trust, none of this is possible."
Chilli gestures widely, indicating all of their surroundings.
Bluey: "What, none of the whole world?"
Chilli: "None of it."
Chilli counts on her fingers.
Chilli: "No libraries, no roads, no power lines."
Bingo: "No power lines?!"
Bluey: "I'm not sure about that. I think we'd still have power lines."
Chilli: "No, we wouldn't."
Bandit: "Mum's right."

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Peter Gleick @petergleick.bsky.social · 04/03/2025

Dear universities, scientists, lawyers, farmers, workers, artists, doctors... Being silent won't protect you.

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Carol Chen @carolchen.bsky.social · 04/03/2025

My alma mater, the University of British Columbia, Dept of Medical Genetics, is hiring for a tenure track junior faculty position specializing in chromatin regulation / gene regulatory mechanisms. Beautiful city and vibrant epigenetics research. Please share! medgen.med.ubc.ca/assistant-pr...

medgen.med.ubc.ca

Assistant Professor (Tenure-Track) | Department of Medical Genetics | Life Sciences Institute (LSI) - Department of Medical Genetics

The Department of Medical Genetics, in collaboration with the Life Sciences Institute (LSI), invites applications for a full-time faculty position at the rank of Assistant Professor, tenure track with...

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Nigel Goldenfeld @nigelgoldenfeld.bsky.social · 28/02/2025

🧪 Wonderful to see UCSD Academic Senate Chair Olivia Graeve encouraging the entire campus to #standupforscience at the rally next Fri March 7 2025 at 12 noon in front of the Geisel Library/Silent Tree! Stand up for science ... and all scholarship at universities. @standupforscience.bsky.social

UCSD Academic Senate Chair Olivia Graeve encouraging the entire campus to #standupforscience at the rally next Fri March 7 2025 at 12 noon in front of the Geisel Library/Silent Tree!

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SD IRACDA @sd-iracda.bsky.social · 27/02/2025

We're #StandingUpforScience at UC San Diego on March 7th! Will you join us?

Flyer for a Stand Up For Science Rally on March 7 at noon at UCSD at the Geisel Library / Silent Tree.

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Jeremy Berg @jeremymberg.bsky.social · 02/03/2025

I am not going to call this a Bluetorial, because I do not want to sully that term (which, at least I, find joyful). Let’s call it a Orwellial.

media.tenor.com

a cartoon of homer simpson holding a card

ALT: a cartoon of homer simpson holding a card

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Annika Barber @annikabarber.bsky.social · 24/02/2025

Wondering if your study section cancelled? I update this sheet daily. As of today, 56/124 study sections that should have met since Jan 2, 2025 have "not met as scheduled." docs.google.com/spreadsheets...

docs.google.com

2025 Study section tracking

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Sofia de Oliveira, Ph.D. @sdeoliveira.bsky.social · 26/02/2025

Join the Department of Developmental & Molecular Biology @einsteinmededu.bsky.social ! 🧬✨ Are you passionate about cutting-edge research and collaborative science? We are looking for you😉 Come be part of a department where curiosity meets impact! 🚀 Learn more and join us👇 #ResearchExcellence #JoinUs

nature.com

Faculty-Tenure Track, Department of Developmental and Molecular Biology - Bronx, New York job with Albert Einstein College of Medicine | 12835514

Faculty-Tenure Track, Department of Developmental and Molecular Biology US-NY-Bronx Job ID: 2025-17126 Type: Research # of Openings: 1 Category: F...

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Lauren N. Girouard, PhD @laurengh.bsky.social · 31/01/2025

I am one of the impacted NSF postdoc research fellows. My funds remain frozen. I rely on these funds as my salary and payment to aid in my research efforts. I am currently without the funds I use to pay my bills, health insurance, etc. and to move my research forward. #NSF #postdoc

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Ferhat Ay @ferhatay.bsky.social · 01/02/2025

If you wonder what will be i doing with the rest of my Friday night, i will be searching for NIH in this stupid dropdown menu of a publisher that makes billions of dollars each year…and yes i also tried typing NIH first..

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Ferhat Ay @ferhatay.bsky.social · 27/01/2025

Happy to share Dante Bolzan’s (ucsd phd student) 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 😂

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Ferhat Ay @ferhatay.bsky.social · 21/01/2025

Differential analysis of HiChIP data is tricky. It is especially challenging to capture differences in long-range loops/interactions. Sourya from my lab (now at Empirico), who also developed FitHiChIP, took on this challenge.

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