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

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.

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”.

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-...

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

🧬 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

Our perspective article is now out

(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),

Postdoc position #1 is live! Please apply / spread the word! lms.mrc.ac.uk/work/vacanci...

Genomic Language Model for Predicting Enhancers and Their Allele-Specific Activity in the Human Genome https://www.biorxiv.org/content/10.1101/2025.03.18.644040v1

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...

#standupforscience rally today at UCSD..

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! 👀☀️

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

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

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

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...

🧪 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

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

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.

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...

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

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

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..

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 😂

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.

Excited to share James Jusuf's preprint: By integrating Micro-C with SuperRes Live-Imaging we can calibrate genomics&imaging to perform absolute quantification of looping (e.g. this loop is present 3%) We quantify mESC 36k loops: <loops> are generally rare (2.3%) www.biorxiv.org/content/10.1...

We're on Bluesky! Hello to all our friends in the #ComputationalBiology community, we're excited to hear all about your amazing #bioinformatics work!

Happy "grad school recommendation letter writing weekend" to those who celebrate!