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!

Genomics, evolution, and more starter pack! Help build community with this starter pack. This list is currently incomplete. Want to be included? Reply and I will remedy that! go.bsky.app/JjvzkWU

ok, I tried to make a starter pack on genome stability/DNA replication/DNA repair etc. Sorry if I couldn't find someone, please nominate yourself and your colleagues in comments or DMs, looking forward to connecting with everyone! go.bsky.app/9jdDNxG

Hi all, just to say thanks for all the enthusiasm about the #epigenetics, Chromatin and Gene Regulation starter pack. The interface is a bit unreliable so a few people I added got missed off 😬. If you notice this applies to you, just message me and I'll try again. go.bsky.app/TKp9YAn

Hi Bluesky! I made a 3D chromatin starter pack. Let me know if you would like to be added. go.bsky.app/6tTQdqQ

Bluesky for Science Starter packs for genomics, bioinformatics, #Rstats, Nextflow. Moderation lists. Feeds. Let's rebuild the old scitwitter community and keep this place nice blog.stephenturner.us/p/bluesky-fo... 🧬🖥️🧪

Both #Cancer #Research starter packs are now completely full! ~300 researchers, oncologists, students, postdocs, patient advocates, and organizations supporting cancer research 🧪🔬⚕️ I hope you'll find these useful to build our community here Pack 1: go.bsky.app/FEoaJMc Pack 2: go.bsky.app/6EcjWNA

We've now filled one #Epigenetics, Chromatin and Gene regulation starter pack. Thanks for all the enthusiasm and support, if you'd like to be listed @raduzabet.bsky.social has been hard at work getting part II up and running: go.bsky.app/SqLa3aw

Ok, I tried to create my own list of people working on developing statistical or machine learning models applied to omics data. I am sure I missed a lot of cool people. If you'd like to be added, let me know. #Stats #ML #Omics go.bsky.app/73rcuJn

Now that the blue bird is X’ed and we are flocking to blue skies, what are good Starter Packs to follow for #bioinformatics #genomics #generegulation #computationalbiology #epigenetics or should we start one?