Ferhat Ay
@ferhatay.bsky.social
Dad x 2, husband, son, brother, computational biologist, genome scientist, associate professor at la jolla institute for immunology (LJI) and UCSD https://www.lji.org/labs/ay/
Pinned
Ferhat Ay
@ferhatay.bsky.social
· May 4
The American Association of Immunologists - Computational Immunology
www.aai.org
(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),
Happy to be serving as a Developer & Director alongside Dan Beiting (U Penn),
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.
November 4, 2025 at 10:58 PM
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.
Reposted by Ferhat Ay
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.
www.washingtonpost.com
September 27, 2025 at 5:36 AM
Important well-explained summary: “NIH has awarded nearly 3,000 fewer research project grants than it did the previous year”.
Reposted by Ferhat Ay
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."
😭
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."
😭
August 19, 2025 at 11:29 PM
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."
😭
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."
😭
Reposted by Ferhat Ay
Funding policy for 2025 from NCI. Was just released: 4 percentile…maybe!
www.cancer.gov/grants-train...
www.cancer.gov/grants-train...
Funding Policy - Research Grants
NCI funding policy for research project grant (RPG) awards reflects the funding goals of the institute, NIH, and HHS.
www.cancer.gov
July 23, 2025 at 9:33 PM
Funding policy for 2025 from NCI. Was just released: 4 percentile…maybe!
www.cancer.gov/grants-train...
www.cancer.gov/grants-train...
Reposted by Ferhat Ay
RegSys Day 2!
Starting the day with a keynote by Roser Vento-Tormo on the cellular components of the placenta and uterus interaction
#ismbeccb2025
Starting the day with a keynote by Roser Vento-Tormo on the cellular components of the placenta and uterus interaction
#ismbeccb2025
July 24, 2025 at 8:26 AM
RegSys Day 2!
Starting the day with a keynote by Roser Vento-Tormo on the cellular components of the placenta and uterus interaction
#ismbeccb2025
Starting the day with a keynote by Roser Vento-Tormo on the cellular components of the placenta and uterus interaction
#ismbeccb2025
Reposted by Ferhat Ay
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.
Join us in room 11BC today and tomorrow.
July 23, 2025 at 7:41 AM
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.
Join us in room 11BC today and tomorrow.
Reposted by Ferhat Ay
#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
July 23, 2025 at 10:34 AM
#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
Reposted by Ferhat Ay
Laura Hinojosa talks about TFs that regulate replication timing
#RegSys #ismbeccb2025 @ferhatay.bsky.social
#RegSys #ismbeccb2025 @ferhatay.bsky.social
July 23, 2025 at 11:56 AM
Laura Hinojosa talks about TFs that regulate replication timing
#RegSys #ismbeccb2025 @ferhatay.bsky.social
#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).
July 23, 2025 at 8:52 AM
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
July 22, 2025 at 10:43 AM
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
July 21, 2025 at 8:29 AM
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
Reposted by Ferhat Ay
Reposted by Ferhat Ay
I'm going to use this clip the next time I explain to my students why they shouldn't use AI to write papers...
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
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
May 29, 2025 at 5:50 PM
I'm going to use this clip the next time I explain to my students why they shouldn't use AI to write papers...
Reposted by Ferhat Ay
🧬 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
Find the full paper here: https://doi.org/10.1093/bioadv/vbaf106
May 14, 2025 at 10:02 AM
🧬 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
Find the full paper here: https://doi.org/10.1093/bioadv/vbaf106
Our perspective article is now out
Our New perspective explores breakthroughs & challenges in regulatory & systems genomics: from cis-regulatory code & 3D chromatin to spatial omics & AI models.
🔗 doi.org/10.1093/bioa...
#Genomics #Bioinformatics #RegulatoryGenomics
🔗 doi.org/10.1093/bioa...
#Genomics #Bioinformatics #RegulatoryGenomics
Perspective on recent developments and challenges in regulatory and systems genomics
Abstract. Predicting how genetic variation affects phenotypic outcomes at the organismal, cellular, and molecular levels requires deciphering the cis-regul
doi.org
May 13, 2025 at 5:12 PM
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),
Happy to be serving as a Developer & Director alongside Dan Beiting (U Penn),
The American Association of Immunologists - Computational Immunology
www.aai.org
May 4, 2025 at 8:23 AM
(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),
Happy to be serving as a Developer & Director alongside Dan Beiting (U Penn),
Reposted by Ferhat Ay
Reposted by Ferhat Ay
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
March 19, 2025 at 6:46 AM
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
Reposted by Ferhat Ay
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...
www.vindy.com/opinion/edit...
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 ...
www.vindy.com
March 17, 2025 at 8:34 PM
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...
www.vindy.com/opinion/edit...
#standupforscience rally today at UCSD..
March 8, 2025 at 12:34 AM
#standupforscience rally today at UCSD..
Reposted by Ferhat Ay
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! 👀☀️
Dr. Francis Collins will be speaking at Stand Up for Science in D.C. on March 7th!
More speaker announcements coming soon, stay tuned! 👀☀️
March 6, 2025 at 12:00 AM
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! 👀☀️
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
March 6, 2025 at 2:19 AM
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
Reposted by Ferhat Ay
I watched a Bluey episode with my three year old this morning about keeping promises. It's fundamental to a functioning society.
March 5, 2025 at 7:01 PM
I watched a Bluey episode with my three year old this morning about keeping promises. It's fundamental to a functioning society.
Reposted by Ferhat Ay
Dear universities, scientists, lawyers, farmers, workers, artists, doctors...
Being silent won't protect you.
Being silent won't protect you.
March 4, 2025 at 1:05 AM
Dear universities, scientists, lawyers, farmers, workers, artists, doctors...
Being silent won't protect you.
Being silent won't protect you.
Reposted by Ferhat Ay
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-pr...
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...
medgen.med.ubc.ca
March 4, 2025 at 2:36 AM
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-pr...