Fereydoun Hormozdiari

These current policies bring to mind that Persian poem, loosely translated as:

"A man was sawing off the branch on which he sat.
The Master of the garden looked on and said,
'If this man does harm, it is not to me,
But to his own self and well-being.'"

D-1 for 2025 Krebs Symposium to honor the legacy of Dr. Edwin G. Krebs, our only Nobel Laureate and founding chair of the Biochemistry and Molecular Medicine Department. Science talk, posters and more. #UCDavisBMM #KrebsSymposium #GenomeResearch #NobelPrize #EdwinKrebs #BiochemIsMyJam

Lossless Pangenome Indexing Using Tag Arrays Pangenome graphs represent the genomic variation by encoding multiple haplotypes within a unified graph structure. However, efficient and lossless indexing of such structures remains challenging due t...

A new preprint on indexing pangenome graphs using an FM-index of the haplotypes and a tag array. Joint work with Parsa Eskandar and @benedictpaten.bsky.social.

The human pangenome continues to grow and improve! Release 2 is here! Click through for the details, but this is a pretty amazing dataset including not just the phased assemblies, but PacBio HiFi, ONT Ultralong, Dovetail/Illumina Hi-C, PacBio Kinnex, and Illumina WGS for all samples

NIH is allowing us to recruit postbacs and postdocs again. Please reach out if you are interested in working with us! Ad: genomeinformatics.github.io/jobs2025/

4 generations help science explore genome mutation rate - UW Medicine | Newsroom

Advanced genomic analysis of 4 generation family offers new knowledge about genetic mutations & their transmission, including inherited variants & those that arise anew
@nature.com @uwgenome.bsky.social @eichlerlab.bsky.social @uwmedicine.bsky.social @utah.edu @pacbio.bsky.social

Efficient near telomere-to-telomere assembly of Nanopore Simplex reads Telomere-to-telomere (T2T) assembly is the ultimate goal for de novo genome assembly. Existing algorithms capable of near T2T assembly all require Oxford Nanopore Technologies (ONT) ultra-long reads w...

Preprint on hifiasm Nanopore-only assembly. Led by Haoyu Cheng: www.biorxiv.org/content/10.1...

Will you join us for the 2025 Krebs Symposium on 05.23.25❓️ Enjoy the weekly trivia Q&As on Dr. Edwin Krebs, and register at bit.ly/2025krebs 🧬🔬👩‍🔬👨‍🔬 #UCDavisSOM #UCDavisBMM #KrebsSymposium #GenomeResearch #NobelPrize #EdwinKrebs #BiochemIsMyJam

minimap2 adds support for short read spliced RNA-seq alignment! lh3.github.io/2025/04/18/s...

Biology of Genomes Cold Spring Harbor Laboratory Meetings & Courses -- a private, non-profit institution with research programs in cancer, neuroscience, plant biology, genomics, bioinformatics.

Biology of Genomes is only 18 days away. The lineup is stellar!
meetings.cshl.edu/meetings.asp...

Reassessing the Heritability of Autism Spectrum Disorders This study reanalyzes Swedish cohort data to assess the stability under alternative assumptions and models of a previous estimate of the heritability of autism spectrum disorder.

Though it's an older result, it's more relevant than ever!

"In a reanalysis of a previous study of the familial risk of ASD, the heritability was estimated to be 83%, suggesting that genetic factors may explain most of the risk for ASD."

jamanetwork.com/journals/jam...

Pan-genome bridges wheat structural variations with habitat and breeding | Nature Wheat is the second largest food crop with a very good breeding system and pedigree record in China. Investigating the genomic footprints of wheat cultivars will unveil potential avenues for future breeding efforts1,2. Here we report chromosome-level genome assemblies of 17 wheat cultivars that chronicle the breeding history of China. Comparative genomic analysis uncovered a wealth of structural rearrangements, identifying 249,976 structural variations with 49.03% (122,567) longer than 5 kb. Cultivars developed in 1980s displayed significant accumulations of structural variations, a pattern linked to the extensive incorporation of European and American varieties into breeding programmes of that era. We further proved that structural variations in the centromere-proximal regions are associated with a reduction of crossover events. We showed that common wheat evolved from spring to winter types via mutations and duplications of the VRN-A1 gene as an adaptation strategy to a changing

China's wheat breeding history unveiled with 17 genome assemblies, revealing 249,976 structural variations, 49.03% over 1 Kb. Insights for breeding progress! PMID:39604736, Nature 2025, @Nature https://doi.org/10.1038/s41586-024-08277-0 #Medsky #Pharmsky #RNA #ASHG #ESHG 🧪

Exciting lineup of talks at this year’s Krebs Symposium, centered on genomics, covering broad topics—from the significance of studying genome diversity to the genomics of cancer, TB susceptibility, Fragile X, and Alzheimers. #UCDavisSOM #UCDavisBMM #KrebsSymposium #GenomeResearch #NobelPrize

Check out our latest work on one of the first multi-modal cell-free RNA foundation models for blood surveillance and liquid biopsy applications, led by @genophoria.bsky.social, @babak-a.bsky.social, @mehrankr.bsky.social and Aiden Sababi

Congrats Sagiv!

Comparison of Research Spending on New Drug Approvals by the NIH vs the Pharmaceutical Industry This cross-sectional study examines National Institutes of Health and pharmaceutical industry investments in recent drug approvals.

99% of new medicines developed by the pharmaceutical industry depend on NIH research jamanetwork.com/journals/jam...

Stands up for science in Sacramento.

HiFi long-read genomes for difficult-to-detect, clinically relevant variants www.cell.com/ajhg/abstrac... 🧬🖥️🧪

Nice work of using graph convolutional neural networks for haplotype assembly!

Tahoe-100M: A Giga-Scale Single-Cell Perturbation Atlas for Context-Dependent Gene Function and Cellular Modeling Building predictive models of the cell requires systematically mapping how perturbations reshape each cell's state, function, and behavior. Here, we present Tahoe-100M, a giga-scale single-cell atlas ...

@thejohnnyyu.bsky.social, @therealnima.bsky.social, and I, are excited to tell you about Tahoe-100M! The largest publicly available single-cell dataset that measures the effect of 1200 genes on 50 cell line models. The Vevo team has outdone itself. #Tahoe100M www.biorxiv.org/content/10.1...

Our recent work, led by Luca Denti, explores pangenome graph augmentation using unassembled long reads.

The single-molecule accessibility landscape of newly replicated mammalian chromatin By developing a long-read sequencing method to simultaneously map replication status and protein-DNA contacts in cells, Ostrowski, Yang, et al. show that newly replicated chromatin is enriched for unw...

The latest from our group, led by Megan Ostrowski and @martyyang.bsky.social, is now published in final form (www.cell.com/cell/fulltex...! Many thanks to our excellent peer reviewers for suggesting several experiments (including CAF-1 perturbation) to really improve the study =) #epigenetics

Rare germline structural variants increase risk for pediatric solid tumors Pediatric solid tumors are a leading cause of childhood disease mortality. In this work, we examined germline structural variants (SVs) as risk factors for pediatric extracranial solid tumors using ge...

Here's our latest, led by Drs. Riaz Gillani & Ryan Collins - we studied a type of inherited genetic event (structural variants) + risk of developing certain cancers in kids:
@danafarber.bsky.social @bostonchildrens.bsky.social @broadinstitute.org @science.org

www.science.org/doi/10.1126/...

A generative framework for enhanced cell-type specificity in rationally designed mRNAs mRNA delivery offers new opportunities for disease treatment by directing cells to produce therapeutic proteins. However, designing highly stable mRNAs with programmable cell type-specificity remains ...

The first preprint of 2025! Together with Matvei, @halfacrocodile.bsky.social, & our amazing team, we are excited to share PARADE: an AI framework for designing mRNA UTRs with enhanced cell-type specificity & stability. www.biorxiv.org/content/10.1...

Neanderthal ancestry through time: Insights from genomes of ancient and present-day humans Gene flow from Neanderthals has shaped genetic and phenotypic variation in modern humans. We generated a catalog of Neanderthal ancestry segments in more than 300 genomes spanning the past 50,000 year...

A new genomic study in Science encompassing more than 300 genomes spanning the last 50,000 years has revealed how a single wave of Neanderthal gene flow into early modern humans left an indelible mark on human evolution. scim.ag/4gkMvpz

🚨 Call for Papers: RECOMB-seq 2025 🚨

🗓️ Dates: April 24-25, 2025

📍 Location: Seoul, South Korea

Key deadlines:
🔹 Abstract registration: Jan 24, 2025
🔹 Submission: Jan 31, 2025

More details: recomb-seq.github.io/papers/

Very excited about this work and the potential applications of of cell-free RNA.

Evo, a 7-billion-parameter genomic foundation model, learns biological complexity from individual nucleotides to whole genomes.

Pretraining a genomic foundation model across prokaryotic life.

Fine-tuning on CRISPR-Cas sequences enables generative design of protein-RNA complexes.

Fig. 4. Fine-tuning on IS200/IS605 sequences enables generative design of transposable biological systems.

Evo: A genomic language model of prokaryote genomes generates functional cas9 proteins and transposons.

@brianhiestand.bsky.social

www.science.org/doi/10.1126/...

The preprint on orphan non-coding RNAs (oncRNAs) as blood-accessible cancer biomarkers is out! Massive project led by Hani Goodarzi (@genophoria.bsky.social). oncRNAs have the potential to transform cancer diagnosis and monitoring, as showcased by @exai.bio.

www.biorxiv.org/content/10.1...