Hani Goodarzi
@genophoria.bsky.social
Core Investigator @ Arc Institute | Associate Professor @ UCSF | {Computational, Systems, Cancer, RNA} biologist | Co-founder @exaibio @vevo_ai
Hundreds of human tRNA genes form a redundant repertoire for decoding the genetic code. But does redundancy imply functional equivalence? A pan-cancer in vivo CRISPRi atlas from @genophoria.bsky.social and Vijay Ramani at @Gladstone Institutes reveals a structured landscape of tRNA dependencies.
The code is on GitHub, with model checkpoints and data on Hugging Face. Learn more about PIE from co-authors Rishi Verma and @genophoria.bsky.social: arcinstitute.org/news/pie Or access the preprint: www.biorxiv.org/content/10.6...
PIE: Generalizing perturbation effects across unseen perturbations, contexts and datasets
Predicting cellular response to perturbations is key to understanding biological mechanisms and selecting therapeutic targets. However, generalizing across cellular contexts, perturbations, and experi...
biorxiv.org
See the full announcement from program organizer @genophoria.bsky.social: arcinstitute.org/news/aixbio-... :
Introducing the 2026 Arc AIxBio Fellows | Arc Institute
Some of the most exciting AI projects I have worked on started not with graduate students or postdocs in my lab, but with undergraduates driven by raw curiosity and technical ambition. So when we laun...
arcinstitute.org
Delighted to share our lab's latest (w/ inimitable @genophoria.bsky.social) in final form at @nature.com. Enormous lift by Sean Wang, @palindromephd.bsky.social & @martyyang.bsky.social to address extensive & constructive reviewer comments & see this through. (1/n) www.nature.com/articles/s41...
Pervasive and programmed nucleosome distortion on single chromatin fibres - Nature
An analytical pipeline called Iteratively Defined Lengths of Inaccessibility (IDLI) maps the genome-wide occupancy of a range of nucleosome types and shows that most nucleosomes exhibit programmed ‘di...
nature.com
But wait! There’s more! So you thought you knew nucleosome structure? Think again! @vram142.bsky.social @gladstoneinst.bsky.social and @genophoria.bsky.social @arcinstitute.org show that there is plenty of distortion largely due to TFs butting in www.nature.com/articles/s41...
Pervasive and programmed nucleosome distortion on single chromatin fibres - Nature
An analytical pipeline called Iteratively Defined Lengths of Inaccessibility (IDLI) maps the genome-wide occupancy of a range of nucleosome types and shows that most nucleosomes exhibit programmed ‘di...
nature.com
Pervasive and programmed nucleosome distortion on single chromatin fibres @nature.com @gladstoneinst.bsky.social @genophoria.bsky.social @arcinstitute.org www.nature.com/articles/s41...
Today in @nature.com, the @genophoria.bsky.social and & Vijay Ramani labs reveal that our picture of how nucleosomes regulate DNA accessibility has been too simple. They find that over 85% of nucleosomes in mammalian cells are structurally distorted, with DNA partially accessible even while wrapped.
While chemotherapy kills some tumor cells, others survive and can drive relapse. This variability isn't fully explained by DNA mutations. In a new preprint, Core Investigator @genophoria.bsky.social and lab identify RNF8 and MIS18A as drivers of tumor cell variability in breast cancer.
Blog post: transitioning to being a PI in the age of AI open.substack.com/pub/arjunraj...
Transitioning to being a PI in the age of AI
Computational biology is in a period of upheaval that is both exhilarating and terrifying.
open.substack.com
Devastated to learn of the passing of the great cancer pioneer J. Michael Bishop. Mentor and friend, it was only a few weeks ago we celebrated his 90th birthday. He taught us that the seeds of cancer lie within us and spent his career combating cancer. 🧪 @ucsfcancer.bsky.social
Over 250 million protein sequences are known, but fewer than 0.1% have confirmed functions. Today, @genophoria.bsky.social, @bowang87.bsky.social & team introduce BioReason-Pro, a multimodal reasoning model that predicts protein function and explains its reasoning like an expert would.
Congratulations @heatherkarner.bsky.social and @tabeamittmann.bsky.social for getting this awesome project across the finish line!
Arc Institute@arcinstitute.org · 7mo agoA protein that stabilizes cancer-suppressing mRNAs turns out to be a key brake on breast cancer metastasis. A paper from Core Investigator @genophoria.bsky.social and lab in Science Advances traces the mechanism to RNA decay and an RNA-binding protein most studies have overlooked.
AI-enabled RNA design for ultra-rare diseases was on stage at PMWC and in a new Charles River feature last week. Two signs of a growing conversation around what is now possible. Link in comments. #RNA #PrecisionMedicine #RareDisease
🎉Proud to present our latest paper, out now in Nature Communications: www.nature.com/articles/s41... RNA Binding Proteins (RBPs) are often full of intrinsically disordered regions (IDRs), but what these regions do during RNA recognition is often unclear. 1/10 #RNA #IDR #RBP
An intrinsically disordered region mediates RNA-binding selectivity and cellular activities of LARP6 - Nature Communications
LARP6 is an EMT-associated RNA-binding protein with diverse RNA targets. Here, the authors show that the N-terminal disordered region of LARP6 promotes RNA-binding selectivity by modulating the adjace...
nature.com
🚨 NEW 🚨 "Systemic hypoxia suppresses solid tumor growth" @ayushmidha.bsky.social @genophoria.bsky.social @ishahjain.bsky.social @arcinstitute.bsky.social @ucsfhealth.bsky.social https://bit.ly/4arkFX8
Systemic hypoxia suppresses solid tumor growth
Local hypoxia is a hallmark of solid tumors and a negative prognostic factor in the progression and treatment of cancer. Here, we showed that systemic hypoxia, in contrast to localized tumor hypoxia, decreases tumor growth in vivo across multiple cancer...
bit.ly
In this Molecular Cell Voices piece, @genophoria.bsky.social comments on how he thinks about bridging bench and computational work: www.cell.com/molecular-ce...
Amazing collaboration with the Jain lab! The impact of systemic hypoxia on cancer!
Ayush Midha@ayushmidha.bsky.social · 8mo agoI am excited to share our latest preprint showing that systemic hypoxia suppresses solid tumor growth: www.biorxiv.org/content/10.6... This has been a tremendous collaborative effort in the labs of Isha Jain @ishahjain.bsky.social and Hani Goodarzi @genophoria.bsky.social.
Arc Core Investigator @genophoria.bsky.social will speak on a free, online panel with @tkaraletsos.bsky.social, @emmalundberg.bsky.social, and @ronalfa.bsky.social on Wed., Oct. 29, as part of GENbio's “The State of AI in Drug Discovery in 2025.” Register at: webinars.liebertpub.com/e/the-state-...
Hear how Arc, Ultima Genomics, and @10xgenomics.bsky.social are partnering to generate perturbation data at the scale needed to train virtual cell models on The Bio Report podcast with guests @genophoria.bsky.social, Gilad Almogy, and Serge Saxonov: thebioreport.podbean.com/e/transformi...
#CELLFIE for CAR T screening—a new mRNA-based platform for screening primary cells. CAR + gRNA library are delivered by lentivirus, CRISPR modifiers as electroporated mRNA. That’s more flexible and effective than existing T cell screening methods. (1/7)
New work from stellar scientists Jeremy Williams and Roman Camarda. Many contributors including the amazing Zena Werb and Atul Butte Work explores how breast cancer cells interact directly with adipocytes via gap junctions, leading to lipid release. @ctbatucsf.bsky.social @ucsfcancer.bsky.social
Tumor cell-adipocyte gap junctions activate lipolysis and contribute to breast tumorigenesis
Nature Communications - Breast cancer cells interact with neighbouring adipocytes, but the mechanisms are not fully understood. Here, the authors show that triple-negative breast cancer (TNBC)...
nature.com
RNA N-glycosylation enables immune evasion and homeostatic efferocytosis by chemically caging acp3U. Excited to report this work lead by Vinnie @vinnieviruses.bsky.social and in collaboration with @vijayrathinam.bsky.social in @nature.com www.nature.com/articles/s41...
My colleagues at Nature Biomedical Engineering @natbiomedeng.nature.com are hiring an associate or senior editor. Ideal applicant will have expertise in immunology, immunotherapy, or immuno-oncology. Please feel to ask me questions! springernature.wd3.myworkdayjobs.com/SpringerNatu...
Associate or Senior Editor, Nature Biomedical Engineering
Job Title: Associate or Senior Editor, Nature Biomedical Engineering Organization: Nature Portfolio Location: New York, Jersey City, Shanghai or Beijing – Hybrid Working Closing date: August 20, 2025 ...
springernature.wd3.myworkdayjobs.com
Go @exai.bio! Looking forward to working with Mike as our incoming CEO and our amazing board members.
exai bio@exai.bio · last yr.We’re excited to welcome Michael Nall as CEO and Board Director and new Board Directors - Steve Kafka, PhD, of S32, Dusan Perovic of Two Sigma Ventures and Emir Sandhu, MD, of Blue Venture Fund. Their leadership will be invaluable as we advance our RNA & AI liquid biopsy platform.
Are you currently in the ERE related field & want to find new collaborative opportunities? Join our Chairs @chiappinellilab.bsky.social, @shenhui1986.bsky.social, Ting & Tao at #EREHD25 this Nov! 🎙️Talk Submission extended to 03 Sept 💰Final few $500 grants remaining Don't Miss out! bit.ly/4eRq9Mp
Our ENS is vital to gut-brain health. When it breaks down, so does health. Treatments? Almost none. Access to functional human enteric neurons at scale powers disease modeling and therapeutic discovery. Grateful to everyone who made this possible. www.nature.com/articles/s41...
Check out this amazing work from @genophoria.bsky.social’s lab, revealing a novel post-transcriptional tumour suppressive programme in breast cancer 👇👇
Hani Goodarzi@genophoria.bsky.social · last yr.Been going back and forth on whether it makes sense to post science in the midst of all that is happening. But here it goes with a couple of days of delay: www.biorxiv.org/content/10.1...
Been going back and forth on whether it makes sense to post science in the midst of all that is happening. But here it goes with a couple of days of delay: www.biorxiv.org/content/10.1...
Integrative analysis of mRNA stability regulation uncovers a metastasis-suppressive program in breast cancer
Heterogeneity in cancer gene expression is typically linked to genetic and epigenetic alterations, yet post-transcriptional regulation likely influences these patterns as well. However, the quantitati...
biorxiv.org
🧬💊 @science.org Programmable gene insertion in human cells with a laboratory-evolved CRISPR-associated transposase | Science www.science.org/doi/10.1126/... @sternberglab.bsky.social @isaacwitte.bsky.social eitzingersimon.bsky.social + al. #CRISPR #Medicine #Science #Evolution #Genome #evoCAST
Programmable gene insertion in human cells with a laboratory-evolved CRISPR-associated transposase
Programmable gene integration in human cells has the potential to enable mutation-agnostic treatments for loss-of-function genetic diseases and facilitate many applications in the life sciences. CRISP...
science.org
Sternberg Lab@sternberglab.bsky.social · last yr.1/10 Today in @science.org in collaboration with the Liu group we report the development of a laboratory-evolved CRISPR-associated transposase (evoCAST) that supports therapeutically relevant levels of RNA-programmable gene insertion in human cells. drive.google.com/file/d/1I-Ub...
