The Dark Matter Project
@darkmatterproject.bsky.social
Studying The Dark Matter of the Genome - everything noncoding 🧬 A collaborative scientific project at NYU Langone. Account managed by Ran Brosh.
www.nature.com/articles/s41... Highly multiplexed mammalian metabolic engineering with a shotgun approach. Congrats Julie Trolle, Sud Pinglay, Jef Boeke et al!
Highly multiplexed mammalian metabolic engineering with a shotgun approach - Nature Biotechnology
Metabolic engineering of mammalian cells is simplified and scaled by screening ‘shotgun’ modifications.
nature.com
How can genome engineering support ecosystem health? What are the ethical considerations? How is it regulated? Free webinars: 🧬 Oct 27: Science talks by Ben Novak & Beth Shapiro ⚖️ Oct 29: Ethics, regulation & governance panel w/ Art Caplan, Alex Erwin & Larisa Rudenko Register: bit.ly/46GXlTQ
ZATELLITE: a toolkit to visualize and manipulate human centromeres in live cells using synthetic zinc fingers biorxiv.org/content/10.6... Congrats to Nestor Saiz et al. from the Center of Synthetic Regulatory Genomics!
ZATELLITE: a toolkit to visualize and manipulate human centromeres in live cells using synthetic zinc fingers
Changes in the number of chromosomes or their spatial organization within the nucleus have critical consequences for cell fate. Yet capturing the karyotype or three-dimensional architecture of chromat...
biorxiv.org
Synthetic biology and genome engineering in support of human, agricultural, and environmental security doi.org/10.3389/fbio... Check out the latest Perspective by Carolyn Chapman et al.
Frontiers | Synthetic biology and genome engineering in support of human, agricultural, and environmental security
The rapid pace of innovation in synthetic biology and genome engineering elicits a need to reevaluate systems of oversight to ensure that biosafety and biose...
doi.org
Happening next week - register now: bit.ly/4urIZQH Learn from world leaders in the fields of Xenotransplantation science, ethics and regulation!!!
The Dark Matter Project@darkmatterproject.bsky.social · 4mo agoInterested in the Science, Ethics and Regulation of Xenotransplantation? Join the next sessions in the "Rewriting Life" series! Register here: bit.ly/4urIZQH
Interested in the Science, Ethics and Regulation of Xenotransplantation? Join the next sessions in the "Rewriting Life" series! Register here: bit.ly/4urIZQH
Interested in the Science, Ethics and Regulation of Xenotransplantation? Join the next sessions in the "Rewriting Life" series! Register here: bit.ly/4urIZQH
Assemblatron: An Automated Workflow for High-Throughput Assembly of Big-DNA Libraries https://www.biorxiv.org/content/10.1101/2025.06.30.662359v1
Happening this Wednesday, 2 PM ET! Register here: nyulangone.zoom.us/webinar/regi...
The Dark Matter Project@darkmatterproject.bsky.social · 5mo agoPlease join us for the “Rewriting Life” series kickoff webinar on May 20th, 2026, 2-3 PM (ET). Register here: nyulangone.zoom.us/webinar/register/WN_tyBjjq2WTHytv_nyovzV9w
Please join us for the “Rewriting Life” series kickoff webinar on May 20th, 2026, 2-3 PM (ET). Register here: nyulangone.zoom.us/webinar/register/WN_tyBjjq2WTHytv_nyovzV9w
We appreciate you sharing your improved toolkit with us! 💙🧑🔬 Find the plasmids here: www.addgene.org/browse/artic...
Addgene: Improved vector toolkit for genome writing in mammalian cells.
addgene.org
The Dark Matter Project@darkmatterproject.bsky.social · 5mo agoPlasmids described in this manuscript are now on Addgene. Check out our Resources page for more info: www.thedarkmatterproject.org/resources
Want to deploy Big-IN or mSwAP-In in your own lab? Check out new plasmids we deposited on Addgene as well as updated protocols: www.thedarkmatterproject.org/resources
Resources — The Dark Matter Project
thedarkmatterproject.org
Please join us for the “Rewriting Life” series kickoff webinar on May 20th, 2026, 2-3 PM (ET). Register here: nyulangone.zoom.us/webinar/register/WN_tyBjjq2WTHytv_nyovzV9w
Improved vector toolkit for genome writing in mammalian cells www.biorxiv.org/content/10.6...
biorxiv.org
Mammalian genome writing: Unlocking new length scales for genome engineering www.sciencedirect.com/science/arti...
Happy to share that our review on mammalian genome writing with Jack Atwater, Ran Brosh, Jef Boeke, @jshendure.bsky.social and Matt Maurano is now out in @cellpress.bsky.social! www.sciencedirect.com/science/arti...
Mammalian genome writing: Unlocking new length scales for genome engineering
The ability to design and engineer mammalian genomes across arbitrary length scales would transform biology and medicine. Such capabilities would enab…
sciencedirect.com
🧬Sign up to our free online 2026 Genome Writing Workshop 🧬 www.thedarkmatterproject.org/2026-genome-...
www.biorxiv.org/content/10.6... Congrats to Dr. Noor Chalhoub who managed to defend her thesis and publish this paper on the same day!
Genome writing and Targeted Delivery of the NKX6-3/ANK1 gene cluster and its Type 2 Diabetes GWAS Variants to Human iPSCs
Genome-wide association studies (GWAS) identified over 600 loci containing single-nucleotide polymorphisms (SNPs) associated with type 2 diabetes (T2D), most of which reside in non-coding regions. Amo...
biorxiv.org
Enhancer cooperativity in the folded genome www.sciencedirect.com/science/arti...
Structure and evolution-guided design of minimal RNA-guided nucleases www.biorxiv.org/content/10.6...
Structure and evolution-guided design of minimal RNA-guided nucleases
The design of RNA-guided nucleases with properties not limited by evolution can expand programmable genome editing capabilities. However, generating diverse multi-domain proteins with robust enzymatic...
biorxiv.org
High-fidelity human chromosome transfer and elimination | Science www.science.org/doi/abs/10.1...
High-fidelity human chromosome transfer and elimination
The synthesis of human genomes and other gigabase-scale genomes will require new strategies. Here, we realized key steps in our pipeline for building synthetic human chromosomes. We established: (i) t...
science.org
How could one engineer a mouse carrying a LETHAL allele? A thread 🧵
One step closer to an LLM that understands novel DNA🧬 𝗜𝘁𝗲𝗿𝗮𝘁𝗶𝘃𝗲 𝗶𝗺𝗽𝗿𝗼𝘃𝗲𝗺𝗲𝗻𝘁 𝗼𝗳 𝗱𝗲𝗲𝗽 𝗹𝗲𝗮𝗿𝗻𝗶𝗻𝗴 𝗺𝗼𝗱𝗲𝗹𝘀 𝘂𝘀𝗶𝗻𝗴 𝘀𝘆𝗻𝘁𝗵𝗲𝘁𝗶𝗰 𝗿𝗲𝗴𝘂𝗹𝗮𝘁𝗼𝗿𝘆 𝗴𝗲𝗻𝗼𝗺𝗶𝗰𝘀. pubmed.ncbi.nlm.nih.gov/41125441 Congrats Andre Ribeiro-Dos-Santos and Matt Maurano!
I am proud to share our work on X-linked Dystonia-Parkinsonism — a rare neurodegenerative movement disorder driven by a SINE-VNTR-Alu retrotransposon insertion in the TAF1 gene. Read our two companion papers: 🔹 www.biorxiv.org/content/10.1... 🔹 www.biorxiv.org/content/10.1... 🧵 Highlights below!
We're thrilled to publish 2 exciting preprints today on the molecular pathology of X-linked Dystonia Parkinsonism! biorxiv.org/content/10.1... AND biorxiv.org/content/10.1... @nyulangone.bsky.social
Megabase-scale human genome rearrangement with programmable bridge recombinases | Science www.science.org/doi/10.1126/...
Megabase-scale human genome rearrangement with programmable bridge recombinases
Bridge recombinases are naturally occurring RNA-guided DNA recombinases that we previously demonstrated can programmably insert, excise, and invert DNA in vitro and in Escherichia coli. In this study,...
science.org
Structure of a polymorphic repeat at the CACNA1C schizophrenia locus | PNAS www.pnas.org/doi/10.1073/... Congrats to Raquel Moya and team!
Structure of a polymorphic repeat at the CACNA1C schizophrenia locus | PNAS
Genetic variation within intron 3 of the CACNA1C calcium channel gene is associated with schizophrenia and other neuropsychiatric disorders, but an...
pnas.org
