Chatting with Jeff about his recent paper on the oat pangenome 🌱🧬. #plants #genome

New Nature Plants study using Proximo™ Hi-C shows how a hybrid eelgrass species inherited low-light tolerance genes from its deep-water parent that could change how we approach coastal restoration.

More from Todd Michael, PhD & team at @salkinstitute.bsky.social l 📄 www.nature.com/articles/s41...

Phase Genomics IRL: a few days together in Portland for real-time collab & creativity. Aligning on new products, pressure-testing ideas, a little fun behind the wheel. It’s how we build even better Hi-C tools for the researchers who rely on them.

A few of our favorite moments👇

"A year and a half ago, we couldn't have resolved this hybrid genome."

New tech (long reads + Hi-C) let researchers separate parental haplotypes in eelgrass revealing which genes drive low-light tolerance. Todd Michael, PhD breaks down how:

Time for our End of Year sale! If you need an excuse to talk to me about science, this is one way to get there (but also, I'll do it for free 🧬 ❤️ )

Hybridization and low-light adaptability in California eelgrass (Zostera spp.) - Nature Plants Seagrass genomes of the deep-water Zostera pacifica and shallow-water Z. marina from the Eastern Pacific Ocean provide evidence for low-light adaptation exemplified in the wild hybrid Z. marina × paci...

🌿 New in @NaturePlants! Researchers used Phase Genomics’ Hi-C to build a haplotype-resolved chromosome-scale #genome of a hybrid eelgrass (Zostera marina × Z. pacifica), revealing genomic clues to low-light tolerance that could boost coastal restoration. www.nature.com/articles/s41...

Phase Genomics’ Hi-C tech helped undergrads assemble the “best duckweed genome yet,” giving them hands-on research experience, boosting PhD prospects, and advancing plant biology. Full story from Alex Harkess at HudsonAlpha on YouTube: na2.hubs.ly/H01P7mG0

Happy #WorldPhageDay.
Tiny, abundant, and anything but boring, phages shape microbial communities, move genes around, and can tip the balance in all kinds of ecosystems.

The catch: to know a #phage only you must know its host. ProxiMeta Hi-C technology gives us that link.

🌳 New chromosome-level Ulmus minor (field elm) genome unlocks clues to Dutch elm disease resistance. Using long reads and Hi-C, the team built this 2.1Gb genome and mapped clusters of resistance genes conserved across elm species to aid restoration.
na2.hubs.ly/H01HQ2Q0

Phages with a broad host range are common across ecosystems - Nature Microbiology Proximity-ligation-based sequencing from 111 samples and 5 environments reveals that a substantial proportion of phages infect multiple species.

In this great new paper, the authors use metagenomic Hi-C to show that #phage with broad host range are fairly common, contrary to the prevailing view on their biology. Cutting edge methods like Hi-C are shedding light on our blind spots in the microbial world.

Join us at the Microbiome Innovation One Health Conference in Oxford on Sept 15! @ivanliachko.bsky.social will present how ProxiMeta™ maps microbes, viruses, plasmids & resistance genes, bringing clarity to complexity across human, animal and environmental health.

🧬 Important Slug News!
Researchers assembled a chromosome-scale #genome for Deroceras laeve using Proximo Hi-C and @pacbio.bsky.social - making it a useful model for study of #genomics, #evolution, and slimyness... Congrats to Alfredo Varela-Echavarría & team!

🔗 academic.oup.com/g3journal/ad...

The Future of Phage Therapy: Can Bacteriophages Replace Antibiotics? | Witness how Phase Genomics revolutionizes DNA analysis through Hi-C technology, enabling breakthroughs in microbiome research, cancer diagnostics, and bacteriophage therapeutics to combat antibiotic r...

Glad I saw @ivanliachko.bsky.social present on mind-blowing applications of proximity ligation, including metagenomics--linking plasmids, phages and genomes across microbiomes. I see major impact for precision #phagetherapy (and #onehealth)
Godspeed @phasegenomics.bsky.social
tinyurl.com/yaubcrpt

A fungus among us: Proximo Hi‑C + @pacbio.bsky.social HiFi produced telomere‑to‑telomere genomes for VCG‑01111/01112, uncovering 4 accessory chromosomes, >3.6 My divergence, SIX6 and novel effectors—pinpointing drivers of high virulence. www.mdpi.com/2309-608X/11...

She doesn’t need a hero, she is the hero we need. 🤩

Comparative genomics of the parasite Trichomonas vaginalis reveals genes involved in spillover from birds to humans - Nature Communications The sexually transmitted human parasite Trichomonas vaginalis belongs to a clade of host-switching trichomonads that parasitize mammals, birds, livestock, and pets. Here the authors describe a chromos...

New study uses long-read + @phasegenomics.bsky.social Hi-C to assemble chromosome-scale #genome of Trichomonas vaginalis and bird-infecting relatives, revealing key genes tied to bird-to-human spillover. Congrats to Jane Carlton, ‪@mikeschatz.bsky.social‬ and team!

Structural variants often go undetected by traditional cytogenetics. A new review in Genes shows how Genomic Proximity Mapping™ (GPM) detects complex SVs right from FFPE. Read more Dr. Patrick Gonzales at the University of Kansas Medical Center: www.mdpi.com/2073-4425/16...

When sample quality is low, insight usually is too. Not with Genomic Proximity Mapping™ (GPM).

Phase Genomics’ GPM works on #FFPE and mosaic samples. It’s just one assay, no metaphase prep, and no tradeoff in resolution. A new preprint shows how: www.medrxiv.org/content/10.1...

Comprehensive cytogenetics from any sample type—including #FFPE—in just one assay:

CytoTerra® delivers genome-wide SV detection with no culture, no HMW DNA, and results in as little as 5 days. Stop by booth 23 & check out our presentations to see it in action at #CGC2025.

This is very cool

🌸 Chromosome-scale genome of Petunia hybrida assembled with Proximo Hi-C, PacBio HiFi, Illumina & Bionano. 7 pseudochromosomes, 99.8% BUSCO with Hi-C being key for resolving repeats. A powerful resource for Solanaceae genetics & breeding. #genome #HiC

📄 hubs.la/Q03ypPmb0

By popular demand by you, #genomics people - this buffer is super useful for Hi-C and we'll give you some if you ask for it, no strings attached.

Haplotype-resolved chromosome-level genome sequence of Elsholtzia splendens (Nakai ex F.Maek.) - Scientific Data Scientific Data - Haplotype-resolved chromosome-level genome sequence of Elsholtzia splendens (Nakai ex F.Maek.)

🌱🧬Researchers released haplotype-resolved, chromosome-level genomes of Eupatorium splendens - a plant known for medicinal properties and ability to thrive in contaminated soils. A powerful resource for studying stress adaptation & secondary metabolism. www.nature.com/articles/s41...

🍓 Meet ‘Yuexin’ - a next-gen #strawberry with smoother texture, better shelf life, and sweeter aroma. Scientists have released its fully phased #genome, revealing the genetic secrets behind these tasty traits. Proximo #HiC +
@pacbio.bsky.social for the win! 🧬

🔗 hubs.la/Q03tZvZD0

Growth Without Venture Capital: The Bootstrapped Biotech Playbook | Ivan Liachko (Part 4/4) YouTube video by The Biotech Startups Podcast | Excedr

“It’s not a brute force technology. It’s a clever technology.”
— Jon Chee, CEO @ Excedr

In the finale of The Biotech Startups Podcast, Jon and @ivanliachko.bsky.social unpack how smart science powers Phase Genomics' impact in cancer research, metagenomics & more👇
youtu.be/fqL6ZvS2sNQ?...

New💩🚰👨‍🔬 study in #EnvMicrobiology uses shotgun & Hi-C metagenomics to reveal rapid shifts in antibiotic resistance genes and their microbial hosts, highlighting the dynamic nature of resistomes. #AMR #Metagenomics

🔗https://hubs.la/Q03tZ1Jf0

TBT: 🧬 Throwing it back to a cool study from Aug 2021! Using proximity ligation, this paper explores the two-compartment genome of R. irregularis, a model arbuscular mycorrhizal symbiont, using Proximo #HiC and @nanoporetech.com sequencing. @Blunt_Microbe

🔗 Full study: hubs.la/Q03tZ6Ch0

How 3D Genome Mapping is Changing Everything We Know About DNA | Ivan Liachko (Part 3/4) YouTube video by The Biotech Startups Podcast | Excedr

“If we don’t commercialize this, it’s going to be a crime against science.” - @ivanliachko.bsky.social, Founder and CEO

Hear how a postdoc aha moment became a platform accelerating #microbiome research, tackling #AMR & more on the Biotech Startups Podcast: www.youtube.com/watch?v=U2UG...

Unleashing the wild side of lupins! 🌕🐺🍃
Researchers built #genomes of rough-seeded lupins - L. cosentinii & L. digitatus - revealing unique #gene expansions tied to stress resilience and seed traits. A howling good resource for legume breeding! #HiC
🔗 hubs.la/Q03v1F2c0

Can’t see the full picture with karyotyping or microarrays?

New research in
@Genes_MDPI
shows how Genomic Proximity Mapping (GPM) detects structural variants other tools miss - translocations, insertions & CN-LOH - even from FFPE!
hubs.la/Q03v2s2N0

#Cancer #Cytogenetics