Phase Genomics

Benchmarking with synthetic communities provides a baseline for virus-host inferences from Hi-C proximity linking Virus discovery has accelerated but linking viruses to hosts remains challenging. This study uses synthetic microbiomes to optimize and benchmark Hi-C for virus-host linkage inference, and applies thi...

New Publication in @plosbiology.org: Optimized Hi-C analysis (Z-score filtering) boosts specificity & reveals virus-host interactions using Phase Genomics’ ProxiMeta™ Hi-C: 79 genus-level matches + 293 new linkages in well-studied, climate-critical soils.

journals.plos.org/plosbiology/...

"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:

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👇

Cell Press: STAR Protocols STAR Protocols is an open access, peer-reviewed journal from Cell Press. We offer structured, transparent, accessible, and repeatable step-by-step experimental and computational protocols from all are...

Tissue prep drives variability early in Hi-C workflows. A new STAR Protocol adds cryogenic tissue grinding before crosslinking, with safe pause points for optimized lab workflows.

See how it improves reproducibility & library quality → star-protocols.cell.com/protocols/4702

Wheels up ✈️ Our CEO Ivan’s headed to Newport Beach for Microbes in Wastewater.

He’ll show how ProxiMeta™ links microbes, phages & the mobilome to track #AMR in wastewater. No coding. Just discovery. If you’ll be in Newport for the conference, say hi to
@ivanliachko.bsky.social

We heard you. Our 25 in ’25 promo is extended through Jan 16.

Save 25% on Phase Genomics Hi-C kits via direct order, book a complimentary bioinformatics consult, and access discounted full-service ProxiMeta™ packages.

Get started → info.phasegenomics.com/25-in-25

Bees carry more than nectar. Their gut microbiomes buzz with plasmids, sharing tetracycline resistance genes across hives. Chris Robinson, PhD from Irene Newton, PhD’s lab used Hi-C to track these mobile elements & explore colony-specific patterns traditional metagenomics misses.

Stuck on Hi-C data? First 25 researchers to email get a free consult with our computational scientists—whether you're using our kits or another provider's.

Email info@phasegenomics.com with "25 in '25 Bioinformatics Promo" in the subject line to claim yours.

Save 25% on Hi-C kits through Dec 31. From complex plant genomes to metagenome binning, Phase Genomics brings clarity to your toughest research questions. Email info@phasegenomics.com with "25 in '25 Kit Promo" in the subject line to claim your discount.

🌿 Scientists produced a high-quality, chromosome-scale genome for American pickleweed, a salt-loving, tetraploid marsh plant. With ~80k genes and detailed methylation data, this resource paves the way for understanding salt-tolerance & supporting salt-marsh conservation.

🔗 bit.ly/3XAQ7vT

New at #AMPath2025: He Fang, PhD, will showcase Genomic Proximity Mapping® (GPM) and CytoTerra® in #sarcoma.

Stop by Level 2, 258ABC on 11/13 from 2:30 – 3:30 pm ET to discover how GPM uncovers hidden structural variants and mosaicism in challenging archival samples.

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...

Big spotlight on Genomic Proximity Mapping® (GPM®) from Elsevier's JMD: See how UW researchers use our GPM platform, CytoTerra®, to detect cryptic structural variants and mosaicism missed by standard tests. Full press release from @elsevierconnect.bsky.social: www.elsevier.com/about/press-...

Phase Genomics Hi-C helped untangle the pomegranate genome, ordering contigs into chromosome-scale scaffolds, clarifying chromosome counts & revealing domestication patterns. Full study from the Volcani Center: link.springer.com/article/10.1...

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

YouTube video by Phase Genomics Hi-C in Action: Faster Discoveries, More Publications, Bigger Impact | with Alex Harkess

Hi-C at scale is reshaping plant biology. With Phase Genomics’ kits, Alex Harkess & HudsonAlpha have published dozens of genomes, uncovered how rising CO₂ alters chromatin structure, and explored how climate change ripples through living systems. 🔗 youtu.be/5-Ub7FnpHzs?...

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

ProxiMeta™ Hi-C fills the missing link in shotgun metagenomics, connecting viruses to hosts & revealing hidden microbial relationships. Hear more from Phil Hugenholtz & Phase Genomics CEO Ivan Liachko on how Hi-C unlocks the microbiome → www.youtube.com/watch?v=DYMv...

Skip the computational guesswork. Hi-C / proximity ligation reveal complete chromosomal architecture based on actual intracellular contacts.

From plant genomes to metagenomes, Phase Genomics delivers chromosome-scale assemblies traditional methods can’t: phasegenomics.com/resources-an...

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.

ProxiMeta™ turns your benchtop box into a Hi-C metagenomics powerhouse. Order before Sept. 30 to lock in 20% savings on the 8-sample ProxiMeta Classic Hi-C Kit, or 50% on the 2-sample ProxiMeta Starter Hi-C Kit.

🔗https://phasegenomics.com/contact-us/

Don’t let your lab’s grant dollars go to waste. Order before September 30 to save 20% on ProxiMeta™ Classic Hi-C Kit, or 50% on the ProxiMeta Starter Hi-C Kit.

✔️ Hands-off workflow ✔️ Flexible timelines ✔️ PGShield™ to keep samples shelf-stable

🔗https://phasegenomics.com/contact-us/

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...

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...

Stanford researchers just achieved another 1st: Using ProxiMeta™, helped isolate p-crAssphage, a common gut virus and shape shifter that can switch between producing viruses and quietly living in bacteria like a plasmid. Read more in @cp-cellhostmicrobe.bsky.social: www.cell.com/cell-host-mi...

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...