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Arang Rhie

@arhie.bsky.social
445 followers 78 following 8 posts
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Adam Phillippy @aphillippy.bsky.social · 30/03/2026
More acrocentric investigations, this one led by @arhie.bsky.social 🕵🏻‍♀️ “Biobank-scale genotyping of Robertsonian translocations reveals hidden structural variation on the human acrocentric chromosomes” 🧵[1/8] 📄 www.biorxiv.org/content/10.6...
biorxiv.org
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Shawn Burgess @burgesslab.bsky.social · 08/04/2025
GRCz12tu is available on Genbank. This will be one of two genomes that will be considered "reference" genomes, there will also be a GRCz12ab assembly coming. It has entered the NCBI annotation pipeline and will also go into the Ensembl annotation pipeline. www.ncbi.nlm.nih.gov/datasets/gen...
ncbi.nlm.nih.gov
Danio rerio genome assembly GRCz12tu
- Danio rerio
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bioRxiv Genomics @biorxiv-genomic.bsky.social · 01/03/2025
A T2T-CHM13 recombination map and globally diverse haplotype reference panel improves phasing and imputation www.biorxiv.org/content/10.1101/202…
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Mikhail Kolmogorov @mishakolmogorov.bsky.social · 14/01/2025
This is becoming a tradition! We are inviting students and postdocs broadly interested in computational cancer to 2025 NCI Spring School on Algorithmic Cancer Biology. Happening Mar 10-14. Please apply and spread the word: ncifrederick.cancer.gov/events/confe...
ncifrederick.cancer.gov
Overview | 2025 NCI Spring School on Algorithmic Cancer Biology | NCIF Conferences
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Adam Phillippy @aphillippy.bsky.social · 09/01/2025
Why was @sexchrlab.bsky.social in snowy Bethesda today? Big news coming later this month! Stay tuned… 🧬
A group of NHRGI scientists having coffee together in a cafe
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Linnea Smeds @linneasmeds.bsky.social · 18/12/2024
Kateryna Makova and I have a new preprint out on non-canonical DNA in human and ape T2T genomes: www.biorxiv.org/content/10.1... Collaboration with Kaivan Kamali, Francesca Chiaromonte, Eduard Kejnovsky, and Iva Kejnovska. Graphical abstract by Dani Zemba.
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Adam Phillippy @aphillippy.bsky.social · 05/09/2024
T2T-F2F 2024 is a wrap! Great to hear about the new discoveries being enabled by complete genomes, and to meet so many new, enthusiastic T2T’ers. Thanks for the great meeting @khmiga.bsky.social @ucscgenomics.bsky.social !! 🎉
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Karen Miga @khmiga.bsky.social · 28/05/2024
We welcome you to join us for the T2T Consortium Face-to-Face (T2T-F2F) Meeting in Santa Cruz, CA 9/2-3. Open to all -- register today.🏄‍♀️ sites.google.com/ucsc.edu/t2t...
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Adam Phillippy @aphillippy.bsky.social · 18/03/2024
We demonstrate a single-platform solution for complete T2T genomes on the ONT PromethION: Duplex + Ultra-long + Pore-C, aka "TNT" 🧨 Expecting rapid improvements in the coming year. Congrats @sergek.bsky.social @zbao.bsky.social @awngs.bsky.social @awngs.bsky.social @khmiga.bsky.social et al.!
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Michael Tress @michaeltress.bsky.social · 12/03/2024
We find that 12 of the 13 WASHC1 paralogues are likely to be pseudogenes, and that the only functional WASHC1 gene is on chromosome 20, not on chromosome 9 as was previously thought. This goes some way to explaining why so little is known about this vital gene, an integral part of the WASH complex.
A. The position of the 13 WASH1 paralogues in the corresponding chromosomes. B-D. The gene neighbours of the old WASHC1 gene, the WASH4P pseudogene, and the functional coding WASH1 gene, LOC124908094.
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Arang Rhie @arhie.bsky.social · 12/03/2024
Congrats!! 👏👏 👏 This is an important piece demonstrating paralogous genes newly found in T2T-CHM13 better represents the coding form while the version in hg38 that was conceived as protein coding turned out to be a pseudogene. Also supported by the #HPRC assemblies. #T2Tgenomes
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bioRxiv Genetics @biorxiv-genetic.bsky.social · 21/12/2023
Rewriting regulatory DNA to dissect and reprogram gene expression www.biorxiv.org/content/10.1101/202…
biorxiv.org
Rewriting regulatory DNA to dissect and reprogram gene expression https://www.biorxiv.org/content/10.1101/2023.12.20.572268v1
Regulatory DNA sequences within enhancers and promoters bind transcription factors to encode cell ty
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bioRxiv Genomics @biorxiv-genomic.bsky.social · 19/12/2023
Cell type specific enrichment of somatic aneuploidy in the mammalian brain www.biorxiv.org/content/10.1101/202…
biorxiv.org
Cell type specific enrichment of somatic aneuploidy in the mammalian brain https://www.biorxiv.org/content/10.1101/2023.12.18.572285v1
Somatic mutations alter the genomes of a subset of an individual's brain cells, impacting gene regul
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Adam Phillippy @aphillippy.bsky.social · 20/12/2023
If you're looking to do long-read sequencing, Katy's awesome!
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Arang Rhie @arhie.bsky.social · 12/12/2023
Pleased to see the Y in here. Full credit for the Y rhyming AI to make it into the title!
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Adam Phillippy @aphillippy.bsky.social · 02/12/2023
Last week we also released updated T2T assemblies for the autosomes as well! Species include: chimp, bonobo, gorilla, Bornean orangutan, Sumatran orangutan, and siamang gibbon. These are making their way to GenBank, but see here for a preview: github.com/marbl/Primates Lots more analyses to come!
github.com
GitHub - marbl/Primates: Complete assemblies of non-human primate genomes
Complete assemblies of non-human primate genomes. Contribute to marbl/Primates development by creating an account on GitHub.
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bioRxiv Genomics @biorxiv-genomic.bsky.social · 01/12/2023
The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes www.biorxiv.org/content/10.1101/202…
biorxiv.org
The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes https://www.biorxiv.org/content/10.1101/2023.11.30.569198v1
Apes possess two sex chromosomes--the male-specific Y and the X shared by males and females. The Y c
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Arang Rhie @arhie.bsky.social · 01/12/2023
What happens when cluster goes down for maintenance. Counter clockwise: @sergek.bsky.social @nancyfhansen.bsky.social @juhyunk.bsky.social @aphillippy.bsky.social playing. @pickettbd.bsky.social taking a break.
Group playing MarioCart in a big conference room.
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Arang Rhie @arhie.bsky.social · 29/11/2023
Come work with us 🙂
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Mikhail Kolmogorov @mishakolmogorov.bsky.social · 20/11/2023
NCI Spring School on Algorithmic Cancer Biology is happening again Apr 1-5 2024! The registration is now open, we invite trainees broadly interested in computational cancer biology to participate. Please apply and spread the word! ncifrederick.cancer.gov/events/confe...
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Fritz Sedlazeck @sedlazeck.bsky.social · 06/11/2023
Tandem repeats are hard! Get your benchmark from @genomeinabottle.bsky.social to compare caller : biorxiv.org/content/10.1... 1.7 mil TR catalog; new tooling to overcome variant representation issues (SNV &SV); insight in complexity. First time we can compare across different techs/caller!
Fig 3 from our preprint to highlight new benchmark approach capable of overcoming allele representation issues etc.
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Dr. Brendan "Doesn't-go-to-Ravenholm" Pinto @drpintothe2nd.bsky.social · 01/11/2023
New preprint out from #NIST in collaboration with @sexchrlab.bsky.social tackling variant calling on the X and Y chromosomes in the human T2T assembly! www.biorxiv.org/content/10.1...
biorxiv.org
Small variant benchmark from a complete assembly of X and Y chromosomes
bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
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bioRxiv Genomics @biorxiv-genomic.bsky.social · 03/11/2023
The complete human diploid reference genome of RPE-1 identifies the phased epigenetic landscapes from multi-omics data www.biorxiv.org/content/10.1101/202…
biorxiv.org
The complete human diploid reference genome of RPE-1 identifies the phased epigenetic landscapes from multi-omics data https://www.biorxiv.org/content/10.1101/2023.11.01.565049v1
Comparative analysis of recent human genome assemblies highlights profound sequence divergence that
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Adam Phillippy @aphillippy.bsky.social · 03/11/2023
NHGRI is searching for new faculty in computational genomics! The NIH intramural program funds labs, not projects, so it's all research and no grant writing. Come work with me at one of the best places in the world to do genomics research! #ASHG23 www.genome.gov/careers-trai...
genome.gov
CGDSR Tenure-Track or Tenure-Eligible Investigator Recruitment
NHGRI seeks to identify outstanding tenure-track or tenure-eligible investigators for the newly established Center for Genomics and Data Science Research (CGDSR) within the Division of Intramural Rese...
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Adam Phillippy @aphillippy.bsky.social · 03/11/2023
Fixed it!
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Arang Rhie @arhie.bsky.social · 03/11/2023
Y chromosome team reunion with Charles and Pille! #ASHG23
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Adam Phillippy @aphillippy.bsky.social · 31/10/2023
We are excited to release v1.0 of our HG002 genome benchmark today! Our goal with the Q100 project is to create a complete and perfectly accurate representation of the diploid HG002 genome to serve as a replacement for current variant-based benchmarks. More info here: github.com/marbl/HG002
github.com
GitHub - marbl/HG002: A complete diploid human genome
A complete diploid human genome. Contribute to marbl/HG002 development by creating an account on GitHub.
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Mikhail Kolmogorov @mishakolmogorov.bsky.social · 24/10/2023
Today we announce the first release of Severus: a new tool for somatic SV calling for long reads! It's designed for complex (and simple) rearrangements in cancer genomes, but also works well for germline github.com/KolmogorovLa...
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Andrew Carroll @acarroll.bsky.social · 24/10/2023
Initial release of DeepSomatic, which identifies subclonal variants when given tumor and normal BAM files. Pre-trained models and case studies available for Illumina and PacBio. Development led by Kishwar Shafin which built off a framework by Pi-Chuan Chang. (github.com/google/deeps...)
github.com
GitHub - google/deepsomatic
Contribute to google/deepsomatic development by creating an account on GitHub.
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Adam Phillippy @aphillippy.bsky.social · 13/09/2023
Kateryna Makova and I were excited to be guests on Science Friday to discuss the Y chromosome. Congrats to the amazing @arhie.bsky.social, Sergey Nurk, and others on completing this last unfinished chromosome! Tune in here if you’re curious about ChrY: www.sciencefriday.com/segments/y-c...
sciencefriday.com
Unraveling the Mysteries Of The Y Chromosome
Assembling the complete sequence of the Y chromosome is an important step toward understanding the human genome.
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