Arang Rhie
@arhie.bsky.social
Reposted by Arang Rhie
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...
www.ncbi.nlm.nih.gov/datasets/gen...
Danio rerio genome assembly GRCz12tu
- Danio rerio
www.ncbi.nlm.nih.gov
April 8, 2025 at 9:44 PM
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...
www.ncbi.nlm.nih.gov/datasets/gen...
Reposted by Arang Rhie
A T2T-CHM13 recombination map and globally diverse haplotype reference panel improves phasing and imputation https://www.biorxiv.org/content/10.1101/2025.02.24.639687v1
March 1, 2025 at 2:33 AM
A T2T-CHM13 recombination map and globally diverse haplotype reference panel improves phasing and imputation https://www.biorxiv.org/content/10.1101/2025.02.24.639687v1
Reposted by Arang Rhie
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...
Overview | 2025 NCI Spring School on Algorithmic Cancer Biology | NCIF Conferences
ncifrederick.cancer.gov
January 14, 2025 at 10:41 PM
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...
Reposted by Arang Rhie
Why was @sexchrlab.bsky.social in snowy Bethesda today? Big news coming later this month! Stay tuned… 🧬
January 9, 2025 at 6:21 PM
Why was @sexchrlab.bsky.social in snowy Bethesda today? Big news coming later this month! Stay tuned… 🧬
Reposted by Arang Rhie
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.
Collaboration with Kaivan Kamali, Francesca Chiaromonte, Eduard Kejnovsky, and Iva Kejnovska. Graphical abstract by Dani Zemba.
December 18, 2024 at 8:10 PM
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.
Collaboration with Kaivan Kamali, Francesca Chiaromonte, Eduard Kejnovsky, and Iva Kejnovska. Graphical abstract by Dani Zemba.
Reposted by Arang Rhie
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 !! 🎉
September 5, 2024 at 6:57 PM
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 !! 🎉
Reposted by Arang Rhie
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...
sites.google.com/ucsc.edu/t2t...
May 28, 2024 at 6:11 PM
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...
sites.google.com/ucsc.edu/t2t...
Reposted by Arang Rhie
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.!
Gapless assembly of complete human and plant chromosomes using only nanopore sequencing https://www.biorxiv.org/content/10.1101/2024.03.15.585294v1
Gapless assembly of complete human and plant chromosomes using only nanopore sequencing https://www.biorxiv.org/content/10.1101/2024.03.15.585294v1
The combination of ultra-long Oxford Nanopore (ONT) sequencing reads with long, accurate PacBio HiFi
www.biorxiv.org
March 18, 2024 at 2:22 PM
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.!
Reposted by Arang Rhie
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.
This goes some way to explaining why so little is known about this vital gene, an integral part of the WASH complex.
March 12, 2024 at 2:13 PM
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.
This goes some way to explaining why so little is known about this vital gene, an integral part of the WASH complex.
Reposted by Arang Rhie
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
March 12, 2024 at 2:23 PM
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
Reposted by Arang Rhie
Rewriting regulatory DNA to dissect and reprogram gene expression https://www.biorxiv.org/content/10.1101/2023.12.20.572268v1
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
www.biorxiv.org
December 21, 2023 at 11:39 AM
Rewriting regulatory DNA to dissect and reprogram gene expression https://www.biorxiv.org/content/10.1101/2023.12.20.572268v1
Reposted by Arang Rhie
Cell type specific enrichment of somatic aneuploidy in the mammalian brain https://www.biorxiv.org/content/10.1101/2023.12.18.572285v1
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
www.biorxiv.org
December 19, 2023 at 7:38 PM
Cell type specific enrichment of somatic aneuploidy in the mammalian brain https://www.biorxiv.org/content/10.1101/2023.12.18.572285v1
Reposted by Arang Rhie
If you're looking to do long-read sequencing, Katy's awesome!
Interested in working in a fast-paced cutting-edge genomic research lab? We're looking for someone to join our team in Seattle, WA, running our PacBio Revio sequencer!
UW Human Resources
University of Washington Human Resources
uwhires.admin.washington.edu
December 20, 2023 at 8:55 PM
If you're looking to do long-read sequencing, Katy's awesome!
Pleased to see the Y in here. Full credit for the Y rhyming AI to make it into the title!
🎇 It's been an amazing year for biotech. 🎇 We're proud to have contributed to two of Nature Biotechnology's top stories of the year, co-leading the creation the new pangenome reference & working with @aphillippy.bsky.social 's team at NHGRI on completing the Y chromosome! go.nature.com/3uMSHnm
December 12, 2023 at 11:54 PM
Pleased to see the Y in here. Full credit for the Y rhyming AI to make it into the title!
Reposted by Arang Rhie
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 - 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.
github.com
December 2, 2023 at 6:31 PM
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!
Reposted by Arang Rhie
The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes https://www.biorxiv.org/content/10.1101/2023.11.30.569198v1
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
www.biorxiv.org
December 1, 2023 at 10:39 PM
The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes https://www.biorxiv.org/content/10.1101/2023.11.30.569198v1
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.
December 1, 2023 at 10:04 PM
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.
Come work with us 🙂
Reposting! This faculty search is open through December
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...
November 29, 2023 at 12:53 AM
Come work with us 🙂
Reposted by Arang Rhie
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...
November 20, 2023 at 9:48 PM
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...
Reposted by Arang Rhie
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!
@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!
November 6, 2023 at 2:29 PM
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!
@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!
Reposted by Arang Rhie
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...
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
www.biorxiv.org
November 1, 2023 at 9:35 PM
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...
Reposted by Arang Rhie
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
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
www.biorxiv.org
November 3, 2023 at 6:34 PM
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
Reposted by Arang Rhie
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...
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...
www.genome.gov
November 3, 2023 at 5:52 PM
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...
Reposted by Arang Rhie
