Adam Phillippy
@aphillippy.bsky.social
Finished a human genome, working on a few more 👨💻
Lab: https://genomeinformatics.github.io
Posts are my own
Lab: https://genomeinformatics.github.io
Posts are my own
If that’s not enough, we threw in a complete, T2T giraffe genome! Giraffe genomes are pretty cool. Almost all of their chromosomes are Robertsonian fusions of the typically telocentric ruminant chromosomes. 🐄 vs. 🦒...
October 10, 2025 at 3:26 PM
If that’s not enough, we threw in a complete, T2T giraffe genome! Giraffe genomes are pretty cool. Almost all of their chromosomes are Robertsonian fusions of the typically telocentric ruminant chromosomes. 🐄 vs. 🦒...
How Robertsonian chromosomes can lead to miscarriage or trisomy explained in one great figure from Human Molecular Genetics (Strachan and Read) that I have referred to many times
September 24, 2025 at 8:27 PM
How Robertsonian chromosomes can lead to miscarriage or trisomy explained in one great figure from Human Molecular Genetics (Strachan and Read) that I have referred to many times
More from HG002: This figure shows the incredible progress of de novo assembly over the past 5 years. Ash1 was a good "collapsed haplotype" assembly from 2020. Now we have single-tech solutions (ONT 6B4) that can produce nearly perfect diploid assemblies out of the (HERRO/Verkko) box 🤯
September 23, 2025 at 1:01 PM
More from HG002: This figure shows the incredible progress of de novo assembly over the past 5 years. Ash1 was a good "collapsed haplotype" assembly from 2020. Now we have single-tech solutions (ONT 6B4) that can produce nearly perfect diploid assemblies out of the (HERRO/Verkko) box 🤯
Assembling and annotating the diploid HG002 genome from “T2T” allowed us to fill in those missing regions and explore the limitations of reference-based variant calling and benchmarking, especially within complex, segmentally duplicated regions of the genome that are often heterozygous [3/14]
September 22, 2025 at 5:02 PM
Assembling and annotating the diploid HG002 genome from “T2T” allowed us to fill in those missing regions and explore the limitations of reference-based variant calling and benchmarking, especially within complex, segmentally duplicated regions of the genome that are often heterozygous [3/14]
Building benchmarks is hard, unglamorous work, but the impact can be huge. Think about how much the GIAB variant benchmarks have shaped the field over the past ~10 years. But did you know these benchmarks omit ~15% of the genome? (And not just in the centromeres...) [2/14]
September 22, 2025 at 5:02 PM
Building benchmarks is hard, unglamorous work, but the impact can be huge. Think about how much the GIAB variant benchmarks have shaped the field over the past ~10 years. But did you know these benchmarks omit ~15% of the genome? (And not just in the centromeres...) [2/14]
Definitely hard to measure, but here is our best attempt from a new benchmarking paper to be preprinted in the next few weeks. Element appears to be the current king of homopolymers. Illumina does worse than HiFi beyond 20 bp. (This is all measured on human DNA)
September 5, 2025 at 12:55 PM
Definitely hard to measure, but here is our best attempt from a new benchmarking paper to be preprinted in the next few weeks. Element appears to be the current king of homopolymers. Illumina does worse than HiFi beyond 20 bp. (This is all measured on human DNA)
As just one example, Verkko2 allowed us to assemble the first T2T Robertsonian chromosomes and pinpoint a particular SST1 satellite repeat array as the fusion site of most ROBs: www.biorxiv.org/content/10.1...
June 17, 2025 at 1:44 PM
As just one example, Verkko2 allowed us to assemble the first T2T Robertsonian chromosomes and pinpoint a particular SST1 satellite repeat array as the fusion site of most ROBs: www.biorxiv.org/content/10.1...
Congrats to @dantipov.bsky.social et al. on the publication of Verkko2! The team put a ton of work into this making it the first assembler that deals with the complexity of human acrocentric chromosomes. Lots of interesting discoveries to come! genome.cshlp.org/content/earl...
June 17, 2025 at 1:39 PM
Congrats to @dantipov.bsky.social et al. on the publication of Verkko2! The team put a ton of work into this making it the first assembler that deals with the complexity of human acrocentric chromosomes. Lots of interesting discoveries to come! genome.cshlp.org/content/earl...
I remember chatting with @sergek.bsky.social and intentionally calling this a "golden threshold" so that it would be a brainworm. Glad our strategy worked and you still remember it 12 years later 😁 This was the original figure from doi.org/10.1186/gb-2...
May 15, 2025 at 8:58 PM
I remember chatting with @sergek.bsky.social and intentionally calling this a "golden threshold" so that it would be a brainworm. Glad our strategy worked and you still remember it 12 years later 😁 This was the original figure from doi.org/10.1186/gb-2...
A project five years in the making, we've now published complete "T2T" genomes for six additional ape species! It turns out that finishing (and analyzing) six genomes is slightly more work than one... doi.org/10.1038/s415...
April 9, 2025 at 9:31 PM
A project five years in the making, we've now published complete "T2T" genomes for six additional ape species! It turns out that finishing (and analyzing) six genomes is slightly more work than one... doi.org/10.1038/s415...
Congrats to Bryce Kille on absolutely smashing his PhD defense at Rice today with advisor @treangen.bsky.social ! Collaborating with Bryce over the past few years has been an absolute delight 👏🎉👏🎉
January 27, 2025 at 8:56 PM
Congrats to Bryce Kille on absolutely smashing his PhD defense at Rice today with advisor @treangen.bsky.social ! Collaborating with Bryce over the past few years has been an absolute delight 👏🎉👏🎉
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… 🧬
I pulled a bunch of old TIGR faculty photos from Wayback Machine for Claire's retirement symposium. Everyone had a formal headshot except you 😄
December 17, 2024 at 6:30 PM
I pulled a bunch of old TIGR faculty photos from Wayback Machine for Claire's retirement symposium. Everyone had a formal headshot except you 😄
Reuniting sci twitter in person with a bearded @blekhman.bsky.social visiting NHGRI today! (and, yes, we both poked Julie to join bsky next)
November 14, 2024 at 9:57 PM
Reuniting sci twitter in person with a bearded @blekhman.bsky.social visiting NHGRI today! (and, yes, we both poked Julie to join bsky next)
Such an honor to speak at Claire Fraser’s retirement symposium today and reflect on how much she shaped my own career. Wonderful to see so many old friends in the same place. What an incredible legacy ❤️🐅 #TIGR
October 8, 2024 at 4:22 PM
Such an honor to speak at Claire Fraser’s retirement symposium today and reflect on how much she shaped my own career. Wonderful to see so many old friends in the same place. What an incredible legacy ❤️🐅 #TIGR
"The formation and propagation of human Robertsonian chromosomes" ROBs are the most common translocation in humans, approx. ~1 per 800 people. Last year we proposed a simple mechanism for ROB formation; This year we prove it by finishing some T2T! New preprint: www.biorxiv.org/content/10.1...
September 27, 2024 at 2:15 PM
"The formation and propagation of human Robertsonian chromosomes" ROBs are the most common translocation in humans, approx. ~1 per 800 people. Last year we proposed a simple mechanism for ROB formation; This year we prove it by finishing some T2T! New preprint: www.biorxiv.org/content/10.1...
"Epigenetic control and inheritance of rDNA arrays" New preprint from the T2T acrocentrics team! We find a tight link between methylation and transcription of the rDNAs, including the occasional silencing of entire arrays www.biorxiv.org/content/10.1...
September 16, 2024 at 10:41 PM
"Epigenetic control and inheritance of rDNA arrays" New preprint from the T2T acrocentrics team! We find a tight link between methylation and transcription of the rDNAs, including the occasional silencing of entire arrays www.biorxiv.org/content/10.1...
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 !! 🎉
Kicking off day 2 of #T2T-F2F in one of my favorite places (redwoods of Santa Cruz) with one of my favorite people (Jen Gerton) presenting our work sequencing Robertsonian chromosomes 🧬
September 4, 2024 at 4:27 PM
Kicking off day 2 of #T2T-F2F in one of my favorite places (redwoods of Santa Cruz) with one of my favorite people (Jen Gerton) presenting our work sequencing Robertsonian chromosomes 🧬
Complete genomes for the apes! We have added bonobo, chimp, gorilla 🦍, orangutan 🦧, and gibbon to the T2T family! Lots of very cool stories buried in these genomes, some of which we have explored here, but I expect many more studies to follow: www.biorxiv.org/content/10.1...
August 1, 2024 at 2:50 PM
Complete genomes for the apes! We have added bonobo, chimp, gorilla 🦍, orangutan 🦧, and gibbon to the T2T family! Lots of very cool stories buried in these genomes, some of which we have explored here, but I expect many more studies to follow: www.biorxiv.org/content/10.1...
So we decided not to stop with human and have finished sex chromosomes for the great apes as well 🙊 They make for the prettiest dotplots, e.g. compare human Y vs. bonobo Y. So many palindromes! 📄 "The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes" www.biorxiv.org/content/10.1...
December 2, 2023 at 6:23 PM
So we decided not to stop with human and have finished sex chromosomes for the great apes as well 🙊 They make for the prettiest dotplots, e.g. compare human Y vs. bonobo Y. So many palindromes! 📄 "The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes" www.biorxiv.org/content/10.1...
