Dmitry Antipov
@dantipov.bsky.social
Genome assemblers and their friends. Postdoc at https://genomeinformatics.github.io/
Molecular Mechanisms in Evolution GRC conference short recap
June 27, 2025 at 7:20 PM
Molecular Mechanisms in Evolution GRC conference short recap
Verkko2 paper is finally published!
genome.cshlp.org/content/earl...
genome.cshlp.org/content/earl...
Verkko2 integrates proximity-ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere genome assembly,
phasing, and scaffolding
An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms
genome.cshlp.org
June 12, 2025 at 10:58 PM
Verkko2 paper is finally published!
genome.cshlp.org/content/earl...
genome.cshlp.org/content/earl...
I believe this to be one of the most important things now. www.theguardian.com/us-news/2024...
Guardian missed that this guy is also a long-time business partner of Peter Thiel and is really influential among those tech bros.
I've read his manifestos. They are frightening and really match the news
Guardian missed that this guy is also a long-time business partner of Peter Thiel and is really influential among those tech bros.
I've read his manifestos. They are frightening and really match the news
He’s anti-democracy and pro-Trump: the obscure ‘dark enlightenment’ blogger influencing the next US administration
Key figures in the incoming administration follow Curtis Yarvin, who’s pushing for an autocratic takeover of the US
www.theguardian.com
February 5, 2025 at 1:05 AM
I believe this to be one of the most important things now. www.theguardian.com/us-news/2024...
Guardian missed that this guy is also a long-time business partner of Peter Thiel and is really influential among those tech bros.
I've read his manifestos. They are frightening and really match the news
Guardian missed that this guy is also a long-time business partner of Peter Thiel and is really influential among those tech bros.
I've read his manifestos. They are frightening and really match the news
Verkko2 paper is finally on the biorxiv
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Verkko2: Integrating proximity ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere genome assembly, phasing, and scaffolding
The Telomere-to-Telomere Consortium recently finished the first truly complete sequence of a human genome. To resolve the most complex repeats, this project relied on the semi-manual combination of lo...
www.biorxiv.org
December 27, 2024 at 7:55 PM
Verkko2 paper is finally on the biorxiv
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Finally on some samples we have all 46 human chromosomes T2T. Update to verkko 2.2, last big release of this summer! github.com/marbl/verkko
GitHub - marbl/verkko: Telomere-to-telomere assembly of accurate long reads (PacBio HiFi, Oxford Nanopore Duplex, HERRO corrected Oxford Nanopore Simplex) and Oxford Nanopore ultra-long reads.
Telomere-to-telomere assembly of accurate long reads (PacBio HiFi, Oxford Nanopore Duplex, HERRO corrected Oxford Nanopore Simplex) and Oxford Nanopore ultra-long reads. - marbl/verkko
github.com
August 31, 2024 at 9:34 PM
Finally on some samples we have all 46 human chromosomes T2T. Update to verkko 2.2, last big release of this summer! github.com/marbl/verkko
Want to discuss a thing about reviewing process. It is far from "ai-generated alpha male rat" level of weirdness, but still weird for me, and I really do not know how it should be fixed.
Let's look on the article on diploid aware polisher. Published just a week ago
www.nature.com/articles/s41...
Let's look on the article on diploid aware polisher. Published just a week ago
www.nature.com/articles/s41...
March 13, 2024 at 11:58 PM
Want to discuss a thing about reviewing process. It is far from "ai-generated alpha male rat" level of weirdness, but still weird for me, and I really do not know how it should be fixed.
Let's look on the article on diploid aware polisher. Published just a week ago
www.nature.com/articles/s41...
Let's look on the article on diploid aware polisher. Published just a week ago
www.nature.com/articles/s41...
Alexey Navalny's death is a disaster for everyone who dreams of free and peaceful Russia
February 16, 2024 at 10:20 PM
Alexey Navalny's death is a disaster for everyone who dreams of free and peaceful Russia
Reposted by Dmitry Antipov
One more opening in my group at Oxford Nanopore. This time in our New York office!
ejnh.fa.em2.oraclecloud.com/hcmUI/Candid...
ejnh.fa.em2.oraclecloud.com/hcmUI/Candid...
February 10, 2024 at 4:34 PM
One more opening in my group at Oxford Nanopore. This time in our New York office!
ejnh.fa.em2.oraclecloud.com/hcmUI/Candid...
ejnh.fa.em2.oraclecloud.com/hcmUI/Candid...
Finally verkko 2.0 is out! github.com/marbl/verkko Waiting for your bug reports;)
My dream for 46 t2t scaffolds on the de novo human genome assemblies out of the box is still a dream, but for some samples we are really close.
My dream for 46 t2t scaffolds on the de novo human genome assemblies out of the box is still a dream, but for some samples we are really close.
February 8, 2024 at 5:49 PM
Finally verkko 2.0 is out! github.com/marbl/verkko Waiting for your bug reports;)
My dream for 46 t2t scaffolds on the de novo human genome assemblies out of the box is still a dream, but for some samples we are really close.
My dream for 46 t2t scaffolds on the de novo human genome assemblies out of the box is still a dream, but for some samples we are really close.
Consider a DAG with edges having both weight and length. Problem: find a path between given vertices with highest _average_ weight (= total_w/total_l). Is it known to be NP-hard in general case? Looks similar to 0-1 knapsack, but I failed to construct polynomial reduction..
October 27, 2023 at 7:37 PM
Consider a DAG with edges having both weight and length. Problem: find a path between given vertices with highest _average_ weight (= total_w/total_l). Is it known to be NP-hard in general case? Looks similar to 0-1 knapsack, but I failed to construct polynomial reduction..
Reposted by Dmitry Antipov
"Minmers are a generalization of minimizers that enable unbiased local jaccard estimation" aka MashMap3 with Bryce Kille, @erikg.bsky.social, and @treangen.bsky.social is now accepted in Bioinformatics! Many thanks to the reviewers for their very careful reviews doi.org/10.1093/bioi...
September 12, 2023 at 7:43 PM
"Minmers are a generalization of minimizers that enable unbiased local jaccard estimation" aka MashMap3 with Bryce Kille, @erikg.bsky.social, and @treangen.bsky.social is now accepted in Bioinformatics! Many thanks to the reviewers for their very careful reviews doi.org/10.1093/bioi...
Ok, let's give this one a try too
September 8, 2023 at 1:09 AM
Ok, let's give this one a try too