Mikhail Kolmogorov

SSACB 2025 rescheduled to Aug 18-22! We are inviting students and postdocs broadly interested in computational cancer to 2025 NCI Summer School on Algorithmic Cancer Biology. Please apply and spread the word: ncifrederick.cancer.gov/events/confe...

ROBIN: A unified nanopore-based assay integrating intraoperative methylome classification and next-day comprehensive profiling for ultra-rapid tumor diagnosis

Really pleased that this paper is out - academic.oup.com/neuro-oncolo... thanks to all our collaborators far and wide who have helped and of course @nanoporetech.com

The Department of Human Genetics at the University of Utah is sponsoring the Rising Stars in Genetics and Genomics symposium!

- We are seeking nominations bu June 1.
- September 18-19, 2025
- Please share with the star postdocs that you know.

docs.google.com/forms/d/e/1F...

Efficient near telomere-to-telomere assembly of Nanopore Simplex reads Telomere-to-telomere (T2T) assembly is the ultimate goal for de novo genome assembly. Existing algorithms capable of near T2T assembly all require Oxford Nanopore Technologies (ONT) ultra-long reads w...

Preprint on hifiasm Nanopore-only assembly. Led by Haoyu Cheng: www.biorxiv.org/content/10.1...

🚨 Pre-print alert! 🚨

We generated chromosome-scale diploid genome assemblies for the widely used fibroblast lines BJ and IMR-90.

These models of replicative senescence and telomere shortening now have fully resolved telomeres, subtelomeres, and centromeres. 🧬

🧵👇

Our lab at the NIH (Bethesda, MD) is looking for postdoctoral fellows to join our team studying the molecular mechanisms of protein trafficking and their links to neurodevelopmental disorders starting on or after 10-1-2025. Send your application to juan.bonifacino@nih.gov. Please share and repost!

A phylogeny of the 7 ape genomes that have now been completed from "T2T", with Homer Simpson representing mankind.

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...

A milestone for our lab! Here's a full access link: rdcu.be/egmYb

Severus detects somatic structural variation and complex rearrangements in cancer genomes using long-read sequencing - Nature Biotechnology Complex structural variations and rearrangements in cancer are identified using long-read sequencing.

Severus detects somatic structural variation and complex rearrangements in cancer genomes using long-read sequencing - @mishakolmogorov.bsky.social go.nature.com/3R334eH

Conservation assessment of human splice site annotation based on a 470-genome alignment Abstract. Despite many improvements over the years, the annotation of the human genome remains imperfect. The use of evolutionarily conserved sequences pro

Check out our new paper in @narjournal.bsky.social on discovering extensive conservation of human introns across hundreds of other mammals, with Ilia Minkin academic.oup.com/nar/article/...

A Broad Survey and Functional Analysis of Immunoglobulin Loci Variation in Rhesus Macaques Rhesus macaques (RMs) are a vital model for studying human disease and invaluable to pre-clinical vaccine research, particularly for the study of broadly neutralizing antibody responses. Such studies ...

Very proud of this collective effort to enhance understanding of immunoglobulin diversity in rhesus macaque @guryaari.bsky.social @williamlees.bsky.social
www.biorxiv.org/content/10.1...
--> NEW and IMPROVED germline sets for this important animal model...explore here: vdjbase.org/reference_bo...

a muppet is sitting at a news desk with the words here is a muppet news flash behind him Alt: a muppet is sitting at a news desk with the words here is a muppet news flash behind him

A new thread for news coverage regarding NIH

a picture of a pikachu with the words " i still have hope " written below it ALT: a picture of a pikachu with the words " i still have hope " written below it

Some glimmers of hope (but mostly confusion) this morning.

I have heard that no intramural tenure track investigators were supposed to be on the termination list although some folks clearly got termination notices.

I am actively checking into this every way I can.

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a man standing in front of a crowd with the words everybody panic Alt: a man standing in front of a crowd with the words everybody panic

Short update on NIH

The situation is very confusing, a not just to me. Folks who were told the were to be terminated did not receive any communication for a day and a half, people who were “on the list” have not received anything as of yet. Some folks who had been terminated have be reinstated

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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...

Biology of Genomes Cold Spring Harbor Laboratory Meetings & Courses -- a private, non-profit institution with research programs in cancer, neuroscience, plant biology, genomics, bioinformatics.

Biology of Genomes 2025 is coming up:
- meeting dates: May 6 - 10, 2025
- abstract deadline: Feb 14, 2025
We hope to see you there for another great meeting with a fantastic speaker lineup!

meetings.cshl.edu/meetings.asp...

Genomics+Bioinformatics Starter Pack 🧬🖥️ Join the conversation

I created a genomics+bioinformatics starter pack. If I left you off, *please* reply and I'll add you! go.bsky.app/B5YYBfq

#Genetics Starter Pack ~100 accounts in genetics and genomics. Apologies to all the lovely people I missed.
go.bsky.app/JcbBNq5

I made a starter pack for algorithmic genomics. It's certainly incomplete, but already has a ton of awesome peeps. Let me know if you know people I should add (with a focus on algorithms and data structures in genomics)

go.bsky.app/TRWCnZs

I created a long-read sequencing starter pack. I'm still finding people on here, so apologies if I missed you. Please suggest people who should be added and I'll add them! go.bsky.app/JGkefsJ

Comparative analysis of metagenomic classifiers for long-read sequencing datasets - BMC Bioinformati... Background Long reads have gained popularity in the analysis of metagenomics data. Therefore, we comprehensively assessed metagenomics classification tools on the species taxonomic level. We analysed ...

Comparative analysis of metagenomic classifiers for long-read sequencing datasets bmcbioinformatics.biomedcentral.com/articles/10.... 🧬🖥️ github.com/lbcb-sci/Met...

Six weeks left until the abstract deadline for Biology of Genomes at CSHL #BoG24! We have a stellar lineup of keynotes and discussion leaders (=~invited speakers), and look forward to another brilliant meeting in May 7-11. Abstract submission & info:
meetings.cshl.edu/meetings.asp...

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...

I am very excited about guest editing a special issue in Genome Research (@genomeresearch.bsky.social )
about long reads DNA Sequencing Applications with Ana Conesa & Alexander Hoischen. This is such a timely and fast moving topic about all its applications, innovations etc. bit.ly/grcallforpap...

GitHub - marbl/HG002: A complete diploid human genome A complete diploid human genome. Contribute to marbl/HG002 development by creating an account on GitHub.

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

If you discovered a novel microbial strain or species, please check out abon - a new program in the zol suite, which lets you easily check the conservation of your sample's BGC-ome (from antiSMASH & GECCO predictions) across target genomes: github.com/Kalan-Lab/zo... #secmet #bgc

Hope it will be helpful! We've tried SURVIVOR, which mostly worked good, but sometimes variants "disappear". Also there is Jasmin and truvari merge, but those were designed mostly for indels (e.g. germline SVs). Also rtg-tools has functinoality to compare BNDs.

GitHub - KolmogorovLab/Severus: A tool for somatic structural variant calling using long reads A tool for somatic structural variant calling using long reads - GitHub - KolmogorovLab/Severus: A tool for somatic structural variant calling using long reads

Another long-read based somatic SV caller:

github.com/KolmogorovLa...

Savana and Severus both seem pretty good, any others in the same category?

Exactly! We actually did develop our own comparison method (for better or worse) - Asher is now tidying up the code and we'll make it available soon. It decomposes SVs from different tools into paired breakpoints and is agnostic to SV types. But overall, parsing different VCFs has been a pain..

Oups! We'll fix that!