Mikhail Kolmogorov
@mishakolmogorov.bsky.social
Tenure-track Stadtman Investigator at NIH/NCI. I like computational/cancer/metagenomics. The views are my own.
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...
Overview | 2025 NCI Spring School on Algorithmic Cancer Biology | NCIF Conferences
ncifrederick.cancer.gov
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
ROBIN: A unified nanopore-based assay integrating intraoperative methylome classification and next-day comprehensive profiling for ultra-rapid tumor diagnosis
academic.oup.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...
Preprint on hifiasm Nanopore-only assembly. Led by Haoyu Cheng: www.biorxiv.org/content/10.1...
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...
biorxiv.org
🚨 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 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...
Severus detects somatic structural variation and complex rearrangements in cancer genomes using long-read sequencing - @mishakolmogorov.bsky.social go.nature.com/3R334eH
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.
go.nature.com
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/...
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
academic.oup.com
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 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 ...
biorxiv.org
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. 1/2
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
media.tenor.com
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 1/2
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
media.tenor.com
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
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...
Biology of Genomes
Cold Spring Harbor Laboratory Meetings & Courses -- a private, non-profit institution with research programs in cancer, neuroscience, plant biology, genomics, bioinformatics.
meetings.cshl.edu
I created a genomics+bioinformatics starter pack. If I left you off, *please* reply and I'll add you! go.bsky.app/B5YYBfq
Genomics+Bioinformatics Starter Pack 🧬🖥️
Join the conversation
go.bsky.app
#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 bmcbioinformatics.biomedcentral.com/articles/10.... 🧬🖥️ github.com/lbcb-sci/Met...
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 ...
bmcbioinformatics.biomedcentral.com
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...
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 - marbl/HG002: A complete diploid human genome
A complete diploid human genome. Contribute to marbl/HG002 development by creating an account on GitHub.
github.com
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
Another long-read based somatic SV caller: github.com/KolmogorovLa... Savana and Severus both seem pretty good, any others in the same category?
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
github.com
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 - google/deepsomatic
Contribute to google/deepsomatic development by creating an account on GitHub.
github.com
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...
I'll be talking about metagenome assemblies at Microbiome Data Congress 2023 (November 13-14 in Boston). Looks like it's going to be fun! Registration: microbiome-data.com/register
