Mikhail Kolmogorov
@mishakolmogorov.bsky.social
Tenure-track Stadtman Investigator at NIH/NCI. I like computational/cancer/metagenomics. The views are my own.
Pinned
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
A milestone for our lab! Here's a full access link: rdcu.be/egmYb
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
June 20, 2025 at 1:31 PM
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...
Reposted by Mikhail Kolmogorov
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
May 21, 2025 at 9:26 AM
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
Reposted by Mikhail Kolmogorov
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...
- 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...
April 28, 2025 at 5:20 PM
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...
- 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...
Reposted by Mikhail Kolmogorov
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...
www.biorxiv.org
April 18, 2025 at 9:54 PM
Preprint on hifiasm Nanopore-only assembly. Led by Haoyu Cheng: www.biorxiv.org/content/10.1...
Reposted by Mikhail Kolmogorov
🚨 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. 🧬
🧵👇
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. 🧬
🧵👇
April 16, 2025 at 6:05 PM
🚨 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. 🧬
🧵👇
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. 🧬
🧵👇
Reposted by Mikhail Kolmogorov
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!
April 13, 2025 at 4:37 PM
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!
Reposted by Mikhail Kolmogorov
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...
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 - @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
April 5, 2025 at 4:40 PM
A milestone for our lab! Here's a full access link: rdcu.be/egmYb
Reposted by Mikhail Kolmogorov
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
April 4, 2025 at 4:04 PM
Severus detects somatic structural variation and complex rearrangements in cancer genomes using long-read sequencing - @mishakolmogorov.bsky.social go.nature.com/3R334eH
Reposted by Mikhail Kolmogorov
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
March 23, 2025 at 1:11 PM
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/...
Reposted by Mikhail Kolmogorov
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...
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 ...
www.biorxiv.org
March 6, 2025 at 7:43 PM
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...
www.biorxiv.org/content/10.1...
--> NEW and IMPROVED germline sets for this important animal model...explore here: vdjbase.org/reference_bo...
Reposted by Mikhail Kolmogorov
A new thread for news coverage regarding NIH
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
media.tenor.com
February 16, 2025 at 10:53 AM
A new thread for news coverage regarding NIH
Reposted by Mikhail Kolmogorov
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
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
February 16, 2025 at 12:44 PM
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
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
Reposted by Mikhail Kolmogorov
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
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
February 16, 2025 at 3:53 PM
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
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
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 Mikhail Kolmogorov
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...
- 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
December 3, 2024 at 7:21 PM
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...
- 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...
Reposted by Mikhail Kolmogorov
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
October 22, 2024 at 12:34 PM
I created a genomics+bioinformatics starter pack. If I left you off, *please* reply and I'll add you! go.bsky.app/B5YYBfq
Reposted by Mikhail Kolmogorov
#Genetics Starter Pack ~100 accounts in genetics and genomics. Apologies to all the lovely people I missed.
go.bsky.app/JcbBNq5
go.bsky.app/JcbBNq5
November 8, 2024 at 6:55 PM
#Genetics Starter Pack ~100 accounts in genetics and genomics. Apologies to all the lovely people I missed.
go.bsky.app/JcbBNq5
go.bsky.app/JcbBNq5
Reposted by Mikhail Kolmogorov
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
go.bsky.app/TRWCnZs
November 12, 2024 at 2:03 PM
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
go.bsky.app/TRWCnZs
Reposted by Mikhail Kolmogorov
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
November 11, 2024 at 5:05 AM
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
Reposted by Mikhail Kolmogorov
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
January 12, 2024 at 12:05 PM
Comparative analysis of metagenomic classifiers for long-read sequencing datasets bmcbioinformatics.biomedcentral.com/articles/10.... 🧬🖥️ github.com/lbcb-sci/Met...
Reposted by Mikhail Kolmogorov
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...
meetings.cshl.edu/meetings.asp...
January 5, 2024 at 1:22 PM
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...
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...
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 Mikhail Kolmogorov
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...
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...
November 6, 2023 at 2:26 PM
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...
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...
Reposted by Mikhail Kolmogorov
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
October 31, 2023 at 10:09 PM
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