Egor Dolzhenko
@egor-dolzhenko.bsky.social
Bioinformatics scientist at PacBio. Opinions are my own.
Reposted by Egor Dolzhenko
I’ll be presenting a poster on Mitorsaw for #PacBio HiFi mitochondrial analysis today! Come see me this afternoon at #ASHG25 poster #4050 to chat about that or other topics!
I'm heading to Boston for #ASHG25 tomorrow, let me know if you'd like to chat about using HiFi sequencing for mitochondrial analyses, pharmacogenomics, or anything else!
ICYMI, also happy to discuss our new Aardvark tool for benchmarking :)
ICYMI, also happy to discuss our new Aardvark tool for benchmarking :)
I'm excited to share our pre-print about a new variant benchmarking tool we've been working on for the past few months!
Aardvark: Sifting through differences in a mound of variants
GitHub: github.com/PacificBiosc...
Some highlights in this thread:
1/N
Aardvark: Sifting through differences in a mound of variants
GitHub: github.com/PacificBiosc...
Some highlights in this thread:
1/N
October 17, 2025 at 11:48 AM
Reposted by Egor Dolzhenko
My new tool Paraviewer is now available for use at github.com/PacificBiosc...! If you use Paraphase, try this new next-step tool - it automates and greatly simplifies variant visualization from Paraphase variant calling. If you're at #ASHG2025, visit me today at poster 4109W. #pacbio
GitHub - PacificBiosciences/Paraviewer
Contribute to PacificBiosciences/Paraviewer development by creating an account on GitHub.
github.com
October 15, 2025 at 2:58 PM
My new tool Paraviewer is now available for use at github.com/PacificBiosc...! If you use Paraphase, try this new next-step tool - it automates and greatly simplifies variant visualization from Paraphase variant calling. If you're at #ASHG2025, visit me today at poster 4109W. #pacbio
Reposted by Egor Dolzhenko
Great to see that sawfish, our new HiFi SV caller, is accepted for publication in Bioinformatics! Sawfish emphasizes local haplotype modeling to improve SV representation and genotyping in both single and joint-sample analysis. Advance-access article now available: (1/n)
doi.org/10.1093/bioi...
doi.org/10.1093/bioi...
Sawfish: Improving long-read structural variant discovery and genotyping with local haplotype modeling
AbstractMotivation. Structural variants (SVs) play an important role in evolutionary and functional genomics but are challenging to characterize. High-accu
doi.org
April 10, 2025 at 3:41 PM
Great to see that sawfish, our new HiFi SV caller, is accepted for publication in Bioinformatics! Sawfish emphasizes local haplotype modeling to improve SV representation and genotyping in both single and joint-sample analysis. Advance-access article now available: (1/n)
doi.org/10.1093/bioi...
doi.org/10.1093/bioi...
Reposted by Egor Dolzhenko
We are excited to announce a call for papers for a special issue of Genome Medicine genomemedicine.biomedcentral.com on "Clinical interpretation of genome variation". The submission deadline is Dec 18, 2025. More info here: go.sn.pub/gskvsk.
Call for papers - Clinical interpretation of genome variation: volume II
go.sn.pub
March 28, 2025 at 10:21 PM
We are excited to announce a call for papers for a special issue of Genome Medicine genomemedicine.biomedcentral.com on "Clinical interpretation of genome variation". The submission deadline is Dec 18, 2025. More info here: go.sn.pub/gskvsk.
Reposted by Egor Dolzhenko
The strchive.org paper is out!!
The paper describes STRchive as a resource to improve the diagnosis of tandem repeat disorders, then goes beyond it to consider what can be learned about childhood onset and population prevalence of these diseases.
🖥️ 🧬
link.springer.com/article/10.1...
The paper describes STRchive as a resource to improve the diagnosis of tandem repeat disorders, then goes beyond it to consider what can be learned about childhood onset and population prevalence of these diseases.
🖥️ 🧬
link.springer.com/article/10.1...
STRchive: a dynamic resource detailing population-level and locus-specific insights at tandem repeat disease loci - Genome Medicine
Approximately 8% of the human genome consists of repetitive elements called tandem repeats (TRs): short tandem repeats (STRs) of 1–6 bp motifs and variable number tandem repeats (VNTRs) of 7 + bp moti...
link.springer.com
March 26, 2025 at 8:01 PM
The strchive.org paper is out!!
The paper describes STRchive as a resource to improve the diagnosis of tandem repeat disorders, then goes beyond it to consider what can be learned about childhood onset and population prevalence of these diseases.
🖥️ 🧬
link.springer.com/article/10.1...
The paper describes STRchive as a resource to improve the diagnosis of tandem repeat disorders, then goes beyond it to consider what can be learned about childhood onset and population prevalence of these diseases.
🖥️ 🧬
link.springer.com/article/10.1...
Reposted by Egor Dolzhenko
A new article from Laurel Hiatt and @hdashnow.bsky.social describing STRchive is now available at Genome Medicine. genomemedicine.biomedcentral.com/articles/10....
Check out the database resource, as STRchive "streamlines TR variant interpretation at disease-associated loci."
strchive.org
Check out the database resource, as STRchive "streamlines TR variant interpretation at disease-associated loci."
strchive.org
STRchive: a dynamic resource detailing population-level and locus-specific insights at tandem repeat disease loci - Genome Medicine
Approximately 8% of the human genome consists of repetitive elements called tandem repeats (TRs): short tandem repeats (STRs) of 1–6 bp motifs and variable number tandem repeats (VNTRs) of 7 + bp moti...
genomemedicine.biomedcentral.com
March 26, 2025 at 7:18 PM
A new article from Laurel Hiatt and @hdashnow.bsky.social describing STRchive is now available at Genome Medicine. genomemedicine.biomedcentral.com/articles/10....
Check out the database resource, as STRchive "streamlines TR variant interpretation at disease-associated loci."
strchive.org
Check out the database resource, as STRchive "streamlines TR variant interpretation at disease-associated loci."
strchive.org
Reposted by Egor Dolzhenko
Exciting Huntington’s disease discovery from the @broadinstitute.org, Harvard, and McLean Hospital using the power of long-read #sequencing!
Learn what surprising mechanism was uncovered, the potential impact on therapeutic developments, & how #PacBio played a role. www.cell.com/cell/fulltex...
Learn what surprising mechanism was uncovered, the potential impact on therapeutic developments, & how #PacBio played a role. www.cell.com/cell/fulltex...
Long somatic DNA-repeat expansion drives neurodegeneration in Huntington’s disease
Single-cell measurement of the Huntington’s disease-causing CAG repeat reveals that
somatic expansion of this repeat drives pathological changes in neurons, providing
insights into disease progression...
www.cell.com
January 21, 2025 at 5:25 PM
Exciting Huntington’s disease discovery from the @broadinstitute.org, Harvard, and McLean Hospital using the power of long-read #sequencing!
Learn what surprising mechanism was uncovered, the potential impact on therapeutic developments, & how #PacBio played a role. www.cell.com/cell/fulltex...
Learn what surprising mechanism was uncovered, the potential impact on therapeutic developments, & how #PacBio played a role. www.cell.com/cell/fulltex...
Reposted by Egor Dolzhenko
Congrats to University of Miami, @broadinstitute.org, and more on deepening our understanding of complex disease! Using #PacBio HiFi long-read #sequencing, the team uncovered critical insights into tandem repeat variability, a challenge for traditional short-read technologies. bit.ly/3C8ZyeU
Detailed tandem repeat allele profiling in 1,027 long-read genomes reveals genome-wide patterns of pathogenicity
Tandem repeats are a highly polymorphic class of genomic variation that play causal roles in rare diseases but are notoriously difficult to sequence using short-read techniques[1][1],[2][2]. Most prev...
bit.ly
January 15, 2025 at 4:01 PM
Congrats to University of Miami, @broadinstitute.org, and more on deepening our understanding of complex disease! Using #PacBio HiFi long-read #sequencing, the team uncovered critical insights into tandem repeat variability, a challenge for traditional short-read technologies. bit.ly/3C8ZyeU
Reposted by Egor Dolzhenko
Image a set of 100 rare disease cases with the most difficult-to-detect mutations a human genetics lab can be faced with. …many of which very difficult or even impossible to detect with (short-read) sequencing methods, and/or requiring additional orthogonal tests…
www.cell.com/ajhg/abstrac...
www.cell.com/ajhg/abstrac...
HiFi long-read genomes for difficult-to-detect, clinically relevant variants
Detecting pathogenic germline variants in the clinic remains technically challenging.
We analyzed 145 previously identified, hard-to-detect variants in 100 samples using
HiFi long-read sequencing (LRS...
www.cell.com
January 13, 2025 at 6:15 PM
Image a set of 100 rare disease cases with the most difficult-to-detect mutations a human genetics lab can be faced with. …many of which very difficult or even impossible to detect with (short-read) sequencing methods, and/or requiring additional orthogonal tests…
www.cell.com/ajhg/abstrac...
www.cell.com/ajhg/abstrac...
Reposted by Egor Dolzhenko
Come and join the lab! we have a position available to work on the analysis of short and long-read DNA and RNA sequencing from patients with repeat expansion diseases
jobs.ac.uk/job/DLG312/bio…
jobs.ac.uk/job/DLG312/bio…
https://jobs.ac.uk/job/DLG312/bio…
January 6, 2025 at 11:35 AM
Come and join the lab! we have a position available to work on the analysis of short and long-read DNA and RNA sequencing from patients with repeat expansion diseases
jobs.ac.uk/job/DLG312/bio…
jobs.ac.uk/job/DLG312/bio…
Reposted by Egor Dolzhenko
Detailed tandem repeat allele profiling in 1,027 long-read genomes reveals genome-wide patterns of pathogenicity https://www.biorxiv.org/content/10.1101/2025.01.06.631535v1
January 8, 2025 at 12:34 AM
Detailed tandem repeat allele profiling in 1,027 long-read genomes reveals genome-wide patterns of pathogenicity https://www.biorxiv.org/content/10.1101/2025.01.06.631535v1
Reposted by Egor Dolzhenko
Very excited (and a bit nervous) to announce that I will be hiring two Postdocs for my new group(!) in Copenhagen to study the Neanderthal and Denisovan DNA which survives in present-day humans. Retweet will be much appreciated :)
Link for application:
candidate.hr-manager.net/ApplicationI...
Link for application:
candidate.hr-manager.net/ApplicationI...
December 2, 2024 at 12:47 PM
Very excited (and a bit nervous) to announce that I will be hiring two Postdocs for my new group(!) in Copenhagen to study the Neanderthal and Denisovan DNA which survives in present-day humans. Retweet will be much appreciated :)
Link for application:
candidate.hr-manager.net/ApplicationI...
Link for application:
candidate.hr-manager.net/ApplicationI...
Reposted by Egor Dolzhenko
I am excited to present STRchive.org v2!
A resource for tandem repeats associated with Mendelian disease. We have resigned the website, added new loci, streamlined our data for easier reuse, added more detailed citations, presented population frequency data and more!
A resource for tandem repeats associated with Mendelian disease. We have resigned the website, added new loci, streamlined our data for easier reuse, added more detailed citations, presented population frequency data and more!
STRchive
An archive of STRs associated with human diseases
STRchive.org
December 12, 2024 at 8:58 PM
I am excited to present STRchive.org v2!
A resource for tandem repeats associated with Mendelian disease. We have resigned the website, added new loci, streamlined our data for easier reuse, added more detailed citations, presented population frequency data and more!
A resource for tandem repeats associated with Mendelian disease. We have resigned the website, added new loci, streamlined our data for easier reuse, added more detailed citations, presented population frequency data and more!
Reposted by Egor Dolzhenko
“StarPhase: Comprehensive Phase-Aware Pharmacogenomic Diplotyper for Long-Read Sequencing Data” is now on biorxiv! In this work, we explore the use of long-read sequencing (#PacBio #HiFi) for #pharmacogenomics #PGx. 1/N
Pre-print: doi.org/10.1101/2024...
Repo: github.com/PacificBiosc...
Pre-print: doi.org/10.1101/2024...
Repo: github.com/PacificBiosc...
GitHub - PacificBiosciences/pb-StarPhase: A phase-aware pharmacogenomic diplotyper for PacBio datasets
A phase-aware pharmacogenomic diplotyper for PacBio datasets - PacificBiosciences/pb-StarPhase
github.com
December 11, 2024 at 2:30 PM
“StarPhase: Comprehensive Phase-Aware Pharmacogenomic Diplotyper for Long-Read Sequencing Data” is now on biorxiv! In this work, we explore the use of long-read sequencing (#PacBio #HiFi) for #pharmacogenomics #PGx. 1/N
Pre-print: doi.org/10.1101/2024...
Repo: github.com/PacificBiosc...
Pre-print: doi.org/10.1101/2024...
Repo: github.com/PacificBiosc...
Reposted by Egor Dolzhenko
Great work by @holtjma.bsky.social to create this PGx caller, StarPhase. Special thanks to the many collaborators who shared data and provided feedback on how to improve the accuracy and user experience.
“StarPhase: Comprehensive Phase-Aware Pharmacogenomic Diplotyper for Long-Read Sequencing Data” is now on biorxiv! In this work, we explore the use of long-read sequencing (#PacBio #HiFi) for #pharmacogenomics #PGx. 1/N
Pre-print: doi.org/10.1101/2024...
Repo: github.com/PacificBiosc...
Pre-print: doi.org/10.1101/2024...
Repo: github.com/PacificBiosc...
GitHub - PacificBiosciences/pb-StarPhase: A phase-aware pharmacogenomic diplotyper for PacBio datasets
A phase-aware pharmacogenomic diplotyper for PacBio datasets - PacificBiosciences/pb-StarPhase
github.com
December 11, 2024 at 4:09 PM
Great work by @holtjma.bsky.social to create this PGx caller, StarPhase. Special thanks to the many collaborators who shared data and provided feedback on how to improve the accuracy and user experience.
Reposted by Egor Dolzhenko
ICYMI my poster at #AMPath24, I'm sharing it here. Folks interested in long reads to resolve complex loci like repeat expansions relevant to neuro disease and carrier screening, check it out! @pacbio.bsky.social collab with @egor-dolzhenko.bsky.social @guilhermesena1.bsky.social and many others
November 23, 2024 at 2:59 PM
ICYMI my poster at #AMPath24, I'm sharing it here. Folks interested in long reads to resolve complex loci like repeat expansions relevant to neuro disease and carrier screening, check it out! @pacbio.bsky.social collab with @egor-dolzhenko.bsky.social @guilhermesena1.bsky.social and many others
Reposted by Egor Dolzhenko
If you were interested but missed it: www.pacb.com/wp-content/u...
www.pacb.com
November 13, 2024 at 7:00 PM
If you were interested but missed it: www.pacb.com/wp-content/u...
Reposted by Egor Dolzhenko
import twitter as x
Import bluesky as bs
del x
bs.activate()
Import bluesky as bs
del x
bs.activate()
November 13, 2024 at 7:40 PM
import twitter as x
Import bluesky as bs
del x
bs.activate()
Import bluesky as bs
del x
bs.activate()
Reposted by Egor Dolzhenko
A little birdie told us we should migrate to bluer skies. 😉 Hello Bluesky world. 👋🌎 Please re-share this post so we can follow you and help to grow the genomics community on here! 🧬✨
November 12, 2024 at 4:15 PM
A little birdie told us we should migrate to bluer skies. 😉 Hello Bluesky world. 👋🌎 Please re-share this post so we can follow you and help to grow the genomics community on here! 🧬✨
Reposted by Egor Dolzhenko
If you missed this poster session at #ASHG24, you can now view the poster online! Happy to have a chat if you're interested in long-read PGx with #PacBio!
www.pacb.com/wp-content/u...
www.pacb.com/wp-content/u...
November 11, 2024 at 6:33 PM
If you missed this poster session at #ASHG24, you can now view the poster online! Happy to have a chat if you're interested in long-read PGx with #PacBio!
www.pacb.com/wp-content/u...
www.pacb.com/wp-content/u...