Egor Dolzhenko
@egor-dolzhenko.bsky.social
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Bioinformatics scientist at PacBio. Opinions are my own.
reposted by
Egor Dolzhenko
Matt Holt
22 days ago
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!
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Egor Dolzhenko
Jon Belyeu
24 days ago
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
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GitHub - PacificBiosciences/Paraviewer
Contribute to PacificBiosciences/Paraviewer development by creating an account on GitHub.
https://github.com/PacificBiosciences/Paraviewer
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reposted by
Egor Dolzhenko
Chris Saunders
7 months ago
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...
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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
https://doi.org/10.1093/bioinformatics/btaf136
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reposted by
Egor Dolzhenko
Heidi Rehm
7 months ago
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
.
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Call for papers - Clinical interpretation of genome variation: volume II
https://go.sn.pub/gskvsk
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reposted by
Egor Dolzhenko
Harriet Dashnow
8 months ago
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...
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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...
https://link.springer.com/article/10.1186/s13073-025-01454-4
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reposted by
Egor Dolzhenko
Aaron Quinlan (he/him)
8 months ago
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
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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...
https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-025-01454-4
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reposted by
Egor Dolzhenko
PacBio
10 months ago
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...
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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...
https://www.cell.com/cell/fulltext/S0092-8674(24)01379-5
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reposted by
Egor Dolzhenko
PacBio
10 months ago
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
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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...
https://bit.ly/3C8ZyeU
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reposted by
Egor Dolzhenko
Alex Hoischen
10 months ago
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...
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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...
https://www.cell.com/ajhg/abstract/S0002-9297(24)00455-5?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0002929724004555%3Fshowall%3Dtrue
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reposted by
Egor Dolzhenko
10 months ago
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…
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https://jobs.ac.uk/job/DLG312/bio…
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reposted by
Egor Dolzhenko
bioRxivpreprint
10 months ago
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
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reposted by
Egor Dolzhenko
Laurits Skov
11 months ago
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...
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reposted by
Egor Dolzhenko
Harriet Dashnow
11 months ago
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!
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STRchive
An archive of STRs associated with human diseases
https://STRchive.org
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reposted by
Egor Dolzhenko
Matt Holt
11 months ago
“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...
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GitHub - PacificBiosciences/pb-StarPhase: A phase-aware pharmacogenomic diplotyper for PacBio datasets
A phase-aware pharmacogenomic diplotyper for PacBio datasets - PacificBiosciences/pb-StarPhase
https://github.com/PacificBiosciences/pb-StarPhase
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reposted by
Egor Dolzhenko
Michael Eberle
11 months ago
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.
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reposted by
Egor Dolzhenko
Sarah Doom
12 months ago
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
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reposted by
Egor Dolzhenko
Jon Belyeu
12 months ago
If you were interested but missed it:
www.pacb.com/wp-content/u...
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https://www.pacb.com/wp-content/uploads/2024-11-08-svtopo_poster.pdf
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reposted by
Egor Dolzhenko
12 months ago
import twitter as x Import bluesky as bs del x bs.activate()
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reposted by
Egor Dolzhenko
PacBio
12 months ago
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! 🧬✨
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reposted by
Egor Dolzhenko
Matt Holt
12 months ago
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...
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