Egor Dolzhenko
@egor_dolzhenko
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A great resource: tandem repeat database in @AllofUsResearch with the expert input of @PacBio @MikeEberle @egor_dolzhenko
biorxiv.org
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...
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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! https://t.co/0rAR1OcChc
Final #ASHG24 poster session is starting now, come say hi if you’re interested in long read PGx, poster 7021!
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Just back from #ashg24 - new record by an automated library prep for a Revio SMRT cell: 8.1 M reads; 133.0 Gb; 16.4 kb avg size; Q34. …and this is before upgrade to SPRQ! Great lab team @GeneticNijmegen @radboudumc! #RevioOlympics
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Deaminase-assisted Fiber-seq (DAF-seq) has arrived! DAF-seq is an amplification-compatible version of #Fiberseq that resolves genetic and chromatin architectures with single-nucleotide, single-molecule, single-haplotype, and single-cell precision.
biorxiv.org
Gene regulation is mediated by the co-occupancy of numerous proteins along individual chromatin fibers. However, our tools for deeply profiling how proteins co-occupy individual fibers, especially at...
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Great talk by Xiao Chen about application of Paraphase in Four Seasons 4. Learn more about the method in last year’s AJHG paper #ASHG24
https://t.co/4ZvZwNGBK4
cell.com
We developed Paraphase, an informatics method that, combined with highly accurate long reads, can resolve the highly homologous SMN1/SMN2 genes involved in spinal muscular atrophy. We characterized...
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Enjoying all the tandem repeat fun at #ASHG24? The Dashnow lab is hiring software developer/data analyst roles. Apply by Nov 13 for best consideration https://t.co/6jWSeBlO2t
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Xiao talking now about using Paraphase and HiFi data to resolve segmental duplications genome wide
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There are plenty of opportunities to make calls this weekend. It's time. Any questions for how? dm. Repost so twitter algo sends out.
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NEW: Learn how the new SPRQ chemistry for #Revio is improving long-read #sequencing performance and affordability like never before: https://t.co/mgNFywDIcR
#PacBio #ASHG24
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I'm happy to announce that SVTopo, a new computational tool from PacBio ( https://t.co/W6sHuB0Ps9), is ready for you to try. SVTopo creates simple images so you can rapidly understand complex changes in genome structure. See me and learn more at ASHG 2024 in Denver, poster 1180W
github.com
Complex structural variant visualization for HiFi sequencing data - PacificBiosciences/SVTopo
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Don’t miss our #ASHG24 platform talk on genome-wide profiling of highly similar paralogous genes using #HiFisequencing. Learn how this powerful approach is helping unravel complex regions of the genome. Details: https://t.co/3ZPGVoXPec
#PacBio #Genomics
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Another #Review highlight: Sequence composition changes in short tandem repeats: heterogeneity, detection, mechanisms and clinical implications https://t.co/PZjcoh7M6k by @IndhuShreeRB, @egor_dolzhenko, @MikeEberle & Jan M. Friedman @UBC @BCCHresearch @PacBio
nature.com
Nature Reviews Genetics - This Review highlights the diversity in sequence composition of disease-related short tandem repeats. The authors discuss how to detect non-canonical motifs in repeat...
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We've been making steady usability updates to the sawfish SV caller thanks to user feedback, including a new feature to output all supporting reads for each SV. The latest binary, user guide, and (new) source code release are available on github here: https://t.co/Sm80gED6HF
github.com
Joint structural variant and copy number variant caller for HiFi sequencing data - PacificBiosciences/sawfish
We assessed our new method on the recent draft GIAB SV benchmark from the T2T-HG002-Q100 assembly, finding sawfish has the highest F1-score among evaluated callers on every tested SV size range and depth level. Other callers required at least 30x depth to reach sawfish at 15x:
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We're recruiting! Join our lab at Baylor College of Medicine to explore the functional role of repetitive DNA, the final frontier of the human genome. We work on rare neurodegenerative diseases and cancer. Postdoc and tech positions available. https://t.co/QLJPyolMYu 1/7
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Tandem repeat catalogs directly affect the sensitivity, cost, and accuracy of TR genotyping studies. In this paper, we discuss TR catalogs and share a new catalog of 4.9 million loci
biorxiv.org
Tandem repeat (TR) catalogs are important components of repeat genotyping studies as they define the genomic coordinates and expected motifs of all TR loci being analyzed. In recent years, genome-w...
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Towards truly unified genomic diagnostics: HiFi long-read genomes for difficult-to-detect clinically relevant variants | medRxiv @ahoischen
medrxiv.org
Clinical short-read exome and genome sequencing approaches have positively impacted diagnostic testing for rare diseases. Yet, technical limitations associated with short reads challenge their use...
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