Yilei Fu
@yileifu.bsky.social
Ph.D. Candidate @ Computer Science Department, Rice University
We introduce trio-barcoded
@nanoporetech.com
adaptive sampling (TBAS), which allows targeted sequencing of one trio in one flowcell. We tested it on HG002-4+13 trios from GREGoR.
TBAS and pipeline accurately report causative SNV, SV&TRs. @sedlazeck.bsky.social
www.medrxiv.org/content/10.1...
@nanoporetech.com
adaptive sampling (TBAS), which allows targeted sequencing of one trio in one flowcell. We tested it on HG002-4+13 trios from GREGoR.
TBAS and pipeline accurately report causative SNV, SV&TRs. @sedlazeck.bsky.social
www.medrxiv.org/content/10.1...
October 24, 2025 at 7:03 PM
We introduce trio-barcoded
@nanoporetech.com
adaptive sampling (TBAS), which allows targeted sequencing of one trio in one flowcell. We tested it on HG002-4+13 trios from GREGoR.
TBAS and pipeline accurately report causative SNV, SV&TRs. @sedlazeck.bsky.social
www.medrxiv.org/content/10.1...
@nanoporetech.com
adaptive sampling (TBAS), which allows targeted sequencing of one trio in one flowcell. We tested it on HG002-4+13 trios from GREGoR.
TBAS and pipeline accurately report causative SNV, SV&TRs. @sedlazeck.bsky.social
www.medrxiv.org/content/10.1...
Reposted by Yilei Fu
The SMaHT marker paper is now live in @nature.com 🧬
This landmark study characterizes somatic variation across 19 tissue types from 150 nondiseased donors, laying the groundwork for future discoveries in health, aging, and disease.
Read the full paper: www.nature.com/articles/s41...
This landmark study characterizes somatic variation across 19 tissue types from 150 nondiseased donors, laying the groundwork for future discoveries in health, aging, and disease.
Read the full paper: www.nature.com/articles/s41...
July 3, 2025 at 12:11 PM
The SMaHT marker paper is now live in @nature.com 🧬
This landmark study characterizes somatic variation across 19 tissue types from 150 nondiseased donors, laying the groundwork for future discoveries in health, aging, and disease.
Read the full paper: www.nature.com/articles/s41...
This landmark study characterizes somatic variation across 19 tissue types from 150 nondiseased donors, laying the groundwork for future discoveries in health, aging, and disease.
Read the full paper: www.nature.com/articles/s41...
Reposted by Yilei Fu
Long reads such as @nanoporetech.com or @pacbio.bsky.social can provide insights into epigenetic. We
@yileifu.bsky.social & @timp0.bsky.social )summarize the latest #Bioinformatics approaches & why this matters! Out now @natrevgenet.bsky.social at:
bit.ly/4cjxUtl
@bcmhouston.bsky.social @jhu.edu
@yileifu.bsky.social & @timp0.bsky.social )summarize the latest #Bioinformatics approaches & why this matters! Out now @natrevgenet.bsky.social at:
bit.ly/4cjxUtl
@bcmhouston.bsky.social @jhu.edu
April 3, 2025 at 4:01 PM
Long reads such as @nanoporetech.com or @pacbio.bsky.social can provide insights into epigenetic. We
@yileifu.bsky.social & @timp0.bsky.social )summarize the latest #Bioinformatics approaches & why this matters! Out now @natrevgenet.bsky.social at:
bit.ly/4cjxUtl
@bcmhouston.bsky.social @jhu.edu
@yileifu.bsky.social & @timp0.bsky.social )summarize the latest #Bioinformatics approaches & why this matters! Out now @natrevgenet.bsky.social at:
bit.ly/4cjxUtl
@bcmhouston.bsky.social @jhu.edu
We summarized state-of-the-art computational methods for DNA methylation analysis using long-read sequencing, covering everything from base calling to sample-level, cell-type-level, and even population-scale analysis. Huge thanks to @sedlazeck.bsky.social and @timp0.bsky.social for this great work!
New online! Computational analysis of DNA methylation from long-read sequencing
Computational analysis of DNA methylation from long-read sequencing
Nature Reviews Genetics, Published online: 28 March 2025; doi:10.1038/s41576-025-00822-5Long-read sequencing technologies can directly profile methylation modifications across the genome. In this Review, Fu et al. overview the long-read computational tools to identify and compare methylation signals, as well as tools that use these methylation signals to analyse cell-type diversity and gain additional genomic insights.
www.nature.com
March 29, 2025 at 12:07 AM
We summarized state-of-the-art computational methods for DNA methylation analysis using long-read sequencing, covering everything from base calling to sample-level, cell-type-level, and even population-scale analysis. Huge thanks to @sedlazeck.bsky.social and @timp0.bsky.social for this great work!
Reposted by Yilei Fu
New online! Diversity and consequences of structural variation in the human genome
Diversity and consequences of structural variation in the human genome
Nature Reviews Genetics, Published online: 21 January 2025; doi:10.1038/s41576-024-00808-9Collins and Talkowski provide a broad overview of structural variation in the human genome that covers their mutational properties, the dynamics of population…
go.nature.com
January 21, 2025 at 1:56 PM
New online! Diversity and consequences of structural variation in the human genome
Reposted by Yilei Fu
Had a great lab retreat on Saturday at rice together with @svillapol.bsky.social and @treangen.bsky.social lab. Amazing talks, discussions and overlap of interests. Won't be the last one :)
April 29, 2024 at 1:45 PM
Had a great lab retreat on Saturday at rice together with @svillapol.bsky.social and @treangen.bsky.social lab. Amazing talks, discussions and overlap of interests. Won't be the last one :)
www.sciencedirect.com/science/arti... Check out our newest paper about comparing long- and short- read metagenome sequencing and EpicPCR when it comes to ARG detection in wastewater. Great collab with Esther Lou and Lauren Stadler lab @RiceCEE and my former lab Qi Wang, @treangen.bsky.social
Sensitivity and consistency of long- and short-read metagenomics and epicPCR for the detection of antibiotic resistance genes and their bacterial hosts in wastewater
Wastewater surveillance is a powerful tool to assess the risks associated with antibiotic resistance in communities. One challenge is selecting which …
www.sciencedirect.com
March 11, 2024 at 8:49 PM
www.sciencedirect.com/science/arti... Check out our newest paper about comparing long- and short- read metagenome sequencing and EpicPCR when it comes to ARG detection in wastewater. Great collab with Esther Lou and Lauren Stadler lab @RiceCEE and my former lab Qi Wang, @treangen.bsky.social
Great day in my life!! Finally defended my Ph.D.!
I can’t do this without the guidance of my Ph.D. advisor
@treangen.bsky.social and my co-advisor @sedlazeck.bsky.social ! I’ll soon join @sedlazeck.bsky.social ’s group at as an postdoc focusing on cancer genetics and cancer epigenetics.
I can’t do this without the guidance of my Ph.D. advisor
@treangen.bsky.social and my co-advisor @sedlazeck.bsky.social ! I’ll soon join @sedlazeck.bsky.social ’s group at as an postdoc focusing on cancer genetics and cancer epigenetics.
November 28, 2023 at 3:14 AM
Great day in my life!! Finally defended my Ph.D.!
I can’t do this without the guidance of my Ph.D. advisor
@treangen.bsky.social and my co-advisor @sedlazeck.bsky.social ! I’ll soon join @sedlazeck.bsky.social ’s group at as an postdoc focusing on cancer genetics and cancer epigenetics.
I can’t do this without the guidance of my Ph.D. advisor
@treangen.bsky.social and my co-advisor @sedlazeck.bsky.social ! I’ll soon join @sedlazeck.bsky.social ’s group at as an postdoc focusing on cancer genetics and cancer epigenetics.