Michael Eberle
@meberle.bsky.social
Head of CompBio at PacBio interested in rare disease, variant calling, population genetics and more. Opinions/views are my own and do not reflect the views of my employer.
Reposted by Michael Eberle
Complex genes can hide critical insights. Hear Xiao Chen from #PacBio explain how Paraphase with HiFi sequencing resolves paralogs and pseudogenes.
Don’t miss her #ASHG25 poster on D4Z4 repeat resolution in facioscapulohumeral muscular dystrophy!
Watch: bit.ly/4mHVhAe
Don’t miss her #ASHG25 poster on D4Z4 repeat resolution in facioscapulohumeral muscular dystrophy!
Watch: bit.ly/4mHVhAe
October 10, 2025 at 3:06 PM
Complex genes can hide critical insights. Hear Xiao Chen from #PacBio explain how Paraphase with HiFi sequencing resolves paralogs and pseudogenes.
Don’t miss her #ASHG25 poster on D4Z4 repeat resolution in facioscapulohumeral muscular dystrophy!
Watch: bit.ly/4mHVhAe
Don’t miss her #ASHG25 poster on D4Z4 repeat resolution in facioscapulohumeral muscular dystrophy!
Watch: bit.ly/4mHVhAe
Reposted by Michael Eberle
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 6, 2025 at 8:07 PM
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
Reposted by Michael Eberle
Please repost -- The Univ. California Davis dept of Plant Pathology is hiring a Fungal biologist / Mycologist
Applications due Dec 1
Application portal: recruit.ucdavis.edu/JPF07339
Screenshot shows part of the job posting (with alt-text of the same text)
Applications due Dec 1
Application portal: recruit.ucdavis.edu/JPF07339
Screenshot shows part of the job posting (with alt-text of the same text)
September 22, 2025 at 6:58 PM
Please repost -- The Univ. California Davis dept of Plant Pathology is hiring a Fungal biologist / Mycologist
Applications due Dec 1
Application portal: recruit.ucdavis.edu/JPF07339
Screenshot shows part of the job posting (with alt-text of the same text)
Applications due Dec 1
Application portal: recruit.ucdavis.edu/JPF07339
Screenshot shows part of the job posting (with alt-text of the same text)
Reposted by Michael Eberle
Heads up: ignore samtools dot org, similarly minimap2 dot com and likely others. It's owned by a known phishing site and while the binaries they offer look valid currently (but note they may be serving us different binaries to others), that could change.
Ie: it's not us (Samtools team)! Be warned
Ie: it's not us (Samtools team)! Be warned
September 15, 2025 at 8:40 AM
Heads up: ignore samtools dot org, similarly minimap2 dot com and likely others. It's owned by a known phishing site and while the binaries they offer look valid currently (but note they may be serving us different binaries to others), that could change.
Ie: it's not us (Samtools team)! Be warned
Ie: it's not us (Samtools team)! Be warned
Reposted by Michael Eberle
minimap2.com is potentially a phishing site. Please don't use anything from that website.
github.com/lh3/minimap2...
github.com/lh3/minimap2...
Phishing site : minimap2.com · Issue #1316 · lh3/minimap2
Not sure how to label this one, but I have come across a website minimap2.com which appears to be AI generated but is serving it's own copy of the Github repository. If you search the address or em...
github.com
September 9, 2025 at 3:40 PM
minimap2.com is potentially a phishing site. Please don't use anything from that website.
github.com/lh3/minimap2...
github.com/lh3/minimap2...
Reposted by Michael Eberle
The human #microbiome holds enormous potential, but only if we can see it clearly.
Join this webinar to learn how #PacBio HiFi sequencing delivers accurate, high-resolution insights with 16S rRNA sequencing and shotgun metagenomics.
Secure your spot: bit.ly/4mYmK1G
Join this webinar to learn how #PacBio HiFi sequencing delivers accurate, high-resolution insights with 16S rRNA sequencing and shotgun metagenomics.
Secure your spot: bit.ly/4mYmK1G
September 8, 2025 at 7:34 PM
The human #microbiome holds enormous potential, but only if we can see it clearly.
Join this webinar to learn how #PacBio HiFi sequencing delivers accurate, high-resolution insights with 16S rRNA sequencing and shotgun metagenomics.
Secure your spot: bit.ly/4mYmK1G
Join this webinar to learn how #PacBio HiFi sequencing delivers accurate, high-resolution insights with 16S rRNA sequencing and shotgun metagenomics.
Secure your spot: bit.ly/4mYmK1G
Reposted by Michael Eberle
The Platinum Pedigree: a long-read benchmark for genetic variants. #HumanGenome #ReferenceGenome #PlatinumPedigree #LongReads #Benchmarking #GeneticVariants @natmethods.nature.com 🧬 🖥️
www.nature.com/articles/s41...
www.nature.com/articles/s41...
August 4, 2025 at 6:39 PM
The Platinum Pedigree: a long-read benchmark for genetic variants. #HumanGenome #ReferenceGenome #PlatinumPedigree #LongReads #Benchmarking #GeneticVariants @natmethods.nature.com 🧬 🖥️
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Michael Eberle
Buongiorno Milano! Ready for a great day 1 of #eshg2025?
Packed program of excellent science 8.30am-8.00pm - plus networking event till 9.30pm to meet many friends, colleagues and collaborators! …andiamo @eshg.bsky.social @eshgyoung.bsky.social
Packed program of excellent science 8.30am-8.00pm - plus networking event till 9.30pm to meet many friends, colleagues and collaborators! …andiamo @eshg.bsky.social @eshgyoung.bsky.social
May 24, 2025 at 4:45 AM
Buongiorno Milano! Ready for a great day 1 of #eshg2025?
Packed program of excellent science 8.30am-8.00pm - plus networking event till 9.30pm to meet many friends, colleagues and collaborators! …andiamo @eshg.bsky.social @eshgyoung.bsky.social
Packed program of excellent science 8.30am-8.00pm - plus networking event till 9.30pm to meet many friends, colleagues and collaborators! …andiamo @eshg.bsky.social @eshgyoung.bsky.social
Reposted by Michael Eberle
Dr Farrow uses @pacbio.bsky.social tools and pipelines in her clinically validated HiFi WGS tests. Shout out to @williamrowell.dev @egor-dolzhenko.bsky.social @guilhermesena1.bsky.social Xiao Chen @meberle.bsky.social
May 7, 2025 at 3:54 PM
Dr Farrow uses @pacbio.bsky.social tools and pipelines in her clinically validated HiFi WGS tests. Shout out to @williamrowell.dev @egor-dolzhenko.bsky.social @guilhermesena1.bsky.social Xiao Chen @meberle.bsky.social
Reposted by Michael Eberle
Nature research paper: Human de novo mutation rates from a four-generation pedigree reference
https://go.nature.com/3GnaA22
https://go.nature.com/3GnaA22
Human de novo mutation rates from a four-generation pedigree reference - Nature
Analysis of more than 95% of each diploid human genome of a four-generation, twenty-eight-member family using five complementary short-read and long-read sequencing technologies provides a truth set to understand the most fundamental processes underlying human genetic variation.
go.nature.com
April 25, 2025 at 12:27 PM
Nature research paper: Human de novo mutation rates from a four-generation pedigree reference
https://go.nature.com/3GnaA22
https://go.nature.com/3GnaA22
Reposted by Michael Eberle
Our Nature paper (rdcu.be/ei1NM) deep sequencing a 4-generation, 28-member family using multiple sequencing technologies to study transmission of all classes of genetic variation is out! @uwgenome.bsky.social @hhmi.org @pacbio.bsky.social @utah.edu
April 24, 2025 at 12:58 AM
Our Nature paper (rdcu.be/ei1NM) deep sequencing a 4-generation, 28-member family using multiple sequencing technologies to study transmission of all classes of genetic variation is out! @uwgenome.bsky.social @hhmi.org @pacbio.bsky.social @utah.edu
Reposted by Michael Eberle
Advanced genomic analysis of 4 generation family offers new knowledge about genetic mutations & their transmission, including inherited variants & those that arise anew
@nature.com @uwgenome.bsky.social @eichlerlab.bsky.social @uwmedicine.bsky.social @utah.edu @pacbio.bsky.social
@nature.com @uwgenome.bsky.social @eichlerlab.bsky.social @uwmedicine.bsky.social @utah.edu @pacbio.bsky.social
4 generations help science explore genome mutation rate - UW Medicine | Newsroom
bit.ly
April 23, 2025 at 8:53 PM
Advanced genomic analysis of 4 generation family offers new knowledge about genetic mutations & their transmission, including inherited variants & those that arise anew
@nature.com @uwgenome.bsky.social @eichlerlab.bsky.social @uwmedicine.bsky.social @utah.edu @pacbio.bsky.social
@nature.com @uwgenome.bsky.social @eichlerlab.bsky.social @uwmedicine.bsky.social @utah.edu @pacbio.bsky.social
Reposted by Michael Eberle
I just released a new preprint! The manuscript describes SVTopo, a software tool that enhances visualization of complex SVs using HiFi data: www.biorxiv.org/content/10.1.... Here’s a summary of the results:
Complex structural variant visualization with SVTopo
Structural variants are genomic variants that impact at least 50 nucleotides and can play major roles in diversity and human health. Many structural variants are complex multi-breakpoint rearrangement...
www.biorxiv.org
April 22, 2025 at 2:21 PM
I just released a new preprint! The manuscript describes SVTopo, a software tool that enhances visualization of complex SVs using HiFi data: www.biorxiv.org/content/10.1.... Here’s a summary of the results:
Reposted by Michael Eberle
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 Michael Eberle
Few more days from now everyone - join us in Milan — submit an abstract by Monday!
Abstract submission deadline extended to Monday, February 03, 23:59 hrs CET (no exceptions). Last chance to submit an abstract for inclusion in the programme of #eshg2025 #hybridconference! More information on: t.co/26f98JviOZ
https://2025.eshg.org/abstracts/
t.co
January 30, 2025 at 1:28 PM
Few more days from now everyone - join us in Milan — submit an abstract by Monday!
Reposted by Michael Eberle
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 Michael Eberle
I’ll be at PAG 2025 presenting on #longread #microbiome species profiling with a talk and a poster. I’ll also be at the PacBio booth some and the party (link to register in reshared post below). Come see me if you or a colleague will be attending. programs.pacb.com/pag2025
January 6, 2025 at 6:17 PM
I’ll be at PAG 2025 presenting on #longread #microbiome species profiling with a talk and a poster. I’ll also be at the PacBio booth some and the party (link to register in reshared post below). Come see me if you or a colleague will be attending. programs.pacb.com/pag2025
Reposted by Michael Eberle
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 Michael Eberle
I've been informed the DOI link is not working yet, here's the bioRxiv URL in the interim:
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
“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 3:21 PM
I've been informed the DOI link is not working yet, here's the bioRxiv URL in the interim:
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
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 Michael Eberle
I'm very impressed by the thorough work @holtjma.bsky.social, @meberle.bsky.social and team have done in building #StarPhase - it really checks all the boxes for reliable calling of #pharmacogenomic star alleles, even for #CYP2D6! 🙌
“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 3:55 PM
I'm very impressed by the thorough work @holtjma.bsky.social, @meberle.bsky.social and team have done in building #StarPhase - it really checks all the boxes for reliable calling of #pharmacogenomic star alleles, even for #CYP2D6! 🙌
Reposted by Michael Eberle
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 Michael Eberle
Post-doc opportunity! 📣📣📣 Our host-virus interaction lab (Institut Cochin, France) is seeking a highly motivated post doctoral researcher for a 2-year position to work on HIV latency. Join us in exploring cutting-edge molecular mechanisms in the beautiful city of Paris!
November 26, 2024 at 12:20 PM
Post-doc opportunity! 📣📣📣 Our host-virus interaction lab (Institut Cochin, France) is seeking a highly motivated post doctoral researcher for a 2-year position to work on HIV latency. Join us in exploring cutting-edge molecular mechanisms in the beautiful city of Paris!
Reposted by Michael Eberle
Late-stage graduate students and junior postdoctoral fellows are invited to attend the 2025 Recruitment Summit for CHOP/Penn Postdoctoral Scholars in Cell Biology and Genomics
careers.chop.edu/us/en/event/...
careers.chop.edu/us/en/event/...
Recruitment Summit for Postdoctoral Scholars in Cell Biology and Genomics | Children’s Hospital of Philadelphia
Recruitment Summit for Postdoctoral Scholars in Cell Biology and Genomics in Philadelphia, Pennsylvania, United States. null at Children’s Hospital of Philadelphia
careers.chop.edu
November 25, 2024 at 5:26 PM
Late-stage graduate students and junior postdoctoral fellows are invited to attend the 2025 Recruitment Summit for CHOP/Penn Postdoctoral Scholars in Cell Biology and Genomics
careers.chop.edu/us/en/event/...
careers.chop.edu/us/en/event/...
Reposted by Michael Eberle
Application review starts 11/30! Please share, new Bluesky friends!
🚨 We're hiring! 🚨 Brandeis University is seeking a tenure-track Assistant Professor in Bioengineering, with a focus on synthetic biology or biomolecular engineering. Please DM me with any questions! academicjobsonline.org/ajo/jobs/28825 (1/2)
Brandeis University, Engineering
Full service online faculty recruitment and application management system for academic institutions worldwide. We offer unique solutions tailored for academic communities.
academicjobsonline.org
November 24, 2024 at 2:47 AM
Application review starts 11/30! Please share, new Bluesky friends!