Reposted by Michael EberleChris Saunders @ctsa.bsky.social · 20/02/2026What if you could improve small variant accuracy, CNV inference, and interpretability of your HiFi WGS data by taking a different approach to read mapping? Our new preprint describes portello, a method which demonstrates the potential for such improvements. (1/5) 12511
Reposted by Michael EberleJohn Greally @greally.bsky.social · 30/01/2026Please spread the word — a 2-year postdoctoral fellowship is available in my group funded by the Simons Foundation Autism Research Initiative (SFARI) to perform a study testing the contribution of functional non-coding variants in glutamatergic neurons to autism. 1/3 143
Reposted by Michael EberlePacBio @pacbio.bsky.social · 10/10/2025Complex 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 031
Reposted by Michael EberleMatt Holt @holtjma.bsky.social · 06/10/2025I'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/Ngithub.comGitHub - PacificBiosciences/aardvark: A tool for sniffing out the differences in vari-AntsA tool for sniffing out the differences in vari-Ants - PacificBiosciences/aardvark 13217
Reposted by Michael EberleTiffany Lowe-Power stands with Minnesota @tlowepower.bsky.social · 22/09/2025Please 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) 257101
Reposted by Michael EberleJames Bonfield @jbonfield.bsky.social · 15/09/2025Heads 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 2145126
Reposted by Michael EberleHeng Li @lh3lh3.bsky.social · 09/09/2025minimap2.com is potentially a phishing site. Please don't use anything from that website. github.com/lh3/minimap2...github.comPhishing site : minimap2.com · Issue #1316 · lh3/minimap2Not 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... 12727
Reposted by Michael EberlePacBio @pacbio.bsky.social · 08/09/2025The 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 064
Reposted by Michael EberleJavier Santoyo @jsantoyo.bsky.social · 04/08/2025The Platinum Pedigree: a long-read benchmark for genetic variants. #HumanGenome #ReferenceGenome #PlatinumPedigree #LongReads #Benchmarking #GeneticVariants @natmethods.nature.com 🧬 🖥️ www.nature.com/articles/s41... 093
Reposted by Michael EberleAlex Hoischen @ahoischen.bsky.social · 24/05/2025Buongiorno 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 0156
Reposted by Michael EberleSarah Doom @sarahdoom.bsky.social · 07/05/2025Dr 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 051
Reposted by Michael EberleNature @nature.com · 25/04/2025Nature research paper: Human de novo mutation rates from a four-generation pedigree reference go.nature.com/3GnaA22go.nature.comHuman de novo mutation rates from a four-generation pedigree reference - NatureAnalysis 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. 0409
Reposted by Michael EberleEichlerLab @eichlerlab.bsky.social · 24/04/2025Our 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.edurdcu.beHuman de novo mutation rates from a four-generation pedigree referenceNature - 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... 1123
Reposted by Michael EberleUW Medicine Newsroom @uwmnewsroom.bsky.social · 23/04/2025Advanced 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.socialbit.ly4 generations help science explore genome mutation rate - UW Medicine | Newsroom 1146
Reposted by Michael EberleJon Belyeu @jonbelyeu.bsky.social · 22/04/2025I 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:biorxiv.orgComplex structural variant visualization with SVTopoStructural 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... 1138
Reposted by Michael EberleChris Saunders @ctsa.bsky.social · 10/04/2025Great 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.orgSawfish: Improving long-read structural variant discovery and genotyping with local haplotype modelingAbstractMotivation. Structural variants (SVs) play an important role in evolutionary and functional genomics but are challenging to characterize. High-accu 24324
Reposted by Michael EberleAlex Hoischen @ahoischen.bsky.social · 30/01/2025Few more days from now everyone - join us in Milan — submit an abstract by Monday! 061
Reposted by Michael EberleAlex Hoischen @ahoischen.bsky.social · 13/01/2025Image 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...cell.comHiFi long-read genomes for difficult-to-detect, clinically relevant variantsDetecting 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... 1169
Reposted by Michael EberleJeremy Wilkinson @jewilki.bsky.social · 06/01/2025I’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/pag2025programs.pacb.comPacBio PAG 2025 0113
Reposted by Michael EberleLaurits Skov @lauritsskov.bsky.social · 02/12/2024Very 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... 9416284
Reposted by Michael EberleMatt Holt @holtjma.bsky.social · 11/12/2024I've been informed the DOI link is not working yet, here's the bioRxiv URL in the interim: www.biorxiv.org/content/10.1... 012
Michael Eberle @meberle.bsky.social · 11/12/2024Great 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. 062
Reposted by Michael EberleLili Milani @lilimilani.bsky.social · 11/12/2024I'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! 🙌 043
Reposted by Michael EberleAaron Quinlan (he/him) @aaronquinlan.bsky.social · 03/12/2024Biology 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...meetings.cshl.eduBiology of GenomesCold Spring Harbor Laboratory Meetings & Courses -- a private, non-profit institution with research programs in cancer, neuroscience, plant biology, genomics, bioinformatics. 16634
Reposted by Michael EberleSarah Gallois-Montbrun @sarahgalloism.bsky.social · 26/11/2024Post-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! 01011
Reposted by Michael EberleStruan Grant @struangrant.bsky.social · 25/11/2024Late-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.eduRecruitment Summit for Postdoctoral Scholars in Cell Biology and Genomics | Children’s Hospital of PhiladelphiaRecruitment Summit for Postdoctoral Scholars in Cell Biology and Genomics in Philadelphia, Pennsylvania, United States. null at Children’s Hospital of Philadelphia 02829
Reposted by Michael EberleAvital Rodal @rodallab.bsky.social · 24/11/2024Application review starts 11/30! Please share, new Bluesky friends! 02723
Reposted by Michael EberleSarah Doom @sarahdoom.bsky.social · 23/11/2024@sedlazeck.bsky.social AMPath24 talk about long reads highlighting TRGT tool by @egor-dolzhenko.bsky.social and @guilhermesena1.bsky.social and others for HiFi sequencing by @pacbio.bsky.social 0176
Reposted by Michael EberleMichel Cayouette @michelcayouette.bsky.social · 21/11/2024bsky.app/profile/mich... 1122
Reposted by Michael EberleWolfgang Huber @wkhuber.bsky.social · 19/11/2024Something that's been bugging me for a while in bioinformatics data analysis is this overreliance on packages, workflows and what's been called "cargo cult science". Can we have more conceptual thinking, more theory? Asking for what we really want to achieve and what we need to do gets us there. 3322134
Reposted by Michael EberlemedRxivpreprint @medrxivpreprint.bsky.social · 20/09/2024HiFi long-read genomes for difficult-to-detect clinically relevant variants www.medrxiv.org/content/10.1101/202… medrxiv.orgHiFi long-read genomes for difficult-to-detect clinically relevant variants https://www.medrxiv.org/content/10.1101/2024.09.17.24313798v1 Clinical short-read exome and genome sequencing approaches have positively impacted diagnostic testi 043
Reposted by Michael EberleAlex Hoischen @ahoischen.bsky.social · 18/11/2024The preliminary #eshg25 program is online. Stellar line-up of invited speakers - full breadth of our amazing field. Grateful to a wonderful SPC @eshg that made this possible. See you all in Milan next year! 2025.eshg.org/programme-at...2025.eshg.orgProgramme at a GlancePre-conference courses Thursday, May 22, 2025 & Friday, May 23, 2025 - TBA Conference programme Saturday, May 24, 2025 08:30 - 10:00 Educational Sessions E01 E01 Single cell genomics and diseases W... 12111
Reposted by Michael EberleChen-Yang Su, PhD @chenyangsu.bsky.social · 17/11/2024 I thought it could be nice to connect the community of researchers in human genetics, so here is the Genetics Starter Pack! 🧬 #academicsky Let me know if you would like to be added or know someone to add. Enjoy and share! go.bsky.app/LN2NRuB 255317
Reposted by Michael EberleSandhya Koushika @wormlockholmes.bsky.social · 17/11/2024Looking for a starter pack to find/join a community? Here is a searchable/browsable link. Love this feature of @bsky.app blueskydirectory.com/starter-pack...blueskydirectory.comAll - Bluesky DirectoryA curated collection of all things relating to the Blue Sky social media platform. 53516
Reposted by Michael EberleAllison Gill @muellershewrote.com · 16/11/2024Try this: move the BlueSky app icon to where your Twitter icon is. Then slide your Twitter icon off your main screen. You’ll notice a vast improvement in your blood pressure. 2436418133383
Reposted by Michael EberleZamin Iqbal @zaminiqbal.bsky.social · 15/11/2024Latest data from AllTheBacteria described in our updated preprint. All illumina WGS bacterial+archaeal sequence data to Aug 2024 consistently assembled, QC, and now AMR profiling. That's 2.4 million genomes. Gene annotations almost done , coming next. Please use! www.biorxiv.org/content/10.1...biorxiv.orgAllTheBacteria - all bacterial genomes assembled, available and searchableThe bacterial sequence data publicly available at the global DNA archives is a vast source of information on the evolution of bacteria and their mobile elements. However, most of it is either unassemb... 413863
Reposted by Michael EberleBen Langmead @benlangmead.bsky.social · 12/11/2024Work by Nate Brown, @vikramshivakumar.bsky.social and I showing how compressed full-text indexes like the move structure can be extended to report "chaining" information alongside exact matches. The extension is called "col-BWT" (1/3) 12510
Reposted by Michael EberleJon Belyeu @jonbelyeu.bsky.social · 13/11/2024 If you were interested but missed it: www.pacb.com/wp-content/u...pacb.com 055
Reposted by Michael EberleJon Belyeu @jonbelyeu.bsky.social · 13/11/2024#ASHG2024 was a blast. I had great discussions with friends and #pacbio collaborators, presented a poster on my new tool SVTopo, welcomed #PacBioVega to the world, and realized than I'm a bigger fan of One Republic than I knew before. Excited for next time! 1111
Reposted by Michael EberleLiz Tseng @magdoll.bsky.social · 14/11/2024Analyzing @pacbio.bsky.social Kinnex full-length (bulk) RNA-Seq data? Here's the troubleshooting guide to help you understand the metrics! Explanation on FLNC reads, SQANTI3/pigeon classification, and artifact filtering. #Bioinformatics 🧬🧪 www.pacb.com/wp-content/u...pacb.com 0113
Reposted by Michael EberlePacBio @pacbio.bsky.social · 12/11/2024A 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! 🧬✨ 617967
Reposted by Michael EberleDr. Julie Claycomb @farmgirlphd.bsky.social · 29/10/2024Please share broadly! We (Molecular Genetics, University of Toronto) are looking for a new faculty member! Deadline Dec 19. Those working on model organisms and using genomics, computational and systems approaches are strongly encouraged to apply! Reach out w/ Qs! jobs.utoronto.ca/job/Toronto-...jobs.utoronto.caAssistant Professor - Molecular Biology and GeneticsAssistant Professor - Molecular Biology and Genetics 085144
Reposted by Michael EberleDanny Miller, MD, PhD @danrdanny.bsky.social · 11/11/2024I created a long-read sequencing starter pack. I'm still finding people on here, so apologies if I missed you. Please suggest people who should be added and I'll add them! go.bsky.app/JGkefsJ 163823
Reposted by Michael EberleMatt Holt @holtjma.bsky.social · 09/02/2024We just added a methylation segmentation algorithm for PacBio HiFi data to our MethBat tooling (beta). If you are interested in trying it out, we would greatly appreciate any feedback on the performance and possible extensions! Release here: github.com/PacificBiosc...github.comRelease MethBat v0.9.0 · PacificBiosciences/MethBatChanges Adds a new segmentation mode based on Circular Binary Segmentation. This mode generates a BED file of methylated, unmethylated, and ASM regions. The mode is executed with methbat segment .... 022
Reposted by Michael EberleDan Portik @dportik.bsky.social · 05/01/2024Very excited to see a new metagenome asssembly algorithm available for PacBio HiFi data! metaMDBG performs extremely well based on my benchmarks and we plan on using it for several deep-sequencing projects. doi.org/10.1038/s415... 0104
Reposted by Michael EberleAaron Quinlan (he/him) @aaronquinlan.bsky.social · 12/11/2023A reminder of this faculty opening in the Dept of Human Genetics at UU. Applications are due Dec. 8. Please share! 01414
Reposted by Michael EberleFritz Sedlazeck @sedlazeck.bsky.social · 06/11/2023Tandem repeats are hard! Get your benchmark from @genomeinabottle.bsky.social to compare caller : biorxiv.org/content/10.1... 1.7 mil TR catalog; new tooling to overcome variant representation issues (SNV &SV); insight in complexity. First time we can compare across different techs/caller! 0157
Reposted by Michael EberleMatt Holt @holtjma.bsky.social · 30/10/2023I'm pleased to announce the release of HiPhase v1.0.0! In addition to phasing small and structural variants from #PacBio #HiFi datasets, HiPhase now also includes support for phasing short tandem repeats (#STR) at the same time! Full release notes can be found here: github.com/PacificBiosc...github.comRelease HiPhase v1.0.0 · PacificBiosciences/HiPhaseChanges Added support for tandem repeat calls from TRGT; minimum supported version - v0.5.0 VCF index files (.tbi) are now automatically generated by HiPhase The reference FASTA file is now a requ... 187
Reposted by Michael EberleMatt Holt @holtjma.bsky.social · 28/10/2023Looking forward to seeing everyone at #ASHG23 next week! This will be my first time attending, and we have some exciting news to share about HiPhase for #PacBio HiFi datasets… 151
Reposted by Michael EberleNandita Garud @nanditagarud.bsky.social · 19/10/2023I am looking for a graduate student and a postdoc to join my group! We are a computational group working on understanding evolution in natural populations with a large emphasis on the microbiome. Please get in touch by dm or email! garud.eeb.ucla.edu 05376