Associate Professor at UCSC; UC Santa Cruz Genomics Institute; Satellite DNA Biologist
Joined February 2014
- Tweets 1,745
- Following 1,222
- Followers 3,571
- Likes 3,307
44 Photos and videos
Karen Miga retweeted
HPRC is building a reference that better reflects global genomic variation.
We're well on our way to advancing assembly technology and tools to power next-gen genomic research!
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Karen Miga retweeted
📢 HPRC Release 2 is here!
Now with phased genomes from 200 individuals, a 5x increase from Release 1.
Explore sequencing data, assemblies, annotations & alignments in our interactive data explorer ⬇️:
humanpangenome.org/hprc-data…
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Karen Miga retweeted
12 Feb 2025
Very excited to share our work @MahlkeMegan in great collaboration with @NAltemose @khmiga Peter Campbell and Rachel O'Neill revealing that human centromeres are heterogenous and naturally evolve over prolonged proliferation. Check it out here biorxiv.org/content/10.1101/…
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Karen Miga retweeted
10 Dec 2024
Meet our plenary speakers!
We are pleased to announce the distinguished plenary speakers for HGM2025. Come and listen to valuable perspectives shared by distinguished experts and leaders!
See you all at HGM2025!
Register Now: hugo-hgm2025.org/registratio…
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Karen Miga retweeted
11 Dec 2024
Final call to submit your abstract for the presentation during HGM2025!
Travel grants for students/post-docs and early-career researchers from LMIC countries are available. Please register and submit abstracts to be awarded.
Submit Abstract: hugo-hgm2025.org/abstract-su…
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Karen Miga retweeted
5 Dec 2024
Meet our speakers!
We are pleased to announce the distinguished speakers for HGM2025.
See you all at HGM2025!
Register Now: hugo-hgm2025.org/registratio…
Submit Abstract: hugo-hgm2025.org/abstract-su…
Apply for Travel Grant: hugo-hgm2025.org/travel-gran…
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Karen Miga retweeted
5 Dec 2024
Release of DeepVariant 1.8. Large speed improvement (~67% faster) via small model for easy sites. New Pangenome-aware option. Reduces error by ~30% for vg-mapped WGS ~10% for BWA WGS ~5% BWA exome. New config for custom model users, see release notes 1/3
github.com/google/deepvarian…
ALT Runtime figure for new version of DeepVariant with and without small model. Showing reduction in runtime of 155 minutes to 101 minutes with Illumina, 174 minutes to 71 minutes with PacBio, and 295 minutes to 114 minutes with Oxford Nanopore.
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Karen Miga retweeted
Accurate genome assemblies are key for research. DeepPolisher uses Pacbio HiFi alignments to improve base-level accuracy, cutting errors by half and reducing indel errors by over 70%.
✍🏼@miramastoras @kishwarshafin @BenedictPaten @MobinAsri
Here's how...
biorxiv.org/content/10.1101/…
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Karen Miga retweeted
Personalized pangenome preferences serve as crucial breakthroughs, furthering HPRC's mission to diversify genetic representation.
@Nature highlights a more customized approach facilitating improvements in genetic diversity and reducing genotyping errors.
nature.com/articles/s41592-0…
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Karen Miga retweeted
26 Sep 2024
I am going on the faculty job market this year, so if your home department is starting a search, I'd love to hear about it. Thanks!
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Karen Miga retweeted
20 Sep 2024
New preprint from our lab 🚨 We explored the variability in ribosomal DNA copy number and activity across humans of the world
with @GertonJennifer @PaxtonKostos @AndresGuarahino @stevenjsolar @erikgarrison @aphillippy and others not on X
biorxiv.org/content/10.1101/…
🧵
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Karen Miga retweeted
17 Sep 2024
Genome sequencing is faster and cheaper than ever – but obstacles to broad adoption remain.
Join @Google’s genomics lead @acarroll_ATG & @ucscgenomics’ @BenedictPaten for a live-streamed discussion on genomic analysis and equity: goo.gle/3ZmPyYO
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Karen Miga retweeted
11 Sep 2024
Published today in @Nature, we describe an approach for single-molecule protein reading on @nanopore arrays. By utilizing ClpX unfoldase to ratchet proteins through a CsgG nanopore, we achieved single-amino-acid sensitivity. nature.com/articles/s41586-0…
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1 Aug 2024
A friendly reminder that today (August 1st) is the last day to register for the T2T-F2F! Hope you can join us (details below and reach out if you have any questions)
23 Jul 2024
We welcome you to join us for the T2T Consortium Face-to-Face (T2T-F2F) Meeting in Santa Cruz, CA Sept 3-4. Open to all -- register before August 1st: sites.google.com/ucsc.edu/t2…
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Karen Miga retweeted
25 Jul 2024
Our fast haplotagging paper is now published (nature.com/articles/s41467-0…) - see the earlier thread for a summary. Thanks to @kishwarshafin @AlexeyKolesni18 for leading the work and collaborators: @Johngorzynski, @gsneha261, @euanashley, @mitenjain, @khmiga, @BenedictPaten
12 Sep 2023
Happy to share this paper which provides more detail about the process we use to assign haplotypes to long reads on-the-fly, which enabled us to speed up the DeepVariant release at v1.4. Implementation by Alexey Kolesnikov, Lead for collaboration, writing, figures @kishwarshafin
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Karen Miga retweeted
23 Jul 2024
🧬Want to learn more about the Telomere-to-Telomere project and the folks involved in the T2T Consortium before the T2T-F2F meeting on Sept 3-4?
👇Watch the presentation @khmiga gave at the Genome Technology Forum held @jacksonlab
in collab w/ @genome_gov
youtu.be/t4kGX373EEQ
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23 Jul 2024
We welcome you to join us for the T2T Consortium Face-to-Face (T2T-F2F) Meeting in Santa Cruz, CA Sept 3-4. Open to all -- register before August 1st: sites.google.com/ucsc.edu/t2…
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23 Jul 2024
With many more speakers scheduled for flash talks. We are also planning interactive discussions focused on T2T sequencing and assembly methods as well as future plans for long-read functional genomics studies.
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23 Jul 2024
We hope you can join us and look forward to seeing you in Santa Cruz!
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