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Karen Shih

@karenyshih.bsky.social
42 followers 44 following 13 posts

Stanford Biology PhD candidate in Dmitri Petrov and Monte Winslow's lab. Cancer Evolution, Cancer Genomics, In Vivo CRISPR Screening & Functional Genomics. kyshih.github.io/karenshih

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Reposted by Karen Shih
Mark Bitter @markcbitter.bsky.social · 01/10/2026
New Perspective w/ @petrovadmitri.bsky.social and Paul Schmidt! We ask what evolution-in-action studies tell us about an old question: what genetic variation matters for fitness, and what maintains it? ecoevorxiv.org/repository/v...
ecoevorxiv.org
Common, consequential, and actively maintained: a neo-balance view of genetic variation
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Karen Shih @karenyshih.bsky.social · 28/08/2026
Really excited to share that work from my PhD is now on bioRxiv! We ask: Is the transcriptional response to high tumor mutational burden (TMB) consistent across cancers, or does it vary by cancer type? www.biorxiv.org/content/10.6...
biorxiv.org
Transcriptional Response to Tumor Mutational Burden Is Consistent Across Cancer Types
Tumor mutational burden (TMB) shapes tumor transcriptional state, but studies typically describe this response as an average effect pooled across cancer types. Whether that average reflects a consiste...
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Reposted by Karen Shih
Nicole Nova @nicole-nova.bsky.social · 23/07/2026
A fundamental question in disease ecology remains unresolved: How can an acute, immunizing virus persist in nature? Theory says viruses like measles need huge pools of susceptible hosts. Our new preprint offers an answer. www.biorxiv.org/content/10.6...
biorxiv.org
Persistent, Multi-Species Outbreaks and Long-Range Transmissions of a Measles-Like Virus
Canine distemper\---|a measles-like disease with high mortality and presently without a cure\---|poses a major threat to wild and domestic carnivores globally. Domestic dogs are generally considered t...
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Reposted by Karen Shih
Olivia Ghosh @oliviamghosh.bsky.social · 30/03/2026
Really excited that this major work from my PhD is finally published in @plosbiology.org ! In it, we were trying to tackle a fundamental question in evolution - how do genetic mutations map onto evolutionary fitness? (1/n) journals.plos.org/plosbiology/...
journals.plos.org
Genotype-fitness mapping of adaptive mutants reveals shifting low-dimensional structure across divergent environments
Predicting the effect of a genetic mutation on fitness is a major challenge in evolutionary biology. This study uses fitness effects of a large collection of adaptive yeast mutants in multiple lab env...
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Reposted by Karen Shih
Dmitri Petrov @petrovadmitri.bsky.social · 11/03/2026
Very proud of this contribution. Beautiful and hyper careful work by @jahemker.bsky.social showing that not all long read assembles are created equal and at times it really does matter to have enough not just long but very long reads. Curious what you all think!
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Karen Shih @karenyshih.bsky.social · 11/03/2026
Huge congrats to star grad student @jahemker.bsky.social in the Petrov lab on this publication! Exciting to see how ultra-long, high-coverage sequencing enables more complete structural variant discovery and opens new possibilities for population genomics.
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Reposted by Karen Shih
Jess Smiley-Rhodes @j-smiley-rhodes.bsky.social · 18/11/2025
Thrilled to finally share the magnum opus of my PhD that focuses on the genetic basis of evolutionary change! Specifically, we know we can map the genetic basis of a trait, but can we tell which genes will underlie the trait shift when it evolves? doi.org/10.1101/2025...
doi.org
High-resolution mapping of a rapidly evolving complex trait reveals genotype-phenotype stability and an unpredictable genetic architecture of adaptation
The extent to which adaptation can be predicted, particularly for traits with complex genetic bases, is unknown. Here, we leveraged a model complex trait, model species, and high-powered longitudinal ...
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Reposted by Karen Shih
Sophie Jean Walton @sophiejwalton.bsky.social · 11/11/2025
Complex microbial communities, like the human gut microbiome, can harbor extensive strain-level diversity, with strains of the same species from different hosts differing by ~10k mutations. However, the fitness consequences of this diversity in community contexts are not well understood. (2/n)
Alt text: Cartoon phylogeny of 4 human hosts and their microbial strains. Arrows indicate that these strains are separate by ~100kya of evolution. ~10k SNVs separate the microbial strains.
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Reposted by Karen Shih
José Aguilar-Rodríguez @jaguilarrod.bsky.social · 22/10/2025
One of the most exciting works of my career, years in the making. We used high-throughput precision genome editing to test the fitness effects of thousands of natural variants. Our findings challenge the long-held assumption that common variants are inconsequential. www.biorxiv.org/content/10.1...
biorxiv.org
Massively parallel interrogation of the fitness of natural variants in ancient signaling pathways reveals pervasive local adaptation
The nature of standing genetic variation remains a central debate in population genetics, with differing perspectives on whether common variants are almost always neutral as suggested by neutral and n...
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Karen Shih @karenyshih.bsky.social · 23/01/2025
Excited to share this amazing paper on how beneficial dominance reversal maintains large-effect functional variation, authored by a star postdoc from the Petrov lab! Huge congrats to Marianna and all the authors! 🎉👏
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