Karen Shih
@karenyshih.bsky.social
Stanford Biology PhD candidate in Dmitri Petrov and Monte Winslow's lab. Cancer Evolution, Cancer Genomics, In Vivo CRISPR Screening & Functional Genomics.
https://kyshih.github.io/karenshih/
https://kyshih.github.io/karenshih/
Reposted by Karen Shih
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...
Common, consequential, and actively maintained: a neo-balance view of genetic variation
ecoevorxiv.org
October 1, 2026 at 6:28 PM
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...
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...
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...
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...
www.biorxiv.org
August 28, 2026 at 10:14 PM
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...
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...
Reposted by Karen Shih
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...
Theory says viruses like measles need huge pools of susceptible hosts. Our new preprint offers an answer.
www.biorxiv.org/content/10.6...
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...
www.biorxiv.org
July 23, 2026 at 6:57 PM
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...
Theory says viruses like measles need huge pools of susceptible hosts. Our new preprint offers an answer.
www.biorxiv.org/content/10.6...
Reposted by Karen Shih
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/plosbiology/...
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...
journals.plos.org
March 30, 2026 at 7:11 PM
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/plosbiology/...
Reposted by Karen Shih
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!
Proud that this work is now published!
We hope it helps orient future #Nanopore long-read sequencing studies hunting for structural variants
Also really happy to share eight new high-coverage (>100x) long-read read pools and assemblies with the #Drosophila community!
doi.org/10.1093/g3jo...
We hope it helps orient future #Nanopore long-read sequencing studies hunting for structural variants
Also really happy to share eight new high-coverage (>100x) long-read read pools and assemblies with the #Drosophila community!
doi.org/10.1093/g3jo...
March 11, 2026 at 3:53 AM
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!
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.
Proud that this work is now published!
We hope it helps orient future #Nanopore long-read sequencing studies hunting for structural variants
Also really happy to share eight new high-coverage (>100x) long-read read pools and assemblies with the #Drosophila community!
doi.org/10.1093/g3jo...
We hope it helps orient future #Nanopore long-read sequencing studies hunting for structural variants
Also really happy to share eight new high-coverage (>100x) long-read read pools and assemblies with the #Drosophila community!
doi.org/10.1093/g3jo...
March 11, 2026 at 4:43 PM
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.
Reposted by Karen Shih
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...
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 ...
doi.org
November 18, 2025 at 12:15 AM
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...
Reposted by Karen Shih
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)
November 11, 2025 at 5:15 PM
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)
Reposted by Karen Shih
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...
www.biorxiv.org/content/10.1...
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...
www.biorxiv.org
October 22, 2025 at 5:46 PM
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...
www.biorxiv.org/content/10.1...
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! 🎉👏
How is functional variation at large-effect loci maintained in natural populations?
Thrilled to share our work showing how beneficial dominance reversal helps fruit flies maintain a resistance polymorphism as selection varies in their environment! A thread 🧵 1/n
www.biorxiv.org/content/10.1...
Thrilled to share our work showing how beneficial dominance reversal helps fruit flies maintain a resistance polymorphism as selection varies in their environment! A thread 🧵 1/n
www.biorxiv.org/content/10.1...
Dominance reversal maintains large-effect resistance polymorphism in temporally varying environments
A central challenge in evolutionary biology is to uncover mechanisms maintaining functional genetic variation1. Theory suggests that dominance reversal, whereby alleles subject to fluctuating selectio...
www.biorxiv.org
January 23, 2025 at 1:07 AM
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! 🎉👏