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Carlo Maley @cmaley

I study cancer from an evolutionary perspective including the dynamics of somatic evolution, therapeutic resistance and the evolution of cancer suppression biodesign.asu.edu/carlo-maley Tempe, AZ Joined August 2007
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Carlo Maley retweeted
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Carlo Maley @cmaley

4 days ago

I'm excited to announce that ASU is hiring a postdoc that can transition into a tenure-track job in comparative genomics (esp. applied to evolutionary med). Applications are due May 17. Apply here apply.interfolio.com/144623 Please spread the word!

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Carlo Maley @cmaley

4 months ago

We are delighted to announce the publication of our mouse study of adaptive therapy for endocrine-resistant but ER+ breast cancer. This is one of the few (third?) published experiments to test adaptive therapy in mice, and the first to test 2 drugs. mdpi.com/2072-6694/16/2…

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Carlo Maley @cmaley

5 months ago

.@EinsteinCross: ALFA-K is available on github - designed and implemented by @Richard_J_Beck #AACRevol23

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Carlo Maley @cmaley

5 months ago

.@EinsteinCross: Want to map a new sample (from TCGA?) onto an existing landscape and test the predicted karyotype evolution from there as a biomarker #AACRevol23

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Carlo Maley @cmaley

5 months ago

.@EinsteinCross: Testing Eigen-Schuster prediction that populations with high mutation rates would tend to cluster on wide fitness peaks rather than high fitness peaks (they tend to fall off of high but narrow peaks) #AACRevol23

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Carlo Maley @cmaley

5 months ago

.@EinsteinCross: Compared landscapes near diploid karyotypes vs near tetraploid karyotypes. Quantified Moran's i to measure ruggedness of the fitness landscape. Tetraploid fitness landscape was significantly smoother #AACRevol23

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Carlo Maley @cmaley

5 months ago

.@EinsteinCross: Took data from Salehi et al. Nature 2021. Found that 4 out of 5 landscapes matched data well. #AACRevol23

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Carlo Maley @cmaley

5 months ago

.@EinsteinCross: Map out fitness of all karyotypes that are no more than 2 chromosome mis-segregations. Infer relative fitness from frequency of changes #AACRevol23

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Carlo Maley @cmaley

5 months ago

.@EinsteinCross: Uses an agent-based model with state as the copy number of each chromosome and occasional mis-segregation of chromosomes. #AACRevol23

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Carlo Maley @cmaley

5 months ago

.@EinsteinCross: There are too many possible karyotypes to be exhaustively characterized. But you can look at local mapping of fitness landscapes #AACRevol23

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Carlo Maley @cmaley

5 months ago

.@EinsteinCross: ALFA-K is the package her lab has developed - forecasting tumor evolution. Juliann Shih et al. Nature 2023 showed that aneuploidy in cancers are shaped by their selective effects. But they interact, so you have to account for epistasis #AACRevol23

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Carlo Maley @cmaley

5 months ago

Last, but certainly not least, @EinsteinCross is talking now about "Adaptive local fitness landscapes for aneuploid karotypes" #AACRevol23

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Carlo Maley @cmaley

5 months ago

.@val_boeva: CDState improved NMF for transcriptional deconvolution #AACRevol23

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Carlo Maley @cmaley

5 months ago

.@val_boeva: Compared most popular methods for bulk deconvolution which didn't do well if pure samples of given cell types are rare #AACRevol23

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Carlo Maley @cmaley

5 months ago

.@val_boeva: Gavish et al. Nature 2023 did a pancancer analysis of transcriptional intratumor heterogeneity #AACRevol23

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Carlo Maley @cmaley

5 months ago

.@val_boeva: Looking for genetic drivers of transcriptional heterogeneity/plasticity #AACRevol23

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Carlo Maley @cmaley

5 months ago

.@val_boeva: Measuring intratumor epigenetic and transcriptional heterogeneity #AACRevol23

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Carlo Maley @cmaley

5 months ago

.@val_boeva is talking next about "Unraveling potential genetic drivers of intratumor transcriptional heterogeneity and phenotypic plasticity in malignant cells" #AACRevol23

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