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  1. Prikvačeni tweet
    24. lip 2019.

    Excited to announce that I’ll be joining Stanford's Applied Physics dept in the fall! Looking for students & postdocs interested in combining tools from statistical physics, popgen, and beyond to understand the ecological and evolutionary dynamics of large microbial communities.

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  2. proslijedio/la je Tweet
    24. sij

    Very excited that the program and I have worked on for years is public on and ready for use. InStrain () is a program for population genomic analysis from metagenomic data and rigorous detection of identical microbial strains(1/6)

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  3. proslijedio/la je Tweet
    15. sij

    Happy to announce that our paper on Acquisition and Transmission of crAssphage is out today! With (and Ami of course)

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  4. 2. sij

    Understanding the generality of these results (across other hosts, other ABX, & other perturbations) -- and their implications for short-term evolution in the microbiome -- are a big focus of our current work. Questions and comments welcome!

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  5. 2. sij

    This suggests that ecological resilience may extend all the way down to the genetic level. Also suggests that quasi-stable coexistence *within species* in this community may be more common than we typically assume (echoing previous finding by & co)

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  6. 2. sij

    Instead, we more commonly observed incomplete genome-wide sweeps involving multiple linked SNPs, many of which were already present in the pre-ABX pop'n. In months following ABX, many sweeping haplotypes eventually returned to their original freqs (at the single bp level!)

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  7. 2. sij

    We observed widespread shifts in genetic composition w/in species during & after ABX. But genetic responses were rarely consistent with simple extinction & recolonization picture. Nor were they consistent with simple model of ABX resistance evol'n via classic selective sweeps.

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  8. 2. sij

    To address these Q's, generated an amazing metagenomic timecourse for a single host microbiome using linked reads. This allowed us to track evolutionary dynamics w/in 36 different species during a period of health, disease, ABX treatment, and recovery

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  9. 2. sij

    But because these pioneering studies were based on 16S data, we know very little about how this ecological robustness is implemented at the strain level. Do species recover bc external strains recolonize the host after treatment? Or do resident strains evolve in response to ABX?

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  10. 2. sij

    Previous work had shown that gut microbial communities can be remarkably resilient after brief ABX perturbations: while ABX can have dramatic effect in short-term, communities often regain much of their baseline composition in weeks following treatment.

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  11. 2. sij

    Happy 2020! With the holidays behind us, wanted to highlight a few key take-aways from our preprint: . Our study focuses on a basic question: how do gut microbial communities respond to routine antibiotic treatments?

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  12. 23. pro 2019.

    Excited to announce a new preprint w/ on the ecological and evolutionary responses of the human gut microbiome during antibiotic treatment. . A lot of surprises in here for me -- will post a longer summary after the holidays.

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  13. proslijedio/la je Tweet

    Here's a thread telling the story of our new technique for genetic recording of lineage history during long term evolution experiments. The work was co-led with and in 's lab. Read the paper here:

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  14. proslijedio/la je Tweet
    13. stu 2019.

    What do you expect evolution to look like in a microbial population? Check out our new study offering a view of that over 1000 generations in yeast in the lab. co-led by , , in 's lab

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  15. proslijedio/la je Tweet
    13. stu 2019.

    What does evolution look like? We developed a rebarcoding approach to observe the travelling wave of adaptation at extremely high resolution. See short summaries by co-authors , in the lab of . Read the paper here:

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  16. proslijedio/la je Tweet
    25. lis 2019.

    We have an open post-doc position in the lab! Core current interests are recombination/reassortment/HGT in microbial evolution, but we can get excited about other questions as well. Please share!

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  17. proslijedio/la je Tweet
    21. lis 2019.

    My new study with comparing influenza's evolution within and between hosts is on bioRxiv! (1/n)

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  18. proslijedio/la je Tweet
    30. ruj 2019.

    How do T cells access many spatial scales in vivo? Excited to share our results in my first preprint, with Stephen Quake: Comments from all communities welcome and with many thanks to 2017.

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  19. proslijedio/la je Tweet
    16. srp 2019.

    Two faculty positions in Computational Genomics at Cornell -- Search starts NOW (July 16, 2019) at the Asst/Assoc level. CB dept has amazing growth potential, exciting colleagues, and soon a new building. Appls due Sept 1. Details here:

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  20. 24. lip 2019.

    Thanks to all for the encouragement and support -- it's quite a privilege to be part of such a great scientific community.

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