Bio

Professional Education


  • Bachelor of Science, Xiamen University (2008)
  • Doctor of Philosophy, Indiana University (2014)

Stanford Advisors


Publications

All Publications


  • Synthetic long-read sequencing reveals intraspecies diversity in the human microbiome NATURE BIOTECHNOLOGY Kuleshov, V., Jiang, C., Zhou, W., Jahanbani, F., Batzoglou, S., Snyder, M. 2016; 34 (1): 64-69

    Abstract

    Identifying bacterial strains in metagenome and microbiome samples using computational analyses of short-read sequences remains a difficult problem. Here, we present an analysis of a human gut microbiome using TruSeq synthetic long reads combined with computational tools for metagenomic long-read assembly, variant calling and haplotyping (Nanoscope and Lens). Our analysis identifies 178 bacterial species, of which 51 were not found using shotgun reads alone. We recover bacterial contigs that comprise multiple operons, including 22 contigs of >1 Mbp. Furthermore, we observe extensive intraspecies variation within microbial strains in the form of haplotypes that span up to hundreds of Kbp. Incorporation of synthetic long-read sequencing technology with standard short-read approaches enables more precise and comprehensive analyses of metagenomic samples.

    View details for DOI 10.1038/nbt.3416

    View details for Web of Science ID 000368758200028

    View details for PubMedID 26655498

  • Sequential evolution of bacterial morphology by co-option of a developmental regulator NATURE Jiang, C., Brown, P. J., Ducret, A., Brun, Y. V. 2014; 506 (7489): 489-?

    Abstract

    What mechanisms underlie the transitions responsible for the diverse shapes observed in the living world? Although bacteria exhibit a myriad of morphologies, the mechanisms responsible for the evolution of bacterial cell shape are not understood. We investigated morphological diversity in a group of bacteria that synthesize an appendage-like extension of the cell envelope called the stalk. The location and number of stalks varies among species, as exemplified by three distinct subcellular positions of stalks within a rod-shaped cell body: polar in the genus Caulobacter and subpolar or bilateral in the genus Asticcacaulis. Here we show that a developmental regulator of Caulobacter crescentus, SpmX, is co-opted in the genus Asticcacaulis to specify stalk synthesis either at the subpolar or bilateral positions. We also show that stepwise evolution of a specific region of SpmX led to the gain of a new function and localization of this protein, which drove the sequential transition in stalk positioning. Our results indicate that changes in protein function, co-option and modularity are key elements in the evolution of bacterial morphology. Therefore, similar evolutionary principles of morphological transitions apply to both single-celled prokaryotes and multicellular eukaryotes.

    View details for DOI 10.1038/nature12900

    View details for Web of Science ID 000332165100038

    View details for PubMedID 24463524

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