Job: Postdoc Fellows: DNA Methylation in Microbiome, Metagenomics and Meta-epigenomics
gravatar for fanggang
2.3 years ago by
United States
fanggang90 wrote:

Job description: Positions for Postdoc Fellows (Exploring and Exploiting DNA Methylation in Microbiome; Computational and/or Experimental) are available at the Mount Sinai School of Medicine (Top-20 medical school in the US) in New York City. Our lab is in the Department of Genetics and Genomic Sciences and the Institute for Genomics and Multi-scale Biology.

Our lab (computation + experiment) pioneered the fast growing field of bacterial epigenomics (Nature Biotechnology, 2012). We also pioneered the use of DNA methylation for high resolution microbiome analysis (Nature Biotechnology, 2017). In our recent work, we presented a binning method that incorporates bacterial DNA methylation signatures, which are detected using single-molecule real-time sequencing. Our method takes advantage of these “hidden” yet highly rich and informative endogenous epigenetic barcodes to resolve individual reads and assembled contigs into species- and strain-level bins. In addition to genome binning, we show that our method links plasmids and other mobile genetic elements to their host species in complex microbiome samples. Incorporation of DNA methylation information into shotgun metagenomics analyses opens a new way to understand microbiome at unprecedented resolution and completeness. We have unique expertise in the use of third generation sequencing (Single Molecule Real-Time by PacBio, ~20kbp read length, and the emerging Oxford Nanopore sequencing technology).

Successful candidates will have unique opportunities to i) build on our unique expertise in third-generation long read sequencing, meta-epigenomics, large scale collection of clinically relevant samples and a strong network of collaborators, ii) take the lead role in multiple projects studying complex mouse and human microbiome in innovative applications with high biological, biomedical and clinical impact. Compensations for successful candidates are highly competitive. Subsidized housing (in New York City) is also available.

Recent publications: Nature Biotechnology, 2017 * Nature, 2016 * Cell Reports, 2016 * Nature Communications, 2015 * PLoS Genetics, 2015 * Biological Psychiatry, 2015 * Nature Communications, 2014 * Molecular Psychiatry, 2014 * PLoS Genetics, 2013 * PLoS Computational Biology, 2013 * Nature Biotechnology, 2012 * Genome Research, 2012

Lab page with details:

General requirements: 1a) Candidates with computational background are expected to have solid training in bioinformatics and metagenomics; experimental skills on microbiome is a plus but not required. 1b) Candidates with experimental background are expected to have rich experience in analyzing mouse and human microbiome samples, bacterial genetics, and molecular biology skills, and an open mind to learn computation. 2) Ability to learn and master new skills, 3) Abilities to lead an independent research direction while adapting to a collaborative environment, 4) An innovative yet critical thinker.

Experience in any of the following (the order does not reflect priority) is a plus, but not required: 1) bacterial genetics, 2) bacterial comparative genomics, 3) metagenomics (16S and/or shotgun), 4) genome and metagenome assembly and annotation, 5) metatranscriptomics, 6) mouse and human gut microbiome, 7) germ-free mice, 8) strain-tracking, 9) fecal transplantation, 10) microbiome and cancer, 11) antibiotics resistance.

How to apply: Please send the following to 1) A brief cover letter, 2) CV with a list of publications, 3) PDF files for the papers in which you are first or co-first author.

Thank you for the interests!

Gang Fang, Assistant Professor, Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, US

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