Welcome to the Microbiome Informatics webinars!

The ‘human microbiome’ is transforming modern medicine, but microbes are also now recognized as major players across diverse ecosystems including plants and animals, soils and the oceans, and engineered systems. Low-cost sequencing and computational advances have flooded the life sciences with new windows into the life and impacts of these hidden movers and shakers. However, Microbiome Science is a relatively new and fast-moving discipline, so there are few opportunities currently available to graduate students and postdocs to immersively train. This webinar series represents a first phase effort to digitize 7 years of a hands-on informatics training course in this space, with a focus that goes beyond 16S-based studies to leverage the power of shotgun sequencing. Each 1.5 – 2 hour webinar will provide a brief concept introduction, and then hands-on practical exercises designed to provide cutting-edge first phase of training in Microbiome Informatics to empower researchers to better understand microbes and their viruses in complex communities.

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***Webinar Resources (including recordings of past sessions) here***

Spring 2021 Agenda overview (Tuesdays 1-3 EST):

March 2, 2021 | Introduction to microbiome science and why OSU ? | Matt Sullivan (OSU)

March 9, 2021 | Introduction to high-performance computing (HPC) | Shareef Dabdoub (OSU)

March 16, 2021 | Introduction to QIIME, Mothur and ecological statistics for microbiomes | Shareef Dabdoub (OSU)

March 23, 2021 | Advanced ecological statistics for microbiomes | Ahmed Zayed (OSU)

March 30, 2021 | Front-end metagenome processing to MAGs (QC, assemble, read map, binning) | Dylan Cronin (OSU)

April 6, 2021 | DRAM and genome-resolved inference | Kayla Borton & Mike Shaffer (Colorado State University)

April 13, 2021 | Genome-based taxonomy and phylogenomics | Donovan Parks (Australian Centre for Ecogenomics)

April 20, 2021 | Viromics 1 – iVirus, KBase and IMG/VR overview of ‘virus’ tools available | Ben Bolduc (OSU)

April 27, 2021 | Viromics 2 – the viral ecogenomic pipeline | Ben Bolduc (OSU)

May 4, 2021 | VirION2 – hybrid short-/long-read metagenomics | Olivier Zablocki (OSU)


Key literature:

Bolduc, B., Youens-Clark, K., Roux, S., Hurwitz, B.L.^, & Sullivan, M.B.^ 2017. iVirus: facilitating new insights into viral ecology with software and community datasets imbedded in a cyberinfrastructure. ISMEJ. 11:7-14.   (^ denotes co-corresponding authors)  LINK

Parks, D.H., Chuvochina, M., Waite, D.W., Rinke, C., Skarshewski, A., Chaumeil, P-A. & Hugenholtz, P. 2018. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nature Biotechnology. 36: 996-1004.  LINK

Jang, H.B., Bolduc, B., Zablocki, O., Kuhn, J., Roux, S., Adriaenssens, E.M., Brister, J.R., Kropinski, A.M., Krupovic, M., Lavigne, R., Turner, D., & Sullivan, M.B. 2019. Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks. Nature Biotechnology. 37:632–639. († denotes co-first authors)  LINK

Parks, D.H., Chuvochina, M., Chaumeil, P-A., Rinke, C., Mussig, A.J. & Hugenholtz, P. 2020. A complete domain-to-species taxonomy for Bacteria and Archaea. Nature Biotechnology. 38: 1079-1086. LINK

Shaffer M.Borton, M.A., McGivern, B.B.Zayed, A.A.La Rosa, S.L.Solden, L.M., Liu, P, Narrowe, A.B., Rodríguez-Ramos, J., Bolduc, B.Gazitua, M.C.Daly, R.A.Smith, G.J.Vik, D.R.Pope, P.B., Sullivan, M.B., Roux, S.Wrighton, K.C. 2020. DRAM for distilling microbial metabolism to automate the curation of microbiome function. Nucleic Acids Research. 48:8883-8900. LINK