Bioinformatics

Vision

Our vision is to harness the power of microbiome bioinformatics for better living.

Mission

The bioinformatics platform at the International Microbiome Centre is a dedicated bioinformatics
support resource for analysis of big data. Our aim is to offer state-of-the art analysis which guarantees high quality results and provide clear answer to research questions.

Key Areas of Expertise

Developing and testing

new methods to analyze 16s
amplicon and shotgun metagenomics data.

Staying up to date

with latest programming advances in interactive and visualization tools.

Focus on supporting researchers

with specific workflows and consistent workspace environments.

Services

The bioinformatics platform of the International Microbiome Centre offers a wide range of individualized bioinformatics services on a contract basis.


16S profiling of microbial diversity and community composition

Characterization of community metabolome, proteome and transcriptome

Statistical analysis of high dimensionality datasets

Next generation sequence pipeline development

Experimental design and sequencing optimization

Custom R package development and documentation

Individualized and group teaching of bioinformatics and statistics

Custom graphics and manuscript figure preparation

Specialization


16s rRNA Analysis

  • Development of a custom pipeline to assess the quality of samples, implemented the most suitable methods to identify sequence variants present and taxonomic assignment.
  • Perform downstream analysis like alpha and beta diversity and differential abundance analysis amongst group and clinical conditions.

Shotgun Metagenomics

  • Provide services for Genome Assembly, biomarker discovery, co-occurrence/ecological analysis and phylogeny reconstruction.

Computing resources

  • Provide access to high-performance computing resources and data storage facility.


Personnel

Dr. Laura Sycuro

Dr. Sycuro is an Assistant Professor at the University of Calgary and Genomics and Bioinformatics Theme Lead for the International Microbiome Centre. Her MSc/PhD dual-degree training in Epidemiology and Molecular Biology at the University of Washington was supported by a National Science Foundation Graduate Research Fellowship. Upon completing her postdoc at Fred Hutchinson Cancer Research Center, Dr. Sycuro focused her independent research program on the microbiome of women and their neonates. Serving as Co-Principal Investigator of the Alberta BLOOM birth cohort initiative, she was recently honoured as a CIHR Early Career Investigator in Maternal Health. In 2018, Dr. Sycuro was also appointed Functional Omics Lead for the IMPACTT Pan-Canadian Microbiome Core. Her work using genetic and genomic approaches to understand how members of the human microbiota cause disease has been published in PLoS Pathogens, the Journal of Infectious Diseases, and Cell.

Alana Schick, PhD, MSc

Alana Schick, PhD, MSc

Alana Schick did her PhD on the genomics of diversification in microbial populations at the University of Ottawa. She brings an evolutionary and ecological approach to the study of microbial diversity. Her expertise encompasses a wide range of computational platforms, primarily on next generation sequence and metabolomic datasets. Most of her work is in the statistical computing language R, but she is competent with an array of other Unix based and scripting approaches. Alana brings expertise in evolutionary modelling to interpreting sequence data and experience in microbiology as well as design and execution of microbial evolution experiments.

Hena R. Ramay, PhD

Hena R. Ramay, PhD

Hena Ramay did her PhD in bioinformatics and computational biology at George Mason University. She has been involved in various projects and has worked on data types included microarrays, genotyping-arrays, exomeseq and RNAseq, Nanostring and a variety of analyses depending on the research question at hand. She has routinely performed Biomarker identification, classification of samples, survival analysis, variant calling, copy number alterations and gene expression analysis of cancer genomics data analysis.

Select Publications

Bomhof, Marc R et. al, Histological improvement of non-alcoholic steatohepatitis with a prebiotic: a pilot clinical trial.European journal of nutrition.1-11.2018

Motta, Jean-Paul et. al, Iron Sequestration in Microbiota Biofilms As A Novel Strategy for Treating Inflammatory Bowel Disease. Inflammatory bowel diseases,24(7):1493-1502,2018

Contact

Shaunna Huston, ACCN RN, BSc, PhD Immunology

Director, Programs and Business, International Microbiome Centre
Phone: 403-220-6074
Email: imc@ucalgary.ca