Xiaoli Dong

Computational scientist in Energy Bioengeering Group

Development and implementation of computational pipelines for metagenomic/metatranscriptomic/metaproteomic data analysis
Administration of big data, scripts and programs.
Mentoring postdoctoral and doctoral students running their own pipelines for data analyses
Independent monitoring of the scientific literature for new developments and adoption/implementation/extension of such developments.
Provide advice and leadership to other U of C investigators on computation, data administration and related practices.
Taking the system administrating roles in Engergy Bioengeering and Geomicrobiology group and responsible for day-to-day maintenance of computatonal servers, including user account management, data access and backup plans, etc.

Metagenomics for Greener Production and Extraction of Hydrocarbon Energy

The target of this project is to develop a database to describe and harness the genetic potential of the microorganisms, genes and biological processes that exist naturally in microbial communities in our oil sands and coal beds. By identifying the genes, bioprocesses and bacteria in the old sands and coal beds, we will improve our understanding of how methane in hydrocarbon resources is generated and identify the enzymes involved in the natural cracking of hydrocarbons that produce methane and carbon dioxide.
My Roles: 1)16s rRNA data (pyrotag) analysis pipeline developement. The pipeline takes high-throughput 16S rRNA sequencing data in studies as input to predict the composition and diversity of natural microbial communities. It outputs taxonomic profile, alpha diversity and beta diversities of the communities. 2) Next-generation metagenome data analysis: seuence (454, Illumina) assembly, gene prediction, metagenome annotation, taxnomic binning, bioinformatics software adaption, modificaiton and development

DOTM: Design oilseeds for tomorrow markets

The target of this project represents a comprehensive and strategically based functional genomics dissection of Brassica seed meal quality. It was sponsored by Genome Alberta and Genome Canada.
My Roles: The transcriptome data analysis such as EST sequence cleaning, assembly, function predictions, user bioinformatics request support, bioinformatics tool development and bioinformatics needs survey of the project.

CAVEman: 4D Mapping of Genomic and Medical Information

The target of this project was to create visual maps of information about diseases that have a genetic component, such as cancer, diabetes, and Alzheimers. Using a virtual reality environment called the CAVE, researchers will integrate a high-resolution digital atlas of the male human body with medical data related to specific diseases.
My Roles: Mapping gene expression and metabolite data to 3D human body

Transplant transcriptome project

funded by Genome Canada and was leading by Dr. Philip Halloran in University of Alberta. The target of this project was to develope tests detecting and measuring organ transplant rejection .
My Roles: developed and maintained the Lab information management system (LIMS). This LIMS includes patitent demographic information management, clinic information management (histology report, pathology report etc), lab information management, sample and operation tracking.

PlasMapper

A web server automatically generates and annotates plasmid maps using only the plasmid DNA sequence as input.
Main roles: was one of the main person who developed it. It has been published on NAR and cited more than 40 times

Canadian Bioinformatics Help Desk (CBHD)

CBHD was the part of "Integrated and Distributed Bioinformatics Platform for Genome Canada" project. It offers a broad range of services to Canadian Researchers: Custom programming, website development, database development, data mining, Batch sequence processing, software advice and assistance.
My Roles: developed Genome Canada LIMS for this project. GC LIMS is a freely available, full-featured, platform-independent, scalable, web supported laboratory information management systems designed for various research labs

PENCE Bioinformatics Core Facility

The Protein Engineering Network of Centres of Excellence is a discovery, research, technology, and development organization that focuses on the study of proteomics and protein engineering.
My Roles: work as a programmer analyst to provide bioinformatics support for PENCE reasearchers

System Administrator

Besides the programming role, I was also taking some of the system administrating roles for Dr. David Wishart Group when I was working in University of Alberta.
My Roles: responsible for day-to-day maintenance of the computers and operating systems(Linux, Windows) in our group, including backup and recovery, adding and deleting user accounts, and performing software and hardware upgrades;Managing and maintaining the groups information systems, including databases, networks, file server and web server; Providing technical support for the group members' business requirements